Microsatellite Unstable Tumors Research Articles

Abstract C154: Clinical, genomic, and socioeconomic factors underlying low survival rates from colorectal cancer in African American patients

Abstract Background: Colorectal cancer (CRC) patients of African ancestry (AFR) have higher incidence, higher mortality, and shorter overall survival (OS) than patients of non-African ancestry (non-AFR) in the United States. This disparity is likely due to a combination of clinical, genomic, and socioeconomic factors. We investigated real-world data of patients from a single tertiary cancer center to delineate the contribution of each of those variables. Methods: We analyzed data from 3,995 CRC patients, including 247 AFR and 3,748 non-AFR patients, diagnosed after 2014 and treated at Memorial Sloan Kettering Cancer Center. Every patient had a specimen sequenced with MSK-IMPACT, a targeted DNA sequencing assay that identifies genomic alterations in 341-505 genes. Genetic ancestry was determined using previously published methods by our group. Clinical annotations included sex, age at diagnosis (Dx), stage at Dx, and tumor location. Billing records were used to identify the type of insurance per patient and estimate their Yost Index (YI), a location-dependent socioeconomic status (SES) percentile score based on household incomes, house values, rent, poverty, education, and employment statistics. A multivariate cox proportional hazards model was used to assess the association between clinical variables (stage at Dx, age at Dx, sex, primary tumor location), genomic features (MSI status, BRAF, APC, SMAD4 alterations, chromosome 20Q amplifications), SES (YI) and OS. Propensity score matching (PSM) was performed using all features included in the multivariate model to assess outcome differences after matching for clinical, genomic, and socioeconomic variables. OS was measured in months from time of Dx to last follow-up and compared using the log-rank test. Results: AFR patients had worse OS compared to non-AFR patients (median OS: AFR, 44.9 vs. non-AFR, 64.3, p<0.001). AFR patients were younger at Dx (median 53 vs. 57 yo, p<0.001), had higher rates of right-sided tumors (41.1% vs. 30.2%, p<0.001), and less often had microsatellite unstable (MSI) tumors (5.26% vs 10.0%, p=0.014). Among microsatellite stable cases, AFR patients had a higher frequency of KRAS (57.1% vs. 44.7%, p=0.004) and a lower frequency of BRAF mutations (4.3% vs. 7.7%, p=0.069). Medicaid was more frequent among AFR patients (10.12% vs. 4.87%, p<0.001). AFR patients had lower SES (median YI 42 vs. 17, p<0.001). In a multivariate model accounting for clinical, genomic and socioeconomic features, AFR ancestry remained associated with worse outcomes (HR: 1.35, p = 0.007). AFR patients also had significantly shorter OS than the set of non-AFR patients matched for clinical, genomic, and socioeconomic features (5-yr OS was 31.6% for AFR vs 45.7% for non-AFR, log-rank p-value = 0.014). Conclusions: Colorectal cancer patients of AFR ancestry had significantly shorter OS than patients of other ancestries after accounting for basic clinical, genomic, and socioeconomic variables. Further research is needed in order to understand the causes of this disparity. Citation Format: Sharafudeen D. Abubakar, Henry Walch, Xuechun Bai, Tejiri Agbamu, Michele Waters, Kanika Arora, Farheen Shah, Christopher Fong, Justin Jee, Hannah Williams, Michael F Berger, Karuna Ganesh, Julio Garcia- Aguilar, Nikolaus Schultz, Rona Yaeger, Walid K Chatila, Francisco Sanchez-Vega. Clinical, genomic, and socioeconomic factors underlying low survival rates from colorectal cancer in African American patients [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C154.

Unique miRNA Expression Profile in MSI- and EMAST-Unstable Sporadic Colon Cancer.

MicroRNAs (miRNAs) are critical post-transcriptional gene regulators and their involvement in sporadic colon cancer (CRC) tumorigenesis has been confirmed. In this study we investigated differences in miRNA expression in microsatellite stable (MSS/EMAST-S), microsatellite unstable marked by high elevated microsatellite alterations at selected tetranucleotide repeats (MSS/EMAST-H), and high microsatellite unstable (MSI-H/EMAST-H) tumor subgroups as well as in tumors with different clinicopathologic characteristics. An RT-qPCR analysis of miRNA expression was carried out on 45 colon cancer and adjacent normal tissue samples (15 of each group). Overall, we found three differentially expressed miRNAs between the subgroups. miR-92a-3p and miR-224-5p were significantly downregulated in MSI-H/EMAST-H tumors in comparison to other subgroups. miR-518c-3p was significantly upregulated in MSS/EMAST-H tumors in comparison to stable and highly unstable tumors. Furthermore, we showed that miR-143-3p and miR-145-5p were downregulated in tumors in comparison to normal tissues in all subgroups. In addition, we showed overexpression of miR-125b-5p in well-differentiated tumors and miR-451a in less advanced tumors. This is the first report on differences in miRNA expression profiles between MSS/EMAST-S, MSS/EMAST-H, and MSI-H/EMAST-H colorectal cancers. Our findings indicate that the miRNA expression signatures differ in CRC subgroups based on their instability status.

Novel WRN Helicase Inhibitors Selectively Target Microsatellite-Unstable Cancer Cells.

