A Phase 1, Open-label, Multicenter Study of SYNB1891 Administered by Intratumoral Injection to Patients With Advanced/Metastatic Solid Tumors and Lymphoma Alone and in Combination With Atezolizumab
Phase: PHASE1
Conditions: Metastatic Solid Neoplasm, Lymphoma
Sponsor: Synlogic

 
 
 
 
CLINICAL STUDY SYNB1891-CP-001 
 
 
Study Title: 
A Phase 1, Open-label, Multicenter Study of SYNB1891 
Administered by Intratumoral Injection to Patients with 
Advanced/Metastatic Solid Tumors or Lymphoma, Alone and in 
Combination with Atezolizumab 
Study Number: 
SYNB1891-CP-001 
Study Phase: 
Phase 1 
Product Name: 
SYNB1891 
Indication: 
Advanced/metastatic solid tumors or lymphoma 
Sponsor: 
Synlogic Operating Company, Inc. 
Protocol Version History: Version 4: 27 July 2020 
Version 3: 27 May 2020 
Version 2: 11 February 2020 
Version 1: 27 June 2019 
 
Synlogic Operating Company, Inc. 
301 Binney Street, Suite 402 
Cambridge, MA 02142 
Phone: (617) 401-9975 
 
CONFIDENTIAL INFORMATION: This protocol contains trade secrets and other confidential information. 
Accordingly, this protocol shall be treated as confidential and restricted to its intended use, namely, the guidance of 
the clinical Investigator. This material is the sole property of Synlogic Operating Company, Inc. and shall not be 
disclosed or used by others except as authorized in writing by Synlogic Operating Company, Inc. This material may 
be disclosed to and used by your staff and associates only to the extent necessary to conduct the clinical study. 

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SIGNATURE PAGE (SPONSOR) 
I have read and understand the contents of the clinical protocol for Clinical Study 
SYNB1891-CP-001 Version 4, dated 27 July 2020, and agree to meet all obligations of Synlogic 
Operating Company, Inc. as detailed in all applicable regulations and guidelines. In addition, I 
will ensure that the Principal Investigators are informed of all relevant information that becomes 
available during the conduct of this study. 
 
______________________________________________  
_____________ 
Richard Riese, MD, PhD 
 
 
 
 
 
Date 
Chief Medical Officer 
Synlogic Operating Company, Inc.  

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PRINCIPAL INVESTIGATOR AGREEMENT 
I have read and understand the contents of the clinical protocol for Clinical Study 
SYNB1891-CP-001 Version 4, dated 27 July 2020, and will adhere to the study requirements as 
presented, including all statements regarding confidentiality. In addition, I will conduct the study 
in accordance with the requirements of this protocol and also protect the rights, safety, privacy 
and well-being of study patients in accordance with the following: 
• International Council for Harmonisation of Technical Requirements for 
Pharmaceuticals for Human Use (ICH) Harmonised Tripartite Guideline for Good 
Clinical Practice (GCP) E6(R2). 
• All applicable laws and regulations, including, without limitation, data privacy laws 
and regulations. 
• Requirements for reporting serious adverse events as defined in Section 9 of this 
protocol. 
• Terms outlined in the Clinical Study Site Agreement. 
My signature also acknowledges that: 
• Neither my Sub-investigators nor I are members of the Institutional Review Board 
reviewing this protocol, or 
• I and/or my Sub-investigators are members of the Institutional Review Board, but 
I/we will not participate in the initial review or continuing review of this study. 
 
 
 
 
Name of Principal Investigator 
 
 
Signature of Principal Investigator 
Date 
 
 
 

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PROTOCOL SYNOPSIS  
Name of Sponsor/Company: 
Synlogic Operating Company, Inc. 
Name of Investigational Product: 
SYNB1891 
Name of Active Ingredient: 
SYNB1891 
Title of Study: 
A Phase 1, Open-label, Multicenter Study of SYNB1891 Administered by Intratumoral Injection to 
Patients with Advanced/Metastatic Solid Tumors or Lymphoma, Alone and in Combination with 
Atezolizumab 
Phase: 1 (first-in-human) 
Study Center: Approximately 8 study centers in the United States 
Number of Patients: Approximately 70 
Objectives and 
Endpoints 
The overall objective is to evaluate the safety and tolerability of escalating doses of 
intratumoral (i.t.) injections of SYNB1891 to determine the single-agent maximum 
tolerated dose (MTD) as monotherapy and the recommended Phase 2 dose (RP2D) 
in combination with atezolizumab. 
Primary objective: 
• 
Incidence of dose-limiting toxicities (DLTs): Percentage of patients 
who experience a DLT 
Secondary objectives: 
• 
Nature, incidence, and severity of all adverse events (AEs) and serious 
adverse events (SAEs) according to the National Cancer Institute 
(NCI) Common Terminology Criteria for Adverse Events (CTCAE), 
version 5.0 
• 
Objective response rate (ORR) in target lesions as determined by the 
Response Evaluation Criteria in Solid Tumors, version 1.1 (RECIST 
1.1), immune-related RECIST (iRECIST), and/or the Lymphoma 
Response to Immunomodulatory Therapy Criteria (LYRIC), with 
evaluations of the SYNB1891-injected tumor(s) and an overall 
response of up to 5 noninjected target lesions 
Exploratory objectives: 
• 
Duration of response or time to progression for evaluated tumors as 
determined by RECIST 1.1, iRECIST, and/or LYRIC 
• 
Pharmacodynamic (PD) response biomarkers including 
tumor-infiltrating lymphocytes (TIL) characterization, 
immunomodulatory cytokine gene expression and interferon (IFN) β 
responsive genes to be monitored in proximal and (if available) distal 
lesion biopsies at baseline and on study; systemic PD effects will be 
evaluated by assessment of changes in serum cytokine levels 
(including but not limited to tumor necrosis factor α [TNFα], 
interleukin [IL] 2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-13, IL1β, IL 1 

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receptor antagonist [IL1RA], IL 2 receptor alpha [IL2Rα], and IFNγ) 
at baseline and while on study 
• 
Kinetics of SYNB1891 within the injected tumor will be assessed by 
quantitative polymerase chain reaction (qPCR) from predose 
(baseline) to predose Cycle 1 Day 8 from a fine needle aspirate 
(FNA); systemic kinetics of SYNB1891 will be monitored by qPCR 
from blood at predose (baseline) and 6 hours and 24 hours postdose in 
Cycle 1 
Design 
Methodology 
This Phase 1, open-label, multicenter, 2-arm study will be conducted using the 
modified toxicity probability interval (mTPI) dose-finding design. Cohorts of 
patients will be enrolled to receive escalating doses of SYNB1891 administered by 
i.t. injection until the target DLT range (approximately 30%) for SYNB1891 
monotherapy is determined based on DLTs observed in Cycle 1 (Arm 1). The dose 
selected as achieving the target DLT range will be considered the MTD. 
After all patients in Arm 1 Cohort 4 have completed their Cycle 1 DLT safety 
evaluation, Arm 2 will enroll its first cohort starting at the Arm 1 Cohort 3 dose 
level, with SYNB1891 administered by i.t. injection in combination with 
atezolizumab administered as an intravenous (IV) infusion at a dose of 1200 mg 
every 3 weeks (Q3W) until the RP2D for the combination regimen is determined. 
The mTPI algorithm will be implemented separately in each arm. 
Assessments 
Eligible patients will be enrolled sequentially and will receive the first dose of 
study treatment within 28 days of screening. 
Safety will be monitored continuously by documentation of AEs, SAEs, clinical 
laboratory measurements, vital signs, and physical examinations. DLTs will be 
evaluated through the end of the first cycle. 
Disease status will be assessed by the local Investigator using appropriate imaging 
every 2 cycles for the duration of study treatment administration to evaluate the 
SYNB1891-injected lesion(s) and an overall response of up to 5 noninjected target 
lesions in accordance with RECIST 1.1, iRECIST, and/or LYRIC. 
Tumor biopsies and blood samples will be collected at baseline and at prespecified 
time points on study to evaluate the pharmacokinetics (PK), as measured by qPCR 
bacterial kinetics, and PD effects of study treatment. 
Study Regimens 
Treatments Administered 
Patients enrolled to Arm 1 may receive up to four 21-day cycles of SYNB1891 
monotherapy. On Days 1, 8, and 15 of Cycle 1 and Day 1 of Cycles 2 through 4, 
patients will receive an i.t. injection of SYNB1891 into an eligible lesion. If the 
initial eligible lesion undergoes complete regression and is no longer injectable (at 
the discretion of the Investigator), a subsequent eligible lesion (until no more 
eligible lesions remain) may be injected. 
At the end of Cycle 4, patients in Arm 1 who do not have progressive disease (i.e., 
those who achieve and sustain complete response [CR], partial response [PR], or 
stable disease [SD]) may receive additional cycles of SYNB1891 administered by 
i.t. injection on Day 1 of each cycle for up to 24 months (i.e., Cycles 5 to 35) after 
the initial dose of study treatment until documentation of progressive disease or 

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other discontinuation criteria, satisfaction of a predefined study stopping rule, or no 
eligible lesions remain. 
Patients enrolled to Arm 2 may receive up to four 21-day cycles with SYNB1891 
administered by i.t. injection into an eligible lesion on Days 1, 8, and 15 of Cycle 1 
and Day 1 of Cycles 2 through 4. In addition, atezolizumab will be administered in 
accordance with its recommended dose and schedule (1200 mg IV Q3W) on Day 1 
of each of the 4 planned cycles. On days when atezolizumab and SYNB1891 are 
both administered, SYNB1891 will be administered first, followed by at least 
1 hour of observation prior to the atezolizumab infusion. Patients in Arm 2 who do 
not have progressive disease (i.e., those who achieve and sustain CR, PR, or SD) at 
the end of Cycle 4 on combination therapy may receive additional cycles of 
SYNB1891 and atezolizumab for up to 24 months (i.e., Cycles 5 to 35) after the 
initial dose of study treatment until documentation of progressive disease or other 
discontinuation criteria, satisfaction of a predefined study stopping rule, or no 
eligible lesions remain.  
Locating and/or injecting the lesion may be performed using guided imaging at the 
discretion of the Investigator. 
Postdose Monitoring 
The initial patient in each Arm 1 cohort (Sentinel patient) will be monitored for at 
least 6 hours following the first (Cycle 1 Day 1) i.t. injection of SYNB1891 (or 
overnight, at the discretion of the Investigator) for evaluation of any procedural 
complication or acute toxicity (i.e., injection reactions or cytokine release 
syndrome) and for collection of postdose blood samples. Safety data must be 
reviewed on or after Day 7 and deemed acceptable by the Investigator and the 
Sponsor and contract research organization (CRO) Medical Monitors before the 
Sentinel patient receives any further injections and before any subsequent patients 
are dosed in that cohort.  
For the remainder of Cycle 1 dosing for the Sentinel patient and for all dosing for 
non-Sentinel patients, SYNB1891 injections will be administered in the outpatient 
setting and patients will be closely observed at the clinic for at least 6 hours 
following each injection for evaluation of any procedural complication or acute 
toxicity (i.e., injection reactions or cytokine release syndrome) and for collection 
of postdose blood samples. All patients will be contacted by telephone on Cycle 1 
Day 3 to monitor for signs of cytokine release syndrome. 
Dose-finding Methodology 
The starting dose of SYNB1891 in the first cohort of Arm 1 will be 1 × 106 live 
cells and will be increased in approximately 3-fold increments in subsequent 
cohorts until MTD determination in accordance with the mTPI algorithm.  
In Arm 2, dosing will begin after all patients in Arm 1 Cohort 4 have completed 
their Cycle 1 DLT safety evaluation. The starting dose of SYNB1891 in the first 
cohort of Arm 2 will be at SYNB1891 Arm 1 Cohort 3 dose level. Dosing in the 
Arm 2 cohorts will increase in approximately 3-fold increments in subsequent 
cohorts until RP2D determination. Once dosing in Arm 2 is initiated, patient 
allocation to cohorts will be managed by the Sponsor to ensure that a dosing level 
within Arm 2 is at least one dose level below the SYNB1891 monotherapy dose 
being evaluated in Arm 1. Combination doses will not be escalated above the 
SYNB1891 single-agent MTD established in Arm 1. The atezolizumab dose will 
remain constant at 1200 mg Q3W for each dose level in Arm 2. 

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In both arms, the escalation schedule may be adjusted based on PK, PD, and safety 
data emerging throughout the study to determine the MTD/RP2D. 
In both study arms, each cohort will initially comprise 3 patients (a Sentinel patient 
and 2 non-Sentinel patients), with subsequent dose level investigation governed by 
the mTPI algorithm in accordance with protocol-mandated criteria. 
Once the RP2D of Arm 2 is determined, up to 20 additional patients may be 
enrolled in the RP2D cohort to fully characterize the safety profile of SYNB1891 
in combination with atezolizumab. 
Definition of Dose-limiting Toxicity 
The occurrence of protocol-specified toxicities during Cycle 1 (e.g., certain 
Grade 3/4 laboratory values; sepsis; or toxicity resulting in death, discontinuation 
of Cycle 1, or delay of Cycle 2; see Section 4.2.4) will be considered a DLT, if 
assessed by the Investigator to be possibly, probably, or definitely related to study 
treatment administration. 
Duration of 
Study 
Participation 
The maximum time of study participation for a patient is up to 26 months, 
including the screening period (up to 28 days), treatment administration period (up 
to 24 months), and safety follow-up period (30 ± 5 days after the last dose). 
Patients in Arm 1 will receive an initial 4 cycles of SYNB1891. Patients who do 
not have progressive disease at the end of Cycle 4 may receive additional cycles of 
SYNB1891 for up to 24 months (i.e., Cycles 5 to 35) after the initial dose of study 
treatment until documentation of progressive disease or other discontinuation 
criteria, satisfaction of a predefined study stopping rule, or no eligible lesions 
remain.  
Patients in Arm 2 will receive an initial 4 cycles of SYNB1891 and atezolizumab. 
Arm 2 patients who do not have progressive disease at the end of Cycle 4 on 
combination therapy may receive additional cycles of SYNB1891 and 
atezolizumab for up to 24 months (i.e., Cycles 5 to 35) after the initial dose of 
study treatment until documentation of progressive disease or other discontinuation 
criteria, satisfaction of a predefined study stopping rule, or no eligible lesions 
remain. 
Eligibility 
Criteria 
 
Inclusion Criteria  
Patients must meet all of the following inclusion criteria to be eligible:  
1. Able and willing to voluntarily complete the informed consent process 
(patient or patient’s representative). 
2. Adults aged ≥ 18 years (on the day of signing informed consent) with 
histologically- or cytologically-confirmed stage III or IV 
advanced/metastatic solid tumor or lymphoma for which no therapeutic 
options are available to extend survival or for which the patient is not a 
candidate for standard-of-care therapy. 
3. Eastern Cooperative Oncology Group performance status ≤ 1. 
4. Life expectancy ≥ 3 months. 
5. ≥ 1 injectable, measurable (≥ 10 mm in diameter, or ≥ 15 mm for nodal 
lesions), eligible lesion as defined by RECIST 1.1 (Eisenhauer et al 2009), 
iRECIST (Seymour et al 2017), and/or LYRIC (Cheson et al 2016) and as 
assessed by the Investigator. Eligible lesions must not be located in the 
thoracic cavity, spleen, pancreas, gastrointestinal tract (liver injection 

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allowed), or cranium and must be amenable to percutaneous injection and 
away from major blood vessels or neurological structures. 
6. Able to provide biopsies for biomarker analysis from injected and (if 
available) noninjected lesions at baseline and other time points during the 
study. 
7. Oxygen saturation > 90% without the use of supplemental oxygen. 
8. Adequate cardiac function, defined as follows: 
a. Left ventricular ejection fraction (LVEF) > 50% by multi-gated 
acquisition (MUGA) scan or echocardiogram (ECHO) performed 
within 6 months prior to the first dose of study treatment provided the 
patient has not received any potential cardiotoxic agents in the 
intervening period. Symptoms relating to left ventricular dysfunction, 
cardiac arrhythmia, or cardiac ischemia must all be Grade < 1 per NCI 
CTCAE version 5.0. 
b. QTc interval corrected for heart rate using Fridericia’s formula (QTcF) 
< 480 msec at screening. 
9. Laboratory values within the following ranges: 
• 
Absolute neutrophil count ≥ 1500/µL 
• 
Lymphocyte count ≥ 500/µL 
• 
Platelets ≥ 100,000/µL without transfusion 
• 
Hemoglobin ≥ 9.0 g/dL (patients may be transfused to meet this 
criterion) 
• 
Estimated glomerular filtration rate (eGFR) > 50 mL/min/1.73 m2 per 
the Cockcroft-Gault formula 
• 
Total bilirubin ≤ 1.5 × upper limit of normal (ULN) OR direct 
bilirubin ≤ ULN for participants with total bilirubin levels 
> 1.5 × ULN or ≤ 3 × ULN for patients with Gilbert’s syndrome 
• 
Aspartate aminotransferase (AST), alanine aminotransferase (ALT), 
and alkaline phosphatase ≤ 2.5 × ULN (AST and ALT ≤ 5 × ULN for 
participants with liver metastases and alkaline phosphatase ≤ 5 × ULN 
for participants with liver or bone metastases) 
• 
International normalized ratio (INR) or prothrombin time (PT) or 
activated partial thromboplastin time (aPTT) ≤ 1.5 × ULN unless 
participant is receiving anticoagulant therapy as long as PT or aPTT is 
within therapeutic range of intended use of anticoagulants 
10. Agree to use an acceptable method of contraception after informed 
consent, throughout the study, and for 5 months after the last dose of 
SYNB1891 or atezolizumab. 
Additional inclusion criteria that apply only to Arm 2 study participants are 
as follows: 
11. Thyroid-stimulating hormone (TSH) must be within the normal reference 
range or the patient must be receiving stable thyroid replacement therapy. 
12. Patients must have received treatment with an anti-programmed cell death 
protein-1 (PD-1)/programmed death-ligand 1 (PD-L1) monoclonal 
antibody (mAb) administered either as monotherapy, or in combination 

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with other checkpoint inhibitors (CPIs) or other therapies, if indicated (if 
CPI therapy is not indicated as a part of standard-of-care therapy, patients 
may be CPI naïve). 
Additional inclusion criteria that apply only to the Arm 2 expansion study 
participants are as follows: 
13. Patients must have progressed on treatment with an anti-PD-1/PD-L1 mAb 
administered either as monotherapy, or in combination with other CPIs or 
other therapies, if indicated (if CPI therapy is not indicated as a part of 
standard-of-care therapy, patients may be CPI naïve). 
PD-1/L1 treatment progression is defined by meeting all of the following 
criteria: 
a. Has received at least 2 doses of an approved anti-PD-1/L1 mAb.  
b. Has demonstrated disease progression after PD-1/L1 as defined by 
RECIST 1.1, iRECIST, and/or LYRIC. The initial evidence of disease 
progression is to be confirmed by a second assessment no less than 
4 weeks from the date of the first documented disease progression, in 
the absence of rapid clinical progression as determined by the 
Investigator. Once disease progression is confirmed, the initial date of 
disease progression documentation will be considered the date of 
disease progression. 
c. Progressive disease has been documented within 12 weeks from the 
last dose of anti-PD-1/L1 mAb. 
Exclusion Criteria 
1. Chemotherapy, radiation, or biological cancer therapy within 14 days prior 
to the first dose of study treatment, or failure of any AEs to recover to 
Baseline or NCI CTCAE version 5.0 Grade 1, except for any grade of 
alopecia caused by cancer therapeutics administered > 28 days earlier. 
2. Systemic immunostimulatory agents (including, but not limited to, IFN 
and IL-2) within 28 days or 5 drug elimination half-lives (whichever is 
longer) prior to initiation of study treatment. Checkpoint inhibitors are not 
considered systemic immunostimulatory agents for this criterion and are 
subject to the washout period listed in exclusion criterion #1. 
3. Allogeneic hematopoietic stem cell transplantation that requires current 
use of immunosuppressors. 
4. Receipt of a live vaccine within 90 days prior to the first dose of study 
treatment or anticipation of a need for such a vaccine during treatment. 
5. Receipt of antibiotics within 7 days prior to the first dose of study 
treatment. 
6. Participation in a study of an investigational agent and receipt of study 
therapy or use of an investigational device within 28 days prior to the first 
dose of study treatment. 
7. Diagnosed immunodeficiency or current use of chronic systemic steroid 
therapy in excess of replacement doses (prednisone ≤ 10 mg/day or 
equivalent is acceptable) or any other form of immunosuppressive 
medication within 7 days prior to the first dose of study treatment. 
8. For injection and biopsy of visceral (deep) lesions: patients must not be on 
long-acting antiplatelet agents such as aspirin or clopidogrel or on 

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therapeutic doses of anticoagulants, with the exception of patients 
receiving a preventative dose of low molecular weight heparin. In patients 
receiving preventative low molecular weight heparin, treatment must be 
stopped 24 hours before the intratumoral injection and resumed again 
24 hours after the injection (Marabelle et al 2018). 
9. Previous or concurrent malignancy, with the exception of: 
a. Adequately treated basal or squamous cell carcinoma, in situ 
carcinoma of the cervix, or ductal carcinoma in situ of the breast; 
b. Localized prostate cancer definitively treated with surgery or radiation 
or stable on hormone therapy; 
c. Other cancer from which the patient has been disease free for at least 
2 years. 
10. Clinically active central nervous system (CNS) metastases and/or 
carcinomatous meningitis (treated brain metastases are permitted if 
radiologically stable for ≥ 28 days prior to the first dose of study 
treatment). 
11. Allergy to antibiotics that precludes treatment for infection with E. coli 
Nissle 1917 (see Appendix 4 for common antibiotics to which E. coli 
Nissle is sensitive). 
12. Hepatitis B or C infection(s) unless screening tests indicate a negative viral 
load, and/or human immunodeficiency virus (HIV) infection unless 
screening tests indicate a negative or below the limit of quantitation viral 
load. 
13. Known active tuberculosis. 
14. Grade 3 or higher infection according to NCI CTCAE within 28 days prior 
to initiation of study treatment, including, but not limited to, 
hospitalization for complications of infection, bacteremia, or severe 
pneumonia. 
15. Failure to fully recover from the effects of major surgery. Surgeries that 
required general anesthesia must be completed > 14 days before the first 
dose of study drug. Surgery requiring regional/epidural anesthesia must be 
completed > 72 hours before the first dose of study treatment and 
participants should be recovered. 
16. Heart failure of New York Heart Association Class 3 or greater, restrictive 
cardiomyopathy, or unstable angina or recent myocardial infarction within 
3 months prior to the first dose of study treatment. 
17. Any other medical condition that might confound the results of the study, 
interfere with the participant’s participation, or is not in the best interest of 
the participant, in the opinion of the treating Investigator. 
18. Pregnant or breastfeeding or anticipated conception or fathering of 
children within the projected duration of the study and for 5 months after 
the last dose of SYNB1891 or atezolizumab. 
Additional exclusion criteria that apply only to Arm 2 study participants are 
as follows: 
19. History of immune-mediated AEs on prior PD-1/PD-L1 therapies 
requiring discontinuation or immunosuppressor therapy, excluding 
endocrinopathies. 

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20. Active or history of underlying autoimmune disease or immune deficiency, 
including, but not limited to, myasthenia gravis, myositis, autoimmune 
hepatitis, systemic lupus erythematosus, rheumatoid arthritis, 
inflammatory bowel disease, antiphospholipid antibody syndrome, 
Wegener granulomatosis, Sjögren syndrome, Guillain-Barré syndrome, or 
multiple sclerosis, with the following exceptions: 
a. Patients with a history of autoimmune-related hypothyroidism who are 
on thyroid replacement hormone are eligible for the study. 
b. Patients with controlled Type 1 diabetes mellitus who are on an insulin 
regimen are eligible for the study. 
c. Patients with eczema, psoriasis, lichen simplex chronicus, or vitiligo 
with dermatologic manifestations only (e.g., patients with psoriatic 
arthritis are excluded) are eligible for the study provided all of 
following conditions are met: 
- Rash must cover < 10% of body surface area; 
- Disease is well controlled at baseline and requires only low-potency 
topical corticosteroids; 
- No occurrence of acute exacerbations of the underlying condition 
requiring psoralen plus ultraviolet A radiation, methotrexate, 
retinoids, biologic agents, oral calcineurin inhibitors, or high potency 
or oral corticosteroids within the previous 12 months. 
21. History of a Grade ≥ 3 allergic anaphylactic reaction following treatment 
with a PD-1 mAb or to chimeric, human, or humanized antibodies or 
fusion proteins. 
22. History of idiopathic pulmonary fibrosis, organizing pneumonia (e.g., 
bronchiolitis obliterans), drug-induced pneumonitis requiring treatment, or 
idiopathic pneumonitis, or evidence of active pneumonitis. 
23. Known hypersensitivity to Chinese hamster ovary cell products or any 
component of the atezolizumab formulation. 
Analytical and 
Statistical 
Methods 
Sample Size Determination 
No formal sample size calculations were performed, as the study is primarily 
designed for empirical evaluation of safety and tolerability in patients with 
advanced solid tumors or lymphoma. The anticipated sample size is approximately 
70 patients, which provides for 4 to 7 dose-finding cohorts in Arm 1, 1 to 5 cohorts 
in Arm 2, and replacement of 1 patient per cohort, as well up to 20 additional 
patients enrolled at the RP2D in Arm 2. Additional cohorts may be required in 
either arm to determine the MTD/RP2D. 
Safety Analysis 
DLTs will be determined for each patient through the end of Cycle 1. This 
timeframe will enable identification of any acute, dose-limiting events that will 
determine suitability for dose escalation. Patients who experience a DLT will 
remain on the study to complete the safety evaluations and follow-up until 
resolution or stabilization of the DLT. AEs and SAEs will be determined to be 
dose-limiting if they occur during the described timeframe and meet the described 
criteria. AEs or SAEs experienced after the end of Cycle 1 will not be reported as 
DLTs but will be documented. 

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All AEs and SAEs will be determined and coded using the Medical Dictionary for 
Regulatory Activities (MedDRA), and severity of AEs and laboratory 
abnormalities will be graded using the NCI CTCAE, version 5.0. Adverse events 
will be tabulated by system organ class (SOC) and preferred term. Incidence tables 
of patients with AEs, SAEs, and DLTs will be presented by maximum severity. 
Efficacy Analysis 
Efficacy analyses using RECIST 1.1, iRECIST, and/or LYRIC will be descriptive 
in nature. The response of SYNB1891-injected lesion(s) and an overall response of 
up to 5 noninjected target lesions will be assessed. Exploratory evaluations for 
proof-of-concept (biopsy-based PD markers) will include change from baseline 
assessment. 
The duration of any response or lack of progression for all evaluated tumors using 
RECIST 1.1, iRECIST, and/or LYRIC will also be assessed. 

