DNA Damage Repair Deficiency Research Articles

#5658 TUBULE-SPECIFIC CYCLIN-DEPENDENT KINASE 12 KNOCKDOWN POTENTIATES KIDNEY INJURY THROUGH TRANSCRIPTIONAL ELONGATION DEFECTS

Abstract Background and Aims Direct tubular injury caused by several medications, especially chemotherapeutic drugs, is a common cause of AKI. Inhibition or loss of cyclin-dependent kinase 12 (CDK12) triggers a transcriptional elongation defect that results in deficiencies in DNA damage repair, producing genomic instability in a variety of cancers. Notably, 10-25% of individuals developed AKI after treatment with a CDK12 inhibitor, and the potential mechanism is not well understood. Method Here, we established a cisplatin-induced AKI mouse model with CDK12 knockdown mice and created stable in vitro models with CDK12 knockdown tubular epithelial cells. Cisplatin nephrotoxicity was induced by intraperitoneal injection of cisplatin (20 mg/kg). After 2 days following cisplatin treatment, blood and kidney tissues were harvested. Renal function and histology were evaluated. DDR, tubular apoptosis, cell proliferation were evaluated by immunofluorescence assays, real-time PCR, flow cytometer and western blot analysis. Notably, we performed single-molecule real-time sequencing (SMRT), a long-read sequencing platform, to identify the formation of novel transcripts involved in the above events. Results We found that CDK12 was downregulated in the renal tubular epithelial cells in both patients with AKI and murine AKI models. Moreover, tubular cell-specific knockdown of CDK12 in mice enhanced cisplatin-induced AKI through promotion of genome instability, apoptosis, and proliferative inhibition, whereas CDK12 overexpression protected against AKI. Using the single molecule real-time (SMRT) platform on the kidneys of CDK12RTEC+/− mice, we found that CDK12 knockdown targeted Fgf1 and Cast through transcriptional elongation defects, thereby enhancing genome instability and apoptosis. Conclusion These data demonstrated that CDK12 knockdown could potentiate the development of AKI by altering the transcriptional elongation defect of the Fgf1 and Cast genes, and more attention should be given to patients treated with CDK12 inhibitors to prevent AKI.

Tumor sensitization to PARP inhibitors by DNA damaging synthetically lethal acylfulvenes.

e15123 Background: 20-30% of solid tumors (ovarian, breast, pancreatic, prostate cancers) harbor some level of deficiency in DNA Damage Repair (DDR) pathways. Such cancers become dependent on alternative DDR pathways to maintain genome integrity, making them selectively vulnerable to DNA damaging agents. The concept of synthetic lethality has been leveraged to treat subsets of such tumors. Clinically, PARP inhibitors (PARPi) have been successful in Homologous Recombination Deficiency (HRD) cancers. LP-100 and LP-184 are acylfulvene (AF) class small molecule prodrugs that are metabolized to active compounds by prostaglandin reductase 1 (PTGR1) that is often elevated in solid tumors. AF-induced DNA lesions are likely selectively processed by repair pathways including BRCA1/2 mediated Homologous Recombination (HR). Methods: Cell Titer Glo based 10 day cell viability assays were used to generate drug IC50 values in vitro. Bliss synergy scores were computed with scores ≥ 10 reflecting synergy. Drug-induced DNA double strand breaks (DSB) were detected and quantified with STRIDE (SensiTive Recognition of Individual DNA Ends) assay in cancer cells. A subcutaneous tumor xenograft model was used to determine tumor volumes in control and drug treated mice. Results: In a BRCA2 mutant ovarian cancer cell line OVCAR3, LP-184 and olaparib co-treatment in vitro showed synergistic effects (Bliss score 10). Similarly in a BRCA2 mutant prostate cancer cell line 22Rv1, LP-100 combination with rucaparib was synergistic (Bliss score 18). 400 nM LP-184 showed a time dependent increase in DNA DSB signals in vitro, 1.7X more so in BRCA2 mutant vs wild type (WT) DLD-1 isogenic colon cancer cell lines up to 24 hours. To validate the hypothesis that AF-induced DSBs remain unresolved if exposed to and further synergize with PARPi in vivo, we tested LP-100 plus olaparib in a DU145 (BRCA2 mutant) prostate cancer xenograft model. LP-100 + olaparib treatment resulted in sustained, durable tumor regression indicating in vivo synergy whereas either agent alone did not produce tumor shrinkage. Day 42 tumor growth inhibition was 66% for 2.5 mg/kg LP-100 alone, 34% for 40 mg/kg olaparib alone and 108% for the combination. Moreover, LP-184 treatment resulted in early onset and complete tumor regression in 7 PDX models of PARPi resistant triple negative breast cancers (TNBC) harboring BRCA1/2 loss whereas olaparib/ niraparib remained entirely ineffective in these. Conclusions: AF response is influenced by tumor DNA repair competence. LP-100 and LP-184 are synthetically lethal resulting from their abilities to cause unresolvable DNA damage where tumor cells express high PTGR1 and are deficient in the HR pathway. LP-184 single agent was superior to PARPi in TNBC and LP-100 combination made an olaparib resistant tumor highly sensitive, thereby facilitating a path to extend the opportunities for both AFs and PARPis and enhance the clinical utilization of PARPi.