Microsatellite-unstable (MSI) cancers require WRN helicase to resolve replication stress due to expanded DNA (TA)n dinucleotide repeats. WRN is a promising synthetic lethal target for MSI tumors, and WRN inhibitors are in development. In this study, we used CRISPR-Cas9 base editing to map WRN residues critical for MSI cells, validating the helicase domain as the primary drug target. Fragment-based screening led to the development of potent and highly selective WRN helicase covalent inhibitors. These compounds selectively suppressed MSI model growth in vitro and in vivo by mimicking WRN loss, inducing DNA double-strand breaks at expanded TA repeats and DNA damage. Assessment of biomarkers in preclinical models linked TA-repeat expansions and mismatch repair alterations to compound activity. Efficacy was confirmed in immunotherapy-resistant organoids and patient-derived xenograft models. The discovery of potent, selective covalent WRN inhibitors provides proof of concept for synthetic lethal targeting of WRN in MSI cancer and tools to dissect WRN biology. Significance: We report the discovery and characterization of potent, selective WRN helicase inhibitors for MSI cancer treatment, with biomarker analysis and evaluation of efficacy in vivo and in immunotherapy-refractory preclinical models. These findings pave the way to translate WRN inhibition into MSI cancer therapies and provide tools to investigate WRN biology. See related commentary by Wainberg, p. 1369.

Abstract B020: Novel WRN helicase inhibitors selectively target microsatellite unstable cancer cells

Abstract Microsatellite-unstable (MSI) cancers require WRN helicase to resolve replication stress due to expanded DNA (TA)n-dinucleotide repeats. WRN is a promising synthetic lethal target for MSI tumours, and WRN inhibitors are in development. Here, we used CRISPR-Cas9 base editing to map WRN residues critical for MSI cells, validating the helicase domain as the primary drug target. Fragment-based screening led to the development of potent and highly selective WRN helicase covalent inhibitors. These compounds selectively suppressed MSI model growth In vitro and In vivo by mimicking WRN loss, inducing DNA double-strand breaks at expanded TA-repeats and DNA damage. Assessment of biomarkers in preclinical models linked TA-repeat expansions and mismatch repair (MMR) alterations to compound activity. Efficacy was confirmed in immunotherapy-resistant organoids and patient-derived xenograft (PDX) models. The discovery of potent, selective covalent WRN inhibitors provides proof of concept for synthetic-lethal targeting of WRN in MSI cancer and tools to dissect WRN biology. Citation Format: Gabriele Picco, Yanhua Rao, Angham Al Saedi, Yang Lee, Shriram Bhosle, Carmen Herranz-Ors, Samantha Walker, Kieron May, Matthew Coelho, Jon Houseley, Benjamin Schwartz, Mathew J. Garnett. Novel WRN helicase inhibitors selectively target microsatellite unstable cancer cells [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B020.

Abstract 5942: Discovery of WRN inhibitors as targeted therapy in the treatment of microsatellite unstable (MSI-H) tumors

Abstract The synthetic lethality resulting from the inhibition of the WRN helicase protein has been observed in tumors characterized by high levels of microsatellite instability (MSI-H). This instability stems from a deficiency in the DNA mismatch repair (MMR) mechanisms, leading to the accumulation of DNA damage. This phenomenon is notably prevalent in 10-30% of colorectal, gastric, endometrial, and ovarian cancers. Specifically, the inhibition of WRN helicase activity induces DNA damage leading to cell cycle arrest and apoptosis exclusively in MSI-H cell lines. This selectivity underscores the therapeutic potential of WRN inhibitors, as they demonstrate efficacy against MSI-H cells while remaining non-toxic to microsatellite stable (MSS) cell lines. Ryvu is developing a chemical series of potent, selective WRN helicase inhibitors. Structure-based optimization facilitated the rapid expansion and delivery of a compound library with novel intellectual property (IP), demonstrating target engagement in cells and selective potency over other RecQ family members. The correlation between the cellular effect and selectivity upon treatment with these ligands was confirmed in the clonogenic assay, specifically in responder, microsatellite instable cell lines only, thereby leaving a substantial safety margin (>100x) relative to non-responder, microsatellite stable lines. Target engagement has been confirmed by dose dependent DNA damage pathway activation concomitant with WRN degradation in in vitro assays. The pharmacokinetic properties of these compounds are favorable for progressing to in vivo studies. The correlation between compound exposure and on-target effect was confirmed in PK/PD and efficacy studies in xenograft MSI-H cancer models. These data provide pharmacological proof-of-concept for the synthetic lethal effect of our inhibitors and support WRN inhibition as a new oncological therapy. Citation Format: Wojciech Schönemann, Agnieszka Ludwig-Słomczyńska, Łukasz Dudek, Marcin Król, Marco Farinone, Urszula Kulesza, Wojciech Jasnosz, Izabela Mac, Karol Zuchowicz, Katarzyna Wierzbicka, Aleksandra Buchcic-Szychowska, Andrzej Gondela, Anna Zagórska, Oliwia Matuszewska, Marta Sowińska, Marcin Nowogródzki, Marianna Girardi, Szymon Paluch, Svitlana Sukhomlinova, Agata Chłopek, Iana Levenets, Kamila Kozłowska-Tomczyk, Katarzyna Łagosz-Ćwik, Mateusz Stoszko, Szymon Woroszyło, Maciej Mikulski, Justyna Jabłońska, Magdalena Wiśniewska, Katarzyna Palus-Chramiec, Paulina Podkalicka-Gołda, Anita Janiga, Sylwia Sudoł-Tałaj, Magdalena Sieprawska-Lupa, Magdalena Miodek, Jacek Faber, Róża Starczak, Bozena Winnik, Agnieszka Świrska, Anna Kowal-Chwast, Dawid Gogola, Sanja Novak Ratajczak, Agata Dudek, Nilesh Gaud, Grzegorz Satała, Agata Stachowicz, Martin Swarbrick, Krzysztof Brzózka, Magdalena I. Zawadzka. Discovery of WRN inhibitors as targeted therapy in the treatment of microsatellite unstable (MSI-H) tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5942.

