Repair Deficiency Research Articles

Abstract 538: Establishment of PARP inhibitor-induced resistant patient-derived ovarian cancer xenograft models

Abstract Introduction: Poly (ADP-ribose) polymerases (PARPs) can recruit DNA repair effectors and cope with DNA single-strand breaks. For DNA double-strand breaks (DSB), there are two main repair mechanisms: non-homologous end joining repair (NHEJ) which is prone to error due to infidelity events, and BRCA1/2 mediated homologous recombination repair (HR) restoring the original sequence. Therefore, inhibition of PARPs may cause both single stranded break repair deficiency and HR deficiency in BRCA1/2 deficient patients, leading to cell death. The concept of “synthetic lethality” has led to the development of PARP inhibitors, including Olaparib, Niraparib and Rucaparib in clinical practice. Despite encouraging efficacy of these PARP inhibitors, acquired resistance, such as HR repair restoration, drug efflux pump upregulation and replication fork protection, has limited their clinical benefits. Therefore, to investigate novel therapeutic strategies which can overcome the acquired resistance, we established patient-derived xenograft (PDX) ovarian cancer models with PARP inhibitor-induced resistance. Methods: OV9402, an ovarian cancer PDX model with BRCA 1 c.3155del, was implanted subcutaneously and treated with Niraparib at 35 mg/kg, daily, for 129 days. Relapse tumors (tumor #1 and tumor #2) were isolated and inoculated into naïve mice. Then the 2nd round of treatment (Niraparib, 35 mg/kg, daily) was given when the mean tumor volume reached 140 mm3. The tumors showing no significant response to Niraparib were collected on either day 32 (#1 derived tumor model) and day 22 (#2 derived tumor model) after randomization and their gene changes were analyzed by RNA sequencing (RNA-seq). Results: Niraparib significantly inhibited OV9402 tumor growth, with complete regression observed in nine out of ten mice on day 54 after the 1st round of treatment. However, tumor regrowth was observed in two out of the nine mice from day 68 onwards. The relapsed tumors (tumor #1 and tumor #2) from these two mice were collected and re-inoculated into 5 naïve mice to establish tumor models for the 2nd round of Niraparib treatment, separately. For #1 derived tumor model, all the tumors presented complete resistance to the Niraparib treatment. RNA-seq data showed that the gene expression of ABCB1, which encodes for efflux pumps, was upregulated. In parallel, complete resistance to Niraparib was observed in all the tumors derived from 2# tumor bearing mice. The RNA-seq data demonstrated that an acquired secondary genetic deletion on BRCA1 genes, which restored the functional protein expression loss in the parental line and restored HR repair, was found in the tumors. Conclusion: Ovarian cancer PDX models that have effectively developed resistance to PARP inhibitors have the potential to serve as valuable preclinical tools to evaluate potential next-generation PARP inhibitors and innovative combination strategies. Citation Format: Li Hua, Shuang Li, Chenpan Nie, Xiaobo Chen, Guo Sheng, Ludovic Bourre, Jingjing Wang. Establishment of PARP inhibitor-induced resistant patient-derived ovarian cancer xenograft models [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 538.

Abstract 4336: Homologous recombination repair deficiency, and not recurrence, determines mutational burden and clonal dynamics in high grade serous ovarian cancer

Abstract High grade serous ovarian cancer (HGSOC) is the most lethal gynecologic malignancy, killing more than 9,000 women each year in the United States. Nearly 80% of patients with HGSOC will experience recurrence within 5 years, but little is known about the mechanisms that drive this process. Up to 60% of the genome in an HGSOC tumor is impacted by structural variant mutations and pronounced intratumoral heterogeneity. Intratumor heterogeneity is believed to be a key feature of recurrence and therapy resistance with some evidence indicating diverse and complex mechanisms of the seeding of metastatic sites and recurrent tumors. We included 35 HGSOC patients for whom paired chemo-naive and chemoresistant tumors as well as germline DNA was available. Whole genome sequencing was used to identify somatic single nucleotide variants (SNV) insertion/deletion variants (indels), and structural variants (SVs) in each tumor. The number of somatic SVs and indels was higher in tumors with homologous recombination repair deficiency (HRD; P=0.000252 SVs, P=0.00385 Indel) but was not affected by recurrent status (P=0.826 SV, P=0.145 SNV/indel). Clonal composition and dynamics were measured using SNVs/indels as tumors progressed from chemo-naïve primary samples to recurrent chemo-resistant tumors. Surprisingly, few changes were observed in clonal abundance and complexity through progression. When this analysis was repeated with SVs homologous recombination repair proficient tumors tend to be polyclonal while HRD tumors tend to be monoclonal. Five denovo structural variant signatures were identified in our cohort and led to three distinct structural variant classes tumors defined by deletion, tumors defined by duplication, and tumors defined by copy number neutral changes (inversions, translocations and balanced complex events). Patients with tumors defined by deletions and copy number neutral changes carry pathogenic SVs correlating with reduced survival (P=0.00023), while DNA gains are less subject to pathogenic alterations. Each class displayed distinct regions of the chromosome that was frequently affected by large scale SV events (>5Mb), which was also observed in the HRP/HRD status. Although no regions were notably altered across recurrence, GO analysis revealed that recurrent tumors have a significantly reduced immune response, which was not seen in the primary tumors. Within a subset of tumors, we are plan to utilize Oxford Nanopore Technologies ultra long read sequencing which will allow for confirmation of SVs observed in the WGS as well as identification of more complex events that cannot be deciphered using WGS techniques. Citation Format: Michael A. Diaz, Nicole Gull, Pei-Chen Peng, Kate Lawrenson, Bobbie J. Rimel, Jenny Lester, Beth Karlan, Simon A. Gayther, Michelle R. Jones. Homologous recombination repair deficiency, and not recurrence, determines mutational burden and clonal dynamics in high grade serous ovarian cancer [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 4336.

