bluuebunny/crossref_metadata_2025 huggingface dataset:
Personalized neoantigen DNA vaccines expand tumor-specific T cells in the periphery which infiltrate the tumor in hepatocellular carcinoma.
Authors: Perales Renzo , Yarchoan Mark , Cooch Neil , Sardesai Niranjan , Perales-Puchalt Alfredo
Published: June 2022

2638

Background: Tumor neoantigens are epitopes derived from tumor-specific mutations that can be incorporated in personalized vaccines to prime T cell responses. DNA vaccines delivered with electroporation have recently shown strong CD8 and CD4 T cell responses in clinical trials. In preclinical studies, DNA-encoded neoantigen vaccines have shown induction of CD8 T cells against 50% of predicted high affinity epitopes with the ability to impact tumor growth. Methods: Paired blood and tumor biopsy samples were collected from a patient with hepatocellular carcinoma before and after treatment with GNOS-PV02 (DNA neoantigen targeted vaccine) + plasmid IL-12 + pembrolizumab. Treatment resulted in a partial response with a decrease in tumor size of 44% by RECIST (168 mm to 94 mm). TCRbeta sequencing was performed on all 4 samples and single cell TCR and transcriptome sequencing was performed from T cells isolated from the post-treatment blood sample. Newly identified TCRs in blood and tumor after vaccination were inserted into an expression vector and used to generate engineered TCR T cells. Engineered TCR T cells were tested against the neoantigens included in the vaccine and their responses characterized by flow cytometry. Results: We identified 67,893 new clones in PBMC after vaccination, 3 of which comprised between 0.1 to 1% of the total T cell clones. Moreover, we identified 5126 new clones in the tumor post vaccination, out of these, 3878 (75.68%) were not found within the patient’s pre vaccination PBMCs and 556 (10.86%) were identified within the pre vaccination PBMC pool. Importantly, of the newly identified T cells infiltrating the tumor post vaccination, we observed high frequency TCR clones of which 44 and 7 clones were above 0.1% and 1%, respectively. The majority of the newly identified T cell clones were CD8 T cells (68.75%) with an activated phenotype. Importantly, the 6 most expanded clones in blood were identified to be activated CD8+CD69+ T cells (81.82%). Engineered TCR T cells generated encoding the TCRs of these newly identified CD8 T cells showed activation when exposed to the tumor neoantigens encoded in the neoantigen DNA vaccine GNOS-PV02. Conclusions: GNOS-PV02, a neoantigen DNA vaccine, in combination with plasmid IL-12 and pembrolizumab resulted in expansion of newly identified T cells, primarily activated CD8, which trafficked to the tumor. These new tumor infiltrating T cells showed TCR specificity against tumor neoantigens encoded in GNOS-PV02 and may account for the observed objective decrease in tumor size.
First-in-human/phase I trial of PE0116 (4-1bb Ig G4 McAb) as single agent in patients with solid tumors progressed after lines of therapies in China.
Authors: Zhao Hui , Gong Yabin , Zhan Xianbao , Jiang Haiping , Zhou Karl , Liu Tianshu
Published: June 2022

2640

Background: The 4-1BB co-stimulatory protein is an important modulator of the adaptive T Cell immune responses, and potentially a vital target for immunotherapies in oncology. HE0116 is a humanized agonist antibody to 4-1BB that promotes proliferation and activation of T cells. The FIH/phase Ia/Ib study was conducted to establish a maximum tolerated dose, identify dose-limiting toxicities (DLTs) and to assess safety, tolerability, and pharmacokinetics of HE0116 as single agent in patients with solid tumors who have progressed on standard of care (SoC) and experimental therapies. Methods: Patients (pts) with histologically confirmed solid tumors who progressed after prior SoC and experimental therapies were enrolled. A Fibonacci 3+3 design was employed for the phase 1a dose escalation of 9 dose levels. HE0116 was administered intravenously once in first 28-day cycle for PK analysis and DLT assessment. Pts continued HE0116 treatment every 3 weeks until experiencing an intolerable toxicity, disease progression or withdrawing consent. Results: As of January 25, 2022, 19 pts were enrolled in the dose-escalation phase). All pts had progressed on multiple lines of therapies, including but not limited to, chemotherapy, hormonal therapy, or/and immunotherapy. As defined in study protocol, pts received HE0116 intravenously at least once at six dose levels: 0.03 mg/kg (n = 1), 0.1 mg/kg (n = 3), 0.3 mg/kg (n = 3), 1 mg/kg (n = 4), 2 mg/kg (n = 3), and 3 mg/kg (n = 5). One DLT of Grade (g) 4 platelets decrease was reported at 3 mg/kg, thus 3 new pts were added at this dose. The grade1 and grade2 HE0116 related adverse events (AEs) per CTCAE v5 that occurred ( < 10% frequency) were ALT and AST increase, platelet decrease, WBC decrease, anemia, hypokalemia, hyponatremia, hypoalbuminemia, hypothyroidism, or bone pain. Three SAE were reported: 1 g2 ascites, 1 g4 dyspnea, 1 g2 fever. To date there was one iPR at 1 mg/kg for a pt with advanced ovarian cancer with liver met after 6 cycles of treatment, and 4 iSD (1 in 2 mg/kg, 3 in 3 mg/kg) were recorded. Conclusions: HE0116 administrated intravenously every 3 weeks is well tolerated with minimal toxicities. Preliminary data are very encouraging as single agent HE0116 showed durable responses with 1 iPR, 4 iSD in several difficult to treat late-stage cancer pts. Dose escalation is ongoing as per study protocol. Phase II in select patient populations, and clinical investigation of the combination of HE0116 with CTLA-4 or PD-1 are warranted. Clinical trial information: CTR20201794.
Dysthyroidism during immune checkpoint inhibitors is associated with improved overall survival in solid tumors: Data-mining of 1,382 electronic patient records.
Authors: Beaufils Mathilde , Amodru Vincent , Tejeda Manuel , Chanez Brice , Chretien Anne Sophie , Gravis Gwenaelle , Madroszyk Anne , Goncalves Anthony , Lisberg Aaron E. , Olive Daniel , Tassy Louis , Castinetti Frédéric , Rochigneux Philippe
Published: June 2022