Abstract 994: Single analyte profiling of the mutational, immune and microbiome landscape in african american colon cancer patients

Abstract Colorectal cancer (CRC) disproportionately affects African American (AA) patients who experience a higher incidence and mortality than any other demographic groups in the United States. Yet molecular profiling in this population is scarce. Here, we performed whole-exome sequencing (WES) of 342 immediately snap-frozen tissues comprising AA CRC and matched, distant normal colon and identified distinct genomic drivers, DNA signatures, and, surprisingly, mosaic pathogenic mutations that are not present in the patient-matched CRC. We inferred T cell infiltration and tissue-resident microbiome (TR-M) directly from WES, enabling integrative analyses. Compared to normal colon, T cell infiltration is strongly decreased in tumours with microsatellite stability (MSS), while microsatellite unstable (MSI) and Polymerase Epsilon (POLE) mutant tumours had similar levels, suggesting immune evasion in MSS rather than increased T cell infiltration in MSI/POLE-mutants. Analyses of matched normal and tumour tissues revealed the evolving TR-M at unprecedented granularity and identified distinct niches of interactions with genomic and tumour-microenvironmental features. Together, this study represents the largest comprehensive genomic analysis of CRC in AA and provides a framework for performing a multi-layered analysis from a single analyte, thus, affording a cost-effective approach to expedite medical discoveries in underrepresented ancestries. Citation Format: Carino Gurjao, Edmond Chan, Michael J. Lee, Sho Hangai, Raul Rabadan, Tal Korem, Hanina Hibshoosh, Benjamin Izar. Single analyte profiling of the mutational, immune and microbiome landscape in african american colon cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 994.

Updates in BRAF V600E-Mutated Metastatic Colorectal Cancer

Colorectal cancer (CRC) is the third most common cancer worldwide, and the second leading cause of cancer death. Approximately one in five patients with CRC present with metastatic disease at diagnosis. The BRAF V600E mutation occurs in 8–12% of patients with metastatic colorectal cancer (mCRC), and is characterised by an aggressive clinical course and poor prognosis. This article is based on a webinar discussion in March 2024, between two experts in gastrointestinal cancers, Chiara Cremolini, University of Pisa, Italy; and Julien Taieb, Georges Pompidou European Hospital, Université Paris-Cité, France, both of whom have a wealth of experience and expertise in the clinical management of CRC. The experts described the most important recent advances in the treatment of BRAF V600E-mutated mCRC, including data presented at the European Society for Medical Oncology (ESMO) Congress in October 2023, and the American Society of Clinical Oncology (ASCO) Gastrointestinal (GI) Cancers Symposium in January 2024. Cremolini and Taieb gave valuable insights into topics such as the aggressive nature of BRAF V600E-mutated mCRC, and how this impacts choice of treatment, patient outcomes, and quality of life, as well as the importance of early testing and monitoring. The experts also discussed how the BRAF V600E mutation impacts treatment response and outcomes in patients with microsatellite unstable (microsatellite instability [MSI]) versus microsatellite stable (MSS) tumours, and recent key clinical trials in BRAF V600E-mutated mCRC. The importance of surgery in the multidisciplinary management of patients with BRAF V600E-mutated mCRC, BRAF as a prognostic marker in resected CRC, and real-world studies in this field were also explored. Finally, Cremolini and Taieb described what the future of the management of patients with BRAF V600E-mutated mCRC might look like, and which advancements in research they would like to see.

Phase 1b/II study of durvalumab (D) and tremelimumab (T) plus PET-adjudicated chemoradiation (CRT) in patients (Pts) with esophageal adenocarcinoma.

355 Background: We previously evaluated adding D, an anti-PD-L1 antibody, to PET-directed CRT and found the combination to be safe and promising in terms of pathologic response and survival outcomes.1 Here, we add T to the combination. Methods: Pts with locally advanced esophageal/GEJ adenocarcinoma were enrolled. Pts received 2 cycles of mFOLFOX6 prior to repeat PET/CT. PET responders (≥35% reduction in SUV (PETr)) received 5-FU/capecitabine and oxaliplatin with RT, while induction PET non-responders (PETnr) received carboplatin/paclitaxel with RT. All Pts received T 300 mg ×1 and D 1,500 mg q4W ×2 starting 2 weeks prior to CRT. Esophagectomy was planned 6-8 weeks after CRT. Pts with R0 resections received adjuvant T 300 mg ×1 and D 1,500mg q4W ×6. The primary endpoint was the pathologic complete response (pCR) rate. Initially, 6 Pts were enrolled to evaluate for toxicity; they received RT to 50.4 Gy. Subsequently, RT was lowered to 41.4 Gy to decrease the length of preop treatment (tx). Results: 16 pts have been enrolled. All Pts had clinical ≥T3 and/or N+ disease. PD-L1 CPS was ≥1 in 9 (60%) of 15 tested. 1 Pt (6%) had a microsatellite unstable (MSI) tumor. 9 (56%) Pts were PETr; 3 Pts (19%) were PETnr but had improved clinical symptoms and other PET parameters (MTV/TLG) and also continued with 5-FU/capecitabine and oxaliplatin during RT. Significant tx-related adverse events (AEs) are shown in the Table. Immune-related AEs (irAEs) were: gd 3 enterocolitis (1 Pt), gd 3/4 colitis (2 Pts, 12%), gd 1 diarrhea (1 Pt), gd 2 pruritis (1 Pt), gd 1 and gd 3 dermatitis (1 Pt each) and gd 2 arthralgias in 1 Pt. 1 Pt died of aspiration pneumonia while being treated for gd 4 colitis during CRT; 1 Pt developed gd 3 enterocolitis and cholecystitis during CRT, achieved a clinical CR and did not undergo surgery. He developed local recurrence and had surgery off-study 16 months after start of tx; 1 Pt developed a bone metastasis after CRT. 4 Pts are awaiting restaging post-CRT. Of 9 Pts who had surgery, 4 achieved a pCR (44%, including the MSI Pt) and 3 (33%) had ypN0 tumors and ³90% tx response. All 9 Pts have initiated/completed adjuvant D+T. Conclusions: The addition of D+T to induction FOLFOX and PET-directed CRT prior to surgery is feasible, although irAEs seem numerically higher than in our prior study of D and CRT. Pathologic response data are promising. Accrual is ongoing and updated data will be presented. 1. Ann Surg 2023;278:e511. Clinical trial information: NCT02962063 . [Table: see text]

