Homologous Recombination Deficiency Research Articles

Abstract 4537: VB15010 is a potent PARP1 selective inhibitor and durable trapper with improved pharmacological activities

Abstract PARP inhibitors have become the backbone of therapy for patients bearing cancers with homologous recombination deficiency (HRD). Currently approved PARP inhibitors, such as olaparib, are pan-PARP inhibitors targeting PARP1, PARP2, and other PARP family members. Emerging evidence suggests that targeting PARP1 is sufficient to exert antitumor effect, whereas targeting PARP2 causes hematological toxicity. Consequently, these pan-PARP inhibitors often lead to dose reduction and treatment discontinuation in clinics. Therefore, developing PARP1 selective inhibitors becomes advantageous to improving patient outcomes and broadening the applications of the targeted therapy. To this end, multiple PARP1 selective inhibitors are currently in preclinical or early clinical development worldwide. We report herein preclinical investigation of a novel, potent PARP1 selective inhibitor and durable DNA trapper, VB15010, which demonstrates improved pharmacokinetic (PK) and pharmacodynamics (PD) properties, and antitumor activity in comparison with an advanced agent in clinical development. Comparatively, VB15010 exhibited higher selectivity for PARP1 over other PARP family members (30 to 8,000-fold) in enzymatic assays, and superior selectivity for PARP1- over PARP2-DNA trapping (>1700-fold) in DNA trapping assays. Genetic knockout of PARP1, but not PARP2, abolished inhibition of PARylation by VB15010 in PARP1/2 wild type cells, further validating its PARP1 selectivity. Besides, VB15010 induced substantially more durable PARP1-DNA trapping when compared to the reference agent. In addition, VB15010 demonstrated potent antiproliferative activity in BRCAm or HRD-positive cancer cell lines (IC50 < 100 nM), as well as induced an increase in DNA damage, cell cycle arrest in G2 phase, and apoptosis in BRCA2-deficient cells in vitro. In vivo, VB15010 showed excellent bioavailability in preclinical animal models. Moreover, VB15010 exerted substantial antitumor activity at a dose range from 0.1 to 30 mg/kg, leading to tumor regression at as low as 0.3 mg/kg in BRCAm human cancer cell line-derived and HRD-positive patient-derived mouse xenograft models with an excellent PK-PD correlation. Tumor-to-plasma ratios of drug exposures indicate that VB15010 displayed a preferable tumor tissue distribution compared with the reference agent. Collectively, with improved PK-PD properties, including durable DNA trapping capability, higher apoptosis-inducing potency, and favorable tumor-to-plasma distribution ratio, as well as potent antitumor activity, VB15010 may achieve enhanced clinical efficacy and reduced hematological toxicity with a higher therapeutic index in patients. Its IND filing is expected in the first quarter of 2024. Citation Format: Douglas D. Fang, Yueqin Liu, Yang Liu, Haolong Zhang, Jinping Wu, Jie Wei, Wei Sha, Charles Z. Ding. VB15010 is a potent PARP1 selective inhibitor and durable trapper with improved pharmacological activities [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 4537.

Abstract 1454: Expanding the therapeutic application of PARP inhibitor: AI evaluation of real-word clinico-genomic data from spontaneous canine tumors

Abstract The widespread application of Poly-ADP ribose polymerase (PARP) inhibitors in anti-cancer therapy is constantly increasing their role as a treatment strategy across various neoplasms, the majority of which are linked with BRCA deficiency. While the most significant advantages are observed in cancers with BRCA1/2 mutations, it is evident that the benefits extend beyond this specific group. Preclinical evidence encourages the exploration of PARP inhibitors in neoplasms demonstrating BRCAness or homologous recombination deficiency (HRD), both as monotherapy and in combination with chemotherapy. This study employs spontaneous canine tumors as a complementary model for cancer research, aiming to seamlessly bridge the transition from preclinical investigations to clinical application. Leveraging the FidoCure® Precision Medicine Platform, we identified biomarkers associated with prognosis and treatment prediction, specifically with the PARP inhibitor olaparib, facilitating a smoother translation from laboratory findings to practical clinical use. Analyzing real-world clinico-genomic data from 1278 dogs with cancer revealed intriguing insights of specific targeted treatments developed for humans showing a positive prognosis when applied to canine tumors with specific genomic alterations. Notably, olaparib exhibited efficacy in TP53 and BRCA1-mutated cases (OS HR 0.34, P < 0.001; HR 0.39, P = 0.004), while rapamycin (mTOR inhibitor) demonstrated promising outcomes in TP53 and RB1-mutated canine tumors (OS HR 0.73, P = 0.028; HR 0.32, P = 0.024). Further stratification by tumor types unveiled noteworthy correlations. TP53 mutant osteosarcomas exhibited improved prognosis with olaparib treatment (OS HR 0.11, P < 0.001), and soft tissue sarcomas with TP53 mutations demonstrated favorable responses to rapamycin and olaparib therapy (OS HR 0.11, P = 0.012; HR 0.07, P = 0.011). These findings underscore the potential of leveraging canine tumor models and clinico-genomic analyses to inform targeted treatment strategies, offering valuable insights for advancing precision medicine in both veterinary and human oncology. Further investigation into the association between TP53 mutation and olaparib response is warranted. The intriguing aspect lies in the role TP53 mutation has been linked in previous studies to heightened chromosomal instability and elevated HRD scores. Utilizing real-world evidence and data tools within the FidoCure dataset, we have effectively pinpointed correlations between gene mutations and survival, particularly in relation to responses to targeted therapy treatment. Canine models, mirroring human diseases with intact immune systems and comparable tumor genomic profiles, as verified by the FidoCure database, expedite clinical studies of novel treatments that face significant scalability challenges. Citation Format: Lucas Rodrigues, Kevin Wu, Garrett Harvey, Gerald Post, Abigail Hull, Aubrey Miller, Lindsay Lambert, Christina Lopes, James Zou. Expanding the therapeutic application of PARP inhibitor: AI evaluation of real-word clinico-genomic data from spontaneous canine 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 1454.

