PDF file - 55K, Kaplan-Meier estimates of (a) overall survival, (b) progression-free survival by NRAS and ERK cluster status.

Organoids contain few or no stroma component and when reinjected in mice originated tumors resembling the corresponding PDXs.

Baseline characteristics of the 349 enrolled patients.

PDF file - 65K, REMARK Flow Chart of E2303 translational research study.

PDF file - 64K, Summary of Biomarker AQUA Scores at Baseline.

PDF file - 67K, Odds Ratio and Hazard Ratio (with 95% Confidence Interval) with A Unit Increase in the Form of log10 Transformation in AQUA Scores by Biomarker.

PDF file - 81K, Primary antibodies Used for Immunohistochemistry.

Background Immune checkpoint inhibitors have revolutionized cancer treatment, but the benefits in refractory patients with esophageal cancer have been modest. Predictors of response as well as new targets for novel therapeutic combinations are needed. In this phase 2 clinical trial, we tested single-agent pembrolizumab in patients with advanced esophageal cancer, who received at least one prior line of therapy. Methods Pembrolizumab 200 mg every 3 weeks was tested in 49 patients with refractory esophageal cancer: 39 with adenocarcinoma and 10 with esophageal squamous cell carcinoma. Major endpoints were radiological response by Immune-related Response Evaluation Criteria In Solid Tumors and survival. Tumor samples were evaluated for programmed cell death ligand 1 (PD-L1) expression, tumor mutational burden (TMB), and immune contexture by both NanoString mRNA expression analysis and flow cytometry. Peripheral blood mononuclear cells and a panel of circulating chemokines were also analyzed. Results The overall response rate (ORR) was 8% (4 of 49 patients; 95% CI 2.3% to 19.6%). Median overall survival (OS) was 5.8 months (95% CI 4.0 to 9.5). ORR and OS were not associated with histology. For PD-L1-positive patients, ORR was 13.3% (95% CI 1.7% to 40.5%) and median OS was 7.9 months (95% CI 4.7 to 15.5). A trend toward improved OS was observed in seven patients with a TMB ≥10 mut/Mb (p=0.086). Tumors with a PD-L1 Combined Positive Score ≥1 showed enrichment of LAG3 (p=0.005) and IDO1 (p=0.04) gene expression. Baseline levels of circulating CXCL10, interleukin 2 (IL2) receptor α (IL2RA) and IL6 were associated with survival: CXCL10 favorably, (HR 0.37, p=0.002 (progression-free survival); HR 0.55, p=0.018 (OS)); IL2RA and IL6 unfavorably (HR 1.57, p=0.020 for IL6 (OS); HR 2.36, p=0.025 for IL2RA (OS)). Conclusions Pembrolizumab monotherapy was modestly effective in refractory esophageal cancer. Circulating CXCL10 at baseline appeared to be a robust predictor of response. Other T cell exhaustion markers are upregulated in PD-L1-positive patients, suggesting that immunotherapy combinations such as anti-LAG3/programmed cell death protein 1 (PD-1) or anti-IDO1/PD-1 may be of promise in refractory esophageal cancer.

11029 Background: In recent years, genomic profiling has become standard of care for several gastrointestinal (GI) cancers. In addition to standard of care indications, comprehensive genomic profiling has led to novel and expanded applications of targeted therapy, chemotherapy, and immunotherapy and facilitated identification of potential clinical trials. A GI molecular tumor board (MTB) was developed with a goal of improving understanding of the biological effects of genomic alterations and their therapeutic implications to enhance personalized therapy. Methods: Foundation Medicine (FM) collaborated with physicians in the GI oncology group of an academic medical center to develop a GI MTB starting March 2019. As of December 2019, 27 GI oncology cases were presented where FoundationOneCDx testing was performed and a clinical question was posed. Cases were discussed by faculty, fellows, research staff, and a clinical genomic scientist and oncologist from FM. Impacted signaling pathways and biomarkers were discussed for each case alongside clinical content so that physicians could consider therapeutic options and clinical trials. Presenting faculty were asked to complete a questionnaire for each case presented to assess the impact of the MTB discussion on clinician knowledge and patient-level treatment recommendations. Results: Of 27 questionnaires sent to 7 providers, 17 (63%) were completed. Respondents indicated that as a result of the MTB, the treatment plan was changed in 2 cases (12%), reinforced in 9 cases (53%) and in 6 cases (35%) there was no effect. On a Likert scale of 1-4 where 1 is “rare/poorly” and 4 is “great” mean scores were as follows: Did this MTB help you understand the biological effects of the main genomic alteration(s) reported in the case presented? 3.3. Did this MTB help you understand the possible therapeutic implications of the main genomic alterations in the case presented? 3.3. Did this MTB improve your understanding of the role of next generation sequencing and comprehensive genomic profiling in making treatment decisions? 3.4. Conclusions: The results of our questionnaire indicate that treatment decisions were changed in a minority of cases based on the MTB. In most cases, clinical decision making was reinforced and understanding of the biological effects of genomic alterations and their therapeutic implications were improved. Based on this feedback we will continue to refine and integrate the GI MTB into clinical care for patients with GI malignancies, and share our experience locally with other disease groups.