A pilot study evaluating somatic mutational burden and signatures among endometrial cancer patients: Is there prognostic benefit to whole genome sequencing?

e17629 Background: Whole genome sequencing (WGS) has emerged as a tool to characterize mutational burden and potentially identify new therapeutic targets and predictive biomarkers. In this study, we describe the mutational landscape of diverse patients with endometrial cancer using WGS and explore associations between mutations and clinicopathologic characteristics. Methods: Patients with endometrial cancer were prospectively consented and WGS was performed on tumors and blood. Using the the New York Genome Center Cancer pipeline, we identified high confidence somatic mutations in our patient cohort (identified by 2 or more variant callers). Somatic variants were categorized into mutational signatures based on the Catalog of Somatic Mutations in Cancer (COSMIC) v2. Associations between COSMIC signatures and clinicopathologic variables were evaluated using ANOVA tests. Results: Sixteen patients with endometrial cancer were enrolled; 10 (62.5%) self-identified as White, 4 (25.0%) as Black, and 2 (12.5%) as Asian. Tumor histology was endometrioid (13, 81.3%) or serous/clear cell (2, 12.5%), with both low grade (9, 56.3%) and high grade (7, 43.8%) tumors. The most frequently mutated genes were PTEN (15, 93.8%), ARID1A (9, 56.3%), PIK3CA (9, 56.3%), and TP53 (6, 37.5%). PIK3CA mutations were found in all mismatch repair (MMR) deficient tumors (5), compared to only 30.0% (3) of patients with intact MMR mechanisms (FDR p = 0.0256). Signature 3, associated with BRCA mutations and loss of DNA double-strand break-repair by homologous recombination, was enriched in p53 mutated tumors (p = 0.0036). Signature 1, associated with age, was enriched in patients with MMR intact tumors (p = 0.0475), while signatures 6 and 20, associated with defective DNA MMR and microsatellite unstable tumors, were enriched in patients with in MMR deficient tumors (p < 0.0001 and p = 0.0022, respectively). Signature 8, of unknown etiology, was enriched in patients with MMR intact tumors, advanced disease (p = 0.0045), disease spread to lymph nodes (p = 0.0231), and disease recurrence (p = 0.0021). Signature 12, also of unknown etiology, was enriched in MMR deficient tumors (p = 0.0005) and stage 1 disease (p = 0.0235). Conclusions: WGS revealed distinct patterns of mutational burden associated with clinicopathologic variables. MMR status was associated with PIK3CA mutations and multiple mutational signatures. Mutational signature 8 was associated with multiple clinicopathologic characteristics associated with poor prognosis, suggesting utility as a biomarker. Further investigation regarding the mechanism of the mutational signatures and correlation with prognostic factors may shed light on disparate biologic endometrial cancer outcomes and serve as a source of hypothesis-generation for the development of targeted therapies.

Preoperative pembrolizumab for MSI high, EBV positive or PD-L1 positive locally advanced gastric cancer followed by surgery and adjuvant chemoradiation with pembrolizumab: Interim results of a phase 2 multi-center trial.

e16073 Background: Certain subtypes of gastric cancer are less responsive to perioperative chemotherapy. Preliminary data suggest that patients with microsatellite unstable tumors (MSI-H), EBV expressing tumors, and tumors with high PD-L1 expression may benefit from immunotherapy. This trial evaluates the benefit of PD-1 checkpoint immunotherapy in this subset of patients with operable gastric cancer. Methods: This is an interim analysis of this Phase II multicenter clinical trial (NCT03257163). Patients with clinically staged T2-T4, N0-N3, M0 gastric adenocarcinoma with MSI-H, EBV positive, or PDL1 expression with CPS>/= 1% were included. Patients receive two cycles of neoadjuvant pembrolizumab followed by gastrectomy. Postoperatively, patients receive one cycle of adjuvant capecitabine + pembrolizumab, then chemoradiation (45 Gy in 25 fractions) with capecitabine + pembrolizumab, then two cycles capecitabine + pembrolizumab, followed by 1-year total of pembrolizumab. Primary endpoint is DFS. Results: 33 patients have been enrolled (planned = 40), median age 67.5 years (range, 44 – 88 years), median follow up duration 18.1 months (range, 2.3-42.5 months). Patients were 30.3% Hispanic, 27% Asian, 24% Black, 24% White. Of the 33 patients, 12 were MSI-H, 3 EBV (+), and 27 had PDL1 expression with CPS >/= 1%. Tumors were of advanced clinical stage with 84.8% ≥ cT3 and 57.6% cN(+). All patients received two cycles of neoadjuvant pembrolizumab. Six patients did not undergo surgical resection: peritoneal disease (n=2), soft tissue metastases (n=1), locally unresectable (n=2), and frailty (n=1). Of the 27 patients who completed surgery, treatment effect was seen in 46%, down-staging in 50%, and complete pathologic response seen in 3 patients, 2 of whom has MSI-H tumors and one whose tumor was PDL1+. Two patients did not receive adjuvant therapy due to postoperative complications. A total of 20 patients have received optimal therapy as defined as postoperative RT and >/=2 cycles of adjuvant pembrolizumab. Four patients had adjuvant pembrolizumab monotherapy (after chemoradiation) stopped due to rash (n=2), pneumonia (n=1), and colitis (n=1). The estimated DFS at 24 months is 60% for the entire cohort (n=33). For the optimal therapy cohort (n=20), the DFS at 24 months is 80%. Conclusions: In this biomarker-driven cohort of operable gastric adenocarcinoma patients, results are promising for patients who receive two cycles of preoperative pembrolizumab followed by postoperative concurrent pembrolizumab with chemoradiation therapy, and chemotherapy. This study presents a novel and effective paradigm for the management of localized gastric cancer and warrants additional evaluation. Clinical trial information: NCT03257163 .

