DNA Damage Response Gene Alterations Research Articles

Abstract C034: First in Human phase 1/2a trial of a macrocyclic ATR inhibitor (ATRN-119) in patients with advanced solid tumors

Abstract Background: ATRN-119 is an oral and highly selective nanomolar inhibitor of Ataxia Telangiectasia and Rad3- related (ATR) kinase, an enzyme that is activated by replication stress and DNA damage and prevents the collapse of DNA replication forks into double strand breaks. ATRN-119 is being studied in advanced solid tumors with dysregulated components of the DNA damage response (DDR) based on the hypothesis that these tumors will be more susceptible to ATR inhibition. Single agent ATRN-119 demonstrates increased cytotoxicity in vitro against a broad spectrum of human colon, breast, pancreatic, sarcoma, ovarian and prostate cancer cell lines that harbor genomic alterations of DDR genes. In vivo, ATRN-119 has demonstrated tumor growth inhibition in human castration-resistant prostate cancer and human colon cancer cell line-derived xenografts (CDX) mice models, and in BRCA mutant high grade serous ovarian cancer patient derived xenografts (PDXs). Trial design: This is a first-in-human Phase 1/2a open-label study (NCT04905914) to evaluate safety, tolerability, pharmacokinetics (PK), and preliminary e!cacy of oral daily ATRN-119 in subjects with advanced solid tumors, conducted in 2 parts. Part 1 consists of a 3+3 dose escalation design at up to 6 dose levels to evaluate the tolerability, PK, dose limiting toxicity (DLT) and maximum tolerated dose (MTD) of repeated daily doses of ATRN-119. Enrollment in Part 1 is ongoing. Subjects must be ≥12 years old with advanced solid tumor, have documented DDR mutations, or advanced Merkel cell carcinoma, must have failed at least one prior standard treatment, have ECOG performance status of 0 or 1, with a life expectancy > 3 months. Primary objective is safety/tolerability and secondary objective is efficacy. After determination of the MTD or maximum feasible dose (MFD) in Part 1, Part 2 will enroll up to 30 additional subjects. The trial is currently recruiting across 4 locations in the United States. Clinical trial identification: ClinicalTrials.gov Identifier: NCT04905914 Citation Format: Fiona Simpkins, Reva Schneider, Amit Mahipal, Patricia LoRusso, Crystal Miller, Eric Brown, Mike Carleton, Joachim Gullbo, Nadeem Q Mirza. First in Human phase 1/2a trial of a macrocyclic ATR inhibitor (ATRN-119) in patients with advanced solid tumors [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C034.

Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer.

There is an urgent need for biomarkers of radiation response in organ-sparing therapies. Bladder preservation with trimodality therapy (TMT), consisting of transurethral tumor resection followed by chemoradiation, is an alternative to radical cystectomy for muscle-invasive bladder cancer (MIBC), but molecular determinants of response are poorly understood. We characterized genomic and transcriptomic features correlated with long-term response in a single institution cohort of patients with MIBC homogeneously treated with TMT. Pretreatment tumors from 76 patients with MIBC underwent whole-exome sequencing; 67 underwent matched transcriptomic profiling. Molecular features were correlated with clinical outcomes including modified bladder-intact event-free survival (mBI-EFS), a composite endpoint that reflects long-term cancer control with bladder preservation. With a median follow-up of 74.6 months in alive patients, 37 patients had favorable long-term response to TMT while 39 had unfavorable long-term response. Tumor mutational burden was not associated with outcomes after TMT. DNA damage response gene alterations were associated with improved locoregional control and mBI-EFS. Of these alterations, somatic ERCC2 mutations stood out as significantly associated with favorable long-term outcomes; patients with ERCC2 mutations had significantly improved mBI-EFS [HR, 0.15; 95% confidence interval (CI), 0.06-0.37; P = 0.030] and improved BI-EFS, an endpoint that includes all-cause mortality (HR, 0.33; 95% CI, 0.15-0.68; P = 0.044). ERCC2 mutant bladder cancer cell lines were significantly more sensitive to concurrent cisplatin and radiation treatment in vitro than isogenic ERCC2 wild-type cells. Our data identify ERCC2 mutation as a candidate biomarker associated with sensitivity and long-term response to chemoradiation in MIBC. These findings warrant validation in independent cohorts.

Impact of DNA damage repair alterations on prostate cancer progression and metastasis.

