Gulhan, D.

Mutations in BRCA1 and BRCA2 genes, whether inherited or somatically acquired, cause homologous recombination deficiency (HRD) in tumor cells. The timing of HRD onset in the emerging tumor lineage is unknown. Here, we present HRDTimer, an algorithm to infer the onset of HRD-driven mutagenesis prior to cancer diagnosis. We estimate that HRD arises at 34% of SBS1-based molecular time---corresponding to a median of 8.3 years (IQR 7.1--10.4) prior to diagnosis in triple-negative breast cancers, and 15.0 years (IQR 12.0--20.6) in ER-positive breast cancers. Bulk sequencing reveals accelerated SBS1 accumulation following neoplastic transformation compared to normal tissue, influencing the estimated age of HRD onset. Single-cell duplex sequencing confirms SBS1 acceleration in tumors and further shows that non-tumor cells largely lack the HRD signature, indicating that HRD is rare in pre-malignant cells, even in BRCA1/2 mutation carriers. Together, our analysis pinpoints the onset of HRD before diagnosis, defining a window for detection and potential interception.

PURPOSE The multicenter, open-label, randomized phase 2 NCI-9944 study ( NCT02595892 ) demonstrated that addition of ATR inhibitor (ATRi) berzosertib to gemcitabine increased progression-free survival (PFS) compared to gemcitabine alone (hazard ratio [HR]=0.57, one-sided log-rank P = .044, which met the one-sided significance level of 0.1 used for sample size calculation). METHODS We report here the final overall survival (OS) analysis and biomarker correlations (ATM expression by immunohistochemistry, mutational signature 3 and a genomic biomarker of replication stress) along with post-hoc exploratory analyses to adjust for crossover from gemcitabine to gemcitabine/berzosertib. RESULTS At the data cutoff of January 27, 2023 (>30 months of additional follow-up from the primary analysis), median OS was 59.4 weeks with gemcitabine/berzosertib versus 43.0 weeks with gemcitabine alone (HR 0.79, 90% CI 0.52 to 1.2, one-sided log-rank P = .18). An OS benefit with addition of berzosertib to gemcitabine was suggested in patients stratified into the platinum-free interval ≤3 months (N = 26) subgroup (HR, 0.48, 90% CI 0.22 to 1.01, one-sided log-rank P =.04) and in patients with ATM-negative/low (N = 24) tumors (HR, 0.50, 90% CI 0.23 to 1.08, one-sided log-rank P = .06). CONCLUSION The results of this follow-up analysis continue to support the promise of combined gemcitabine/ATRi therapy in platinum resistant ovarian cancer, an active area of investigation with several ongoing clinical trials.

