Phase II Trial of Rifaximin in Patients With Early Stage HER2 Positive Breast Cancer With Gastrointestinal Toxicities Related to Pertuzumab-Based Therapy
Phase: PHASE2
Conditions: Anatomic Stage I Breast Cancer AJCC v8, Anatomic Stage IA Breast Cancer AJCC v8, Anatomic Stage IB Breast Cancer AJCC v8, Anatomic Stage II Breast Cancer AJCC v8, Anatomic Stage IIA Breast Cancer AJCC v8, Anatomic Stage IIB Breast Cancer AJCC v8, Anatomic Stage III Breast Cancer AJCC v8, Anatomic Stage IIIA Breast Cancer AJCC v8, Anatomic Stage IIIB Breast Cancer AJCC v8, Anatomic Stage IIIC Breast Cancer AJCC v8, HER2 Positive Breast Carcinoma, Prognostic Stage I Breast Cancer AJCC v8, Prognostic Stage IA Breast Cancer AJCC v8, Prognostic Stage IB Breast Cancer AJCC v8, Prognostic Stage II Breast Cancer AJCC v8, Prognostic Stage IIA Breast Cancer AJCC v8, Prognostic Stage IIB Breast Cancer AJCC v8, Prognostic Stage III Breast Cancer AJCC v8, Prognostic Stage IIIA Breast Cancer AJCC v8, Prognostic Stage IIIB Breast Cancer AJCC v8, Prognostic Stage IIIC Breast Cancer AJCC v8
Sponsor: Mayo Clinic

Protocol Version Date: 27April2022 
 
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Document History 
Pre-Activation Amendment, dated 09Apr2020  
Amendment 1 (Activation), dated 29Jul2020 
Amendment 2, dated 17Dec2020 
Amendment 3, dated 13Ju12021 
Amendment 4, dates 27April2022 
(Effective Date) 
May 15, 2020 
August 28, 2020 
March 5, 2021 
August 13, 2021 
Pending approval 
MC18C3 
Mayo Clinic Cancer Center 
Phase II trial of Rifaximin in patients with early stage HER2 positive breast cancer with 
gastrointestinal toxicities related to pertuzumab-based therapy 
Study Chairs: 
 
 
 
 
 
Study Cochairs: 
 
 
 
 
 
Statistician: 
Study contributor(s) not responsible for patient care 
Drug Availability 
Drug Company supplied 
Salix Pharmaceuticals: Rifaximin (IND #14692) 
 

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Protocol Resources 
 
Questions: 
Contact Name: 
Patient eligibility*, test schedule, treatment 
delays/interruptions/adjustments, dose 
modifications, adverse events, 
forms completion and submission 
 
 
  
Forms completion and submission 
  
 
  
Protocol document, consent form, regulatory 
issues 
 
  
 
 
Non-paraffin biospecimens 
  
 
  
Serious Adverse Event Reporting 
  
 
  
*No waivers of eligibility allowed 

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Table of Contents 
Protocol Resources ....................................................................................................................................... 2 
Table of Contents .......................................................................................................................................... 3 
Schema .......................................................................................................................................................... 4 
1.0 
2.0 
3.0 
4.0 
5.0 
6.0 
7.0 
8.0 
9.0 
10.0 
11.0 
12.0 
13.0 
14.0 
15.0 
16.0 
17.0 
18.0 
19.0 
20.0 
Background ................................................................................................................................... 6 
Goals ............................................................................................................................................. 8 
Patient Eligibility .......................................................................................................................... 9 
Test Schedule .............................................................................................................................. 12 
Stratification Factors OR Grouping Factor ................................................................................. 15 
Registration Procedures .............................................................................................................. 15 
Protocol Treatment...................................................................................................................... 18 
Dosage Modification Based on Adverse Events ......................................................................... 19 
Ancillary Treatment/Supportive Care ......................................................................................... 22 
Adverse Event (AE) Monitoring and Reporting ......................................................................... 23 
Treatment Evaluation/Measurement of Effect ............................................................................ 31 
Descriptive Factors ..................................................................................................................... 31 
Treatment/Follow–up Decision at Evaluation of Patient ............................................................ 31 
Body Fluid Biospecimens ........................................................................................................... 32 
Drug Information ........................................................................................................................ 35 
Statistical Considerations and Methodology............................................................................... 37 
Pathology Considerations/Tissue Biospecimens: ....................................................................... 42 
Records and Data Collection Procedures .................................................................................... 42 
Budget ......................................................................................................................................... 43 
References ................................................................................................................................... 44 
Appendix I 
Appendix II 
Appendix III 
Appendix IV 
Appendix V 
ECOG Performance Status ............................................................................................... 46 
Patient Medication Diary .................................................................................................. 47 
NCI CTCAE v5.0 for Gastrointestinal toxicities .............................................................. 49 
4 point Likert scale questionnaire ..................................................................................... 50 
Bristol Stool Scale ............................................................................................................ 51 
 

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Schema 
Sample size: 34 patients 
Patient population: Stage I-III HER2 overexpressed breast cancer patients who will receive adjuvant and 
neoadjuvant pertuzumab-based chemotherapy. 
PreRegistration 
Initiation of pertuzumab-based 
chemotherapy 
Registration 
Treatment Cycle = 21 days (± 7 day window) 
Rifaximin treatment will be for 5 days concurrently with subsequent cycles of pertuzumab-based 
chemotherapy in patients with Grade ≥ 2 PIGT 
End of Treatment = 21 days after the last dose of pertuzumab-based chemotherapy 
*Patients that develop ≥ grade 2 PIGT ONLY according to NCI CTCAE v5.0 after initiation of 
pertuzumab-based chemotherapy will be eligible to receive rifaximin for 5 days on subsequent cycles of 
pertuzumab-based chemotherapy. Rifaximin will be given as 550 mg orally twice daily for 5 days 
starting on day 1 of the pertuzumab cycle. This will be repeated every 3 weeks on subsequent 
Pertuzumab induced gastrointestinal toxicities (PIGT) including abdominal distension, abdominal pain, 
diarrhea, dyspepsia, stomach pain, and typhlitis, according to NCI CTCAE v5.0. 
End of Treatment 
 
 
 
 
Off study 
 
Study Treatment: 
Continue subsequent cycles of 
pertuzumab-based 
chemotherapy: Cycles 1-5 (Day 
1) of study 
 
Study Treatment*: 
Rifaximin: Cycles 1-5 (Days 1-5) 
Continue subsequent cycles of 
pertuzumab-based chemotherapy: 
Cycles 1-5 (Day 1) of study 
Arm 1: 
Grade ≥ 2 PIGT 
 
Arm 2: 
Grade ≤ 1 PIGT 
 
 
 
 
 
 
 
 
 
 
 
 
 

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Generic name: Rifaximin 
Brand name(s): Xifaxan 
Mayo Abbreviation: 
Availability: Mayo Clinic Pharmacy 
 

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1.0 
Background 
1.1 
HER2 positive breast cancer 
Breast cancer is one of the most common malignancies among women worldwide. 
Human epidermal growth factor receptor 2 (HER2)-positive breast cancer is a unique 
subset of breast cancer, which accounts for approximately 15-30% of breast cancers 
(Owens MA, 2004). 
Patients with HER2 positive breast cancer in addition to traditional chemotherapy are 
also treated with HER2 targeted therapies such as pertuzumab and trastuzumab. HER2 
targeted therapies have revolutionized the treatment outcome for patients with HER2 
positive breast cancer. However, gastrointestinal toxicities are common adverse events of 
pertuzumab in particular. The gastrointestinal toxicities can be severe enough that the 
immediate consequences are to reduce, delay or interrupt the planned treatment which 
could potentially affect the oncologic outcome. 
1.2 
Pertuzumab induced gastrointestinal toxicities 
Pertuzumab-induced gastrointestinal toxicities (PIGT) are common side effects from 
pertuzumab, which has been reported in up to 70% of patients receiving pertuzumab 
(Swain et al, 2017). The gastrointestinal toxicities appear to be intensified when 
pertuzumab is given in combination with chemotherapy. 
In the pivotal phase III CLEOPATRA trial, which evaluated pertuzumab in combination 
with trastuzumab and docetaxel in patients with metastatic HER2-positive breast cancer, 
all grade diarrhea was reported in 66.8% of patients receiving pertuzumab compared to 
46.3% of patients receiving docetaxel and trastuzumab with placebo (Baselga J et al., 
2012). Among patients with early stage HER2-positive breast cancer, all grade episodes 
of diarrhea were reported in the range of 43-72.4% in patients receiving pertuzumab 
combination. 
The incidence of all grade diarrheas was highest in the TCH+P regimen in the 
TRYPHAENA trial with 72.4% of patients receiving this regimen had any grade diarrhea 
and 11.8% of those patients had ≥ grade 3 diarrhea (Schneeweiss A et al., 2013). 
In the NEOSPHERE trial the incidence of all grade diarrheas reported in the THP arm 
was 51% (Gianni et al. 2012). 
1.3 
Etiology of PIGT 
PIGT is likely a result of a combination of different etiologies. There are several potential 
mechanisms for diarrhea associated with epidermal growth factor receptor (EGFR)/HER2 
signaling blockade, including dysregulation of ion channels in intestinal epithelial cells, 
which leads to excess chloride secretion; altered gut motility; changes in intestinal 
microbiome, including small intestinal bacterial overgrowth and altered nutrient 
metabolism. 
1.31 
Hydrogen Breath Test 
Hydrogen breath test is a non-invasive diagnostic tool to evaluate small intestine 
bacterial overgrowth and carbohydrate malabsorption, such as lactose, fructose, 
 

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and sorbitol malabsorption. The test is performed after a short period of fasting 
of about 8-12 hours. Bacteria in the bowel generally produce hydrogen gas on 
fermentation of carbohydrates. In bowel, bacteria can only do this when dietary 
carbohydrates are not absorbed in small intestine and stay as undigested material 
as it travels along the digestive tract into large intestine. Though some of the 
hydrogen gas produced by the bacteria is expelled as flatus or in making other 
molecules such as sulphides, acetate and short chain fatty acids but most of the 
gas is absorbed across the lining of the large intestine into blood stream. The gas 
is then transported to lungs via the blood stream and from blood it is exchanged 
into the airways of lungs and breathed out. The only source of hydrogen gas in 
the breath can be from bacterial fermentation in the bowel. The same applies to 
the gas called methane which is exhaled by some people and not all. The bacteria 
in their large bowel make methane from the hydrogen. The amount of hydrogen 
and methane gases breathed out from the lungs can be easily measured by taking 
a breath sample, and measuring by a breath-testing machine. (Rezaie et al., 2017) 
1.4 
Treatment approaches for PIGT 
Pharmacologic approaches to treat PIGT are not specific and mainly focus on 
symptomatic relief. 
For the treatment of diarrhea and other PIGT, the standard of care is to use antidiarrheal 
agents such as loperamide, diphenoxylate/atropine, etc., however even with the use of 
these agents, the gastrointestinal toxicities can persist. No other drugs are approved for 
the treatment of pertuzumab induced gastrointestinal toxicities. 
A recent case report demonstrated the safe and effective use of rifaximin in the treatment 
of pertuzumab induced gastrointestinal toxicities (Soyano AE et al., 2017). In this case, 
rifaximin was thought to reduce the small intestinal bacterial overgrowth contributing to 
diarrhea. 
New research on this area is needed as these side effects can be disabling and negatively 
affect quality of life and survivorship of patients. New treatment approaches are needed 
to help to safely decrease the incidence and severity of gastrointestinal toxicities without 
having to reduce, delay or interrupt the chemotherapy schedule as that also may 
negatively affect the oncologic outcome. 
1.5 
Rifaximin 
Rifaximin is a poorly absorbed bactericidal, which is a derivative of rifamycin. Rifaximin 
irreversibly inhibits bacterial protein synthesis by binding to the beta-subunit of the 
bacterial DNA-dependent RNA polymerase (RpoB) (Hartmann et al., 1967). Previous 
study demonstrated that rifaximin has minimal systemic absorption with < 0.4% 
bioavailability (Descombe et al., 1994). Due to poor absorption, previous clinical studies 
showed no significant drug-drug interaction with other medications (Pentikis et al., 2007; 
Trapnell et al., 2007). Rifaximin has been studied using multiple dosing and frequency. 
The 550 mg twice daily dosing is based on several clinical trials for traveler’s diarrhea1,2, 
irritable bowel syndrome3, and hepatic encephalopathy4. The 5-day duration was based 
on previous clinical trials of rifaximin for the treatment of travelers’ diarrhea (TD) which 
showed that 5-day course of rifaximin is safe and resulted in a trend for shorter duration 
of diarrhea compared to TMP-SMX (160/800 mg twice a day)5. Given the fact that 
 