2659

Background: Medical treatment of solid tumors cancer has irreversibly changed since the development of immune checkpoint inhibitors (ICI). However, immune-related adverse events (irAE) are challenging in routine practice. Dysthyroidism is the most common endocrine irAE and small series suggest that dysthyroidism might be associated with ICI efficacy. This led us to explore the association between ICI-induced dysthyroidism and overall survival (OS) in a large cohort of solid tumor patients (pts) using data mining of electronic patient records (EPR). Methods: ConSoRe is a new generation data analytics solution using natural language processing to search aggregated data and perform advanced data mining. It was used for data extraction from EPR of pts treated with ICI for solid tumors in Institut Paoli-Calmettes (Marseille Cancer Center, France), with validation using manual screening of 28.8% EPR. All dysthyroidism were verified and only dysthyroidism ICI-induced were retained. Survival analyses were performed by Kaplan-Meier method and compared using the log-rank test (survminer R package). In the uni/multivariate analysis, the Cox proportional-hazards model was used to estimate the variables associated with OS, using hazard ratio (HR) and its associated 95% confidence interval. Results: Data extraction identified 1,385 pts treated with ICI in 2011-2021. Dysthyroidism was observed in 90 pts (6.5%), including 22 hyperthyroidism (24%), 36 hypothyroidism (40%) and 32 hyperthyroidism and hypothyroidism (36%). In this cohort, 81 % of the dysthyroidism were related to PD(L)-1 inhibitors and 19 % to CTLA-4/PD(L)-1 inhibitors combination. No statistical difference was observed in term of tumor location between patients with or without dysthyroidism. Dysthyroidism was associated with improved OS (HR=0.46, 95%CI 0.29-0.70, p=0.0005) with a median OS of 65 months (mo) vs. 30 mo in patients without dysthyroidism. Survival impact of dysthyroidism was consistent using a 2-mo landmark analysis, fixed on median time to dysthyroidism. In multivariate analysis including sex, age, tumor localization, line numbers and type of ICI, dysthyroidism was independently associated with an improved OS (HR=0.49, 95%CI 0.32-0.75, p=0.001), as presented in the Table. Conclusions: Data mining identified a large number ICI-induced dysthyroidism, associated with an improved OS. The onset of dysthyroidism might help oncologist detecting patients more likely to benefit from ICI. [Table: see text]
The impact of pembrolizumab on patients with pre-existing autoimmune diseases.
Authors: Bazerbashi Noor , Muhsen Ibrahim , Burns Ethan , Abdelrahim Maen
Published: June 2022

2660

Background: Immune checkpoint inhibitors (ICI) have changed the therapeutic landscape across a range of solid and hematologic malignancies. With the mechanistic activation of the adaptive immune response and known unique development of immune-related adverse effects (irAE), there is a theoretical risk of causing detrimental effects on patients with pre-existing autoimmune diseases (AID). However, this patient population was excluded from many clinical trials, and there is limited and conflicting retrospective data speculating upon the impacts of using ICI therapy in patients with AID. This study aims to report the impact of pembrolizumab in patients with AID. Methods: Patients who received pembrolizumab for treatment of any type of cancer between 1/1/2017-8/1/2021 were retrospectively reviewed, and patients with AID (rheumatologic or non-rheumatologic) were identified. Data including age, gender, race, ECOG, and primary cancer diagnosis were collected. AID was characterized by type, activity (symptomatic vs. asymptomatic at ICI initiation), and immunosuppressive treatment (IST) use. Outcomes included flare of AID, irAE, and ICI discontinuation. Results: Out of 810 patients, 12 with pre-existing AID were found and being treated for non-small cell lung cancer (NSCLC) (58% N=7), renal cell carcinoma (RCC) (16.6% N=2), colorectal cancer (CRC) (8% N=1), head and neck cancer (8% N=1), and cervical cancer (8% N=1). Around 67% of these patients were females with a median age of 65 years (50-77). Median ECOG was 1 (0-2). 9 patients (75%) had rheumatologic disease (5 rheumatoid arthritis (RA), 1 systemic lupus erythematosus (SLE), 2 psoriatic arthritis, and 1 systemic sclerosis (SS)). 3 patients (25%) had non-rheumatologic AID (1 multiple sclerosis (MS), 1 autoimmune hepatitis, and 1 Evan’s syndrome). All patients were asymptomatic prior to initiation of therapy. At the time of ICI initiation, 11 patients (92%) were on therapy, including steroids, methotrexate, and other IST. Due to concern for severe flare, pembrolizumab was discontinued in 3 (25%) MS, RA, and SS patients treated for RCC, CRC, and NSCLC, respectively. 3 patients (25%) developed irAE unrelated to their AID (pneumonitis, dermatitis, arthritis, gastritis) and received steroids. 4 patients (33.3%) had documented flares while on pembrolizumab requiring escalation of their ongoing therapy, and 1 NSCLC patient had a severe exacerbation of SS requiring cyclophosphamide and rituximab infusions. Conclusions: This analysis adds to the limited available literature that patients with an AID and on IST appear to have minimal AID-associated flares requiring intervention and tolerate pembrolizumab with a similar rate of irAE compared to patients without AID. Additional larger studies are needed to assess the efficacy of treatment in this population.
Immune-related adverse effects of long-term PD-1/PD-L1 inhibtor treatment.
Authors: Kim Sarah , Colevas A. Dimitrios , Tse Stephanie , On Sandy , Cheung Edna
Published: June 2022