5512 Background: The multicenter, open-label, randomized phase 2 NCI-9944 study (NCT02595892) demonstrated that addition of ATR inhibitor (ATRi) berzosertib to gemcitabine increased progression-free survival (PFS) compared to gemcitabine alone (HR = 0.57, one-sided log-rank p = 0.044, which met the one-sided significance level of 0.1 used for sample size calculation). Final overall survival (OS) and corresponding biomarker analyses are reported here. Methods: Patients (pts) with platinum-resistant high-grade serous ovarian cancer and unlimited previous lines of cytotoxic therapy in the platinum-sensitive setting but no more than one line of cytotoxic therapy in the platinum-resistant setting, were randomized 1:1 to gemcitabine/berzosertib versus gemcitabine alone. Randomization was stratified based on platinum free interval (PFI), PFI≤3 months versus > 3 months. Crossover from gemcitabine to gemcitabine/berzosertib was allowed upon disease progression by RECIST 1.1. OS was a secondary endpoint while preplanned exploratory correlative studies included assessment of DNA repair pathways and replication stress (RS) alterations by targeted gene sequencing and/or immunohistochemistry (IHC). Results: Seventy pts were randomly assigned to treatment with gemcitabine/berzosertib (34 pts) or gemcitabine alone (36 pts); 15 pts crossed over from gemcitabine to gemcitabine/berzosertib. At the final OS analysis (92.9% maturity), median follow-up was 53.2 weeks in the gemcitabine/berzosertib and 43 weeks in the gemcitabine alone groups. Median OS in the intent-to-treat (ITT) population was 59.4 weeks in the gemcitabine/berzosertib group versus 43.0 weeks in the gemcitabine alone group (HR 0.79, 90% CI 0.52-1.2, one-sided p = 0.18). However, when patients who crossed over to gemcitabine/berzosertib were excluded from analysis, a significant OS benefit was observed with gemcitabine/berzosertib (HR 0.60, 90%CI 0.37−0.97); HR was 0.26 (90% CI 0.1−0.7) in pts with PFI≤3 months and 0.89 (90%CI 0.50−1.59) in pts with PFI > 3 months. Furthermore, significant OS benefit was observed in pts with RS-low tumors (HR 0.39, 90%CI 0.17−0.91, defined as tumors harboring no genomic RS alterations related to loss of RB pathway regulation and/or oncogene-induced RS) but not in pts with RS-high tumors (HR 0.74, 90%CI 0.35−1.56). Additional targeted gene sequencing and IHC analyses as well as analyses adjusting for patient crossover will be reported at the meeting. Conclusions: In the ITT population, gemcitabine/berzosertib did not significantly improve OS versus gemcitabine alone. Pts with PFI≤3 months and pts with RS-low tumors may derive a survival advantage from addition of berzosertib to gemcitabine in the platinum-resistant setting. Clinical trial information: NCT02595892 .

e13003 Background: The emergence of somatic KMT2C mutations has been associated with resistance to various treatments, including chemotherapy and endocrine therapy in patients with estrogen receptor-positive breast cancers. The impact of these mutations in patients treated with poly-ADP ribose polymerase inhibitors (PARPi) and phosphatidylinositol-3-kinase inhibitors (PI3Ki) is unknown. Methods: Circulating tumor DNA (ctDNA) was obtained from plasma and peripheral blood at different time points from 38 patients prior to treatment with the combination of the PARPi olaparib with the alpha-specific PI3Ki alpelisib (NCT01623349). CtDNA was also collected immediately before the first cycle and at the time of disease progression. CtDNA underwent deep targeted sequencing (tumor-normal pairs, 397 genes (2Mb) at 25,000x somatic and 10,000x germline) at the Broad Institute of MIT and Harvard. Variants that were exonic, non-synonymous, and predicted to lead to loss-of-function were considered mutations. Cohorts were stratified according to the presence or absence of the genomic alteration, and progression-free survival was compared with the Kaplan-Meier method and log-rank test. A Cox regression was performed using age, tumor type, germline BRCA1/2 mutation status, performance status, and number of previous lines of treatment as covariates. Results: The KMT2C gene was one of the 3 genes most frequently mutated in our cohort, affecting 5 patients (15%) after the exclusion of those with variants with non-deleterious alterations. The other 2 commonly mutated genes were TP53 (76%) and PIK3CA (15%). In the comparison of patients based on these most common mutations, we identified that patients with somatic KMT2C mutations (n=5) have longer mPFS than those that were wild type (n=28): mPFS 386 vs. 151 days, log-rank p = 0.025. Cox proportional hazards model accounting for age, tumor type, germline BRCA1/2 mutation status, performance status, and number of previous lines revealed a hazard ratio of 0.16; p = 0.007. All somatic KMT2C mutations were proximal to the SET domain critical for methyltransferase activity. Upon progression, the KMT2C-mutated clones were suppressed to below the detection level of mutation calling algorithms. Analysis of the raw files revealed that the clones were suppressed but not eliminated. Conclusions: While the emergence of KMT2C has been reported to be associated with cancer progression and resistance to different therapies, patients with deleterious KMT2C mutations in the ctDNA may benefit from therapy with PARPi and PI3Ki.