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patients with PIGT do not have an established infection, this dosing schedule is likely to 
be adequate to prevent small intestinal bacterial overgrowth which may contribute to 
PIGT. 
2.0 
Goals 
2.1 
Primary Goal 
To evaluate the reduction rate of grade ≥ 2 abdominal toxicities, including abdominal 
distension, abdominal pain, diarrhea, dyspepsia, stomach pain, and typhlitis according to 
the National Cancer Institute Common Terminology for Adverse Events version 5.0 (NCI 
CTCAE v5.0) with the use of rifaximin in stage II-III HER-2 positive breast cancer 
patients with pertuzumab induced gastrointestinal toxicities. 
Secondary Goals 
2.2 
2.21 
Evaluate dose reductions, dose delays and discontinuation of treatment with 
pertuzumab due to gastrointestinal side effects. 
Evaluate and measure the change in the Bristol stool scale before and after 
rifaximin treatment. 
Evaluate and measure the change in the 4-point Likert scale patient questionnaire 
before and after rifaximin treatment. 
2.22 
2.23 
2.3 
Correlative Study Goals 
2.31 
Evaluate changes in the fecal microbiome, hydrogen breath test, and permeability 
test before and after rifaximin. 
Evaluate changes in the fecal microbiome, hydrogen breath test, and permeability 
test before and after pertuzumab-based chemotherapy. 
Evaluate the difference in the fecal microbiome, hydrogen breath test, and 
permeability test among patients with or without PIGT. 
2.32 
2.33 
 

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3.0 
Patient Eligibility 
3.1 
Pre-registration – Inclusion Criteria 
3.11 
3.12 
Age ≥18 years 
Histological confirmation of HER2 positive breast cancer stage I-III per AJCC 
staging 8th edition. 
Provide written informed consent. 
Breast cancer patients who will be receiving pertuzumab-based chemotherapy 
with either TCHP (docetaxel, carboplatin, trastuzumab, and pertuzumab) or 
docetaxel/paclitaxel, trastuzumab, and pertuzumab. 
ECOG Performance Status (PS) 0, 1, or 2 (Appendix I). 
The following laboratory values obtained ≤30 days prior to pre-registration: 
− Hemoglobin ≥ 10.0 g/dL 
− Absolute neutrophil count (ANC) ≥ 1.5 x 109/L 
− Platelet count ≥ 100 x 109/L 
− Total Bilirubin ≤ 1.5 x ULN (institutional upper limit of normal) 
− AST (SGOT)/ALT (SGPT) ≤ 2.5 x ULN 
− Serum or plasma creatinine ≤ 1.5 x ULN 
− Calculated creatinine clearance ≥45 ml/min using the Cockcroft-Gault 
formula below: 
3.13 
3.14 
3.15 
3.16 
3.17 
Negative serum pregnancy test done ≤30 days prior to pre-registration, for person 
of childbearing potential only. 
Willingness to return to enrolling institution for follow-up (during the Active 
Monitoring Phase of the study). 
Willingness to provide mandatory stool  specimen for correlative research 
(see section 14.0) 
Ability to complete questionnaire(s) by themselves or with assistance. 
3.18 
3.19a 
3.19b 
3.2 
Pre-registration - Exclusion criteria 
3.21 
History of myocardial infarction ≤6 months prior to pre-registration, or 
congestive heart failure requiring use of ongoing maintenance therapy for life- 
threatening ventricular arrhythmias. 
Failure to recover from acute, reversible effects of prior therapy regardless of 
interval since last treatment. 
EXCEPTION: Grade 1 peripheral (sensory) neuropathy that has been stable for 
at least 3 months since completion of prior treatment. 
Uncontrolled intercurrent non-cardiac illness including, but not limited to: 
3.22 
3.23 
Cockcroft-Gault Equation: 
Creatinine clearance for males = 
(140 - age)(weight in kg) 
(72)(serum creatinine in mg/dL) 
Creatinine clearance for females = 
(140 - age)(weight in kg)(0.85) 
(72)(serum creatinine in mg/dL) 
 
 
 
 

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• 
• 
• 
Ongoing or active infection 
Psychiatric illness/social situations 
Dyspnea at rest due to complications of advanced malignancy or other 
disease that requires continuous oxygen therapy 
Any other conditions that would limit compliance with study requirements 
• 
3.24 
Immunocompromised patients and patients known to be HIV positive and 
currently receiving antiretroviral therapy. 
NOTE: Patients known to be HIV positive, but without clinical evidence of an 
immunocompromised state, are eligible for this trial. 
Receiving any other investigational agent which would be considered as a 
treatment for the primary neoplasm. (adjust to protocol if applicable) 
Any of the following because this study involves an agent whose genotoxic, 
mutagenic and teratogenic effects on the developing fetus and newborn are 
unknown 
• 
Pregnant women 
3.25 
3.26 
• 
• 
Nursing women 
Women of childbearing potential who are unwilling to employ adequate 
contraception 
3.27 
Current Colostomy or ileostomy 
3.28 
History of inflammatory bowel disease 
3.29a 
History of irritable bowel syndrome 
3.29b History of arteriovenous malformations 
3.29c 
History of gastrointestinal bleeds 
3.29d Previous surgical resection of the small bowel or colon 
3.29e 
Previous allergy to rifaximin or its derivatives 
3.3 
Registration – Inclusion Criteria 
3.31 
Received pertuzumab based regimens in the adjuvant or neoadjuvant setting. 
The following laboratory values obtained ≤ 14 days prior to registration: 
− Hemoglobin ≥ 8.0 g/dL 
− Absolute neutrophil count (ANC) ≥ 1.5 x 109/L 
− Platelet count ≥ 100 x 109/L 
− Total Bilirubin ≤ 1.5 x ULN (institutional upper limit of normal) 
− AST (SGOT)/ALT (SGPT) ≤ 2.5 x ULN 
− Serum or plasma creatinine ≤ 1.5 x ULN 
− Calculated creatinine clearance ≥45 ml/min using the Cockcroft-Gault 
formula below: 
3.32 
 

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Cockcroft-Gault Equation: 
Creatinine clearance for males = 
(140 - age)(weight in kg) 
(72)(serum creatinine in mg/dL) 
Creatinine clearance for females = 
(140 - age)(weight in kg)(0.85) 
(72)(serum creatinine in mg/dL) 
 
 
 
 

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4.0 Test Schedule 
4.1 
Test schedule for early stage HER2 positive breast cancer with and without gastrointestinal toxicities* 
Tests and procedures 
 
Preregistration*** 
 
 
7-14 days 
after initiation 
of 
pertuzumab- 
based 
chemotherapy
Registration 
(21 days after 
initiation of 
pertuzumab- 
based 
chemotherapy
)
Cycle 1, 
Day 110 
 
Cycle 1, 
Day 7 
 
Cycle 
2-5, 
Day 1 
 
End of 
Treatment (21 
Days 
after last dose of 
pertuzumab-
based 
Window 
 
 
+7 days/-3 days +3 days/-3 
days 
+ 7 days 
± 7 
days 
+ 7 days 
History, ECOG 
(PS),physical exam1 
X 
 
X 
X 
 
X 
X 
Height 
X 
 
 
 
 
 
 
CBC with 5 part 
differential, total 
bilirubin, direct bilirubin 
(if total bilirubin is 
elevated), AST (SGOT), 
ALT (SGPT), serum, or 
plasma creatinine11 
X 
 
 
X11 
 
X 
 
 
X 
 
X 
 
Chemistry group2, 11 
 
 
X11 
X 
 
X 
X 
Pregnancy test, serum3 
X 
 
 
 
 
 
 
PIGT grading 
assessment 
 
 
X 
X 
 
X 
X 
Adverse event 
assessment 
 
 
 
X 
 
X 
X 
4-Point Likert Scale 
(Appendix IV)4 
X 
 
 
 
X 
 
 
X 
 
X 
 
Bristol 
stool 
scale 
and 
stool 
diary 
(Appendix V)5 
X 
 
 
 
X 
 
 
X 
 
X 
 
(Optional) Hydrogen 
breath test6, R 
X 
X 
 
X 
X 
 
X 
 

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Cycle = 21 days (± 7 day window) 
*Pertuzumab induced gastrointestinal toxicities (PIGT) include abdominal distension, abdominal pain, diarrhea, dyspepsia, stomach pain, and 
typhlitis, according to NCI CTCAE v5.0. 
**21 days after the last dose of pertuzumab-based chemotherapy. In patients who receive pertuzumab-based chemotherapy in the adjuvant and 
neoadjuvant setting, this follow up should be prior to surgery in patients who will proceed with surgery. 
***Test/Procedures completed ≤30 days prior to pre-registration are not to be repeated. 
1. 
2. 
History and physical exam including weight and performance status. 
Alkaline phosphatase, BUN, albumin, total protein, uric acid, bicarbonate, calcium, chloride, glucose, LDH, magnesium, phosphorus, 
potassium, sodium 
For Women of childbearing potential only. Must be 30 days prior to registration. 
The 4-point Likert scale questionnaire (Appendix IV) will be completed by the patient at preregistration, prior to Initiation of pertuzumab- 
based chemotherapy, and on Day 1 of Cycles 1-5 of Rifaximin treatment, and at the end of treatment. Questionnaire will be completed on Day 
1 of each subsequent cycle. 
3. 
4. 
5. Bristol stool scale and stool diary (Appendix V) will be completed by the patient on days 1-14 of each pertuzumab- based chemotherapy 
cycle. Study staff will provide the patient with 14 pages of stool diaries. The diaries will be collected on the 1st day of each subsequent cycle 
and at the end of treatment. 
6. OPTIONAL: Hydrogen breath test (See Lactulose Breath Test For Bacterial Overgrowth, Appendix VII) will be collected and submitted at 
preregistration, 7-14 days after initiation of pertuzumab-based chemotherapy, Cycle 1, Day 1, Cycle 1 (day 7-14), and at the end of treatment. 
Tests and procedures 
 
Preregistration*** 
 
 
7-14 days 
after initiation 
of 
pertuzumab- 
based 
chemotherapy
Registration 
(21 days after 
initiation of 
pertuzumab- 
based 
chemotherapy
)
Cycle 1, 
Day 110 
 
Cycle 1, 
Day 7 
 
Cycle 
2-5, 
Day 1 
 
End of 
Treatment (21 
Days 
after last dose of 
pertuzumab-
based 
Research stool 
collection (see section 
14.0) 7, R 
X 
 
X 
 
 
X 
 
X 
 
 
X 
 
(Optional) Research 
urine collection (See 
section 14.0)8, R 
X 
 
X 
 
 
X 
 
X 
 
 
X 
 
Patient Medication 
Diary9 
 
 
 
 
 
X 
 
Concomitant 
Medications 
X 
X12 
X12 
X 
 
X 
X 
 

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The hydrogen breath test and the urine permeability test must be ≥48 hours apart. Hydrogen breath test is an optional test and will be performed 
at physician discretion. 
Stool kit will be given to patient prior to collection. Stool will be collected and submitted, At preregistration, 7-14 days after pertuzumab based 
treatment, Cycle 1, Day 1, Cycle 1 (day 7-14), and at the end of treatment. 
OPTIONAL: Research Urine for the permeability test will be collected preregistration, 7-14 days after initiation of pertuzumab-based 
chemotherapy, Cycle 1, Day 1, Cycle 1 (day 7-14), and at the end of treatment. The hydrogen breath test (optional) and the urine permeability 
test (optional) must be ≥48 hours apart. 
(ARM 1 only) The patient medication diary must begin the day the patient starts taking the medication and must be completed per protocol and 
returned to the treating institution OR compliance must be documented in the medical record by any member of the care team. (See Appendix 
II) 
7. 
8. 
9. 
10. If test/procedure was completed prior to C1D1, do not repeat. Exam and labs must be completed prior to study treatment. 
11. Laboratory values obtained ≤ 14 days prior to registration. 
12.If concomitant medications are not recorded during preregistration, they may be collected 7-14 days after initiation of pertuzumab-based 
therapy OR at registration (21 days after initiation of pertuzumab-based chemotherapy). 
R Research funded (see Section 19.0) 
4.2 
Survival Follow-up 
This study does not follow patient survival. Once patients complete study intervention, they are off study. 
 