Prostate cancer is among the most common diseases worldwide. Despite recent progress with treatments, patients with advanced prostate cancer have poor outcomes and there is a high unmet need in this population. Understanding molecular determinants underlying prostate cancer and the aggressive phenotype of disease can help with design of better clinical trials and improve treatments for these patients. One of the pathways often altered in advanced prostate cancer is DNA damage response (DDR), including alterations in BRCA1/2 and other homologous recombination repair (HRR) genes. Alterations in the DDR pathway are particularly prevalent in metastatic prostate cancer. In this review, we summarise the prevalence of DDR alterations in primary and advanced prostate cancer and discuss the impact of alterations in the DDR pathway on aggressive disease phenotype, prognosis and the association of germline pathogenic alterations in DDR genes with risk of developing prostate cancer.

Camonsertib in DNA damage response-deficient advanced solid tumors: phase 1 trial results

Predictive biomarkers of response are essential to effectively guide targeted cancer treatment. Ataxia telangiectasia and Rad3-related kinase inhibitors (ATRi) have been shown to be synthetic lethal with loss of function (LOF) of ataxia telangiectasia-mutated (ATM) kinase, and preclinical studies have identified ATRi-sensitizing alterations in other DNA damage response (DDR) genes. Here we report the results from module 1 of an ongoing phase 1 trial of the ATRi camonsertib (RP-3500) in 120 patients with advanced solid tumors harboring LOF alterations in DDR genes, predicted by chemogenomic CRISPR screens to sensitize tumors to ATRi. Primary objectives were to determine safety and propose a recommended phase 2 dose (RP2D). Secondary objectives were to assess preliminary anti-tumor activity, to characterize camonsertib pharmacokinetics and relationship with pharmacodynamic biomarkers and to evaluate methods for detecting ATRi-sensitizing biomarkers. Camonsertib was well tolerated; anemia was the most common drug-related toxicity (32% grade 3). Preliminary RP2D was 160 mg weekly on days 1–3. Overall clinical response, clinical benefit and molecular response rates across tumor and molecular subtypes in patients who received biologically effective doses of camonsertib (>100 mg d−1) were 13% (13/99), 43% (43/99) and 43% (27/63), respectively. Clinical benefit was highest in ovarian cancer, in tumors with biallelic LOF alterations and in patients with molecular responses. ClinicalTrials.gov registration: NCT04497116.

Erratum to “Landscape of DNA damage response gene alterations in breast cancer: A comprehensive investigation”

Erratum to “Landscape of DNA damage response gene alterations in breast cancer: A comprehensive investigation”

Comparative outcomes of metastatic prostate cancer (mPC) patients (pts) with DNA damage response gene alterations (DDR-a): A single-center experience.

169 Background: DDR-a are prevalent in mPC pts. The clinical behaviour of these pts is not well defined. We sought to investigate how DDR-a affects prognosis and treatment outcomes in mPC pts. Methods: Eligible pts were age ≥18 with mPC who had undergone germline (G) and/or somatic (S) next generation sequencing (NGS) at the Cross Cancer Institute 2016-2021. Pts were considered DDR-a if a pathogenic/likely pathogenic variant (P/LP-v) in a DDR gene was identified on G or S NGS; patients were considered DDR-p if no P/LP-v was identified on S NGS. Data from electronic medical records were collected. The primary endpoint was overall survival (OS) from diagnosis of mPC. Secondary endpoints included: OS and progression free survival (PFS) from initial diagnosis of prostate cancer (PC); PSA response after 12 weeks, and PFS and OS from the start time of 1st and 2nd line therapies. Time based endpoints were analyzed using the Kaplan-Meier (KM) method, and log-rank statistics were used to compare the KM curves. PSA responses were compared using chi-squared testing. Results: 23 DDR-a and 48 DDR-p pts were identified. The most frequent DDR-a were BRCA2 (n=11) and ATM (n=6). Baseline characteristics including age at diagnosis were similar between the two groups. 1st line systemic therapy was androgen deprivation therapy (ADT) alone in 73.9% of DDR-a and 77.0% of DDR-p. 2nd line therapy was abiraterone or enzalutamide in 65% of DDR-a and 92% of DDR-p. Olaparib was received by 52% of DDR-a pts. No difference in OS from mPC (65.7 vs 51.0 mos, p=0.487), OS from initial diagnosis (94.1 vs 88.9 mos, p=0.865), PFS on 1st line therapy (33.2 vs 31.0 mos, p=0.847), OS on 1st line therapy (85.6 vs 78.6 mos, (p=0.799) PFS on 2nd line therapy (8.4 vs 13.1 mos, p=0.569) or OS on 2nd line therapy (32.5 vs 35.8 mos, p=0.901) was seen for DDR-a vs DDR-p, respectively. PSA responses to 1st and 2nd line therapies were similar and will be presented as waterfall plots. Conclusions: In this single-center cohort, no difference in clinical characteristics or outcomes were seen in DDR-a compared to DDR-p pts. While this study is limited by small numbers and retrospective nature, it adds to the growing literature characterizing the clinical behaviour of DDR-a mPC. Collaborative efforts are required to better define this molecular cohort of pts.