2661

Background: Immune-related adverse effects (irAE) are autoimmune-like toxicities caused by immune checkpoint inhibitor (ICI) treatment and often necessitate interventions such as corticosteroids, treatment interruptions/discontinuation, or hospital admission. Although ICI related irAEs are well described in literature, data on the toxicity profile associated with long-term ICI use remains limited. Since the optimal duration of therapy with ICI agents is currently unknown, it is crucial to assess the risks of long-term ICI use. Methods: This was a retrospective, observational, single-center study of adult oncology patients who received at least 1 year of programed death 1 (PD-1) inhibitor or programmed death ligand-1 (PD-L1) inhibitor treatment. The objective of this study was to characterize late-onset irAEs defined as greater than 1 year with long-term ICI treatment. Clinically significant irAEs were defined as those requiring corticosteroid treatment, hospital admission, treatment interruption or treatment discontinuation. This study included patients who received at least 1 year of nivolumab, pembrolizumab, atezolizumab or durvalumab between January 2016 and September 2021. Disease states included head and neck cancer, renal cell carcinoma, non-small cell lung cancer, and melanoma. Patients with concurrent exposure to other treatment such as chemotherapy, radiation, surgery, tyrosine kinase inhibitors and monoclonal antibodies while on ICI treatment were included in the study. Exclusion criteria included patients with treatment breaks of greater than 6 months, two malignancies undergoing active treatment, and treatment administration outside of the study center. Results: Of 282 patients assessed, 143 met study inclusion criteria. The median ICI treatment duration was 19 months (IQR 14-27). There was a 30% incidence of late-onset irAEs, of which 22% were clinically significant. Most late-onset irAEs were low in severity, as 45 (90%) were grade 1-2 and 5 (10%) were grade 3. The most common late-onset irAEs were pulmonary (8%) and gastrointestinal (7%). Univariate analysis suggests risk factors potentially associated with late-onset irAEs include concurrent exposure to additional therapies during ICI treatment and past medical history of rheumatologic disease. Conclusions: Although the optimal duration of ICI therapy is unknown, this study suggests that long-term ICI use was associated with a low but notable incidence of toxicities, of which most were low in severity. [Table: see text]
Immune checkpoint inhibitor–induced diabetes mellitus across NCI trials.
Authors: Quandt Zoe E. , Hill Vanessa , Dib Joe E. , Burian Jason , Tessler Sapir , Naqash Abdul Rafeh , Anderson Mark S , Othus Megan , Sharon Elad
Published: June 2022

2668

Background: Immune checkpoint inhibitors (CPI) are known to rarely cause new onset diabetes (CPI DM). While rare, this adverse event is quite challenging for patients and clinicians to manage. Therefore, it is important to identify risk factors and clinical characteristics. This is the first comprehensive, multi-institutional study of CPI-DM across multiple agents and cancer types. Methods: The NCI Cancer Therapy Program (CTEP) database of adverse events (AEs) was queried for AEs related to diabetes (Grade 3 or 4 hyperglycemia, Acidosis including Diabetic Ketoacidosis (DKA), glucose intolerance and diabetes mellitus) among 6,925 patients who had been treated with a PD-(L)1 inhibitor alone or in combination from 6/2015 to 12/2019. Each AE report was reviewed and classified as due to CPI DM, new onset type 2 diabetes mellitus (T2DM), T2DM exacerbation without medication non-compliance, existing DM with medication non-compliance, or association with steroids (SDM). CPI DM was diagnosed based on: evidence of insulin deficiency either through presentation in DKA or low c-peptide with need for long term basal bolus insulin to maintain euglycemia and/or positive islet autoantibodies. Results: In total, there were 82 cases with at least one of these AEs; 41 had CPI-DM, 22 had SDM, 1 had new T2DM, 4 had T2DM exacerbation, 3 had medication noncompliance and 11 had acidosis not attributable to diabetes or had insufficient data. After excluding non-hyperglycemic acidosis, 57.8% had CPI-DM. Furthermore, if not on steroids and in good compliance with diabetes medications, 89.1% had CPI-DM. The incidence of CPI-DM was 0.59%; it was most common on combination PD-1/CTLA-4 inhibitor therapy (0.85%, 15/1767), followed by PD-(L)1 inhibitor monotherapy (0.54%, 18/3354), followed by CPIs combined with additional agents including chemotherapy and targeted agents (0.44%, 8/1804)(p = 0.25). Hospitalization was required for 87.5% of CPI-DM cases with 74.3% of those requiring an inpatient endocrine consult. All but one CPI-DM case had an endocrine consult at as either an inpatient or outpatient. Conclusions: While rare, this cohort shows the large health care burden of CPI-DM and that any hyperglycemia, and especially marked hyperglycemia, should be treated as CPI-DM until proven otherwise. [Table: see text]
A phase Ia/Ib study of CBP-1008, a bispecific ligand drug conjugate, in patients with advanced solid tumors.
Authors: Wu Lingying , Shen Lin , Hu Xichun , Li Ning , Liu Dan , Zhang Jian , Huang Robert , Teng Yan , Li Li , Zhang Bin , Zhang Youzhong , Huang Yi , Wang Ying , Wu Junyan , Zheng Yulong , Luo SuXia , Ba Yi , Tong Zhongsheng , Wang Xian , Lou Ge
Published: June 2022