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5.0 
Grouping Factor: 
PIGT Grade: ≤ 1 VS. ≥ 2. 
6.0 
Registration Procedures 
6.1 
Pre-Registration (Step 0) 
6.11 
Registering a patient 
To register a patient, access the Mayo Clinic Cancer Center (MCCC) web page 
and enter the registration application. The registration application is available 24 
hours a day, 7 days a week. Back up and/or system support contact information is 
available on the website. If unable to access the website, call the MCCC 
Registration Office at 
between the hours of 8 a.m. and 5:00 p.m. 
Central Time (Monday through Friday). 
The instructions for the registration application are available on the MCCC web 
page 
and detail the process for 
completing and confirming patient registration. Prior to initiation of protocol 
treatment, this process must be completed in its entirety and an MCCC subject ID 
number must be available as noted in the instructions. It is the responsibility of 
the individual and institution registering the patient to confirm the process has 
been successfully completed prior to release of the study agent. Patient 
registration via the registration application can be confirmed in any of the 
following ways: 
• 
Contact the MCCC Registration Office 
 If the 
patient was fully registered, the MCCC Registration Office staff can 
access the information from the centralized database and confirm the 
registration. 
• 
Refer to “Instructions for Remote Registration” in section 
“Finding/Displaying Information about A Registered Subject.” 
6.12 
Verification of information 
Prior to accepting the pre-registration, the registration application will verify the 
following: 
• 
IRB approval at the registering institution 
• 
• 
• 
Patient pre-registration eligibility 
Existence of a signed consent form 
Existence of a signed authorization for use and disclosure of protected health 
information. 
6.13 
Pre-registration tests/procedures 
Pre-registration tests/procedures (see Section 4.0) must be completed within the 
guidelines specified on the test schedule. 
6.14 
Correlative Research 
6.141 Mandatory - A mandatory correlative research component is part of this study, 
the patient will be automatically registered onto this component (see Sections 3.19a, 
14.0) 
 
6.142 Optional – An optional research component is part of this study, there will be 
an option to select if the patient is to be registered onto this component (see Section 
14.0) 
• 
Patient has/has not given permission to give his/her urine sample for 
research testing. 
 

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6.15 
Kits - Stool collection kits and urine containers are available on site. 
Registration (Step 1): 
6.2 
6.211 Registering a patient 
To register a patient, access the Mayo Clinic Cancer Center (MCCC) web page 
and enter the registration application. The registration application is available 24 
hours a day, 7 days a week. Back up and/or system support contact information is 
available on the website. If unable to access the website, call the MCCC 
Registration Office at 
between the hours of 8 a.m. and 4:30 p.m. 
Central Time (Monday through Friday). 
The instructions for the registration application are available on the MCCC web 
page 
and detail the process for 
completing and confirming patient registration. Prior to initiation of protocol 
treatment, this process must be completed in its entirety and an MCCC subject ID 
number must be available as noted in the instructions. It is the responsibility of 
the individual registering the patient to confirm the process has been successfully 
completed prior to release of the study agent. Patient registration via the 
registration application can be confirmed in any of the following ways: 
• 
Contact the MCCC Registration Office 
If the patient 
was fully registered, the MCCC Registration Office staff can access 
the information from the centralized database and confirm the 
• 
Refer to “Instructions for Remote Registration” in section 
“Finding/Displaying Information about A Registered Subject.” 
6.3 
Verification of materials 
Prior to accepting the registration, registration application will verify the following: 
• 
IRB approval at the registering institution 
• 
• 
• 
Patient eligibility 
Existence of a signed consent form 
Existence of a signed authorization for use and disclosure of protected health 
information 
6.4 
Documentation of IRB approval 
Documentation of IRB approval must be on file in the Registration Office before an 
investigator may register any patients. 
In addition to submitting initial IRB approval documents, ongoing IRB approval 
documentation must be on file (no less than annually) at the Registration Office 
 
If the necessary documentation is not submitted in advance of 
attempting patient registration, the registration will not be accepted and the patient may 
not be enrolled in the protocol until the situation is resolved. 
When the study has been permanently closed to patient enrollment, submission of annual 
IRB approvals to the Registration Office is no longer necessary. 
6.5 
Treatment on protocol 
Treatment on this protocol must commence at Mayo Clinic Florida under the supervision 
of a medical oncologist. 
 

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6.6 
Treatment start 
Rifaximin treatment cannot begin prior to registration and must begin 3 days after 
registration. 
6.7 
Baseline symptoms 
All required baseline symptoms (see Section 10.6) must be documented and graded. 
6.8 
Study drug 
Study drug is available on site. 
6.9b 
Study Conduct 
The clinical trial will be conducted in compliance with regulations (21 CFR 312, 50, and 
56), guidelines for Good Clinical Practice (ICH Guidance E6), and in accordance with 
general ethical principles outlined in the Declaration of Helsinki; informed consent will 
be obtained from all participating patients; the protocol and any amendments will be 
subject to approval by the designated IRB prior to implementation, in accordance with 
21 CFR 56.103(a); and subject records will be stored in a secure location and subject 
confidentiality will be maintained. The investigator will be thoroughly familiar with the 
appropriate use of the study drug as described in the protocol and Investigator’s 
Brochure. Essential clinical documents will be maintained to demonstrate the validity of 
the study and the integrity of the data collected. Master files should be established at the 
beginning of the study, maintained for the duration of the study and retained according 
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7.0 
Protocol Treatment 
7.1 
Treatment Schedule 
7.11 
Treatment medication table 
Cycle Length = 21 days 
Treatment Window = ± 7 days 
Patients that develop ≥ grade 2 PIGT ONLY according to NCI CTCAE v5.0 after 
initiation of pertuzumab-based chemotherapy and prior to registration will be eligible to 
receive rifaximin for 5 days on subsequent cycles of pertuzumab-based chemotherapy. 
Rifaximin will be given as 550 mg orally twice daily for 5 days starting on day 1 of the 
pertuzumab cycle. This will be repeated every 3 weeks on subsequent pertuzumab cycles. 
Return to consenting institution 
For this protocol, the patient must return to the consenting institution for evaluation at 
least every 21±7 days during treatment and once 21 Days after last dose of pertuzumab- 
based chemotherapy. 
Treatment by local medical doctor (LMD) is not allowed. 
7.2 
7.3 
Agent 
Starting Dose 
Route 
Administration 
Rifaximin 
550 mg 
PO 
Twice daily 
(Cycles 1-5, 
 

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8.0 
Dosage Modification Based on Adverse Events 
If the patient develops any clinically significant adverse event attributed to rifaximin use, 
strictly follow the modifications in this table for the first three cycles, until individual 
treatment tolerance can be ascertained. Thereafter, these modifications should be regarded as 
guidelines to produce mild-to-moderate, but not debilitating, side effects. If multiple adverse 
events are seen, administer dose based on greatest reduction required for any single adverse 
event observed. Reductions or increases apply to treatment given in the preceding cycle and 
are based on adverse events observed since the prior dose. The patient should continue to be 
followed according to protocol criteria; this includes completing questionnaires. 
8.1 
Dose Levels (Based on Adverse Events in Tables 8.2 and 8.3) 
*Dose level 0 refers to the starting dose. 
If dose reduction goes below -2 level then rifaximin should be discontinued. 
For patients who do not tolerate the 550 mg BID x 5 days dosing schedule, dose 
adjustment to 550 orally daily x 5 days is permitted in order to allow the patient to 
continue on study drug. The following guidelines need to be applied and these changes 
must be recorded on the on the specific section of the patient record. 
Missed/skipped doses will not be made up (i.e. the patient should not double their dose if 
the previous dose was missed). When the adverse event that resulted in a dose reduction 
improves to and remains stable at Grade 1 or less for a minimum of 14 days, the dose can 
be re-escalated at the investigators discretion provided there are no other concomitant 
adverse events. 
Dose reduction/interruption/discontinuation decisions should be based on the CTCAE 
grade of the adverse event (AE) and the guidelines provided below. In general, doses 
should not be reduced or interrupted for Grade 1 events, but treatment to control 
symptoms should be provided as appropriate. All AEs should be followed weekly or as 
clinically appropriate until stabilization or resolution. 
A patient with a Grade 4 AE may resume treatment at the lower dose level if the AE 
recovers to grade ≤1 within 21 days of interrupting drug and, if in the opinion of the 
Investigator and Medical Monitor, the event is not life-threatening, and the patient can be 
managed and monitored for recurrence of AE. Dose interruptions of more than 21 days 
are not allowed unless approved by the Investigator. 
Dose 
Level 
Rifaximin 
0* 
550 mg orally twice daily x 5 days 
-1 
550 mg orally daily x 5 days 
-2 
550 mg orally x 3 days 
-3 
Discontinue 
 

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Please refer to the table below for dose adjustment recommendations for rifaximin 
induced adverse events. 
8.2 
Dose Modifications Based on Interval Adverse Events 
CTCAE 
System/Organ/Class 
(SOC) 
ADVERSE EVENT 
Grade 
ACTION FOR RIFAXIMIN 
Nervous system 
disorders 
 
Dizziness 
 
Grade 1 
Maintain same dose of Rifaximin 
Grade 2 
 
Omit rifaximin for current cycle. Reassess for next 
cycle. If dizziness worsens or does not improve, omit 
rifaximin until resolved to Grade ≤1. If AE does not 
resolve ≤ 3 weeks, resume rifaximin at 1 reduced dose 
level. 
Grade 3 
 
Omit rifaximin for current cycle. 
Reassess for next cycle. If dizziness worsens or does 
not improve, hold rifaximin until resolved to Grade 
≤1. If AE does not resolve ≤ 3 weeks, resume 
rifaximin at 2 reduced dose level. 
Skin and 
subcutaneous tissue 
disorders 
 
Rash maculo- 
papular 
 
Grade 1 
Maintain same dose of Rifaximin 
Grade 2 
 
First occurrence: 
- 
Maintain dose of Rifaximin and monitor 
rash closely 
Second Occurrence: 
- 
Omit rifaximin for current cycle and 
monitor rash 
- 
Reassess for next cycle. If rash worsens or 
does not improve, Omit rifaximin until 
resolved to Grade ≤1. If AE does not resolve 
≤ 3 weeks, resume rifaximin at 1 reduced 
dose level 
Grade 3 
 
Omit rifaximin for current cycle and monitor rash 
Reassess for next cycle. If rash worsens or does not 
improve, Omit rifaximin until resolved to Grade ≤1. If 
AE does not resolve ≤ 3 weeks, resume rifaximin at2 
reduced dose level 
Skin and 
subcutaneous tissue 
disorders 
 