Abstract 7036: Integrative biomarker profiling for predicting immunotherapy outcomes in gynecologic cancers

Abstract Immunotherapy with immune checkpoint inhibitors (ICI) has proven effective for various solid tumors, such as those in the lungs, urinary tract, and skin. However, its efficacy in gynecologic (GYN) cancers has been limited, with response rates of 11-17% in recurrent cases. Only a minority of patients with DNA mismatch repair deficiencies exhibit favorable responses to PD-1 inhibitors. The predictability of PD-L1 expression in GYN cancers remains inconsistent. Our research aimed to identify and prioritize biomarkers and mechanisms linked to ICI resistance in GYN oncology, targeting those who could benefit from these treatments.We gathered clinical and pathological data from 49 patients with ovarian, endometrial, and cervical cancers at various stages, all treated with ICI. We performed comprehensive analyses, including transcriptome-based immune cell abundance estimation, signaling pathway enrichment, and correlation with ICI treatment responses and survival outcomes. Our previous work highlighted TGF-β and CD47's roles in immunotherapy resistance, facilitating an immunosuppressive environment within our GYN cancer cohort. Moreover, we conducted a stoichiometry constraint-based genome-scale metabolic model and computed correlation-grouped metabolic activity scores (cgScore) using metabolic enzyme gene expression as constraints. Among 1533 metabolic reactions, pyruvate transport and folate metabolism stood out as the most upregulated in responders versus those who progressed.Upon identifying several promising biomarkers, we used logistic regression classifiers to decipher the predictive value of each. Our model included clinical-demographic (age, BMI, cancer type, stage) and molecular-genomic features (immune marker gene expression, TopTGF-β score, immune cell abundance from transcriptomic deconvolution, and the top 2 cgScores). Analysis divided into training and testing sets highlighted features such as stage, BMI, eosinophils, CD274, CD47, and the pyruvate transport reaction as significant predictors of ICI response. The model achieved an 80% accuracy rate on the test set, confirmed by permutation importance from scikit-learn. We also used a Regularized Cox model to link predictors with progression-free survival, emphasizing the roles of BMI, plasma cells, CD276, pyruvate transport reaction, and folate metabolism. In conclusion, there are immunological and metabolic markers have the potential to serve as predictive indicators for ICI treatment response and survival in GYN cancers. Understanding these predictors can profoundly influence clinical decision-making in immunotherapy, ultimately leading to enhanced patient outcomes and personalized treatment approaches. Citation Format: Gideon Idumah, Lin Li, Haider Mahdi, Ying Ni. Integrative biomarker profiling for predicting immunotherapy outcomes in gynecologic cancers [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 7036.

Abstract 5610: Investigating the role of BRCA2 in the development of pediatric rhabdomyosarcoma

Abstract Introduction: In a large-scale exome sequencing study of pediatric rhabdomyosarcoma (RMS) patients, we identified a statistical enrichment of patients with germline variants in BRCA2 (Li, et al. JNCI, 2020), which prompted this study to assess the role of heterozygous BRCA2 variants in the development of pediatric RMS in both precursor cell and mouse models. Methods: We engineered BRCA2 loss of function (LoF) variants in lines of immortalized mesenchymal stem cells, a potential precursor cell to RMS, using CRISPR and Prime Editing (PE). CRISPR was used to induce frameshift alleles in Exons 10 and 11 and with PE, we created two RMS patient specific LOF variants in Exons 5 and 17. We generated a genetically engineered mouse model (GEMM) with heterozygous excision of Exon 11 of Brca2. This allele is now being crossed into two different previously established GEMMs of RMS: a myoblast-specific (MyoD1-Cre) conditional loss of p53, and a gain-of-function mutant p53, LSL-p53R172H (Nakahata, et al. Dis. Model. Mech., 2022), to assess changes in the pace of tumorigenesis and metastatic potential. Through an X01 agreement with the Gabriella Miller Kids First Program, we have submitted paired tumor-normal samples for additional whole-genome sequencing and RNA sequencing (tumor only) on >500 patients with RMS, including those with germline variants in BRCA2. Results: Using CRISPR, we generated cell lines heterozygous for the frameshift variants c.1345dup, c.5680del, and c.5680dup. With Prime Editing, we created heterozygous lines mimicking two specific variants detected in the RMS cohort, c.462_463del and c.7857G>A. Generation of a C57BL6 GEMM with a heterozygous removal of Exon 11 in Brca2 has been successful. No homozygous mice were obtained following 7 heterozygous crosses (50 pups), a departure from Mendelian ratios (p=0.0001) consistent with embryonic lethality. Heterozygous Brca2 mice derived from crosses into two RMS models are being monitored for tumor development. We have completed tumor-normal whole-genome and tumor RNA sequencing for 609 RMS patients, including 228 subjects not previously analyzed. We will directly assess whether there is evidence for mutation or loss of expression of the remaining BRCA2 allele in tumors and whether these tumor genomes exhibit signatures of DNA repair deficiency. Conclusions: The goal of this project is to determine the molecular basis for the enrichment in germline BRCA2 LOF variants in pediatric malignancies, including RMS. Ongoing experiments using the engineered heterozygous BRCA2 in vitro cell line models will assess genomic stability, homologous recombination proficiency, and DNA replication fork stability. Assessment of the effect of heterozygous Brca2 variants in GEMMs of RMS, and subsequent analysis of additional sequencing data, will further elucidate what role this gene may play in increasing risk or progression of pediatric cancers. Citation Format: P. Adam Weinstein, Ryan Zabriskie, Cem Ozdemir, Kyle M. Miller, Olga Medina-Martinez, Jason D. Heaney, Aniko Sabo, Philip J. Lupo, Sharon E. Plon. Investigating the role of BRCA2 in the development of pediatric rhabdomyosarcoma [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 5610.