DNA Damage Response Gene Signature as Potential Treatment Markers for Oral Squamous Cell Carcinoma.

Oral squamous cell carcinoma (OSCC) is a rapidly progressive cancer that often develops resistance against DNA damage inducers, such as radiotherapy and chemotherapy, which are still the standard of care regimens for this tumor. Thus, the identification of biomarkers capable of monitoring the clinical progression of OSCC and its responsiveness to therapy is strongly required. To meet this need, here we have employed Whole Genome Sequencing and RNA-seq data from a cohort of 316 patients retrieved from the TCGA Pan-Cancer Atlas to analyze the genomic and transcriptomic status of the DNA damage response (DDR) genes in OSCC. Then, we correlated the transcriptomic data with the clinical parameters of each patient. Finally, we relied on transcriptomic and drug sensitivity data from the CTRP v2 portal, performing Pearson's correlation analysis to identify putative vulnerabilities of OSCC cell lines correlated with DDR gene expression. Our results indicate that several DDR genes show a high frequency of genomic and transcriptomic alterations and that the expression of some of them correlates with OSCC grading and infection by the human papilloma virus. In addition, we have identified a signature of eight DDR genes (namely CCNB1, CCNB2, CDK2, CDK4, CHECK1, E2F1, FANCD2, and PRKDC) that could be predictive for OSCC response to the novel antitumor compounds sorafenib and tipifarnib-P1. Altogether, our data demonstrate that alterations in DDR genes could have an impact on the biology of OSCC. Moreover, here we propose a DDR gene signature whose expression could be predictive of OSCC responsiveness to therapy.

Landscape of DNA damage response gene alterations in breast cancer: A comprehensive investigation.

DNA damage response (DDR) gene alterations are prevalent in breast cancer (BC) and important for treatment decisions. Intensive studies on DDR alterations in BC are still needed. The authors included 438 patients with metastatic breast cancer from their next-generation sequencing database and 1091 patients with early-stage breast cancer from The Cancer Genome Atlas (TCGA) database in the analysis to characterize molecular alterations in the DDR pathway. Germline DDR mutations were more prevalent in younger patients and those with HER2-negative cancers. Tumors with germline DDR mutations more commonly had somatic DDR mutations, especially those with germline Fanconi anemia (FA) pathway mutations. Notably, 66.67% (four of six) of patients with germline PALB2 mutations had tumors that harbored somatic PALB2 mutations. No differences in prognosis were observed in patients with germline or tumor somatic DDR mutations compared to patients and tumors that were wild-type. Compared to early BC, the frequency of somatic DDR mutations in metastatic cancers was significantly higher (24.89% vs. 16.02%, p<.001). Higher tumor mutation burdens were observed in cancers with somatic DDR mutations, but not in cancers with germline DDR mutations. Furthermore, tumors with somatic DDR mutations showed an abundance of anticancer immunological phenotypes. Somatic FA and mismatch repair pathway mutations were associated with increased expression of immune checkpoint molecules. Although most DDR genes were significantly positively associated with expression of proliferation-related genes, PARP3 expression was negatively correlated with MKI67 expression. Lower PARP3 expression was associated with a worse prognosis in TCGA database by multivariate Cox analysis. Patients with germline FA mutations more frequently have tumors with somatic DDR mutations. Somatic DDR mutations lead to anticancer immunological phenotypes in BC. No differences in prognosis according to germline or somatic DDR mutations were found.

BRCA Mutations in Ovarian and Prostate Cancer: Bench to Bedside.