Pruritus 
 
Grade 1 
 
First occurrence: 
- 
Maintain dose of Rifaximin and 
monitor closely 
Second Occurrence: 
- 
Omit rifaximin for current cycle and monitor 
- 
Reassess for next cycle. If rash worsens or 
does not improve, hold rifaximin until 
resolved. If AE does not resolve ≤ 3 weeks, 
resume rifaximin at 1 reduced dose level 
Grade 2 
 
Omit rifaximin for current cycle and monitor pruritus 
Reassess for next cycle. If rash worsens or does not 
improve, omit rifaximin until resolved to Grade ≤1. If 
AE does not resolve ≤ 3 weeks, resume rifaximin at 2 
reduced dose level 
Grade 3 
Permanently discontinue rifaximin 
Investigations 
Serum Alanine 
Grade 1 
Maintain dose of Rifaximin and monitor closely 
 

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** Use the following to describe actions in the Action column: 
➢ Hold/Delay = The current dose(s) of all drugs during a cycle is delayed. The patient 
does make up the delayed dose(s) when the patient meets the protocol criteria to restart 
drugs. 
➢ Discontinue = The specified drug(s) are totally stopped. 
➢ Omit= The current dose(s) for the specified drug(s) during a cycle is skipped. The 
patient does not make up the omitted dose(s) at a later time. 
NOTE: If patient experiences an adverse event and rifaximin was omitted for 2 consecutive cycles, 
discontinue rifaximin. 
NOTE: If the patient experiences a significant adverse event requiring a dose reduction at the start of the 
next cycle, then the dose will remain lowered for that entire subsequent cycle. If that cycle is completed 
with no further adverse events >Grade 2, then the dose may be increased, at the investigator’s discretion, 
one level at a time, in the following cycles. 
NOTE: Adverse events requiring a dose-reduction step for any or all drugs beyond the two dose- 
reduction steps (levels –1 and –2) will be at the discretion of the treating physician, if the decision is made 
for the patient to be kept on study. These dose reductions must be clearly recorded in reported clinical 
8.3 
Warnings and Precautions 
8.31 
Clostridium difficile-associated diarrhea (CDAD) 
CDAD has been reported with use of nearly all antibacterial agents, including 
rifaximin. Therefore, CDAD must be considered in patients who present with 
diarrhea. If CDAD is confirmed, rifaximin should be discontinued. Appropriate 
antibiotic treatment for CDAD, fluid and electrolyte management, protein 
supplementation, and surgical evaluation should be instituted as clinically 
indicated. 
8.32 
Development of drug resistant bacteria 
Due to potential increased risk of drug-resistant bacteria, rifaximin should be 
discontinued in patients who are confirmed to have multi-drug resistant bacterial 
infection that is felt to be related to rifaximin at the discretion of the attending 
physician. 
CTCAE 
System/Organ/Class 
(SOC) 
ADVERSE EVENT 
Grade 
ACTION FOR RIFAXIMIN 
 
Aminotransferase 
(ALT) 
 
Grade 2 
 
Omit rifaximin for current cycle and monitor 
Reassess for next cycle. If ALT worsens or does not 
improve, hold rifaximin until resolved to Grade ≤1 . 
If AE does not resolve ≤ 3 weeks, resume rifaximin at 
1 reduced dose level 
Grade 3 
 
Omit rifaximin for current cycle and monitor. 
Reassess for next cycle. If ALT worsens or does not 
improve, omit rifaximin until resolved to Grade ≤1. If 
AE does not resolve ≤ 3 weeks, resume rifaximin at 2 
reduced dose level 
Grade 4 
Permanently discontinue rifaximin 
 

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9.0 
Ancillary Treatment/Supportive Care 
9.1 
Full supportive care 
Patients should receive full supportive care while on this study. This includes blood 
product support, antibiotic treatment, and treatment of other newly diagnosed or 
concurrent medical conditions. Other treatment as necessary for the control of 
chemotherapy related symptoms is allowed. All blood products and concomitant 
medications such as antidiarrheals, analgesics, and/or antiemetics received from the first 
day of study treatment administration until 30 days after the final dose will be recorded in 
the medical records. 
Blood products and growth factors 
Blood products and growth factors should be utilized as clinically warranted and 
following institutional policies and recommendations. The use of growth factors should 
follow published guidelines of the Journal of Clinical Oncology, Volume 33, No 28 
(October 1), 2015: pp. 3199-3212 (WBC growth factors) AND Journal of Clinical 
Oncology, Volume 28, No 33 (November 20), 2010: pp. 4955-5010 
(darbepoetin/epoetin). 
Antiemetics 
Antiemetics may be used at the discretion of the attending physician. 
Diarrhea 
The use of loperamide and/or atropine/diphenoxylate is allowed. In the event of Grade 3 
or 4 diarrhea, the following supportive measures are allowed: hydration, octreotide, and 
antidiarrheals. 
9.2 
9.3 
9.4 
 

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10.0 
Adverse Event (AE) Monitoring and Reporting 
The site principal investigator is responsible for reporting any/all serious adverse events to the 
sponsor as described within the protocol, regardless of attribution to study agent or treatment 
procedure. 
The sponsor/sponsor-investigator is responsible for notifying FDA and all participating 
investigators in a written safety report of any of the following: 
• 
• 
Any suspected adverse reaction that is both serious and unexpected. 
Any findings from laboratory animal or in vitro testing that suggest a significant risk for 
human subjects, including reports of mutagenicity, teratogenicity, or carcinogenicity. 
Any findings from epidemiological studies, pooled analysis of multiple studies, or 
clinical studies, whether or not conducted under an IND and whether or not conducted 
by the sponsor, that suggest a significant risk in humans exposed to the drug 
Any clinically important increase in the rate of a serious suspected adverse reaction over 
the rate stated in the protocol or Investigator’s Brochure (IB). 
Summary of SAE Reporting for this study 
(please read entire section for specific instructions): 
• 
• 
Definitions 
Adverse Event 
Any untoward medical occurrence associated with the use of a drug in humans, whether or 
not considered drug related. 
Suspected Adverse Reaction 
Any adverse event for which there is a reasonable possibility that the drug caused the adverse 
event. 
Expedited Reporting 
Events reported to sponsor within 24 hours, 5 days or 10 days of study team becoming aware 
of the event. 
Routine Reporting 
Events reported to sponsor via case report forms 
Events of Interest 
Events that would not typically be considered to meet the criteria for expedited reporting, but 
that for a specific protocol are being reported via expedited means in order to facilitate the 
review of safety data (may be requested by the FDA or the sponsor). 
WHO: 
WHAT form: 
WHERE to send: 
All sites 
 
Pregnancy Reporting 
 
 
Mayo Sites – attach to MCCC 
Electronic SAE Reporting Form 
 
Mayo Clinic 
Sites 
 
Mayo Clinic Cancer Center SAE Reporting Form: 
 
Will automatically be sent to 
 
 
 
 
 

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Unanticipated Adverse Device Event (UADE) 
Any serious adverse effect on health or safety or any life-threatening problem or death caused 
by, or associated with, a device, if that effect, problem, or death was not previously identified 
in nature, severity, or degree of incidence in the investigational plan or application (including 
a supplementary plan or application), or any other unanticipated serious problem associated 
with a device that relates to the rights, safety, or welfare of subjects 
10.1 
Adverse Event Characteristics 
CTCAE term (AE description) and grade: The descriptions and grading scales found 
in the revised NCI Common Terminology Criteria for Adverse Events (CTCAE) version 
5.0 will be utilized for AE reporting. All appropriate treatment areas should have access 
to a copy of the CTCAE version 5.0. A copy of the CTCAE version5.0 can be 
downloaded from the CTEP web site: 
 
a. 
b. 
c. 
Identify the grade and severity of the event using the CTCAE version 5.0. 
Determine whether the event is expected or unexpected (see Section 10.2). 
Determine if the adverse event is related to the study intervention (agent, treatment or 
procedure) (see Section 10.3). 
Determine whether the event must be reported as an expedited report. If yes, 
determine the timeframe/mechanism (see Section 10.4). 
Determine if other reporting is required (see Section 10.5). 
Note: All AEs reported via expedited mechanisms must also be reported via the 
routine data reporting mechanisms defined by the protocol (see Sections 10.6 and 
18.0). 
d. 
e. 
f. 
NOTE: A severe AE is NOT the same as a serious AE, which is defined in Section 10.4. 
Expected vs. Unexpected Events 
Expected events - are those described within the Section 15.0 of the protocol, the study 
specific consent form, package insert (if applicable), and/or the investigator brochure, (if 
an investigator brochure is not required, otherwise described in the general 
investigational plan). 
Unexpected adverse events or suspected adverse reactions are those not listed in Section 
15.0 of the protocol, the study specific consent form, package insert (if applicable), or in 
the investigator brochure (or are not listed at the specificity or severity that has been 
observed); if an investigator brochure is not required or available, is not consistent with 
the risk information described in the general investigational plan. 
Unexpected also refers to adverse events or suspected adverse reactions that are 
mentioned in the investigator brochure as occurring with a class of drugs but have not 
been observed with the drug under investigation. 
An investigational agent/intervention might exacerbate the expected AEs associated with a 
commercial agent. Therefore, if an expected AE (for the commercial agent) occurs with a 
higher degree of severity or specificity, expedited reporting is required. 
NOTE: *The consent form may contain study specific information at the discretion of the 
Principal Investigator; it is possible that this information may NOT be included in the 
protocol or the investigator brochure. Refer to protocol or IB for reporting needs. 
Attribution to agent(s) or procedure 
10.2 
10.3 
 

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When assessing whether an adverse event (AE) is related to a medical agent(s) medical or 
procedure, the following attribution categories are utilized: 
Definite - The AE is clearly related to the agent(s)/procedure. 
Probable - The AE is likely related to the agent(s)/procedure. 
Possible - The AE may be related to the agent(s)/procedure. 
Unlikely - The AE is doubtfully related to the agent(s)/procedure. 
Unrelated - The AE is clearly NOT related to the agent(s)/procedure. 
10.31 AEs Experienced Utilizing Investigational Agents and Commercial Agent(s) on 
the SAME (Combination) Arm 
NOTE: When a commercial agent(s) is (are) used on the same treatment arm as 
the investigational agent/intervention (also, investigational drug, biologic, 
cellular product, or other investigational therapy under an IND), the entire 
combination (arm) is then considered an investigational intervention for 
reporting. 
• An AE that occurs on a combination study must be assessed in accordance with the 
guidelines for investigational agents/interventions. 
• An AE that occurs prior to administration of the investigational agent/intervention 
must be assessed as specified in the protocol. In general, only Grade 4 and 5 AEs 
that are unexpected with at least possible attribution to the commercial agent 
require an expedited report, unless hospitalization is required. Refer to Section 10.4 
for specific AE reporting requirements or exceptions. 
An investigational agent/intervention might exacerbate the expected AEs associated 
with a commercial agent. Therefore, if an expected AE (for the commercial agent) 
occurs with a higher degree of severity or specificity, expedited reporting is 
required. 
• An increased incidence of an expected adverse event (AE) is based on the 
patients treated for this study at their site. A list of known/expected AEs is 
reported in the package insert or the literature, including AEs resulting from 
a drug overdose. 
• Commercial agent expedited reports must be submitted to the FDA via 
MedWatch 3500A for Health Professionals (complete all three pages of the 
form). 
 