Abstract 1755: Integrative genomic and transcriptomic profiles from a prospective cervical cancer study (RAIDs)

Abstract Background: Cervical cancer (CC) remains a leading cause of gynecological cancer related mortality worldwide and constitutes the third most common malignancy in women. We have previously reported a “metagene” of genomic markers in the PI3K pathway and epigenetic regulators associated with poor outcome. Immune therapy recently showed promising results yet new biomarkers for targeted therapeutic approaches in this type of cancer remain to be determined. Patients & Methods: Patients included in this study were enrolled in BioRAIDs [NCT02428842]. Whole exome sequencing (WES), shallow whole genome sequencing (sWGS) and RNA sequencing were performed on quality-controlled primary frozen tumor samples in 297, 306 and 280 patients, respectively who subsequently had received primary radio chemotherapy. Multi-omics bioinformatics analyses were performed to identify alterations representing new valid drug targets in CC. Tumor-stromal characteristics such as transcriptome deconvolution, CD8+, CD45+, CD68+ staining cells, PD-L1 expression, tumor infiltrating lymphocytes (TILs) together with the degree of tumor necrosis were assessed. Results: 273/306 were HPV positive (89%). Most frequently altered (≥10%) oncogenes were PIK3CA (30%) and TERT promoter (14%). Most frequently altered (≥10%) tumor suppressor genes were FBXW7 (14%), KMT2D (11%), KMT2C (11%) and FAT1 (11%).Microsatellite instability (MSI) was detected in 8/297 (3%) patients, homologous recombination deficiency (HRD)-high status in 8/297 (3%) patients and TMB-high (>10mut/Mb) in 32/297 (11%) patients. The most frequent mutational signatures were APOBEC, deaminase and MMR (DNA mismatch repair deficiency (74%, 28% and 11% respectively). Interestingly, FGFR3 fusions were detected in 8/297 patients (3%). Transcriptomic analyses showed 510 differentially expressed genes between HPV positive and HPV negative CC (adjusted p-value<0.01 and |log2FC|>1). No significantly differentially expressed genes were detected between FIGO 2018 stages (I/II vs III-IV). Both stages as well as tumor necrosis were highly significantly associated with progression-free survival (PFS), with tumor necrosis as an independent prognostic factor in a multivariable analysis (p<0.001).Presence or absence of CD8-positive lymphocytes, or CD68-positive cells of the myeloid cell compartment, histopathological subtype or number of TILs did not correlate with PFS. Conclusion: Our results confirm the high level of altered genes involved in chromatin remodeling with or without PI3K pathway mutations suggesting the relevance of epidrugs in CC. FGFR3 fusions and HRD tumors - although being rare (3%) - to be considered as new targeted approaches. Additionally, MSI and TMB high are of interest for immunotherapy beyond PD-L1 expression. Integrative analyses of omics and pathology data and correlation with PFS are ongoing and will be presented in the meeting. Citation Format: Maud Kamal, Solenn Barraud, Lolita Lecompte, Maral Halladjian, Emmanuelle Jeannot, Elodie Girard, Sylvain Baulande, Patricia Legoix, Fabrice Lecuru, Léa Pauly, Mathilde Saint-Ghislain, Stacy Cyrille, Célia Dupain, Constance Lamy, Olfa Chouchane-Mlik, Alexandra Oniga, Michel Mittelbronn, Christophe Le Tourneau, Aurélien Latouche, Nicolas Servant, Suzy Scholl, Ivan Bièche. Integrative genomic and transcriptomic profiles from a prospective cervical cancer study (RAIDs) [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 1755.

Abstract 7563: Efficacy of JPI-547, novel dual PARP inhibitor, in endometrial cancer cell line

Abstract Objectives: PARP inhibitor is effective in treating DNA repair deficiency endometrial cancer. Endometrial cancer (EC) is one of the most common gynecological cancers in developed countries and its incidence is increasing, and the prognosis of patients with early stage and low-risk EC is very good, but the prognosis of progressive and recurrent EC is poor. Novel PARP inhibitor JPI-547 is a PARP and tankyrase dual inhibitor, and in cancer cells, tankyrase inhibitor plays an important role in DNA repair, telomere maintenance, and cell survival. This experiment was conducted to determine whether the reactivity of the PTEN mutant EEC was increased by using the Novel PARP inhibitor. Method: Human endometrioid endometrial cancer cell lines, Hec-1A, Hec-1B and Ishikawa were obtained. Cell viability assay for the drugs Olaparib and JPI-547 were assessed. Colonies consisting of at least 50 cells were counted. The number of dead cells was counted in five different areas of the hemocytometer, and the experiment was performed three times. The percentage of dead cells was analyzed compared to the untreated group. We confirmed the efficacy by siRNA transfection and immunofluorescence. Result: When treated with Olaparib, there was no change in cell viability in the rest of the cells except for Ishikawa cells, which are PTEN mutations. It decreased by 35.4% in Ishikawa cells, whereas when treated with JPI-547, all cell lines Hec-1A, Hec-1B, and Ishikawa cell viability decreased by 28%, 34.3%, and 48.7%, respectively. PTEN knock-down reduced cell visibility by 28% when treated with olaparib, whereas when treated with JPI-547, Hec-1A (siCont) and Hec-1A (siPTEN) decreased by 26% and 42%, respectively, in all cells regardless of whether PTEN knock-down is present. When treated with Olaparib, dead cells were identified only in PTEN knock-down cells, increasing by 22%. When treated with JPI-547, dead cells increased by 25.5% and 33% in all cells of Hec-1A (siCont) and Hec-1A (siPTEN), respectively. It was confirmed that JPI-547 can reduce cell viability regardless of the formation of Rad51 according to PTEN. Conclusion: JPI-547, a novel PARP inhibitor, showed good efficacy in PTEN mutation and PTEN-wild-type EEC cell lines than in conventional PARP inhibitor. The effect of reducing survival of ECC cell line with JPI-547 was confirmed with or without PTEN mutation. Further evaluation and in vivo experiments are needed to prove the efficacy of JPI-547 in EC. Citation Format: Shin-Wha Lee, So-Hyun Nam, Su-Bin Park. Efficacy of JPI-547, novel dual PARP inhibitor, in endometrial cancer cell line [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 7563.

Leveraging Off-Target Reads in Panel Sequencing for Homologous Recombination Repair Deficiency Screening in Tumor

Targeted tumor only sequencing has become a standard practice in cancer diagnostics. This study aims to develop an approach for robust copy number variant (CNV) calling in tumor samples using only off-target region (OTR) reads. We also established a clinical use case for homologous recombination deficiency (HRD) score estimation (HRDest) using the sum of telomeric allelic imbalance (TAI) and large-scale state transitions (LST) scores without the need for loss of heterozygosity (LOH) information. We demonstrated a strong correlation between HRD score and the sum of TAI + LST in the TCGA cohort (rho = 0.99, p < 2.2x 10-16) and in a clinical in-house cohort of 34 tumors (rho = 0.9, p = 5.1 x 10-13) comparing WES and targeted sequencing data. We compared HRDest scores from 1086 clinical cases to the TCGA data set and showed that there were no significant differences in HRD score distribution within the analyzed tumor types. As a control, commercially available HRD standards were also sequenced and the HRDest scores obtained from the OTR reads were well within the HRD reference range provided by the manufacturer. In conclusion, we showed that OTR reads of tumor-only panel sequencing can be used to determine genome-wide CNV profiles and to approximate HRD scores.