Simple SummaryDNA damage is one of the hallmarks of cancer. Epithelial ovarian cancer (EOC) —especially the high-grade serous subtype—harbors a defect in at least one DNA damage response (DDR) pathway. Defective DDR results from a variety of lesions affecting homologous recombination (HR) and nonhomologous end joining (NHEJ) for double strand breaks, base excision repair (BER), and nucleotide excision repair (NER) for single strand breaks and mismatch repair (MMR). Apart from the EOC, mutations in the DDR genes, such as BRCA1 and BRCA2, are common in prostate cancer as well. Among them, BRCA2 lesions are found in 12% of metastatic castration-resistant prostate cancers, but very rarely in primary prostate cancer. Better understanding of the DDR pathways is essential in order to optimize the therapeutic choices, and has led to the design of biomarker-driven clinical trials. Poly(ADP-ribose) polymerase (PARP) inhibitors are now a standard therapy for EOC patients, and more recently have been approved for the metastatic castration-resistant prostate cancer with alterations in DDR genes. They are particularly effective in tumours with HR deficiency.DNA damage repair (DDR) defects are common in different cancer types, and these alterations can be exploited therapeutically. Epithelial ovarian cancer (EOC) is among the tumours with the highest percentage of hereditary cases. BRCA1 and BRCA2 predisposing pathogenic variants (PVs) were the first to be associated with EOC, whereas additional genes comprising the homologous recombination (HR) pathway have been discovered with DNA sequencing technologies. The incidence of DDR alterations among patients with metastatic prostate cancer is much higher compared to those with localized disease. Genetic testing is playing an increasingly important role in the treatment of patients with ovarian and prostate cancer. The development of poly (ADP-ribose) polymerase (PARP) inhibitors offers a therapeutic strategy for patients with EOC. One of the mechanisms of PARP inhibitors exploits the concept of synthetic lethality. Tumours with BRCA1 or BRCA2 mutations are highly sensitive to PARP inhibitors. Moreover, the synthetic lethal interaction may be exploited beyond germline BRCA mutations in the context of HR deficiency, and this is an area of ongoing research. PARP inhibitors are in advanced stages of development as a treatment for metastatic castration-resistant prostate cancer. However, there is a major concern regarding the need to identify reliable biomarkers predictive of treatment response. In this review, we explore the mechanisms of DDR, the potential for genomic analysis of ovarian and prostate cancer, and therapeutics of PARP inhibitors, along with predictive biomarkers.

Abstract 3494: Characterizing the relationship between genotype and phenotype in DNA damage response-altered pancreatic cancer models

Abstract Alterations in DNA damage response (DDR) proteins are prevalent across cancers and present unique opportunities for the therapeutic induction of synthetic lethality (i.e., two gene deficiencies in the same pathway synergize to kill tumor cells). In pancreatic adenocarcinoma, patients harboring alterations in DDR genes, such as in homology-directed repair (HDR), comprise the 10-20% of patients that may benefit from the recent FDA approval of Olaparib, a poly (ADP-ribose) polymerase inhibitor that disrupts non-homologous end joining (NHEJ). Despite being the best-in-class targeted therapy for DDR-altered pancreatic cancers, a subset of patients fails to respond to Olaparib and those that initially respond eventually go on to develop resistance. The mechanisms underlying resistance are poorly elucidated but suggest that some patients harboring DDR-altered tumors are HDR-proficient or revert to HDR-proficiency during therapy, bypassing the second gene deficiency requisite for synthetic lethal induction with targeted therapy (e.g., Olaparib). Utilizing patient-derived models of cancer, we are actively investigating DDR-altered, pancreatic tumor cell lines and exploring the relationship between DDR-alterations and HDR-deficiency with three goals: [1] To evaluate the prevalence of HDR-proficiency in BRCA-altered tumors, [2] to understand the extent to which patient-derived models of cancer are concordant and predictive of clinical outcomes, and [3] to identify novel therapeutic strategies for resistant patients. So far, we have observed HDR-proficiency by functional assays (e.g., RAD51 foci formation) in DDR-altered patient-derived cell lines that corresponds with poor response to Olaparib in vitro, and resistance to platinum therapy clinically. Whereas DDR-altered HDR-deficient lines had greater sensitivity to Olaparib and platinum therapy. These early data suggest that measures of HDR by functional assay may be more predictive of clinical therapeutic responses than the use of genetic signatures alone. Citation Format: James R. Carroll, Jason M. Link, Jonathan R. Brody. Characterizing the relationship between genotype and phenotype in DNA damage response-altered pancreatic cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3494.

Abstract 1951: Circulating tumor cell-derived explant models reveal DNA damage response-based therapeutic opportunities in non-small cell lung cancer