 
 
 
 
Instructions for completing the MedWatch 3500A: 
 
 

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10.4 
Expedited Reporting Requirements for IND/IDE Agents 
10.41 Phase 1 and Early Phase 2 Studies: Expedited Reporting Requirements for 
Adverse Events that Occur on Studies under an IND/IDE within 30 Days 
of the Last Administration of the Investigational Agent/Intervention 1, 2 
10.42 General reporting instructions 
The Mayo IND Coordinator will assist the sponsor-investigator in the processing 
of expedited adverse events and forwarding of suspected unexpected serious 
adverse reactions (SUSARs) to the FDA and IRB. 
FDA REPORTING REQUIREMENTS FOR SERIOUS ADVERSE EVENTS (21 CFR Part 312) 
NOTE: Investigators MUST immediately report to the sponsor ANY Serious Adverse Events, whether or not they 
are considered related to the investigational agent(s)/intervention (21 CFR 312.64) 
An adverse event is considered serious if it results in ANY of the following outcomes: 
1) 
Death 
2) 
A life-threatening adverse event 
3) 
An adverse event that results in inpatient hospitalization or prolongation of existing hospitalization for ≥ 24 
hours 
4) 
A persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions 
5) 
A congenital anomaly/birth defect. 
6) 
Important Medical Events (IME) that may not result in death, be life threatening, or require hospitalization 
may be considered serious when, based upon medical judgment, they may jeopardize the patient or subject 
and may require medical or surgical intervention to prevent one of the outcomes listed in this definition. 
(FDA, 21 CFR 312.32; ICH E2A and ICH E6). 
ALL SERIOUS adverse events that meet the above criteria MUST be immediately reported to the sponsor within 
the timeframes detailed in the table below. 
Hospitalization 
Grade 1 and Grade 2 Timeframes 
Grade 3-5 
Timeframes 
Resulting in 
Hospitalizatio
n 
24 h
7 Calendar Days 
 
24-Hour 3 Calendar 
Days 
 
Not resulting 
in 
Hospitalization 
Not required 
 
Expedited AE reporting timelines are defined as: 
o “24-Hour; 3 Calendar Days” - The AE must initially be reported within 24 hours of learning of the 
AE, followed by a complete expedited report within 3 calendar days of the initial 24-hour report. 
o “7 Calendar Days” - A complete expedited report on the AE must be submitted within 7 calendar 
days of learning of the AE. 
1Serious adverse events that occur more than 30 days after the last administration of investigational 
agent/intervention and have an attribution of possible, probable, or definite require reporting as follows: 
Expedited 24-hour notification followed by complete report within 3 calendar days for: 
• All Grade 3, 4, and Grade 5 AEs 
Expedited 7 calendar day reports for: 
• Grade 2 AEs resulting in hospitalization or prolongation of hospitalization 
2 For studies using PET or SPECT IND agents, the AE reporting period is limited to 10 radioactive half-lives, 
rounded UP to the nearest whole day, after the agent/intervention was last administered. Footnote “1” above 
applies after this reporting period. 
Effective Date: May 5, 2011 
 
 
 

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Use Mayo Expedited Event Report form 
 
for investigational agents 
or commercial/investigational agents on the same arm. 
For commercial agents: 
 
 
 
To Pharmaceutical Company (Salix Pharmaceuticals): 
Submit all SAEs and Pregnancy Reports to Valeant Drug Safety 
 
Reporting of re-occurring SAEs 
ALL SERIOUS adverse events that meet the criteria outlined in table10.41 
MUST be immediately reported to the sponsor within the timeframes detailed 
in the corresponding table. This reporting includes, but is not limited to SAEs 
that re-occur again after resolution. 
10.43 
10.5 
Other Required Reporting 
10.51 Unanticipated Problems Involving Risks to Subjects or Others (UPIRTSOS) 
Unanticipated Problems Involving Risks to Subjects or Others (UPIRTSOS) in 
general, include any incident, experience, or outcome that meets all of the 
following criteria: 
1. Unexpected (in terms of nature, severity, or frequency) given (a) the research 
procedures that are described in the protocol-related documents, such as the 
IRB-approved research protocol and informed consent document; and (b) the 
characteristics of the subject population being studied; 
Related or possibly related to participation in the research (in this guidance 
document, possibly related means there is a reasonable possibility that the 
incident, experience, or outcome may have been caused by the procedures 
involved in the research); and 
2. 
3. Suggests that the research places subjects or others at a greater risk of harm 
(including physical, psychological, economic, or social harm) than was 
previously known or recognized. 
Some unanticipated problems involve social or economic harm instead of the 
physical or psychological harm associated with adverse events. In other cases, 
unanticipated problems place subjects or others at increased risk of harm, but no 
harm occurs. 
Note: If there is no language in the protocol indicating that pregnancy is not 
considered an adverse experience for this trial, and if the consent form does not 
indicate that subjects should not get pregnant/impregnate others, then any 
pregnancy in a subject/patient or a male patient’s partner (spontaneously 
reported) which occurs during the study or within 120 days of completing the 
study should be reported as a UPIRTSO. 
 
 

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Mayo Clinic Cancer Center (MCCC) Institutions: 
If the event meets the criteria for IRB submission as a Reportable 
Event/UPIRTSO, provide the Reportable Event coversheet and appropriate 
documentation to 
The Mayo Regulatory 
Affairs Office will review and process the submission to the Mayo Clinic IRB. 
Death 
Note: A death on study requires both routine and expedited reporting 
regardless of causality, unless as noted below. Attribution to treatment or 
other cause must be provided. 
Any death occurring within 30 days of the last dose, regardless of attribution to 
an agent/intervention under an IND/IDE requires expedited reporting within 24-
hours. 
Any death occurring greater than 30 days with an attribution of possible, 
probable, or definite to an agent/intervention under an IND/IDE requires 
expedited reporting within 24-hours. 
Reportable categories of Death 
10.52 
• 
• 
Death attributable to a CTCAE term. 
Death Neonatal: A disorder characterized by cessation of life during the 
first 28 days of life. 
Death NOS: A cessation of life that cannot be attributed to a CTCAE term 
associated with Grade 5. 
Sudden death NOS: A sudden (defined as instant or within one hour of the 
onset of symptoms) or an unobserved cessation of life that cannot be 
attributed to a CTCAE term associated with Grade 5. 
Death due to progressive disease should be reported as Grade 5 “Disease 
Progression” under the system organ class (SOC) of the General 
disorders and administration site conditions. Evidence that the death 
was a manifestation of underlying disease (e.g., radiological changes 
suggesting tumor growth or progression: clinical deterioration associated 
with a disease process) should be submitted. 
• 
• 
• 
10.53 Secondary Malignancy 
• 
A secondary malignancy is a cancer caused by treatment for a previous 
malignancy (e.g., treatment with investigational agent/intervention, radiation 
or chemotherapy). A secondary malignancy is not considered a metastasis of 
the initial neoplasm. 
All secondary malignancies that occur following treatment with an agent under 
an IND/IDE will be reported. Three options are available to describe the event: 
o Leukemia secondary to oncology chemotherapy (e.g., Acute Myeloctyic 
Leukemia [AML]) 
o Myelodysplastic syndrome (MDS) 
o Treatment-related secondary malignancy 
Any malignancy possibly related to cancer treatment (including AML/MDS) 
should also be reported via the routine reporting mechanisms outlined in each 
protocol. 
• 
• 
10.54 Second Malignancy 
 

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A second malignancy is one unrelated to the treatment of a prior malignancy (and is 
NOT a metastasis from the initial malignancy). Second malignancies require ONLY 
routine reporting unless otherwise specified. 
Pregnancy, Fetal Death, and Death Neonatal 
If a female subject (or female partner of a male subject) taking investigational 
product becomes pregnant, the subject taking should notify the Investigator, and 
the pregnant female should be advised to call her healthcare provider 
immediately. The patient should have appropriate follow-up as deemed necessary 
by her physician. If the baby is born with a birth defect or anomaly, a second 
expedited report is required. 
Prior to obtaining private information about a pregnant woman and her infant, the 
investigator must obtain consent from the pregnant woman and the newborn 
infant’s parent or legal guardian before any data collection can occur. A consent 
form will need to be submitted to the IRB for these subjects if a pregnancy 
occurs. If informed consent is not obtained, no information may be collected. 
In cases of fetal death, miscarriage or abortion, the mother is the patient. In cases 
where the child/fetus experiences a serious adverse event other than fetal death, 
the child/fetus is the patient. 
NOTE: When submitting Mayo Expedited Adverse Event Report reports for 
“Pregnancy”, “Pregnancy loss”, or “Neonatal loss”, the potential risk of exposure 
of the fetus to the investigational agent(s) or chemotherapy agent(s) should be 
documented in the “Description of Event” section. Include any available medical 
documentation. Include this form: 
 
 
10.55 
10.551 
Pregnancy 
Pregnancy should be reported in an expedited manner as Grade 3 
“Pregnancy, puerperium and perinatal conditions - Other 
(pregnancy)” under the Pregnancy, puerperium and perinatal 
conditions SOC. Pregnancy should be followed until the outcome is 
known. 
Fetal Death 
Fetal death is defined in CTCAE as “A disorder characterized by death 
in utero; failure of the product of conception to show evidence of 
respiration, heartbeat, or definite movement of a voluntary muscle after 
expulsion from the uterus, without possibility of resuscitation.” 
Any fetal death should be reported expeditiously, as Grade 4 
“Pregnancy loss” under the Pregnancy, puerperium and perinatal 
conditions SOC. 
Death Neonatal 
Neonatal death, defined in CTCAE as “A disorder characterized by 
cessation of life occurring during the first 28 days of life” that is felt by 
the investigator to be at least possibly due to the investigational 
agent/intervention, should be reported expeditiously. 
A neonatal death should be reported expeditiously as Grade 4 
“Neonatal loss” under the General disorders and administration SOC. 
10.552 
10.553 
 

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10.6 
Required Routine Reporting 
10.61 Baseline and Adverse Events Evaluations 
Pretreatment symptoms/conditions to be graded at baseline and adverse events to 
be graded at each evaluation. 
Grading is per CTCAE v5.0 unless alternate grading is indicated in the table 
below: 
10.62 All other AEs 
All AEs and SAEs will be recorded regardless of whether or not they are 
considered related to the study drug(s) in the subjects’s medical record and on the 
appropriate study specific CRF form. 
10.7 
Late Occurring Adverse Events 
Refer to the instructions in the Forms Packet (or electronic data entry screens, as 
applicable) regarding the submission of late occurring AEs following completion of the 
Active Monitoring Phase (i.e., compliance with Test Schedule in Section 4.0). 
CTCAE 
System/Organ/Class 
(SOC) 
Adverse event/Symptoms 
Baseline 
Each 
evaluation 
Nervous system disorders 
Dizziness 
X 
X 
Skin and subcutaneous 
tissue disorders 
Rash maculo-papular 
X 
X 
Skin and subcutaneous 
tissue disorders 
Pruritus 
X 
X 
Investigations 
Alanine aminotransferase 
increased 
X 
X 
Gastrointestinal disorders 
 
Number of Stools 
X 
 
Diarrhea 
 
X 
 

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11.0 
Treatment Evaluation/Measurement of Effect 
Measurement of effect will be determined based on whether a patient have improvement in grade 
2 abdominal adverse events; details related to the primary endpoint and its assessment are found 
in the statistics section of this protocol. 
12.0 
Descriptive Factors 
None. 
13.0 Treatment/Follow–up Decision at Evaluation of Patient 
13.1 
A patient is deemed ineligible if after registration, it is determined that at the time of 
registration, the patient did not satisfy each and every eligibility criteria for study entry. 
The patient may continue treatment off-protocol at the discretion of the physician as long 
as there are no safety concerns, and the patient was properly registered. The patient will 
go directly off study. 
• 
If the patient received treatment, all data up until the point of 
confirmation of ineligibility must be submitted. 
• 
If the patient never received treatment, on-study material must be 
submitted. 
13.2 
A patient is deemed a major violation, if protocol requirements regarding treatment in 
cycle 1 of the initial therapy are severely violated that evaluability for primary end point 
is questionable. All data up until the point of confirmation of a major violation must be 
submitted. The patient will go off study. The patient may continue treatment off-protocol 
at the discretion of the physician as long as there are no safety concerns, and the patient 
was properly registered. 
13.3 
A patient is deemed a cancel if he/she is removed from the study for any reason before 
any study treatment is given. On-study material and the End of Active Treatment/Cancel 
Notification Form must be submitted. No further data submission is necessary. 
13.4 
If the patient stops rifaximin but continues pertuzumab, the patient should continue to fill 
out questionnaires on-study as long as the patient is on pertuzumab based chemotherapy. 
13.5 
At the end of the pertuzumab based chemotherapy treatment, the patient will continue to 
the End of treatment Visit as indicated in Section 4.0. 
13.6 
If the rifaximin dose is delayed, missed, or skipped, the patient should continue to fill out 
questionnaires. 
 