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TABLE OF CONTENTS 
SIGNATURE PAGE (SPONSOR) ..................................................................................................2 
PRINCIPAL INVESTIGATOR AGREEMENT .............................................................................3 
PROTOCOL SYNOPSIS ................................................................................................................4 
TABLE OF CONTENTS ...............................................................................................................13 
LIST OF ABBREVIATIONS ........................................................................................................19 
1. 
INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE .................23 
2. 
INTRODUCTION ......................................................................................................24 
2.1. 
Targeted Immunotherapy in Advanced Cancer ..........................................................24 
2.2. 
Investigational Medicinal Product ..............................................................................25 
2.2.1. 
Nonclinical Studies .....................................................................................................27 
2.2.1.1. 
Summary of the Nonclinical Development Program ..................................................30 
2.3. 
Background of Atezolizumab .....................................................................................30 
2.4. 
Rationale for the Study ...............................................................................................31 
3. 
STUDY OBJECTIVES AND ENDPOINTS ..............................................................32 
3.1. 
Primary .......................................................................................................................32 
3.2. 
Secondary ...................................................................................................................32 
3.3. 
Exploratory .................................................................................................................32 
4. 
STUDY DESIGN .......................................................................................................33 
4.1. 
Study Design Overview ..............................................................................................33 
4.2. 
Study Dosing Regimens .............................................................................................35 
4.2.1. 
Treatments Administered ............................................................................................35 
4.2.2. 
Postdose Monitoring ...................................................................................................35 
4.2.3. 
Dose-finding with the mTPI Algorithm .....................................................................36 
4.2.4. 
Definition of Dose-limiting Toxicity ..........................................................................38 
4.3. 
Intrapatient Dose Modification ...................................................................................39 
4.3.1. 
Dosing Delays and Interruptions ................................................................................39 
4.3.2. 
Dose Reductions .........................................................................................................40 
4.3.2.1. 
Dose Reductions for SYNB1891 ................................................................................40 
4.3.2.2. 
Dose Reductions for Atezolizumab ............................................................................40 
4.4. 
Toxicity Management .................................................................................................40 
4.4.1. 
Adverse Events Associated with SYNB1891 .............................................................40 

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4.4.2. 
Adverse Events Associated with Atezolizumab .........................................................42 
4.4.2.1. 
Pulmonary Events .......................................................................................................42 
4.4.2.2. 
Hepatic Events ............................................................................................................43 
4.4.2.3. 
Gastrointestinal Events ...............................................................................................44 
4.4.2.4. 
Endocrine Events ........................................................................................................45 
4.4.2.5. 
Ocular Events ..............................................................................................................48 
4.4.2.6. 
Immune-mediated Myocarditis ...................................................................................49 
4.4.2.7. 
Infusion-related Reactions and Cytokine Release Syndrome .....................................50 
4.4.2.8. 
Pancreatic Events ........................................................................................................53 
4.4.2.9. 
Dermatologic Events ..................................................................................................55 
4.4.2.10. 
Neurologic Disorders ..................................................................................................55 
4.4.2.11. 
Immune-mediated Meningoencephalitis ....................................................................56 
4.4.2.12. 
Renal Events ...............................................................................................................57 
4.4.2.13. 
Immune-mediated Myositis ........................................................................................58 
4.4.2.14. 
Systemic Immune Activation .....................................................................................60 
4.5. 
Stopping Rules ............................................................................................................63 
4.6. 
Duration of Study Participation ..................................................................................63 
5. 
PATIENT POPULATION ..........................................................................................64 
5.1. 
Number of Patients .....................................................................................................64 
5.2. 
Selection of Patients ...................................................................................................64 
5.2.1. 
Eligibility Criteria .......................................................................................................64 
5.2.1.1. 
Inclusion Criteria ........................................................................................................64 
5.2.1.2. 
Exclusion Criteria .......................................................................................................66 
6. 
INVESTIGATIONAL MEDICINAL PRODUCT AND CONCOMITANT 
MEDICATIONS .........................................................................................................69 
6.1. 
Investigational Product Supply and Administration ...................................................69 
6.1.1. 
SYNB1891 ..................................................................................................................69 
6.1.1.1. 
Manufacturing and Formulation .................................................................................69 
6.1.1.2. 
Packaging and Labeling ..............................................................................................69 
6.1.1.3. 
Shipping, Storage, and Handling ................................................................................69 
6.1.1.4. 
Dispensing and Administration ..................................................................................69 
6.1.2. 
Atezolizumab ..............................................................................................................69 
6.2. 
Accountability and Dosing Compliance .....................................................................70 

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6.3. 
Concomitant Medications ...........................................................................................70 
7. 
STUDY PROCEDURES AND ASSESSMENTS......................................................71 
7.1. 
Screening ....................................................................................................................71 
7.2. 
Safety Assessments .....................................................................................................71 
7.2.1. 
Medical History ..........................................................................................................71 
7.2.2. 
Adverse Events ...........................................................................................................71 
7.2.2.1. 
Monitoring for Signs and Symptoms of Infection ......................................................72 
7.2.3. 
Vital Signs ..................................................................................................................72 
7.2.4. 
Physical Examination .................................................................................................72 
7.2.5. 
Clinical Laboratory Measurements.............................................................................72 
7.2.5.1. 
Local Laboratory Measurements ................................................................................73 
7.2.5.2. 
Central Laboratory Measurements .............................................................................74 
7.2.6. 
Electrocardiograms .....................................................................................................75 
7.2.7. 
Multi-gated Acquisition Scan or Echocardiogram .....................................................75 
7.3. 
Efficacy Assessments .................................................................................................75 
7.4. 
Pharmacodynamic Assessments .................................................................................75 
7.5. 
Follow-up Assessments ..............................................................................................76 
7.5.1. 
End-of-Treatment Visit ...............................................................................................76 
7.5.2. 
Safety Follow-up Visit ................................................................................................76 
7.6. 
Sample Retention for Exploratory Analyses ..............................................................76 
8. 
STUDY DISCONTINUATION .................................................................................81 
8.1. 
Sponsor Discontinuation Criteria ...............................................................................81 
8.2. 
Study Discontinuation for Individual Patients ............................................................81 
8.2.1. 
Patient Replacement ...................................................................................................82 
9. 
ADVERSE EVENTS..................................................................................................83 
9.1. 
Adverse Event .............................................................................................................83 
9.1.1. 
Assessment of Severity ...............................................................................................83 
9.1.2. 
Assessment of Causality .............................................................................................83 
9.2. 
Serious Adverse Event ................................................................................................84 
9.2.1. 
Clarification of Serious Adverse Event Definition .....................................................84 
9.2.2. 
Serious, Unexpected, Suspected Adverse Reactions ..................................................85 
9.3. 
Adverse Events of Special Interest .............................................................................85 
9.4. 
Reporting of Adverse Events ......................................................................................86 

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9.5. 
Pregnancy ...................................................................................................................86 
9.6. 
Clinical Laboratory Abnormalities .............................................................................86 
9.7. 
Review of Safety Data ................................................................................................87 
10. 
STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE ...........88 
10.1. 
Populations for Analysis .............................................................................................88 
10.2. 
Safety Variables ..........................................................................................................88 
10.3. 
Efficacy Variables ......................................................................................................88 
10.4. 
Pharmacodynamic Variables ......................................................................................89 
10.5. 
Kinetic Variables ........................................................................................................89 
10.6. 
Determination of Sample Size ....................................................................................89 
10.7. 
Randomization and Blinding ......................................................................................89 
10.8. 
Changes in the Conduct of the Study or Planned Analysis ........................................89 
11. 
DATA RECORDING, RETENTION AND MONITORING ....................................90 
11.1. 
Case Report Forms .....................................................................................................90 
11.2. 
Data Retention ............................................................................................................90 
11.3. 
Data Monitoring ..........................................................................................................90 
11.4. 
Quality Control and Quality Assurance ......................................................................91 
12. 
REGULATORY, ETHICAL, AND LEGAL OBLIGATIONS .................................92 
12.1. 
Good Clinical Practice ................................................................................................92 
12.2. 
Institutional Review Board Approval .........................................................................92 
12.3. 
Regulatory Authority Approval ..................................................................................92 
12.4. 
Other Required Approvals ..........................................................................................92 
12.5. 
Informed Consent .......................................................................................................92 
12.6. 
Patient Confidentiality ................................................................................................93 
12.7. 
Disclosure of Information ...........................................................................................93 
12.8. 
Publication of Study Data ...........................................................................................93 
12.9. 
Ethical Standards ........................................................................................................94 
13. 
REFERENCES ...........................................................................................................95 
APPENDIX 1. RESPONSE EVALUATION CRITERIA IN SOLID TUMORS, 
VERSION 1.1 .............................................................................................................98 
APPENDIX 2. IMMUNE-RELATED RESPONSE EVALUATION CRITERIA IN 
SOLID TUMORS .....................................................................................................105 

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APPENDIX 3. LYMPHOMA RESPONSE TO IMMUNOMODULATORY 
THERAPY CRITERIA ............................................................................................108 
APPENDIX 4. E. COLI NISSLE SENSITIVITY AND RESISTANCE AGAINST 
COMMON ANTIBIOTICS ......................................................................................111 
LIST OF TABLES 
Table 1: 
Dose-finding Rules per mTPI Design .........................................................................37 
Table 2: 
Toxicity Management for Adverse Events Considered Potentially Associated 
with SYNB1891..........................................................................................................41 
Table 3: 
Management Guidelines for Pulmonary Events, Including Pneumonitis ...................43 
Table 4: 
Management Guidelines for Hepatic Events ..............................................................44 
Table 5: 
Management Guidelines for Gastrointestinal Events .................................................45 
Table 6: 
Management Guidelines for Endocrine Events ..........................................................46 
Table 7: 
Management Guidelines for Ocular Events ................................................................49 
Table 8: 
Management Guidelines for Immune-mediated Myocarditis .....................................50 
Table 9: 
Management Guidelines for Infusion-related Reactions and Cytokine 
Release Syndrome ......................................................................................................51 
Table 10: Management Guidelines for Pancreatic Events, Including Pancreatitis .....................54 
Table 11: Management Guidelines for Dermatologic Events .....................................................55 
Table 12: Management Guidelines for Neurologic Disorders ....................................................56 
Table 13: Management Guidelines for Immune-mediated Meningoencephalitis .......................57 
Table 14: Management Guidelines for Renal Events .................................................................58 
Table 15: Management Guidelines for Immune-mediated Myositis ..........................................59 
Table 16: Systemic Immune Activation Diagnosis and Management ........................................62 
Table 17: Local Laboratory Parameters ......................................................................................74 
Table 18: Central Laboratory Parameters ...................................................................................75 
Table 19: Schedule of Events (Arm 1) .......................................................................................77 
Table 20: Schedule of Events (Arm 2) .......................................................................................79 
Table 21: Criteria for Overall Response at a Single Time Point: Patients with Target 
Lesions (with or without Nontarget Lesions) ...........................................................103 
Table 22: Guidelines for Evaluation of Lesions to Support iRECIST Response 
Assessment after Disease Progression per RECIST 1.1 ...........................................107 
Table 23: Guidelines for the Classification of Disease Status According to LYRIC ...............108 
 

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LIST OF FIGURES 
Figure 1: 
Design of the Engineered E. coli Nissle Strain SYNB1891 .......................................26 
Figure 2: 
In Vitro CDA Production and Biological Activity of SYNB1891 .............................27 
Figure 3: 
Antitumor, Pharmacologic and Systemic Immunity Activity of SYNB1891 ............29 
Figure 4: 
SYNB1891-CP-001 Study Design .............................................................................34 

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LIST OF ABBREVIATIONS 
Abbreviation or Specialist Term 
Explanation 
AE 
adverse event 
AESI 
adverse event of special interest 
ALT 
alanine aminotransferase 
ANC 
absolute neutrophil count 
APC 
antigen-presenting cell 
aPTT 
activated partial thromboplastin time 
AST 
aspartate aminotransferase 
ATP 
adenosine triphosphate 
BAL 
bronchoscopic alveolar lavage 
°C 
degree(s) Celsius 
CBC 
complete blood count 
CD 
cluster of differentiation 
CDA 
cyclic-di-AMP 
CDN 
cyclic dinucleotide 
CNS 
central nervous system 
CPI 
checkpoint inhibitor 
CR 
complete response 
CRA 
clinical research associate 
CRO 
contract research organization 
CRS 
cytokine release syndrome 
CT 
computed tomography 
CTCAE 
Common Terminology Criteria for Adverse Events 
CV 
curriculum vitae 
dacA or DacA 
di-adenylate cyclase gene or enzyme 
DAP 
diaminopimelic acid 
DILI 
drug-induced liver injury 
DLT 
dose-limiting toxicity 
dTMP 
2’-deoxythymidine-5’-monophosphate 
dUMP 
2’-deoxyuridine-5’-monophosphate 
ECG 
electrocardiogram 
ECHO 
echocardiogram 
ECMO 
extracorporeal membrane oxygenation 
EcN 
Escherichia coli Nissle 1917 

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Abbreviation or Specialist Term 
Explanation 
eCRF 
electronic case report form 
EDC 
electronic data capture 
eGFR 
estimated glomerular filtration rate 
ELISA 
enzyme-linked immunosorbent assay 
EOT 
End of Treatment 
°F 
degree(s) Fahrenheit 
FDA 
Food and Drug Administration 
FNA 
fine needle aspirate 
FNR 
fumarate and nitrate reductase 
FT4 
free thyroxine 
g 
gram(s) 
GCP 
Good Clinical Practice 
GLP 
Good Laboratory Practice 
GM-CSF 
granulocyte-macrophage colony-stimulating factor 
h 
hour 
hCG 
human chorionic gonadotropin 
HIV 
human immunodeficiency virus 
HLH 
hemophagocytic lymphohistiocytosis 
HNSTD 
highest nonseverely toxic dose 
ICH 
International Council for Harmonisation of Technical Requirements for 
Pharmaceuticals for Human Use 
ICU 
intensive care unit 
IgG1 
immunoglobulin G1 
IFN 
interferon 
IL 
interleukin 
IL1RA 
interleukin 1 receptor antagonist 
IL2Rα 
interleukin 2 receptor alpha 
INR 
International normalized ratio 
IRB 
Institutional Review Board 
iRECIST 
immune-related Response Evaluation Criteria in Solid Tumors 
IRR 
infusion-related reaction 
i.t. 
intratumoral 
IV 
intravenous 
kb 
kilobase 
kg 
kilogram 

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Abbreviation or Specialist Term 
Explanation 
L 
liter(s) 
LC-MS/MS 
liquid chromatography/tandem mass-spectrometry 
LDH 
lactate dehydrogenase 
LFT 
liver function test 
LPS 
lipopolysaccharide 
LVEF 
left ventricular ejection fraction 
LYRIC 
Lymphoma Response to Immunomodulatory Therapy Criteria 
m2 
meter(s) squared 
mAb 
monoclonal antibody 
MAS 
macrophage activation syndrome 
MedDRA 
Medical Dictionary for Regulatory Activities 
mg 
milligram(s) 
min 
minute(s) 
mL 
milliliter(s) 
mM 
millimolar(s) 
MRI 
magnetic resonance imaging 
MTD 
maximum tolerated dose 
mTPI 
modified toxicity probability interval 
MUGA 
multi-gated acquisition scan 
NCI 
National Cancer Institute 
NSAID 
nonsteroid anti-inflammatory drug 
ORR 
objective response rate 
PD 
pharmacodynamic(s) 
PD-1 
programmed cell death protein-1 
PfnrS 
fumarate and nitrate reductase regulator promoter [ 
PK 
pharmacokinetic(s) 
PD-L1 
programmed death-ligand 1 
PR 
partial response 
PRR 
pattern recognition receptor 
PT 
prothrombin time 
Q3W 
every 3 weeks 
qPCR 
quantitative polymerase chain reaction 
QTcF 
QT interval corrected for heart rate using Fridericia’s formula 
RAW 
immortalized murine macrophage cells 

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Abbreviation or Specialist Term 
Explanation 
RP2D 
recommended Phase 2 dose 
RECIST 
Response Evaluation Criteria in Solid Tumors 
SAE 
serious adverse event 
SAP 
statistical analysis plan 
SD 
stable disease 
SOC 
system organ class 
SRC 
Safety Review Committee 
STING 
STimulator of INterferon Genes 
SUSAR 
serious, unexpected, suspected adverse reaction 
THY 
thymidine 
TIL 
tumor-infiltrating lymphocytes 
TLR 
toll-like receptor 
TME 
tumor microenvironment 
TNFα 
tumor necrosis factor α 
TSH 
thyroid-stimulating hormone 
ULN 
upper limit of normal 
US 
United States 
VAD 
ventricular assist device 

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1. 
INVESTIGATORS AND STUDY ADMINISTRATIVE 
STRUCTURE 
The Principal Investigator is the person responsible for the conduct of the study at the 
investigational site. A Sub-investigator is any member of the clinical study team designated and 
supervised by the Principal Investigator to perform critical study-related procedures and/or to 
make important study-related decisions. 
Prior to study initiation, the Principal Investigator at each site must provide to Synlogic 
Operating Company, Inc. (also referred to as “Synlogic” or “Sponsor”) a signed protocol 
signature page, a fully executed and signed United States (US) Food and Drug Administration 
(FDA) Form 1572, a current curriculum vitae (CV) and medical license and a financial 
disclosure form. Financial disclosure forms, current CVs and medical licenses must also be 
provided for all Sub-investigators listed on Form 1572 who will be directly involved in the 
evaluation of patients. 
The study will be administered and monitored by employees or representatives of Synlogic in 
accordance with all applicable regulations. Clinical research associates (CRAs) will monitor each 
site on a periodic basis and perform verification of source documentation for each patient. 
Synlogic or designee will be responsible for ensuring timely reporting of expedited serious 
adverse event (SAE) reports to regulatory authorities and Investigators. 

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2. 
INTRODUCTION 
SYNB1891 is being developed for the treatment of patients with advanced/metastatic solid 
tumors or lymphoma. 
2.1. 
Targeted Immunotherapy in Advanced Cancer 
As the immuno-oncology field matures and as more therapies are evaluated in the clinic, our 
appreciation for the complexity of tumor-immune cell interactions deepens. While 
immunotherapies have become the standard-of-care for numerous cancers, significant unmet 
medical need persists primarily for the 55-87% of patients failing to respond to checkpoint 
inhibitors (CPIs) (Darvin et al 2018). Addressing the question of why some patients respond to 
checkpoint inhibition while others do not is currently an active area of investigation. However, 
one emerging biomarker correlated with response is intratumoral immune cell infiltration 
(Zou et al 2016) where patients with higher levels of immune cell infiltration prior to therapy 
exhibit higher response rates to CPIs. Combination therapies seek to expand response rates by 
driving higher levels of immune cell infiltration into tumors, triggering antigen-presenting cell 
(APC) activation and promoting productive tumor-antigen presentation to effector T cells 
(Zou et al 2016). To this end, an interest in innate immune agonists has emerged, such as the use 
of toll-like receptor (TLR) agonists (Adams 2009; Iribarren et al 2016) and STimulator of 
INterferon Genes (STING) agonists (Fu et al 2015; Corrales et al 2015; Woo et al 2014). 
The crucial role that Type 1 inteferons (IFNs) play in infection and inflammation has been 
known for decades (Isaacs et al 1957), and the many pathways that revolve around this first 
described cytokine (now known as IFN-β) have been determined over time (Ivashkiv et al 2014). 
These findings provide some insight as to why initial work with intratumoral injections of active 
bacteria (Coley’s toxin) led to many anecdotal responses in malignant tumors, defining the link 
between infection, inflammation and cancer. Since the “treatment era” that began in 1891, the 
importance of lipopolysaccharide (LPS), endotoxin and ultimately Type 1 IFN in adaptive 
immunity, tumor immunology and immune surveillance has been elucidated (Trinchieri 2010). 
Recent tumor immunology work has directly related Type 1 IFN-related gene expression 
signatures to the amount of T-cell infiltration in tumors (Fuertes et al 2011), leading investigators 
to use the cytokine to turn immune-unreactive tumors without lymphocyte infiltration (cold) into 
immunoreactive tumors (hot). The observation that Type 1 IFN signatures were associated with 
tumors in ipilimumab-responding melanoma patients (Chiappinelli et al 2015) was an important 
link in the chain, and there is currently little doubt that the Type 1 IFN pathway is essential for 
the efficacy of cancer immunotherapy (Zamarin et al 2014).  
Over the last decade, several modern therapeutic strategies designed to upregulate the Type 1 
IFN pathway as a potential cancer treatment have been devised. Because the STING pathway is 
required in immune recognition and elimination of tumors through Type 1 IFN (Woo et al 2014), 
agonists of STING provide a promising approach to elicit Type 1 IFN production (Ishikawa et al 
2008). Unique nucleic acids called cyclic dinucleotides (CDNs), like cyclic-di-AMP (CDA), 
which function as signaling molecules in bacteria, have also been shown to induce a 
STING-dependent Type 1 IFN response intracellularly (Corrales et al 2015) and thus small 
molecule analogs were developed, with some evaluated clinically. While small molecule STING 
agonists have been shown to be potent inducers of antitumor immunity (Corrales et al 2015; 
Fu et al 2015; Woo et al 2014), “off-target” activation of STING in effector T cells can lead to 

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T cell apoptosis (Larkin et al 2017) and impede the establishment of immunological memory 
(Sivick et al 2018). To reduce nontargeted, systemic effects and improve “on-target” efficacy, 
new means of localized and targeted STING activation are needed. 
2.2. 
Investigational Medicinal Product 
SYNB1891 is a strain of modified live probiotic bacterium (Escherichia coli [E. coli] Nissle 
1917) (EcN) programmed as a live immuno-biotherapeutic agent designed to treat patients with 
cancer. It is a genetically modified strain of EcN that, under hypoxic conditions, is designed to 
produce CDA, which functions as a STING agonist. Figure 1 presents the structure of 
SYNB1891. 
Cyclic di-AMP functions as a STING agonist. Activation of STING results in the induction of 
Type I IFNs, like IFNβ, and in the context of cancer can trigger the initiation of antitumor 
immunity through the activation of APCs and the presentation of tumor-antigens to effector 
T cells (Corrales et al 2015). In addition to the production of CDA to stimulate APCs and innate 
immunity, the bacterial chassis itself provides supplementary immune stimulation within the 
TME via activation of pattern recognition receptors (PRRs) such as the activation of TLR4 by 
the gram-negative bacterial cell wall component endotoxin or LPS. Upon i.t. administration, 
SYNB1891 is taken up by APCs, such as dendritic cells and macrophages, within the TME. 
Once the SYNB1891 bacteria are phagocytosed by APCs, this leads to the intracellular release of 
the CDA contained inside of the SYNB1891 bacteria, which activates the STING pathway and 
leads to upregulation of Type I IFNs. In addition, parallel pathways of innate immune activation 
are triggered through PRRs, such as endotoxin stimulation of TLR4, which lead to the release of 
additional cytokines. The release of these pro-inflammatory cytokines and activation of APCs 
subsequently initiates and promotes antitumor immunity and immune rejection of the tumor. 
SYNB1891 was engineered with several biocontainment and safety features to target the 
production of CDA to the TME and inhibit the proliferation of the bacterial chassis both inside 
and outside the tumor. Genomic insertion of a gene encoding DacA, a di-adenylate cyclase from 
the bacterium Listeria monocytogenes, was made within the EcN chromosome. The DacA 
enzyme catalyzes the production of CDA from two molecules of adenosine triphosphate (ATP). 
The dacA gene was placed under the regulatory control of an anaerobic-inducible promoter (the 
fumarate and nitrate reductase regulator promoter [PfnrS]) and the anaerobic-responsive 
transcriptional activator fumarate and nitrate reductase (FNR). These regulatory components are 
meant to ensure that the generation of CDA only takes place in the anoxic environment of the 
tumor. From a safety and control perspective, SYNB1891 was engineered to be an auxotrophic 
strain through a deletion of the dapA gene encoding 4-hydroxy-tetrahydropicolinate synthase and 
a thyA gene encoding the thymidylate synthase. DapA deletion renders SYNB1891 unable to 
synthesize diaminopimelic acid (DAP), thereby preventing the proper formation of the bacterial 
cell wall unless the strain is supplemented with DAP exogenously. Thymidylate synthase 
catalyzes the reductive methylation of 2’-deoxyuridine-5’-monophosphate (dUMP) to 
2’-deoxythymidine-5’-monophosphate (dTMP) and without that, SYNB1891 can only grow 
in a thymidine-rich environment. For contract manufacturing facility access, SYNB1891 was 
also modified with a deletion of an approximately 9 kilobase (kb) pair segment of an endogenous 
prophage sequence, Φ, which prevents the cells from being able to express infectious 
bacteriophage particles. Finally, all antibiotic resistance genes utilized during the engineering 

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and development of SYNB1891 were removed to ensure antibiotic sensitivity and enable 
clearance of bacteria by available treatments. 
Figure 1: 
Design of the Engineered E. coli Nissle Strain SYNB1891 
 
Abbreviations: ΔΦ = deletion of the prophage sequence endogenous to E. coli Nissle; ATP = adenosine 
triphosphate; CDA = cyclic-di-AMP; dacA or DacA = di-adenylate cyclase gene or enzyme; ΔdapA = deletion of 
dapA gene leading to diaminopimelate auxotrophy; LPS = lipopolysaccharide or endotoxin; Pfnrs = fumarate and 
nitrate reductase regulator promoter; PRR = pattern recognition receptor; ΔthyA = deletion of thyA gene leading to 
thymidine auxotrophy; TME = tumor microenvironment 
The combination of a genetically modified strain of bacteria engineered to deliver a STING 
agonist (like CDA) would be a strategy that marries both the targeted delivery of STING 
agonists to phagocytic APCs and the complimentary stimulation of the innate immune system 
through the activation of PRRs. The utilization of microbial based therapies for the treatment of 
human cancer can be charted back to the work of Dr. William B. Coley in 1891 when he began 
treating patients with living bacterial cultures after observing spontaneous regressions in patients 
with streptococcal infections (McCarthy 2006). Over the following 125 years, numerous 
bacterial based therapies for cancer have been investigated, with the majority utilizing attenuated 
pathogens such as Salmonella typhimurium, Clostridium novyi, and Listeria monocytogenes 
(Felgner et al 2016). Unfortunately, efforts to improve safety via strain attenuation often led to 
reductions in efficacy and attempts to improve efficacy by engineering in additional functions 
are often limited due to a lack of tools and approaches for genetic manipulation. Synthetic 
biology represents a promising means to develop novel therapies with combinatorial, rationally 
designed functionalities and safety features (Bashor et al 2018; Kitada et al 2018).  
With these consideration in mind, the rationale for the development of SYNB1891 was to utilize 
synthetic biology techniques to create a live biotherapeutic that provides multi-pathway innate 
immune activation localized to the TME and STING pathway induction targeted to phagocytic 
APCs. By utilizing the nonpathogenic EcN as a “vector” for the delivery of the STING agonist 
CDA, SYNB1891 has both broad innate immune activating and APC target STING activating 
functionalities. From a safety and control perspective, SYNB1891 was engineered to produce 
CDA under the hypoxic conditions found in tumors, contains dual DAP and thymidine 

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auxotrophies to inhibit bacterial proliferation and does not contain any antibiotic resistance 
genes. The administration of SYNB1891 as an immunotherapy for cancer is a promising 
approach and has shown activity and safety in several experimental models of cancer. 
2.2.1. 
Nonclinical Studies 
To evaluate the in vitro activity of the engineered bacteria SYNB1891, bacterial cells were 
expanded under anaerobic conditions to induce its agonist-producing genetic circuit. After 
4 hours of culture, bacterial cell pellets were harvested, and intracellular CDA levels were 
analyzed by liquid chromatography/tandem mass-spectrometry (LC-MS/MS). The data shown in 
Figure 2A are representative of these types of studies and demonstrate the capacity of the 
SYNB1891 to produce high levels of the STING-agonist molecule, CDA, as compared to 
nonengineered bacteria (SYN differs from SYNB1891 in that it lacks the dacA gene insertion). 
To evaluate the biological activity of SYNB1891, bacteria were expanded in vitro and induced 
under anaerobic conditions as above to express CDA. Immortalized murine macrophage cells 
(RAW cells) were co-cultured at various ratios of bacteria-to-mammalian cells with either a 
nonengineered bacteria (SYN) or SYNB1891. Two hours post-treatment, culture supernatants 
were harvested and IFNβ was quantified by an enzyme-linked immunosorbent assay (ELISA). 
The data shown in Figure 2B are representative of these types of studies and demonstrate 
dose-dependent biological activity of SYNB1891 for the activation of the STING pathway in a 
biologically relevant antigen presenting cell and subsequent downstream production of IFNβ.  
Figure 2: 
In Vitro CDA Production and Biological Activity of SYNB1891  
A 
 
B 
 
  
To demonstrate the antitumor activity of SYNB1891 in vivo, we employed two different 
syngeneic mouse models of cancer: the B16.F10 melanoma model and the A20 lymphoma 
model. These tumor models are representative of tumors lacking significant immune infiltrate 
and are known as “cold tumors”. They are also representative of the tumor types we intend to 
treat in the Phase 1 clinical trial. In data not shown here, the pharmacokinetic and 
pharmacodynamic activity of SYNB1891 in B16.F10 tumors after a single i.t. administration 
were evaluated. In these studies, dose and time dependent increases in tumoral levels of CDA, 
IFNα and β (IFNα1 and IFNβ1) and other pro-inflammatory cytokines (IL-6, granulocyte-

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macrophage colony-stimulating factor [GM-CSF]) were observed after a single i.t. 
administration of SYNB1891. Moreover, there was a dose- and time-dependent profile observed 
for the bacterial persistence of SYNB1891 in the tumor, with lower doses of SYNB1891 being 
cleared from the tumor more rapidly than higher doses. In addition, blood analysis demonstrated 
no detectable SYNB1891 present at any dose or time point evaluated in this study. These 
experiments demonstrated that SYNB1891 can produce CDA in vivo in the tumor, this CDA is 
biologically active and capable of activation of the STING pathway and additionally, the EcN 
bacterial chassis elicits further innate immune pathway activation (through for example 
LPS-mediated activation of TLR4), as expected. 
To assess the antitumor activity of SYNB1891, B16.F10 tumor bearing mice were established 
and treated with three (3) doses separated by 3 days (Q3D × 3) of either of SYNB1891 or 
unengineered EcN (1 × 109 live cells/dose), or saline controls and tumor growth was monitored 
over the timeframe of the study (21 days). The data in Figure 3A show that compared to both the 
saline and unengineered EcN controls (SYNB), SYNB1891 administration results in significant 
antitumor control. Moreover, only SYNB1891 treatment led to complete tumor regressions 
(CRs). However, the administration of the unengineered EcN control still led to some level of 
tumor growth inhibition, supporting in vivo the contribution of chassis-mediated activation of 
PRRs to the antitumor activity of SYNB1891. To explore the pharmacologic activity of 
SYNB1891, we established A20 lymphoma tumors in mice and then treated them with 
3 different dose levels of SYNB1891 (1 × 108, 5 × 108, 1 × 109 live cells/dose; every 3 days × 3) 
and monitored tumor growth throughout the time frame of the study. The results shown in 
Figure 3B show that administration of SYNB1891 demonstrates dose-dependent antitumor 
activity and importantly, dose-dependent generation of CRs. Finally, to investigate the potential 
for SYNB1891 to systemic antitumor immunity, we treated A20 tumor bearing mice with either 
SYNB1891 or saline control. Mice that underwent complete tumor regression in response to 
SYNB1891 treatment (CRs) were then monitored for additional ~35 days after regression to 
verify CRs and then these animals were re-challenged with A20 tumor cells and tumor growth 
after re-challenge was compared to tumor growth in naïve age-matched controls. Figure 3C 
shows that the re-challenge of mice that were previously cured of their tumors by SYNB1891 
treatment were immune to tumor re-establishment whereas naïve, age-matched control animals 
demonstrated robust tumor growth similar to what had been observed with the initial saline 
control treated animals. 

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Figure 3: 
Antitumor, Pharmacologic and Systemic Immunity Activity of SYNB1891 
A 
 
B 
 
C 
 
From a safety perspective, as mentioned above, SYNB1891 has been engineered with dual 
auxotrophies, deletion of dapA and thyA genes (∆dapA, ∆thyA), as biosafety and control features. 
These genetic alterations render SYNB1891 unable to proliferate in absence of exogenous 
addition of the products of dapA and thyA (dipimelate and thymidine, respectively). These 
molecules are found at extremely low to negligible levels in tissues and systemic circulation as 
well as the external environment. Studies of in vitro bacterial cell cultures and in vivo in mice 
have demonstrated the inability of SYNB1891 to grow without the addition of these molecules. 
Additionally, SYNB1891 also lacks any antibiotic resistance cassettes and has been shown to be 
sensitive to a broad panel of antibiotics, further strengthening the safety control over SYNB1891. 
A Good Laboratory Practice (GLP) toxicology study was performed in A20 tumor-bearing male 
and female mice. Intratumoral administration of SYNB1891 was given weekly for 4 weeks at 
doses of 4.7 × 107, 4.7 × 108, and 4.7 × 109 live cells/dose. SYNB1891was well tolerated in mice 
at the dose level of 4.7 × 107 live cells/dose. Based on the SYNB1891-related toxicological 
profile (mild injection site reactions and elevations in serum cytokine levels, no significant 
changes in body weight, slight increases in spleen weights and splenic extramedullary 
hematopoiesis), the biodistribution observations (no SYNB1891 was found in any tissue or body 
fluid examined for the 4.7 × 107 live cell/dose level) and the lack of mortality, the low dose of 
4.7 × 107 live cells/dose was considered the highest nonseverely toxic dose (HNSTD) of 
SYNB1891. This dose, 4.7 × 107, is 47 times higher than the proposed starting dose of 
SYNB1891 (1 × 106 live cells/dose) in the Phase 1 study. 