Background/Aim: Early-stage gastric cancer has a high risk of recurrence, despite trimodality therapy with surgery, chemotherapy and radiation. To improve patient selection for adjuvant chemoradiotherapy, we evaluated the prognostic significance of immunohistochemical and genetic biomarkers in patients with resected gastric adenocarcinoma. Patients and Methods: Tumors from 119 patients were subjected to immunohistochemistry for 12 protein biomarkers, as well as next-generation sequencing. Clinical and biomarker data were available for 91 patients. Results: EBV- positive tumors and tumors with mutations had higher intratumoral CD8 tumor-infiltrating lymphocyte density (p=0.009 and p=0.017, respectively). PIK3CA mutations were correlated with VEGFA overexpression (p=0.042), while KRAS mutations and HER2 expression were mutually exclusive (p=0.036). PTEN expression univariately confirmed longer overall survival (HR=0.27; p=0.046), while there was a trend between the presence of KRAS mutations and inferior disease free and overall survival. Conclusion: PTEN protein expression and KRAS mutations may predict disease outcome in early-stage gastric cancer. These results need to be further validated in larger cohorts.

The application of genomic profiling assays using plasma circulating tumor DNA (ctDNA) is rapidly evolving in the management of patients with advanced solid tumors. Diverse plasma ctDNA technologies in both commercial and academic laboratories are in routine or emerging use. The increasing integration of such testing to inform treatment decision making by oncology clinicians has complexities and challenges but holds significant potential to substantially improve patient outcomes. In this review, the authors discuss the current role of plasma ctDNA assays in oncology care and provide an overview of ongoing research that may inform real-world clinical applications in the near future.

Abstract Gastric cancer is the world's third leading cause of cancer mortality. In spite of significant therapeutic improvements, the clinical outcome for patients with advanced gastric cancer is poor; thus, the identification and validation of novel targets is extremely important from a clinical point of view. We generated a wide, multilevel platform of gastric cancer models, comprising 100 patient-derived xenografts (PDX), primary cell lines, and organoids. Samples were classified according to their histology, microsatellite stability, Epstein–Barr virus status, and molecular profile. This PDX platform is the widest in an academic institution, and it includes all the gastric cancer histologic and molecular types identified by The Cancer Genome Atlas. PDX histopathologic features were consistent with those of patients' primary tumors and were maintained throughout passages in mice. Factors modulating grafting rate were histology, TNM stage, copy number gain of tyrosine kinases/KRAS genes, and microsatellite stability status. PDX and PDX-derived cells/organoids demonstrated potential usefulness to study targeted therapy response. Finally, PDX transcriptomic analysis identified a cancer cell–intrinsic microsatellite instability (MSI) signature, which was efficiently exported to gastric cancer, allowing the identification, among microsatellite stable (MSS) patients, of a subset of MSI-like tumors with common molecular aspects and significant better prognosis. In conclusion, we generated a wide gastric cancer PDX platform, whose exploitation will help identify and validate novel “druggable” targets and optimize therapeutic strategies. Moreover, transcriptomic analysis of gastric cancer PDXs allowed the identification of a cancer cell–intrinsic MSI signature, recognizing a subset of MSS patients with MSI transcriptional traits, endowed with better prognosis. Significance: This study reports a multilevel platform of gastric cancer PDXs and identifies a MSI gastric signature that could contribute to the advancement of precision medicine in gastric cancer.