Efficacy and predictors of response of nivolumab in treatment-refractory MSI solid tumors: Results of a tumor-agnostic DRUP cohort.

2590 Background: Microsatellite unstable (MSI) tumors represent 4% of all cancer diagnoses and are known to be sensitive to immune checkpoint inhibitors (ICI). Despite the progress made, a significant proportion of patients with MSI tumors does not respond, highlighting the urgent need to identify additional predictive biomarkers. In this study, we evaluated the efficacy of the PD-1 inhibitor nivolumab across pre-treated solid MSI tumors and performed extensive biomarker analysis to better characterize ICI-effectiveness in this setting. Methods: Adult patients with MSI tumors who exhausted all standard of care treatment options were eligible for inclusion and were enrolled in the Drug Rediscovery Protocol (DRUP), a clinical trial that treats cancer patients with approved targeted- and immunotherapies outside their registered indication, based on their tumor molecular profile (NCT0295234). Patients were treated with nivolumab (four cycles of 240 mg every 2 weeks, followed by 480 mg every 4 weeks) until disease progression or unmanageable toxicity. Primary endpoint was clinical benefit (CB, objective response (OR) or stable disease ≥ 16 weeks). Whole genome sequencing and RNA sequencing were performed on pre-treatment biopsies to reveal potential predictors of response or resistance to anti-PD1. Results: 130 evaluable patients were enrolled with in total 16 different tumor types. CB was observed in 62% (95% CI 46 – 54) ( N = 80) with an OR in 45% (95% CI 53 – 70) ( N = 58). After a median follow-up of 14.5 months (95% CI 13 – 19), median progression free survival was 18 months (95% CI 9 – not reached) and median overall survival was not reached. HLA class I status and mutational burden were not significantly associated with CB. However, in depth biomarker analyses identified that mutational burden was predictive of CB in HLA-wildtype patients (52%) but not in HLA class I mutants (48%). Strikingly, in contrast to the paradigm that neoantigen-specific adaptive immunity is primarily involved in clearing MSI tumors, transcriptomics indicated that, compared to non-CB, CB was characterized by significantly higher expression of key modulators in innate immunity, including non-classical HLA transcripts (P = 4.2x10-3), NKGD2 ligands MICA/MICB (P = 6.4x10-3), killer immunoglobulin-like receptors ( P = 0.047) and butyrophilins ( P = 0.024). Conclusions: Nivolumab proved highly effective in pre-treated, advanced solid MSI tumors. Genomic analysis revealed that neoantigen burden only determined ICI-effectiveness in patients with wildtype HLA class I. Furthermore, transcriptomics revealed a central role of innate immunity in ICI-effectiveness in MSI tumors, which aligns with the fact that these tumors frequently lose HLA class I antigen presentation. Together, these results inform novel biomarker strategies to further refine precision medicine in this patient population. Clinical trial information: NCT0295234 .

Treatment with lenvatinib plus pembrolizumab in recurrent or advanced endometrial cancer: A systematic review and meta-analysis.