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14.0 
Body Fluid Biospecimens: 
14.1 
Summary Table of Stool to be collected 
14.2 
Collection and Processing 
All samples should be labeled with the study number (MC18C3), the patient’s study ID, and the designated specimen timepoint as 
indicated in section 14.1. 
14.21 Fecal Microbiome 
Collect two 2ml tubes and ship with cold pack. 
14.22 Permeability Test 
Collect two 5 mL 13x75 mm polypropylene tubes. The samples should be shipped frozen overnight on dry ice. 
14.3 
Shipping and Handling 
14.31 Stool kits will be used for this study. Kits will be supplied by the Biospecimen Accessioning and Processing Share Resource 
(BAP) in Florida. 
Research 
 
Mandatory 
or     
Optional 
 
Specimen 
collected 
 
Volume to 
collect per tube 
(# of tubes to 
be collected) 
 
≤30 days prior to 
Preregistration 
 
7-14 days after 
initiation of 
pertuzumab- 
based 
chemotherapy 
 
Cycle 
1, Day 
1 
 
Cycle 1, 
(Day 7) 
 
End of 
Treatment 
(21 Days 
after last dose 
of pertuzumab- 
based 
chemotherapy) 
Process 
at site? 
(Yes or 
No) 
 
Temperature 
Conditions for 
Storage /Shipping 
 
Fecal 
microbiome 
test 
 
Mandatory 
 
Stool 
 
2 mL (2) 
 
X 
 
X 
 
X 
 
X 
 
X 
 
No 
 
Cold, Ice pack 
 
Permeability 
Test 
 
Optional 
Urine 
 
5 mL (2) 
 
X 
 
X 
 
X 
 
X 
 
X 
 
Yes 
 
Frozen, Dry Ice 
 
 

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14.311 Stool Collection kits prepared by BAP will be provided to the patients. Participating institutions may obtain kits by 
submitting the supply order form to 
Because we are charged for all outgoing kits, a small, but 
sufficient, supply of the specimen collection kits should be ordered prior to patient entry. Supply Order Forms must be 
filled in completely and legibly for quick processing. 
14.312 Each stool kit will contain 2 or more stool collection vials that contain a collection spoon. Each kit will also contain a 
toilet hat, gloves, ice packs, and any other material deemed necessary for sanitary collection of stool by the patient in their 
home. Instructions for collection will be included with each kit. 
Prior to being provided to the patient, each stool kit and vial will be labeled with the protocol number and patient ID 
number. Information regarding the date and time of collection will be added to the containers. 
Fecal specimens may be collected by the patient at any day of the week, as long as the specimen is maintained at freezing 
temperature until shipping. Returning of the kit can be done in two ways: (a) in person, by depositing the kit with samples 
maintained under a cold temperature with ice pack to Mayo Clinic Florida; (b) by shipping the kit with samples 
maintained under a cold temperature with the ice pack by FedEx overnight shipping Monday – Friday ONLY (cost 
covered by the study). 
Shipping Specimens 
Stool samples will be sent to the following address at the end of the study via batch shipment: 
 
 
 
 
14.313 
14.314 
14.315 
14.32 Specimen kits will be used for this study. Kits will be supplied by the Biospecimen Accessioning and Processing Share Resource 
(BAP) in Florida. 
14.321 
14.322 
Urine collection containers will be provided to the patients. 
Each vial will be labeled with the protocol number and patient ID number. Information regarding the date and time of 
collection will be added to the vial. 
Urine specimens may be collected by the patient at any day of the week, as long as the specimen is maintained at freezing 
temperature until shipping. When samples are ready to be shipped, an email notification must be submitted. They are to 
be shipped frozen overnight on dry-ice (Mon – Wed only) with a sample sheet that is to be completed and electronically 
returned for each batch shipped. 
Shipping Specimens 
14.323 
14.324 
 

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Urine Samples for permeability test must be shipped to: 
 
 
 
 
 
 
14.4 
Background and Methodology 
14.41 Fecal microbiome characterization 
Microbial DNA will be extracted from the stool samples using the MoBio PowerSoil ® DNA Isolation Kit according to 
manufacturer’s protocol at the University of Minnesota Genomics Center. After extraction and quality assurance, amplicons will 
be generated from the 16S rDNA V4 region using barcoded reverse primers and sequenced using the Illumina MiSeq platform. 
Reads will then be aligned using a custom multiple alignment tool (Jeraldo 2014) that merges paired end reads into a single 
multiple alignment and obtain bacterial taxa calls to assess bacterial abundance and diversity. Alpha diversity measures will be 
performed to evaluate the sample bacterial diversity observed. Distance metrics will be applied to compare the microbiome 
diversity of the samples before and after treatment, and with and without PIGT. A generalized mixed-effects model will be fit to 
the taxa counts to determine the significance of differential abundances of individual and groups of taxa across the subjects. 
Permeability Test 
Gastrointestinal permeability is known to play a role in a number of chronic gastrointestinal disorders such as inflammatory bowel 
disease, celiac disease, and irritable bowel syndrome. Performing this test measures the integrity of the intestinal barrier using 
probe sugars to assess the absorptive ability of the intestines. We shall use the urinary excretion of mannitol, and lactulose, to 
measure small intestinal and colonic permeability (Camilleri et al submitted 2009). The chemical analysis is refinement of the 
method of Lostia et al (2008) with 2 improvements: first, we use HPLC-tandem mass spectrometry to increase assay accuracy and 
test sensitivity; second, we use the sugars administered in solution or a delayed- release capsule (that dissolves at the ileocolonic 
junction), to identify which urine samples correspond to small intestinal or colonic absorption. 
14.42 
 

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15.0 
Drug Information 
IND number (study specific) or IND exempt 
 
 
 
15.1 
Rifaximin 
15.11 Background: Rifaximin is a semi-synthetic derivative of rifampin and acts by 
binding to the beta-subunit of bacterial DNA-dependent RNA polymerase 
blocking one of the steps in transcription. This results in inhibition of bacterial 
protein synthesis and consequently inhibits the growth of bacteria. 
15.12 Formulation: Rifaximin tablets for oral administration are film-coated and 
contain 200 mg or 550 mg of rifaximin. 
The 200 mg tablet is a pink-colored, round, biconvex tablet with “Sx” debossed 
on one side and plain on the other. 
The 550 mg tablet is a pink-colored, oval, biconvex tablet with “rfx” debossed on 
one side and plain on the other. 
15.13 Preparation and storage: Store rifaximin tablets at 20° to 25°C (68° to 77°F); 
excursions permitted to 15° to 30°C (59° to 86°F). 
15.14 Administration: Rifaximin may be taken with or without food. 
15.15 Pharmacokinetic information: 
Absorption: 
In healthy subjects, the mean time to reach peak rifaximin plasma concentrations 
was about an hour and the mean Cmax ranged 2.4 to 4 ng/mL after a single dose 
and multiple doses of rifaximin 550 mg. 
Distribution: Rifaximin is moderately bound to human plasma proteins. In vivo, 
the mean protein binding ratio was 67.5% in healthy subjects and 62% in patients 
with hepatic impairment when rifaximin was administered. 
Metabolism: In an in vitro study rifaximin was metabolized mainly by CYP3A4. 
Rifaximin accounted for 18% of radioactivity in plasma suggesting that the 
absorbed rifaximin undergoes extensive metabolism. 
Half-life elimination: The mean half-life of rifaximin in healthy subjects at 
steady-state was 5.6 hours. 
Excretion: In a mass balance study, after administration of 400 mg 14C- 
rifaximin orally to healthy volunteers, of the 96.94% total recovery, 96.62% of 
the administered radioactivity was recovered in feces mostly as the unchanged 
drug and 0.32% was recovered in urine mostly as metabolites with 0.03% as the 
unchanged drug. 
 

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15.16 Potential Drug Interactions: 
An in vitro study suggests that rifaximin is a substrate of CYP3A4. In vitro 
rifaximin is a substrate of P-glycoprotein, OATP1A2, OATP1B1, and 
OATP1B3. Rifaximin is not a substrate of OATP2B1. 
However, rifaximin has minimal systemic absorption with < 0.4% bioavailability. 
In previous clinical studies, rifaximin has shown no significant effect on drug 
metabolism by cytochrome P450 isoenzymes. 
P-glycoprotein Inhibitors 
Caution should be exercised when concomitant use of rifaximin and a P-gp 
inhibitor such as cyclosporine is needed. Concomitant administration of 
cyclosporine, an inhibitor of P-gp and OATPs significantly increased the 
systemic exposure of rifaximin. In patients with hepatic impairment, a potential 
additive effect of reduced metabolism and concomitant P-gp inhibitors may 
further increase the systemic exposure to rifaximin. 
Warfarin 
Changes in INR have been reported post marketing in patients receiving 
rifaximin and warfarin concomitantly. Monitor INR and prothrombin time. Dose 
adjustment of warfarin may be needed to maintain target INR range. See 
prescribing information for warfarin. 
CYP3A4 Substrates 
An in vitro study has suggested that rifaximin induces CYP3A4. However, in 
patients with normal liver function, rifaximin at the recommended dosing 
regimen is not expected to induce CYP3A4. It is unknown whether rifaximin can 
have a significant effect on the pharmacokinetics of concomitant CYP3A4 
substrates in patients with reduced liver function who have elevated rifaximin 
concentrations. 
15.17 Known potential toxicities 
Common known potential toxicities, > 10%: 
Cardiovascular: Peripheral edema 
Central nervous system: Dizziness, fatigue 
Hepatic: Ascites 
Gastrointestinal: Nausea 
Less common known potential toxicities, 2% - 10: 
Central nervous system: Headache, depression 
Dermatological: Pruritus, skin rash 
Gastrointestinal: Abdominal pain, pseudomembranous colitis 
Hematologic & oncologic: Anemia 
Hepatic: Increased serum ALT 
Neuromuscular & skeletal: Muscle spasm, arthralgia, increased creatine 
phosphokinase 
Respiratory: Nasopharyngitis, dyspnea, epistaxis 
Miscellaneous: Fever 
 

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Rare known potential toxicities: <2%: Anaphylaxis, angioedema, Clostridium 
difficile associated diarrhea, exfoliative dermatitis, flushing, hypersensitivity 
reaction, urticaria 
15.18 Drug procurement: Rifaximin will be provided free of charge to patients by 
Salix Pharmaceuticals. 
15.19 Nursing Guidelines: 
1. Assess for patients concomitant medications. There are several drug to drug 
interactions with rifaximin. For patients receiving concomitant warfarin, 
INR and PT will need to be monitored carefully with dose adjustments of 
warfarin as necessary. 
2. Patients may experience peripheral edema. Instruct patients to report this and 
manage symptomatically. 
3. 
4. 
Dizziness has been seen with this agent. Warn patients of this possibility. 
Monitor LFT’s while patient is on therapy as increased LFT’s have been seen 
as has ascites. 
Rifaximin may be taken with or without food. 
Rarely anaphylaxis (angioedema, flushing, and hypersensitivity reaction, 
urticarial) has been seen with this agent. Instruct patient to report any signs 
or symptoms of allergic reaction to the study team immediately and/or seek 
out emergency medical care. 
Gastrointestinal side effects have been seen including diarrhea, abdominal 
pain, and nausea. Due to the possibility of c-difficle colitis, patients should 
be instructed to notify the team of any diarrhea and not to self-medicate. 
5. 
6. 
7. 
16.0 
Statistical Considerations and Methodology 
16.1 
Statistical Endpoints and analysis 
16.11 Primary Endpoint 
The primary endpoint is to evaluate the reduction rate of ≥ grade 2 abdominal toxicities 
including abdominal distension, abdominal pain, diarrhea, dyspepsia, stomach pain, and 
typhlitis based on the NCI CTCAE with the use of rifaximin in stage I-III HER-2 
positive breast cancer patients with PIGT after initiation of pertuzumab-based 
chemotherapy. 
16.12 Secondary endpoints 
16.121 Dose reductions, dose delays and discontinuation of treatment with 
pertuzumab due to gastrointestinal side effects 
16.122 Change in the Bristol stool scale before and after rifaximin treatment. 
16.123 Other PIGT such as abdominal pain, bloating and flatulence as measured 
by a 4 point Likert scale. 
16.13 Correlative Endoints 
16.131 Evaluation of changes in the fecal microbiome, hydrogen breath test, and 
permeability test before and after rifaximin. 
 