A phase 1/2 study of bay 18953444 (Elimusertib) in pediatric patients with relapsed or refractory solid tumors: Initial report of the phase 1 results of PEPN2112.

e15131 Background: Elimusertib is a highly selective oral inhibitor of the Ataxia telangiectasia and Rad3 related (ATR) kinase, which is required for efficient end-joining repair of double-stranded breaks, particularly during DNA replication. Many pediatric cancers involve potential ATR susceptibilities such as increased replication stress due to oncogenic fusions, specific DNA damage repair (DDR) deficiencies, oncogenic activation of DNA damage and nucleases such as PGBD5, as well as alternative lengthening of telomeres. We report the initial phase 1 results of PEPN2112 (NCT05071209), an ongoing pediatric phase 1/2 clinical trial of elimusertib monotherapy. Methods: Eligible patients (pts) included children, adolescents, and young adults with relapsed or refractory tumors with: (1) Ewing sarcoma or related EWSR1 fusion positive tumors (EWS), (2) alveolar rhabdomyosarcoma, PAX3-FOXO1 fusion positive (aRMS), or (3) non-CNS primary tumors exhibiting specific DDR pathway defects anticipated to sensitize to ATR inhibition. For pts < 18 years (yrs), a rolling-six design was used to evaluate elimusertib administered BID x3 days/week of a 28-day cycle starting at the adult equivalent recommended phase 2 dose (RP2D) of 24 mg/m2/dose (max 40 mg) with a potential de-escalation to 18 mg/m2/dose (max 30 mg). The pediatric RP2D determination was based upon dose limiting toxicity (DLT) criteria (CTCAEv5) during cycle 1. Pharmacokinetic (PK) studies were performed. Pts > 18 yrs could enroll onto the phase 2 cohorts at the adult RP2D simultaneously with the pediatric phase 1. Once the pediatric RP2D was defined, pts < 18 yrs accrued to the phase 2 cohorts and a PK expansion for pts < 12 yrs was opened. Results: 8 eligible pts were enrolled (4 males) on the phase 1 part of the study. 2 pts were inevaluable for DLT as they received < 75% of protocol therapy. Median (range) age was 13 (10-17) yrs. Diagnoses included: EWS (n = 4) and 1 pt each with aRMS, adrenocortical carcinoma, clear cell sarcoma, and osteosarcoma. At 24 mg/m2/dose, no DLTs were observed. Toxicities were hematologic, with grade 3 toxicities including anemia (n = 3), neutropenia (n = 4), and decreased white blood cells (n = 1). One pt experienced grade 4 lymphopenia. There were no grade 3/4 non-hematologic toxicities. Day 1 mean ± SD values of Tmax, Cmax, AUC0-8h and t1/2 were 1.6 ± 0.5 h, 1532 ± 385 ng/mL, 5863 ± 1841 h*ng/mL and 3.6 ± 0.9 h, respectively. Conclusions: Elimusertib-related toxicities were primarily hematologic. The RP2D for elimusertib monotherapy in pediatric pts is 24 mg/m2/dose (max 40 mg) orally BID x3 days/week continuously, analogous to dosing in adults with similar PK. Phase 2 and PK expansion cohorts as well as pharmacodynamic studies are ongoing. Clinical trial information: NCT05071209 .