Abstract Background: DNA damage and genomic instability contribute to non-small cell lung cancer (NSCLC) etiology and progression. However, their therapeutic exploitation is disappointing. CTC-derived eXplants (CDX) offer systems for mechanistic investigation of CTC metastatic potency and biology-driven therapeutic testings. We perform in-depth molecular and functional characterization of CDX models and demonstrate that targeting defects in the DNA damage response (DDR) and genome integrity regulators impedes CTC-driven metastasis in NSCLC. Methods: CTCs were enriched from 30 mL blood samples of 56 advanced NSCLC patients and implanted subcutaneously into Nod/Scid-IL2Rγ-/- (NSG) mice. Tumors were palpable within a median of 108 days. Among the four CDX models established, three CDX-derived cell lines (GR-CDXL1, GR-CDXL3, GR-CDXL4) were obtained. CDX and cell lines were characterized by immunofluorescence (IF), immunohistochemistry and whole-exome sequencing (WES). Chromosomal instability (CIN) and DDR activity were evaluated by IF and western blot. Gene expression was quantified by qRT-PCR. Tumorigenic potential of CDX-derived cell lines was assessed in the chick embryo chorioallantoic membrane and NSG mice engrafted intravenously. IC50 was assessed using CellTiter-Glo®. Results: Four CDX models and three CDX-derived cell lines were established from NSCLC CTCs and recapitulated patient tumor histology (available for three patients) and response to platinum-based chemotherapy. WES analysis showed considerable mutational landscape similarity between the CDX (GR-CDXL1, GR-CDXL2, GR-CDXL3, GR-CDXL4), corresponding patient tumor biopsy and/or single CTCs. Truncal alterations in key DDR and genome integrity-related genes were prevalent across models and assessed as therapeutic targets in vitro, in ovo and in vivo. GR-CDXL1 presented homologous recombination deficiency linked to bi-allelic BRCA2 mutation, FANCA deletion and unrepaired DNA lesions post-mitosis. GR-CDXL1 cells were sensitive to PARP inhibitor (PARPi) olaparib, despite chemoresistance, which challenges the current clinical hypothesis claiming that chemosensitive NSCLC patients should respond to PARPi. Targeting CIN through centrosome clustering inhibition in GR-CDXL3 impeded tumor growth in ovo and in vivo. In GR-CDXL4, olaparib sensitivity was dictated by SLFN11 overexpression, which also correlated with increased neuroendocrine marker expression at patient disease progression, suggesting a predictive value of SLFN11 in histological transformation of NSCLC into SCLC. Conclusion: This study unravels distinct DDR profiles as a central mechanism underpinning CTC metastatic potency. Our CDX models provide a robust platform for ex vivo drug testing of DDR-targeted strategies to expand patient categories that may benefit from precision medicine in metastatic NSCLC. Citation Format: Tala Tayoun, Vincent Faugeroux, Marianne Oulhen, Olivier Deas, Judith Michels, Laur Brulle-Soumare, Stefano Cairo, Jean-Yves Scoazec, Virginie Marty, Agathe Aberlenc, David Planchard, Jordi Remon, Santiago Ponce, Benjamin Besse, Patricia Kannouche, Jean-Gabriel Judde, Patrycja Pawlikowska, Françoise Farace. Circulating tumor cell-derived explant models reveal DNA damage response-based therapeutic opportunities in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1951.

Comprehensive genomic profiling to identify gene alterations in DNA repair pathway across solid tumors.

3124 Background: Deleterious events in DNA damage response (DDR) are hallmarks of cancer associated with sensitivity to PARP inhibitors (PARPi) and immune checkpoint inhibitors (CPI). This study investigated DDR pathway alterations across solid tumors. Methods: Samples were sequenced with the Oncomap ExTra assay using tumor-normal paired whole-exome DNA sequencing to detect single base substitutions, indels, and copy number alterations that were clinically actionable, defined as associated with FDA approved drugs or clinical trial enrollment. Here, we report the frequency of MSI-high and TMB-high (&gt;10 mutations/Mb), and clinically-actionable alterations for the following 49 DDR genes: ARID1A, ATM, ATR, ATRX, BAP1, BARD1, BLM, BRCA1/2, BRIP1, CDK12, CHEK1/2, EPCAM, ERCC1/2/3/4/5, FANCA/C/D2/E/F/G/I/L/M, MLH1, MRE11A, MSH2/6, MUTYH, NBN, PALB2, PMS2, PPP2R2A, PTEN, RAD21/50/51/51B/51C/51D/52/54L, XRCC1/2/3. Results: Of the 6055 patient samples profiled, 1633 (27.0%) had clinically actionable alterations in DDR genes; DDR alterations varied from 0-64.3% across tumor types. For the 5657 samples with TMB/MSI data, 429 (7.6%) had high TMB and 193 (3.4%) were MSI-high; MSI-high samples were usually TMB-high (n = 180; 93.2%). The percent of cancers that were TMB-high or MSI-high varied from 0-64.8% and 0-20.8% respectively. Actionable BRCA1/2 gene alterations were present in 319 patients (5.3%, range 0-15.3%). Three cancers (biliary, brain and liver) had BRCA1/2 alterations in less than 2% of patients but across the 49 DDR genes alterations were present in more than 20% of patients, representing a greater than 10-fold difference. Across solid tumors, this analysis identifies a group of 1314 patients (21.7%) who harbor a DDR gene alteration other than BRCA1/2. Conclusions: Defective DNA repair as detected by deleterious alterations in DDR genes along with TMB/MSI status has the potential to guide clinicians to FDA-approved therapy or clinical trial enrollment in a large percentage of patients across solid tumor types.[Table: see text]

Targeting DNA Damage Response and Immune Checkpoint for Anticancer Therapy.