e17630 Background: Endometrial cancer (EC) is the second most prevalent gynecological cancer. After failure to first-line platinum-based chemotherapy, treatment options are sparse, but recent studies have investigated new approaches with promising results. We conducted a systematic review and meta-analysis to evaluate the efficacy and safety of Lenvatinib plus Pembrolizumab in patients with advanced or recurrent EC. Methods: PubMed, Web of Science, Cochrane, Scopus, and LILACS databases, Central Register of Clinical Trials, and congresses publication websites were searched for studies using Lenvatinib plus Pembrolizumab in advanced or recurrent EC with progression after platinum-based chemotherapy. Outcomes of interest were best overall response rate (BORR) and disease control rate (DCR), on intention-to-treat (ITT) and per-protocol analyses, and according to mismatch repair status. Progression free-survival (PFS) and overall survival (OS) were also assessed. Heterogeneity was examined with the Cochran Q test and I2 statistics. We use a DerSimonian and Laird random-effects model. Results: Four studies, with 637 patients, were included: two clinical trials and two retrospective observational cohorts. Endometrioid EC was the predominant histology (53%), and most patients had mismatch repair-proficient tumors (pMMR, 86.5%). In a pooled analysis, with a medium follow-up of 12.2 months, BORR was 31% (95%CI 26, 37), and DCR was 74% (95%CI 65, 83) on ITT. CR, PR, and SD were documented in 37 (5.8%),168 (26.3%) and 284 (44.5%) patients, respectively. BORR was 48% in microsatellite unstable tumors compared to 31% in stable microsatellite disease (p = 0.07), while DCR was similar in both groups (p = 0.33). Median progression-free survival was 7.2 months (95%CI 3.2, 7.4), and median overall survival was 18.3 months (95%CI 8.6, 18.3) in patients receiving Lenvatinib and Pembrolizumab. The most common treatment-related adverse events (AE) included diarrhea 277/514 (53.8%), nausea 244/514 (47.4%), hypothyroidism 288/562 (39.1%), hypertension 338/632 (36.9%), fatigue 213/632 (31.0%), and vomiting 178/514 (34.6%). Grades 3 or 4 AE was reported in 436/514 (79.6%) patients. Overall, dose reductions, treatment interruptions, and discontinuation due to toxicities were required in 61%, 63%, and 27% of patients, respectively. Conclusions: This systematic review and meta-analysis reinforce the antitumor activity of the combination of Pembrolizumab and Lenvatinib in patients with advanced or recurrent EC, regardless of MMR status. Despite high rates of serious adverse events related to treatment, most were manageable.

Cancer-specific functional profiling in microsatellite-unstable (MSI) colon and endometrial cancers using combined differentially expressed genes and biclustering analysis.

Microsatellite-unstable (MSI) cancers have distinct genetic and clinical features from microsatellite-stable cancers, but the molecular functional differences between MSI cancers originating from different tissues or organs have not been well studied because the application of usual differentially expressed gene (DEG) analysis is error-prone, producing too many noncancer-specific normally functioning genes. To maximize therapeutic efficacy, biomarkers reflecting cancer-specific differences between MSI cancers of different tissue origins should be identified. To identify functional differences between MSI colon and endometrial cancers, we combined DEG analysis and biclustering instead of DEG analysis alone and refined functionally relevant biclusters reflecting genuine functional differences between the 2 tumors. Specifically, using The Cancer Genome Atlas and genome-tissue expression as data sources, gene ontology (GO) enrichment tests were performed after routinely identifying DEGs between the 2 tumors with the exclusion of DEGs identified in their normal counterparts. Cancer-specific biclusters and associated enriched GO terms were obtained by biclustering with enrichment tests for the preferences for cancer type (either colon or endometrium) and GO enrichment tests for each cancer-specific bicluster, respectively. A novel childness score was developed to select functionally relevant biclusters among cancer-specific biclusters based on the extent to which the enriched GO terms of the biclusters tended to be child terms of the enriched GO terms in DEGs. The selected biclusters were tested using survival analysis to validate their clinical significance. We performed multiple sequential analyses to produce functionally relevant biclusters from the RNA sequencing data of MSI colon and endometrial cancer samples and their normal counterparts. We identified 3066 cancer-specific DEGs. Biclustering analysis revealed 153 biclusters and 41 cancer-specific biclusters were selected using Fisher exact test. A mean childness score over 0.6 was applied as the threshold and yielded 8 functionally relevant biclusters from cancer-specific biclusters. Functional differences appear to include gland cavitation and the TGF-β receptor, G protein, and cytokine pathways. In the survival analysis, 6 of the 8 functionally relevant biclusters were statistically significant. By attenuating noise and applying a synergistic contribution of DEG results, we refined candidate biomarkers to complement tissue-specific features of MSI tumors.

Metastatic Prostate Cancers with BRCA2 versus ATM Mutations Exhibit Divergent Molecular Features and Clinical Outcomes.

In patients with metastatic prostate cancer (mPC), ATM and BRCA2 mutations dictate differences in PARPi inhibitor response and other therapies. We interrogated the molecular features of ATM- and BRCA2-mutated mPC to explain the divergent clinical outcomes and inform future treatment decisions. We examined a novel set of 1,187 mPCs after excluding microsatellite-instable (MSI) tumors. We stratified these based on ATM (n = 88) or BRCA2 (n = 98) mutations. As control groups, mPCs with mutations in 12 other homologous recombination repair (HRR) genes were considered non-BRCA2/ATM HRR-deficient (HRDother, n = 193), whereas lack of any HRR mutations were considered HRR-proficient (HRP; n = 808). Gene expression analyses were performed using Limma. Real-world overall survival was determined from insurance claims data. In noncastrate mPCs, only BRCA2-mutated mPCs exhibited worse clinical outcomes to AR-targeted therapies. In castrate mPCs, both ATM and BRCA2 mutations exhibited worse clinical outcomes to AR-targeted therapies. ATM-mutated mPCs had reduced TP53 mutations and harbored coamplification of 11q13 genes, including CCND1 and genes in the FGF family. BRCA2-mutated tumors showed elevated genomic loss-of-heterozygosity scores and were often tumor mutational burden high. BRCA2-mutated mPCs had upregulation of cell-cycle genes and were enriched in cell-cycle signaling programs. This was distinct from ATM-mutated tumors. Tumoral ATM and BRCA2 mutations are associated with differential clinical outcomes when patients are stratified by treatments, including hormonal or taxane therapies. ATM- and BRCA2-mutated tumors exhibited differences in co-occurring molecular features. These unique molecular features may inform therapeutic decisions and development of novel therapies.