Abstract 2663: Determining the role of tumor mutational burden in a pre-clinical model of glioblastoma

Abstract Despite advances in care in many cancer types, patients with glioblastoma (GBM) have a grim prognosis of 15 to 21 months and unchanged standard therapy since 2005. These tumors have a profoundly immunosuppressive tumor immune microenvironment. Immunotherapy, including the checkpoint inhibitors (ICIs) targeting PD-1 and CTLA-4, has transformed the treatment of many cancers but has failed in trials of both newly diagnosed and recurrent GBM. Tumor mutational burden (TMB) has been proposed as a predictor of response to ICI treatment, presumably through an increase in neoantigens that can be recognized by cytotoxic CD8+ T cells leading to tumor rejection. GBM typically has a low TMB, a feature speculated as a contributor to poor response to ICI treatment. However, cases with an extremely high TMB (i.e., patients with the biallelic mismatch repair deficiency syndrome) do show response to immunotherapy. To begin to investigate the impact of mutational burden on immune response in GBM, we created a murine syngeneic tumor model using CRISPR-Cas9 to knockout (KO) the mismatch repair protein Msh2, the lynchpin to mismatch recognition, in the SB28 GBM model that has a low TMB (108 mutations) at baseline. Msh2 KO increased the TMB from 2 to 12-fold depending on single cell sorted clone, resulting in between 150 and 200 predicted strong MHC-I binding neoantigens estimated by the NetMHC algorithm. Preliminary studies have demonstrated that in vitro proliferation is similar amongst low TMB and high TMB SB28 clones. Flank implantation of high TMB SB28 clones revealed slower growth compared to the low TMB SB28 tumors. Furthermore, treatment with ICIs did provide a survival advantage in this flank model. However, no survival advantage was noted when the high TMB clones were implanted intracranially either with or without ICI treatment. These results suggested that either there is poor immune cell trafficking to the intracranial tumors, or a robust immune response was causing increased intracranial pressure that is prematurely causing death. Use of dexamethasone starting at day 11 to control cerebral edema has shown some survival improvement with ICI treatment, supporting that an inflammatory response is at least partially responsible for the lack of improved survival in early studies. We are currently evaluating CD4+ and CD8+ T cell clonality, earlier timepoints to evaluate the immune infiltrate and anti-tumor immune response, and alterations in chemokines/cytokines in the tumor microenvironment. By creating high mutation burden clones from a GBM with a low mutational burden, we will be able to interrogate potential mechanisms of heightened immunogenicity that has been reported in other cancers. Citation Format: Kevin Breen, Tuesday Haynes, Masashi Watanabe, Mark Gilbert. Determining the role of tumor mutational burden in a pre-clinical model of glioblastoma [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 2663.

Abstract 5129: Subcellular MLH1 protein as first in class biomarker for CDK4/6 response in endocrine resistant ER+/HER2- breast cancer

Abstract Over 175,000 diagnoses of estrogen receptor-positive breast cancer are made every year in the US. Of these, &amp;gt;40,000 patients will go on to die of their disease. We recently identified defects in a principal mismatch repair (MMR) gene, MLH1, as a driver of resistance to standard-care treatment and poor patient outcomes. Moreover, we demonstrated increased sensitivity to palbociclib, a CDK4/6 inhibitor, in experimental model systems in vitro and in vivo and in clinical trial data. MLH1 is mutated in 5-10% of treatment-resistant tumors, i.e., 4,000 patient tumors every year. However, most of these mutations are missense and variants of unknown significance (VUS). The impact of these mutations on mismatch repair capability and on treatment resistance remains uncertain. Here, we use experimental model systems to phenotype MLH1 VUS´ in vitro and in vivo using xenograft systems.Specifically, we use nuclear localization of MLH1 and repair of mismatches through a mismatch repair deficiency assay to test for mismatch repair capability in ER+ breast cancer cells engineered to express mutations in MLH1 that are found in patient tumors associated with poor survival. Second, we assess the ability of variants of MLH1 to induce activation of G1/S cell cycle checkpoints by activating Chk2. Lastly, we directly test the ability of variants in MLH1 to induce resistance to standard-care endocrine therapies and sensitivity to palbociclib, using 2D and 3D growth assays and xenograft experiments. Results from these experiments serve to systematically catalog VUS´ in MLH1 based on their predictive potential. We identified for the first-time specific mutation in MLH1 that induces resistance to endocrine therapy by stalling nuclear translocation of MLH1 which inhibits Chk2 activation. Cells with impaired Chk2 activation maintain a high CDK4/6 levels and are therefore more sensitive to CDK4/6 inhibition. Currently, there are few tests available in the clinic to predict response to therapies early in the timeline of ER+ breast cancer patients. Due to the nature of the disease, this can result in years of overtreatment. Overtreatment comes at great financial, physical, and emotional cost to patients and their families. Simultaneously, a lack of predictive markers can result in missed opportunities of presenting patients likely to relapse on standard care with personalized alternative therapeutic strategies. Based on our findings, cytoplasmic MLH1 may serve as first in-class biomarker for CDK4/6 response in ER+/HER2- patients. Citation Format: Aloran Mazumder, Elena Oropeza, Nindo Punturi, Svasti Haricharan. Subcellular MLH1 protein as first in class biomarker for CDK4/6 response in endocrine resistant ER+/HER2- breast cancer [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 5129.