Abstract A Phase I study of A166, a Novel Anti-HER2 Antibody-Drug Conjugate (ADC), in Patients with Locally Advanced/Metastatic Solid Tumors. Purpose: A166 is an Antibody Drug Conjugate (ADC) targeting HER2-expressing cancer cells, aiming for post trastuzumab/TDM1 population and patients with HER2 expressing cancers not commonly treated with trastuzumab and TDM1. The antibody has the same amino acid sequence as trastuzumab, and it is designed to provide uniform distribution of payload molecules, using an innovative antibody-drug linker and duostatin-5 (an MMAF derivative) as payload. This ongoing phase I, open-label, first-in-human study is evaluating the safety, pharmacokinetics (PK), and dose-limiting toxicities (DLT) of A166 to determine the Maximum-Tolerated Dose (MTD) and/or recommended phase II dose (RP2D). Methods: Patients with advance solid tumors received escalating doses of A166 (0.3, 1.2, 3.6, and 4.8 mg/kg), administered intravenously (IV) every three weeks. Patients must have had documented HER2 positivity defined as positive, or amplified on in situ hybridization (ISH) or next-generation sequencing (NGS), or HER2 expression, defined as at least 1+ by validated immunohistochemistry (IHC) test or an activating HER2 mutation. Dose escalations were guided by a Bayesian logistic regression model (BLRM). Assessments include archival tumor molecular status, PK, and efficacy by Response Evaluation Criteria in Solid Tumors (RECIST). Results: 23 subjects [median age 68 (range 50-83), 17 female, 6 male, PS 0-1], have been treated. All patients had metastatic disease: 7 breast, 7 GC/GEJ/EC; 4 CRC, 5 other (lacrimal gland, vulvar, bladder, NSCLC, and ovarian). HER2 expression was available for all 23 patients: 12 (3+), 2 (2+ and amplified), 7 (amplified), 1 (1+), and 1 (HER2 mutated), and most had received previous HER2 targeted therapies (1-7 lines). No significant > Grade 3 AEs at doses below 3.6 mg/kg have been observed. Based on safety and efficacy outcomes, dose levels (DLs) 3.6 and 4.8 mg/kg were expanded to a total of 7 and 8 patients respectively. In these two cohorts, 4 patients experienced grade 2 ophthalmic toxicities involving the ocular surface (3 keratitis, 1 blurred vision), and 2 had Grade 3 keratitis. Treatment was discontinued (n=3) or delayed (n=3), and patients were treated with topical steroids and aggressive lubrication. All patients have resolved/resolving status of the ophthalmic toxicities, with a duration from onset to recovery/improvement of symptoms of 2-3 weeks. Other common drug-related and reversible Grade 1-2 AEs include blurry vision (n=4), peripheral neuropathy (n=3), anemia (n=2), leukopenia (n=2), thrombocytopenia (n=2). No cardiac or liver toxicities have been noted. Preliminary response assessment found that efficacy is evident at DL 3.6 and 4.8 mg/kg. Of 8 evaluable patients at 3.6-4.8 DL, 4/8 had PR, and 6/8 had DCR. Among PRs, 3 had prior anti-HER2 therapies, including 2/3 with prior TDM1. Conclusion: A166 has been well tolerated and shows promising anti-tumor activity in patients with heavily pre-treated HER2-positive cancers. The ophthalmic AEs have been reversible and manageable with supportive management. A detailed regimen for early diagnosis and intervention has been developed to further investigate the management of these toxicities in future cohorts, and three additional dose levels (6.0, 7.2, 8.4 mg/kg) will be added to the escalation phase. Citation Format: Diana M Lopez, Minal Barve, Judy Wang, Andrea J. Bullock, Eirini Pectasides, Ulka Vaishampayan, Alexander I. Spira, Susanna Ulahannan, Amita Patnaik, Rachel E. Sanborn, Dragan Cicic, Qiuqing Ang, Gregory Bergonio, Jordi Rodon Ahnert. A phase I study of A166, a novel anti-HER2 antibody-drug conjugate (ADC), in patients with locally advanced/metastatic solid tumors [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B005. doi:10.1158/1535-7163.TARG-19-B005

e16072 Background: There are limited treatment (tx) options for metastatic esophageal cancer patients (pts). We sought to determine the safety and efficacy of pembro among US pts with previously treated metastatic esophageal cancer. Methods: Eligible pts had metastatic esophageal cancer, or Sievert type 1 GEJ adenocarcinoma (ADC), ECOG of 0 or 1, and had progressed on at least 1 line of therapy. Squamous cell carcinoma (SCC) pts were enrolled on a compassionate use basis. Fresh baseline biopsy for PD-L1 and correlatives was required; patients could enroll regardless of PD-L1 status. Pembro was given at 200mg q3 weeks. Pts were restaged q9 weeks with RECIST v1.1 by independent review. Primary endpoint was overall response rate (ORR = CR+PR) among ADC pts. Results: Of 45 pts enrolled, 39 had ADC and 6 had SCC, 36 were men, median age was 62 (range 34-78), 14 pts had received 1 prior line of therapy, 17 had received 2, 10 had received 3, and 4 had received 4. 13 pts were PD-L1 positive, 25 were negative, 6 unevaluable, 1 pending. Among 44pts (1 too early), 4 PR's (9.1%) were observed, 3 with ADC and one with SCC. Duration of response was 10.6+ mo, 6.2 mo, 5.8 mo, and 2.3 mo, with PD-L1 H-scores of 220, 10, 6, and 0, respectively. 9 pts (20%) had stable disease. 11 pts discontinued pembro prior to restaging but are included in this analysis. Only 3 pts (7%) had grade 3-4 toxicity attributed to pembro: one grade 3 pneumonitis, one grade 4 myasthenia gravis, and one grade 3 joint pain. There were no treatment related deaths. We are currently evaluating immunologic correlates of response, profiling pre-treatment biopsies and on-treatment biopsies using flow cytometry and gene expression analysis. Conclusions: Pembro is active in US pts with previously treated metastatic esophageal cancer. The safety profile is similar to other studies with this agent. Supported by Merck & Co, Inc. Clinical trial information: NCT02971956.ORR N = Percent 95% CI All 44 9.1 2.5-21.7 ADC 38 7.9 1.7-21.4 SCC 6 16.7 0.4-64.1 PFS N = Months 95% CI All 45 1.97 1.84-2.73 ADC 39 1.97 1.84-2.14 SCC 6 2.99 1.71- OS N = Months 95% CI All 45 5.03 3.02- ADC 39 4.67 2.73- SCC 6 Too early