Abstract 1370: Overexpression of the small GTPase Rab27B regulates autophagy flux and contributes to tumor growth in colorectal cancer

Abstract Rab27B is a member of the Rab small GTPases that belong to the RAS-like GTPase superfamily. Rab27B has been shown to regulate endosomal trafficking, exosome secretion, and delivery of secretory granules. However, the role of Rab27B in colorectal cancer (CRC) tumor biology is unknown. Using CRC tissue microarrays, a significant upregulation of Rab27B was detected in staged adenocarcinoma compared to normal colon tissue. Interestingly, microsatellite unstable (MSI) tumors showed a higher increase in Rab27B (2.4-fold) than microsatellite stable (MSS) tumors (1.6-fold), consistent with TCGA data. To study the role of Rab27B in CRC, we targeted Rab27B in MSI HCT116 cell line by CRISPR-Cas9 deletion and siRNA knockdown. In both cases, loss of Rab27B resulted in a dysregulation of cellular autophagy and reduction in extracellular vesicle secretion. Rab27B-depleted cells showed an abnormal accumulation of autophagy vesicles and increase in autophagy markers LC3-II and p62, indicating a defect in autophagy flux. To characterize this autophagy defect, we used eGFP-mCherry-LC3 reporter, lysotracker and Cyto-ID staining to identify that autophagy flux is blocked at the autophagosome/lysosome fusion step when Rab27B is lost. To test whether the GTPase activity of Rab27B is needed for the autophagy role, we added back constitutively active and dominant negative GTPase mutants of Rab27B in Rab27B KO cells and observed autophagy phenotype rescue with only wildtype and constitutively active GTPase forms. As autophagy has been shown to have a pro-survival role in tumor growth and stress response, we hypothesized that this defect in autophagy flux resulting from Rab27B deletion will impact cellular stress response and reduce tumor growth. While Rab27B knockout (KO) cells show similar in vitro 2D-growth characteristics as wildtype cells under normal conditions, loss of Rab27B resulted in a 60% reduction in cell viability in response to starvation conditions. Similarly, a 94% reduction in colony formation was observed when grown in soft agar, along with deficiencies in spheroid formation. In vivo, Rab27B KO cells showed a major reduction (p<0.0001) in tumor growth xenografts compared to wildtype HCT116 cells. Taken together, these results demonstrate a new role of Rab27B in the autophagy trafficking process in CRC. Futures studies will focus on further characterizing the relationship among Rab27B overexpression, microsatellite instability, and autophagy in vitro and in vivo using Rab27B knockout mouse model, as well as investigating whether Rab27B can be targeted as a potential new therapeutic strategy. Citation Format: Sahida Afroz, Ranjan Preet, Vikalp Vishwakarma, Dan A. Dixon. Overexpression of the small GTPase Rab27B regulates autophagy flux and contributes to tumor growth in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1370.

B7H4 Expression Is More Frequent in MSS Status Colorectal Cancer and Is Negatively Associated with Tumour Infiltrating Lymphocytes.

The immunotherapies based on ICIs in CRC are nowadays limited to microsatellite unstable tumours which are approximately 15% of all CRC cases. There are a few new immune checkpoints belonging to the B7 family, including B7H4. B7H4 expression is associated with so-called "cold tumours", and its function is linked to the downregulation of various immune cell populations. Our study aimed to investigate whether B7H4 expression is dependent on microsatellite status in CRC and on elucidating the immunological context in which the expression of B7H4 occurs. We enrolled 167 patients in the study. We prepared the homogenates from tumour tissues and healthy adjacent tissue to assess the B7H4 levels and the Bio-Plex Pro Human 48-cytokine panel. We assessed the microsatellite status of the tumour, B7H4 expression, CD8+ T cell population, and the TILs and budding in H + E stained slides by the IHC method. We used an online available database for further exploring the biological characteristics of B7H4. The expression of B7H4 was more frequent in microsatellite stable tumours, and was negatively associated with TILs. B7H4 is positively correlated with antitumour immunosuppressive iTME, thus contributing to the immunosuppressive environment in CRC.

DeltaMSI: artificial intelligence-based modeling of microsatellite instability scoring on next-generation sequencing data

BackgroundDNA mismatch repair deficiency (dMMR) testing is crucial for detection of microsatellite unstable (MSI) tumors. MSI is detected by aberrant indel length distributions of microsatellite markers, either by visual inspection of PCR-fragment length profiles or by automated bioinformatic scoring on next-generation sequencing (NGS) data. The former is time-consuming and low-throughput while the latter typically relies on simplified binary scoring of a single parameter of the indel distribution. The purpose of this study was to use machine learning to process the full complexity of indel distributions and integrate it into a robust script for screening of dMMR on small gene panel-based NGS data of clinical tumor samples without paired normal tissue.MethodsScikit-learn was used to train 7 models on normalized read depth data of 36 microsatellite loci in a cohort of 133 MMR proficient (pMMR) and 46 dMMR tumor samples, taking loss of MLH1/MSH2/PMS2/MSH6 protein expression as reference method. After selection of the optimal model and microsatellite panel the two top-performing models per locus (logistic regression and support vector machine) were integrated into a novel script (DeltaMSI) for combined prediction of MSI status on 28 marker loci at sample level. Diagnostic performance of DeltaMSI was compared to that of mSINGS, a widely used script for MSI detection on unpaired tumor samples. The robustness of DeltaMSI was evaluated on 1072 unselected, consecutive solid tumor samples in a real-world setting sequenced using capture chemistry, and 116 solid tumor samples sequenced by amplicon chemistry. Likelihood ratios were used to select result intervals with clinical validity.ResultsDeltaMSI achieved higher robustness at equal diagnostic power (AUC = 0.950; 95% CI 0.910–0.975) as compared to mSINGS (AUC = 0.876; 95% CI 0.823–0.918). Its sensitivity of 90% at 100% specificity indicated its clinical potential for high-throughput MSI screening in all tumor types.Clinical Trial Number/IRB B1172020000040, Ethical Committee, AZ Delta General Hospital.