Acquired DNA damage repairs deficiency-driven immune evolution and involved immune factors of local versus distant metastases in non-small cell lung cancer

ABSTRACT The evolution of immune profile from primary tumors to distant and local metastases in non-small cell lung cancer (NSCLC), as well as the impact of the immune background of primary tumors on metastatic potential, remains unclear. To address this, we performed whole-exome sequencing and immunohistochemistry for 73 paired primary and metastatic tumor samples from 41 NSCLC patients, and analyzed the change of immune profile from primary tumors to metastases and involved genetic factors. We found that distant metastases tended to have a decreased CD8+ T cell level along with an increased chromosomal instability (CIN) compared with primary tumors, which was partially ascribed to acquired DNA damage repair (DDR) deficiency. Distant metastases were characterized by immunosuppression (low CD8+ T cell level) and immune evasion (high PD-L1 level) whereas local metastases (pleura) were immune-competent with high CD8+ T cell, low CD4+ T cell and low PD-L1 level. Primary tumors with high levels of CD4+ T cells were associated with distant metastases rather than local metastases. Analysis of TCGA data and a single-cell RNA-sequencing dataset revealed a decreasing trend of major immune cells, such as CD8+ T cells, and an increasing trend of CD4 T helper cells (Th2 and Th1) in primary tumors with metastases from local to distant sites. Our study indicates that there are differences in the immune evolution between distant and local metastases, and that acquired DDR deficiency contributes to the immunosuppression in distant metastases of NSCLC. Moreover, the immune background of primary tumors may affect their metastatic potential.

Genomic hallmarks and therapeutic implications of G0 cell cycle arrest in cancer

BackgroundTherapy resistance in cancer is often driven by a subpopulation of cells that are temporarily arrested in a non-proliferative G0 state, which is difficult to capture and whose mutational drivers remain largely unknown.ResultsWe develop methodology to robustly identify this state from transcriptomic signals and characterise its prevalence and genomic constraints in solid primary tumours. We show that G0 arrest preferentially emerges in the context of more stable, less mutated genomes which maintain TP53 integrity and lack the hallmarks of DNA damage repair deficiency, while presenting increased APOBEC mutagenesis. We employ machine learning to uncover novel genomic dependencies of this process and validate the role of the centrosomal gene CEP89 as a modulator of proliferation and G0 arrest capacity. Lastly, we demonstrate that G0 arrest underlies unfavourable responses to various therapies exploiting cell cycle, kinase signalling and epigenetic mechanisms in single-cell data.ConclusionsWe propose a G0 arrest transcriptional signature that is linked with therapeutic resistance and can be used to further study and clinically track this state.

Management of Advanced Prostate Cancer in the Precision Oncology Era.

Prostate cancer (PC) is the second leading cause of cancer death in men in the United States. While diversified and improved treatment options for aggressive PC have improved patient outcomes, metastatic castration-resistant prostate cancer (mCRPC) remains incurable and an area of investigative therapeutic interest. This review will cover the seminal clinical data supporting the indication of new precision oncology-based therapeutics and explore their limitations, present utility, and potential in the treatment of PC. Systemic therapies for high-risk and advanced PC have experienced significant development over the past ten years. Biomarker-driven therapies have brought the field closer to the goal of being able to implement precision oncology therapy for every patient. The tumor agnostic approval of pembrolizumab (a PD-1 inhibitor) marked an important advancement in this direction. There are also several PARP inhibitors indicated for patients with DNA damage repair deficiencies. Additionally, theranostic agents for both imaging and treatment have further revolutionized the treatment landscape for PC and represent another advancement in precision medicine. Radiolabeled prostate-specific membrane antigen (PSMA) PET/CT is rapidly becoming a standard of care for diagnosis, and PSMA-targeted radioligand therapies have gained recent FDA approval for metastatic prostate cancer. These advances in precision-based oncology are detailed in this review.