3000

Background: Folate receptor α (FRα) and vanilloid subfamily member 6 of transient receptor potential channels (TRPV6) are overexpressed in many solid tumors hence could be promising therapeutic targets. CBP-1008 is a first-in-class bi-specific ligand drug targeting FRα and TRPV6 carrying monomethyl auristatin E (MMAE) as payload. Here we report the first-in-human, multicenter, phase Ia/Ib study designed to explore the safety, pharmacokinetics and efficacy of CBP-1008 in advanced solid tumors. Methods: CBP-1008 was administered by intravenous infusion. Phase Ia study included a dose-escalation period initiated by accelerated titration (0.015, 0.03mg/kg d1,15; q28d) and then switched to 3+3 scheme (0.12, 0.15, 0.17, 0.18mg/kg d1,15; q28d) and a dose expansion period. Phase Ib clinical expansion study included 3 cohorts, platinum-resistant ovarian cancer (OC), metastatic triple negative breast cancer (TNBC) and other solid tumors. The primary objective was to assess the safety and preliminary efficacy. Results: As of January 13, 2022, 106 patients received at least one dose of study drug were enrolled (phase Ia: n = 30; phase Ib: n = 76) and received median 3 prior regimens. Included tumor species were OC (n = 52), TNBC (n = 20), ER+/Her2+ breast cancer (BC) (n = 16), lung cancer (n = 3), pancreatic cancer (n = 2) and others (n = 13). In phase Ia study, DLTs were observed in 3 patients (0.12, 0.15, 0.18mg/kg, n = 1 each), including grade 4 hypophosphatemia, neutropenia, febrile neutropenia, and grade 3 hyperglycemia, alanine aminotransferase (ALT). MTD was not yet reached. Majority of adverse events were mild to moderate. The most common grade 3/4 treatment-emerging adverse events (TEAEs) were neutropenia (37.7%), AST elevation (6.6%), ALT elevation (5.7%), hyperglycemia (2.8%), hypohemoglobinemia (2.8%) and nausea (1.9%). Drug-related death was not observed. A total of 69 patients at dose of 0.15mg/kg or above were evaluable for efficacy assessment. There were 11 patients achieved partial response (PR) (OC n = 8, ER+/Her2+ BC n = 2, TNBC n = 1) and 30 patients achieved stable disease (SD). In 32 advanced platinum-resistant OC patients with FRα and/or TRPV6-positive expression, 6 PR and 16 SD were observed. Moreover, 6/18 PR (33.3%) and 8/18 SD (44.4%) were observed in enriched OC patients who showed high score of FRα/TRPV6 receptor. Conclusions: The preliminary results showed that CBP-1008 has manageable safety profile. Antitumor activity was observed in patients with FRα/TRPV6 receptor expression, especially in platinum-resistant OC cohort with high score of the two receptors. Clinical trial information: NCT04740398.
A phase Ia/Ib, dose-escalation/expansion study of the MDM2–p53 antagonist BI 907828 in patients with solid tumors, including advanced/metastatic liposarcoma (LPS).
Authors: Gounder Mrinal M. , Yamamoto Noboru , Patel Manish R. , Bauer Todd Michael , Schöffski Patrick , Grempler Rolf , Durland-Busbice Sara , Geng Junxian , Maerten Angela , LoRusso Patricia
Published: June 2022

3004

Background: The highly potent MDM2–p53 antagonist BI 907828 showed antitumor efficacy in vivo, particularly in TP53 wild-type, MDM2-amplified de-differentiated LPS (DDLPS) patient-derived xenografts and syngeneic models. This phase I study (NCT03449381) is assessing BI 907828 monotherapy in patients with advanced solid tumors, including LPS. In Part A (dose escalation), patients received one of two BI 907828 dosing schedules: Arm A, day 1 of 21-day cycles (q3w); Arm B, days 1 and 8 of 28-day cycles. Based on previously reported results from Part A (LoRusso ASCO 2021), the MTD was 60 mg q3w and the recommended dose for expansion (RDE) was selected as 45 mg q3w. Methods: In Part B (dose expansion), patients received BI 907828 45 mg q3w. The primary endpoint was PFS. Secondary endpoints/objectives included objective response rate, overall survival, the number of patients with grade ≥3 treatment-related AEs, and PK parameters. Here, we report overall safety data and efficacy data in the subgroup of patients with advanced LPS. Results: As of January 10, 2022, 90 patients had been enrolled; 49 (54.4%) were male, 55 (61.1%)/34 (37.8%) were ECOG PS 0/1, the median number of prior systemic therapies was 2 (range, 0–11), 44 had advanced LPS (28 DDLPS, 16 well-differentiated LPS [WDLPS]). At data cut-off, 31/90 patients (34.4%) had received treatment for ≥6 months. In the 41 evaluable patients with advanced LPS, best response of PR or SD was observed in 24/27 patients with DDLPS (88.9%) and 13/14 patients with WDLPS (92.9%). Two DDLPS and 4 WDLPS patients achieved a PR; all had MDM2-amplified disease. In Part A, 5/11 DDLPS patients and 4/8 WDLPS patients have achieved PFS ≥10.5 months. In the 42 patients who received the RDE of 45 mg q3w, 18 patients (42.9%) had grade ≥3 AEs; the most common grade ≥3 AEs were neutropenia (23.8%), thrombocytopenia (21.4%), and anemia (11.9%). Seven patients (16.7%) had SAEs; the most common were thrombocytopenia (4.8%) and pyrexia (4.8%). PK analysis showed that mean plasma exposures (Cmax and AUC0-inf) increased with dose and showed no significant deviation from linearity in the dose range 10–60 mg. A correlation was observed between exposure and GDF-15 levels in plasma, as a target engagement marker. Conclusions: BI 907828 showed a manageable safety profile, high plasma exposure, target engagement and encouraging signs of antitumor activity in patients with advanced DDLPS and WDLPS. The Part B dose expansion is ongoing. Clinical trial information: NCT03449381.
Tumor agnostic efficacy and safety of erdafitinib in patients (pts) with advanced solid tumors with prespecified fibroblast growth factor receptor alterations (FGFRalt) in RAGNAR: Interim analysis (IA) results.
Authors: Loriot Yohann , Schuler Martin H. , Iyer Gopa , Witt Olaf , Doi Toshihiko , Qin Shukui , Tabernero Josep , Reardon David A. , Massard Christophe , Palmer Daniel , Lugowska Iwona , Coward Jermaine , Corassa Marcelo , Stuyckens Kim , Liao Huimin , Najmi Saltanat , Hammond Constance , Santiago-Walker Ademi E. , Sweiti Hussein , Pant Shubham
Published: June 2022