Abstract 1746: KRAS mutant lung adenocarcinoma is associated with distinct mutational signature profiles

Abstract Background: Lung cancer is the 3rd most common cancer in the UK and leading cause of cancer mortality worldwide. Somatic RAS mutations are the most common oncogenes in human cancer, and KRAS mutations are the largest molecular subset of lung adenocarcinoma (LUAD). Each cancer genome accumulates a unique combination of somatic mutations, and these mutational signatures provide a genetic imprint of mutational processes that have occurred during tumorigenesis. Mutational signatures provide information on tumor aetiology/maintenance and could highlight potential therapeutic targets. This is the largest study to date to profile KRAS mutant LUAD mutational signatures using whole genome sequencing (WGS) data. Methods: Paired tumor and germline WGS data were obtained through the 100 000 Genomes Project (Genomics England). KRAS mutations were profiled using Ensembl Variant Effect Predictor (VEP) v109.0. Single base substitution (SBS), doublet base substitution (DBS), small insertion and deletions (ID) and copy number (CN) mutational signature extraction was performed using SigProfiler (COSMIC version 3.3). Statistical analysis and plotting were performed in R; a two-tailed p-value <0.05 was considered statistically significant. Results: 680 LUAD patients were included; 301 KRAS mutant (44%), 379 KRAS wild type (63%). Common KRAS variants were present, including G12C (38.9%), G12V (15.9%) and G12D (14.0%). 17 SBS, 9 DBS, 10 ID and 9 CN signatures were extracted and present in both KRAS mutant and wild type cohorts. KRAS mutant samples were enriched in smoking related signatures (SBS4, DBS2, ID3; odds (OR) ratio 5.54, 3.80, 4.97 respectively, p <0.001) and diploid CN signature (CN1, OR 1.41, p = 0.03). Conversely, KRAS mutant samples were less likely to have clocklike (ID5, OR 0.61, p = 0.012; ID8, OR 0.44, p <0.001), APOBEC (SBS2, OR 0.49, p <0.001; SBS13; 0.50, p <0.001), chromosomal instability (CN9, OR 0.63, p = 0.019), loss of heterozygosity (CN14, OR 0.47, p = 0.015), or homologous recombination deficiency (CN17, OR 0.58, p <0.001) signatures. Discussion: These results show distinct mutational signature profiles between KRAS mutant and wild type LUAD. As previously described, KRAS mutant LUAD is dominated by smoking related signatures; however, the majority of remaining signatures were more common in the KRAS wild type cohort where there was a statistically significant difference. This data suggests different mutational processes are observed in KRAS mutant compared to wild type LUAD. KRAS mutations are commonly clonal and thought to initiate tumorigenesis: timing signatures relative to KRAS mutations is necessary to further our understanding of KRAS cancer evolution and the subject of future work. Combined with clinical data integration, mutational signatures could provide prognostic information and inform predictive models. Citation Format: Laura Woodhouse, Aliah Hawari, Andreas Gruber, Colin Lindsay, David Wedge. KRAS mutant lung adenocarcinoma is associated with distinct mutational signature profiles [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 1746.

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 2938: Comprehensive genomic profiling of solid tumor patients with the OncoDEEP assay for broad analysis in clinical diagnostics

Abstract Somatic multi-gene analysis by Next Generation Sequencing (NGS) becomes standardly integrated in medical oncology for clinical decision making. However, with the fast-growing number of recommended and required genomic biomarkers, small panels have become vastly insufficient for most tumor types. Comprehensive Genomic Profiling (CGP) is amenable to screen for single nucleotide variants (SNVs) and subtle insertions and deletions (indels) in several hundreds of genes. Moreover, it provides information on copy number variations (CNVs) and gene fusions of the most relevant genes for optimal patient management. Currently, most comprehensive panels also allow for screening of tumor-agnostic genomic biomarkers, including microsatellite instability (MSI), tumor mutation burden (TMB) and homologous recombination deficiency (HRD), which are implemented as prognostic and therapeutic signatures in a wide variety of solid tumors. So far, only a handful of CGP assays have been validated for their diagnostic utility in routine laboratory practice for the care of cancer patients. In this study we report on an extensive multicentric analysis across multiple centers in Belgium and The Netherlands comparing the novel OncoDEEP CGP assay (OncoDNA) with the diagnostically validated TSO500 assay (Illumina). We describe the technical differences between both assays as well as their outcome and shortcomings. Detection of clinically relevant SNVs, indels and CNVs was very similar and differences were often due to assay-specific settings. Similarly, TMB, MSI and HRD data were concordant for most samples but those with scores close to the cut-offs could deviate. For fusion detection, concordance was found for the limited number of 11 clinically-actionable driver genes covered by the OncoDEEP kit. The uniformity of coverage was much higher with the OncoDEEP assay thereby allowing to pool 2- to 3-times more samples per NGS run. For the diagnostic implementation of the OncoDEEP assay we then performed an extensive validation with clinical samples representing a wide variety of solid tumor types, as well as reference samples. All performance metrics passed the validation criteria. In conclusion, the OncoDEEP kit can be used for reliable diagnostic comprehensive profiling of solid tumors, but currently, extensive fusion analysis requires an additional screening method. Citation Format: Ernst-Jan M. Speel, Pieter-Jan Volders, Joni Van der Meulen, Aaron De Cock, Stefanie Vermeire, Jacques Van Huysse, Marie De Barsy, Gabriela Beniuga, Wendy de Leng, Anne Jansen, Sharon Thijssen, Hendrikus Jan Dubbink, Zeliha Ozgur, Wilfred van Ijcken, Brigitte Maes, Guy Froyen. Comprehensive genomic profiling of solid tumor patients with the OncoDEEP assay for broad analysis in clinical diagnostics [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 2938.

Abstract 4562: Activity of PARP1-selective inhibitor SNV-001 in models of HRD cancers as monotherapy and in combination

Abstract Current FDA approved poly (ADP-ribose) polymerase inhibitors (PARPi) inhibit both PARP1 and PARP2. Genetic studies indicate that loss of PARP1 is synthetic lethal with homologous recombination deficiency (HRD), including BRCA1/2 mutations, and PARP2 depletion may be linked to hematologic toxicity. To date, no first generation PARPi has been successfully combined with standard of care (SoC) agents in the clinic without significant reduction in dosing intensity because of overlapping toxicities. A selective inhibitor could potentially improve the therapeutic index and provide additional opportunities in combination strategies especially with drugs that are prone to myelosuppression. SNV-001 potently and selectively inhibits PARP1 in biochemical and cellular assays. SNV-001 inhibits PARylation in the low nanomolar range with over 500-fold selectivity against PARP2. SNV-001 did not inhibit any other PARP family member tested up to 10 uM in biochemical assays confirming its selectivity for PARP1. In human erythroid and myeloid colony formation assays, the IC50s of SNV-001 for both lineages were approximately 100-times higher than the target efficacious concentration based on the IC95 for inhibition of DLD1 (BRCA2 -/-) colony formation. In a subcutaneous MDA-MB-436 (BRCA1mut) xenograft model, oral administration of SNV-001 once daily resulted in a dose-dependent tumor regression. SNV-001 showed greater efficacy at lower doses compared to olaparib at 100 mg/kg or at equivalent doses of AZD9574. SNV-001 showed promising synergy with SoC chemotherapies or DDR inhibitors in cell proliferation assays. SNV-001 enhanced cytotoxicity of the DNA-damaging agent topotecan or carboplatin in Capan-1 (BRCA2mut) and HCC1395 (BRCA1mut) cells. Synergy was seen between SNV-001 and cell cycle check point inhibitors camonsertib (ATRi) or adavosertib (WEE1i) in DLD1 (BRCA2 -/-) and UWB1.289 (BRCA1mut) cells, as DNA damage induced by PARP1 trapping relies on cell cycle modulation for repair. Combination of SNV-001 with polymerase theta inhibitor ART558 or USP1 inhibitor KSQ4279 exhibited synergistic effects in DLD1 (BRCA2 -/-) or UWB1.289 (BRCA1mut) cells. These results suggest that inhibition of microhomology-mediated end-joining and translesion synthesis pathways may further exacerbate SNV-001-induced DDR in certain cellular contexts.In summary, the PARP1 selective inhibitor SNV-001 demonstrates potent antitumor activity and shows promising synergy between SoC chemotherapies or DDR inhibitors. Current data highlight a potential strategy for improving treatment efficacy and overcoming resistance. Further clinical investigations are warranted to validate this combination strategy. Citation Format: Zhentian Li, Qipeng Fan, Mingming Gao, Jun Pan, Liangxing Wu, Wenqing Yao, Phillip C. Liu. Activity of PARP1-selective inhibitor SNV-001 in models of HRD cancers as monotherapy and in combination [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 4562.