Survival improvement for patients with metastatic colorectal cancer over twenty years

Over the past two decades of successive clinical trials in metastatic colorectal cancer (CRC), the median overall survival of both control and experimental arms has steadily improved. However, the incremental change in survival for metastatic CRC patients not treated on trial has not yet been quantified. We performed a retrospective review of 1420 patients with de novo metastatic CRC who received their primary treatment at the University of Texas M.D. Anderson Cancer Center (UTMDACC) from 2004 through 2019. Median OS was roughly stable for patients diagnosed between 2004 and 2012 (22.6 months) but since has steadily improved for those diagnosed in 2013 to 2015 (28.8 months), and 2016 to 2019 (32.4 months). Likewise, 5-year survival rate has increased from 15.7% for patients diagnosed from 2004 to 2006 to 26% for those diagnosed from 2013 to 2015. Notably, survival improved for patients with BRAFV600E mutant as well as microsatellite unstable (MSI-H) tumors. Multivariate regression analysis identified surgical resection of liver metastasis (HR = 0.26, 95% CI, 0.19–0.37), use of immunotherapy (HR = 0.44, 95% CI, 0.29–0.67) and use of third line chemotherapy (regorafenib or trifluridine/tipiracil, HR = 0.74, 95% CI, 0.58–0.95), but not year of diagnosis (HR = 0.99, 95% CI, 0.98–1), as associated with better survival, suggesting that increased use of these therapies are the drivers of the observed improvement in survival.

Phase II study (daNIS-1) of the anti–TGF-β monoclonal antibody (mAb) NIS793 with and without the PD-1 inhibitor spartalizumab in combination with nab-paclitaxel/gemcitabine (NG) versus NG alone in patients (pts) with first-line metastatic pancreatic ductal adenocarcinoma (mPDAC).

TPS761 Background: Overall survival remains short for pts with mPDAC despite approved therapies, highlighting the need for more effective treatment options. While TGF-β can act as a tumor suppressor in normal tissue and early-stage PDAC, it is associated with tumorigenic processes (such as enhanced genomic instability, neoangiogenesis, epithelial-to-mesenchymal transition, and metastasis) observed in late-stage PDAC. Within the pancreatic tumor microenvironment (TME), TGF-β activates stellate cells and cancer-associated fibroblasts, thereby promoting fibrotic network development and immune exclusion, maintaining an immunosuppressive TME. Preclinical data in murine models have shown that addition of TGF-β blockade to anti-PD-1 therapy or NG augmented the antitumor activity of those agents, leading to tumor regression. These data provide the rationale for combining TGF-β-targeting agents with chemotherapy and/or immunotherapy. This study investigates NIS793, a human IgG2 mAb that binds TGF-β1 and 2, with and without spartalizumab (PD-1 antagonist) combined with NG in treatment-naïve mPDAC. Methods: This is a phase II open-label, randomized study (NCT04390763) with a safety run-in period followed by randomization. Eligible pts are adults with previously untreated mPDAC with measurable disease as per RECIST 1.1 and ECOG performance status score ≤1. Pts are excluded if they have a microsatellite-unstable tumor. The safety run-in was completed and confirmed a dose of NIS793 (intravenously [IV] 2100 mg Q2W) + spartalizumab (IV 400 mg Q4W) + nab-paclitaxel (IV 125 mg/m2 on Days 1, 8, and 15) + gemcitabine (IV 1000 mg/m2 on Days 1, 8, and 15). In the randomized part, pts will be randomized 1:1:1 to NIS793 + spartalizumab + NG (n = 50) or NIS793 + NG (n = 50) or NG (n = 50). Treatment will continue until disease progression, unacceptable toxicity, discontinuation by investigator’s/pt’s choice, or withdrawal of consent. The primary objective is to evaluate the progression-free survival per RECIST v1.1 of NIS793 + NG with or without spartalizumab, versus NG alone. Secondary objectives include safety and tolerability, antitumor activity, overall survival, change in tumoral CD8 and PD-L1 status, and characterization of immunogenicity and pharmacokinetics. Efficacy will be assessed by investigator per RECIST v1.1 and iRECIST at screening, every 8 weeks for 1 year and then every 12 weeks until disease progression. The study is ongoing and has an estimated enrollment of 161 pts. There are currently 31 sites participating across 14 countries. The study is funded by Novartis. Clinical trial information: NCT04390763 .

Incorporation of Combination Immunotherapy into the Treatment Paradigms of Gastrointestinal Cancers

Immune checkpoint inhibitors allow innate immune cells to recognize and attack tumour cells by removing inhibitory signals associated with tumours and their microenvironment. These agents can induce durable responses and they have transformed the management of many cancer types. There have been great efforts to incorporate immunotherapy (IO) into the treatment of gastrointestinal (GI) cancers. However, most of the GI cancers, except for microsatellite unstable tumours, are largely resistant to IO, especially when used as monotherapy. Increased efficacy has been observed when these agents are combined with other drugs, including chemotherapy, other immune checkpoint inhibitors, or targeted drugs. This review will summarize recent advances in the management of GI cancers with the incorporation of immune checkpoint inhibitors into current treatment paradigms. It will review pivotal studies that led to these practice updates and highlight potentially practice-changing ongoing clinical studies that involve IO agents.