Abstract 6102: Targeting BARD1 slows PDAC growth in vitro and in vivo and sensitizes cells to DNA damaging agents

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the most prevalent malignant neoplasm of the pancreas, responsible for over 90% of pancreatic cancer cases. Despite recent therapeutic advances, the five-year overall survival rate for PDAC is only 11% and therapies remain limited. It is now known that deficiency in DNA damage repair (DDR) renders PDAC cells vulnerable to certain DNA damage agents, for example, poly (ADP-ribose) polymerase inhibitors (PARPi). Most of the DDR genes mutated in PDAC are crucial for the proper functioning of the homologous recombination repair (HRR) pathway, and loss-of-function alterations in DDR genes sensitize cells to DNA-damaging agents. Since this treatment strategy is currently limited to 5-10% of PDAC cases with known mutations in the DDR genes, it underscores a dire need to understand new therapeutic avenues and expand the PDAC patient population that could benefit from this therapeutic approach. We have recently published that BARD1 (BRCA1- Associated- Ring- Domain- 1), an obligate binding partner of BRCA1, is upregulated in PDAC cells exposed to PARPi/platinums. We found that transient inhibition of BARD1 rendered PDAC cells extremely sensitive to olaparib (PARPi)/oxaliplatin (platinum), and enhanced DNA damage. Based on these results, we created two genetic models of BARD1 inhibition and utilized these model systems to investigate if loss of BARD1 chemo-sensitizes PDAC cells to other PARPis and DNA damage agents. Doxycycline inducible shRNA and BARD1 CRISPR KO models were created to inhibit gene expression of BARD1 in PDAC cells. We first characterized these model systems to confirm the loss of BARD1 protein and mRNA expression by western blot and qRT-PCR analyses. Using colony formation and Pico green cell survival assays, we found that inhibiting BARD1 resulted in slower growth of pancreatic cancer cells in vitro. Moreover, expression of several cell cycle genes from G2-M phase was significantly decreased (p=0.05). These studies were recapitulated in a mouse xenograft subcutaneous model, where BARD1 KO and WT PDAC cells were injected subcutaneously and tumor growth was analyzed over 25-30 days. Kaplan-Meier curves were calculated and plotted using Log-rank test. We found that inhibiting BARD1 significantly (p=0.026) delayed formation of PDAC tumors in vivo. Next, we analyzed the efficacies of various DNA damaging agents when BARD1 was inhibited. Silencing or CRISPR KO of BARD1 enhanced efficacy of mitomycin C, irinotecan, as well as other PARPis, which are currently in clinical trials (rucaparib, veliparib) in vitro and lowered their IC50s. These results indicate that targeting BARD1 has the potential to benefit patients in terms of novel or improved treatments. Our ongoing and future studies will expand on these findings to understand BARD1-mediated pathway and evaluate sensitivity of multiple DNA damage agents by screening a library of > 250 compounds. Citation Format: Sohum Patel, Anoohya Arkala, Avinoam Nevler, Carolyn Coats, Charles J. Yeo, Aditi Jain. Targeting BARD1 slows PDAC growth in vitro and in vivo and sensitizes cells to DNA damaging agents. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6102.

Abstract 6519: Haploinsufficiency for BRCA2 leads to common fragile site instability in human mammary epithelial cells