Abstract 2520: CD133 expression is associated with less DNA repair, better response to chemotherapy, and survival in ER-positive/ER-negative breast cancer

Abstract Introduction: Cancer stem cells (CSC) constitute only 0.1-1% of all the cells in a bulk tumor, yet they play a crucial role in treatment resistance and relapses. Its role in breast cancer (BC) has been studied but a consensus remains elusive. We focused on gene expression of a CSC marker CD133 and studied its clinical significance in ER-positive/HER2-negative (ER+/HER2-) BC, the most prevalent subtype. We utilized multiple independent large patient cohorts of gene expression and clinical variables for transcriptome analysis. Methods: A total of 2969 patients from The Cancer Genome Atlas (TCGA, n=1065) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC, n=1904) BC cohorts, as well as BC patients who underwent neoadjuvant chemotherapy (NAC; GSE25066, GSE20194, GSE32646 cohorts) were analyzed. Results: By analyzing SCP1039 and SCP1106 single-cell sequencing cohorts, we found that epithelial cells were the predominant source of CD133 gene expression in the tumor microenvironment. High expression of CD133 in ER+/HER2- BC correlated with elevated gene expressions of the other CSC markers; CD24, NOTCH1, DLL1, and ALDH1A1 (all p<0.001), and significantly enriched WNT/β-Catenin, Hedgehog, and Notch signaling (all FDR<0.25), which are all known pathways related with CSC in TCGA and validated in METABRIC cohort. Consistent with CSC phenotype, CD133-high BC was negatively enriched with Hallmark cell proliferation-related gene sets, such as E2F Targets, G2M Checkpoint, MYC Targets V1, Ki67 gene expression and proliferation score (FDR<0.25 and p<0.001, respectively) in both cohorts. CD133-high BC was negatively associated with DNA repair genes, such as BRCA1, E2F7 in both cohorts (all p<0.001). In agreement, CD133-high BC was associated with less homologous recombination deficiency, lower silent and non-silent mutation rates. Surprisingly, CD133-high BC exhibited a proinflammatory microenvironment, as represented by higher cytolytic activity in the METABRIC and higher lymphocyte infiltrations, TGF-beta response, and TCR richness in TCGA (both p<0.001), but less Th1 cells, M1 macrophages and dendritic cell infiltrations consistently in both cohorts. It also enriched signaling pathways related to inflammation and immune responses such as inflammatory response, allograft rejection, TNF-alpha, IL-6, TGF-beta signaling, and complement signaling (all FDR<0.25). CD133-high tumors had better pathological complete response after NAC in GSE25066 cohort and improved Disease-Free Survival and Overall Survival in both TCGA and METABRIC cohorts (all p<0.05). Conclusion: CD133-high ER+/HER2- BC is associated with CSC phenotype, reduced cell proliferation, and impaired DNA repair, but enhanced inflammation, potentially explaining the better response to NAC and favorable patient prognosis. Citation Format: Takumi Sato, Masanori Oshi, Jing Lee, Arya M. Roy, Kohei Chida, Itaru Endo, Masato Obayashi, Kazuaki Takabe. CD133 expression is associated with less DNA repair, better response to chemotherapy, and survival in ER-positive/ER-negative 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 2520.

Abstract 6422: Comprehensive proteogenomic profiling and biomarker analyses in resected extrahepatic cholangiocarcinoma: A prespecified exploratory analysis of the phase 2 STAMP trial

Abstract Background: Biliary tract cancer constitutes a heterogeneous group of diseases with a limited understanding of its molecular characteristics and prognostic/predictive biomarkers. We performed prespecified exploratory analyses of the STAMP trial, a multicenter randomized phase 2 trial of adjuvant capecitabine (CAP) or gemcitabine plus cisplatin (GemCis) for patients with resected extrahepatic cholangiocarcinoma (EH-CCA) with regional lymph node metastasis. Methods: Among 101 patients included in the intention-to-treat population of the STAMP trial, a total of 89 patients (45 in the GemCis group and 44 in the CAP group) were included in the current biomarker analysis after excluding 12 patients without available tissue and blood samples. Whole exome sequencing and proteomics were performed using surgical specimens. Results: TP53 (63%), SMAD4 (20%), and KRAS (18%) mutations were the most frequent in the pooled population. Somatic mutations in homologous recombination deficient (HRD) genes were present in 20% of patients, while one patient (1%) had a germline ATM mutation. The prevalence of microsatellite instability was 1%. Somatic mutations in known targetable genes were observed in 54 patients (60.7%) and proteogenomic integrative analysis revealed significant HER2 pathway alteration with HER2 amplification in 4 patients (7%). The characteristics of prognostic biomarkers varied by the adjuvant regimen used. In the adjuvant GemCis group, somatic mutations were associated with poor disease-free survival (DFS) and overall survival (OS), including KRAS (log-rank p=0.004 for DFS and p=0.003 for OS), FBXW7 (p=0.021 for DFS and p=0.011 for OS), and PIK3CA (p<0.001 for DFS and p=0.042 for OS) mutations. In the adjuvant CAP group, copy number alterations (CNAs) such as 8q24.21 amplification (p=0.006 for DFS and p=0.707 for OS) and 3q26.1 amplification (p=0.020 for DFS and p=0.026 for OS) were associated with poor survival, while 11q13.3 amplification (p=0.017 for DFS and p=0.099 for OS) was associated with improved survival. Additionally, a higher HRD score showed a tendency toward better DFS and OS in the GemCis group, but not in the CAP group, although it did not reach statistical significance in both groups (p>0.05). Non-negative matrix clustering of proteomics data classified patients into 4 clusters. Among those, cluster 2, which showed alterations in the metabolism pathway, was associated with higher CNA level, higher tendency of HRD scores, and favorable survival with GemCis (p=0.039 for DFS and p=0.100 for OS) but not with CAP. Conclusions: Comprehensive proteogenomic analyses enable the identification of prognostic biomarkers and may guide the selection of adjuvant chemotherapy in resected EH-CCA. Citation Format: Hyehyun Jeong, Ji-Hye Oh, Hee-Sung Ahn, Baek-Yeol Ryoo, Kyu-pyo Kim, Jae Ho Jeong, Inkeun Park, Seung-Mo Hong, Jinho Shin, Chae Won Park, Yoo Sook Cho, Kyunggon Kim, Chang Ohk Sung, Changhoon Yoo. Comprehensive proteogenomic profiling and biomarker analyses in resected extrahepatic cholangiocarcinoma: A prespecified exploratory analysis of the phase 2 STAMP trial [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 6422.