Abstract Background Breast cancers in women with a germline BRCA1/2 mutation (gBRCAm) have homologous recombination deficiency (HRD) and are sensitive to therapies causing double-strand DNA breaks. In TBCRC 031 (INFORM), both neoadjuvant cisplatin and doxorubicin/cyclophosphamide (“AC”) in gBRCAm carriers resulted in a complete pathologic response in 18% and 26% respectively in patients with newly diagnosed HER2–negative breast cancer. Herein, we describe molecular features from tumor whole exome (WES) and transcriptome sequencing (RNAseq) associated with response. Methods TBCRC 031 (the INFORM Trial - NCT01670500) was a randomized phase II neoadjuvant trial comparing the efficacy of cisplatin versus AC in gBRCAm carriers with stage I-III HER2–negative breast cancer. Of 118 patients enrolled, 92 patients provided fresh frozen research biopsies, collected prior to chemotherapy initiation, which were subjected to WES and RNAseq. Variants were called using GATK best practices and intratumoral heterogeneity was inferred from mutations and variant allele frequencies using Mutant Allele Tumor Heterogeneity (MATH) scores. Mutational Signature 3 (Sig3) and Genomic Instability Score (GIS) were calculated with SigMA and scarHRD, respectively. RNAseq data were utilized to perform differential gene expression and functional analyses, while cellular deconvolution was performed with CIBERSORTx trained against breast cancer single cell data. Patients were grouped according to their residual cancer burden (RCB) as responders (RCB-0 or 1), or non-responders (RCB-2 or 3). P-values ≤ 0.05 were considered statistically significant and when appropriate, adjustment for multiple testing was performed using a false discovery rate ≤ 5%. Results Of the 92 patients with gBRCAm, 59 (64%) had triple-negative and 33 (36%) were hormone-receptor positive HER2-negative breast cancer, 40 (43%) were classified as responders and 52 (57%) as non-responders. WES analysis revealed that indices of HRD were high (Sig3 exposure predominant and GIS ≥ 42) across most samples irrespective of receptor status and not significantly different among responders and non-responders. In contrast, responders exhibited lower levels of intratumor heterogeneity than non-responders (median MATH 42.9 vs. 33.5, p = 0.01). 223 genes were differentially expressed between responders and non-responders following control for tumor hormone receptor status, BRCA1/2 mutation, and menopausal status. Pathways identified as significantly enriched in upregulated genes were indicative of intrinsic immune activation in responders (e.g., T-cell activation, immune response-signaling, and regulation of leukocyte activation). Cellular deconvolution of the tumor microenvironment confirmed that responders presented a higher proportion of T-cells (p = 0.025) and myeloid cells (p = 0.003) in the tumor samples, while perivascular-like cells were enriched in non-responders (p = 0.034). Conclusion In this analysis of the largest cohort of treatment-naïve gBRCAm breast cancer to date, we found that response to cytotoxic chemotherapy is associated with a transcriptional program of intrinsic immune activation and an increased population of intratumoral T-cells and myeloid cells. Lower levels of intratumor heterogeneity and higher immune activation were associated with response to chemotherapy gBRCAm carriers while HRD scores were not. Citation Format: Felipe Batalini, Doga C. Gulhan, Xanthi Lida Katopodi, Nikolas Kalavros, Antuan Tran, Dimitra Karagkouni, Emily Stern-Gatof, Stuart Schnitt, Judy E. Garber, Gerburg M. Wulf, Peter J. Park, Ioannis Vlachos, Nadine Tung. Intratumor heterogeneity and intrinsic immune activation are associated with response to chemotherapy in BRCA-related breast cancers [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-12-03.

We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 with schizophrenia, and 59 with autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, brains had 20 to 60 detectable single-nucleotide mutations, but ~6% of brains harbored hundreds of somatic mutations. Hypermutability was associated with age and damaging mutations in genes implicated in cancers and, in some brains, reflected in vivo clonal expansions. Somatic duplications, likely arising during development, were found in ~5% of normal and diseased brains, reflecting background mutagenesis. Brains with autism were associated with mutations creating putative transcription factor binding motifs in enhancer-like regions in the developing brain. The top-ranked affected motifs corresponded to MEIS (myeloid ectopic viral integration site) transcription factors, suggesting a potential link between their involvement in gene regulation and autism.