Abstract Individuals with germline heterozygous mutations of breast cancer susceptibility genes BRCA1 or BRCA2 have a 50 to 80% lifetime risk of developing breast cancer, yet the mechanisms of these cancers remain largely unknown. There is growing evidence that BRCA1 and BRCA2 heterozygosity confer haploinsufficiency in normal human mammary epithelial cells for their multiple known functions. Haploinsufficiency for BRCA1 leads to defects in differentiation, replication stress response, premature senescence and genomic instability in human mammary epithelial cells. Deficiencies in error-free DNA damage repair has been observed in genetically engineered cells as well as primary human mammary epithelial cells carrying BRCA1 heterozygous mutations. There is relatively less research on understanding the role of haploinsufficiency for BRCA2 in human mammary epithelial cells. It has been reported that haploinsufficiency for BRCA2 leads to genomic instability via unscheduled R-loops. We previously showed that accumulation of sub-chromosomal copy number variations (CNVs) and replication stress-induced DNA damage, together with attenuated checkpoint and apoptotic responses, constitute a haplo-insufficient phenotype in mammary epithelial cells of BRCA2 mutation carrier patients. Common fragile sites (CFS) are found in all individuals and represent a normal component of chromosome structure. Numerous studies have shown that CFSs are prone to deletions and rearrangements in many cancers, a situation referred as CFS instability. Importantly, Fanconi Anemia/BRCA pathway has been previously reported to have a role in regulating CFS instability. In this study, we further explored a link between BRCA2 haploinsufficiency and CFS instability. We induced replication stress with DNA polymerase inhibitor aphidicolin (APH) treatment in control and BRCA2- deficient human mammary epithelial cells. We then performed DAPI banding to map and score the cytogenic lesions in metaphase spreads cells, in the absence or presence of APH treatment. Our results demonstrated that BRCA2- deficient human mammary epithelial cells showed increased frequency of CFS regions such as FRA18B. Correspondingly, BRCA2-deficient cells exhibited a failure to activate CHK1, a central coordinator of the response to replication stress and DNA damage, in response to APH treatment, despite normal levels of total CHK1 protein. ATR/CHK1 pathway is a major regulator of CFS stability. Thus, our results provide support for BRCA2 haploinsufficiency leading to CFS instability in human mammary epithelial cells. These studies will yield unanticipated opportunities for improved risk assessment and prevention strategies in high-risk patients. Citation Format: Mihriban Karaayvaz, Kavya Vipparthi, Antony Caputo. Haploinsufficiency for BRCA2 leads to common fragile site instability in human mammary epithelial cells. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6519.

Abstract 6241: LP-184, an acylfulvene class small molecule therapeutic, is synthetically lethal in DNA damage repair deficient cancers

Abstract As many as one third of solid tumors (ovarian, breast, pancreatic, prostate cancers) harbor deficiency in some DNA Damage Repair (DDR) pathways. Such cancers become dependent on alternative DDR pathways to maintain genome integrity, making them selectively vulnerable to DDR inhibitors. The concept of synthetic lethality has been successfully applied to develop strategies to treat subsets of such tumors. Clinically, PARP inhibitors (PARPi) have been successful particularly in Homologous Recombination Deficiency (HRD) cancers. Other agents have also been designed to target these DDR deficiencies in cancer cells and have potential to be clinically beneficial. LP-184 is a next generation acylfulvene prodrug metabolized to an active compound by prostaglandin reductase 1 (PTGR1) that is often elevated in multiple tumors. LP-184-induced DNA lesions are likely repaired by the Nucleotide Excision Repair (NER) and Homologous Repair (HR) pathways. Reduced activities of multiple DDR-related pathways in solid tumor models correlated with increased sensitivities to LP-184 as indicated by Gene Set Enrichment Analysis. Chinese Hamster Ovary cells with NER mutations (ERCC1/2/6) were at least 4 fold more sensitive to LP-184 relative to otherwise isogenic parental cells. ERCC2 or BRCA2 depletion enhanced LP-184 sensitivity 5-8X in a metastatic prostate cancer cell line. LP-184 showed ~120 fold higher potency (IC50 77 nM) compared to Olaparib in HRD prostate cancer organoid model LuCaP 96 (BRCA2/CHEK2 inactivating mutations). Across 14 patient-derived pancreatic, lung and prostate tumor models harboring HR mutations (BRCA1/2, CHEK1/2, ATM/ATR, PALB2, PARP1/2, RAD51, FANCA/B), LP-184 showed ex vivo IC50s in the range of 30-300 nM, whereas Olaparib IC50s ranged from 1700-6900 nM. LP-184 treatment resulted in complete tumor regression (107-141% TGI) in 10/10 HR deficient triple negative breast cancer PDX models of which 7/10 were resistant Olaparib/Niraparib and to Doxorubicin/Cyclophosphamide. LP-184 treatment resulted in complete and durable tumor regression in HRD (BRCA1/ATR mutant) pancreatic cancer PDX models (112-140% TGI). In the ovarian cancer cell line OVCAR3 having HRD/NERD phenotype, LP-184 IC50 was 13 nM, Olaparib IC50 was 145 nM and their combination Bliss Synergy Score was 16 indicating synergy. LP-184 is synthetic lethal resulting from its abilities to cause unresolvable DNA damage if tumor cells express high PTGR1 and are deficient in NER/HR genes. Unlike PARPi, LP-184 has striking activity in both NERD as well as HRD cancers. These strong data have prompted the development of a soon to be launched clinical trial to translate the broad preclinical anticancer activity of LP-184 in solid tumors with HR/NER pathway defects, such as pancreatic, prostate, ovarian and breast cancers. Citation Format: Aditya Kulkarni, Jianli Zhou, Neha Biyani, Kishor Bhatia, Panna Sharma. LP-184, an acylfulvene class small molecule therapeutic, is synthetically lethal in DNA damage repair deficient cancers. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6241.