Abstract 3909: PARG inhibitor sensitivity is correlated with accumulation of single strand DNA gaps in preclinical models of ovarian cancer

Abstract Poly (ADP-ribose) glycohydrolase (PARG) is a dePARylating enzyme which promotes DNA repair in conjunction with PARP1 by removal of poly (ADP-ribose) (PAR). Loss or inhibition of PARG results in replication stress and sensitizes cancer cells to DNA damaging agents, suggesting it is a potential therapeutic target for cancer therapy. Indeed, PARG inhibitors are now undergoing clinical development for patients having tumors with homologous recombination deficiency (HRD), such as ovarian and breast cancer patients with BRCA1/2-mutation. In this study, we investigated PARG inhibitor (PARGi)-PDD00017273 activity in preclinical models of ovarian cancer cell lines and primary patient-derived organoids. PARGi exhibited sensitivity in a subset of ovarian cancer cell lines that was distinct from PARP inhibitor sensitivity. Initially, we evaluated a PARGi-sensitive cell line, RMUGS. By gradually increasing the concentration of PARGi, we generated drug resistant cells. PARGi treatment resulted in increased S phase specific PAR, DNA-PARylation, DNA damage, and replication stress in the sensitive cells but not in cells with de novo or acquired resistance. In the sensitive cells, PARGi exposure also increased accumulation of PAR at the replication fork resulting from unligated Okazaki fragment processing. More importantly, PARGi treatment or PARG loss caused accumulation of single strand DNA (ssDNA) gaps in sensitive cells, as detected by the DNA fiber assays combined with S1 nuclease treatment. Regardless of the BRCA-status, the induction of ssDNA gaps in ovarian cancer cells correlated with PARGi sensitivity. Consistent with an increase in ssDNA gaps, PARGi exposure increased p-RPA, a ssDNA surrogate, at the replication fork in sensitive cells. p-RPA sites also colocalized with PAR suggesting that accumulation of PAR occurs at the ssDNA sites, perhaps, leading to the ssDNA gaps. Collectively, these results suggested that toxic accumulation of PAR at the replication fork leads to accumulation of ssDNA gaps due to Okazaki fragment processing defects and ovarian cancer cell killing after PARG inhibition. We further assessed PARG inhibition in patient-derived organoids (PDOs) and patient-derived xenograft (PDX)-derived organoids (PDXOs) as model systems of ovarian cancer. PARGi exhibited monotherapy activity in specific HR-deficient PDOs and PDXOs with BRCA1 or RAD51C mutation and in a HR-proficient PDXO model. Importantly, PARGi exposure resulted in accumulation of ssDNA gaps in organoids of ovarian cancer and this phenotype directly correlated with drug sensitivity. PDOs can therefore be a useful model system for testing PARGi sensitivity. The detection of ssDNA gaps in PDOs may provide a functional biomarker to predict the response to PARG inhibitors in clinical trials. Citation Format: Ramya Ravindranathan, Ozge Somuncu, Yuqing Jiao, Alexandre André B A da Costa, Benjamin P Lamarre, David B Martignetti, Gabriella A Zambrano, Sirisha Mukkavalli, Joyce Liu, Bose Kochupurakkal, Jean-Bernard Lazaro, Kalindi Parmar, Geoffrey I Shapiro, Alan D. D'Andrea. PARG inhibitor sensitivity is correlated with accumulation of single strand DNA gaps in preclinical models of 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 3909.

Abstract 406: Characterization of whole genome duplication in a genomic cohort of over 14000 cell free DNA samples

Abstract Background: Wide-scale rates of whole genome duplication (WGD) have previously been demonstrated in studies performed in tissue among genomically characterized tumors. Such studies report varied rates of WGD depending on tumor type and stage. Hallmarks of WGD include widespread loss-of-heterozygosity as well as associations with tumor proliferation and specific oncogenic driver events such as loss of function TP53 mutations. It has been proposed that presence of WGD could be a poor prognostic biomarker, leading to interest in profiling this genomic landmark in large retrospective cohorts to inform future clinical studies. Methods: Samples that were run through the GuardantOMNI high content genomic profiling assay using cfDNA extracted from blood were analyzed. Only samples originating from individuals with primary breast, colorectal, or prostate cancer were considered due to limited sample size in other indications. We deployed a likelihood-based copy-number variant caller, which jointly selects tumor purity and ploidy while fitting normalized coverage and germline variant allele frequencies across genome-wide data. Only samples where we predicted to have greater than 10% tumor fraction from copy number variant (CNV) profiles were considered for statistical analysis. The presence of whole genome duplication was assessed by counting the median major chromosomal copy number. Presence of SNV/InDels were annotated, assessed for pathogenicity, and filtered to those with a pathogenic allele frequency greater than 10%. Results: A total of 14,076 samples were analyzed, with 5362 passing the 10% observed tumor fraction cutoff. WGD was annotated in 2195 (41%) samples with varying rates across sub-cohorts (31%, 36%, and 54% of breast, colorectal, and prostate cancer, respectively). Mutation in TP53 was associated with a large increase in rate of WGD (odds ratio 6.9, 95% CI 6.1-7.8) which is consistent but higher in magnitude to similar studies in tissue samples. Amplification of CCNE1 and homozygous deletion of genes including WRN and RB1 were also associated with WGD, independent of TP53 mutation status and overall rates of aneuploidy. Conclusion: WGD was detected in 41% of samples with greater than 10% tumor fraction in cell-free DNA across three cancer types. While this represents a substantial percentage of advanced cancers, more research needs to be done regarding the impact of these events on clinical outcomes and treatment response. Additionally, co-occurrence of these events with other advanced cancer biomarkers such as microsatellite instability or homologous recombination deficiency was not reported. Given the high rates of these events, future retrospective studies are warranted to correlate presence of WGD with patient outcomes and response. Citation Format: Andrew Gross, Hao Wang, Denis Tolkunov, Colby Jenkins, Sara Wienke, Catalin Barbacioru, Han-Yu Chuang. Characterization of whole genome duplication in a genomic cohort of over 14000 cell free DNA samples [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 406.