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2.2.1.1. 
Summary of the Nonclinical Development Program 
In summary, SYNB1891 is an engineered strain of EcN that was designed to efficiently deliver 
the STING pathway agonist CDA to the TME and elicit activation of innate immune system. In 
vitro experiments demonstrate that CDA is produced at high levels under anaerobic conditions 
and that the CDA is biologically active in a macrophage cell-based assay, respectively. Studies in 
tumor-bearing mice demonstrate that SYNB1891 delivered by intratumoral administration is able 
to produce CDA locally within the TME leading to acute increases in tumoral levels of both 
IFNβ and pro-inflammatory cytokines. These increases in innate immune signaling correlate with 
dose dependent antitumor activity and complete tumor regressions. Importantly, the complete 
tumor regressions elicited by SYNB1891 led to the generation of long-term systemic immunity 
as evidenced by tumor rejections upon re-challenge in mice that had previously undergone 
complete regressions.  
Finally, a GLP toxicology study in tumor-bearing mice did not reveal any adverse findings at the 
dose of 4.7 × 107 live cells/dose given once weekly for 24 days; therefore, this dose level was 
determined to be the HNSTD of SYNB1891. The preclinical development program therefore 
supports the further development of SYNB1891 as an immunotherapeutic treatment for cancer, 
as outlined further in Section 2.4. 
2.3. 
Background of Atezolizumab 
Atezolizumab is a humanized immunoglobulin G1 (IgG1) monoclonal antibody that targets 
PD-L1 and inhibits the interaction between programmed death-ligand 1 (PD-L1) and its 
receptors, programmed cell death protein-1 (PD-1) and B7-1 (also known as cluster of 
differentiation [CD] 80), both of which function as inhibitory receptors expressed on T cells. 
Therapeutic blockade of PD-L1 binding by atezolizumab has been shown to enhance the 
magnitude and quality of tumor specific T-cell responses, resulting in improved antitumor 
activity (Fehrenbacher et al 2016; Rosenberg et al 2016). Atezolizumab has minimal binding to 
Fc receptors, thus eliminating detectable Fc effector function and associated antibody-mediated 
clearance of activated effector T cells. 
Atezolizumab is currently approved in the United States as a single agent or as a component of 
combination therapy for several indications, including urothelial carcinoma, nonsmall cell lung 
cancer, triple-negative breast cancer, and small cell lung cancer. Atezolizumab has demonstrated 
antitumor activity in both nonclinical models and cancer patients and is being investigated as a 
potential therapy (as a single agent or in combination with chemotherapy, targeted therapy, or 
immunotherapy) in a wide variety of malignancies in addition to the approved indications. 
The most frequently reported adverse reactions (≥ 20% of patients) observed with atezolizumab 
as a single agent have included fatigue/asthenia, nausea, cough, dyspnea, and decreased appetite. 
Alopecia, constipation, and diarrhea have also been observed in ≥ 20% of patients when 
atezolizumab is administered in combination with other agents. Adverse events with potentially 
immune-related causes consistent with an immunotherapeutic agent, including rash, influenza-
like illness, endocrinopathies, hepatitis or transaminitis, pneumonitis, colitis, and myasthenia 
gravis, have been observed. To date, these events have been manageable with treatment and/or 
interruption of atezolizumab treatment. 

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Refer to the atezolizumab Investigator’s Brochure for nonclinical and clinical study results and 
detailed safety information. 
2.4. 
Rationale for the Study 
As outlined in Section 2.1, the ability to engineer a modified strain of nonpathological bacteria 
(EcN with DAP and thymidine [THY] auxotrophies, and no antibiotic resistance genes) with the 
ability to deliver a STING agonist (c-di-AMP) that is active only under hypoxic conditions (like 
a tumor, not in normal tissue or blood) is a strategy that combines both the known stimulation of 
the innate immune system with a target important to the release of Type 1 IFN. 
This rationale lends support to the investigation of i.t. administration of SYNB1891, which in 
preclinical studies in mouse tumor models, is taken up by APCs leading to CDN production, 
STING activation and the release of type 1 interferons (IFN-α1 and IFN-β1). In addition, 
chassis-mediated engagement of PRRs on APCs (through for example the interaction of 
bacterial-derived LPS with its cognate receptor TLR4) further stimulates innate immunity. This 
ability of SYNB1891 to dually activate the innate immune system subsequently promotes the 
initiation of antitumor immune responses in the injected tumor, as well as the demonstration of 
long-term immunological memory. 
The strategy of the current clinical development plan for SYNB1891 is based on an initial 
priming of the tumor microenvironment with SYNB1891, followed by targeted checkpoint 
inhibition with atezolizumab administered concurrently in continuous cycles to induce an 
optimal tumor response. Agonism of the STING pathway (and other PRRs) by SYNB1891 will 
lead to productive T cell priming and trafficking, but sustained antitumor activity is likely to 
require inhibition of the PD-1/PD-L1 pathway to address the T cell “exhaustion” that develops 
after priming. Therefore, the scientific rationale underlying the combination of SYNB1891 with 
atezolizumab is to stimulate multiple components of the immune response to cancer; innate 
immune activation, effector T cell activation, reinvigorating exhausted tumor-associated T cells, 
and prevention of further T cell exhaustion. 
Study SYNB1891-CP-001 represents the first clinical study of SYNB1891. As such, a modified 
toxicity probability interval (mTPI) dose-finding algorithm (Ji et al 2013) will be implemented to 
determine the maximum tolerated dose (MTD) of single-agent therapy with SYNB1891 and 
recommended Phase 2 dose (RP2D) of SYNB1891 in combination with atezolizumab in patients 
with advanced/metastatic solid tumors or lymphoma. In preclinical toxicology studies, 
SYNB1891 was well tolerated in mice at doses up to 4.7 × 107 live cells per dose, which was 
considered to be the HNSTD of SYNB1891. This HNSTD is 47 times higher than the proposed 
starting dose of SYNB1891 (1 × 106 live cells/dose) in this first-in-human Phase 1 study. Upon 
demonstration of tolerability in accordance with the mTPI algorithm, the dose of SYNB1891 in 
Arm 1 will be subsequently escalated in approximately 3-fold increments. 
After all patients in Arm 1 Cohort 4 have completed their Cycle 1 DLT safety evaluation, Arm 2 
will investigate SYNB1891 starting at the Arm 1 Cohort 3 dose level, when given in 
combination with atezolizumab (1200 mg IV Q3W) in patients with advanced/metastatic solid 
tumors or lymphoma. Although the primary purpose of the study is to define the MTD/RP2D of 
study treatment, the broad patient population and standard frequency of disease assessments 
(every 2 cycles on treatment) may also enable the evaluation of any preliminary clinical activity 
elicited by the single-agent and/or combination regimens. 

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3. 
STUDY OBJECTIVES AND ENDPOINTS 
The overall objective is to evaluate the safety and tolerability of escalating doses of i.t. injections 
of SYNB1891 to determine the single-agent MTD as monotherapy and the RP2D in combination 
with atezolizumab. 
3.1. 
Primary 
Incidence of dose-limiting toxicities (DLTs): Percentage of patients who experience a DLT 
3.2. 
Secondary 
Secondary objectives include evaluation of the following: 
• Nature, incidence, and severity of all adverse events (AEs) and SAEs according to the 
National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events 
(CTCAE), version 5.0 
• Objective response rate (ORR) in target lesions as determined by the Response 
Evaluation Criteria in Solid Tumors, version 1.1 (RECIST 1.1) (Eisenhauer et al 
2009), immune-related RECIST (iRECIST) (Seymour et al 2017), and/or the 
Lymphoma Response to Immunomodulatory Therapy Criteria (LYRIC) (Cheson et al 
2016), with evaluations of the SYNB1891-injected tumor(s) and an overall response 
of up to 5 noninjected target lesions 
3.3. 
Exploratory 
Exploratory objectives include evaluation of the following: 
• Duration of response or time to progression for evaluated tumors as determined by 
RECIST 1.1, iRECIST, and/or LYRIC 
• Pharmacodynamic (PD) response biomarkers including tumor-infiltrating 
lymphocytes (TIL) characterization, immunomodulatory cytokine gene expression 
and IFNβ responsive genes to be monitored in proximal and (if available) distal lesion 
biopsies at baseline and on study; systemic PD effects will be evaluated by 
assessment of changes in serum cytokine levels (including but not limited to tumor 
necrosis factor α [TNFα], interleukin [IL] 2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-13, 
IL1β, IL 1 receptor antagonist [IL1RA], IL 2 receptor alpha [IL2Rα], and IFNγ) at 
baseline and while on study 
• Kinetics of SYNB1891 within the injected tumor will be assessed by quantitative 
polymerase chain reaction (qPCR) from predose (baseline) to predose Cycle 1 Day 8 
from a fine needle aspirate (FNA); systemic kinetics of SYNB1891 will be monitored 
by qPCR from blood at predose (baseline) and 6 hours and 24 hours postdose in 
Cycle 1 

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4. 
STUDY DESIGN 
4.1. 
Study Design Overview 
This Phase 1, open-label, multicenter, 2-arm study will be conducting using the mTPI 
dose-finding design (Ji et al 2013). Cohorts of patients will be enrolled to receive escalating 
doses of SYNB1891 administered by i.t. injection until the target DLT range (approximately 
30%) for SYNB1891 monotherapy is determined based on DLTs observed in Cycle 1 (Arm 1). 
The dose selected as achieving the target DLT range will be considered the MTD. After all 
patients in Arm 1 Cohort 4 have completed their Cycle 1 DLT safety evaluation, Arm 2 will 
enroll its first cohort starting at the Arm 1 Cohort 3 dose level, with SYNB1891 administered by 
i.t. injection in combination with atezolizumab administered as an intravenous (IV) infusion at a 
dose of 1200 mg every 3 weeks (Q3W) until the RP2D for the combination regimen is 
determined (see Figure 4). 
The mTPI algorithm (as further discussed in Section 4.2.3) will be implemented separately in 
each arm. 
Eligible patients will be enrolled sequentially and will receive the first dose of study treatment 
within 28 days of screening. 
Safety will be monitored continuously by documentation of AEs, SAEs, clinical laboratory 
measurements, vital signs, and physical examinations. DLTs, as defined in Section 4.2.4, will be 
evaluated through the end of the first cycle. 
Disease status will be assessed by the local Investigator using appropriate imaging every 2 cycles 
for the duration of study treatment administration to evaluate the SYNB1891-injected lesion(s) 
and an overall response of up to 5 noninjected target lesions in accordance with RECIST 1.1 
(Eisenhauer et al 2009 and Appendix 1), iRECIST (Seymour et al 2017 and Appendix 2), and/or 
LYRIC (Cheson et al 2016 and Appendix 3). 
Tumor biopsies and blood samples will be collected at baseline and at prespecified time points 
on study to evaluate the pharmacokinetics (PK), as measured by qPCR bacterial kinetics, and PD 
effects of study treatment. 
 

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Figure 4: 
SYNB1891-CP-001 Study Design 
  
 
Abbreviations: CPI = checkpoint inhibitor; DLT = dose-limiting toxicity; MTD = maximum tolerated dose; mTPI = modified toxicity probability interval; 
RP2D = recommended Phase 2 dose; SRC = Safety Review Committee 

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4.2. 
Study Dosing Regimens 
4.2.1. 
Treatments Administered 
Patients enrolled to Arm 1 may receive up to four 21-day cycles of SYNB1891 monotherapy. On 
Days 1, 8, and 15 of Cycle 1 and Day 1 of Cycles 2 through 4, patients will receive an i.t. 
injection of SYNB1891 into an eligible lesion. If the initial eligible lesion undergoes complete 
regression and is no longer injectable (at the discretion of the Investigator), a subsequent eligible 
lesion (until no more eligible lesions remain) may be injected.  
At the end of Cycle 4, patients in Arm 1 who do not have progressive disease (i.e., those who 
achieve and sustain complete response [CR], partial response [PR], or stable disease [SD]) may 
receive additional cycles of SYNB1891 administered by i.t. injection on Day 1 of each cycle for 
up to 24 months (i.e., Cycles 5 to 35) after the initial dose of study treatment until documentation 
of progressive disease or other discontinuation criteria, satisfaction of a predefined study 
stopping rule, or no eligible lesions remain.  
Patients enrolled to Arm 2 may receive up to four 21-day cycles with SYNB1891 administered 
by i.t. injection into an eligible lesion on Days 1, 8, and 15 of Cycle 1 and Day 1 of Cycles 2 
through 4. In addition, atezolizumab will be administered in accordance with its recommended 
dose and schedule (1200 mg IV Q3W) on Day 1 of each of the 4 planned cycles. On days when 
atezolizumab and SYNB1891 are both administered, SYNB1891 will be administered first, 
followed by at least 1 hour of observation prior to the atezolizumab infusion. Patients in Arm 2 
who do not have progressive disease (i.e., those who achieve and sustain CR, PR, or SD) at the 
end of Cycle 4 on combination therapy may receive additional cycles of SYNB1891 and 
atezolizumab for up to 24 months (i.e., Cycles 5 to 35) after the initial dose of study treatment 
until documentation of progressive disease or other discontinuation criteria, satisfaction of a 
predefined study stopping rule, or no eligible lesions remain. 
Locating and/or injecting the lesion may be performed using guided imaging at the discretion of 
the Investigator. 
4.2.2. 
Postdose Monitoring 
The initial patient in each Arm 1 cohort (Sentinel patient) will be monitored for at least 6 hours 
following the first (Cycle 1 Day 1) i.t. injection of SYNB1891 (or overnight, at the discretion of 
the Investigator) for evaluation of any procedural complication or acute toxicity (i.e., injection 
reactions or cytokine release syndrome) and for collection of postdose blood samples. Safety 
data must be reviewed on or after Day 7 and deemed acceptable by the Investigator and the 
Sponsor and contract research organization (CRO) Medical Monitors before the Sentinel patient 
receives any further injections and before any subsequent patients are dosed in that cohort. 
For the remainder of Cycle 1 dosing for the Sentinel patient and for all dosing for non-Sentinel 
patients, SYNB1891 injections will be administered in the outpatient setting and patients will be 
closely observed at the clinic for at least 6 hours following each injection for evaluation of any 
procedural complication or acute toxicity (i.e., injection reactions or cytokine release syndrome) 
and for collection of postdose blood samples. All patients will be contacted by telephone on 
Cycle 1 Day 3 to monitor for signs of cytokine release syndrome (see Section 4.4).  

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4.2.3. 
Dose-finding with the mTPI Algorithm 
In both study arms, each cohort will initially comprise 3 patients (a Sentinel patient and 
2 non-Sentinel patients), with subsequent dose escalation governed by an mTPI design 
(Ji et al 2013). 
The starting dose of SYNB1891 in the first cohort of Arm 1 will be 1 × 106 live cells and will be 
increased in approximately 3-fold increments in subsequent cohorts until MTD determination. If 
no MTD is identified, then the MTD will be considered the maximum dose at which a sufficient 
number of patients have been treated such that if 14 patients were administered that dose then 
either escalation or staying at the current dose would be recommended according to Table 1. For 
example, if 8 patients were administered a dose level with 0 DLTs observed, even if all 
remaining 6 patients had a DLT, Table 1 would indicate “stay at the current dose”; thus, the 
remaining 6 patients are not required to evaluate the MTD. 
A mTPI design with a target DLT rate of approximately 30% will be applied for dose escalation 
and confirmation to determine the MTD/RP2D. In Arm 1, predetermined dose levels of 1 × 106, 
3 × 106, 1 × 107, 3 × 107, 1 × 108, 3 × 108, and 1 × 109 live cells will be explored independently, 
with additional dose levels as necessary to determine the MTD. A de-escalation dose of 3 × 105 
live cells is available if the starting dose is deemed not tolerable. All dose escalation and de-
escalation decisions will be based on the occurrence of DLTs at a given dose during Cycle 1 and 
will be made jointly by the Investigators and the Sponsor. 
In Table 1, the number of patients treated is indicated in the columns and the number of patients 
who experienced a DLT is indicated in the rows. Dosing decisions include escalate to the next 
higher dose (E), stay at the current dose (S), de-escalate to the next lower dose (D), and 
de-escalate to a lower dose and never test this dose again (i.e., unacceptably toxic dose; DU). 
During dose escalation, a minimum of 3 patients are required at each dose. Depending on accrual 
rate and occurrence of DLTs, 3, 4, 5 or 6 patients may be enrolled at each new dose until the last 
of those patients completes the Cycle 1 DLT assessment period. For example, the dose escalation 
rules will proceed as follows if 3 patients are enrolled: if 0 of the first 3 patients at a given dose 
level develops a DLT, then the dose can be escalated to the next level without further expansion. 
If 1 of the first 3 patients at a given dose level develops a DLT, no more than an additional 3 
patients should be enrolled at this dose level until additional DLT data are available since this 
dose would be considered unacceptably toxic if all 3 of the additional patients experience a DLT 
(i.e., 4 of 6 patients). If 2 of the first 3 patients at a given dose level develop a DLT, the dose will 
be de-escalated to the next lower level. If 3 of the first 3 patients at a given dose level develop a 
DLT, this dose will be considered unacceptably toxic (i.e., the dose will be de-escalated and 
never re-escalated to that dose again). The same principle will be applied whether 3, 4, 5 or 6 
patients are enrolled in the same dose cohort according to Table 1. 
Based on the mTPI design, the number of patients who are enrolled at a dose, but are not yet 
fully evaluable for DLT assessment, may not exceed the number of remaining patients who are at 
risk of developing a DLT before the dose would be considered unacceptably toxic (denoted as 
DU in Table 1). To determine how many more patients can be enrolled at a dose level, one can 
count steps in a diagonal direction (down and to the right) from the current cell to the first cell 
marked DU. In total, 3 to 14 patients may be enrolled at a given dose level. 
Dose escalation and confirmation will end after 14 patients have been treated at any of the 
selected doses. The pool-adjacent-violators-algorithm (Ji et al 2013) will be used to estimate the 

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DLT rates across doses. The dose with an estimated DLT rate closest to 30% may be treated as a 
preliminary MTD. Using the mTPI algorithm, the totality of the data will be considered before a 
dose is selected to carry forward to the next cohort, and the escalation schedule may be adjusted 
based on PK, PD, and safety data emerging throughout the study to determine the MTD/RP2D. 
Note that while 30% was the target toxicity rate used to generate the guidelines in Table 1, the 
observed rates of patients with DLTs at the MTD may be slightly above or below 30%. 
Table 1: 
Dose-finding Rules per mTPI Design 
Number of participants 
with at least 1 DLT 
Number of Participants Evaluable for DLT at Current Dose 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 
0 
E 
E 
E 
E 
E 
E 
E 
E 
E 
E 
E 
E 
1 
S 
S 
S 
E 
E 
E 
E 
E 
E 
E 
E 
E 
2 
D 
S 
S 
S 
S 
S 
S 
S 
E 
E 
E 
E 
3 
DU 
DU 
D 
S 
S 
S 
S 
S 
S 
S 
S 
S 
4 
 
DU 
DU 
DU 
D 
D 
S 
S 
S 
S 
S 
S 
5 
 
 
DU 
DU 
DU 
DU 
DU 
D 
S 
S 
S 
S 
6 
 
 
 
DU 
DU 
DU 
DU 
DU 
DU 
D 
S 
S 
7 
 
 
 
 
DU 
DU 
DU 
DU 
DU 
DU 
DU 
D 
8 
 
 
 
 
 
DU 
DU 
DU 
DU 
DU 
DU 
DU 
9 
 
 
 
 
 
 
DU 
DU 
DU 
DU 
DU 
DU 
10 
 
 
 
 
 
 
 
DU 
DU 
DU 
DU 
DU 
11 
 
 
 
 
 
 
 
 
DU 
DU 
DU 
DU 
12 
 
 
 
 
 
 
 
 
 
DU 
DU 
DU 
13 
 
 
 
 
 
 
 
 
 
 
DU 
DU 
14 
 
 
 
 
 
 
 
 
 
 
 
DU 
E = escalate to the next higher dose; S = stay at the current dose; D = de-escalate to the next lower dose; 
DU = the current dose is unacceptably toxic. 
Target toxicity rate = 30% 
Flat noninformative prior Beta (1,1) is used as a prior and ε1=ε2=0.03 
 
After all patients in Arm 1 Cohort 4 have completed their Cycle 1 DLT safety evaluation, dosing 
will begin in Arm 2 starting at the Arm 1 Cohort 3 dose level. Dosing in the Arm 2 cohorts will 
increase in approximately 3-fold increments in subsequent cohorts until RP2D determination. 
Combination doses will not be escalated above the SYNB1891 single-agent MTD established in 
Arm 1. Once dosing in Arm 2 is initiated, patient allocation to cohorts will be managed by the 
Sponsor to ensure that a dosing level within Arm 2 is at least one dose level below the 
SYNB1891 monotherapy dose being evaluated in Arm 1. The atezolizumab dose will remain 
constant at 1200 mg Q3W for each dose level in Arm 2. 
In both study arms, enrollment will proceed in accordance with the following rules: 
• Review of the safety data for the first patient in a cohort (Sentinel patient) must be 
completed on or after Day 7 before the remaining 2 patients (non-Sentinel) in that 
cohort may be dosed (these 2 patients may be dosed concurrently). Observation of 
DLT(s) in a Sentinel patient will not necessarily preclude enrollment of subsequent 

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patients at the same dose level; rather, DLTs occurring in Sentinel patients will be 
reviewed individually by the SRC (consisting of the Sponsor Medical Monitor, the 
CRO Medical Monitor, all active Investigators, and other study personnel as needed) 
to determine appropriate dosing for subsequent patients. 
• After all patients in a cohort have been assessed for DLTs (i.e., after each patient 
either experiences a DLT or completes the end of Cycle 1 safety assessment, 
whichever occurs first), the SRC will review all available safety data from the cohort 
and determine whether to escalate to the next higher SYNB1891 dose, enroll 
additional patients at the current dose, de-escalate to the next lower dose, or declare 
that the study objectives or stopping rules have been met. The decision will be 
informed by the mTPI algorithm recommendation to achieve the targeted toxicity 
interval. 
• Patients must either experience a DLT during Cycle 1 or receive at least 2 of the 
3 planned SYNB1891 injections to be considered evaluable for DLT evaluations and 
contribute to dose-escalation decisions for a given cohort. Patients who withdraw 
from the study for any reason other than DLTs prior to receiving the second injection 
of SYNB1891 in Cycle 1 may be replaced. 
Once the RP2D of Arm 2 is determined, up to 20 additional patients may be enrolled in the 
RP2D cohort to fully characterize the safety profile of SYNB1891 in combination with 
atezolizumab. 
4.2.4. 
Definition of Dose-limiting Toxicity 
The occurrence of any of the following toxicities during Cycle 1 will be considered a DLT, if 
assessed by the Investigator to be possibly, probably, or definitely related to study treatment 
administration. 
1. Grade 4 nonhematologic toxicity (not laboratory) 
2. Grade 4 hematologic toxicity lasting ≥ 7 days, except thrombocytopenia: 
• Grade 4 thrombocytopenia of any duration 
• Grade 3 thrombocytopenia associated with clinically significant bleeding 
3. Any nonhematologic AE Grade ≥ 3 in severity should be considered a DLT, with the 
following exceptions: Grade 3 fatigue lasting ≤ 3 days; Grade 3 diarrhea, nausea, or 
vomiting without use of antiemetics or antidiarrheals per standard of care; Grade 3 rash 
without use of corticosteroids or anti-inflammatory agents per standard of care 
4. Any Grade 3 or Grade 4 nonhematologic laboratory value if: 
• Clinically significant medical intervention is required to treat the patient, or 
• The abnormality leads to hospitalization, or 
• The abnormality persists for > 1 week, or 
• The abnormality results in a drug-induced liver injury (DILI)  
• Exceptions: clinically nonsignificant, treatable, or reversible laboratory abnormalities 
including liver function tests, uric acid, etc. 
5. Febrile neutropenia Grade 3 or Grade 4: 

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• Grade 3 is defined as absolute neutrophil count (ANC) < 1000/mm3 with a single 
temperature of > 38.3°C (101°F) or a sustained temperature of ≥ 38°C (100.4°F) for 
more than 1 hour 
• Grade 4 is defined as ANC < 1000/mm3 with a single temperature of > 38.3°C 
(101°F) or a sustained temperature of ≥ 38°C (100.4°F) for more than 1 hour, with 
life-threatening consequences and urgent intervention indicated 
6. Sepsis, severe abscesses and/or ulcerations requiring surgical management 
7. Prolonged delay (>2 weeks) in initiating Cycle 2 due to treatment-related toxicity 
8. Investigator decision to discontinue study treatment for a treatment-related toxicity 
during Cycle 1 
9. Missing > 33% of study drug doses as a result of Grade 3 drug-related AE(s) during the 
first cycle 
10. Grade 5 toxicity 
4.3. 
Intrapatient Dose Modification 
Every effort should be made to administer study treatment on the planned dose and schedule. 
4.3.1. 
Dosing Delays and Interruptions 
Study treatment dosing delays will be permitted in any treatment cycle if unforeseen 
circumstances prevent the patient from returning to the clinic on the scheduled day(s). A 
maximum delay of 2 days in Cycle 1 will be permitted. If administration of study treatment is 
delayed by > 2 days in Cycle 1, that dose is considered missed and the patient should receive the 
next dose at the next visit. 
If a patient misses ≥ 2 SYNB1891 doses in Cycle 1, then the patient will be discontinued 
permanently from treatment and may be replaced (see Section 8.2.1). In Cycle 2 and beyond, if a 
patient misses the dose of SYNB1891, then the patient may be discontinued permanently from 
treatment, unless the Investigator’s assessment of the benefit/risk suggests otherwise (after 
consultation with Sponsor). If treatment is permanently discontinued, patients will continue to be 
followed for safety as indicated for end of treatment and follow-up. 
SYNB1891 treatment interruption can occur due to treatment-related toxicity, including Grade 3 
or higher infections or local inflammation requiring antibiotics, and the start of a new cycle may 
not occur until the following criteria have been met: 
• Nonhematologic toxicities have returned to either baseline or Grade ≤ 1, or at the 
Investigator’s discretion, Grade ≤ 2 if not considered a safety risk. This condition 
must be met within 14 days of the initial treatment interruption. 
• Hematologic toxicities: ANC ≥ 1000/mm3 or have returned to baseline levels; platelet 
count ≥ 50,000/ mm3 or has returned to baseline levels. This condition must be met 
within 14 days of the initial treatment interruption. 
• If a patient requires treatment with a systemic antibiotic on study, SYNB1891 should 
be held for the duration of the antibiotic regimen and for 5 half-lives after the last 
dose of antibiotics. Once the patient is apyretic after completion of the antibiotic 
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If the patient cannot meet the above conditions within the specified time frame, then study 
treatment should be permanently discontinued, unless the Investigator’s assessment of the 
benefit/risk suggests otherwise (after consultation with Sponsor). The patient may be replaced 
(see Section 8.2.1). 
Atezolizumab treatment may be temporarily suspended in patients experiencing toxicity 
considered to be related to study treatment. If corticosteroids are initiated for treatment of 
immune-mediated toxicity, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 
mg/day oral prednisone before atezolizumab can be resumed. If atezolizumab is withheld for > 
12 weeks after event onset, the patient will be discontinued from atezolizumab. However, 
atezolizumab may be withheld for > 12 weeks to allow for patients to taper off corticosteroids 
prior to resuming treatment. Atezolizumab can be resumed after being withheld for > 12 weeks if 
the Medical Monitor(s) agrees that the patient is likely to derive clinical benefit. Atezolizumab 
treatment may be suspended for reasons other than toxicity (e.g., surgical procedures) with 
Medical Monitor approval. The Investigator and the Medical Monitor(s) will determine the 
acceptable length of treatment interruption. 
4.3.2. 
Dose Reductions 
4.3.2.1. 
Dose Reductions for SYNB1891 
No dose reductions of SYNB1891 will be permitted in Cycle 1; any patient who requires such a 
modification will be permanently discontinued and may be replaced (see Section 8.2.1). After 
Cycle 1, SYNB1891 dose reductions are permitted in approximately 3-fold decrements after 
consultation with the Sponsor. While no specific dose reductions are required for Grade 1 or 2 
treatment-related toxicities, the Investigator should always manage patients according to medical 
judgment and assessment of risk/benefit for that patient. Patients experiencing recurrent or 
intolerable Grade 2 toxicity may resume dosing at the next lower dose level once the toxicity has 
resolved or recovery to Grade 1 or baseline has occurred. 
If more than 1 dose reduction is required, then the patient(s) are permanently discontinued from 
treatment but will be followed for end of treatment and follow-up assessments. 
Once a dose has been reduced, the patient should continue to receive that dose for all subsequent 
doses. In this setting, intrapatient dose escalation is not permitted. 
4.3.2.2. 
Dose Reductions for Atezolizumab 
No dose reductions of atezolizumab will be permitted in this study. 
4.4. 
Toxicity Management 
Participants should receive appropriate supportive care measures as deemed necessary by the 
treating Investigator. 
4.4.1. 
Adverse Events Associated with SYNB1891 
Guidelines for the management of patients who experience AEs considered to be potentially 
associated with SYNB1891 are provided in Table 2. 