Abstract 889: Machine learning-enhanced targeted versus whole-exome sequencing as a guide to cancer care

Abstract Targeted DNA sequencing of cancer-associated genes has been widely adopted clinically. In addition, the increasing availability of targeted and whole-exome/genome sequencing (WES/WGS)-derived big data suggests avenues of computationally enhancing power of targeted assays via machine learning. We directly compared targeted (MSK-IMPACT) and WES in a cohort of 1,483 cancer patients using the same DNA libraries. We found high sensitivity and specificity of mutation detection by WES for overlapping genes. Comparatively higher estimates of tumor mutation burden by MSK-IMPACT arose from enrichment of oncogenic mutations in the targeted gene set. WES had minimal value in identifying actionable alterations beyond those from MSK-IMPACT, whereas RNA-sequencing identified additional targetable fusions that led to durable responses. We developed a deep learning-based algorithm (DeepSig) that enhances power of mutational signature detection, enabling detection of a select group of signatures with mutation counts of ~5 or less. Hypermutation-associated signatures, including POLE, temozolomide, and mismatch repair deficiency could be detected robustly using targeted sequencing data. In summary, WES had limited clinical value over targeted sequencing panels and future clinical diagnostic development should focus on transcriptome and WGS that can detect additional signatures and gene fusions. Citation Format: Hyung Jun Woo, Shweta S. Chavan, Aphrothiti J. Hanrahan, Allison L. Richards, Anne Marie Noronha, Ahmet Zehir, Alexander Drilon, Michael F. Berger, David B. Solit, Mark T. Donoghue. Machine learning-enhanced targeted versus whole-exome sequencing as a guide to cancer care [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 889.

Abstract 4532: Discovery of DAT-1000A, a potent Polθ inhibitor that significantly enhances anti-tumor efficacy in combination with PARP inhibitor in homologous-recombination-deficient tumors

Abstract Cancers exhibiting homologous recombination (HR) repair deficiencies due to mutations in genes like BRCA1 or BRCA2 rely on alternative DNA damage response (DDR) pathways to uphold genomic integrity. This vulnerability allows for the targeted disruption of these pathways through synthetic lethality approaches. DNA polymerase theta (Polθ, encoded by POLQ) assumes a crucial role in mending DNA double-strand breaks (DSB) via microhomology-mediated end-joining (MMEJ), one of the principal pathways for repairing DNA DSB. Notably, Polθ expression is minimal in normal tissues but becomes upregulated in HR-deficient cancer cells, positioning Polθ as a prime target for synthetic lethality in HRD cancers. Reversion mutations in HR-related genes frequently employ micro-homology deletion mechanisms. Consequently, the inhibition of Polθ holds the potential to thwart the emergence of PARPi resistance, primarily driven by BRCA reversion mutations. In this context, we introduce DAT-1000A, a novel small-molecule Polθ inhibitor exhibiting potent activity with a single-digital nanomolar IC50 value. Its efficacy in MMEJ functional assays validates its on-target cellular activity. Assessments of cell viability in HR-deficient BRCA2-KO DLD-1 cells, compared to their parental counterparts, reveal a striking synthetic lethality window exceeding 500-fold. Additionally, DAT-1000A displays synergistic anti-proliferative effects when combined with PARP inhibitors in BRCA1/2-mutated cells. In BRCA1/2-mutated xenograft models, DAT-1000A demonstrates robust and sustained tumor regression, as evidenced by the level of γH2AX, a common marker for double-strand breaks, which closely correlates with anti-tumor efficacy. Importantly, high-dose DAT-1000A treatment in mice elicits no significant abnormalities, underscoring its excellent tolerability. Collectively, DAT-1000A emerges as a novel Polθ inhibitor, offering both potent activity and a favorable safety profile, and holds promise for advancing therapeutic options in the realm of HRD cancer treatment. Citation Format: Dan Yan, Yao Zhang, Yan Zhang, Jingxi Zhang, Bin Wang, Huixian Chen, Jingxue Shi, Xiaoling Lin, Jincong Zhuo, Kevin Zhou. Discovery of DAT-1000A, a potent Polθ inhibitor that significantly enhances anti-tumor efficacy in combination with PARP inhibitor in homologous-recombination-deficient 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 4532.

Abstract 6462: Somatic mutational profile in MUTYH- associated colorectal cancers (MUTYH-CRCs)

Abstract Background: Biallelic inactivation of MUTYH leads to hereditary predisposition to colorectal polyposis and CRC. Herein we evaluated co-alterations in somatic next-generation sequencing (NGS) in patients with MUTYH-CRC, mainly KRAS G12C, high tumor mutational burden and microsatellite instability (MSI-H)/mismatch repair deficiency (dMMR). Methods: Data was collected on patients with MUTYH-CRC in the period between 2015 and 2023 at Moffitt Cancer Center (Tampa, Florida, United States). All patients with MUTYH-CRC were included regardless disease stage. Different germline panels were used to detect MUTYH and Foundation One, Caris and Moffitt STAR (in house NGS) were used to detect somatic co-alterations. Results: A total of 36 patients were identified with MUTYH- CRC, the median age at diagnosis was 44-year-old, 55% were men. All patients had a somatic NGS available, 18 patients (50%) had KRAS mutation, and specifically KRAS G12C was detected in 9 patients (24%), 6 patients (17%) had MSI-H/dMMR, 5 patients (14%) had BRAF mutation and 4 patients (11%) with BRCA2 mutation. Conclusion: MUTYH-CRC is associated with a high incidence of targetable alterations including KRAS G12C and BRAF. Considering unique characteristics in MUTYH-CRC tumor microenvironment, including T cell infiltrate, trials combining KRAS G12C/BRAF inhibitors and immune checkpoint inhibitors are warranted. Citation Format: David Kaldas, Tiago Biachi de Castria. Somatic mutational profile in MUTYH- associated colorectal cancers (MUTYH-CRCs) [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 6462.

Abstract 3892: Systematic generation of a clinicogenomic harmonized oncologic real-world dataset (MSK-CHORD)