Abstract 5070: Landscape of clonal hematopoiesis prior to PARP inhibitor treatment in patients with ovarian cancer

Abstract Background: Poly (ADP-ribose) polymerase inhibitors (PARPi) are an important tool for treatment of ovarian and other cancers, particularly for those with mutations in BRCA1 or 2 genes or homologous recombination deficiency. The risk of developing secondary hematologic malignancy, particularly myelodysplastic syndrome or acute myeloid leukemia (MDS/AML), is substantially higher (4-12%) after PARPi maintenance or treatment in the second line and beyond in patients with ovarian cancer. This elevated risk necessitates additional investigation into the pathogenesis of PARPi-related secondary malignancy. Clonal hematopoiesis of indeterminate potential (CHIP) has been associated with the development of therapy-related myeloid neoplasms. We aim to understand the patterns of CHIP in patients with high grade serous ovarian carcinoma who receive PARPi therapy. Methods: We performed ultra-high-depth whole exome sequencing of plasma derived cfDNA or white blood cells (WBCs) barcoded with unique molecular identifiers from patients with high grade serous ovarian carcinoma who were treated with multiple lines of chemotherapy (n=6) or with PARPi in addition to chemotherapy (n = 10). Using spike-in mutated DNAs as positive controls, we detected variant alleles as low as 1% variant allele frequency. Gene set enrichment analysis was performed on identified groups. Results: We identified 7162 recurrent variants among our patients. We began by comparing quantities of CHIP between the samples from patients who eventually receive PARPi and those who do not. Samples contained a median of 2030 recurrent CHIP variants and 4300 total variants. No differences in total CHIP quantity or mutation type was discernable among samples from patients who will receive PARPi (BRCA1/2 enriched) vs those who will not. Among our 16 patients, 14 ultimately developed secondary hematologic malignancy (t-MN+ Comparison of t-MN+ (n=14) and t-MN- (n=2) defined a group of 14 variants enriched in the t-MN+ population and a group of 85 variants depleted in the t-MN+ population. The t-MN+ enriched variants we identified were not previously associated with CHIP and had significant overlaps with alkyl transferase activity (FDR q val < 0.01) and nucleotide binding gene sets (FDR q val < 0.01). Conclusions: We used a novel methodology to identify unbiased low variant mutational changes in the hematopoietic system. These results suggest that baseline clonal hematopoiesis variants are similar among patients newly diagnosed with ovarian carcinoma. We have also identified a signature potentially related to future risk of leukemia requiring further validation. Citation Format: Amma Asare, Sara Corvigno, Jun Yao, Li Zhao, Nicole D. Fleming, Joseph Celestino, Richard A. Hajek, Mark S. Kim, Alejandra Flores Legarreta, Karen H. Lu, Koichi Takahashi, P Andrew Futreal, Amir A. Jazaeri, Shannon N. Westin, Anil K. Sood, Sanghoon Lee. Landscape of clonal hematopoiesis prior to PARP inhibitor treatment in patients with 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 5070.

Abstract 909: Enhancing genomic analysis in cancer diagnostics: A machine learning approach for removing artifacts in FFPE specimens

Abstract Formalin-Fixed Paraffin-Embedded (FFPE) specimens, widely utilized in clinical cancer diagnostics, present significant challenges by introducing artifacts into genomic data. This study aimed to profile these FFPE-induced genomic alterations, with a particular focus on single-nucleotide variants (SNVs), small insertions and deletions (indels), and copy-number variations (CNVs), and to develop computational methods for filtering out such artifacts. Our primary focus was twofold: first, to comprehensively characterize the unique error profile of FFPE specimens observed through whole-genome sequencing (WGS), and second, to construct artifact classifiers and noise filters for SNV/indels and CNVs. We utilized machine learning (ML) and signal-processing techniques on a dataset of FFPE and matched fresh-frozen (FF) samples. The dataset of 52 FFPE-FF pairs were obtained from four different medical institutes and from various cancers including liver, breast, colon, stomach, and lung cancer, with varied FFPE archiving times. We also analyzed additional FFPE-only samples to refine our methods. Our methodology incorporated advanced computational approaches, including stacking ensemble, transfer learning, and wavelet transform, to enhance robustness and accuracy. The method's design was centered around the notion of not only achieving high performance in distinguishing true signals from FFPE-induced artifacts but also addressing the real-world challenges posed by the varying quality and conditions of clinical FFPE samples. In the analysis, we found peculiar patterns of FFPE-specific error profile, including well-known cytosine deamination and novel mutational signatures. The classifier, building on our findings, effectively differentiated true genomic variants from FFPE-induced artifacts for both SNVs and indels, demonstrating a sensitivity of 0.97, specificity of 0.87, and an F1 score of 0.94 for SNVs. For indels, it achieved a sensitivity of 0.91, specificity of 0.91, and an F1 score of 0.91. The CNV filter notably enhanced the signal-to-noise ratio (SNR) of CNV depth profiles, increasing it from 13dB to 17.5dB on average. Furthermore, we conducted evaluations on two critical measures in cancer and clinical genomics: homologous recombination deficiency (HRD) and tumor mutational burden (TMB), achieving post-filtering concordance rates of 0.99 for HRD—correctly identifying all 8 HRD-positive patients in our dataset—and 0.96 for SNV-based TMB and 0.87 for indel-based TMB. Additionally, a post hoc procedure for sensitive detection of cancer driver mutations resulted in concordance rates of 0.94 for SNVs, 0.91 for indels, and 0.95 for oncogene amplification. Taken together, our study advances FFPE WGS analysis in cancer diagnostics by effectively filtering artifacts and addressing challenges with older, degraded samples, enhancing clinical applicability. Citation Format: Joonoh Lim, Seongyeol Park, Won-Chul Lee, Ryul Kim, Sangmoon Lee, Jeong Seok Lee, Brian Baek-Lok Oh, Young Seok Ju. Enhancing genomic analysis in cancer diagnostics: A machine learning approach for removing artifacts in FFPE specimens [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 909.