3007

Background: Erdafitinib (erda) is an oral selective pan-FGFR tyrosine kinase inhibitor approved to treat locally advanced or metastatic urothelial carcinoma (UC) in adults with susceptible FGFR3/2alt who have progressed during or after ≥ 1 line of platinum containing chemotherapy . FGFRalt are observed across a wide range of malignancies and may function as oncogenic drivers independent of the underlying tumor type. RAGNAR (NCT04083976) is an ongoing phase 2 open label, single arm tumor agnostic trial investigating the efficacy and safety of erda in pretreated adult and pediatric pts with advanced solid tumors and FGFRalt. Here, we report results from a planned IA of RAGNAR. Methods: Pts aged ≥ 6 y with advanced or metastatic solid tumors of any histology (except UC) with predefined FGFR1-4alt (mutations/fusions based on local/central test) and documented disease progression on ≥ 1 prior line of systemic therapy (tx) and no alternative standard tx received oral erda until disease progression or intolerable toxicity. The primary end point is objective response rate (ORR) by independent review committee (IRC). Secondary end points include investigator assessed ORR, duration of response (DOR), disease control rate (DCR), clinical benefit rate (CBR), PFS, OS, and treatment emergent adverse events (TEAEs). Results: As of the IA data cutoff, 178 pts were treated (median age 56.5 y [range 12-79], median 2 prior systemic tx). Only 9.0% of pts responded to last line of tx prior to study entry. ORR by IRC was 29.2% (95% CI, 22.7-36.5). Investigator assessed ORR was 26.4% (95% CI, 20.1-33.5). Responses were observed in 14 distinct tumor types, including gliomas, thoracic, gastrointestinal, gynecological, and rare tumors (Table). ORR in pts with FGFR mutations vs fusions was comparable (26.8% vs 27.0%, respectively). Median DOR, PFS, and OS were 7.1 mo (95% CI, 5.5-9.3), 5.2 mo (95% CI, 4.0-5.6), and 10.9 mo (95% CI, 7.9-14.3), respectively; DCR was 75.3% and CBR was 48.9%. All pts experienced TEAEs, including 69.1% with grade ≥ 3. Treatment-related serious TEAEs occurred in 7.3% of pts. Conclusions: RAGNAR data show, for the first time, evidence of efficacy for erda in heavily pretreated pts with a variety of hard to treat advanced FGFR+ malignancies, including glioblastoma, pancreatic, and salivary gland cancers. Safety was consistent with the known erda safety profile. Clinical trial information: NCT04083976. [Table: see text]
Expanding clinical actionability in individual patient profiles with the Molecular Oncology Almanac.
Authors: Reardon Brendan Michael , Van Allen Eliezer Mendel
Published: June 2022

3015

Background: The clinical care of oncology patients is routinely informed by tumor and inherited genetic profiles. This is accomplished by molecular pathologists synthesizing the growing body of clinical guidelines and scientific evidence that associates cancer genome alterations and therapeutic response, and applying that knowledge during case reviews. Many academic medical centers formalize this process in the form of molecular tumor boards. As the number of cases for review and literature continue to increase, there is opportunity to leverage clinical interpretation algorithms to computationally prioritize molecular features and both enhance and automate the sample contextualization process. Here, we present the Molecular Oncology Almanac (MOAlmanac) to enable the rapid assessment of tumor actionability. Methods: Molecular Oncology Almanac is an open source clinical interpretation algorithm and paired knowledge base for precision cancer medicine. It is used to rapidly characterize and identify genomic features related to therapeutic sensitivity and resistance and of prognostic relevance. This is performed by assessing not only individual genomic features (e.g. somatic variants, copy number alterations, germline variants, and fusions) but also interactions between these events as well as secondary features such as mutational burden, mutational signatures, MSI status, and aneuploidy. MOAlmanac summarizes all clinically relevant findings into a web-based actionability report. The underlying knowledge base can be accessed through our API endpoints and web browser, and entries may be recommended through either Github or our browser extension. In addition, we developed a cloud-based web portal on top of the Terra framework to increase accessibility. Results: A total of 32,108 samples from 30,607 patients across 66 cancer types received targeted sequencing to characterize somatic variants, copy number alterations, and fusions from PROFILE’s Oncopanel and were evaluated with MOAlmanac. Based on Oncopanel’s tier 1 and tier 2 criteria for clinical actionability, we observed that 8,285 samples (26%, 0 - 69% by cancer type) of patients harbored at least one alteration suggesting therapeutic sensitivity based on FDA approvals or clinical guidelines. Actionability increases to 18,117 samples (56%, 0 - 85% by cancer type) when considering an expanded set of evidence to include relationships captured from clinical trials, clinical, preclinical, and inferential evidence; consequently providing at least one therapeutic hypothesis to otherwise variant-negative patients. Conclusions: Clinical actionability of molecular tumor data was increased in individual patients by expanding the set of evidence considered. Source code and a web portal for this project are available at moalmanac.org .
Enabling circulating cell-free mRNA theranostics from PD-L1, ALK, ROS1, NTRK to transcriptomic profiling.
Authors: Yeh Chen-Hsiung
Published: June 2022