Abstract Clinical data storage in unstructured notes and siloed datasets present a major challenge for large-scale cancer informatics. Whether natural language processing (NLP) combined with multimodal integration across datasets can produce a mineable resource and improve discovery of relationships between tumor genomics and clinical phenotypes is unknown. We hypothesized that NLP could automatically annotate a pan-cancer corpus of 82,464 patients with tumor genomic sequencing. To develop algorithms to annotate free-text reports, we leveraged the AACR Project GENIE Biopharma Collaborative (BPC), a structured curation of EMR from five cancer types (non-small cell lung (NSCLC), breast, colorectal, prostate, and pancreatic cancer), to train and validate several Transformer and rule based-based NLP models. After automating the generation of NLP annotations alongside medication, demographic, tumor registry, survival, and tumor genomic sequencing data, we tested whether clinicogenomic relationships not apparent in the smaller BPC cohort might be discoverable in the larger cohort. In 5-fold cross-validation, NLP Transformers accurately annotated the presence of cancer (AUC=0.99), cancer progression (AUC=0.97), and sites of disease (AUC=0.99) from radiology reports, and presence of prior outside treatment (AUC=0.98) and hormone receptor (HR) and HER2 receptor status (AUC=0.98, 0.98) from clinician notes. In addition, rule-based models, trained on non-BPC data and validated on the whole BPC cohort, annotated smoking status from clinician notes (ACC=0.95), and Gleason score (ACC=1.0), PD-L1 status (ACC=0.98), and mismatch repair deficiency (ACC=0.98) from histopathology reports. NLP annotations were merged with genomic and other structured clinical data to create a Clinicogenomic, Harmonized Oncologic Real-world Dataset (MSK-CHORD). Finally, we tested if associations not apparent in the BPC might be discoverable in MSK-CHORD. We found positive associations between Gleason score and gene-level alterations in prostate cancer including TP53, PTEN and BRCA2 (q&amp;lt;0.1), none of which were adequately powered for detection in the BPC. We found PD-L1 status was associated with better survival following immunotherapy treatment in NSCLC, but only in the larger MSK-CHORD was this association statistically significant. In breast cancer, NF1 mutations were associated with prior therapy in both cohorts, but this association was only significant in MSK-CHORD. The infrastructure generating MSK-CHORD uses a combination of on-premise and cloud computing resources and open-source development operation applications to automate processes. Once annotations are created, data is imported into a local instance of cBioPortal, where researchers can visualize data and perform analyses. The system generating MSK-CHORD demonstrates how large-scale data delivery and integration can fuel cancer research. Citation Format: Christopher J. Fong, Karl Pichotta, Thinh Tran, Michele Waters, Tom Fu, Mono Pirun, Mirella Altoe, Brooke Mastrogiacomo, Anisha Luthra, Mehnaj Ahmed, Arfath Pasha, Armaan Kohli, Raymond Lim, Tom Pollard, Darin Moore, Benjamin Gross, Avery Wang, Calla Chennault, Ritika Kundra, Ramyasree Madupuri, Ino de Bruijn, Aaron Lisman, Walid K. Chatila, Subhiksha Nandakumar, Anika Begum, Doori Rose, Kenneth L. Kehl, Deborah Schrag, Michael Berger, Jian Carrot-Zhang, Pedram Razavi, Bob Li, Peter Stetson, Nikolaus Schultz, Justin Jee. Systematic generation of a clinicogenomic harmonized oncologic real-world dataset (MSK-CHORD) [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 3892.

Abstract 4534: HSK40495, a highly selective PARP1 inhibitor with improved hematopoietic safety for the treatment of HRD cancers

Abstract It is well known that several PARP inhibitors have been approved for tumors with homologous recombination repair deficiencies (HRD), such as BRCA mutations. However, the common side effect of these inhibitors is hematologic toxicity, which limits their therapeutic index and combination potential with first-line chemotherapies. One possible reason is that currently approved PARP inhibitors do not specifically target PARP1, and might also affect other PARP family members. Recent studies have shown that the synthetic lethality caused by PARP trapping with HRD is mainly dependent on PARP1 inhibition, but not other PARP family members. Accordingly, we developed a selective PARP1 inhibitor that effectively inhibits tumor growth with less hematologic toxicity. HSK40495 is a potent PARP1 inhibitor with highly selectivity of PARP2. HSK40495 inhibited PARP1 enzymatic activity with a single digit nanomolar potency and with greater than 5000-fold selectivity against PARP2 in the protein binding assay. In addition, HSK40495 exhibited potent anti-proliferation activity in both DLD1(BRCA KO) cell and MDA-MB-436 cell, while had minimal effects against BRCA-WT DLD1 cell up to 30 µM in an anti-proliferation assay. In a subcutaneous MDA-MB-436 xenograft tumor model, HSK40495 administered orally once daily achieved excellent tumor growth inhibition of 100% at 3mg/kg. HSK40495 demonstrated significant PARylation inhibition in tumor tissues. Importantly, in CD34+ human bone marrow progenitor cell, HSK40495 showed improved cytotoxicity when compare to first-generation PARP inhibitor, Talazoparib. Meanwhile, in a lineage-specific hematotoxicity assay, HSK40495 exhibited improved cytotoxic safety in the process of differentiation of myeloid, erythroid and megakaryocyte compared with Talazoparib treatment. In summary, HSK40495, a highly selective PARP1inhibitor over other PARP family members, exhibits excellent pharmacological and safety properties, and also has the favorable pharmacokinetics profile in preclinical studies. All these findings suggest that HSK40495 has the great potential to be a promising PARP1 inhibitor for further development in the patients with HRD tumors. Citation Format: Fan Li, Xiaoli Gou, Lei Chen, Qingyuan Meng, Yao Li, Hongjiao Dong, Pingming Tang, Ju Wang, Pangke Yan. HSK40495, a highly selective PARP1 inhibitor with improved hematopoietic safety for the treatment of HRD cancers [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 4534.

Abstract 7115: Mutational signatures in PDXs for improved understanding of drug response and companion biomarkers identification

Abstract Genomic DNA editing is a continuous process that occurs during the entire cell life span. The type and frequency of these modifications can be related to the physiological or pathological activity of intrinsic mechanisms such as DNA surveillance and repair or to extrinsic events that may induce an alteration of DNA sequence by exposure to agents that directly or indirectly induce accumulations of DNA alterations. In the past few years, large-scale analyses have revealed mutational signatures across human cancer types. These signatures can be used as markers of defective internal processes, such as DNA repair deficiency, or external exposures, such as carcinogens, like tobacco, or genotoxic therapies such as radiation and chemotherapy. Our TumorGraft platform, a collection of 1500 patient-derived xenograft generated from more than 50 different types of cancer, is one of the most comprehensive preclinical oncology platforms worldwide, and aims to recapitulate the variety of the patient population and tumor biology complexity. This platform is currently used to evaluate the efficacy of new drugs, and all our models are very well characterized at the molecular level, including whole transcriptome, proteomics and phospho-proteomics, quantification, and genomic variation calls. This allows accurate selection of models with the molecular characteristics of the target patient population, as well as to identify biomarkers predictive of treatment efficacy. This could eventually lead to the development of companion biomarkers in the clinical setting to improve the identification of patients that will benefit from the treatment and those that should be spared. To maximize the chances of identifying relevant molecular traits associated with tumor response, we have been utilizing the Pharmaco-Pheno-Multiomic (PPMO) integration workflow, a machine learning approach which combines phenotypic and therapeutic response profiles with multiple omics datatypes to generate complex biomarker profiles. To provide additional insights on the molecular characteristics of our tumors, we decided to perform the mutational signatures profiling of our models by using whole exome sequencing data. The results obtained were crossed with patient’s clinical history and showed good correlation between the mutational signatures identified and the treatments received by the patient, in particular for exposure to platinum salts. The addition of PDXs mutational signatures strongly improves our knowledge on these models and confers an important parameter for model selection. Moreover, the integration of mutational signature profiles in the PPMO workflow would make a significant contribution for companion biomarkers identification. Citation Format: Haia Khoury, Stefano Cairo, Mara Gilardi, Michael Ritchie, Gilad Silberberg. Mutational signatures in PDXs for improved understanding of drug response and companion biomarkers identification [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 7115.