Abstract Gastroesophageal adenocarcinoma (GEA) is a lethal disease where targeted therapies, even when guided by genomic biomarkers, have had limited efficacy. A potential reason for the failure of such therapies is that genomic profiling results could commonly differ between the primary and metastatic tumors. To evaluate genomic heterogeneity, we sequenced paired primary GEA and synchronous metastatic lesions across multiple cohorts, finding extensive differences in genomic alterations, including discrepancies in potentially clinically relevant alterations. Multiregion sequencing showed significant discrepancy within the primary tumor (PT) and between the PT and disseminated disease, with oncogene amplification profiles commonly discordant. In addition, a pilot analysis of cell-free DNA (cfDNA) sequencing demonstrated the feasibility of detecting genomic amplifications not detected in PT sampling. Lastly, we profiled paired primary tumors, metastatic tumors, and cfDNA from patients enrolled in the personalized antibodies for GEA (PANGEA) trial of targeted therapies in GEA and found that genomic biomarkers were recurrently discrepant between the PT and untreated metastases. Divergent primary and metastatic tissue profiling led to treatment reassignment in 32% (9/28) of patients. In discordant primary and metastatic lesions, we found 87.5% concordance for targetable alterations in metastatic tissue and cfDNA, suggesting the potential for cfDNA profiling to enhance selection of therapy. Significance: We demonstrate frequent baseline heterogeneity in targetable genomic alterations in GEA, indicating that current tissue sampling practices for biomarker testing do not effectively guide precision medicine in this disease and that routine profiling of metastatic lesions and/or cfDNA should be systematically evaluated. Cancer Discov; 8(1); 37–48. ©2017 AACR. See related commentary by Sundar and Tan, p. 14. See related article by Janjigian et al., p. 49. This article is highlighted in the In This Issue feature, p. 1

Background: To identify predictive markers for responders in lapatinib-treated patients and to demonstrate molecular changes during lapatinib treatment via cell-free genomics. Patients and methods: We prospectively evaluated the efficacy of combining lapatinib with capecitabine and oxaliplatin as first line neoadjuvant therapy in patients with previously untreated, HER2-overexpressing advanced gastric cancer. A parallel biomarker study was conducted by simultaneously performing immunohistochemistry and next-generation sequencing (NGS) with tumor and blood samples. Results: Complete response was confirmed in 7/32 patients (21.8%), 2 of whom received radical surgery with pathologic-confirmed complete response. Fifteen partial responses (46.8%) were observed, resulting in a 68.6% overall response rate. NGS of the 16 tumor specimens demonstrated that the most common co-occurring copy number alteration was CCNE1 amplification, which was present in 40% of HER2+ tumors. The relationship between CCNE1 amplification and lack of response to HER2-targeted therapy trended toward statistical significance (66.7% of non-responders versus 22.2% of responders harbored CCNE1 amplification; P = 0.08). Patients with high level ERBB2 amplification by NGS were more likely to respond to therapy, compared with patients with low level ERBB2 amplification (P = 0.02). Analysis of cfDNA showed that detectable ERBB2 copy number amplification in plasma was predictive to the response (100%, response rate) and changes in plasma-detected genomic alterations were associated with lapatinib sensitivity and/or resistance. The follow-up cfDNA genomics at disease progression demonstrated that there are emergences of other genomic aberrations such as MYC, EGFR, FGFR2 and MET amplifications. Conclusions: The present study showed that HER2+GC patients respond differently according to concomitant genomic aberrations beyond ERBB2, high ERBB2 amplification by NGS or cfDNA can be a positive predictor for patient selection, and tumor genomic alterations change significantly during targeted agent therapy.