Abstract 3947: Non-BRCA variants in hereditary breast and ovarian cancer patients in the Northern Mexico population

Abstract Background: Hereditary cancer syndromes explain 5-10% of all cancer cases. Germline pathogenic variants in BRCA1 and BRCA2 genes (BRCA) are present in 2-3% of all breast cancer (BC), and 15% of all ovarian cancer (OC) cases. BRCA1 and BRCA2 pathogenic variants (PV) represent 25-28% of BC and 40% of OC patients with a positive familial history. BRCAs are the most studied genes for the prevalence, family history, preventive surgeries, and target treatment options in both BC and OC. There are other genes, important in the diagnosis, pathogenesis, and treatment options of the patients: TP53, PALB2, CHEK2, among others. This study aims to identify the prevalence of non- BRCA genes related to the development of hereditary breast and ovarian cancer syndrome in patients of Northeast Mexico. Methods: This is a multicenter study that recruited patients from two reference oncology centers in Nuevo Leon, Mexico: the CECIL (The CUCC Early Cancer Detection Clinic) Hereditary Cancer Registry and Hereditary Cancer Program from Tec Salud. From March of 2016 to March of 2023, a total of 872 patients meeting NCCN criteria were evaluated by Medical Geneticists from both centers and were tested with NGS multigene cancer panels. Results: A total of 665 (76.26%) patients with a clinical diagnosis of HBOC (Hereditary Breast Hereditary Cancer Syndrome) were included. We found 310 (46.6%) patients had at least one variant, 180 (58%) with at least one pathogenic variant, and 130 (41%) with a VUS (a variant of uncertain significance). BRCA1 was found in 79 (43.8%) and BRCA2 in 32 (17.7%) of all PV. Non-BRCA PV were found in 69 (38.3%) patients: 4 ATM, 2 BLM, 3 BRIP1, 22 CHEK2, 4 CDKN2A, 5 MUTYH, 10 PALB2, 4 RAD51C, 2 SDHA, 2 TP53, 2 WRN, CDH1, CDK4, DICER, MSH3, NBN, PTEN, RAD50, USH2A one of each. Is remarkable that 19 of the 22 patients with CHEK2 and 5 of the 10 patients with PALB2 had the recurrent PV c.707T>C and c.2167_2168del, respectively. Conclusions: Non-BRCA PV in Northern Mexico corresponds to one-third of the BC and OC cases, including HRD (homologous recombination deficiency) genes. HDR patient carriers are potential targets of iPARP therapies. This project reinforces the fact that multigene panels should be employed to ensure a complete diagnosis in hereditary cancer patients. Citation Format: Carlos H. Burciaga-Flores, Diana C. Perez-Ibave, Maria L. Garza-Rodriguez, Oscar Vidal-Gutierrez, Cynthia M. Villarreal-Garza, Dione Aguilar y Mendez. Non-BRCA variants in hereditary breast and ovarian cancer patients in the Northern Mexico population [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 3947.

Abstract 670: Preclinical candidate LAE120, a novel selective USP1 inhibitor shows effective anticancer and combination activity with PARP inhibitor

Abstract The Fanconi anemia (FA) and translesion synthesis (TLS) are DNA damage tolerance and repair pathways that have been found to be regulated by reversible ubiquitination in which ubiquitin-specific protease 1 (USP1) plays a key role. Numerous studies have indicated that USP1 inhibitors have therapeutic effects on tumors with homologous recombination deficiency (HRD), including mutations in BRCA1/2. Due to the emergence of resistance to PARP inhibitors in clinical applications, new strategies are needed to address this issue. Here we present LAE120, a novel, allosteric and highly potent USP1 inhibitor, displayed monotherapy potency and combination activity with PARP inhibitor in HRD cancers. LAE120 has a unique tail group distinct from all the published USP1 inhibitors and is predicted to induce a different conformational change at the USP1 allosteric site. In the biochemical assay, LAE120 strongly inhibited USP1 enzymatic activity with IC50 of 5.6 nM. LAE120 potently inhibited proliferation of BRCA-mutated MDA-MB-436 breast cancer cell (IC50:19 nM) and exhibited anti-proliferative activity in NCI-H1792 (IC50: 69 nM) and K562 (IC50: 38 nM) cell lines. In the xenograft model of MDA-MB-436 cells with BRCA mutations, LAE120 demonstrated robust single-agent tumor inhibitory activity (TGI: 88%, 10 mg/kg BID) and a favorable dose-dependent response (TGI: 106%, 25 mg/kg BID). We also observed strong tumor-inhibition efficacy of LAE120 as a single agent in the K562 xenograft model with Bcr-Abl expression (TGI: 86%, 10 mg/kg BID). Current research indicates that USP1 inhibitors exhibit synergistic activity in combination with PARP inhibitors and re-sensitizes PARP refractory tumors. Similar results have been confirmed in the xenograft model of BRCA-mutated MDA-MB-436 cells. The combination of LAE120 and Olaparib (PARP inhibitor) yielded a more robust and durable anti-tumor efficacy at low dose (TGI: 110%, LAE120, 5 mg/kg BID + Olaparib, 50 mg/kg QD). LAE120 also displayed favorable ADME properties and PK profiles. Preclinical-tox studies indicated the molecule was well tolerated without significant toxicities and hematological observations. Both in vitro and in vivo data strongly support further investigation of LAE120, whether as a single agent or in combination therapy. Citation Format: Jintao Wang, Yan Chen, Junyan Chen, Ling Jiang, Xiaofen Lin, Chaojun Cai, Minhua Zhang, Ming Li, Justin Gu. Preclinical candidate LAE120, a novel selective USP1 inhibitor shows effective anticancer and combination activity with PARP inhibitor [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 670.

Abstract 2549: Activity-regulated cytoskeleton-associated protein (ARC) gene expression is associated with high infiltration of stromal cells and immune cells, but with less cancer cell proliferation and better overall survival in ER-positive/HER2-negative breast cancers

Abstract Introduction: Recently peritumoral lidocaine infiltration prior to removal was reported to be associated with better survival in early-stage breast cancer (BC). This led us to hypothesize that innervation to the tumor affects its biology and patient survival. Activity-regulated cytoskeleton-associated protein (ARC) gene expression is known to be regulated by neuronal activity. Therefore, we studied the clinical relevance of ARC gene expression as a surrogate of neuronal activity in BC. Methods: Sweden Cancerome Analysis Network-Breast (SCAN-B (GSE96058), n=3273) cohort was analyzed, and the results were validated using The Cancer Genome Atlas (TCGA, n=1069). Results: ER+/HER2- and Luminal A type cancers expressed significantly higher ARC compared to the other subtypes in both cohorts (p<0.005). In the tumor microenvironment, the stromal cells (fibroblasts, endothelial cells and adipocytes) were all found to be significantly infiltrated in high ARC BC (p<0.01). Multiple immune cells were significantly infiltrated in high ARC BC, including CD8, CD4 memory cells, helper type II T cells, regulatory T cells, M1 and M2 macrophages, dendritic cells and B cells (all p<0.03 in both cohorts). In terms of cancer characteristics, there was no difference in silent or nonsilent mutations, single nucleotide variant or indel neoantigens between tumors with low or high ARC expression. However, high ARC BC was significantly associated with less homologous recombination deficiency, intratumor heterogeneity and fraction altered mutation rate compared to low ARC BC in TCGA (p<0.001). High ARC expression was significantly associated with smaller tumor size (p<0.001) and without lymph node metastasis in the SCAN-B cohort (p<0.02), and less Stage IV disease in the TCGA cohort (p<0.02); however, these results were not validated by the other. High ARC BC was significantly associated with lower Nottingham histologic grade and lower MKi67 expression in both cohorts (p<0.001). Cell proliferation-related gene sets in the Hallmark collection (E2F targets, G2M checkpoint, and MTORC1 signaling) were significantly less enriched to high ARC BC consistently in both cohorts. Overall survival (OS) was significantly better in high ARC BC in the ER+/HER2- subtype consistently in both cohorts (p<0.01) and when including all subtypes in the SCAN-B cohort (p<0.001); however this was not validated in TCGA. No significant difference in OS was found between low and high ARC gene expression in triple negative BC in either cohort. Conclusion: ARC gene expression as a surrogate of neuronal activity in BC was associated with high infiltration of stromal cells and immune cells but with less cancer cell proliferation and better overall survival, particularly in the ER+/HER2- subtype. Citation Format: Gabrielle Yee, Rongrong Wu, Takashi Ishikawa, Kazuaki Takabe. Activity-regulated cytoskeleton-associated protein (ARC) gene expression is associated with high infiltration of stromal cells and immune cells, but with less cancer cell proliferation and better overall survival in ER-positive/HER2-negative breast 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 2549.