Abstract 4533: Identification of DAT-2000A, a novel potent PARG inhibitor that selectively inhibits PARPi-resistant and homologous-recombination-deficient tumors

Abstract A significant portion of patients with homologous recombination repair deficiencies(HRD) do not respond to PARP inhibitors, and even among those who initially respond, resistance often develops after PARP inhibitor treatment. This underscores the unmet clinical need to address the challenges in the treatment of HRD patients. Poly (ADP-ribose) glycohydrolase (PARG) plays a key role in hydrolyzing PAR chains from PARylated protein substrates, such as PARP1, serving as a critical checkpoint in DNA damage repair and the control of DNA replication stress. Therefore, PARG has emerged as a promising target for cancer therapy. Cancer cells experiencing replication stress, such as HRD breast cancer cells and those resistant to PARPi, exhibit sensitivity to PARG inhibition. DAT-2000A is a potent, selective, orally bioavailable small-molecule inhibitor of PARG, which directly binds to the catalytic domain of PARG, inducing the accumulation of poly-PAR chains at DNA lesions, and exhibits notable anti-proliferative activity across a wide range of HRD tumors both in vitro and in vivo. Biochemical assays confirm DAT-2000A's high potency and selectivity as an inhibitor of PAR-chain hydrolysis. In cellular assays, DAT-2000A demonstrates selective sensitivity in HRD cells, distinguishing itself from PARPi across various indications. Preclinical studies involving CDX and PDX xenograft models reveal that DAT-2000A exerts robust anti-tumor effects in both PARPi-sensitive and -resistant settings. Furthermore, it induces a dose and time-dependent accumulation of PAR chains, which may serve as a reliable pharmacodynamic biomarker indicative of PARG target engagement. In conclusion, DAT-2000A represents an innovative targeted therapy that warrants further investigation in clinical trials for the treatment of HRD cancers and beyond. Citation Format: Dan Yan, Yan Zhang, Zhangqi Yu, Yao Zhang, Jingxi Zhang, Bin Wang, Huixian Chen, Jingxue Shi, Zhiwei Bao, Xiaoling Lin, Jincong Zhuo, Kevin Zhou. Identification of DAT-2000A, a novel potent PARG inhibitor that selectively inhibits PARPi-resistant and homologous-recombination-deficient 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 4533.

Abstract 6845: MAGEA3 expression and secretion in MMR-MSH6 and MMR-PMS2 microsatellite-stable colorectal cancer

Abstract Despite the breakthrough of PD-1/PD-L1 blockade therapy in the recent years, mixed responses have been shown across multiple tumor types, including in colorectal cancer (CRC), the second leading cause of death worldwide. This immunotherapy has proven to be successful for a subtype of CRC that carries mismatch repair deficiency (dMMR) and high microsatellite instability (MSI-H), despite a lack of response by microsatellite-stable CRC. For these types of non-responsive cancers, new immunotherapy targets are currently being investigated for alternative therapy such as the MAGE-A cancer testis antigen family whose expression is restricted to germline cells in normal tissue but is overexpressed in many cancer cells. In this study, we examine the relationship between MAGEA3 and MMR proteins MSH6 and PMS2. Immunohistochemical staining of CRC tissues demonstrated co-expression between MAGEA3 with both MSH6 and PMS2. Immune cells were observed to express MAGEA3 in CRC as well. To investigate the possibility of secreted MAGEA3 from tumor cells, we performed western blot analysis of CRC cell lines, ELISA, and binding assay on cell lines and the positive results suggest that MAGEA3 protein is secreted. The results suggest that MAGE-A3 may be a promising target for microsatellite-stable colorectal cancer immunotherapy. Citation Format: Jina Yom, Rachel Gonzalez, Bailey Gilmore, Zhaoying Guo, Andy Han, Eden Zewdu, Dehe Kong, Tianli Qu, Hailey Guo, Alex Strom, Zoe Zhao, Xiaomin Hu, Qi Ren, Yan Ma, Ranran Zhang, Zhaohui Wu, Xuan Liu, Wei Fu. MAGEA3 expression and secretion in MMR-MSH6 and MMR-PMS2 microsatellite-stable colorectal cancer [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 6845.

Abstract 4244: Clinical response assessment of immune checkpoint inhibitors in mismatch repair-deficient endometrial cancer using a T cell organoid coculture system

Abstract Endometrial cancers with the mismatch repair deficiency (MMR-D) phenotype exhibit characteristics such as an increased burden of tumor mutations and the presence of tumor-infiltrating lymphocytes (TILs) involved in tumor invasion. While monotherapy using immune checkpoint inhibitors (ICIs) has shown clinical improvement in MMR-D endometrial cancer (EC), observed response rates ranging from 30% to 50% suggest the existence of inherent resistance mechanisms. One notable feature of MMR-D tumors is the high proportion of tumor-infiltrating lymphocytes (TILs) encompassing various lymphocytes with diverse effects on immune interactions. Therefore, we aim to assess the feasibility of a self T-cell-tumor organoid co-culture platform for individual MMR-D endometrial cancer patients. We provide evidence that co-culturing self-tumor organoids with peripheral blood lymphocytes can be utilized to evaluate ICI responsiveness in MMR-D endometrial cancer patients. The application of a specific T-cell organoid co-culture platform to a cohort of patient resistant to monotherapy ICIs offers a means to anticipate the timing for minimal immunotherapeutic intervention and the appropriate timing for combination therapy. Citation Format: Ju Hee Oh, Eun Hye Choi, Ji Eun Lee, Eun Ji Nam. Clinical response assessment of immune checkpoint inhibitors in mismatch repair-deficient endometrial cancer using a T cell organoid coculture system [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 4244.