Deficiency in DNA damage response (DDR) genes leads to impaired DNA repair functions that will induce genomic instability and facilitate cancer development. However, alterations of DDR genes can serve as biomarkers for the selection of suitable patients to receive specific therapeutics, such as immune checkpoint blockade (ICB) therapy. In addition, certain altered DDR genes can be ideal therapeutic targets through adapting the mechanism of synthetic lethality. Recent studies indicate that targeting DDR can improve cancer immunotherapy by modulating the immune response mediated by cGAS-STING-interferon signaling. Investigations of the interplay of DDR-targeting and ICB therapies provide more effective treatment options for cancer patients. This review introduces the mechanisms of DDR and discusses their crucial roles in cancer therapy based on the concepts of synthetic lethality and ICB. The contemporary clinical trials of DDR-targeting and ICB therapies in breast, colorectal, and pancreatic cancers are included.

Abstract 1640: Correlations of DNA damage response gene alterations with response to immune checkpoint inhibitors are different in solid tumors

Abstract Background: The DNA damage response (DDR), which is frequently disrupted in cancer, is a signal transduction pathway that responds to DNA damage and DNA replication blocks. Genomic alterations in DDR genes are associated with increased genomic instability and higher tumor mutational burden (TMB). A better understanding of DDR alterations will not only expand our knowledge of cancer development but also led to new cancer treatments. TMB has different predictive values among multiple cancer types. We hypothesized that the prediction values of DDR alterations for response to immune checkpoint inhibitors (ICIs) are also varied. In the present work, we explored the associations between DDR alterations and ICIs efficacy in different solid tumors. Methods: In a cohort of 3396 patients at our center were enrolled. The following tumor types are included: NSCLC (n=1080), colorectal cancer (n=509), gastric cancer (n=269), bile duct cancer (n=122), pancreatic cancer (n=199), hepatocellular carcinoma (n=309), glioma (n=778), melanoma (130). Targeted next-generation sequencing and PD-L1 immunohistochemistry (22C3 antibody) were performed. The ICIs treatment cohort from the Memorial Sloan Kettering Cancer Center (MSKCC) was also selected. Results: Across all 3396 patients, the mutational frequencies of DDR genes were 23.4%. Hepatocellular carcinoma, colorectal cancer, and NSCLC were the tumor types in which DDR alterations were most frequent-30.4%, 30.1% , and 29.1%, respectively. About 7.6% of patients have high microsatellite instability (MSI-H) in the DDR alterations group, while 0.2% of patients display MSI-H in the control group (P &amp;lt; 0.0001). For all patients, the median TMB was significantly higher in the DDR alterations group (8.92 vs 4.69 muts/Mb, P &amp;lt; 0.0001). Furthermore, 39.7% of patients had PD-L1 expression (TPS≥10%) in the DDR alterations group and 29.9% of patients had PD-L1 expression in the control group (P = 0.016). For the entire MSKCC cohort, patients in the DDR alterations group had significantly longer median overall survival after ICIs therapy (34 vs 15 months, P &amp;lt; 0.0001). However, DDR alterations display divergent predictive roles in different cancer types. DDR alterations are associated with ICIs efficacy in melanoma (P = 0.0007), colorectal cancer (P = 0.0012), NSCLC (P = 0.0224), bladder cancer (P = 0.0439), and breast cancer (P = 0.0451). There were no associations between DDR alterations and benefit from ICIs in renal cell carcinoma, glioma, esophagogastric, and head and neck cancers. Conclusions: Our data indicated that DDR alterations are associated with increased TMB, MSI-H, and higher PD-L1 expression. Furthermore, DDR alterations were associated with better response to ICIs in pan-cancer analysis. It's worth noting that DDR alterations can predict patient responses to ICIs in some cancer types, but not in all types of cancer. Citation Format: Tao Li, Yanling Niu, Tonghui Ma, Danhua Wang, Dong-Dong Jia. Correlations of DNA damage response gene alterations with response to immune checkpoint inhibitors are different in solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1640.

Abstract 2062: Comprehensive molecular profiling of DNA damage response (DDR) deficiencies in advanced solid tumors using a real-world genomic database