Abstract 1893: OBI-992, a novel TROP2 targeting antibody-drug conjugate, displayed excellent antitumor efficacy in various animal models

Abstract Background: TROP2 is a validated therapeutic target for cancer treatment. OBI-992 is an antibody-drug conjugate (ADC) derived from a novel TROP2 antibody linked with a topoisomerase 1 inhibitor payload, exatecan, through conjugation with an enzyme-cleavable linker. Upon binding to TROP2 on the surface of cancer cells, OBI-992 is internalized into the cell and trafficked to lysosomes where the linker is cleaved by cathepsin B, releasing the payload exatecan to kill the cancer cells. This study aims to evaluate the antitumor efficacy of OBI-992 in vitro and in vivo, including cell-based cytotoxicity, cell line-derived xenografts (CDX), and patient-derived xenografts (PDX) models. Methods: The cytotoxicity of OBI-992 was evaluated in cell lines with different levels of TROP2 expression. In vivo efficacy was evaluated using CDX and PDX models of various cancer types. Bystander killing effect of OBI-992 was examined in a xenograft model containing a premixture of TROP2 positive and TROP2 negative cancer cells. Moreover, the impact of overexpression of P-glycoprotein (Pgp) or breast cancer resistance protein (BCRP) on the antitumor efficacy of TROP-2 ADCs was evaluated. OBI-992 in combination with PARP inhibitors such as olaparib and talazoparib was examined for potential synergistic effects in a homologous recombination deficiency (HRD) xenograft model. Results: The cytotoxicity of OBI-992 was positively associated with the TROP2 RNA levels in different cell lines. In various CDX and PDX models, a single dose of OBI-992 at 3 or 10 mg/kg exhibited remarkable tumor growth inhibition. Notably, the antitumor efficacy of OBI-992 surpassed that of datopotamab deruxtecan (Dato-DXd) across different CDX and PDX models. OBI-992 demonstrated a bystander killing effect as OBI-992 was able to kill TROP2-negative xenografts in the presence of nearby TROP2-positive cells. OBI-992 showed superior efficacy to Dato-DXd in the CDX model overexpressing Pgp or BCRP. These findings suggest that OBI-992 was not affected by the Pgp- and BCRP-mediated multidrug resistance. In the HRD CDX model at suboptimal doses, combination of OBI-992 with olaparib or talazoparib displayed remarkable synergistic effects. Conclusions: OBI-992 exhibited excellent antitumor efficacy and outperformed the benchmark Dato-DXd in CDX and PDX models of various cancer types. A strong bystander killing effect indicated that OBI-992 will be effective for tumors with heterogenous expression of target antigen. OBI-992 retained its antitumor effect upon overexpression of Pgp and BCRP, suggesting that OBI-992 may overcome the multidrug resistance. Outstanding synergistic effect with the combination of OBI-992 with PARP inhibitors was observed. These results warrant further studies of OBI-992 in the clinical setting. Citation Format: Wan-Fen Li, Ming-Feng Chiang, Hao-Cheng Weng, Jhih-Jie Yang, Hsin-Shan Wu, Chun-Jung Lin, Ping-Tzu Chiu, Ming-Tain Lai. OBI-992, a novel TROP2 targeting antibody-drug conjugate, displayed excellent antitumor efficacy in various animal 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 1893.

Abstract 975: Genomic landscape of circulating tumor DNA in cervical cancer in Asia: NCCH1905/A-TRAIN trial

Abstract Background: Cervical cancer is the second most common cancer among women worldwide, with over 500,000 new cases diagnosed annually and a 50% mortality rate in Asia. The incidence and prevalence of cervical cancer is high in Asia due to limited screening, awareness of HPV infection, and access to vaccines. The purpose of this study is to evaluate the comprehensive genomic profiles of circulating tumor DNA (ctDNA) in Asian cervical cancer patients with different histological subtypes and their association with clinicopathological features. Methods: This is an Asian multicenter prospective observational study conducted by nine institutions in Japan, Singapore, Malaysia, Thailand, and Vietnam (NCT05099978, ClinicalTrials.gov). Eligible patients had histological diagnosis of cervical cancer with metastatic or recurrent disease. Patients on chemotherapy or radiotherapy were excluded. ctDNA was analyzed in blood samples collected at newly initial diagnosis of metastatic disease and/or at disease progression. Genomic profiling was conducted by Guardant360 (Guardant Health). Results: Ninety-nine samples from 101 cervical cancer patients were analyzed. ctDNA was detected in 70 (70.7%) samples; median time to test results was 11 days. The median number of genomic abnormalities was 1 (range, 0-22). The most frequently altered genes were PIK3CA (n=28. 28.3%), TP53 (n=18, 18.2%), KRAS (n=12, 12.1%) and STK11 (n=6, 6.1%). Clinical trial-related genomic abnormalities were detected in 59 patients (59.6%) with 40 associated with approved drugs in other indication, including those targeting PIK3CA mutation (n=28), homologous recombination deficiency (BRCA1/2, ATM and CDK12 mutation) (n=5), ERBB2 amplification (n=4) and FGFR3alterations (n=3). In squamous cell carcinoma (n=59), commonly altered genes were PIK3CA (n=21, 35.6%), TP53(n=12, 20.3%), ERBB2 (n=5, 8.5%), NOTCH1 (n=5, 8.5%) and ARID1A (n=5, 8.5%). In adenocarcinoma (n=36), commonly altered genes were KRAS (n=7, 19.4%), PIK3CA (n=6, 16.7%) and TP53 (n=5, 13.9%). The number of patients with genomic alterations relevant for clinical trials was 39 (66.1%) and 19 (52.8%) for squamous cell carcinoma and adenocarcinoma, respectively. There were no differences in the number of genomic alterations according to prior chemotherapy or radiation therapy. Conclusion: Comprehensive genomic profiling using liquid biopsy can rapidly identify potential candidates for targeted therapy in cervical cancer patients, regardless of histopathology. Clinical studies of precision medicines in Asia are encouraged for such patients. Citation Format: Prathepamalar Yehgambaram, Yuki Kojima, Kazuki Sudo, Shu Yazaki, Momoko Tokura, Munehiro Ito, Mai Hoshino, Wong Yoke Fui, Pei Jye Voon, David SP Tan, Arb-aroon Lertkhachonsuk, Anh Tuan Pham, Thinh Dang Huy Quoc, Wan Zamaniah Wan Ishak, Hiroshi Yoshida, Shinji Kohsaka, Yukari Nagasaka, Ryunosuke Machida, Tomomi Hata, Kenichi Nakamura, Kan Yonemori. Genomic landscape of circulating tumor DNA in cervical cancer in Asia: NCCH1905/A-TRAIN trial [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 975.