Abstract 4349: Characterization of a centrosome loss-induced tumorigenic signature in prostate epithelial cells

Abstract Prostate cancer (PCa) stands as the second leading cause of cancer death in American men, with overtreatment being common given the difficulty in distinguishing between indolent and aggressive cases. Unlike many cancers, PCa lacks hallmark mutations in key oncogenes and tumor-suppressor genes. Instead, PCa exhibit extensive genomic rearrangements and chromosomal instability (CIN). CIN occurs during PCa progression, producing ETS gene family fusions, PTEN loss and androgen receptor amplification. Importantly, the mechanism underlying CIN in PCa remains unclear. Previously, we found that cell within early-grade human primary prostate adenocarcinomas (PRAD) frequently lack centrosomes, and this frequency correlates with tumor grade. We demonstrated that transient removal of centrosomes within non-tumorigenic human prostate epithelial cells (hPrEC) induces CIN and was, strikingly, sufficient to transform subpopulations of cells capable of producing xenograft tumors in mice. To unravel the molecular mechanisms underlying this path to tumorigenesis, we isolated DNA and RNA from parental hPrECs, clonal lines subjected to transient centrosome loss, and xenograft tumor cells and performed whole genome sequencing (WGS) and bulk RNA-seq. This allowed us to characterize the genomic profiles induced by centrosome loss and to identify an associated mutational signature. We used MUTECT2 to identify single nucleotide variants. Kataegis loci were observed on multiple chromosomes in all transient centrosome removal samples. Copy number variations were also detected in these samples using FACETS and SEQUENZA. Next, we extracted the copy number (CN) signature with SigProfiler and Sigminer, comparing it to COSMIC CN signatures and WGS data from PRAD patients. Our results revealed that the transient centrosome loss signature bears similarity to CN signatures associated with chromothripsis, loss of heterozygosity, and homologous recombination repair deficiency. Patients with PRAD displaying the centrosome loss CN signature had a poorer prognosis. Additionally, our CN analysis discovered that centrosome loss induced mosaic loss of chromosome Y in our samples. To detect structural variations, we employed DELLY, MANTA, SVABA, revealing a high occurrence of both non-clustered and clustered translocations in transient centrosome loss samples. These translocations were validated in our RNA-seq data using STAR-Fusion. Ongoing analyses include inferring CNV from PCa scRNA-seq data, and determining cell populations with the centrosome loss CN-signature and their associated transcriptome features. This work unveils a comprehensive genomic profile stemming from centrosome loss and demonstrates its role in driving oncogenesis in PCa. These findings have the potential to establish centrosome loss as a hallmark in PCa stratification, and lead to a significant advancement in prostate tumor treatment. Citation Format: Jiawen Yang, Diogo de Oliveira Pessoa, John M. Ryniawec, Emily Loertscher, Anne E. Cress, Megha Padi, Gregory C. Rogers. Characterization of a centrosome loss-induced tumorigenic signature in prostate epithelial cells [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 4349.

Abstract 5150: An immunohistochemical survey of predictive biomarkers for immunotherapy in ampullary carcinoma identifies strata with unique prognostic signatures

Abstract Introduction: Carcinomas located in the ampulla of Vater are a low incidence malignancy. Therapeutic options for early stage disease largely consist of pancreaticoduodenectomy followed by adjuvant chemotherapy with or without radiation. We explored the localization of CD8 and CD3 positive cells in addition to PDL-1 staining and mismatch repair deficiency markers to gain insight into the potential applicability of immunotherapy for patients with this disease. Methods: Excess material from clinically diagnosed cases collected between 1997 - 2013 were used to construct a duplicate 0.6mm core tissue microarray (TMA). All cases were derived from the Vancouver Coastal Health Region. Immunohistochemical staining was performed with the following markers: CD8, CD3, PD-L1, and the mismatch repair (MMR) markers: MSH2, MSH6, MLH1 and PMS2. CD3 and CD8 were quantified using localization within the tissue. PD-L1 was considered positive with &amp;gt;1% of cells stating positive. MMR markers were confirmed using full section and cases with convincing loss of any MMR marker were considered MMR deficient. Univariable disease specific survival analysis was performed to identify unique prognostic signatures and contingency analysis was performed to identify co-expression of the aforementioned biomarkers. Results: Ninety-eight cases were evaluable for all markers. The median age of the cohort was 69 [41 - 84] years. Forty-two percent were female. Adjuvant chemotherapy was provided to 15% of patients with the remainder undergoing post-surgical observation. Almost 90% were pT3 or pT4 and 48% had regional lymph node metastasis. CD3+ T-cells were either localized in the tumor stroma only (59%) or in both the stroma and epithelial compartments (41%). CD8+ T-cells were principally located in the stroma (66%) and both the epithelial and stroma (24%). Ten percent of cases had no CD8+ T-cells. PD-L1 staining was found in 10% of cases. MMR deficiency was found in 5% of cases. Improved prognostic signatures were found for cases with CD3+ and CD8+ T-cells in both the epithelial and stromal compartments (p &amp;lt;= 0.02). A trend towards a negative prognostic signature was observed for MMR deficient cases and for PD-L1 positive cases. The only significant positive association between biomarkers was found for CD3+ and CD8+ in both the epithelial and stromal compartments. Conclusions: The results of this analysis suggest that enhancement of an immune response yielding an increase CD3+ and CD8+ T-cells in the epithelial compartment may have a beneficial effect on prognosis. The relative scarcity of MMR deficiency in this disease is within the expected prevalence supported by other studies. Further exploration of the potential role of immunotherapy in immune enhanced subgroups of ampullary cancers is warranted. Citation Format: Steve E. Kalloger, Joanna Karasinska, James Topham, Daniel J. Renouf, David F. Schaeffer. An immunohistochemical survey of predictive biomarkers for immunotherapy in ampullary carcinoma identifies strata with unique prognostic signatures [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 5150.