A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes

Specific classes of DNA damage repair (DDR) defect can drive sensitivity to emerging therapies for metastatic prostate cancer. However, biomarker approaches based on DDR gene sequencing do not accurately predict DDR deficiency or treatment benefit. Somatic alteration signatures may identify DDR deficiency but historically require whole-genome sequencing of tumour tissue. We assembled whole-exome sequencing data for 155 high ctDNA fraction plasma cell-free DNA and matched leukocyte DNA samples from patients with metastatic prostate or bladder cancer. Labels for DDR gene alterations were established using deep targeted sequencing. Per sample mutation and copy number features were used to train XGBoost ensemble models. Naive somatic features and trinucleotide signatures were associated with specific DDR gene alterations but insufficient to resolve each class. Conversely, XGBoost-derived models showed strong performance including an area under the curve of 0.99, 0.99 and 1.00 for identifying BRCA2, CDK12, and mismatch repair deficiency in metastatic prostate cancer. Our machine learning approach re-classified several samples exhibiting genomic features inconsistent with original labels, identified a metastatic bladder cancer sample with a homozygous BRCA2 copy loss, and outperformed an existing exome-based classifier for BRCA2 deficiency. We present DARC Sign (DnA Repair Classification SIGNatures); a public machine learning tool leveraging clinically-practical liquid biopsy specimens for simultaneously identifying multiple types of metastatic prostate cancer DDR deficiencies. We posit that it will be useful for understanding differential responses to DDR-directed therapies in ongoing clinical trials and may ultimately enable prospective identification of prostate cancers with phenotypic evidence of DDR deficiency.

Phase II trial of lurbinectedin combined with avelumab as maintenance therapy for metastatic urothelial carcinoma with stable or responding disease following platinum-based chemotherapy.