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Table 2: 
Toxicity Management for Adverse Events Considered Potentially Associated 
with SYNB1891 
Event 
NCI CTCAE Grade 
Recommended Medical 
Management 
Premedication and 
Subsequent Dosing 
Cytokine release 
syndrome (may include 
associated AEs, e.g., 
fever, tachypnea, 
headache, tachycardia, 
hypotension, rash, 
hypoxia) 
Grade 1 
Fever with or without 
constitutional 
symptoms 
Increase vital sign and oxygen 
saturation monitoring as 
medically indicated until the 
patient is deemed medically 
stable in the opinion of the 
Investigator. 
Administer as planned 
Grade 2 
Hypotension 
responding to fluids; 
hypoxia responding to 
< 40% oxygen 
Increase vital sign and oxygen 
saturation monitoring as 
medically indicated until the 
patient is deemed medically 
stable in the opinion of the 
Investigator. 
Additional appropriate 
therapy may include, but is 
not limited to: 
IV fluids 
NSAIDs 
Acetaminophen 
Narcotics 
Oxygen 
Evaluate for infectious 
etiologies and treat 
neutropenia if present. 
Patient may be 
premedicated 1.5 hours 
(± 30 minutes) prior to 
study treatment 
administration with oral 
acetaminophen (500 to 
1000 mg) or equivalent 
dose of antipyretics. 
Grade 3 
Hypotension managed 
with one pressor; 
hypoxia requiring ≥ 
40% oxygen 
Appropriate therapy may 
include, but is not limited to: 
IV fluids 
NSAIDs 
Acetaminophen 
Narcotics 
Oxygen 
Pressors 
Corticosteroids 
Anti-IL6 (e.g., 
tocilizumab) 
Empiric antibiotics 
Monitor patients closely; 
consider an intensive care 
setting 
Discuss with the Sponsor 
prior to the resumption of 
study treatment. Upon 
approval by the Sponsor, 
resume SYNB1891 at a 
reduced dose upon AE 
resolution to baseline or 
Grade 1. 
 
Patient may be 
premedicated 1.5 hours 
(± 30 minutes) prior to 
study treatment 
administration with oral 
acetaminophen (500 to 
1000 mg) or equivalent 
dose of antipyretics. 

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Event 
NCI CTCAE Grade 
Recommended Medical 
Management 
Premedication and 
Subsequent Dosing 
Grade 4 
Life-threatening 
consequences; urgent 
intervention indicated 
Appropriate therapy may 
include, but is not limited to: 
IV fluids 
NSAIDs 
Acetaminophen 
Narcotics 
Oxygen 
Pressors 
Corticosteroids 
Anti-IL6 (e.g., 
tocilizumab) 
Empiric antibiotics 
Monitor patients closely; 
consider an intensive care 
setting. 
Permanently discontinue 
study treatment. 
Systemic infection 
Grade 3 or higher 
Appropriate therapy may 
include, but is not limited to: 
IV fluids 
NSAIDs 
Acetaminophen 
Narcotics 
Oxygen 
Pressors 
Empiric antibiotics 
Refer to Appendix 4 for 
EcN-sensitive antibiotics 
Perform local blood and urine 
cultures and sensitivities. 
Perform serum qPCR specific 
for EcN. 
Patients who require 
systemic antibiotic 
treatment should 
postpone dosing with 
SYNB1891 for the 
duration of the antibiotic 
regimen and for 
5 half-lives after the last 
dose of antibiotics and 
until the patient is 
apyretic. 
Local injection site 
reactions (may include 
associated AEs, e.g., 
abscess, infection, 
ulceration or necrosis, or 
severe tissue damage) 
Grade 3 or higher 
Consider surgical intervention 
as needed in addition to and in 
accordance with local 
standard of care, which may 
include, but is not limited to: 
NSAIDs 
Acetaminophen 
Antibiotics  
Permanently discontinue 
study treatment. 
Abbreviations: AE = adverse event; CTCAE = Common Terminology Criteria for Adverse Events; EcN = E. coli 
Nissle; IL = interleukin; IV = intravenous; NCI = National Cancer Institute; NSAID = nonsteroidal anti-
inflammatory drug; qPCR = quantitative polymerase chain reaction 
4.4.2. 
Adverse Events Associated with Atezolizumab 
4.4.2.1. 
Pulmonary Events 
Dyspnea, cough, fatigue, hypoxia, pneumonitis, and pulmonary infiltrates have been associated 
with the administration of atezolizumab. Patients will be assessed for pulmonary signs and 
symptoms throughout the study and will have imaging (e.g., computed tomography [CT] scans) 
of the chest performed at every tumor assessment. 

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All pulmonary events should be thoroughly evaluated for other commonly reported etiologies 
such as pneumonia or other infection, lymphangitic carcinomatosis, pulmonary embolism, heart 
failure, chronic obstructive pulmonary disease, or pulmonary hypertension. Management 
guidelines for pulmonary events are provided in Table 3. 
Table 3: 
Management Guidelines for Pulmonary Events, Including Pneumonitis 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Pulmonary event 
Grade 1 
• Continue atezolizumab and monitor closely. 
• Re-evaluate on serial imaging. 
• Consider patient referral to pulmonary specialist. 
Grade 2 
• Withhold atezolizumab for up to 12 weeks after event onset. a 
• Refer patient to pulmonary and infectious disease specialists 
and consider bronchoscopy or BAL. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day oral prednisone. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding 
atezolizumab, permanently discontinue atezolizumab and 
contact Medical Monitor(s). 
• For recurrent events, treat as a Grade 3 or 4 event. 
Grade 3 or higher 
• Permanently discontinue atezolizumab and contact Medical 
Monitor(s). 
• Bronchoscopy or BAL is recommended. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day oral prednisone. 
• If event does not improve within 48 hours after initiating 
corticosteroids, consider adding an immunosuppressive agent. 
• If event resolves to Grade 1 or better, taper corticosteroids over 
≥ 1 month. 
Abbreviations: BAL = bronchoscopic alveolar lavage; CTCAE = Common Terminology Criteria for Adverse Events; 
NCI = National Cancer Institute 
a Atezolizumab may be withheld for a longer period of time (i.e., > 12 weeks after event onset) to allow for corticosteroids 
(if initiated) to be reduced to the equivalent of ≤ 10 mg/day oral prednisone. The acceptable length of the extended period 
of time must be agreed upon by the Investigator and the Medical Monitor(s). 
b If corticosteroids have been initiated, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 mg/day oral 
prednisone before atezolizumab can be resumed. 
4.4.2.2. 
Hepatic Events 
Immune-mediated hepatitis has been associated with the administration of atezolizumab. Eligible 
patients must have adequate liver function, as manifested by measurements of total bilirubin and 
hepatic transaminases, and liver function will be monitored throughout study treatment. 
Management guidelines for hepatic events are provided in Table 4. 
Patients with right upper-quadrant abdominal pain and/or unexplained nausea or vomiting should 
have liver function tests (LFTs) performed immediately and reviewed before administration of 
the next dose of study drug. 

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For patients with elevated LFTs, concurrent medication, viral hepatitis, and toxic or neoplastic 
etiologies should be considered and addressed, as appropriate. 
Table 4: 
Management Guidelines for Hepatic Events 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Hepatic event 
Grade 1 
• Continue atezolizumab. 
• Monitor LFTs until values resolve to within normal limits or to 
baseline values. 
Grade 2 
All events: 
• Monitor LFTs more frequently until return to baseline values.  
Events of > 5 days duration: 
• Withhold atezolizumab for up to 12 weeks after event onset. a 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day oral prednisone. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding 
atezolizumab, permanently discontinue atezolizumab and 
contact Medical Monitor(s). 
Grade 3 or higher 
• Permanently discontinue atezolizumab and contact Medical 
Monitor(s). 
• Consider patient referral to gastrointestinal specialist for 
evaluation and liver biopsy to establish etiology of hepatic 
injury.  
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day oral prednisone. 
• If event does not improve within 48 hours after initiating 
corticosteroids, consider adding an immunosuppressive agent. 
• If event resolves to Grade 1 or better, taper corticosteroids over 
≥ 1 month. 
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; LFT = liver function test; NCI = National 
Cancer Institute 
a Atezolizumab may be withheld for a longer period of time (i.e., > 12 weeks after event onset) to allow for corticosteroids 
(if initiated) to be reduced to the equivalent of ≤ 10 mg/day oral prednisone. The acceptable length of the extended period 
of time must be agreed upon by the Investigator and the Medical Monitor(s). 
b If corticosteroids have been initiated, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 mg/day oral 
prednisone before atezolizumab can be resumed. 
4.4.2.3. 
Gastrointestinal Events 
Immune-mediated colitis has been associated with the administration of atezolizumab. 
Management guidelines for diarrhea or colitis are provided in Table 5. 
All events of diarrhea or colitis should be thoroughly evaluated for other more common 
etiologies. For events of significant duration or magnitude or associated with signs of systemic 
inflammation or acute-phase reactants (e.g., increased C-reactive protein, platelet count, or 
bandemia): perform sigmoidoscopy (or colonoscopy, if appropriate) with colonic biopsy, with 
3 to 5 specimens for standard paraffin block to check for inflammation and lymphocytic 
infiltrates to confirm colitis diagnosis. 

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Table 5: 
Management Guidelines for Gastrointestinal Events 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Diarrhea or colitis 
Grade 1 
• Continue atezolizumab. 
• Initiate symptomatic treatment. 
• Endoscopy is recommended if symptoms persist for > 7 days. 
• Monitor closely. 
Grade 2 
• Withhold atezolizumab for up to 12 weeks after event onset. a 
• Initiate symptomatic treatment. 
• Patient referral to GI specialist is recommended. 
• For recurrent events or events that persist > 5 days, initiate 
treatment with corticosteroids equivalent to 1−2 mg/kg/day oral 
prednisone.  
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding 
atezolizumab, permanently discontinue atezolizumab and 
contact Medical Monitor(s). 
Grade 3 
• Withhold atezolizumab for up to 12 weeks after event onset. a 
• Refer patient to GI specialist for evaluation and confirmatory 
biopsy. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day IV methylprednisolone and convert to 
1−2 mg/kg/day oral prednisone or equivalent upon 
improvement. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding 
atezolizumab, permanently discontinue atezolizumab and 
contact Medical Monitor(s). 
Grade 4 
• Permanently discontinue atezolizumab and contact Medical 
Monitor(s). 
• Refer patient to GI specialist for evaluation and confirmation 
biopsy. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day IV methylprednisolone and convert to 
1−2 mg/kg/day oral prednisone or equivalent upon 
improvement. 
• If event does not improve within 48 hours after initiating 
corticosteroids, consider adding an immunosuppressive agent. 
• If event resolves to Grade 1 or better, taper corticosteroids over 
≥ 1 month. 
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; GI = gastrointestinal; IV = intravenous; 
NCI = National Cancer Institute 
a Atezolizumab may be withheld for a longer period of time (i.e., > 12 weeks after event onset) to allow for corticosteroids 
(if initiated) to be reduced to the equivalent of ≤ 10 mg/day oral prednisone. The acceptable length of the extended period 
of time must be agreed upon by the Investigator and the Medical Monitor(s). 
b If corticosteroids have been initiated, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 mg/day oral 
prednisone before atezolizumab can be resumed. 
4.4.2.4. 
Endocrine Events 
Thyroid disorders, adrenal insufficiency, diabetes mellitus, and pituitary disorders have been 
associated with the administration of atezolizumab. Management guidelines for endocrine events 
are provided in Table 6. 
Patients with unexplained symptoms such as headache, fatigue, myalgias, impotence, 
constipation, or mental status changes should be investigated for the presence of thyroid, 
pituitary, or adrenal endocrinopathies. The patient should be referred to an endocrinologist if an 
endocrinopathy is suspected. Thyroid-stimulating hormone (TSH) and triiodothyronine and 

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thyroxine levels should be measured to determine whether thyroid abnormalities are present. 
Pituitary hormone levels and function tests (e.g., TSH, growth hormone, luteinizing hormone, 
follicle-stimulating hormone, testosterone, prolactin, adrenocorticotropic hormone levels, and 
adrenocorticotropic hormone stimulation test) and magnetic resonance imaging (MRI) of the 
brain (with detailed pituitary sections) may help to differentiate primary pituitary insufficiency 
from primary adrenal insufficiency. 
Table 6: 
Management Guidelines for Endocrine Events 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Hypothyroidism 
(Asymptomatic) 
Not applicable 
• Continue atezolizumab. 
• Initiate treatment with thyroid replacement 
hormone. 
• Monitor TSH weekly. 
Hypothyroidism 
(Symptomatic) 
Not applicable 
• Withhold atezolizumab. 
• Initiate treatment with thyroid replacement 
hormone. 
• Monitor TSH weekly. 
• Consider patient referral to endocrinologist. 
• Resume atezolizumab when symptoms are 
controlled and thyroid function is improving. 
Hyperthyroidism 
(Asymptomatic) 
Not applicable 
TSH ≥ 0.1 mU/L and < 0.5 mU/L: 
• Continue atezolizumab. 
• Monitor TSH every 4 weeks. 
TSH < 0.1 mU/L: 
• Follow guidelines for symptomatic 
hyperthyroidism. 
Hyperthyroidism 
(Symptomatic) 
Not applicable 
• Withhold atezolizumab. 
• Initiate treatment with antithyroid drug such as 
methimazole or carbimazole as needed. 
• Consider patient referral to endocrinologist. 
• Resume atezolizumab when symptoms are 
controlled and thyroid function is improving. 
• Permanently discontinue atezolizumab and contact 
Medical Monitor(s) for life-threatening immune-
mediated hyperthyroidism. 

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Event 
NCI CTCAE Grade 
Recommended Medical Management 
Symptomatic adrenal 
insufficiency  
Grade 2 or higher 
• Withhold atezolizumab for up to 12 weeks after 
event onset. a 
• Refer patient to endocrinologist. 
• Perform appropriate imaging. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day IV methylprednisolone and convert 
to 1−2 mg/kg/day oral prednisone or equivalent 
upon improvement. 
• If event resolves to Grade 1 or better and patient is 
stable on replacement therapy, resume 
atezolizumab. b 
• If event does not resolve to Grade 1 or better or 
patient is not stable on replacement therapy while 
withholding atezolizumab, permanently discontinue 
atezolizumab and contact Medical Monitor(s). 
Hyperglycemia 
Grade 1 or 2 
• Continue atezolizumab. 
• Investigate for diabetes. If patient has Type 1 
diabetes, treat as a Grade 3 event. If patient does 
not have Type 1 diabetes, treat as per institutional 
guidelines. 
• Monitor for glucose control. 
Grade 3 or higher 
• Withhold atezolizumab. 
• Initiate treatment with insulin. 
• Monitor for glucose control. 
• Resume atezolizumab when symptoms resolve and 
glucose levels are stable. 
Hypophysitis 
(pan-hypopituitarism)  
Grade 2 or 3 
• Withhold atezolizumab for up to 12 weeks after 
event onset. a 
• Refer patient to endocrinologist. 
• Perform brain MRI (pituitary protocol). 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day IV methylprednisolone and convert 
to 1−2 mg/kg/day oral prednisone or equivalent 
upon improvement. 
• Initiate hormone replacement if clinically indicated. 
• If event resolves to Grade 1 or better, resume 
atezolizumab. b 
• If event does not resolve to Grade 1 or better while 
withholding atezolizumab, permanently discontinue 
atezolizumab and contact Medical Monitor(s). 
• For recurrent hypophysitis, treat as a Grade 4 event. 

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Event 
NCI CTCAE Grade 
Recommended Medical Management 
Hypophysitis 
(pan-hypopituitarism)  
Grade 4 
• Permanently discontinue atezolizumab and contact 
Medical Monitor(s). 
• Refer patient to endocrinologist. 
• Perform brain MRI (pituitary protocol). 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day IV methylprednisolone and convert 
to 1−2 mg/kg/day oral prednisone or equivalent 
upon improvement. 
• Initiate hormone replacement if clinically indicated. 
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; IV = intravenous; MRI = magnetic resonance 
imaging; NCI = National Cancer Institute; TSH = thyroid-stimulating hormone 
a Atezolizumab may be withheld for a longer period of time (i.e., > 12 weeks after event onset) to allow for corticosteroids 
(if initiated) to be reduced to the equivalent of ≤ 10 mg/day oral prednisone. The acceptable length of the extended period 
of time must be agreed upon by the Investigator and the Medical Monitor(s). 
b If corticosteroids have been initiated, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 mg/day oral 
prednisone before atezolizumab can be resumed. 
4.4.2.5. 
Ocular Events 
An ophthalmologist should evaluate visual complaints (e.g., uveitis, retinal events). Management 
guidelines for ocular events are provided in Table 7. 

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Table 7: 
Management Guidelines for Ocular Events 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Ocular event 
Grade 1 
• Continue atezolizumab. 
• Patient referral to ophthalmologist is strongly recommended. 
• Initiate treatment with topical corticosteroid eye drops and 
topical immunosuppressive therapy. 
• If symptoms persist, treat as a Grade 2 event. 
Grade 2 
• Withhold atezolizumab for up to 12 weeks after event onset. a 
• Patient referral to ophthalmologist is strongly recommended. 
• Initiate treatment with topical corticosteroid eye drops and 
topical immunosuppressive therapy. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding 
atezolizumab, permanently discontinue atezolizumab and 
contact Medical Monitor(s). 
Grade 3 or higher 
• Permanently discontinue atezolizumab and contact Medical 
Monitor(s). 
• Refer patient to ophthalmologist. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day oral prednisone. 
• If event resolves to Grade 1 or better, taper corticosteroids over 
≥ 1 month. 
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; NCI = National Cancer Institute 
a Atezolizumab may be withheld for a longer period of time (i.e., > 12 weeks after event onset) to allow for corticosteroids 
(if initiated) to be reduced to the equivalent of ≤ 10 mg/day oral prednisone. The acceptable length of the extended period 
of time must be agreed upon by the Investigator and the Medical Monitor(s). 
b If corticosteroids have been initiated, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 mg/day oral 
prednisone before atezolizumab can be resumed. 
 
4.4.2.6. 
Immune-mediated Myocarditis 
Immune-mediated myocarditis has been associated with the administration of atezolizumab. 
Immune-mediated myocarditis should be suspected in any patient presenting with signs or 
symptoms suggestive of myocarditis, including, but not limited to, laboratory (e.g., B-type 
natriuretic peptide) or cardiac imaging abnormalities, dyspnea, chest pain, palpitations, fatigue, 
decreased exercise tolerance, or syncope. Immune-mediated myocarditis needs to be 
distinguished from myocarditis resulting from infection (commonly viral, e.g., in a patient who 
reports a recent history of gastrointestinal illness), ischemic events, underlying arrhythmias, 
exacerbation of preexisting cardiac conditions, or progression of malignancy. 
All patients with possible myocarditis should be urgently evaluated by performing cardiac 
enzyme assessment, an electrocardiogram (ECG), a chest X-ray, an echocardiogram, and a 
cardiac MRI as appropriate per institutional guidelines. A cardiologist should be consulted. An 
endomyocardial biopsy may be considered to enable a definitive diagnosis and appropriate 
treatment, if clinically indicated. 
Patients with signs and symptoms of myocarditis, in the absence of an identified alternate 
etiology, should be treated according to the guidelines in Table 8. 

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Table 8: 
Management Guidelines for Immune-mediated Myocarditis 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Immune-mediated 
myocarditis 
Grade 2 
• Withhold atezolizumab for up to 12 weeks after event onset a 
and contact Medical Monitor(s). 
• Refer patient to cardiologist. 
• Initiate treatment as per institutional guidelines and consider 
antiarrhythmic drugs, temporary pacemaker, ECMO, or VAD 
as appropriate. 
• Consider treatment with corticosteroids equivalent to 
1−2 mg/kg/day IV methylprednisolone and convert to 
1−2 mg/kg/day oral prednisone or equivalent upon 
improvement. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding 
atezolizumab, permanently discontinue atezolizumab and 
contact Medical Monitor(s). 
Grade 3 or higher 
• Permanently discontinue atezolizumab and contact Medical 
Monitor(s). 
• Refer patient to cardiologist. 
• Initiate treatment as per institutional guidelines and consider 
antiarrhythmic drugs, temporary pacemaker, ECMO, or VAD 
as appropriate. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day IV methylprednisolone and convert to 
1−2 mg/kg/day oral prednisone or equivalent upon 
improvement. 
• If event does not improve within 48 hours after initiating 
corticosteroids, consider adding an immunosuppressive agent. 
• If event resolves to Grade 1 or better, taper corticosteroids 
over ≥ 1 month. 
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; ECMO = extracorporeal membrane 
oxygenation; IV = intravenous; NCI = National Cancer Institute; VAD = ventricular assist device 
a Atezolizumab may be withheld for a longer period of time (i.e., > 12 weeks after event onset) to allow for corticosteroids 
(if initiated) to be reduced to the equivalent of ≤ 10 mg/day oral prednisone. The acceptable length of the extended period 
of time must be agreed upon by the Investigator and the Medical Monitor(s). 
b If corticosteroids have been initiated, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 mg/day oral 
prednisone before atezolizumab can be resumed. 
4.4.2.7. 
Infusion-related Reactions and Cytokine Release Syndrome 
No premedication is indicated for the administration of Cycle 1 of atezolizumab. However, 
patients who experience an infusion-related reaction (IRR) or cytokine release syndrome with 
atezolizumab may receive premedication with antihistamines, anti-pyretics, and/or analgesics 
(e.g., acetaminophen) for subsequent infusions. Metamizole (dipyrone) is prohibited in treating 
atezolizumab-associated IRRs because of its potential for causing agranulocytosis. 
IRRs are known to occur with the administration of monoclonal antibodies and have been 
reported with atezolizumab. These reactions, which are thought to be due to release of cytokines 

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and/or other chemical mediators, occur within 24 hours of atezolizumab administration and are 
generally mild to moderate in severity. 
Cytokine release syndrome is defined as a supraphysiologic response following administration of 
any immune therapy that results in activation or engagement of endogenous or infused T cells 
and/or other immune effector cells. Symptoms can be progressive, always include fever at the 
onset, and may include hypotension, capillary leak (hypoxia), and end-organ dysfunction 
(Lee et al 2019). Cytokine release syndrome has been well documented with chimeric antigen 
receptor T-cell therapies and bispecific T-cell engager antibody therapies but has also been 
reported with immunotherapies that target PD-1 or PD-L1 (Rotz et al 2017; Adashek et al 2019), 
including atezolizumab. 
There may be significant overlap in signs and symptoms of IRRs and cytokine release syndrome, 
and in recognition of the challenges in clinically distinguishing between the two, consolidated 
guidelines for medical management of IRRs and cytokine release syndrome are provided in 
Table 9. 
Table 9: 
Management Guidelines for Infusion-related Reactions and Cytokine Release 
Syndrome 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Fevera with or 
without 
constitutional 
symptoms 
Grade 1b 
• Immediately interrupt infusion 
• Upon symptom resolution, wait for 30 minutes and then restart 
infusion at half the rate being given at the time of event onset. 
• If the infusion is tolerated at the reduced rate for 30 minutes, the 
infusion rate may be increased to the original rate. 
• If symptoms recur, discontinue infusion of this dose. 
• Administer symptomatic treatment,c including maintenance of 
IV fluids for hydration. 
• In case of rapid decline or prolonged CRS (> 2 days) or in 
patients with significant symptoms and/or comorbidities, 
consider managing as per Grade 2. 
• For subsequent infusions, consider administration of oral 
premedication with antihistamines, anti-pyretics, and/or 
analgesics, and monitor closely for IRRs and/or CRS. 
Fevera with 
hypotension not 
requiring 
vasopressors 
 
and/or 
 
Hypoxia requiring 
low-flow oxygend 
by nasal cannula 
or blow-by 
Grade 2b 
• Immediately interrupt infusion. 
• Upon symptom resolution, wait for 30 minutes and then restart 
infusion at half the rate being given at the time of event onset. 
• If symptoms recur, discontinue infusion of this dose. 
• Administer symptomatic treatment.c 
• For hypotension, administer IV fluid bolus as needed. 
• Monitor cardiopulmonary and other organ function closely (in 
the ICU, if appropriate). Administer IV fluids as clinically 
indicated, and manage constitutional symptoms and organ 
toxicities as per institutional practice. 
• Rule out other inflammatory conditions that can mimic CRS 
(e.g., sepsis). If no improvement within 24 hours, initiate 
workup and assess for signs and symptoms of HLH or MAS. 
• Consider IV corticosteroids (e.g., methylprednisolone 
2 mg/kg/day or dexamethasone 10 mg every 6 hours). 

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Event 
NCI CTCAE Grade 
Recommended Medical Management 
• Consider anti-cytokine therapy.e 
• Consider hospitalization until complete resolution of symptoms. 
If no improvement within 24 hours, manage as per Grade 3, that 
is, hospitalize patient (monitoring in the ICU is recommended), 
permanently discontinue atezolizumab, and contact Medical 
Monitor. 
• If symptoms resolve to Grade 1 or better for 3 consecutive days, 
the next dose of atezolizumab may be administered. For 
subsequent infusions, consider administration of oral 
premedication with antihistamines, antipyretics, and/or 
analgesics and monitor closely for IRRs and/or CRS. 
• If symptoms do not resolve to Grade 1 or better for 
3 consecutive days, inform the Medical Monitor. 
Fevera with 
hypotension 
requiring a 
vasopressor (with 
or without 
vasopressin) 
 
and/or 
 
Hypoxia requiring 
high-flow 
oxygend by nasal 
cannula, face 
mask, non 
rebreather mask, 
or venturi mask 
Grade 3b 
• Permanently discontinue atezolizumab and contact Medical 
Monitor(s). 
• Administer symptomatic treatment.c 
• For hypotension, administer IV fluid bolus and vasopressor as 
needed. 
• Monitor cardiopulmonary and other organ function closely; 
monitoring in the ICU is recommended. Administer IV fluids as 
clinically indicated and manage constitutional symptoms and 
organ toxicities as per institutional practice. 
• Rule out other inflammatory conditions that can mimic CRS 
(e.g., sepsis). If no improvement within 24 hours, initiate 
workup and assess for signs and symptoms of HLH or MAS. 
• Administer IV corticosteroids (e.g., methylprednisolone 
2 mg/kg/day or dexamethasone 10 mg every 6 hours). 
• Consider anti-cytokine therapy.e 
• Hospitalize patient until complete resolution of symptoms. If no 
improvement within 24 hours, manage as per Grade 4, that is, 
admit patient to ICU and initiate hemodynamic monitoring, 
mechanical ventilation, and/or IV fluids and vasopressors as 
needed; for patients who are refractory to anti-cytokine therapy, 
experimental treatments may be considered at the discretion of 
the investigator and in consultation with the Medical Monitor. 
Fevera with 
hypotension 
requiring multiple 
vasopressors 
(excluding 
vasopressin) 
 
and/or 
 
Hypoxia requiring 
oxygen by 
positive pressure 
(e.g., continuous 
positive airway 
pressure, bi-level 
Grade 4b 
• Permanently discontinue atezolizumab and contact Medical 
Monitor. 
• Administer symptomatic treatment.c 
• Admit patient to ICU and initiate hemodynamic monitoring, 
mechanical ventilation, and/or IV fluids and vasopressors as 
needed. Monitor other organ function closely. Manage 
constitutional symptoms and organ toxicities as per institutional 
practice. 
• Rule out other inflammatory conditions that can mimic CRS 
(e.g., sepsis). If no improvement within 24 hours, initiate 
workup and assess for signs and symptoms of HLH or MAS. 
• Administer IV corticosteroids (e.g., methylprednisolone 
2 mg/kg/day or dexamethasone 10 mg every 6 hours). 

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Event 
NCI CTCAE Grade 
Recommended Medical Management 
positive airway 
pressure, 
intubation and 
mechanical 
ventilation) 
• Consider anti-cytokine therapy.e For patients who are refractory 
to anti-cytokine therapy, experimental treatmentsf may be 
considered at the discretion of the investigator (inform the 
Medical Monitor of such treatments). 
• Hospitalize patient until complete resolution of symptoms. 
Abbreviations: CRS = cytokine release syndrome; CTCAE = Common Terminology Criteria for Adverse Events; 
HLH = hemophagocytic lymphohistiocytosis; ICU = intensive care unit; IRR = infusion-related reaction; IV = intravenous; 
MAS = macrophage activation syndrome; NCI = National Cancer Institute 
Note:  The management guidelines have been adapted from National Comprehensive Cancer Network guidelines for 
management of chimeric antigen receptor T-cell-related toxicities (Version 2.2019). 
a 
Fever is defined as temperature ≥ 38°C not attributable to any other cause. In patients who develop CRS and then receive 
anti-pyretic, anti-cytokine, or corticosteroid therapy, fever is no longer required when subsequently determining event 
severity (grade). In this case, the grade is driven by the presence of hypotension and/or hypoxia. 
b 
Grading system for management guidelines is based on American Society for Transplantation and Cellular Therapy  
consensus grading for CRS. NCI CTCAE version 5.0 should be used when reporting severity of IRRs, CRS, or organ 
toxicities associated with CRS. Organ toxicities associated with CRS should not influence overall CRS grading. 
c 
Symptomatic treatment may include oral or IV antihistamines, anti-pyretics, analgesics, bronchodilators, and/or oxygen. 
For bronchospasm, urticaria, or dyspnea, additional treatment may be administered as per institutional practice. 
d Low flow is defined as oxygen delivered at ≤ 6 L/min, and high flow is defined as oxygen delivered at > 6 L/min. 
e 
There are case reports where anti-cytokine therapy has been used for treatment of CRS with immune checkpoint inhibitors 
(Rotz et al 2017; Adashek et al 2019), but data are limited, and the role of such treatment in the setting of antibody-
associated CRS has not been established. 
f 
Refer to Riegler et al (2019) for information on experimental treatments for CRS. 
 
4.4.2.8. 
Pancreatic Events 
Symptoms of abdominal pain associated with elevations of amylase and lipase, suggestive of 
pancreatitis, have been associated with the administration of atezolizumab. The differential 
diagnosis of acute abdominal pain should include pancreatitis. Appropriate workup should 
include an evaluation for ductal obstruction, as well as serum amylase and lipase tests. 
Management guidelines for pancreatic events, including pancreatitis, are provided in Table 10. 