3033

Background: Circulating cell-free mRNA (cfmRNA) expression can be considered as a compendium of transcripts collected from all organs. It has the capability of integrating functional and genetic information of tissues, highlighting this analyte’s unique potential as a non-invasive biomarker in early detection, therapy selection and patient follow-up of cancer management. Plasma cfmRNA is usually made up of degraded small fragments of smaller than 200 nucleotides, very low concentration, and with different terminal modification, these properties make it difficult to detect. We have developed, validated and automated a cfmRNA clinical testing workflow for simultaneous measurement of PD-L1 expression, ALK, ROS1 and NTRK fusions. This proprietary real-time qPCR-based process is exosome-free, highly sensitive and requires only half milliliter of plasma with 72-hour turnaround. A plasma cfmRNA profiling database covering 750 genes in 9 major cancer pathways was also established with novel cancer type-specific characteristics. Methods: Circulating cfRNA was extracted from 400 uL of plasma and reverse transcribed to cDNA. The cDNA pool then served as the universal source for multi-biomarker tests. All target primer and probe sets were selected based on RNA secondary structures. Plasma PD-L1 expression, ALK, ROS1, NTRK fusions and transcriptomic profiling were performed by Circulogene CLIA/CAP-complied testing platform. Results: Limit of detection (LOD) for PD-L1, ALK/ROS1 and NTRK were 1.0 copy/uL, 17.5 copies/uL and 28 copies/uL, respectively. For scoring of PD-L1 expression, based on Keynote trials, we used the 30th percentile Ct value as cutoff in qPCR which corresponded to IHC ≥ 50% TPS; while the 66th percentile Ct value corresponded to IHC ≥ 1% TPS. PD-L1 cfmRNA was demonstrated to be an excellent surrogate marker of tissue PD-L1 protein for clinical outcomes with immunotherapy. In a global cfmRNA landscape, a functional transcriptomic databank was also established, including differential gene expression, classification, functional clustering and cancer type-specific signatures. Conclusions: Liquid biopsy qPCR tests targeting PD-L1 expression, ALK, ROS1 and NTRK fusions are commercially available and filling the gap of tissue-based assays and NGS. Our groundbreaking cfmRNA work has research, clinical, and diagnostic value, and provides greater dimensionality to the current knowledge of cfmRNA research and makes a significant jump into understanding and devising strategies to tailor cancer Dx and Rx.
Early detection of cancer using cell-free DNA (cfDNA) size analysis on a multiplexed amplicon-based next-generation sequencing (NGS) platform.
Authors: Choudhury Yukti , Pinweha Pannapa , Poh Jonathan , Lim Jing Shan , Tan Min-Han
Published: June 2022

3041

Background: Tumor-derived cfDNA fragments are observed to be shorter in length than normal cfDNA. This size (length) difference can be analyzed as a tumor-specific signal. Whole genome or probe hybridization-based NGS methods can capture cfDNA fragments of native sizes. However, amplicon-based NGS assays are not directly amenable to cfDNA size analysis due to predetermination of amplicon sizes by design. Here we present a method to extract relative distribution of cfDNA fragment lengths from a targeted amplicon-based assay and show its utility in cancer detection. Methods: The LiquidHALLMARK cfDNA assay is an amplicon-based NGS test for the sensitive detection of genomic alterations in 80 genes. Although panel design is optimized for cfDNA with average amplicon length of ̃150 bp, the consecutive tiling design of amplicons for genes with contiguously targeted regions, e.g. BRCA permits the formation of longer amplicons (> 150 bp) from physically subsequent primer pairs, provided longer template cfDNA molecules are present. Cancer samples (n = 281), clinically tested by LiquidHALLMARK during Sep 2020-Sep 2021, and healthy samples (n = 28) were included for analysis. For each sample, fragment lengths were inferred from sequencing alignment files, and binned into “short” (0-150 bp) and “long” (151-500 bp) groups. A relative “size ratio” of the total number of short vs. long fragments per sample was calculated, and examined with clinical features, plasma cfDNA concentration (cfDNA/ml) and highest mutation allele frequency (AF%), in a model to predict cancer. Results: Calculated size ratios (relative abundance of short fragments) were higher in cancer than normal samples (median 47.6 vs. 31.2, p < 0.001). Cholangiocarcinoma and colorectal cancer samples had the highest size ratios (medians: 62.9 and 60.9, respectively) in agreement with a genome-wide NGS study that profiled cfDNA sizes. Size ratios were higher in metastatic (n = 143) compared to early stage (n = 30) lung cancers (p = 0.0039), indicating a stage-dependent accumulation of shorter cfDNA fragments. Size ratio was correlated with cfDNA/ml ( r= 0.63, p < 0.01) and AF% ( r= 0.42, p < 0.01). In 20-fold cross-validation of a logistic regression model trained to predict cancer, average area under curve (AUC) was 0.82 using size ratio, 0.86 using cfDNA/ml, and increased to 0.95 with the two features combined. Conclusions: Our analysis shows that it is feasible to derive meaningful cfDNA fragment size information from amplicon-based NGS data. Importantly, relative fragment size distributions observed in cancer and healthy plasma samples by this method are concordant with alternate target capture methods. Fragment size ratios derived from relatively small, targeted amplicon panels are a novel feature that, combined with other molecular and clinical features, can enhance non-invasive methods of cancer detection.
PD-L1 is overexpressed on tumorspheres cultured from circulating cancer stem cells in patients with breast cancer.
Authors: Pizon Monika , Schott Dorothea , Pachmann Ulrich A. , Pizon Marek , Pachmann Katharina
Published: June 2022