TPS590 Background: Maintenance avelumab following stable/responding disease after 4-6 cycles of platinum-based chemotherapy is a conventional first-line therapy for metastatic urothelial carcinoma (mUC). Given the attrition of patients between lines of systemic therapy, there is a role for extending the benefits of maintenance avelumab by combinations with tolerable and active agents. Lurbinectedin (Lurbi) is an alkylating agent and selective inhibitor of oncogenic transcription. Lurbi is approved by the US FDA for treating small cell lung cancer with progression on platinum-based chemotherapy with typical dosing as 3.2 mg/m2 intravenously (IV) every 3 weeks. The activity of lurbi in the presence of DNA damage repair (DDR) alterations, multiple transcriptomic drivers and preclinical synergism with and feasibility of co-administration with immune checkpoint inhibitors (ICI) suggests potential activity of combination lurbi and ICI in mUC. Patients with stable or responding disease following platinum-based chemotherapy are phenotypically selected for deficiencies in DDR. Lurbi may be tolerable in this setting given mostly reversible myelosuppression and no serious non-hematologic toxicities especially neurotoxicity. Thus, the combination of lurbi with maintenance avelumab may warrant evaluation in mUC. Methods: A non-randomized multicenter (Advent Health Cancer Institute, Moffitt Cancer Center) phase II trial (n=36) is designed to evaluate combination avelumab (800 mg IV every 2 weeks) and lurbi (3·2 mg/m2 IV as a 1-h infusion every 4 weeks) for those with stable or responding disease following 4-6 cycles of platinum-based first-line platinum-based chemotherapy for mUC. Therapy is continued till progression of disease, intolerable toxicities or patient decision. Patients are seen for a clinical examination every 4 weeks (1 cycle) with laboratory evaluation every 2 weeks. Radiographic imaging is performed every 8 weeks for 6 months and then every 12 weeks thereafter to assess disease. Premedication for lurbi includes corticosteroids (dexamethasone 8 mg or equivalent) and serotonin antagonists. Mandatory granulocyte-colony stimulating factor (G-CSF) prophylaxis will be administered to all patients. Baseline archival tumor tissue and periodic blood is collected for correlative studies (tumor genomics/PD-L1 expression, circulating tumor DNA and immune markers). Given a median progression-free survival (PFS) with avelumab alone of 3.7 months, an alternative median PFS of 6 months is of interest warranting further development. We will enroll 33 evaluable patients to achieve 90% power at a 1-sided alpha level 0.1 to detect hazard ratio of 0.62. Given ~10% of enrolled patients may be inevaluable, we may enroll up to 36 patients. Clinical trial ID: NCT05574504. Clinical trial information: NCT05574504 .

Atypical ATMs: Broadening the phenotypic spectrum of ATM-associated hereditary cancer.

Heterozygous, loss-of-function germline variants in ATM have been associated with an increased lifetime risk of breast, pancreas, prostate, stomach, ovarian, colorectal, and melanoma cancers. We conducted a retrospective review of thirty-one unrelated patients found to be heterozygous for a germline pathogenic variant in ATM and identified a significant proportion of patients in this cohort with cancers not currently associated with the ATM hereditary cancer syndrome, including carcinomas of the gallbladder, uterus, duodenum, kidney, and lung as well as a vascular sarcoma. A comprehensive review of the literature found 25 relevant studies where 171 individuals with a germline deleterious ATM variant have been diagnosed with the same or similar cancers. The combined data from these studies were then used to estimate the prevalence of germline ATM pathogenic variants in these cancers, which ranged between 0.45% and 2.2%. Analysis of tumor sequencing performed in large cohorts demonstrated that the frequency of deleterious somatic ATM alterations in these atypical cancers equaled or exceeded the alteration frequency in breast cancer and occurred at a significantly higher rate than in other DNA-damage response tumor suppressors, namely BRCA1 and CHEK2. Furthermore, multi-gene analysis of somatic alterations in these atypical cancers demonstrated significant co-occurrence of pathogenic alterations in ATM with BRCA1 and CHEK2, while there was significant mutual exclusivity between pathogenic alterations in ATM and TP53. This indicates that germline ATM pathogenic variants may play a role in cancer initiation and progression in these atypical ATM malignancies, potentially influencing these cancers to be driven toward DNA-damage repair deficiency and away from loss of TP53. As such, these findings provide evidence for broadening of the ATM-cancer susceptibility syndrome phenotype to improve the recognition of affected patients and provide more efficacious, germline-directed therapies.

DNA repair deficiency as circulating biomarker in prostate cancer.