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16.132 Evaluation of changes in the fecal microbiome, hydrogen breath test, 
and permeability test before and after pertuzumab-based chemotherapy. 
16.133 Evaluation the difference in the fecal microbiome, hydrogen breath test, 
and permeability test among patients with or without PIGT. 
Study Design 
We plan to conduct a single center, phase II trial of rifaximin in stage II-III HER2- 
positive breast cancer patients with PIGT (defined as ≥ National Cancer Institute 
Common Terminology Criteria for Adverse Events, NCI CTCAE v5.0, grade 2 
gastrointestinal toxicities) despite standard antidiarrheal agents after the initiation of 
pertuzumab-based neoadjuvant or adjuvant chemotherapy. A parallel arm will comprise 
patients without PIGT (defined as ≤ 1 NCI CTCAE v5.0 grade gastrointestinal toxicities. 
No formal statistical comparisons are planned for the primary and secondary endpoints; 
however, we will evaluate between arm differences for the correlative endpoints in a 
descriptive and explorative fashion. 
16.2 
16.21 Decision Rule: The largest success proportion where the proposed treatment 
regimen would be considered ineffective in this population is 10%, and the 
smallest success proportion that may warrant subsequent studies with the 
proposed regimen in this patient population is 30%. The following 2-stage 
design uses 7 or 18 evaluable patients to test the null hypothesis that the true 
success proportion in a given patient population is at most 30%. We call it a 
success if the patient has reduction of ≥ grade 2 abdominal toxicities after cycle 
1. 
16.211 STAGE 1: Enter 7 evaluable patients into the study. If no success is 
observed in the first 7 evaluable patients, we may consider this regimen 
ineffective in this patient population and terminate this study. Otherwise, 
if the number of successes is at least 1, we will proceed to Stage 2. 
16.212 STAGE 2: Enter an additional 11 evaluable patients into the study. If 3 
or fewer successes are observed in the first 18 evaluable patients, we 
may consider this regimen ineffective in this patient population. If 4 or 
more successes are observed in the first 18 evaluable patients, we may 
recommend further testing of this regimen in subsequent studies in this 
population. 
NOTE: We will not suspend accrual between stages because long-term 
suspension of accrual for the first-stage analysis is likely to lead to poor 
accrual in the second stage. We feel that safety will not be compromised 
due to real time adverse event monitoring. We will consider closing 
accrual in the event of rapid accrual or high incidence of adverse events. 
16.213 
16.3 
Sample Size 
The sample size was determined based on the primary endpoint measured in the rifaximin 
arm and is based on a Simon's two-stage design (Simon, 1989), which is fully described 
in section 16.21. A minimum of 7 and a maximum of 18 evaluable patients will be 
accrued onto this phase II study unless undue adverse events are encountered. We 
anticipate accruing an additional 2 patients to account for ineligibility, cancellation, 
major treatment violation, or other reasons. Given the incidence of ≥ grade 2 diarrhea is 
 

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approximately 60% with pertuzumab-based chemotherapy; we expect to enroll a total of 34 
patients to achieve 20 patients receiving rifaximin, of which 18 will be evaluable. Note that 
the total sample size will be determined by number of patients in the rifaximin arm, once there 
are 18 patients deemed evaluable in the rifaximin arm , the study will close accrual. 
Assuming that the number of successes is binomially distributed, the significance level is 
≤10% and the probability of declaring that this regimen warrants further studies (i.e. 
statistical power) under various success proportions and the probability of stopping 
accrual after the first stage can be tabulated as a function of the true success proportion as 
shown in the following table. 
16.4 
Analysis Plan 
The statistical analyses will be handled in a descriptive manner. 
16.41 Primary endpoint: 
The proportion of successes will be estimated by the number of successes divided 
by the total number of evaluable patients. Confidence intervals for the true 
success proportion will be calculated according to the approach of Duffy and 
Santner (1987). 
16.42. Secondary Endpoints 
16.421. Descriptive statistics (frequency table) and histogram will be used to 
summarize dose reductions, dose delays and discontinuation of treatment with 
pertuzumab due to gastrointestinal side effects. 
16.422 Descriptive statistics (frequency table) and histogram will be used to 
summarize the Bristol stool scale during the study. 
16.423 Descriptive statistics (frequency table) and histogram will be used 
to summarize other PIGT such as abdominal pain, bloating and flatulence as 
measured by a 4 point Likert scale during the study. 
16.43 Correlative Endpoints 
16.431. Descriptive statistics (mean, sd, median, iqr) and longitudinal plots (raw 
value, change, change in percentage) will be used to summarize the baseline 
levels of hydrogen/methane peak by hydrogen breath test , diversity of gut 
microbiome(number of species) and specific species by fecal microbiome, and 
levels of urine mannitol and lactulose by permeability test before and after 
rifaximin. 
16.432 Descriptive statistics (mean, sd, median, iqr) and longitudinal plots (raw 
value, change, change in percentage) will be used to summarize the baseline 
levels of hydrogen/methane peak by hydrogen breath test, diversity of gut 
microbiome(number of species) and specific species by fecal microbiome, and 
If the true success proportion is . . . . 
0.10 0.15 
0.20 0.25 
0.30 
then the probability of declaring that the 
regimen warrants further studies is . . . . 
0.09 
 
0.26 
 
0.47 
 
0.66 
 
0.80 
 
and the probability of stopping at stage 1 is . . . . 
0.48 0.32 
0.21 0.13 
0.08 
 
 

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levels of urine mannitol and lactulose by permeability test before and after 
pertuzumab-based chemotherapy. 
16.433 Descriptive statistics (mean, sd, median, iqr) and longitudinal plots (raw 
value, change, change in percentage) will be used to the fecal microbiome, 
hydrogen breath test, and permeability test among patients with or without PIGT. 
The study is not powered to detect any differences between the two arms; the 
main purpose is to quantify and evaluate differences descriptively between 
patients who develop and do not develop PIGT (between arm 1 and arm 2) to 
inform subsequent research.  
Accrual and duration of study 
This trial will be conducted at Mayo Clinic in Florida. Based on past experience of 
patient accrual in previous trials and the frequency of pertuzumab therapy we estimate an 
accrual rate of approximately 1-2 patients per months. Therefore, we expect to complete 
accrual within 30 months. With a follow-up time of 6 months, the expected total duration 
of the study is about 3 years. 
Data and Safety Monitoring 
The principal investigator(s) and the study statistician will review the study monthly to 
identify accrual, adverse event, and any endpoint problems that might be developing. The 
Mayo Clinic Cancer Center (MCCC) Data Safety Monitoring Board (DSMB) is 
responsible for reviewing accrual and safety data for this trial at least biannually, based 
on reports provided by the MCCC Statistical Office. 
Adverse Event Stopping Rule 
16.5 
16.6 
16.7 
16.71 The stopping rule specified below is based on the knowledge available at study 
development. We do note that the Adverse Event Stopping Rule may be adjusted 
in the event of either (1) the study re-opening to accrual or (2) at any time during 
the conduct of the trial and in consideration of newly acquired information 
regarding the adverse event profile of the treatment(s) under investigation. The 
study team may choose to suspend accrual because of unexpected adverse event 
profiles that have not crossed the specified rule below. 
16.72 Accrual will be temporarily suspended to this study if at any time we observe 
events that the study team considers to be at least possibly related to study 
treatment (i.e., an adverse event with attribute specified as “possible,” 
“probable,” or “definite”) that satisfy the following: 
16.73 If there are ≥ 2 patients who receive rifaximin develop the same grade 3 or higher 
adverse events based on the NCI CTCAE v5.0 or if ≥ 1 patient develops grade 4 
or higher adverse events that the study team considers to be at least possibly 
related to rifaximin (i.e., an adverse event with attribute specified as “possible,” 
“probable,” or “definite”). 
16.74 We note that we will review grade 4 and 5 adverse events deemed “unrelated” or 
“unlikely to be related” to verify their attribution and to monitor the emergence 
of a previously unrecognized treatment-related adverse event. 
16.8 
Gender and minority accrual considerations 

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This study is open to patients for all races. 
Ethnic 
Categories: 
Hispanic or Latino – a person of Cuban, Mexican, Puerto Rican, South or Central 
American, or other Spanish culture or origin, regardless of race. The term “Spanish 
origin” can also be used in addition to “Hispanic or Latino.” 
Not Hispanic or Latino 
American Indian or Alaskan Native – a person having origins in any of the original 
peoples of North, Central, or South America, and who maintains tribal affiliations or 
community attachment. 
Asian – a person having origins in any of the original peoples of the Far East, 
Southeast Asia, or the Indian subcontinent including, for example, Cambodia, China, 
India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and 
Vietnam. (Note: Individuals from the Philippine Islands have been recorded as Pacific 
Islanders in previous data collection strategies.) 
Black or African American – a person having origins in any of the black racial 
groups of Africa. Terms such as “Haitian” or “Negro” can be used in addition to 
“Black or African American.” 
Native Hawaiian or other Pacific Islander – a person having origins in any of the 
original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. 
White – a person having origins in any of the original peoples of Europe, the Middle 
East, or North Africa. 
Racial 
Categories: 
Accrual Targets 
Ethnic Category 
Sex/Gender(%) 
Females 
Males 
Unknown 
Total 
Hispanic or Latino 
1 
0 
0 
1 
Not Hispanic or Latino 
33 
0 
0 
33 
Ethnic Category: Total of all subjects 
34 
0 
0 
34 
Racial Category 
American Indian or Alaskan Native 
1 
0 
0 
1 
Asian 
0 
0 
0 
0 
Black or African American 
4 
0 
0 
4 
Native Hawaiian or other Pacific Islander 
0 
0 
0 
0 
White 
29 
0 
0 
29 
Racial Category: Total of all subjects 
34 
0 
0 
34 

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17.0 
Pathology Considerations/Tissue Biospecimens: 
None. 
18.0 
Records and Data Collection Procedures 
18.1 
Submission Timetable 
Data submission instructions for this study can be found in the Data Submission 
Schedule. 
Survival Follow-up 
See Section 4.2. 
CRF completion 
This study will use Medidata Rave® for remote data capture (rdc) of all study data. Data 
collection for this study will be done exclusively through the Medidata Rave® clinical 
data management system. Access to the trial in Rave is granted through the iMedidata 
application to all persons with the appropriate roles assigned in Regulatory Support 
System (RSS). To access Rave via iMedidata, the site user must have an active account 
and the appropriate Rave role (Rave CRA, Read-Only, Site Investigator) on either the 
organization roster at the enrolling site. 
Site responsibilities 
Each site will be responsible for insuring that all materials contain the patient’s initials, 
MCCC registration number, and MCCC protocol number. Patient’s name must be 
removed. 
Supporting documentation 
This study requires supporting documentation for diagnosis prior to study. These 
documents should be submitted within 30 days of preregistration (for prior to study entry 
materials). 
Labelling of materials 
Each site will be responsible for insuring that all materials contain the patient’s initials, 
MCCC registration number, and MCCC protocol number. Patient’s name must be 
removed. 
Incomplete materials 
Any materials deemed incomplete by the MCCC Operations Office will be considered 
“not received” and will not be edited or otherwise processed until the missing 
information is received. A list of the missing documents will be made available to the 
appropriate co-sponsor/participant. 
Overdue lists 
A list of overdue materials and forms for study patients will be generated monthly. The 
listings will be sorted by location and will include the patient study registration number. 
The appropriate co-sponsor/participant will be responsible to obtain the overdue material. 
18.2 
18.3 
18.4 
18.5 
18.6 
18.7 
18.8 
18.9 
Corrections forms 
 