Abstract Purpose: DNA damage response (DDR) deficiency is a hallmark of cancer and can be exploited with therapeutic interventions such as the use of PARP inhibitors and PD-1/PD-L1 immune checkpoint inhibitors. To understand the relationship between clinically actionable DDR genomic alterations (GA) and DDR deficiency biomarkers, we investigated the distribution of the GA in the most common DDR genes and explored the association with DDR deficiency biomarkers by utilizing the Foundation Medicine comprehensive genomic database across different cancer types. These data may provide essential information to refine and define the clinical translational strategies for innovative cancer therapies in clinical development. Methods: Molecular profiles from a total of 269,371 clinically advanced and diverse malignancies were analyzed using FoundationInsightsTM. Genomic alterations including short variants, copy number alterations and rearrangements in 35 DDR genes, more complex biomarkers (tumor mutation burden [TMB], genome-wide loss of heterozygosity [gLOH], microsatellite instability [MSI] status) and PD-L1 expression were studied. Only functional alterations (known or likely oncogenic) were analyzed. Results: DDR gene alterations are frequent and non-uniformly distributed by type and frequency across cancer types including breast, ovarian, colorectal, esophagus, biliary track, gastric, head and neck, pancreas, melanoma, lung, bladder, and prostate. TP53 is the most frequently altered DDR gene across all cancers as expected (59%), followed by ARID1A (9%), ATM (4%), SMARCA4 (3%), MDM2 (3%), BRCA2 (3%), BRCA1 (2%), CHK2 (2%), MUTYH (2%), whereas many other DDR genes are rarely altered (≤1%). Excluding TP53 from the analysis, bladder cancer has the highest cumulative rate of cases with mutations in DDR genes (46.59%), while other cancers have rates ranging between 20-40%. Further analyses including the relative distribution of TMB, MSI, gLOH and PD-L1 expression by tumor type and their association with DDR GA are ongoing. Conclusion: Identifying associations of DDR alterations and immuno-oncology associated predictive biomarkers (TMB, PD-L1) as well as assessment of signatures of genomic instability (MSI, gLOH) are critical for enabling biomarker-driven precision oncology. We systematically analyzed somatic alterations using the Foundation Medicine comprehensive genomic database and provide a comprehensive molecular profiling of DDR deficiencies in advanced solid tumors. It is anticipated that this data will collectively contribute to identify molecularly defined tumor subsets, where single and/or combination therapies such as DDR inhibitors, immunotherapies, targeted therapies etc. may result in increased clinical benefit for patients with cancer. Citation Format: Danyi Wang, Brian Elenbaas, Karthikeyan Murugesan, Lee A. Albacker, Julien Doudement, Juergen Scheuenpflug, Giuseppe Locatelli, Zheng Feng. Comprehensive molecular profiling of DNA damage response (DDR) deficiencies in advanced solid tumors using a real-world genomic database [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2062.

MA13.03 DNA Damage Response Gene Alterations and their Association with Tumor Mutation Burden and Response to Immunotherapy in NSCLC and SCLC

MA13.03 DNA Damage Response Gene Alterations and their Association with Tumor Mutation Burden and Response to Immunotherapy in NSCLC and SCLC

Natural history, response to systemic therapy, and genomic landscape of plasmacytoid urothelial carcinoma

BackgroundPlasmacytoid urothelial carcinoma (PUC) is a rare, aggressive histologic variant of urothelial cancer characterised by a diffuse growth pattern and CDH1 mutation. We studied the efficacy of preoperative platinum-based chemotherapy in nonmetastatic PUC and immune checkpoint inhibitors (ICIs) in advanced PUC.MethodsCases of nonmetastatic PUC and advanced PUC treated with ICIs at our institution were identified. Outcomes were compared to those of a published cohort of patients with urothelial carcinoma not otherwise specified.ResultsWe identified 81 patients with nonmetastatic PUC. Of the patients with localised disease who underwent neoadjuvant chemotherapy, pathologic complete response and downstaging rates were 12 and 21%, respectively. Pathologic downstaging was not associated with significant improvement in clinical outcomes. Up to 18% of localised disease and 28% of locally advanced cases had unresectable disease at the time of surgery. ICI-treated advanced PUC (N = 21) had progression-free and overall survival of 4.5 and 10.5 months, respectively, and a 38% response rate. FGFR3 and DNA damage response gene alterations were observed in 3 and 15% of cases, respectively.ConclusionsPUC is associated with high disease burden and poor chemosensitivity. Increased awareness and recognition of this disease variant will allow for new treatment strategies.

ATM Loss Confers Greater Sensitivity to ATR Inhibition Than PARP Inhibition in Prostate Cancer.

Alterations in DNA damage response (DDR) genes are common in advanced prostate tumors and are associated with unique genomic and clinical features. ATM is a DDR kinase that has a central role in coordinating DNA repair and cell-cycle response following DNA damage, and ATM alterations are present in approximately 5% of advanced prostate tumors. Recently, inhibitors of PARP have demonstrated activity in advanced prostate tumors harboring DDR gene alterations, particularly in tumors with BRCA1/2 alterations. However, the role of alterations in DDR genes beyond BRCA1/2 in mediating PARP inhibitor sensitivity is poorly understood. To define the role of ATM loss in prostate tumor DDR function and sensitivity to DDR-directed agents, we created a series of ATM-deficient preclinical prostate cancer models and tested the impact of ATM loss on DNA repair function and therapeutic sensitivities. ATM loss altered DDR signaling, but did not directly impact homologous recombination function. Furthermore, ATM loss did not significantly impact sensitivity to PARP inhibition but robustly sensitized to inhibitors of the related DDR kinase ATR. These results have important implications for planned and ongoing prostate cancer clinical trials and suggest that patients with tumor ATM alterations may be more likely to benefit from ATR inhibitor than PARP inhibitor therapy. SIGNIFICANCE: ATM loss occurs in a subset of prostate tumors. This study shows that deleting ATM in prostate cancer models does not significantly increase sensitivity to PARP inhibition but does sensitize to ATR inhibition.See related commentary by Setton and Powell, p. 2085.