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Table 10: 
Management Guidelines for Pancreatic Events, Including Pancreatitis 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Amylase 
and/or 
lipase 
elevation 
Grade 2 
Amylase and/or lipase > 1.5 − 2.0 × ULN: 
• Continue atezolizumab. 
• Monitor amylase and lipase weekly. 
• For prolonged elevation (e.g., > 3 weeks), consider treatment with 
corticosteroids equivalent to 10 mg/day oral prednisone. 
Asymptomatic with amylase and/or lipase > 2.0 − 5.0 × ULN: 
• Treat as a Grade 3 event. 
Grade 3 or higher 
• Withhold atezolizumab for up to 12 weeks after event onset. a 
• Refer patient to GI specialist. 
• Monitor amylase and lipase every other day. 
• If no improvement, consider treatment with corticosteroids equivalent to 
1−2 mg/kg/day oral prednisone. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding atezolizumab, 
permanently discontinue atezolizumab and contact Medical Monitor(s). 
• For recurrent events, permanently discontinue atezolizumab and contact 
Medical Monitor(s). 
Immune-
mediated 
pancreatitis 
Grade 2 or 3 
• Withhold atezolizumab for up to 12 weeks after event onset. a 
• Refer patient to GI specialist. 
• Initiate treatment with corticosteroids equivalent to 1−2 mg/kg/day IV 
methylprednisolone and convert to 1−2 mg/kg/day oral prednisone or 
equivalent upon improvement. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding atezolizumab, 
permanently discontinue atezolizumab and contact Medical Monitor(s). 
• For recurrent events, permanently discontinue atezolizumab and contact 
Medical Monitor(s).  
Grade 4 
• Permanently discontinue atezolizumab and contact Medical Monitor(s). 
• Refer patient to GI specialist. 
• Initiate treatment with corticosteroids equivalent to 1−2 mg/kg/day IV 
methylprednisolone and convert to 1−2 mg/kg/day oral prednisone or 
equivalent upon improvement. 
• If event does not improve within 48 hours after initiating corticosteroids, 
consider adding an immunosuppressive agent. 
• If event resolves to Grade 1 or better, taper corticosteroids over ≥ 1 month. 
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; GI = gastrointestinal; IV = intravenous; 
NCI = National Cancer Institute; ULN = upper limit of normal 
a Atezolizumab may be withheld for a longer period of time (i.e., > 12 weeks after event onset) to allow for corticosteroids (if 
initiated) to be reduced to the equivalent of ≤ 10 mg/day oral prednisone. The acceptable length of the extended period of 
time must be agreed upon by the Investigator and the Medical Monitor(s). 
b If corticosteroids have been initiated, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 mg/day oral prednisone 
before atezolizumab can be resumed. 

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4.4.2.9. 
Dermatologic Events 
Treatment-emergent rash has been associated with atezolizumab. The majority of cases of rash 
were mild in severity and self-limiting, with or without pruritus. A dermatologist should evaluate 
persistent and/or severe rash or pruritus. A biopsy should be considered unless contraindicated. 
Management guidelines for dermatologic events are provided in Table 11. 
Table 11: 
Management Guidelines for Dermatologic Events 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Dermatologic 
event 
Grade 1 
• Continue atezolizumab. 
• Consider treatment with topical corticosteroids and/or other 
symptomatic therapy (e.g., antihistamines). 
Grade 2 
• Continue atezolizumab. 
• Consider patient referral to dermatologist. 
• Initiate treatment with topical corticosteroids. 
• Consider treatment with higher-potency topical corticosteroids if 
event does not improve. 
Grade 3 
• Withhold atezolizumab for up to 12 weeks after event onset. a 
• Refer patient to dermatologist. 
• Initiate treatment with corticosteroids equivalent to 10 mg/day 
oral prednisone, increasing dose to 1−2 mg/kg/day if event does 
not improve within 48−72 hours. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding 
atezolizumab, permanently discontinue atezolizumab and 
contact Medical Monitor(s). 
Grade 4 
• Permanently discontinue atezolizumab and contact Medical 
Monitor(s). 
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; NCI = National Cancer Institute 
a Atezolizumab may be withheld for a longer period of time (i.e., > 12 weeks after event onset) to allow for corticosteroids 
(if initiated) to be reduced to the equivalent of ≤ 10 mg/day oral prednisone. The acceptable length of the extended period 
of time must be agreed upon by the Investigator and the Medical Monitor(s). 
b If corticosteroids have been initiated, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 mg/day oral 
prednisone before atezolizumab can be resumed. 
4.4.2.10. Neurologic Disorders 
Myasthenia gravis and Guillain-Barré syndrome have been observed with single-agent 
atezolizumab. Patients may present with signs and symptoms of sensory and/or motor 
neuropathy. Diagnostic workup is essential for an accurate characterization to differentiate 
between alternative etiologies. Management guidelines for neurologic disorders are provided in 
Table 12. 

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Table 12: 
Management Guidelines for Neurologic Disorders 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Immune-mediated 
neuropathy 
Grade 1 
• Continue atezolizumab. 
• Investigate etiology. 
Grade 2 
• Withhold atezolizumab for up to 12 weeks after event onset. a 
• Investigate etiology. 
• Initiate treatment as per institutional guidelines. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding 
atezolizumab, permanently discontinue atezolizumab and 
contact Medical Monitor(s). 
Grade 3 or higher 
• Permanently discontinue atezolizumab and contact Medical 
Monitor(s).  
• Initiate treatment as per institutional guidelines. 
Myasthenia gravis 
and Guillain-
Barré syndrome 
Any grade 
• Permanently discontinue atezolizumab and contact Medical 
Monitor(s). 
• Refer patient to neurologist. 
• Initiate treatment as per institutional guidelines. 
• Consider initiation of corticosteroids equivalent to 
1−2 mg/kg/day oral or IV prednisone. 
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; IV = intravenous; NCI = National Cancer 
Institute 
a Atezolizumab may be withheld for a longer period of time (i.e., > 12 weeks after event onset) to allow for corticosteroids 
(if initiated) to be reduced to the equivalent of ≤ 10 mg/day oral prednisone. The acceptable length of the extended period 
of time must be agreed upon by the Investigator and the Medical Monitor(s). 
b If corticosteroids have been initiated, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 mg/day oral 
prednisone before atezolizumab can be resumed. 
4.4.2.11. Immune-mediated Meningoencephalitis 
Immune-mediated meningoencephalitis is an identified risk associated with the administration of 
atezolizumab. Immune-mediated meningoencephalitis should be suspected in any patient 
presenting with signs or symptoms suggestive of meningitis or encephalitis, including, but not 
limited to, headache, neck pain, confusion, seizure, motor or sensory dysfunction, and altered or 
depressed level of consciousness. Encephalopathy from metabolic or electrolyte imbalances 
needs to be distinguished from potential meningoencephalitis resulting from infection (bacterial, 
viral, or fungal) or progression of malignancy, or secondary to a paraneoplastic process. 
All patients being considered for meningoencephalitis should be urgently evaluated with a CT 
scan and/or MRI scan of the brain to evaluate for metastasis, inflammation, or edema. If deemed 
safe by the treating physician, a lumbar puncture should be performed and a neurologist should 
be consulted. 
Patients with signs and symptoms of meningoencephalitis, in the absence of an identified 
alternate etiology, should be treated according to the guidelines in Table 13. 

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Table 13: 
Management Guidelines for Immune-mediated Meningoencephalitis 
Event 
NCI CTCAE 
Grade 
Recommended Medical Management 
Immune-mediated 
meningoencephalitis 
All grades 
• Permanently discontinue atezolizumab and contact 
Medical Monitor(s). 
• Refer patient to neurologist. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day IV methylprednisolone and convert to 
1−2 mg/kg/day oral prednisone or equivalent upon 
improvement. 
• If event does not improve within 48 hours after initiating 
corticosteroids, consider adding an immunosuppressive 
agent. 
• If event resolves to Grade 1 or better, taper corticosteroids 
over ≥ 1 month. 
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; IV = intravenous; NCI = National Cancer 
Institute 
4.4.2.12. Renal Events 
Immune-mediated nephritis has been associated with the administration of atezolizumab. 
Eligible patients must have adequate renal function, and renal function, including serum 
creatinine, should be monitored throughout study treatment. Patients with abnormal renal 
function should be evaluated and treated for other more common etiologies (including prerenal 
and postrenal causes, and concomitant medications such as nonsteroidal anti-inflammatory 
drugs). Refer the patient to a renal specialist if clinically indicated. A renal biopsy may be 
required to enable a definitive diagnosis and appropriate treatment. 
Patients with signs and symptoms of nephritis, in the absence of an identified alternate etiology, 
should be treated according to the guidelines in Table 14. 

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Table 14: 
Management Guidelines for Renal Events 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Renal event 
Grade 1 
• Continue atezolizumab. 
• Monitor kidney function, including creatinine, closely until 
values resolve to within normal limits or to baseline values.  
Grade 2 
• Withhold atezolizumab for up to 12 weeks after event onset. a 
• Refer patient to renal specialist. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day oral prednisone. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding 
atezolizumab, permanently discontinue atezolizumab and 
contact Medical Monitor(s). 
Grade 3 or higher 
• Permanently discontinue atezolizumab and contact Medical 
Monitor(s).  
• Refer patient to renal specialist and consider renal biopsy. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day oral prednisone. 
• If event does not improve within 48 hours after initiating 
corticosteroids, consider adding an immunosuppressive agent. 
• If event resolves to Grade 1 or better, taper corticosteroids over 
≥ 1 month. 
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; NCI = National Cancer Institute 
a Atezolizumab may be withheld for a longer period of time (i.e., > 12 weeks after event onset) to allow for corticosteroids 
(if initiated) to be reduced to the equivalent of ≤ 10 mg/day oral prednisone. The acceptable length of the extended period 
of time must be agreed upon by the Investigator and the Medical Monitor(s). 
b If corticosteroids have been initiated, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 mg/day oral 
prednisone before atezolizumab can be resumed. 
4.4.2.13. Immune-mediated Myositis 
Immune-mediated myositis has been associated with the administration of atezolizumab. 
Myositis or inflammatory myopathies are a group of disorders sharing the common feature of 
inflammatory muscle injury; dermatomyositis and polymyositis are among the most common 
disorders. Initial diagnosis is based on clinical (muscle weakness, muscle pain, skin rash in 
dermatomyositis), biochemical (serum creatine kinase increase), and imaging 
(electromyography/MRI) features, and is confirmed with a muscle biopsy. 
Patients with signs and symptoms of myositis, in the absence of an identified alternate etiology, 
should be treated according to the guidelines in Table 15. 

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Table 15: 
Management Guidelines for Immune-mediated Myositis 
Event 
NCI CTCAE Grade 
Recommended Medical Management 
Immune-mediated 
myositis 
Grade 1 
• Continue atezolizumab. 
• Refer patient to rheumatologist or neurologist.  
• Initiate treatment as per institutional guidelines. 
Grade 2 
• Withhold atezolizumab for up to 12 weeks after event onset a 
and contact Medical Monitor(s). 
• Refer patient to rheumatologist or neurologist. 
• Initiate treatment as per institutional guidelines. 
• Consider treatment with corticosteroids equivalent to 
1−2 mg/kg/day IV methylprednisolone and convert to 
1−2 mg/kg/day oral prednisone or equivalent upon 
improvement. 
• If corticosteroids are initiated and event does not improve 
within 48 hours after initiating corticosteroids, consider adding 
an immunosuppressive agent. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding 
atezolizumab, permanently discontinue atezolizumab and 
contact Medical Monitor(s). 
Grade 3 
• Withhold atezolizumab for up to 12 weeks after event onset a 
and contact Medical Monitor(s). 
• Refer patient to rheumatologist or neurologist. 
• Initiate treatment as per institutional guidelines. Respiratory 
support may be required in more severe cases. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day IV methylprednisolone, or higher-dose bolus if 
patient is severely compromised (e.g., cardiac or respiratory 
symptoms, dysphagia, or weakness that severely limits 
mobility); convert to 1−2 mg/kg/day oral prednisone or 
equivalent upon improvement. 
• If event does not improve within 48 hours after initiating 
corticosteroids, consider adding an immunosuppressive agent. 
• If event resolves to Grade 1 or better, resume atezolizumab. b 
• If event does not resolve to Grade 1 or better while withholding 
atezolizumab, permanently discontinue atezolizumab and 
contact Medical Monitor(s). 
• For recurrent events, treat as a Grade 4 event. 

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Event 
NCI CTCAE Grade 
Recommended Medical Management 
Immune-mediated 
myositis 
Grade 4 
• Permanently discontinue atezolizumab and contact Medical 
Monitor(s). 
• Refer patient to rheumatologist or neurologist. 
• Initiate treatment as per institutional guidelines. Respiratory 
support may be required in more severe cases. 
• Initiate treatment with corticosteroids equivalent to 
1−2 mg/kg/day IV methylprednisolone, or higher-dose bolus if 
patient is severely compromised (e.g., cardiac or respiratory 
symptoms, dysphagia, or weakness that severely limits 
mobility); convert to 1−2 mg/kg/day oral prednisone or 
equivalent upon improvement. 
• If event does not improve within 48 hours after initiating 
corticosteroids, consider adding an immunosuppressive agent. 
• If event resolves to Grade 1 or better, taper corticosteroids over 
≥ 1 month. 
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; IV = intravenous; NCI = National Cancer 
Institute 
a Atezolizumab may be withheld for a longer period of time (i.e., > 12 weeks after event onset) to allow for corticosteroids 
(if initiated) to be reduced to the equivalent of ≤ 10 mg/day oral prednisone. The acceptable length of the extended period 
of time must be agreed upon by the Investigator and the Medical Monitor(s). 
b If corticosteroids have been initiated, they must be tapered over ≥ 1 month to the equivalent of ≤ 10 mg/day oral 
prednisone before atezolizumab can be resumed. 
4.4.2.14. Systemic Immune Activation 
Systemic immune activation is a rare condition characterized by an excessive immune response. 
Given the mechanism of action of atezolizumab, systemic immune activation is considered a 
potential risk for atezolizumab. 
Recommendations regarding early identification and management of systemic immune activation 
are provided below. In the event of suspected systemic immune activation, atezolizumab should 
be withheld and clinical specialists (e.g., rheumatology, clinical immunology, or solid organ or 
hematopoietic stem cell transplant specialists) and the Medical Monitor(s) should be informed. 
Early disease recognition is critical, and systemic immune activation should be suspected if, in 
the absence of an alternative etiology, the patient meets two or more of the following criteria: 
• Hypotension that is refractory to aggressive IV fluid challenge (vasopressor support 
may be required). 
• Respiratory distress that requires aggressive supportive care (supplemental oxygen 
and intubation may be required). 
• Fever > 38.5°C 
• Acute renal or hepatic failure 
• Bleeding from coagulopathy 
• Any of the following unexplained laboratory abnormalities (change from baseline): 
cytopenias (in two or more lineages), significant transaminitis, or coagulopathy 

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For patients with suspected systemic immune activation, an initial evaluation should include the 
following: 
• Complete blood count with peripheral smear 
• Prothrombin time (PT), activated partial thromboplastin time (aPTT), fibrinogen, and 
D-dimer 
• Ferritin 
• Soluble IL-2 receptor (soluble CD25) 
• Triglycerides 
• Aspartate aminotransferase (AST), alanine aminotransferase (ALT), and direct 
bilirubin 
• Lactate dehydrogenase (LDH) 
• Complete neurologic and abdominal examination (assess for hepatosplenomegaly) 
Laboratory tests with normal results should be repeated frequently in patients for whom a high 
clinical suspicion of systemic immune activation exists. 
If neurologic abnormalities are present, consider cerebrospinal fluid analysis and/or an MRI of 
the brain. 
If cytopenias are present (Grade ≥ 2 in two or more lineages) or ferritin is ≥ 3000 ng/mL, the 
following evaluations should also be performed: 
• Bone marrow biopsy and aspirate (assess for evidence of hemophagocytosis) 
• Adenovirus, cytomegalovirus, Epstein Barr virus, herpes simplex virus, and human 
herpes virus 6, 7, and 8 evaluation (for reactivated or active disease) 
Diagnostic criteria and recommended management for systemic immune activation are provided 
in Table 16. The diagnostic criteria apply only when alternative etiologies have been excluded. 
An AE of systemic immune activation should be reported on the Adverse Event electronic case 
report form (eCRF) if the event meets the criteria for “consistent with systemic immune 
activation” or “probable systemic immune activation” as outlined in Table 16. 

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Table 16: 
Systemic Immune Activation Diagnosis and Management 
Systemic Immune Activation Diagnostic Criteria (Applicable Only When Alternative Etiologies are 
Excluded) 
Major Criteria 
Minor Criteria 
• Fever ≥ 38.5°C on more than one occasion 
• Ferritin ≥ 3000 ng/mL 
• Cytopenias (Grade ≥ 2 in two or more lineages) 
• Age-adjusted soluble interleukin-2 receptor 
elevated by ≥ 2 standard deviations 
• Severe (Grade ≥ 3) or progressive dysfunction in 
two or more organs 
• Decreased fibrinogen 
• Splenomegaly  
• Hemophagocytosis in bone marrow, spleen, or lymph 
nodes 
• Elevated gamma-glutamyl transpeptidase or liver 
function tests (aspartate aminotransferase, alanine 
aminotranferase, or direct bilirubin) 
• Elevated triglycerides 
• Elevated lactate dehydrogenase 
• Decreased natural killer cell activity 
Diagnosis and Management of Systemic Immune Activation 
Number of Criteria 
Diagnosis 
Action to Be Taken 
≥ 4 major criteria 
Consistent with 
systemic 
immune 
activation 
• Permanently discontinue atezolizumab. 
• Consider treatment with an immunosuppressive agent (i.e., cytokine 
inhibitors) and intravenous corticosteroids (i.e., methylprednisolone 
1 g once daily or equivalent, or dexamethasone ≥ 10 mg/m2 once 
daily if neurologic abnormalities are present). 
• Inform the Medical Monitor(s). 
• Consider HLH-2004 protocol (Henter et al 2007) if there is no 
clinical improvement. 

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3 major criteria 
OR 
2 major plus 
≥ 3 minor criteria 
Probable 
systemic 
immune 
activation 
• Depending on clinical severity, follow guidelines for “Consistent 
with systemic immune activation” or “Possible systemic immune 
activation” diagnosis. 
• Clinical specialists may be contacted for recommendations and the 
Medical Monitor(s) should be informed. 
2 major plus 
≤ 2 minor criteria 
OR 
1 major plus 
≥ 4 minor criteria 
Possible 
systemic 
immune 
activation 
• Withhold atezolizumab. 
• Consider treatment with intravenous corticosteroids. 
• Clinical specialists may be contacted for additional recommendations 
and the Medical Monitor(s) should be informed. 
• Follow guidelines for “Consistent with systemic immune activation” 
diagnosis if there is no clinical improvement or if clinical worsening 
occurs. 
• If clinical improvement occurs, atezolizumab may be resumed 
following a benefit-risk assessment by the Medical Monitor(s). 
Notes: Criteria are adapted from a Delphi Survey of 26 experts who provided helpful criteria in the positive diagnosis of 
hemophagocytic syndrome in adult patients (Hejblum et al 2014). 
Grades are based on National Cancer Institute Common Terminology Criteria for Adverse Events. 
These recommendations do not replace clinical judgment and are intended as suggested guidance. 
4.5. 
Stopping Rules 
The Sponsor may stop this study at any time. Investigators will be notified by the Sponsor or its 
designee if the study is stopped. The occurrence of the following events will require that further 
enrollment in the study be stopped: 
• Grade 3 or higher systemic infection assessed as definitely related to SYNB1891. 
• Death assessed as at least possibly related to study treatment. 
• The Investigator, Medical Monitor(s), and/or Sponsor determines that an event or 
current data warrant stopping the study. 
The SRC will review the data concerning these event(s), along with all other available data. 
Based on the results of their investigation, the SRC will determine appropriate follow-up and 
decide whether the study should be continued, amended or stopped. 
If the study is stopped, the events will be investigated, and the study will be closed to further 
enrollment. Patients already participating in the study at the time the study is stopped will not 
receive further study treatment and the evaluations for the End-of-treatment (EOT)/Early 
Termination visit will be performed. 
4.6. 
Duration of Study Participation 
The maximum time of study participation for a patient is up to 26 months, including the 
screening period (up to 28 days), treatment administration period (up to 24 months; see 
Section 4.2.1), and safety follow-up period (30 ± 5 days after the last dose). 

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5. 
PATIENT POPULATION 
5.1. 
Number of Patients 
Approximately 70 patients are anticipated for enrollment, which provides for 4 to 7 dose-finding 
cohorts in Arm 1, 1 to 5 cohorts in Arm 2, and replacement of 1 patient per cohort, as well up to 
20 additional patients enrolled at the RP2D in Arm 2. Additional cohorts may be required in 
either arm to determine the MTD/RP2D. 
5.2. 
Selection of Patients 
5.2.1. 
Eligibility Criteria 
This study will comprise patients with advanced/metastatic solid tumors or lymphoma. Patients 
will be eligible for enrollment regardless of gender or race/ethnicity. 
5.2.1.1. 
Inclusion Criteria 
Patients must meet all of the following inclusion criteria to be eligible: 
1. Able and willing to voluntarily complete the informed consent process (patient or 
patient’s representative). 
2. Adults aged ≥ 18 years (on the day of signing informed consent) with histologically- or 
cytologically-confirmed stage III or IV advanced/metastatic solid tumor or lymphoma for 
which no therapeutic options are available to extend survival or for which the patient is 
not a candidate for standard-of-care therapy. 
3. Eastern Cooperative Oncology Group performance status ≤ 1. 
4. Life expectancy ≥ 3 months. 
5. ≥ 1 injectable, measurable (≥ 10 mm in diameter, or ≥ 15 mm for nodal lesions), eligible 
lesion as defined by RECIST 1.1 (Eisenhauer et al 2009), iRECIST (Seymour et al 2017), 
and/or LYRIC (Cheson et al 2016) and as assessed by the Investigator. Eligible lesions 
must not be located in the thoracic cavity, spleen, pancreas, gastrointestinal tract (liver 
injection allowed), or cranium and must be amenable to percutaneous injection and away 
from major blood vessels or neurological structures. 
6. Able to provide biopsies for biomarker analysis from injected and (if available) 
noninjected lesions at baseline and other time points during the study. 
7. Oxygen saturation > 90% without the use of supplemental oxygen. 
8. Adequate cardiac function, defined as follows: 
a. Left ventricular ejection fraction (LVEF) > 50% by multi-gated acquisition (MUGA) 
scan or echocardiogram (ECHO) performed within 6 months prior to the first dose of 
study treatment provided the patient has not received any potential cardiotoxic agents 
in the intervening period. Symptoms relating to left ventricular dysfunction, cardiac 
arrhythmia, or cardiac ischemia must all be Grade < 1 per NCI CTCAE version 5.0. 
b. QTc interval corrected for heart rate using Fridericia’s formula (QTcF) < 480 msec at 
screening. 

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9. Laboratory values within the following ranges: 
• Absolute neutrophil count ≥ 1500/µL 
• Lymphocyte count ≥ 500/µL 
• Platelets ≥ 100,000/µL without transfusion 
• Hemoglobin ≥ 9.0 g/dL (patients may be transfused to meet this criterion) 
• Estimated glomerular filtration rate (eGFR) > 50 mL/min/1.73 m2 per the Cockcroft-
Gault formula 
• Total bilirubin ≤ 1.5 × the upper limit of normal (ULN) OR direct bilirubin ≤ ULN 
for participants with total bilirubin levels > 1.5 × ULN or ≤ 3 × ULN for patients with 
Gilbert’s syndrome 
• AST, ALT, and alkaline phosphatase ≤ 2.5 × ULN (AST and ALT ≤ 5 × ULN for 
participants with liver metastases and alkaline phosphatase ≤ 5 × ULN for 
participants with liver or bone metastases) 
• International normalized ratio (INR) or PT or aPTT ≤ 1.5 × ULN unless participant is 
receiving anticoagulant therapy as long as PT or aPTT is within therapeutic range of 
intended use of anticoagulants 
10. Agree to use an acceptable method of contraception after informed consent, throughout 
the study, and for 5 months after the last dose of SYNB1891 or atezolizumab. 
Additional inclusion criteria that apply only to Arm 2 study participants are as follows: 
11. TSH must be within the normal reference range or the patient must be receiving stable 
thyroid replacement therapy. 
12. Patients must have received treatment with an anti-PD-1/L1 monoclonal antibody (mAb) 
administered either as monotherapy, or in combination with other CPIs or other therapies, 
if indicated (if CPI therapy is not indicated as a part of standard-of-care therapy, patients 
may be CPI naïve). 
Additional inclusion criteria that apply only to the Arm 2 expansion study participants 
are as follows: 
13. Patients must have progressed on treatment with an anti-PD-1/L1 mAb administered 
either as monotherapy, or in combination with other CPIs or other therapies, if indicated 
(if CPI therapy is not indicated as a part of standard-of-care therapy, patients may be CPI 
naïve). 
PD-1/L1 treatment progression is defined by meeting all of the following criteria: 
a. Has received at least 2 doses of an approved anti-PD-1/L1 mAb.  
b. Has demonstrated disease progression after PD-1/L1 as defined by RECIST 1.1, 
iRECIST, and/or LYRIC. The initial evidence of disease progression is to be 
confirmed by a second assessment no less than 4 weeks from the date of the first 
documented disease progression, in the absence of rapid clinical progression as 
determined by the Investigator. Once disease progression is confirmed, the initial date 

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of disease progression documentation will be considered the date of disease 
progression. 
c. Progressive disease has been documented within 12 weeks from the last dose of 
anti-PD-1/L1 mAb. 
5.2.1.2. 
Exclusion Criteria 
Patients meeting any of the following criteria are not eligible for study enrollment: 
1. Chemotherapy, radiation, or biological cancer therapy within 14 days prior to the first 
dose of study treatment, or failure of any AEs to recover to Baseline or NCI CTCAE 
version 5.0 Grade 1, except for any grade of alopecia caused by cancer therapeutics 
administered > 28 days earlier. 
2. Systemic immunostimulatory agents (including, but not limited to, IFN and IL-2) within 
28 days or 5 drug elimination half-lives (whichever is longer) prior to initiation of study 
treatment. Checkpoint inhibitors are not considered systemic immunostimulatory agents 
for this criterion and are subject to the washout period listed in exclusion criterion #1. 
3. Allogeneic hematopoietic stem cell transplantation that requires current use of 
immunosuppressors. 
4. Receipt of a live vaccine within 90 days prior to the first dose of study treatment or 
anticipation of a need for such a vaccine during treatment. 
5. Receipt of antibiotics within 7 days prior to the first dose of study treatment. 
6. Participation in a study of an investigational agent and receipt of study therapy or use of 
an investigational device within 28 days prior to the first dose of study treatment. 
7. Diagnosed immunodeficiency or current use of chronic systemic steroid therapy in excess 
of replacement doses (prednisone ≤ 10 mg/day or equivalent is acceptable) or any other 
form of immunosuppressive medication within 7 days prior to the first dose of study 
treatment. 
8. For injection and biopsy of visceral (deep) lesions: patients must not be on long-acting 
antiplatelet agents such as aspirin or clopidogrel or on therapeutic doses of 
anticoagulants, with the exception of patients receiving a preventative dose of low 
molecular weight heparin. In patients receiving preventative low molecular weight 
heparin, treatment must be stopped 24 hours before the intratumoral injection and 
resumed again 24 hours after the injection (Marabelle et al 2018). 
9. Previous or concurrent malignancy, with the exception of: 
a. Adequately treated basal or squamous cell carcinoma, in situ carcinoma of the cervix, 
or ductal carcinoma in situ of the breast; 
b. Localized prostate cancer definitively treated with surgery or radiation or stable on 
hormone therapy; 
c. Other cancer from which the patient has been disease free for at least 2 years. 
10. Clinically active central nervous system (CNS) metastases and/or carcinomatous 
meningitis (treated brain metastases are permitted if radiologically stable for ≥ 28 days 
prior to the first dose of study treatment). 

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11. Allergy to antibiotics that precludes treatment for infection with E. coli Nissle 1917 (see 
Appendix 4 for common antibiotics to which E. coli Nissle is sensitive). 
12. Hepatitis B or C infection(s) unless screening tests indicate a negative viral load, and/or 
human immunodeficiency virus (HIV) infection unless screening tests indicate a negative 
or below the limit of quantitation viral load. 
13. Known active tuberculosis. 
14. Grade 3 or higher infection according to NCI CTCAE within 28 days prior to initiation of 
study treatment, including, but not limited to, hospitalization for complications of 
infection, bacteremia, or severe pneumonia. 
15. Failure to fully recover from the effects of major surgery. Surgeries that required general 
anesthesia must be completed > 14 days before the first dose of study drug. Surgery 
requiring regional/epidural anesthesia must be completed > 72 hours before the first dose 
of study treatment and participants should be recovered. 
16. Heart failure of New York Heart Association Class 3 or greater, restrictive 
cardiomyopathy, or unstable angina or recent myocardial infarction within 3 months prior 
to the first dose of study treatment. 
17. Any other medical condition that might confound the results of the study, interfere with 
the participant’s participation, or is not in the best interest of the participant, in the 
opinion of the treating Investigator. 
18. Pregnant or breastfeeding or anticipated conception or fathering of children within the 
projected duration of the study and for 5 months after the last dose of SYNB1891 or 
atezolizumab. 
Additional exclusion criteria that apply only to Arm 2 study participants are as follows: 
19. History of immune-mediated AEs on prior PD-1/PD-L1 therapies requiring 
discontinuation or immunosuppressor therapy, excluding endocrinopathies. 
20. Active or history of underlying autoimmune disease or immune deficiency, including, but 
not limited to, myasthenia gravis, myositis, autoimmune hepatitis, systemic lupus 
erythematosus, rheumatoid arthritis, inflammatory bowel disease, antiphospholipid 
antibody syndrome, Wegener granulomatosis, Sjögren syndrome, Guillain-Barré 
syndrome, or multiple sclerosis, with the following exceptions: 
a. Patients with a history of autoimmune-related hypothyroidism who are on thyroid 
replacement hormone are eligible for the study. 
b. Patients with controlled Type 1 diabetes mellitus who are on an insulin regimen are 
eligible for the study. 
c. Patients with eczema, psoriasis, lichen simplex chronicus, or vitiligo with 
dermatologic manifestations only (e.g., patients with psoriatic arthritis are excluded) 
are eligible for the study provided all of following conditions are met: 
- Rash must cover < 10% of body surface area; 
- Disease is well controlled at baseline and requires only low-potency topical 
corticosteroids; 

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- No occurrence of acute exacerbations of the underlying condition requiring psoralen 
plus ultraviolet A radiation, methotrexate, retinoids, biologic agents, oral 
calcineurin inhibitors, or high potency or oral corticosteroids within the previous 
12 months. 
21. History of a Grade ≥ 3 allergic anaphylactic reaction following treatment with a PD-1 
mAb or to chimeric, human, or humanized antibodies or fusion proteins. 
22. History of idiopathic pulmonary fibrosis, organizing pneumonia (e.g., bronchiolitis 
obliterans), drug-induced pneumonitis requiring treatment, or idiopathic pneumonitis, or 
evidence of active pneumonitis. 
23. Known hypersensitivity to Chinese hamster ovary cell products or any component of the 
atezolizumab formulation. 