Abstract 3563: Multi-modal mutational signatures elucidate the comprehensive consequences of mutational processes

Abstract The development of mutational signatures defined individually in the contexts of single/double base substitutions, insertions and deletions, structural variants and copy number variation have led to improved understanding of cancer mutagenesis and potential for improved patient stratification. We hypothesized that combining these contexts into a multi-modal mutational signature framework may improve the accuracy of assigning mutational processes to samples, and provide a holistic view of the full repertoire of mutations conferred from such processes. In order to develop multi-modal signatures, bespoke feature engineering was required for each mutational modality to enhance signal, in addition to individual modality matrix normalization so that the data could be harmonized and analyzed as a whole. These methods, and subsequent signature extraction were developed on 2,438 whole genome sequenced cancers from 21 distinct cancer types from the PCAWG consortium for which all modalities of data were available, incorporating a 348 channel signature definition. Deployment of these methods identified multi-modal signatures that encompass multiple mutation types known to associate with specific processes, for example SBS, indel and rearrangement channels defining a signature of homologous recombination deficiency. In contrast, some signatures remain defined by a single mutational modality, highlighting the distinction between broadly mutational processes, and more focused mutation processes. Multi-modal signatures show promise in increasing accuracy for difficult to assign signatures, such as those for homologous recombination deficiency, and therefore in improving patient stratification for life-saving treatment. Citation Format: Christopher D. Steele, Ludmil Alexandrov, Azhar Khandekar. Multi-modal mutational signatures elucidate the comprehensive consequences of mutational processes [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 3563.

Abstract 5073: Advancing precision oncology: Insights from pan-cancer proteogenomic signatures

Abstract Somatic mutations in cancer genomes arise from diverse mutational processes, leaving distinct mutational signatures. However, the proteogenomic implications of these signatures and their connections to environmental influences and immune interactions remain largely unexplored. In this study, we comprehensively investigated these signatures from a broader proteogenomic perspective to further discern their genetic, proteomic, phosphoproteomic, and environmental ramifications. The harmonized dataset of 1064 samples across ten cancer types from the Clinical Proteomics Tumor Analysis Consortium (CPTAC) pan-cancer resource was utilized for this investigation. Beyond genetic alterations and mutational signatures, we harnessed high-throughput multi-omics data to detect critical changes and infer expression signatures associated with the transitions to seven tumor-linked phenotypes: aging, Apolipoprotein B mRNA Editing Catalytic Polypeptide (APOBEC), Homologous Recombination Deficiency (HRD), Microsatellite Instability (MSI), Polymerase Epsilon (POLE), smoking, and ultraviolet (UV) light exposure at the pan-cancer level. We prioritized the top differentially expressed markers uniquely found at the protein and phosphoprotein levels and developed a quantitative score predicting each phenotype status, such as MSI. Respectively, we pinpointed potential candidates as actionable therapeutic targets by linking the identified markers to druggable databases. This offers additional cues to optimize therapeutic options for patients. Specifically, directing attention to genes up-regulated in HRD tumors treated with PARP1 inhibitors shows potential promise in overcoming resistance. Moreover, we explored environmental exposure-related tumor proteogenomic signatures and their association with immune infiltration levels and phenotypes. Notably, smoking strongly influenced the tumor microenvironment (TME) and prognosis in lung cancer. In summary, our identification of expression signatures facilitates phenotype prediction and unveils their molecular mechanisms. We anticipate clinical utility in classifying samples using proteogenomics, particularly in cases where a solely genomic assessment is inconclusive. Citation Format: Yize Li, Nadezhda V. Terekhanova, Michael C. Wendl, Feng Chen, Li Ding. Advancing precision oncology: Insights from pan-cancer proteogenomic 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 5073.

Abstract 3371: PRMT blockade induces defective DNA replication stress response via ATR suppression and synergizes with PARP inhibition

Abstract Aberrant protein arginine methylation has been observed in multiple cancer types, making it an attractive drug target. Proteins can undergo asymmetric arginine methylation by type I protein arginine methyltransferases (PRMTs), predominately by PRMT1 and to a lesser extent PRMT4, or symmetric arginine methylation by type II PRMTs, predominately PRMT5. Here, we performed targeted proteomics following inhibition of PRMT1, PRMT4, and PRMT5 across cancer cell lines. We found that inhibition of both type I and type II PRMTs suppressed levels of total and phosphorylated ATR protein in cancer cell lines, and down-regulated expression of the ATR gene. Loss of ATR from PRMT inhibition resulted in defective DNA replication stress response activation in following exogenous replication stress. Since PARP inhibitors are known to induce replication stress, we next combined PRMT inhibition with PARP inhibition and found inhibition of PRMT1 or PRMT5 greatly exacerbated PARP inhibitor induced DNA damage. Based on this observation, we assessed the combination of PARP and PRMT inhibition in a panel of cell lines. While inhibition of both type I and type II PRMTs were synergistic with PARP inhibition in both cells with intact and deficient homologous recombination, type I PRMT inhibition resulted in higher toxicity in non-malignant cells. Therefore, we validated the synergy of combined PARP/PRMT5 inhibition in primary patient-derived organoids. Finally, we demonstrate that the combination of PARP and PRMT5 inhibition improves overall survival in both BRCA-mutant and wild-type patient-derived xenograft models without any detectable hematological toxicities typically associated with PARPi combination therapies. Taken together, these results demonstrate that PRMT5 inhibition may be a well-tolerated approach to improve tumor sensitivity to PARP inhibition. Citation Format: Deepa Bisht, Yang Li, Lacey E. Dobrolecki, Christina Sallas, Xudong Zhang, Travis D. Kerr, Yalong Wang, Sharad Awasthi, Babita Kaundal, Siqi Wu, Weiyi Peng, Marc L. Mendillo, Yiling Lu, Collene R. Jeter, Guang Peng, Jinsong Liu, Shannon N. Westin, Anil K. Sood, Michael T. Lewis, Jishnu Das, S. Stephen Yi, Mark T. Bedford, Daniel J. McGrail, Nidhi Sahni. PRMT blockade induces defective DNA replication stress response via ATR suppression and synergizes with PARP inhibition [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 3371.