Prognostic Value of DNA Damage Response Genomic Alterations in Relapsed/Advanced Urothelial Cancer.

DNA damage response (DDR) genomic alterations may play an important role in clinical outcomes of patients with urothelial cancer (UC). However, data on the prognostic role of DDR gene alterations in patients with advanced UC remain unclear. We retrospectively collected data of three independent patient cohorts with relapsed or advanced UC including 81 and 91 patients from four institutions who underwent FoundationOne genomic sequencing as well as 129 patients selected from The Cancer Genome Atlas bladder cohort. Fisher's exact test was used to determine differences of mutation frequency among the three cohorts. Logistic regression analysis was performed to calculate odds ratio (OR) and 95% confidence interval (CI). Overall survival (OS) was measured from time of initial diagnosis and Cox proportional hazard regression analysis was performed to calculate the hazard ratio (HR) and 95% CI. DDR genomic alterations were present in 76.5% (62/81), 40.7% (37/91), and 51.2% (66/129) of the three cohorts. ATM alterations consistently correlated with significantly shorter OS, whereas other DDR alterations (excluding ATM) were associated with better prognosis. In 152 patients treated with platinum pooled from the three cohorts, the prognostic value of alterations in ATM as compared with other predefined DDR genes was substantially different (ATM: adjusted HR [HR], 2.03; 95% CI, 1.03-4; p = .04; other DDR: adjusted HR, 0.49; 95% CI, 0.31-0.8; p = .003). Genomic alterations in ATM and other DDR genes may have opposite prognostic value in relapsed and/or advanced UC. ATM may have a complex role in UC progression. Somatic mutations of DNA damage response (DDR) genes are frequently found in urothelial cancer and appear to play an important role in tumorigenesis, progression, treatment response, and outcomes. In a set of DDR genes, ATM alterations were associated with worse survival, while other alterations were associated with better survival in advanced urothelial cancer. The results of this study suggest a complex role of ATM in tumor progression and call for further studies to determine the underlying mechanisms and biomarker clinical utility.

Treatment response comparisons between ATM and BRCA2 germline carriers for mCRPC.

63 Background: Over 10% of men with metastatic prostate cancer (PC) have germline DNA damage response gene alterations; most studies have reported BRCA2 alone or an aggregate of BRCA1, BRCA2 and ATM. Emerging data suggest ATM mutations have distinct effects and warrant individual gene evaluation. We hypothesize that, compared to patients (pts) carrying germline BRCA2 mutations (g BRCA2mut), pts carrying germline ATM mutations (g ATMmut) may have different treatment response to androgen-receptor-targeted agents, docetaxel, platinum therapy and PARP inhibitors (PARPi). Methods: This is an international, multicenter, retrospective case-control study of pts with PC who underwent clinical germline genetic testing between 2014-2019. We identified pts with g ATMmut and matched pts with g BRCA2mut by stage at diagnosis and year of testing. IRB-approved medical records review, χ² and log rank tests were performed. Results: 39 g ATMmut cases and 39 matched g BRCA2mut cases were identified for total of 78. A third (13/39) of pts in each cohort had metastases at diagnosis. Of those diagnosed with localized stage, 81% (21/26) of gATMmut and 73% (19/26) of g BRCA2mut developed metastasis (median times to metastasis 69 vs 49 months, respectively (p=0.1)). Pts in g ATMmut and g BRCA2mut cohorts had similar age, Gleason grade, and PSA at diagnosis. We did not observe a difference in PSA50 response rates to abiraterone, enzalutamide, docetaxel, or carboplatin for mCRPC (Table). g BRCA2mut pts were more likely to respond to PARPi for mCRPC; where available, somatic loss of heterozygosity (LOH) data will be reported at final presentation. Conclusions: While response to standard therapies appears similar between g ATMmut and g BRCA2mut cohorts, response to PARPi in g ATMmut appears to be attenuated compared to g BRCA2mut. More studies are needed and pts with g ATMmut warrant prioritization for novel treatment strategies.[Table: see text]