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6. 
INVESTIGATIONAL MEDICINAL PRODUCT AND 
CONCOMITANT MEDICATIONS 
6.1. 
Investigational Product Supply and Administration 
Within this protocol, “study treatment” refers to SYNB1891 and/or atezolizumab. 
6.1.1. 
SYNB1891 
Detailed instructions for the storage, handling, and administration of SYNB1891 will be 
provided in the Pharmacy Manual and may override instructions provided in the following 
protocol sections. 
6.1.1.1. 
Manufacturing and Formulation 
SYNB1891 investigational drug product is formulated in buffer composed of 15% glycerol, 5% 
trehalose, 10 mM Tris at pH 7.5. 
6.1.1.2. 
Packaging and Labeling 
SYNB1891 is packaged aseptically into AT-closed vials at a volume of 0.6 mL and will be 
labeled for clinical study use. 
6.1.1.3. 
Shipping, Storage, and Handling 
Labeled, packaged SYNB1891 will be shipped from Synlogic’s manufacturing site to a central 
drug vendor. SYNB1891 must be stored at ≤ -65°C in a secured freezer with controlled access. 
6.1.1.4. 
Dispensing and Administration 
The manufactured SYNB1891 drug product has a concentration of 1× 1011 live cells/mL. To 
obtain appropriate doses, vial(s) of concentrated drug product will be thawed and appropriately 
diluted to a volume of 5 mL in room temperature 5% dextrose in water for injection and held at 
room temperature while handling prior to administration. The time between the thaw of vials 
containing SYNB1891 and injection should not exceed 2 hours. If the 2-hour stability window is 
exceeded, discard and prepare another dose. 
The preparation of SYNB1891 doses must be performed in a biosafety cabinet while wearing 
sterile sleeves, sterile gloves, and a facemask to minimize contamination. 
Once the dilutions have been prepared, withdraw 0.3 mL of the prepared cell concentration, 
change the needle to the appropriate length for the tumor to be treated prior to injection, and 
follow local protocol to obtain the final dose volume of 0.1 mL. 
6.1.2. 
Atezolizumab 
Atezolizumab will be supplied by the manufacturer as a sterile liquid in a single-use, 20-mL 
glass vial and labeled and shipped to each investigational site. Atezolizumab (1200 mg/vial) will 
be prepared in accordance with the current Investigator’s Brochure and administered as an IV 
infusion at a dose of 1200 mg Q3W. 

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6.2. 
Accountability and Dosing Compliance 
All doses of SYNB1891 and atezolizumab will be administered in the clinic by trained study 
personnel. Dosing details (e.g., lot/batch number, date/time of administration) will be 
documented in the eCRF. 
Unless other arrangements are agreed to in writing, all unused clinical trial material should be 
returned to Synlogic at the completion of the study. Interim returns are permissible after drug 
accountability has been performed by the monitor and as agreed upon by the Sponsor. 
6.3. 
Concomitant Medications 
All concomitant medications and dietary supplements received within 28 days prior to the first 
dose of study treatment through 30 days after the last dose of study treatment will be recorded in 
the eCRFs, using generic drug names when possible. 
No restrictions on concomitant medications will be implemented, other than those mentioned in 
the eligibility criteria (see Section 5.2.1) or the toxicity management guidelines (see Section 4.4). 
Concomitant medications can be administered at the Investigator’s discretion to conform to 
standard practice during the dosing period; however, Investigators should use caution when 
prescribing concomitant medications, as SYNB1891 has not been previously investigated in the 
clinical setting. Investigators should contact the Medical Monitor(s) when they are unsure 
whether a drug should be prescribed to a patient. If there is a clinical indication for any 
medication or vaccination specifically prohibited during the study, discontinuation from study 
treatment may be required at the discretion of the Medical Monitor(s). 
 
 
 

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7. 
STUDY PROCEDURES AND ASSESSMENTS 
Before recruitment of patients into the study, written Institutional Review Board (IRB) approval 
of the protocol, informed consent, and any additional patient information must be obtained. 
The various assessments that will be conducted during this study are summarized in Table 19 
(Schedule of Events for Arm 1) and Table 20 (Schedule of Events for Arm 2). 
Detailed instructions regarding sample collection, shipping, and handling, as well as all 
laboratory procedures, will be provided to the study site in separate study manuals. Site-specific 
handling instructions for hematology and clinical chemistry samples should be followed. 
7.1. 
Screening 
For both study arms, screening procedures must be performed to determine eligibility for 
enrollment within 28 days prior to the first dose of study treatment. If a particular assessment is 
repeated, the results obtained closest to the first dose of study treatment should be used to assess 
eligibility. 
During screening, a unique identification number will be assigned to each patient who signs 
informed consent for the study. If a patient meets all the inclusion criteria and none of the 
exclusion criteria and is selected to participate in the study, s/he will be enrolled and only be 
identified by the unique identification number. 
The Investigator or designee is responsible for verifying that the patient is eligible before 
requesting an identification number. At the site, the Investigator will maintain a log for all 
screened patients (including patients who failed screening after signing informed consent) and all 
enrolled patients. Patients may be re-screened. Eligibility assessments from the initial screening 
may only be used for re-screening if performed within the screening period as defined in the 
protocol or within 14 days following the screening period only after consultation with the 
medical monitor. 
Patients must be dosed within 5 calendar days of the registration/enrollment date (i.e., the date 
that a patient is assigned to a given dose cohort). 
7.2. 
Safety Assessments 
7.2.1. 
Medical History 
Past and present medical history, including prior cancer diagnoses, will be recorded. Any 
ongoing condition and signs and symptoms observed prior to signing of the informed consent 
should be recorded as medical history. 
7.2.2. 
Adverse Events 
Adverse events will be assessed continuously by direct observation and patient interviews. The 
severity of AEs will be evaluated using the NCI CTCAE, version 5.0 (US DHHS 2017). All AEs 
occurring from the time a patient signs informed consent through the Safety Follow-up visit 
(30 ± 5 days after the last dose of study treatment) will be recorded, regardless of causality. After 
the Safety Follow-up visit, only SAEs that are considered related to study treatment will be 
recorded, if clinically indicated. 

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Postdose monitoring for AEs will be performed as described in Section 4.2.2, including 
telephone contact on Cycle 1 Day 3 to monitor for signs of cytokine release syndrome (see 
Section 4.4). If these symptoms are present, patients will be instructed on the appropriate next 
steps. 
7.2.2.1. 
Monitoring for Signs and Symptoms of Infection 
If clinical presentation warrants, including but not limited to cases in which patients develop 
persistent (> 24 hours) fever or a change in vital signs suggestive of clinical infection resulting 
from a study treatment or procedure, then blood and urine cultures (performed and analyzed 
locally) will be performed and weight will be recorded. 
If a patient is treated for systemic infection such that blood culture tubes are drawn locally, an 
additional blood culture tube should be drawn for analysis for the presence of SYNB1891, if 
possible. For this purpose, patients will be provided with an identification card containing study 
contact information (see Central Laboratory manual for collection, shipping, and other 
processes). 
7.2.3. 
Vital Signs 
Vital signs (systolic blood pressure, diastolic blood pressure, body temperature, pulse, and pulse 
oximetry) will be collected while patients are in a seated or supine position at screening, on 
Cycle 1 Day 1 (predose and 30 minutes, 1 hour, 2 hours, 3 hours, 6 hours, and 24 hours 
postdose), on all other study treatment days (predose and 30 minutes, 1 hour, 2 hours, 3 hours, 
and 6 hours postdose), at EOT/Early Termination and Safety Follow-up, and as clinically 
indicated (see Table 19 and Table 20). A ± 15-minute window is permitted at all time points. 
7.2.4. 
Physical Examination 
Complete physical examinations will be performed by trained medical personnel at screening 
and Baseline, with symptom-directed physical examinations performed at subsequent time points 
(see Table 19 and Table 20). Height will be collected at screening only, and weight will be 
collected at the time points indicated in Table 19 and Table 20. Any abnormal findings will be 
recorded as AEs. 
As a part of the physical examination and prior to each dose, a photograph of the visible injected 
and/or noninjected lesion(s) should be taken at the discretion of the Investigator. 
7.2.5. 
Clinical Laboratory Measurements 
Clinical laboratory tests will be performed (predose unless otherwise specified) at the time points 
indicated in Table 19 and Table 20. Baseline laboratory measurements do not need to be repeated 
if screening measurements were performed within 3 days prior to Cycle 1 Day 1. 
Screening for HIV and hepatitis B and C will also be performed prior to study dosing. Serum 
pregnancy testing will be performed at screening, with urine pregnancy testing performed at 
subsequent time points (see Table 19 and Table 20). 
Screening results will be assessed by the Investigator for inclusion of patients in the study. 
Additionally, unscheduled clinical laboratory tests can be obtained at any time during the study 

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at the Investigator’s discretion. The diagnosis corresponding to any clinically significant 
abnormality, or abnormality requiring treatment/intervention, must be recorded as an AE. 
7.2.5.1. 
Local Laboratory Measurements 
Table 17 outlines the clinical laboratory measurements that will be reviewed at the local 
laboratory.  
On dosing days, prior to receiving study treatment, patients must meet the laboratory value 
criteria outlined in Section 5.2.1.1, with the exception that platelets may be ≥ 75,000/µL without 
transfusion and hemoglobin may be ≥ 8.5 g/dL (patients may be transfused to meet this 
criterion). 

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Table 17: 
Local Laboratory Parameters 
Panel 
Parameters 
Hematology 
Must be Reviewed Predose: 
Calculated absolute neutrophil count  
White blood cell  
Red blood cell  
Red cell indices 
Hemoglobin  
Hematocrit  
Platelet count 
 
Neutrophils  
Lymphocytes  
Monocytes  
Eosinophils  
Basophils 
Chemistry 
Must be Reviewed Predose: 
 
Calcium  
Chloride  
Total protein  
Potassium  
Glucose  
Sodium  
Blood urea nitrogen  
Creatinine  
Bicarbonate  
Albumin  
Uric acid 
Phosphorus 
Magnesium 
Alkaline phosphatase 
Aspartate aminotransferase 
Alanine aminotransferase 
Lactate dehydrogenase 
Direct bilirubin 
Indirect bilirubin  
Total bilirubin 
 
 
 
 
 
Thyroid 
Function 
May be Reviewed Pre- or Postdose: 
Free T4 
Thyroid-stimulating hormone 
Coagulation 
May be Reviewed Pre- or Postdose: 
Prothrombin time and/or activated partial thromboplastin time 
International normalized ratio 
 
Urinalysis 
May be Reviewed Pre- or Postdose: 
Dipstick: 
pH  
Glucose 
Protein 
Bilirubin 
Ketones  
Leukocytes  
Blood  
Microscopic (if dipstick is positive): 
White blood cell count  
Red blood cell count 
Casts 
7.2.5.2. 
Central Laboratory Measurements 
Table 18 outlines the clinical laboratory measurements that will be reviewed at the central 
laboratory as specified in the Central Laboratory Manual. 

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Table 18: 
Central Laboratory Parameters 
Panel 
Parameters 
Cytokines 
TNFα, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-13, IL1β, IL1RA, IL2Rα, and IFNγ 
qPCR 
• Tumor tissue quantitative polymerase chain reaction (qPCR) from fine needle aspirate and 
whole blood 
• qPCR from blood cultures 
Other 
Blood samples collected for exploratory analyses in preservation tubes 
7.2.6. 
Electrocardiograms 
Semi-supine single 12-lead ECGs will be performed at screening and reviewed locally. 
7.2.7. 
Multi-gated Acquisition Scan or Echocardiogram 
MUGA or ECHO will be performed within 6 months prior to the first dose of study treatment 
provided the patient has not received any potential cardiotoxic agents in the intervening period. 
If potential cardiotoxic agents have been administered within 6 months, patients must undergo a 
MUGA/ECHO during the screening period. 
7.3. 
Efficacy Assessments 
Disease response status will be assessed in the SYNB1891-injected lesion(s), and an overall 
analysis of potential responses in up to 5 noninjected target lesions will be performed using 
appropriate imaging at screening and every 2 cycles on study (i.e., at the end of every even-
numbered cycle) for the duration of the treatment period and at the EOT visit (unless imaging 
has been performed within 8 weeks prior to the EOT visit). Every effort should be made to assess 
each lesion that is measured at screening using the same imaging method(s) throughout the study 
to enable a consistent comparison. Injected lesions that are reduced in size on study to the extent 
that they are no longer able to sustain injections will continue to be monitored for response. 
Tumor response will be evaluated by the local Investigator using appropriate imaging in 
accordance with RECIST 1.1 (Eisenhauer et al 2009 and Appendix 1), iRECIST 
(Seymour et al 2017 and Appendix 2), and/or LYRIC (Cheson et al 2016 and Appendix 3). 
7.4. 
Pharmacodynamic Assessments 
Blood samples for qPCR will be collected during the first 24-hour period of Cycle 1 and will be 
analyzed to assess for the presence of circulating SYNB1891. 
An FNA of the eligible lesion will be performed predose on Cycle 1 Day 1 (within 7 days prior 
to Cycle 1 Day 1) and predose on Cycle 1 Day 8 and analyzed for bacterial kinetics by qPCR. 
Core biopsies of the intended SYNB1891-injected lesion will be performed predose on Cycle 1 
Day 1 (within 7 days prior) and predose on Cycle 2 Day 1 (within 3 days prior). For patients who 
withdraw from the study prior to Cycle 2 Day 1, the second biopsy should be performed at the 
EOT visit (see Section 7.5.1). While not required for study entry, second biopsiable lesions, if 
present, will undergo a mandatory biopsy at the same time points.  

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To optimize the quality of the biopsy samples obtained, 3 core samples should be obtained at 
each time point for each lesion, when feasible in the opinion of the Investigator. Biopsy tissue 
will be evaluated at various time points for IFN-responsive cytokines, TILs, PD-1, and PD-L1. 
Refer to the study manuals for details on the procedures for collecting, shipping, and handling 
biopsy material. 
7.5. 
Follow-up Assessments 
7.5.1. 
End-of-Treatment Visit 
Within 14 days after the last dose of study treatment (or premature treatment discontinuation), an 
EOT visit will be performed and every effort should be made to perform the procedures specified 
in Table 19 and Table 20. 
7.5.2. 
Safety Follow-up Visit 
All patients will attend a Safety Follow-up visit 30 ± 5 days after the last dose of study treatment.  
7.6. 
Sample Retention for Exploratory Analyses 
De-identified blood samples may be stored for future analyses related to cancer and immune 
responses for up to 5 years from the time the sample is collected. Any unused samples will be 
destroyed. 
 
 

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Table 19: 
Schedule of Events (Arm 1) 
Study Period 
Protocol 
Section Screening 
Cycle 1 
Cycles 
2-4 
Additional 
Cycles1 
EOT/Early 
Termination 
Visit 
Safety 
Follow-
up Visit 
Study Day 
7 
-28 to 0 
1 
2 
(24 ± 2 
hours 
postdose) 
3 
(48 ± 2 
hours 
postdose) 
8 ± 
1 day 
15 ± 
1 day 
1 ± 
1 day 
1 ± 
1 day 
Within 14 
days after 
last dose 
30 ± 5 
 days 
after last 
dose 
Baseline 
(predose) 
Dose 
(6 ± 1 
 hours 
postdose) 
Informed consent/enrollment  
7.1 
 
 
 
 
 
 
 
 
 
 
 
 
Medical history 
7.2.1 
 
 
 
 
 
 
 
 
 
 
 
 
Physical examination 
7.2.4 
 
 
 
 
 
 
 
 
 
 
 
 
Height 
7.2.4 
 
 
 
 
 
 
 
 
 
 
 
 
Weight 
7.2.4 
 
 
 
 
 
 
 
 
 
 
 
 
Vital signs (blood pressure, body temperature, 
pulse, and pulse oximetry) 2 
7.2.3 
 
 
 
 
 
 
 
 
 
 
 
 
Screening for hepatitis B, C and HIV 
7.2.5 
 
 
 
 
 
 
 
 
 
 
 
 
ECGs 
7.2.6 
 
 
 
 
 
 
 
 
 
 
 
 
MUGA/ECHO 
7.2.7  
 
 
 
 
 
 
 
 
 
 
 
 
Hematology (CBC with differential) 
7.2.5.1 
 
 
 
 
 
 
 
 
 
 
 
 
Blood chemistry, including LFTs 
7.2.5.1 
 
 
 
 
 
 
 
 
 
 
 
 
Coagulation (PT/aPTT) 
7.2.5.1 
 
 
 
 
 
 
 
 
 
 
 
 
Thyroid function (FT4, TSH) 
7.2.5.1 
 
 
 
 
 
 
 
 
 3 
 3 
 
 
Urinalysis 
7.2.5.1 
 
 
 
 
 
 
 
 
 
 
 
 
Cytokine blood draw 
7.2.5.2 
 
 
 
 
 
 
 4 
 4 
 4 
 
 
 
Blood preservation tube for exploratory 
analyses 
7.2.5.2 
 
 
 
 
 
 
 5 
 
 5,6 
 
 
 
Kinetics of SYNB1891 (qPCR blood assay) 
7.4 
 
 
 
 
 
 
 
 
 
 
 
 
Serum hCG (women of childbearing 
potential) 
7.2.5 
 
 
 
 
 
 
 
 
 
 
 
 
Urine hCG (women of childbearing potential) 
7.2.5 
 
 
 
 
 
 
 
 
 
 
 
 
Telephone call 
7.2.2 
 
 
 
 
 
 
 
 
 
 
 
 
Fine needle aspirate of eligible lesion 
pre-injection 
7.4 
 
 7 
 
 
 
 
 5 
 
 
 
 
 

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Study Period 
Protocol 
Section Screening 
Cycle 1 
Cycles 
2-4 
Additional 
Cycles1 
EOT/Early 
Termination 
Visit 
Safety 
Follow-
up Visit 
Study Day 
7 
-28 to 0 
1 
2 
(24 ± 2 
hours 
postdose) 
3 
(48 ± 2 
hours 
postdose) 
8 ± 
1 day 
15 ± 
1 day 
1 ± 
1 day 
1 ± 
1 day 
Within 14 
days after 
last dose 
30 ± 5 
 days 
after last 
dose 
Baseline 
(predose) 
Dose 
(6 ± 1 
 hours 
postdose) 
Biopsy of eligible lesion 
7.4 
 
 7 
 
 
 
 
 
 
 8 
 
 9 
 
Biopsy of noninjected lesion (if applicable) 
7.4 
 
 7 
 
 
 
 8 
 
 9 
 
Administration of SYNB1891 intratumorally  
4.2 
 
 
 
 
 
 
 
 
 
 
 
 
Tumor response using appropriate imaging 
 7.3  
 
 
 
 
 
 
 
 
 10 
 10 
 
 
Adverse event reporting 
7.2.2 
Continuously from the time of informed consent through the Safety Follow-up visit 
Monitoring for symptoms and signs of 
infection 
7.2.2.1 
Continuously from the time of informed consent through the Safety Follow-up visit 
Abbreviations: aPTT = activated partial thromboplastin time; CBC = complete blood count; ECG = electrocardiogram; ECHO = echocardiogram; EOT = end of treatment; 
FT4 = free thyroxine; hCG = human chorionic gonadotropin; HIV = human immunodeficiency virus; LFT = liver function test; MUGA = multi-gated acquisition; qPCR = 
quantitative polymerase chain reaction; PT = prothrombin time; TSH = thyroid stimulating hormone 
1 Patients who do not have progressive disease (i.e., those who achieve and sustain a complete/partial response or stable disease) may receive additional cycles of SYNB1891 given 
on Day 1 of each cycle for up to 24 months (i.e., Cycles 5 to 35) after the initial dose of study treatment until documentation of progressive disease or other discontinuation criteria, 
satisfaction of a predefined stopping rule, or no eligible lesions remain.  
2 Collected while patients are in a seated or supine position at screening, on Cycle 1 Day 1 (predose and 30 minutes, 1 hour, 2 hours, 3 hours, 6 hours, and 24 hours postdose), on all 
other study treatment days (predose and 30 minutes, 1 hour, 2 hours, 3 hours, and 6 hours postdose), at EOT/Early Termination and Safety Follow-up, and as clinically indicated.  
NOTE: A ± 15-minute window is permitted for each timepoint. 
3 Day 1 of odd-numbered cycles only. 
4 Predose and 6 hours postdose (as indicated) after every SYNB1891 injection. 
5 Predose. 
6 Day 1 of Cycle 3 only. 
7 The predose (baseline) biopsies and fine needle aspirate may be performed up to 7 days prior to Cycle 1 Day 1. 
8 Core biopsies will be collected predose on (or up to 3 days prior to) Day 1 of Cycle 2 only (i.e., not Day 1 of Cycles 3 or 4). 
9 For patients who withdraw from the study prior to Cycle 2 Day 1, the second biopsy should be performed at the EOT visit. 
10 At the end of even-numbered cycles only. 
 

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Table 20: 
Schedule of Events (Arm 2) 
Study Period 
Protocol 
Section Screening 
Cycle 1 
Cycles 
2-4  
Additional 
Cycles 1 
EOT/Early 
Termination 
Visit 
Safety 
Follow-
up Visit 
Study Day 
7 
-28 to 0 
1 
2 
(24 ± 2 
hours 
postdose) 
3 
(48 ± 2 
hours 
postdose) 
8 ± 
1 day 
15 ± 
1 day 
1 ± 
1 day 
1 ± 
1 day 
Within 14 
days after 
last dose 
30 ± 5 
days 
after 
last 
dose 
Baseline 
(predose) 
Dose 
(6 ± 1 
hours 
 postdose) 
Informed consent/enrollment  
7.1 
 
 
 
 
 
 
 
 
 
 
 
 
Medical history 
7.2.1 
 
 
 
 
 
 
 
 
 
 
 
 
Physical examination 
7.2.4 
 
 
 
 
 
 
 
 
 
 
 
 
Height 
7.2.4 
 
 
 
 
 
 
 
 
 
 
 
 
Weight 
7.2.4 
 
 
 
 
 
 
 
 
 
 
 
 
Vital signs (blood pressure, body temperature, 
pulse, and pulse oximetry) 2 
7.2.3 
 
 
 
 
 
 
 
 
 
 
 
 
Screening for hepatitis B, C and HIV 
7.2.5 
 
 
 
 
 
 
 
 
 
 
 
 
ECGs 
7.2.6 
 
 
 
 
 
 
 
 
 
 
 
 
MUGA/ECHO 
7.2.7  
 
 
 
 
 
 
 
 
 
 
 
 
Hematology (CBC with differential) 
7.2.5.1 
 
 
 
 
 
 
 
 
 
 
 
 
Blood chemistry, including LFTs 
7.2.5.1 
 
 
 
 
 
 
 
 
 
 
 
 
Coagulation (PT/aPTT) 
7.2.5.1 
 
 
 
 
 
 
 
 
 
 
 
 
Thyroid function (FT4, TSH) 
7.2.5.1 
 
 
 
 
 
 
 
 
 3 
 3 
 
 
Urinalysis 
7.2.5.1 
 
 
 
 
 
 
 
 
 
 
 
 
Cytokine blood draw 
7.2.5.2 
 
 
 
 
 
 
 4 
 4 
 4 
 
 
 
Blood preservation tube for exploratory analyses 
7.2.5.2 
 
 
 
 
 
 
 5 
 
 5,6 
 
 
 
Kinetics of SYNB1891 (qPCR blood assay) 
7.4 
 
 
 
 
 
 
 
 
 
 
 
 
Serum hCG (women of childbearing potential) 
7.2.5 
 
 
 
 
 
 
 
 
 
 
 
 
Urine hCG (women of childbearing potential) 
7.2.5 
 
 
 
 
 
 
 
 
 
 
 
 
Telephone call 
7.2.2 
 
 
 
 
 
 
 
 
 
 
 
 
Fine needle aspirate of eligible lesion 
pre-injection 
7.4 
 
 7 
 
 
 
 
 5 
 
 
 
 
 
Biopsy of eligible lesion 
7.4 
 
 7 
 
 
 
 
 
 
 8 
 
9 
 

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Study Period 
Protocol 
Section Screening 
Cycle 1 
Cycles 
2-4  
Additional 
Cycles 1 
EOT/Early 
Termination 
Visit 
Safety 
Follow-
up Visit 
Study Day 
7 
-28 to 0 
1 
2 
(24 ± 2 
hours 
postdose) 
3 
(48 ± 2 
hours 
postdose) 
8 ± 
1 day 
15 ± 
1 day 
1 ± 
1 day 
1 ± 
1 day 
Within 14 
days after 
last dose 
30 ± 5 
days 
after 
last 
dose 
Baseline 
(predose) 
Dose 
(6 ± 1 
hours 
 postdose) 
Biopsy of noninjected lesion (if applicable) 
7.4 
 
 7 
 
 
 
 
 8 
 
9 
 
Administration of SYNB1891 intratumorally  
4.2 
 
 
 
 
 
 
 
 
 
 
 
 
Administration of atezolizumab by IV infusion 
4.2 
 
 
 
 
 
 
 
 
 
 
 
 
Tumor response using appropriate imaging 
 7.3  
 
 
 
 
 
 
 
 
 10 
 10 
 
 
Adverse event reporting 
7.2.2 
Continuously from the time of informed consent through the Safety Follow-up visit 
Monitoring for symptoms and signs of infection 
7.2.2.1  
Continuously from the time of informed consent through the Safety Follow-up visit 
Abbreviations: aPTT = activated partial thromboplastin time; CBC = complete blood count; ECG = electrocardiogram; ECHO = echocardiogram; EOT = end of treatment; 
FT4 = free thyroxine; hCG = human chorionic gonadotropin; HIV = human immunodeficiency virus; IV = intravenous; LFT = liver function test; MUGA = multi-gated acquisition; 
qPCR = quantitative polymerase chain reaction; PT = prothrombin time; TSH = thyroid stimulating hormone 
1 Patients who do not have progressive disease (i.e., those who achieve and sustain a complete/partial response or stable disease) at the end of Cycle 4 on combination therapy may 
receive additional cycles of study treatment for up to 24 months (i.e., Cycles 5 to 35) after the initial dose of study treatment until documentation of progressive disease or other 
discontinuation criteria, satisfaction of a predefined stopping rule, or no eligible lesions remain. 
2 Collected while patients are in a seated or supine position at screening, on Cycle 1 Day 1 (predose and 30 minutes, 1 hour, 2 hours, 3 hours, 6 hours, and 24 hours postdose), on all 
other study treatment days (predose and 30 minutes, 1 hour, 2 hours, 3 hours, and 6 hours postdose), at EOT/Early Termination and Safety Follow-up, and as clinically indicated. 
NOTE: A ± 15-minute window is permitted for each timepoint. 
3 Day 1 of odd-numbered cycles only. 
4 Predose and 6 hours postdose (as indicated) after every SYNB1891 injection. 
5 Predose. 
6 Day 1 of Cycle 3 only. 
7 The predose (baseline) biopsies and fine needle aspirate may be performed up to 7 days prior to Cycle 1 Day 1. 
8 Core biopsies will be collected predose on (or up to 3 days prior to) Day 1 of Cycle 2 only (i.e., not Day 1 of Cycles 3 or 4).  
9 For patients who withdraw from the study prior to Cycle 2 Day 1, the second biopsy should be performed at the EOT visit. 
10 At the end of even-numbered cycles only. 
 
 
 

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8. 
STUDY DISCONTINUATION 
8.1. 
Sponsor Discontinuation Criteria 
This study may be discontinued at any time due to safety concerns (including, but not limited to, 
the stopping rules described in Section 4.5), failure to meet expected enrollment goals, 
administrative reasons, or at the discretion of the Sponsor. Should the study be terminated 
prematurely, the Sponsor will provide written notification to the Investigator and regulatory 
authorities and will specify the reason(s) for early termination. The Investigator must inform the 
IRB promptly and provide the reason(s) for the termination. 
8.2. 
Study Discontinuation for Individual Patients 
Determination of whether a patient should discontinue further study treatment administration and 
withdraw from the study will depend on whether one of the following qualifying events (except 
for withdrawal of consent) occurs prior to or after the patient receives SYNB1891: 
• The patient withdraws consent. 
• The Investigator or Sponsor notes a significant noncompliance with protocol 
procedures. 
• The Investigator determines that the patient must discontinue further study dosing for 
medical reasons. 
• Discontinuation of treatment with SYNB1891 may be considered for participants in 
whom all eligible injected lesion have undergone complete regression and are no 
longer injectable (at the discretion of the Investigator). In Arm 1, patients will 
continue in follow-up and in Arm 2, patients may continue on atezolizumab.  
• Discontinuation of treatment with atezolizumab may be considered for participants 
who have attained a confirmed CR and have been treated for at least 8 cycles (at least 
24 weeks), receiving at least 2 doses of atezolizumab beyond the date when the initial 
CR was declared. It is anticipated that these participants will have discontinued 
SYNB1891. 
In patients who meet the criteria for permanent discontinuation due to intolerable toxicity, 
resumption of study treatment may be considered if the patient is deriving benefit and has fully 
recovered from the immune-related event. Patients can be re-challenged with study treatment 
only after approval has been documented by both the Investigator (or an appropriate delegate) 
and the Sponsor. 
Patients may withdraw their consent at any time for any reason without prejudice to their future 
medical care by the physician or at the institution. If a patient withdraws consent, the date and 
stated reason for consent withdrawal should be documented. Patient data collected up to the date 
of consent withdrawal will be included in the analyses. 
Patients who withdraw from the study prior to receiving the first dose of study treatment are not 
required to complete any further visits. Patients who withdraw from the study after receiving the 
first dose of study treatment must complete the EOT and Safety Follow-up visits, unless consent 
for follow-up is withdrawn. Patients who discontinue study treatment and withdraw from the 

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study will not be allowed to enroll again at a later date. If a patient who withdraws from the 
study has an ongoing SAE, every effort will be made to follow the SAE until the event has 
resolved, stabilized, or returned to baseline status. The Sponsor must be notified of all study 
withdrawals within 24 hours. 
8.2.1. 
Patient Replacement 
Patients who terminate participation in the study for any reason other than DLTs prior to 
receiving the second injection of SYNB1891 in Cycle 1 will be considered ineligible for the 
safety assessment required for dose-escalation decisions and may be replaced. 