3052

Background: Circulating cancer cells, and in particular their very rare subpopulation, circulating cancer stem cells (cCSCs), are responsible for recurrence and metastasis. The exact role of cCSCs in escape of cancer from immunosurveillance is still unknown, but recent studies revealed that enhanced PDL-1 expression in cancer stem cells is linked to immune evasion and could crucially contribute to the maintenance of CSC self-renewal. Understanding the mechanisms behind this PDL-1 overexpression in cancer stem cells is critical for developing more effective anti-PD-1/PD-L1 therapy. Therefore the aim of the study was to determine the number of tumorspheres and expression of PD-L1 on tumorspheres cultured from cCSC in breast cancer patients. Methods: 110 patients with breast cancer in different stages of disease were included in this study. The determination of circulating cancer stem cells was performed using the sphere-forming assay. Additionally anti-PDL-1 antibody staining was applied to examine PDL-1 expression on breast tumorspheres. Results: We have developed an innovative in vitro platform for detection of cCSCs from peripheral blood of cancer patients. The number of tumorspheres increased significantly with tumor progression and aggressiveness of primary tumor. Patients with metastatic disease had statistically more tumorspheres as compared to patients without metastasis (30 vs 10/100µl blood, p < 0.05). Patients with multiple metastasis had more tumorspheres compared to patients with single metastases (60 vs 30/100µl blood, p < 0.05). The number of tumorspheres was positively correlated with Ki-67, Her2 status and grade score in primary breast tumors. We observed high PDL-1 expression and their considerable heterogeneity in enriched tumorspheres. Conclusions: The number of tumorspheres cultured from peripheral blood directly reflects aggressiveness and proliferation capacity of primary tumor. The presence of tumorspheres with expression of PDL-1 might suggest their immunregulatory potential. Better understanding of the interaction between cCSCs and tumor immunology may help to identify strategies to eradicate the minor subpopulation that escapes conventional therapy attack, thus providing a solution to the problem of drug resistance and metastasis.
Tracking changes in circulating stromal cells and circulating tumor cells predicts responsiveness of new line induction in metastatic breast cancer after 1 cycle of therapy.
Authors: Adams Daniel L , Alpaugh R. Katherine , Lapidus Rena G. , Chumsri Saranya , Reduzzi Carolina , Tang Cha-Mei , Williams William , Cristofanilli Massimo
Published: June 2022

3056

Background: In metastatic Breast Cancer (mBC), Circulating Tumor Cells (CTCs) are established prognostic indicators of patients (pts) not responding to new lines of therapy and who have poor clinical outcomes. However, CTCs are typically found in < 20% of mBC pts and many pts without CTCs will also progress. Recently an inflammatory pro-tumorigenic macrophage emanating from tumor stroma (i.e. Cancer associated macrophage-like cell [CAML]) was found in > 90% of mBC pts and were also indicative of poor clinical outcomes. As CTCs & CAMLs are isolated in conjunction from a single blood sample, and both are prognostic for therapy response, we evaluated CTCs & CAMLs before and after initiation of new therapies in mBC to determine their combined prognostic/predictive values. Methods: An observational prospective 2-year multi-institutional study was undertaken to evaluate CTCs & CAMLs before, and after, induction of any new line of therapy in pts with diagnosed mBC (n = 101). Anonymized and blinded blood samples were taken at baseline (BL), prior to starting a new systemic therapy, and a 2nd sample (T1) taken after therapy initiation (̃30 days). Blood was filtered by CellSieve filtration. The quantities and subtypes of CTCs & CAMLs were analyzed based on RECIST v1.1 for progression-free survival (PFS) and overall survival (OS) hazard ratios (HRs) by censored univariate & multivariate analysis at 2 years. Results: CTCs were identified in 35% (n = 35/101) of pts at BL & 24% (n = 24/101) at T1, with a single CTC at T1 being highly prognostic for worse PFS HR = 6.2 95%CI 3.0-13.2, p < 0.001 & OS (HR = 5.1 95%CI 2.0-13.4, p = 0.002. In parallel, CAMLs were found in 93% of BL and 86% of T1 samples, and whose decreases were significantly prognostic for improved PFS (HR = 2.7, 95%CI 1.4-5.1, p = 0.006) and OS (HR = 4.4 95%CI 1.5-13.2, p = 0.018) when CTCs were absent. Overall ≥1 CTC at T1 (n = 24) had median PFS = 2.4 & mOS = 4.8 months (mos), however, in pts without CTCs plus an increase in CAMLs (n = 36) had mPFS = 5.9 & mOS = 14.1 mos, while in pts without CTCs plus a decrease in CAMLs (n = 41) had mPFS = 14.8 & mOS = 18.8 mos. Conclusions: Our data confirms that pts with persistent CTCs have the worst clinical outcomes. Further, simultaneous CAML quantification provided a new dynamic predictive blood based biomarker in pts without detectable CTCs which may be useful to better individualize therapy and improve outcomes, though future studies are need to validate these findings.
Resolution ctDx FIRST plasma assay as a companion diagnostic for adagrasib and its application to longitudinal monitoring.
Authors: Pekker Ira , Pollak Julia , Potts Kristy , Chan PuiYee , Tsai Chen-Hsun , Liao Angela , Garrison Carly , Brown Taylor , Stull Paul , Bianchi-Frias Daniella , Li Zhen , Baker Christine , Garg Kavita
Published: June 2022