 

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If a correction is necessary the QAS will query the site. The query will be sent to the 
appropriate site to make the correction and return the query and documentation of 
correction back to the QAS. 
19.0 
Budget 
19.1 
19.2 
Costs charged to patient: routine clinical care 
Tests to be research funded: Rifaximin (study drug), Stool kit and test, Hydrogen breath 
test, and Permeability collection and test. 
Other budget concerns: 
Salix Pharmaceuticals, Inc will provide Mayo Clinic with funding to support costs of 
running this study and will provide study drug, rifaximin, for use in this study. 
19.3 

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20.0 
1. 
References 
Baselga J et al. Pertuzumab plus trastuzumab plus docetaxel for metastatic breast cancer. N Engl 
J Med (2012) 366(2):109-19. 
2. Bass NM, Mullen KD, Sanyal A, et al: Rifaximin treatment in hepatic encephalopathy. N Engl J 
Med 362:1071-81, 2010. 
3. Descombe JJ, Dubourg D, Picard M, et al: Pharmacokinetic study of rifaximin after oral 
administration in healthy volunteers. Int J Clin Pharmacol Res 14:51-6, 1994. 
4. DuPont HL, Jiang ZD, Okhuysen PC, et al: Antibacterial chemoprophylaxis in the prevention of 
traveler's diarrhea: evaluation of poorly absorbed oral rifaximin. Clin Infect Dis 41 Suppl 8:S571- 
6, 2005. 
5. DuPont HL, Jiang ZD, Ericsson CD, et al: Rifaximin versus ciprofloxacin for the treatment of 
traveler's diarrhea: a randomized, double-blind clinical trial. Clin Infect Dis 33:1807-15, 2001. 
6. DuPont HL, Ericsson CD, Mathewson JJ, et al: Rifaximin: a nonabsorbed antimicrobial in the 
therapy of travelers' diarrhea. Digestion 59:708-14, 1998 
7. Gianni et al. Efficacy and safety of neoadjuvant pertuzumab and trastuzumab in women with 
locally advanced, inflammatory, or early HER2-positive breast cancer (NeoSphere): a randomised 
multicentre, open-label, phase 2 trial. Lancet Oncol (2012) 13(1):25-32. 
8. Jeraldo, Patricio et al. IM-TORNADO: A Tool for Comparison for 16S Reads from Paired-End 
Libraries. PLoS ONE 9(12): e114804. https://doi.org/10.1371/journal.pone.0114804. 
9. Lewis, SJ et al. Stool form scale as useful guide to intestinal transit time. Scandinavian Journal of 
Gastronenterology. (1997) 32: 920-924. 
10. Owens MA et al. HER2 amplification ratios by fluorescence in situ hybridization and correlation 
with immunohistochemistry in a cohort of 6556 breast cancer tissues. Clin Breast Cancer. 
2004;5:63-69. 
11. Pentikis HS, Connolly M, Trapnell CB, et al: The effect of multiple-dose, oral rifaximin on the 
pharmacokinetics of intravenous and oral midazolam in healthy volunteers. Pharmacotherapy 
27:1361-9, 2007. 
12. Pimentel, M. et al. Rifaximin therapy for patients with irritable bowel syndrome without 
constipation. N Engl J Med. (2011) 364:22-32. 
13. Rezaie, A. et al. Hydrogen and methan-based breath testing in gastrointestinal disorders: the north 
American consensus. American Journal of Gastroenterology. (2017) 112(5):775-784. 
14. Schneeweiss A et al. Pertuzumab plus trastuzumab in combination with standard neoadjuvant 
anthracycline-containing and anthracycline-free chemotherapy regimens in patients with HER2- 
positive early breast cancer: a randomized phase II cardiac safety study (TRYPHAENA). Ann 
Oncol (2013) 24(9):2278-84. 

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15. Sharara AI, Aoun E, Abdul-Baki H, et al: A randomized double-blind placebo-controlled trial of 
rifaximin in patients with abdominal bloating and flatulence. Am J Gastroenterol 101:326-33, 
2006. 
16. Simon R (1989). Controlled Clinical Trials 10: 1-10 
17. Soyano AE et al. Rifaximin for Pertuzumab-Related GI Toxicities. Front. Oncol.(2017) 7:168. 
2017 
18. Swain et al. Pertuzumab, trastuzumab, and docetaxel in HER2-positive metastatic breast cancer. 
N Engl J Med (2015) 372(8):724-34. 
19. Trapnell CB, Connolly M, Pentikis H, et al: Absence of effect of oral rifaximin on the 
pharmacokinetics of ethinyl estradiol/norgestimate in healthy females. Ann Pharmacother 
41:222-8, 2007. 
20. Vazquez-Roque et al. A Controlled trial of gluten-free diet in patients with irritable bowel 
syndrome-diarrhea: effects on bowel frequency and intestinal function. Gastroenterology (2013) 
144(5), 903-911. https://doi.org/10.1053/j.gastro.2013.01.049 

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Appendix I 
ECOG Performance Status 
*As published in Am. J. Clin. Oncol.: 
Oken, M.M., Creech, R.H., Tormey, D.C., Horton, J., Davis, T.E., McFadden, E.T., Carbone, P.P.: 
Toxicity And Response Criteria Of The Eastern Cooperative Oncology Group. Am J Clin Oncol 5:649- 
655, 1982. 
The ECOG Performance Status is in the public domain therefore available for public use. To duplicate the 
scale, please cite the reference above and credit the Eastern Cooperative Oncology Group, Robert Comis 
M.D., Group Chair. 
 
ECOG PERFORMANCE STATUS* 
Grade ECOG 
0 
Fully active, able to carry on all pre-disease performance without restriction 
1 
 
Restricted in physically strenuous activity but ambulatory and able to carry out 
work of a light or sedentary nature, e.g., light house work, office work 
2 
 
Ambulatory and capable of all selfcare but unable to carry out any work 
activities. Up and about more than 50% of waking hours 
3 
 
Capable of only limited selfcare, confined to bed or chair more than 50% of 
waking hours. 
4 
 
Completely disabled. Cannot carry on any selfcare. Totally confined to bed or 
chair. 
5 
Dead 

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Appendix II Patient Medication Diary (Arm 1 only) 
Name _ 
 
Study ID Number 
 
Please complete this diary on a daily basis. Write in the amount of the dose of rifaximin that you 
took in the appropriate “Day” box. 
Rifaximin may be taken with or without food. On the days that you do not take any study drug or 
miss a dose, please write in “0” for any dose that was missed. If you forget to take your daily 
dose, please write in “0”, but remember to take your prescribed dose at the next regularly 
scheduled time. Rifaxmin is required to be taken on Days 1-5. If you miss Day 5 doses, do not 
continue to take the drug the next day. 
If you experience any health/medical complaints please record this information. 
Week of: 
Week of: 
Week of: 
Week of: 
Week of: 
Patient signature:   
 
Health or medical complaints during this time: 
 
Study Drug 
Day 1 
Day 2 
Day 3 
Day 4 
Day 5 
Rifaximin 1st dose 
 
 
 
 
 
Rifaximin 2nd dose 
 
 
 
 
 
Study Drug 
Day 1 
Day 2 
Day 3 
Day 4 
Day 5 
Rifaximin 1st dose 
 
 
 
 
 
Rifaximin 2nd dose 
 
 
 
 
 
Study Drug 
Day 1 
Day 2 
Day 3 
Day 4 
Day 5 
Rifaximin 1st dose 
 
 
 
 
 
Rifaximin 2nd dose 
 
 
 
 
 
Study Drug 
Day 1 
Day 2 
Day 3 
Day 4 
Day 5 
Rifaximin 1st dose 
 
 
 
 
 
Rifaximin 2nd dose 
 
 
 
 
 
Study Drug 
Day 1 
Day 2 
Day 3 
Day 4 
Day 5 
Rifaximin 1st dose 
 
 
 
 
 
Rifaximin 2nd dose 
 
 
 
 
 
 
 
 

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Other medications or supplements taken during this time: 
Use a separate sheet of paper if more space is needed. 
Study Coordinator Use Only 
Number of vials returned:   
  
Verified by   
 
Number of pills returned   
  
Discrepancy Yes  
/No  
 
Date  
 
 
 
 
 
My next scheduled visit is:   
 
If you have any questions, please call:   
 
Name of medication or 
supplement 
How much did you take? 
(example: Two 500mg pills) 
When did you take it 
(examples: Every day 
Or Day 19 and Day 20) 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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Appendix III NCI CTCAE v5.0 for Gastrointestinal toxicities 
ADL: activities of daily living 
Adverse 
Event 
Grade 1 
 
Grade 2 
 
Grade 3 
 
Grade 4 
 
Grade 5 
 
Diarrhea 
 
Increase of 
<4 stools per 
day 
 
Increase of 4- 
6 stools per 
day over 
baseline 
 
Increase of ≥7 
stools per day 
over baseline; 
hospitalization 
indicated; 
limiting self 
care ADL 
Life- 
threatening 
consequences, 
urgent 
intervention 
indicated 
 
Death 
 
Abdominal 
pain 
 
Mild pain 
 
Moderate 
pain; limiting 
instrumental 
ADL 
Severe pain; 
limiting self 
care ADL 
 
- 
 
- 
 
Bloating 
 
No change in 
bowel 
function or 
oral intake 
 
Symptomatic; 
decreased 
oral intake; 
change in 
bowel 
function 
- 
 
- 
 
- 
 
Flatulence 
 
Mild 
symptoms; 
intervention 
not indicated 
Moderate; 
persistent; 
psychosocial 
sequelae 
- 
 
- 
 
- 
 

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Appendix IV 4 point Likert scale questionnaire 
Name _ 
 
Study ID Number 
 
A. How would you rate the severity of abdominal pain experienced during the past 3 
weeks? 
0. 
1. 
2. 
3. 
None 
Mild 
Moderate 
Severe 
B. How would you rate the severity of abdominal bloating experienced during the past 
3 weeks? 
0. None 
1. Mild 
2. Moderate 
3. Severe 
C. How would you rate the severity of flatulence/gas experienced during the past 3 
weeks? 
0. None 
1. Mild 
2. Moderate 
3. Severe 
D. How would you rate the severity of diarrhea experienced during the past 3 weeks? 
0. 
1. 
2. 
3. 
None 
Mild 
Moderate 
Severe 
E. Do you consider your symptoms have improved since starting the study drug? 
(Only fill if you have received the study drug) 
0. Yes 
1. No 
See reference: 
Pimentel, Mark et al.: Rifaxmin therapy for patients with irritable bowel syndrome without constipation. 
The New England Journal 2011; 364:22-32. 
 
 

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Appendix V 
Bristol Stool Scale and Stool Diary 
See Reference: 
Lewis, SJ et al. Stool form scale as useful guide to intestinal transit time. Scandinavian Journal of 
Gastronenterology. (1997) 32: 920-924. 

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See Reference: 
Vazquez-Roque et al. A Controlled trial of gluten-free diet in patients with irritable bowel syndrome-diarrhea: effects on 
bowel frequency and intestinal function. Gastroenterology (2013) 144(5), 903-911. 
https://doi.org/10.1053/j.gastro.2013.01.049 

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