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9. 
ADVERSE EVENTS 
9.1. 
Adverse Event 
An AE is any untoward medical occurrence, including the exacerbation of a pre-existing 
condition, in a patient administered a pharmaceutical product, regardless of causality. 
9.1.1. 
Assessment of Severity 
The severity rating of an AE refers to its intensity. The severity of each AE will be categorized 
using the NCI CTCAE, version 5.0 (US DHHS 2017). For any term that is not specifically listed 
in the CTCAE scale, intensity should be assigned a grade of 1 through 5 using the following 
CTCAE guidelines: 
Grade 1: Mild; asymptomatic or mild symptoms; clinical or diagnostic observations only; 
intervention not indicated 
Grade 2: Moderate; minimal, local or noninvasive intervention indicated; limiting  
age-appropriate instrumental activities of daily living 
Grade 3: Severe or medically significant but not immediately life-threatening; 
hospitalization or prolongation of hospitalization indicated; disabling; limiting 
self-care activities of daily living 
Grade 4: Life-threatening consequences; urgent intervention indicated 
Grade 5: Death related to AE 
9.1.2. 
Assessment of Causality 
Medical judgment should be used to determine the cause of the AE, considering all relevant 
factors such as (but not limited to) the underlying study indication, coexisting disease, 
concomitant medication, relevant history, pattern of the AE, temporal relationship to study 
treatment (with separate causality assessments for SYNB1891 and atezolizumab), and 
de-challenge or re-challenge. 
Yes (possibly, probably, or definitely related): there is a reasonable possibility that study 
treatment caused the event; one or more of the following criteria apply: 
• The event follows a reasonable temporal sequence from administration of study 
treatment. 
• The event could not be reasonably attributed to the known characteristics of the 
patient’s clinical state, environmental or toxic factors, or other modes of therapy 
administered to the patient. 
• The event follows a known pattern of response to study treatment. 
• The event disappears or decreases on cessation or reduction in dose. (It should be 
noted that in some situations an AE will not disappear or decrease in intensity upon 
discontinuation of study dosing despite other clear indications of relatedness). 

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No (unlikely, probably not related, or definitely not related): there is no reasonable possibility 
that study treatment caused the event; one or more of the following criteria apply: 
• The event does not follow a reasonable temporal sequence from administration of 
study treatment.  
• The event could be reasonably attributed to the known characteristics of the patient’s 
clinical state, concurrent illness, environmental or toxic factors, or other modes of 
therapy administered to the patient. 
• The event does not follow a known pattern of response to study treatment. 
• The event does not disappear or decrease on cessation or reduction in dose(ing), and 
it does not reappear or worsen when dosing is resumed. 
9.2. 
Serious Adverse Event 
An SAE is any untoward medical occurrence that meets any of the following criteria: 
• Results in death. 
• Is immediately life-threatening (refers to an event in which the patient is at risk of 
death at the time of the event; it does not refer to an event, which hypothetically 
might have caused death if it were more severe). 
• Requires inpatient hospitalization or prolongation of existing hospitalization. 
• Results in a persistent or significant incapacity or substantial disruption of the ability 
to conduct normal life functions. 
• Is a congenital anomaly/birth defect. 
• Based on appropriate medical judgment, represents an important medical event that 
may jeopardize the patient or may require intervention to prevent one of the other 
outcomes described above. 
9.2.1. 
Clarification of Serious Adverse Event Definition 
• Progression of malignancy should be documented through appropriate methodology 
(e.g., as per iRECIST) and designated as progression of disease in the disease 
assessment eCRF, but should not be reported as an AE/SAE unless a causal 
relationship to study treatment is suspected. 
• Death is an outcome of an SAE and not an SAE in itself. When death is an outcome, 
the event(s) resulting in death should be reported (e.g., “pulmonary embolism” with a 
fatal outcome). The appropriate diagnosis or term should be recorded and assigned 
severity Grade 5. 
• In instances of death due ultimately to the underlying disease, the cause of death 
should be indicated as the specific event or condition resulting in death to the extent 
possible. If no appropriate term with a Grade 5 severity in the CTCAE can be 
identified, then a term should be selected from the CTCAE category “Death”. 

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• “Life-threatening” means that the patient was at immediate risk of death from the 
event as it occurred. This does not include an event that might have led to death if it 
had occurred with greater severity. Grade 4 events (e.g., thrombocytopenia) are not 
always serious unless they have life-threatening consequences or result in 
hospitalization. 
• Preplanned or elective hospitalizations including social and/or convenience situations 
(e.g., respite care) are excluded from SAE reporting. In addition, “admissions” under 
23-hour observation or emergency room visits are excluded from SAE reporting; 
however, such events should still be reported on the appropriate eCRF page. 
• Overdose of either study treatment or concomitant medication without any overdose 
signs or symptoms unless the event meets SAE criteria (e.g., hospitalization) are 
excluded from SAE reporting; however, such events should still be reported on the 
appropriate eCRF page. 
• SAEs that occur within the safety follow-up period but are related to subsequent 
therapies are excluded from SAE reporting: 
− Patients who have completed study treatment administration or who terminate 
from the study and then undergo subsequent therapies during the safety follow-up 
period and experience an SAE specifically related to the administration of the 
subsequent therapy will not have those events reported as SAEs. This exclusion 
will include “elective” hospitalizations necessary for the administration of such 
therapies. 
9.2.2. 
Serious, Unexpected, Suspected Adverse Reactions 
In accordance with regulatory requirements, the Sponsor or designee will notify regulatory 
authorities as required per local law (i.e., 21 CFR 312.32 in the United States). The Sponsor or 
designee will also notify the Investigators, who will in turn notify their IRB as necessary, of any 
AE associated with study treatment administration or study procedures that is a serious, 
unexpected, suspected adverse reaction (SUSAR) or any finding from tests in laboratory animals 
that suggests a significant risk for human patients, including reports of mutagenicity, 
teratogenicity, or carcinogenicity. An AE or suspected adverse reaction is considered 
“unexpected” if it is not listed in the Investigator’s Brochure or is not listed at the specificity or 
severity that has been previously observed. 
9.3. 
Adverse Events of Special Interest 
Adverse events of special interest (AESIs) (serious or nonserious) are a subset of events to 
monitor scientific and medical concern, for which ongoing monitoring by the Investigator to the 
Sponsor is required. An AESI may warrant further investigation and reporting in accordance 
with local regulatory requirements.  

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Adverse events of special interest for SYNB1891 are as follows: 
• Cytokine release syndrome (may include associated AEs, e.g., fever, tachypnea, 
headache, tachycardia, hypotension, rash, hypoxia) graded in accordance with 
NCI CTCAE, version 5.0 
• Systemic infection (Grade 3 or higher in accordance with NCI CTCAE, version 5.0) 
• Local injection site reactions (Grade 3 or higher; may include associated AEs, e.g., 
abscess, infection, ulceration or necrosis, or severe tissue damage) graded in 
accordance with NCI CTCAE, version 5.0 
9.4. 
Reporting of Adverse Events 
All AEs, serious and nonserious, will be fully documented on the appropriate eCRF. For each 
AE, the Investigator must provide its duration (start and end dates or ongoing), intensity, 
assessment of causality, and whether specific action or therapy was required. 
All AEs occurring from the time a patient signs informed consent through the Safety Follow-up 
visit must be recorded on the eCRF. 
All SAEs, regardless of relationship to study treatment, must be reported to the Sponsor within 
24 hours of the Investigator’s knowledge. This should be done by faxing the completed SAE 
Report Form to the Sponsor at the number provided on the SAE Report Form. After the Safety 
Follow-up visit, only SAEs that are considered related to study treatment will be recorded, if 
clinically indicated. 
Investigators must follow patients with AEs/SAEs until event resolution or stabilization, 
withdrawal of consent, patient loss to follow-up, or death, whichever occurs first. 
9.5. 
Pregnancy 
If a patient becomes pregnant during the study, study treatment administration is to be 
discontinued immediately. 
Pregnancies (both those of female patients and female partners of male patients) must be 
reported to the Sponsor or designee within 24 hours of the Investigator’s knowledge using the 
designated pregnancy reporting form. Investigators should make every effort to obtain 
permission to follow and report the outcome of the pregnancy to the Sponsor. 
Pregnancies themselves are not considered AEs or SAEs. However, any AEs or SAEs occurring 
during pregnancy (or the outcome of the pregnancy) are to be reported following AE and SAE 
reporting guidelines. 
9.6. 
Clinical Laboratory Abnormalities 
It is the responsibility of the Investigator to assess the clinical significance of all abnormal 
laboratory values as defined by the appropriate reference ranges. All abnormal values assessed to 
be of clinical concern and at least possibly related to study treatment or of uncertain causality 
should be repeated. Persistent abnormal values and changes of possible clinical concern that 
remain within the normal range should be followed at the discretion of the Investigator. 

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An abnormal laboratory value that is not already associated with an AE is to be recorded as an 
AE if an action on study treatment dosing is made as a result of the abnormality, if intervention 
for management of the abnormality is required, or at the discretion of the Investigator. 
9.7. 
Review of Safety Data 
The Sponsor Medical Monitor in collaboration with the CRO Medical Monitor will be 
responsible for the ongoing review and evaluation of safety data, including AEs, clinical 
laboratory data, and any other safety evaluations, for the duration of the study. 
The Sponsor will host Investigator teleconferences on a regular basis during the study. In 
addition, the Safety Review Committee (SRC; consisting of the Sponsor Medical Monitor, the 
CRO Medical Monitor, all active Investigators, and other study personnel as needed) will 
convene when all patients have completed the first cycle of study treatment in a given cohort and 
review all available safety information, including DLTs and all NCI CTCAE Grade 2 or higher 
toxicity data, as well as any other (e.g., PK/PD) data as indicated. Updated safety data on other 
ongoing patients, including data from later cycles, will be discussed as well.  

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10. 
STATISTICAL METHODS AND DETERMINATION OF 
SAMPLE SIZE 
All evaluations and tabulations will be carried out as described in detail in a statistical analysis 
plan (SAP), which will be finalized and approved prior to database lock. 
10.1. 
Populations for Analysis 
The following populations will be defined: 
• The safety population includes participants who were enrolled, allocated to treatment, 
and received at least one dose of investigational product. 
• The efficacy population includes participants who received study drug and had an 
on-treatment response assessment (including “Not Evaluable”) or who discontinued 
study before any response assessment was performed due to disease progression. 
• The PK/PD population includes participants who received study drug and had at least 
one PK or PD assessment. 
Additional populations may be defined in the SAP, as required. 
10.2. 
Safety Variables 
Patients in the safety population will be included in safety analyses. 
Adverse events will be coded using the Medical Dictionary for Regulatory Activities 
(MedDRA), and the severity of AEs and laboratory abnormalities will be graded using the NCI 
CTCAE, version 5.0 (US DHHS 2017). AEs will be tabulated by system organ class (SOC) and 
preferred term. Incidence tables of patients with AEs, SAEs, and DLTs will be presented by 
maximum severity. 
Clinical laboratory data, ECGs, and other safety assessments will be presented in by-patient 
listings and will be presented in tabular format, including absolute values and changes from 
baseline (if applicable), by dose cohort, cycle, and study day. 
10.3. 
Efficacy Variables 
Efficacy analyses will be descriptive in nature. The response of SYNB1891-injected lesion(s) 
and an overall response of up to 5 noninjected target lesions will be assessed. Exploratory 
evaluations for proof-of-concept (biopsy-based PD markers) will include change from baseline 
assessment. 
The duration of any response or lack of progression for all evaluated tumors will also be assessed 
using RECIST 1.1 (Eisenhauer et al 2009 and Appendix 1), iRECIST (Seymour et al 2017 and 
Appendix 2), and/or LYRIC (Cheson et al 2016 and Appendix 3). 
Results will be presented in by-patient listings and will be presented in tabular format, including 
absolute values and changes from baseline (if applicable), by dose cohort, cycle, and study day. 

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10.4. 
Pharmacodynamic Variables 
Pharmacodynamic data will be presented in by-patient listings and will be presented in tabular 
and/or graphical format, including absolute values and changes from baseline, by dose cohort 
and study day. 
10.5. 
Kinetic Variables 
Kinetics of SYNB1618 will be presented in by-patient listings and will be presented in tabular 
format and figures by dose cohort, cycle, and study day. 
10.6. 
Determination of Sample Size 
No formal sample size calculations were performed, as the study is primarily designed for 
empirical evaluation of safety and tolerability in patients with advanced solid tumors or 
lymphoma. The anticipated sample size is approximately 70 patients, which provides for 4 to 
7 dose-finding cohorts in Arm 1, 1 to 5 cohorts in Arm 2, and replacement of 1 patient per 
cohort, as well up to 20 additional patients enrolled at the RP2D in Arm 2 to fully characterize 
the safety profile of SYNB1891 in combination with atezolizumab. Additional cohorts may be 
required in either arm to determine the MTD/RP2D. 
10.7. 
Randomization and Blinding 
This first-in-human, dose-finding study will be nonrandomized with open-label study treatment. 
10.8. 
Changes in the Conduct of the Study or Planned Analysis 
Only the Sponsor may modify the protocol. Amendments to the protocol will be made only after 
consultation and agreement between the Sponsor and the Investigator. The only exception is 
when the Investigator considers that a patient’s safety is compromised without immediate action. 
In these circumstances, the Investigator should inform the Sponsor and the full IRB within 
1 working day after the emergency occurred. All amendments that have an impact on patient risk 
or the study objectives or require revision of the informed consent document must receive 
approval from the IRB prior to implementation. 

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11. 
DATA RECORDING, RETENTION AND MONITORING 
11.1. 
Case Report Forms 
Data will be collected using source documents through an electronic data capture (EDC) system 
at the clinical site. The Investigator or designee will record data specified in the protocol using 
eCRFs. Changes or corrections to eCRFs will be made by the Investigator or an authorized 
member of the study staff according to the eCRF completion guidelines. It is expected that the 
site will enter all data within 5 days of a patient visit. 
It is the Investigator’s responsibility to ensure eCRFs are complete and accurate, regardless of 
whether this responsibility has been delegated in whole or in part. Following review and 
approval, the Investigator or designee will electronically sign and date the pages, which certifies 
that the Investigator has thoroughly reviewed and confirmed all data on the eCRF.  
11.2. 
Data Retention 
Data retention practices will follow International Council for Harmonisation of Technical 
Requirements for Pharmaceuticals for Human Use (ICH) guidelines, which note that essential 
documents should be retained for a minimum of 2 years after the last approval of a marketing 
application in an ICH region and until there are no pending or contemplated marketing 
applications in an ICH region or at least 2 years have elapsed since the formal discontinuation of 
clinical development of SYNB1891. However, these documents should be retained for a longer 
period if required by the applicable legal requirements.  
11.3. 
Data Monitoring 
This study will be closely monitored by representatives of the Sponsor or designee throughout its 
duration. Monitoring will include personal visits with the Investigator and study staff as well as 
appropriate communications by telephone, fax, mail, email, or use of the EDC system, as 
applicable. It is the monitor’s responsibility to inspect eCRFs at regular intervals throughout the 
study to verify the completeness, accuracy, and consistency of the data and to confirm adherence 
to the study protocol and to Good Clinical Practice (GCP) guidelines. The Investigator agrees to 
cooperate with the monitor to ensure that any problems detected during the course of this study 
are resolved promptly. The Investigator and site will permit study-related monitoring, audits, 
IRB review, and regulatory inspection, including direct access to source documents. 
It is understood that study monitors and any other personnel authorized by the Sponsor may 
contact and visit the Investigator and will be permitted to inspect all study records (including 
eCRFs and other pertinent data) on request, provided that patient confidentiality is maintained 
and that the inspection is conducted in accordance with local regulations. 
Every effort will be made to maintain the anonymity and confidentiality of patients during this 
study. However, because of the experimental nature of SYNB1891, the Investigator agrees to 
allow representatives of the Sponsor and authorized representatives of regulatory authorities to 
inspect the facilities used in the conduct of this study and to inspect, for purposes of verification, 
the hospital or clinic records of all patients enrolled in the study. 

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11.4. 
Quality Control and Quality Assurance 
Quality control procedures will be conducted according to the Sponsor and CRO’s internal 
procedures. The study site may be audited by a quality assurance representative of the Sponsor. 
All necessary data and documents will be made available for inspection. 

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12. 
REGULATORY, ETHICAL, AND LEGAL OBLIGATIONS 
12.1. 
Good Clinical Practice 
The study will be performed in accordance with the protocol, guidelines for GCP established by 
the ICH and applicable local regulatory requirements and laws.  
12.2. 
Institutional Review Board Approval 
The Investigator must inform and obtain approval from the IRB for the conduct of the study at 
named sites, the protocol, informed consent documents, and any other written information that 
will be provided to the patients and any advertisements that will be used. Written approval must 
be obtained prior to recruitment of patients into the study and shipment of 
SYNB1891/atezolizumab. 
Proposed amendments to the protocol (see Section 10.8) and aforementioned documents must be 
submitted to the Sponsor for review and approval, then to the IRB. Amendments may be 
implemented only after a copy of the approval letter from the IRB has been transmitted to the 
Sponsor. 
Per GCP guidelines, the Investigator will be responsible for ensuring that an annual update is 
provided to the IRB until the study is completed (i.e., finalization of the clinical study report) to 
facilitate continuing review of the study and that the IRB is informed about the end of the study. 
Copies of the update, subsequent approvals, and final letter must be sent to the Sponsor. 
12.3. 
Regulatory Authority Approval 
The study will be performed in accordance with the requirements of the US FDA and will also 
meet all of the requirements of ICH GCP guidance. Amendments to the protocol will be 
submitted to the FDA prior to implementation in accordance with applicable regulations. 
12.4. 
Other Required Approvals 
In addition to IRB and regulatory authority approval, all other required approvals (e.g., approval 
from the local research and development board or scientific committee) will be obtained prior to 
recruitment of patients into the study and shipment of SYNB1891/atezolizumab. 
12.5. 
Informed Consent 
Informed consent is initiated prior to the patient’s agreeing to participate in the study and 
continues throughout the patient’s study participation. It is the Investigator’s responsibility (or 
designee) to obtain written informed consent from each patient after adequate explanation of the 
aims, methods, anticipated benefits, and potential hazards of the study and before any study 
procedures are initiated. Each patient should be given a copy of the informed consent document 
and associated materials. The original copy of the signed and dated informed consent document 
must be retained at the site and is patient to inspection by representatives of the Sponsor or 
regulatory authorities. If any amendments occur throughout the course of the study that affect the 
informed consent form (i.e., when new study procedures or assessments have been added), all 
active patients should be reconsented using the same process for the initial consent. 

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12.6. 
Patient Confidentiality 
The Investigator must ensure that the patient’s privacy is maintained. On eCRFs and other 
documents submitted to the Sponsor, patients will be identified by their assigned patient number. 
Documents that are not submitted to the Sponsor (e.g., signed informed consent documents) 
should be kept in a confidential file by the Principal Investigator. 
The Investigator shall permit authorized representatives of the Sponsor, regulatory authorities, 
and Ethics Committees to review the portion of the patient’s medical record that is directly 
related to the study. As part of the required content of informed consent documents, the patient 
must be informed that his/her records will be reviewed in this manner. 
12.7. 
Disclosure of Information 
Information concerning the study, patent applications, processes, scientific data, or other 
pertinent information is confidential and remains the property of the Sponsor. The Principal 
Investigator may use this information for the purposes of the study only. 
It is understood by the Principal Investigator that the Sponsor will use information obtained in 
this clinical study in connection with the clinical development program, and therefore may 
disclose it as required to other clinical Investigators and to regulatory authorities. In order to 
allow the use of the information derived from this clinical study, the Principal Investigator 
understands that he/she has an obligation to provide complete test results and all data obtained 
during this study to the Sponsor. 
Verbal or written discussion of results prior to study completion and full reporting should only 
be undertaken with written consent from the Sponsor. 
12.8. 
Publication of Study Data 
The Sponsor encourages the scientific publication of data from clinical research studies. 
However, Investigators may not present or publish partial or complete study results individually 
without participation of the Sponsor. The Principal Investigator and the Sponsor may propose 
appropriate scientific manuscripts or abstracts from the study data. All proposed publications 
must be reviewed and commented on by the Sponsor before submission for publication. The 
detailed procedures for the review of publications are set out in the clinical trial agreement 
entered into with the Sponsor in connection with this study. These procedures are in place to 
ensure coordination of study data publication and adequate review of data for publication against 
the validated study database for accuracy.  
Qualification of authorship will follow the requirements of the International Committee of 
Medical Editors (www.icmje.org). The names of Investigators and Sponsor representatives 
responsible for designing the study and analyzing the results will be included in the 
publication(s). This custom can be adjusted upon mutual agreement of the authors and Synlogic. 
In addition, other than clinical pharmacology studies in healthy volunteers or Phase 1 trials, all 
clinical trials must be registered with ClinicalTrials.gov. 

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12.9. 
Ethical Standards 
We are committed to designing, implementing, conducting, analyzing and reporting these trials 
in compliance with the highest ethical and scientific standards. Protection of patient safety is the 
overriding concern in the design of clinical trials. In all cases, Synlogic clinical trials will be 
conducted in compliance with local and/or national regulations and in accordance with the 
ethical principles that have their origin in the Declaration of Helsinki.  

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13. 
REFERENCES 
Adams S. Toll-like receptor agonists in cancer therapy. Immunotherapy 2009; 1(6):949-64. 
Adashek ML, Feldman M. Cytokine release syndrome resulting from anti-programmed death-1 
antibody: raising awareness among community oncologist. J Oncol Practice 2019; 15:502-504. 
Bashor CJ, Collins JJ. Understanding biological regulation through synthetic biology. Annu Rev 
Biophys 2018; 47:399-423. 
Cheson BD, Ansell S, Schwartz L, et al. Refinement of the Lugano Classification lymphoma 
response criteria in the era of immunomodulatory therapy. Blood 2016; 128(21):2489-96. 
Chiappinelli KB, Strissel PL, Desrichard A, et al. Inhibiting DNA methylation causes an 
interferon response in cancer via dsRNA including endogenous retroviruses. Cell 2015; 
162(5):974-86. 
Corrales L, Glickman LH, McWhirter SM, et al. Direct activation of STING in the tumor 
microenvironment leads to potent and systemic tumor regression and immunity. Cell Rep 2015; 
11(7):1018-30. 
Darvin P, Toor SM, Sasidharan Nair V, Elkord E. Immune checkpoint inhibitors: recent progress 
and potential biomarkers. Exp Mol Med 2018; 50(12):165. 
Eisenhauer EA, Therasse P, Bogaerts J. New response evaluation criteria in solid tumours: 
revised RECIST guideline (version 1.1). Eur J Cancer 2009; 45(2):228-47. 
Fehrenbacher L, Spira A, Ballinger M, et al. Atezolizumab versus docetaxel for patients with 
previously treated non-small-cell lung cancer (POPLAR): a multicentre, open label, phase 2 
randomised controlled trial. Lancet 2016; 387:1837-46. 
Felgner S, Kocijancic D, Frahm M, Weiss S. Bacteria in cancer therapy: renaissance of an old 
concept. Int J Microbiol 2016; 2016:8451728. 
Fu J, Kanne DB, Leong M, et al. STING agonist formulated cancer vaccines can cure established 
tumors resistant to PD-1 blockade. Sci Transl Med 2015; 7(283):283ra52. 
Fuertes MB, Kacha AK, Kline J, et al. Host type I IFN signals are required for antitumor CD8+ 
T cell responses through CD8α+ dendritic cells. J Exp Med 2011; 208(10):2005-16. 
Hejblum G, Lambotte O, Galicier L, et al. A web-based Delphi study for eliciting helpful criteria 
in the positive diagnosis of hemophagocytic syndrome in adult patients. PLoS ONE 2014; 
9(4):e94024. 
Henter JI, Horne A, Aricó M, et al. HLH-2004: diagnostic and therapeutic guidelines for 
hemophagocytic lymphohistiocytosis. Pediatr Blood Cancer 2007; 48:124-31. 

SYNB1891 
 
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27 July 2020 
 
Iribarren K, Bloy N, Buque A, et al. Trial watch: immunostimulation with toll-like receptor 
agonists in cancer therapy. Oncoimmunology 2015; 5(3):e1088631. 
Isaacs A, Lindenmann J. Virus interference. I. The interferon. Proc Roy Soc London 1957; 
147(927): 258. 
Ishikawa H, Barber GN. STING is an endoplasmic reticulum adaptor that facilitates innate 
immune signalling. Nature 2008; 455(7213):674-8. 
Ivashkiv LB, Donlin LT. Regulation of type I interferon responses. Nat Rev Immunol 2014; 
14(1):36-49. 
Ji Y, Wang SJ. Modified toxicity probability interval design: a safer and more reliable method 
than the 3 + 3 design for practical phase 1 trials. J Clin Oncol 2013; 31(14):1785-91. 
Kitada T, DiAndreth B, Teague B, Weiss R. Programming gene and engineered-cell therapies 
with synthetic biology. Science 2018; 359(6376) pii:eaad1067. 
Larkin B, Ilyukha V, Sorokin M, et al. Cutting edge: activation of STING in T cells induces 
Type I IFN responses and cell death. J Immunol 2017; 199(2):397-402. 
Lee DW, Santomasso BD, Locke FL, et al. ASTCT consensus grading for cytokine release 
syndrome and neurologic toxicity associated with immune effector cells. Biol Blood Marrow 
Transplant 2019; 25(4):625-638. 
Marabelle A, Andtbacka R, Harrington K, et al. Starting the fight in the tumor: expert 
recommendations for the development of human intratumoral immunotherapy (HIT-IT). Ann 
Oncol 2018; 29(11):2163-74. 
McCarthy EF. The toxins of William B. Coley and the treatment of bone and soft-tissue 
sarcomas. Iowa Orthop J 2006; 26:154-8.  
Riegler LL, Jones GP, Lee DW. Current approaches in the grading and management of cytokine 
release syndrome after chimeric antigen receptor T-cell therapy. Ther Clin Risk Manag 2019; 
15:323-335. 
Rosenberg JE, Hoffman-Censits J, Powles T, et al. Atezolizumab in patients with locally 
advanced and metastatic urothelial carcinoma who have progressed following treatment with 
platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial. Lancet 2016; 387:1909-
20. 
Rotz SJ, Leino D, Szabo S, et al. Severe cytokine release syndrome in a patient receiving PD-1-
directed therapy. Pediatr Blood Cancer 2017; 64:e26642. 

SYNB1891 
 
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Seymour L, Bogaerts J, Perrone A, et al. iRECIST: guidelines for response criteria for use in 
trials testing immunotherapeutics. Lancet Oncol 2017; 18(3):e143-e152. 
Sivick KE, Desbien AL, Glickman LH, et al. Magnitude of therapeutic STING activation 
determines CD8+ T cell-mediated anti-tumor immunity. Cell Rep 2018; 25(11):3074-85. 
Sonnenborn U, Schulze J. The non-pathogenic Escherichia coli strain Nissle 1917 – features of a 
versatile probiotic. Microb Ecol Health Dis 2009; 21:122-58. 
Trinchieri G. Type I interferon: friend or foe? J Exp Med 2010; 207(10):2053-63. 
US Department of Health and Human Services. Common Terminology Criteria for Adverse 
Events (CTCAE) Version 5.0. Published 27 Nov 2017. Available at: 
<https://ctep.cancer.gov/protocolDevelopment/electronic_applications/docs/CTCAE_v5_Quick_
Reference_5x7.pdf> Accessed 17 May 2019. 
Woo SR, Fuertes MB, Corrales L, et al. STING-dependent cytosolic DNA sensing mediates 
innate immune recognition of immunogenic tumors. Immunity 2014; 41(5):830-42. 
Zamarin D, Holmgaard RB, Subudhi SK, et al. Localized oncolytic virotherapy overcomes 
systemic tumor resistance to immune checkpoint blockade immunotherapy. Sci Transl Med 
2014; 6(226):226ra32. 
Zou W, Wolchok JD, Chen L. PD-L1 (B7-H1) and PD-1 pathway blockade for cancer therapy: 
Mechanisms, response biomarkers, and combinations. Sci Transl Med 2016; 8(328):328rv4. 
 
 
 

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APPENDIX 1. RESPONSE EVALUATION CRITERIA IN SOLID 
TUMORS, VERSION 1.1 
The following immune-related response criteria, adapted from the RECIST, version 1.1, 
guidelines (Eisenhauer et al 2009), should be implemented to assess disease status for patients 
with solid tumors. 
Tumor Measurability 
At baseline, tumor lesions/lymph nodes will be categorized as measurable or nonmeasurable as 
described below. All measurable and nonmeasurable lesions should be assessed at screening and 
at subsequent protocol-specified tumor assessment time points. Additional assessments may be 
performed as clinically indicated for suspicion of progression. 
Definition of Measurable Lesions 
Tumor Lesions 
Tumor lesions must be accurately measured in at least one dimension (longest diameter in the 
plane of measurement is to be recorded) with a minimum size as follows:  
• 10 mm by computed tomography (CT) or magnetic resonance imaging (MRI) scan 
(CT/MRI scan slice thickness/interval ≤ 5 mm) 
• 10-mm caliper measurement by clinical examination (lesions that cannot be accurately 
measured with calipers should be recorded as nonmeasurable) 
• 20 mm by chest X-ray 
Malignant Lymph Nodes 
To be considered pathologically enlarged and measurable, a lymph node must be ≥ 15 mm in the 
short axis when assessed by CT scan (CT scan slice thickness recommended to be ≤ 5 mm). At 
baseline and follow-up, only the short axis will be measured and followed. Additional 
information on lymph node measurement is provided below (see “Identification of Target and 
Nontarget Lesions” and “Calculation of Sum of Diameters”). 
Definition of Nonmeasurable Lesions 
Nonmeasurable tumor lesions encompass small lesions (longest diameter < 10 mm or 
pathological lymph nodes with short axis ≥ 10 mm but ≤ 15 mm) as well as truly nonmeasurable 
lesions. Lesions considered truly nonmeasurable include leptomeningeal disease, ascites, pleural 
or pericardial effusion, inflammatory breast disease, lymphangitic involvement of skin or lung, 
peritoneal spread, and abdominal mass/abdominal organomegaly identified by physical 
examination that is not measurable by reproducible imaging techniques. 
Special Considerations Regarding Lesion Measurability 
Bone lesions, cystic lesions, and lesions previously treated with local therapy require particular 
comment, as outlined below. 
Bone Lesions: 
• Technetium-99m bone scans, sodium fluoride positron emission tomography scans, and 
plain films are not considered adequate imaging techniques for measuring bone lesions. 