3057

Background: KRAS is one of the most commonly mutated oncogenes in cancer. There is a significant need for new treatment options for patients with non–small cell lung cancer (NSCLC) harboring the KRAS G12C mutation. Adagrasib is an investigational, highly selective, oral small molecule inhibitor of KRAS G12C that has demonstrated clinical benefit in patients with KRAS G12C–mutant NSCLC and CRC. Detection of KRAS G12C in cfDNA is minimally invasive and is of benefit to NSCLC patients, many without lesions accessible by tissue biopsy testing. Methods: Resolution ctDx FIRST is a 113 gene comprehensive genomic profiling assay that identifies oncogenic alterations including substitutions, insertions, deletions, gene fusions, and homozygous deletions using targeted NGS sequencing of cfDNA. The Resolution ctDx FIRST assay is being developed as a companion diagnostic for adagrasib in NSCLC patients of the Mirati Study 849-001. Results: The LOD95 for SNVs and indels in KRAS and EGFR at a cfDNA input level of 15ng ranged from 0.34% to 0.82%. No false positives were detected in any samples from healthy donors (N = 60). A total of 230 NSCLC plasma samples were orthogonally tested using a ddPCR assay for KRAS G12C, using 76 plasma samples from Study 849-001 where KRAS G12C positive results had previously been obtained by a tissue assay, and 154 commercially procured NSCLC samples representative of the trial population. The PPA and NPA for Resolution ctDx FIRST plasma testing relative to ddPCR assay (95% CI) were 87.0% (75.1–94.6%) and 97.6% (94.1–99.4%) respectively. Of 112 Study 849-001 patients, 71 (63.4%) were tested for KRAS G12C mutations with Resolution ctDx FIRST in pretreatment plasma samples. Seventy-four commercially procured matched tissue and plasma samples were tested by Resolution ctDx FIRST and tissue assay. The PPA and NPA for Resolution ctDx FIRST plasma testing relative to tissue assay (95% CI) were 66.2% (54.0-77.0%) and 100% (94.7-100%) respectively. The detection of EGFR variants in the Resolution ctDx FIRST assay was compared to results from a ddPCR assay for each variant. A total of 165 NSCLC plasma samples generated a total of 317 comparative valid results. PPA was 100% for EGFR L858R, 88.9% for EGFR T790M, and 91.3% for EGFR Exon 19 Deletions. NPA was 97.8% for EGFR L858R, 100% for EGFR T790M, and 100% for EGFR Exon 19 Deletions. Application of the assay in longitudinally collected NSCLC and CRC patient samples will be presented highlighting changes of VAF over time including identification of oncogenes involved in emerging resistance. Conclusions: The Resolution ctDx FIRST assay offers highly sensitive, specific, and robust test results, and meets analytical requirements for clinical applications. [Table: see text]
T-cell receptor repertoire analysis based on RNA sequencing data from tumor cells and tumor-infiltrating lymphocytes.
Authors: Du Cheng , Cui Lili , Wang Meiling , Li Long , Zheng Zhendong , Liu Danni , Li Yingmei , Mu Tianhao
Published: June 2022

3058

Background: T-cell receptor (TCR) repertoire has been thought to be indicative in cancer progression and treatment response. Previous methods mainly focused on peripheral blood or fresh tumor tissue, which were sometimes logistically limited in clinical settings. Tumor-infiltrating lymphocytes (TILs), which harbored TCR characteristics, were also mingled with tumor cells (TCs), which brought hurdles in extracting TCR signals from bulk RNA sequencing data. Here we employed a set of RNA sequencing data from paired FFPE tumor samples and their micro-dissected TILs, to analyze and compare the TCR features in tumor cells and TILs. Methods: RNA sequencing data of 14 tumor cell samples and matched TILs were downloaded from NCBI-SRA (accession: PRJEB36554). Raw data were cleaned up by Trim Galore (v0.6.2). TCR clonotypes were assembled and quantified from clean fastq files by MiXCR (v3.0.4). Diversity and clonality metrics were analyzed using VDJtools (v1.2.1) and in-house Pearl scripts. Results: The median mapping rates of sequencing reads to TCR regions were 0.29% and 1.80% for TCs and TILs respectively (p = 0.00051). TCR diversity of TCs and TILs was characterized by Shannon and Simpson index respectively. The median Shannon index was 1.889 and 2.694 in TCs and TILs (p = 0.00034, unpaired Wilcoxon rank-sum test); the median Simpson index was 0.8724 and 0.9420 in TCs and TILs (p = 0.0058). Conclusions: RNA isolated from clinical FFPE samples could be used for TCR analysis. Micro-dissection of TILs could enhance TCR signals of unprocessed tumor tissues.
Frequency of practice-changing findings identified by comprehensive genomic profiling in non-myeloid hematologic malignancies.
Authors: Zhou Katherine I. , Lin Chenyu , Green Michelle , Caughey Bennett Adam , Datto Michael , Strickler John H , McKinney Matthew
Published: June 2022

3060

Background: Comprehensive genomic profiling (CGP) is increasingly used to guide management of myeloid and advanced solid malignancies, but its role in non-myeloid hematologic malignancies is less clear. Studies have found a high rate of potentially actionable variants by CGP in this population, but these do not always translate into clinical practice changes. We aimed to determine the rate at which variants found on CGP changed clinical practice. Methods: We retrospectively reviewed a cohort of 101 consecutive patients with non-myeloid hematologic malignancies at Duke, comprising a total of 105 samples that were sent for CGP by FoundationOne Heme (104) or HemeComplete (1) in 2014–2021. We identified variants of clinical significance and classified them by evidence level according to the AMP/ASCO/CAP 2017 guidelines (e.g., for therapies, level A: FDA-approved / in guidelines; B: expert consensus; C: clinical trial / FDA-approved in different tumor type; D: preclinical data). We further identified documented changes in clinical practice that occurred in direct response to CGP results. Results: Commonly cited reasons for CGP included guiding therapy selection (27), identifying resistance mutations (19), refining prognosis (14), and clarifying diagnosis (11). Of the 105 samples sent for sequencing, 92 (88%) yielded at least one pathogenic or likely pathogenic variant. CGP resulted after death in 12 patients and within 1 month of death in another 11 patients. Seventy-three out of 101 patients (72%) had at least one variant with therapy sensitizing, diagnostic, or prognostic significance (levels A–C) or associated with therapy resistance (levels A/D). While 61 patients (60%) had a therapy sensitizing variant, only 6 patients (10%) were offered a biomarker-directed therapy. In contrast, the presence of a resistance mutation led to discontinuation of current therapy or influenced future therapy selection in 9 of 13 patients (69%). The absence of a resistance mutation influenced choice of therapy in another 4 patients. Sequencing results also helped clarify a previously uncertain diagnosis in 4 patients and led to medical genetics referrals in 3 patients. Conclusions: Comprehensive genomic profiling of non-myeloid hematologic malignancies identified variants of clinical significance in 72% of patients and led to changes in practice in 22% of patients. CGP was often sent late in the clinical course. [Table: see text]