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However, these techniques can be used to confirm the presence or disappearance of bone 
lesions. 
• Lytic bone lesions or mixed lytic-blastic lesions with identifiable soft tissue components 
that can be evaluated by cross-sectional imaging techniques such as CT or MRI can be 
considered measurable lesions if the soft tissue component meets the definition of 
measurability described above. 
• Blastic bone lesions are nonmeasurable. 
Cystic Lesions: 
• Lesions that meet the criteria for radiographically defined simple cysts should not be 
considered malignant lesions (neither measurable nor nonmeasurable) since they are, by 
definition, simple cysts. 
• Cystic lesions thought to represent cystic metastases can be considered measurable 
lesions if they meet the definition of measurability described above. However, if 
noncystic lesions are present in the same patient, these are preferred for selection as 
target lesions. 
Lesions with Prior Local Treatment: 
• Tumor lesions situated in a previously irradiated area or in an area subjected to other 
loco-regional therapy are usually not considered measurable unless there has been 
demonstrated progression in the lesion. 
Methods For Assessing Lesions 
All measurements should be recorded in metric notation, using calipers if clinically assessed. All 
baseline evaluations should be performed as close as possible to the treatment start and never 
more than 4 weeks before the beginning of the treatment. 
The same method of assessment and the same technique should be used to characterize each 
identified and reported lesion at baseline and during the study. Imaging-based evaluation should 
always be the preferred option. 
Clinical Lesions 
Clinical lesions will only be considered measurable when they are superficial and ≥ 10 mm in 
diameter as assessed using calipers (e.g., skin nodules). For the case of skin lesions, 
documentation by color photography, including a ruler to estimate the size of the lesion, is 
suggested. 
Chest X-Ray 
Chest CT is preferred over chest X-ray, particularly when progression is an important endpoint, 
since CT is more sensitive than X-ray, particularly in identifying new lesions. However, lesions 
on chest X-ray may be considered measurable if they are clearly defined and surrounded by 
aerated lung. 
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CT is the best currently available and reproducible method to measure lesions selected for 
response assessment. In this guideline, the definition of measurability of lesions on CT scan is 
based on the assumption that CT slice thickness is ≤ 5 mm. When CT scans have slice thickness 
of > 5 mm, the minimum size for a measurable lesion should be twice the slice thickness. MRI is 
also acceptable. 
If prior to enrollment it is known that a patient is unable to undergo CT scans with intravenous 
(IV) contrast because of allergy or renal insufficiency, the decision as to whether a noncontrast 
CT or MRI (without IV contrast) will be used to evaluate the patient at baseline and during the 
study should be guided by the tumor type under investigation and the anatomic location of the 
disease. For patients who develop contraindications to contrast after baseline contrast CT is 
done, the decision as to whether noncontrast CT or MRI (enhanced or nonenhanced) will be 
performed should also be based on the tumor type and the anatomic location of the disease, and 
should be optimized to allow for comparison with the prior studies if possible. Each case should 
be discussed with the radiologist to determine if substitution of these other approaches is possible 
and, if not, the patient should be considered not evaluable from that point forward. Care must be 
taken in measurement of target lesions and interpretation of nontarget disease or new lesions on a 
different modality, since the same lesion may appear to have a different size using a new 
modality. 
Endoscopy, Laparoscopy, Ultrasound, Tumor Markers, Cytology, Histology 
Endoscopy, laparoscopy, ultrasound, tumor markers, cytology, and histology cannot be used for 
objective tumor evaluation . 
Assessment of Tumor Burden 
To assess objective response or future progression, it is necessary to estimate the overall tumor 
burden at baseline and use this as a comparator for subsequent measurements. 
Identification of Target and Nontarget Lesions 
When more than one measurable lesion is present at baseline, all lesions up to a maximum of 
5 lesions total (and a maximum of two lesions per organ) representative of all involved organs 
should be identified as target lesions and will be recorded and measured at baseline. This means 
that, for instances in which patients have only one or two organ sites involved, a maximum of 
two lesions (one site) and four lesions (two sites), respectively, will be recorded. Other lesions 
(albeit measurable) in those organs will be considered nontarget lesions. 
Target lesions should be selected on the basis of their size (lesions with the longest diameter) and 
should be representative of all involved organs, but in addition should lend themselves to 
reproducible repeated measurements. It may be the case that, on occasion, the largest lesion does 
not lend itself to reproducible measurement, in which circumstance the next largest lesion that 
can be measured reproducibly should be selected. 
Lymph nodes merit special mention since they are normal anatomical structures that may be 
visible by imaging even if not involved by tumor. As noted above, pathological nodes that are 
defined as measurable and may be identified as target lesions must meet the criterion of a short 
axis of ≥ 15 mm by CT scan. Only the short axis of these nodes will contribute to the baseline 
sum. The short axis of the node is the diameter normally used by radiologists to judge if a node is 
involved by solid tumor. Lymph node size is normally reported as two dimensions in the plane in 

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which the image is obtained (for CT, this is almost always the axial plane; for MRI, the plane of 
acquisition may be axial, sagittal, or coronal). The smaller of these measures is the short axis. 
For example, an abdominal node that is reported as being 20 mm × 30 mm has a short axis of 
20 mm and qualifies as a malignant, measurable node. In this example, 20 mm should be 
recorded as the node measurement. All other pathological nodes (those with short axis ≥ 10 mm 
but ≤ 15 mm) should be considered nontarget lesions. Nodes that have a short axis of < 10 mm 
are considered nonpathological and should not be recorded or followed. 
All lesions (or sites of disease) not selected as target lesions (measurable or nonmeasurable), 
including pathological lymph nodes, should be identified as nontarget lesions and should also be 
recorded at baseline. Measurements are not required. It is possible to record multiple nontarget 
lesions involving the same organ as a single item on the eCRF (e.g., “multiple enlarged pelvic 
lymph nodes” or “multiple liver metastases”). 
Calculation of Sum of Diameters 
A sum of the diameters (longest diameter for nonlymph node lesions, short axis for lymph node 
lesions) will be calculated for all target lesions at baseline and at each subsequent tumor 
assessment as a measure of tumor burden. 
Measuring Lymph Nodes 
Lymph nodes identified as target lesions should always have the actual short axis measurement 
recorded (measured in the same anatomical plane as the baseline examination), even if the node 
regresses to < 10 mm during the study. Thus, when lymph nodes are included as target lesions, 
the sum of diameters may not be zero even if complete response criteria are met, since a normal 
lymph node is defined as having a short axis of < 10 mm. 
Measuring Lesions That Become Too Small to Measure 
During the study, all target lesions (lymph node and nonlymph node) recorded at baseline should 
have their actual measurements recorded at each subsequent evaluation, even when very small 
(e.g., 2 mm). However, sometimes lesions or lymph nodes that are recorded as target lesions at 
baseline become so faint on CT scan that the radiologist may not feel comfortable assigning an 
exact measurement and may report them as being too small to measure. When this occurs, it is 
important that a value be recorded on the eCRF, as follows: 
• If it is the opinion of the radiologist that the lesion has likely disappeared, the 
measurement should be recorded as 0 mm. 
• If the lesion is believed to be present and is faintly seen but too small to measure, a 
default value of 5 mm should be assigned and “too small to measure” should be 
ticked. (Note: It is less likely that this rule will be used for lymph nodes since they 
usually have a definable size when normal and are frequently surrounded by fat such 
as in the retroperitoneum; however, if a lymph node is believed to be present and is 
faintly seen but too small to measure, a default value of 5 mm should be assigned in 
this circumstance as well and “too small to measure” should also be ticked). 
To reiterate, however, if the radiologist is able to provide an actual measurement, that should be 
recorded, even if it is < 5 mm, and in that case “too small to measure” should not be ticked. 
Measuring Lesions That Split or Coalesce on Treatment 

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When nonlymph node lesions fragment, the longest diameters of the fragmented portions should 
be added together to calculate the sum of diameters. Similarly, as lesions coalesce, a plane 
between them may be maintained that would aid in obtaining maximal diameter measurements 
of each individual lesion. If the lesions have truly coalesced such that they are no longer 
separable, the vector of the longest diameter in this instance should be the maximum longest 
diameter for the coalesced lesion. 
Evaluation of Nontarget Lesions 
Measurements are not required for nontarget lesions, except that malignant lymph node 
nontarget lesions should be monitored for reduction to < 10 mm in short axis. Nontarget lesions 
should be noted at baseline and should be identified as “present” or “absent” and (in rare cases) 
may be noted as “indicative of progression” at subsequent evaluations. In addition, if a lymph 
node lesion shrinks to a nonmalignant size (short axis < 10 mm), this should be captured on the 
eCRF as part of the assessment of nontarget lesions. 
Response Criteria 
Criteria for Target Lesions 
Definitions of the criteria used to determine objective tumor response for target lesions are 
provided below: 
• Complete response (CR): Disappearance of all target lesions 
− Any pathological lymph nodes must have reduction in short axis to < 10 mm. 
• Partial response (PR): At least a 30% decrease in the sum of diameters of all target 
lesions, taking as reference the baseline sum of diameters, in the absence of CR 
• Progressive disease (PD): At least a 20% increase in the sum of diameters of target 
lesions, taking as reference the smallest sum of diameters at prior time points 
(including baseline)  
− In addition to the relative increase of 20%, the sum of diameters must also 
demonstrate an absolute increase of ≥ 5 mm. 
• Stable disease (SD): Neither sufficient shrinkage to qualify for CR or PR nor 
sufficient increase to qualify for PD 
Criteria for Nontarget Lesions 
Definitions of the criteria used to determine the tumor response for the group of nontarget lesions 
are provided below. While some nontarget lesions may actually be measurable, they need not be 
measured and instead should be assessed only qualitatively at the time points specified in the 
schedule of activities. 
• CR: Disappearance of all nontarget lesions and (if applicable) normalization of tumor 
marker level 
− All lymph nodes must be nonpathological in size (< 10 mm short axis). 
• Non-CR/Non-PD: Persistence of one or more nontarget lesions and/or (if applicable) 
maintenance of tumor marker level above the normal limits 

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• PD: Unequivocal progression of existing nontarget lesions 
Special Notes on Assessment of Progression of Nontarget Lesions 
For patients with both measurable and nonmeasurable disease to achieve unequivocal 
progression on the basis of the nontarget lesions, there must be an overall level of substantial 
worsening in nontarget lesions in a magnitude that, even in the presence of SD or PR in target 
lesions, the overall tumor burden has increased sufficiently to merit discontinuation of therapy. A 
modest increase in the size of one or more nontarget lesions is usually not sufficient to qualify 
for unequivocal progression status. The designation of overall progression solely on the basis of 
change in nontarget lesions in the face of SD or PR in target lesions will therefore be extremely 
rare. 
New Lesions 
The appearance of new malignant lesions denotes disease progression; therefore, some 
comments on detection of new lesions are important. There are no specific criteria for the 
identification of new radiographic lesions; however, the finding of a new lesion should be 
unequivocal, that is, not attributable to differences in scanning technique, change in imaging 
modality, or findings thought to represent something other than tumor (for example, some “new” 
bone lesions may be simply healing or flare of preexisting lesions). This is particularly important 
when the patient's baseline lesions show PR or CR. For example, necrosis of a liver lesion may 
be reported on a CT scan report as a “new” cystic lesion, which it is not. 
A lesion identified during the study in an anatomical location that was not scanned at baseline is 
considered a new lesion and will indicate disease progression. 
If a new lesion is equivocal, for example because of its small size, continued therapy and follow-
up evaluation will clarify if it represents truly new disease. If repeat scans confirm there is 
definitely a new lesion, progression should be declared using the date of the initial scan. 
Criteria for Overall Response at a Single Time point 
Table 21 provides a summary of the overall response status calculation at each response 
assessment time point for patients who have measurable disease at baseline. 
Table 21: 
Criteria for Overall Response at a Single Time Point: Patients with Target 
Lesions (with or without Nontarget Lesions) 
Target Lesions 
Nontarget Lesions 
New Lesions 
Overall Response 
CR 
CR 
No 
CR 
CR 
Non-CR/non-PD 
No 
PR 
CR 
Not all evaluated 
No 
PR 
PR 
Non-PD or not all evaluated 
No 
PR 
SD 
Non-PD or not all evaluated 
No 
SD 
Not all evaluated 
Non-PD 
No 
NE 
PD 
Any 
Yes or no 
PD 
Any 
PD 
Yes or no 
PD 
Any 
Any 
Yes 
PD 
Abbreviations: CR = complete response; NE = not evaluable; PD = progressive disease; PR = partial response; 
SD = stable disease 
 

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Missing Assessments and Not-Evaluable Designation 
When no imaging/measurement is done at all at a particular time point, the patient is not 
evaluable at that time point. If measurements are made on only a subset of target lesions at a 
time point, usually the case is also considered not evaluable at that time point, unless a 
convincing argument can be made that the contribution of the individual missing lesions would 
not change the assigned time point response. This would be most likely to happen in the case of 
PD. For example, if a patient had a baseline sum of 50 mm with three measured lesions and 
during the study only two lesions were assessed, but those gave a sum of 80 mm, the patient will 
have achieved PD status, regardless of the contribution of the missing lesion. 
Special Notes on Response Assessment 
Patients with a global deterioration in health status requiring discontinuation of treatment without 
objective evidence of disease progression at that time should be reported as “symptomatic 
deterioration.” Every effort should be made to document objective progression even after 
discontinuation of treatment. Symptomatic deterioration is not a descriptor of an objective 
response; it is a reason for stopping study therapy. The objective response status of such patients 
is to be determined by evaluation of target and nontarget lesions as shown in Table 21. 
For equivocal findings of progression (e.g., very small and uncertain new lesions; cystic changes 
or necrosis in existing lesions), treatment may continue until the next scheduled assessment. If at 
the next scheduled assessment, progression is confirmed, the date of progression should be the 
earlier date when progression was suspected. 

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APPENDIX 2. IMMUNE-RELATED RESPONSE EVALUATION 
CRITERIA IN SOLID TUMORS 
Conventional response criteria may not be adequate to characterize the antitumor activity of 
immunotherapeutic agents, which can produce delayed responses that may be preceded by initial 
apparent radiographic progression, including the appearance of new lesions. Therefore, 
immunotherapy-specific response criteria adaptations to RECIST 1.1 (Eisenhauer et al 2009) 
have been developed to allow for unconventional response and progression patterns. These 
include modified RECIST 1.1 for immune-based therapeutics (iRECIST; Seymour et al 2017), 
which was developed by the RECIST working group in an effort to create a common set of 
criteria that the cancer immunotherapy field could apply to clinical trials. 
Response evaluation through use of iRECIST requires collection of tumor assessment data after 
radiographic progression per RECIST 1.1. Details regarding lesion evaluation are described 
below. When not otherwise specified, RECIST 1.1 conventions will apply. 
Criteria for determining overall response at a single time point per iRECIST are also summarized 
below. Of note, overall response per iRECIST will not be captured in the eCRF, but will instead 
be calculated programmatically by the Sponsor on the basis of Investigator-assessed individual 
lesion data recorded in the eCRF. 
iRECIST response status is not a specific component of treatment discontinuation criteria, 
including decisions about whether to continue treatment beyond progression per RECIST 1.1. 
Investigators should instead take into account radiologic data and clinical status in making such 
decisions. 
Evaluation of Lesions to Support IRECIST Response Assessment after Disease Progression 
per RECIST 1.1  
iRECIST is an extension of RECIST 1.1 that allows for response assessment following disease 
progression per RECIST 1.1. RECIST 1.1 rules for categorizing lesions as measurable or 
nonmeasurable and measuring lesions (see Appendix 1) also apply to iRECIST. After disease 
progression per RECIST 1.1, the same target and nontarget lesions selected at baseline will 
continue to be followed, along with any new lesions that develop, to support iRECIST response 
evaluations, as described below and summarized in Table 22. Once a lesion has been categorized 
as a target, nontarget, or new lesion, it will remain classified as such. 
Target Lesions 
The target lesions selected at baseline should continue to be measured at all tumor assessment 
time points after disease progression per RECIST 1.1, according to RECIST 1.1 conventions. 
Nontarget Lesions 
Nontarget lesions selected at baseline should continue to be followed at all tumor assessment 
time points after disease progression per RECIST 1.1. At each time point, nontarget lesions 
should continue to be categorized as “absent” (complete response [CR]), “unequivocal 
progression” relative to baseline (progressive disease [PD]), or “present without unequivocal 
progression” (non-CR/non-PD), as defined by RECIST 1.1. In addition, any nontarget lesions 
that were categorized as PD at the previous time point should be evaluated to determine whether 
there has been any further increase in size. 

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New Lesions 
New lesions identified after baseline will be evaluated for measurability with use of the same 
criteria applied to prospective target lesions at baseline per RECIST 1.1 (e.g., nonlymph node 
lesions must be ≥ 10 mm on the longest diameter; new lymph nodes must be ≥ 15 mm on the 
short axis [see note below]). All new lesions (measurable or nonmeasurable) must be assessed 
and recorded at the time of identification and at all subsequent tumor assessment time points. 
Up to a maximum of 5 measurable new lesions total (with a maximum of two lesions per organ) 
should be selected and measured at each time point. New lesions that are not measurable at first 
appearance but meet measurability criteria at a subsequent time point should be measured from 
that point on, if the maximum number of measurable new lesions has not been reached. 
However, for calculation of the sum of diameters for new lesions, iRECIST excludes 
measurements from new lesions that were not measurable at first appearance. 
All nonmeasurable new lesions (including those that subsequently become measurable) and 
additional measurable new lesions (in excess of 5 total or two per organ) should be assessed to 
determine whether there is any increase in size relative to the previous assessment time point. 
Note regarding new lymph node lesions: If at first appearance the short axis of a lymph node 
lesion is ≥ 15 mm, it will be considered a measurable new lesion. If at first appearance the short 
axis of a lymph node lesion is ≥ 10 mm and < 15 mm, the lymph node will not be considered 
measurable but will still be considered a new lesion and should be identified as a nonmeasurable 
new lesion. If at first appearance the short axis of a lymph node is < 10 mm, the lymph node 
should not be considered pathological and should not be considered a new lesion. A lymph node 
can subsequently become measurable, when the short axis is ≥ 15 mm. Measurable new lymph 
node lesions should continue to be measured at all subsequent time points, even if the short axis 
decreases to < 15 mm (or even < 10 mm). 

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Table 22: 
Guidelines for Evaluation of Lesions to Support iRECIST Response 
Assessment after Disease Progression per RECIST 1.1 
Lesion Type 
Evaluation of Lesions to Support iRECIST Response Assessment after 
Disease Progression per RECIST 1.1 
Target lesions 
• Measurements should be continued according to RECIST 1.1 conventions. 
Nontarget lesions 
• Nontarget lesions should continue to be categorized as absent (CR), 
unequivocal progression (PD), or present without unequivocal progression 
(non-CR/non-PD), as defined by RECIST 1.1. In addition, any nontarget 
lesions that were categorized as PD at the previous time point should be 
evaluated to determine whether there has been any further increase in size. 
New lesions 
• New lesions should be evaluated for measurability per RECIST 1.1. 
• All new lesions (measurable or nonmeasurable) must be assessed and 
recorded at the time of identification and at all subsequent tumor 
assessment time points. 
• Up to a maximum of five measurable new lesions total (with a maximum 
of two lesions per organ) should be selected and measured at each 
time point. 
• All nonmeasurable new lesions (including those that subsequently become 
measurable) and additional measurable new lesions (in excess of five total 
or two per organ) should be assessed to determine whether there is any 
increase in size relative to the previous assessment time point. 
Abbreviations: CR = complete response; iRECIST = modified RECIST 1.1 for immune-based therapeutics; 
PD = progressive disease; RECIST 1.1 = Response Evaluation Criteria in Solid Tumors, Version 1.1 

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APPENDIX 3. LYMPHOMA RESPONSE TO IMMUNOMODULATORY 
THERAPY CRITERIA 
Immunomodulatory agents may be associated with clinical and imaging findings during 
treatment that are suggestive of progressive disease despite evidence of clinical benefit (e.g., 
tumor flare or pseudo-progression). The response criteria outlined below, which have been 
adapted from the Lymphoma Response to Immunomodulatory Therapy Criteria (LYRIC) 
(Cheson et al 2016), should be implemented to assess disease status for patients with lymphoma 
who receive immunomodulatory agents. 
Table 23: 
Guidelines for the Classification of Disease Status According to LYRIC 
Complete Response 
Partial Response 
Progressive Disease 
PET-CT score 1, 2, 
or 3* with or without 
a residual mass on 
5PS† 
OR 
On CT, target 
nodes/nodal masses 
must regress to ≤ 1.5 
cm in LDi. 
PET-CT score 4 or 5 
with reduced uptake 
compared with 
baseline and residual 
mass(es) of any size. 
OR 
On CT, ≥ 50% 
decrease in SPD of 
up to 6 target 
measurable nodes 
and extranodal sites. 
PET-CT score 4 or 5 with an increase in intensity of uptake from 
baseline and/or new FDG-avid foci consistent with lymphoma at 
interim or end-of-treatment assessment. 
OR 
On CT, an individual node/lesion must be abnormal with: 
LDi > 1.5 cm and increase by ≥ 50% from PPD nadir and an 
increase in LDi or SDi from nadir 0.5 cm for lesions > 2 cm 
1.0 cm for lesions > 2 cm 
In the setting of splenomegaly, the splenic length must increase 
by > 50% of the extent of its prior increase beyond baseline 
(e.g., a 15-cm spleen must increase to > 16 cm). If no prior 
splenomegaly, must increase by ≥ 2 cm from baseline. New or 
recurrent splenomegaly 
New or clear progression of pre-existing nonmeasured lesions 
Regrowth of previously resolved lesions 
A new node > 1.5 cm in any axis or a new extranodal site 
> 1.0 cm in any axis; if < 1.0 cm in any axis, its presence must 
be unequivocal and must be attributable to lymphoma 
Assessable disease of any size unequivocally attributable to 
lymphoma 
AND/OR new or recurrent involvement of the bone marrow 
The above criteria apply with the following exceptions for IR: 
IR(1): ≥ 50% increase in SPD in first 12 weeks of therapy 
IR(2): < 50% increase in SPD with 
a. New lesion(s), or 
b. ≥ 50% increase in PPD of a lesion or set of lesions at any time 
during treatment 
IR(3): Increase in FDG uptake without a concomitant increase in 
lesion size or number meeting criteria for PD 
Abbreviations: CT = computed tomography; FDG = fluorodeoxyglucose; IR = immune response; LDi = longest 
diameter; PET = positron emission tomography; PPD = product of the perpendicular diameters; SDi = short 
diameter; SPD = sum of the product of diameters; 5PS = 5-point scale. 
*A score of 3 in many patients indicates a good prognosis with standard treatment, especially if at the time of an 
interim scan. However, in trials involving PET where de-escalation is investigated, it may be preferable to consider 
a score of 3 as inadequate response (to avoid undertreatment). 
†PET 5PS: 1 = no uptake above background; 2 = uptake ≤ mediastinum; 3 = uptake > mediastinum but ≤ liver; 
4 = uptake greater than liver; 5 = uptake markedly higher than liver (2-3 times SUVmax in normal liver) and/or 
new lesions; X = new areas of uptake unlikely to be related to lymphoma. 

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The term “immune response” (IR) does not make direct reference to the underlying mechanism, 
recognizing that a delayed response and an immune-mediated flare can both occur in the early 
treatment period and may be difficult to distinguish from progression by physical examination or 
imaging alone. Moreover, the term provides the flexibility to allow patients to continue treatment 
past IR in some circumstances with a subsequent evaluation within 12 weeks to confirm or refute 
true progressive disease. A patient will be considered to have IR in 1 or more of the 3 following 
circumstances. 
1. Increase in overall tumor burden (as assessed by sum of the product of the 
diameters [SPD]) of ≥ 50% of up to 6 measurable lesions in the first 12 weeks of 
therapy, without clinical deterioration [IR(1)]. This pattern may be seen as a 
consequence of either delayed response or early immune-mediated flare. At least within 
the context of clinical trials, a biopsy is encouraged in this case because this may help to 
distinguish the two and, if positive, will confirm the impression of progressive disease. 
However, if negative for lymphoma, it will support the concept of pseudo-progression 
and contribute to our understanding of this phenomenon. When such a biopsy is neither 
safe nor feasible, decisions should be based on a repeat scan 12 weeks after the initial 
determination of IR. 
It is recognized that “clinical deterioration” is subjective. In some cases, the simple 
growth of a nodal or tumor mass could worsen the symptoms mechanically related to that 
mass, such as pain at the tumor site, compression of adjacent structures, etc. Such an 
increase in symptoms that can be directly attributed to the size of the tumor mass may not 
be considered as clinical deterioration in this context. However, in most cases, patients 
should be experiencing clinical stability or improvement by Investigator assessment to be 
considered as having IR, and in all cases, the patient must be considered likely to tolerate 
continued treatment and not at risk of serious complications should further tumor growth 
occur. 
2. Appearance of new lesions or growth of one or more existing lesion(s) ≥ 50% at any 
time during treatment; occurring in the context of lack of overall progression (< 
50% increase) of overall tumor burden, as measured by SPD of up to 6 lesions at 
any time during the treatment [IR(2)]. This phenomenon may occur early or late in the 
treatment course, and therefore, unlike IR(1), is not defined by its temporal relationship 
to treatment initiation. Both within and outside the context of clinical trials, a biopsy is 
strongly encouraged in such cases. If the biopsy does not confirm the presence of viable 
tumor in the new or enlarging lesion(s), then the lesion(s) are not considered active 
disease and should not be used in subsequent SPD assessments. 
3. Increase in FDG uptake of 1 or more lesion(s) without a concomitant increase in 
lesion size or number [IR(3)]. Increased immune activity at the site of tumor may 
manifest as an increase in FDG uptake. Therefore, by itself, changes in uptake should not 
trigger an assignment of progressive disease with checkpoint inhibitors. The magnitude 
of increase in uptake in an immune-mediated flare compared with that in true tumor 
progression is not yet known. It is important to investigate this finding, especially in 
conjunction with biopsies of the lesion in question.  

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An increase in FDG avidity of 1 or more lesions suggestive of lymphoma, without a 
concomitant increase in size of those lesions meeting progressive disease criteria does not 
constitute progressive disease.  
It is possible that, at a single time point, a patient could fulfill criteria for both IR(1) or 
IR(2) and IR(3): for example, there could be a new FDG avid lesion in the absence of 
overall progression [IR(2)], and, at the same time, increase in FDG uptake of a separate 
lesion [IR(3)]. In such cases, the designation of IR(1 or 2) should take priority [e.g., IR 
(2)] in the above example. 
In patients categorized as having any of the above types of IR, repeat imaging should be obtained 
after an additional 12 weeks (or earlier if clinically indicated). At that time, response should be 
re-evaluated, and the patient should be considered to have true progressive disease if the SPD of 
target lesion has increased further, with the considerations below: 
• In the case of IR(1), the comparison should be between the first IR(1) and the current 
SPD, with an increase of ≥ 10% constituting progressive disease. In addition, there 
should be an increase of ≥ 5 mm (in either dimension) of ≥ 1 lesion for lesions ≤ 2 cm 
and 10 mm for lesions > 2 cm. The 10% threshold is empiric but designed to account for 
variability in measurement, especially when taken along with the minimum increase. If 
the target SPD increase is < 10%, the response would still be categorized as IR(1), and 
the patient could continue treatment until a subsequent scan shows either true progressive 
disease [≥ 10% increase from first IR(1) time point and an increase of > 5 mm in either 
dimension of ≥ 1 lesion] or response (≥ 50% decrease from baseline). In this situation, it 
is reasonable to repeat imaging in 4 to 8 weeks of the original IR(1) time point to ensure 
absence of significant further increase. 
• In the case of IR(2), the new or growing lesion(s) (unless biopsy proven to be benign) 
should be added to the target lesion(s), up to a total of no more than 6 total lesions. If the 
SPD of the newly defined set of target lesions has increased ≥ 50% from their nadir value 
(which may precede the IR time point), the patient should be considered to have 
progressive disease. 
• In the case of IR(3), because inflammatory responses may result in an increase in the 
standardized uptake value of a lesion, the patient will not be considered to have PD 
unless there is evidence of PD by an increase in lesion size or the development of new 
lesions, as noted above. 
Importantly, if a patient is assessed as having IR and then “true” progressive disease at a 
subsequent time point (without an intervening objective response between IR and progressive 
disease), the IR assessment should subsequently be corrected to progressive disease for reporting 
purposes to the date of the prior designation of IR. While these lesions may remain stable during 
the time of observation, the initial designation of IR should be changed to progressive disease. 
 
 

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APPENDIX 4. E. COLI NISSLE SENSITIVITY AND RESISTANCE AGAINST COMMON 
ANTIBIOTICS 
E. coli Nissle sensitive to 
E. coli Nissle resistant against a 
Amikacin 
Imipenem 
Cefsulodin 
Amoxicillin/clavulanic acid 
Latamoxef 
Clindamycin 
Ampicillin 
Mezlocillin 
Erythromycin 
Azlocillin 
Nitrofurantoin 
Metronidazole 
Cefaclor 
Norfloxacin 
Penicillin G 
Cefazolin  
Pipemidic acid 
Quinupristin/dalfopristin 
Cefoperazone 
Piperacillin 
Rifampin 
Cefotaxime 
Rifampicin 
Teicoplanin 
Ceftriaxone 
Streptomycin 
Vancomycin 
Cephalothin 
Tetracycline 
 
Chloramphenicol 
Ticarcillin 
 
Ciprofloxacin  
Tobramycin 
 
Doxycycline 
Trimethoprim/sulfamethoxazole 
 
Gentamicin 
 
 
Adapted from Sonnenborn et al 2009 
a 
Like E. coli in general, E. coli Nissle shows natural resistance against the listed antibiotics. As an isolate from the pre-antibiotic era, E. coli Nissle 
has no acquired resistance, and no antibiotic resistance plamids are present.