Deleterious aberrations in DNA repair genes are actionable in approximately 25% of metastatic castration-resistant prostate cancers (mCRPC) patients. Homology recombination repair (HRR) is the DNA damage repair (DDR) mechanism most frequently altered in prostate cancer; of note BRCA2 is the most frequently altered DDR gene in this tumor. Poly ADP-ribose polymerase inhibitors showed antitumor activity with a improvement in overall survival in mCRPC carrying somatic and/or germline alterations of HHR. Germline mutations are tested on peripheral blood samples using DNA extracted from peripheral blood leukocytes, while the somatic alterations are assessed by extracting DNA from a tumor tissue sample. However, each of these genetic tests have some limitations: the somatic tests are related to the sample availability and tumor heterogeneity, while the germline testing are mainly related to the inability to detect somatic HRR mutations. Therefore, the liquid biopsy, a non-invasive and easily repeatable test compared to tissue test, could identified somatic mutation detected on the circulating tumor DNA (ctDNA) extracted from a plasma. This approach should better represent the heterogeneity of the tumor compared to the primary biopsy and maybe helpful in monitoring the onset of potential mutations involved in treatment resistance. Furthermore, ctDNA may inform about timing and potential cooperation of multiple driver genes aberration guiding the treatment options in patients with mCRPC. However, the clinical use of ctDNA test in prostate cancer compared to blood and tissue testing are currently very limited. In this review, we summarize the current therapeutic indications in prostate cancer patients with DDR deficiency, the recommendation for germline and somatic-genomic testing in advanced PC and the advantages of the use liquid biopsy in clinical routine for mCRPC.

The effects of altered DNA damage repair genes on mutational processes and immune cell infiltration in esophageal squamous cell carcinoma.

Defects in DNA damage repair (DDR) pathways lead to genomic instability and oncogenesis. DDR deficiency is prevalent in esophageal squamous cell carcinoma (ESCC), but the effects of DDR alterations on mutational processes and tumor immune microenvironment in ECSS remain unclear. Whole-exome and transcriptome sequencing data of 45 ESCC samples from Taizhou, China, were used to identify genomic variations, gene expression modulation in DDR pathways, and the abundance of tumor-infiltrating immune cells. Ninety-six ESCC cases from The Cancer Genome Atlas (TCGA) project were used for validation. A total of 57.8% (26/45) of the cases in the Taizhou data and 70.8% (68/96) of the cases in the TCGA data carried at least one functional impact DDR mutation. Mutations in the DDR pathways were associated with a high tumor mutation burden. Several DDR deficiency-related mutational signatures were discovered and were associated with immune cell infiltration, including T cells, monocytes, dendritic cells, and mast cells. The expression levels of two DDR genes, HFM1 and NEIL1, were downregulated in ESCC tumor tissues and had an independent effect on the infiltration of mast cells. In the Taizhou data, increased expression of HFM1 was associated with a poor prognosis, and the increased expression of NEIL1 was associated with a good outcome, but no reproducible correlation was observed in the TCGA data. This research demonstrated that DDR alterations could impact mutational processes and immune cell infiltration in ESCC. The suppression of HFM1 and NEIL1 could play a crucial role in ESCC progression and may also serve as prognostic markers.

Clinicopathological and immunological profiles of prostate adenocarcinoma and neuroendocrine prostate cancer

BackgroundBiomarkers of DNA damage repair deficiency provide opportunities for personalized treatment with immunotherapy. However, there is limited research on the immune microenvironment of adeno-neuroendocrine prostate cancer (NEPC). In this study, we aimed to assess and describe the comprehensive clinicopathological manifestations of NEPC to improve diagnosis and predict prognosis.MethodsA retrospective medical record review of 66 patients with prostate cancer (PCa) was performed. PCa samples from the 66 patients were analyzed using immunohistochemical staining for the detection of chromogranin, neural cell adhesion molecule 1, and synaptophysin. For tumor-associated immune microenvironment analysis, PD-L1, CD3, and CD8 were labeled in tissue slides. The effect of clinicopathological factors on the survival of patients with Adeno-NEPC was analyzed.ResultsTwenty patients presented with adeno-NEPC, whereas 46 presented with adeno-PCa. The median age of patients at PCa diagnosis was 67.86 ± 7.05 years (68.65 ± 7.23 years, adeno-NEPC; 67.52 ± 7.02 years, adeno-PCa). Eleven patients with adeno-NEPC underwent prostatectomy, whereas nine received primary androgen deprivation therapy (ADT). Additionally, 30 patients with adeno-PCa underwent prostatectomy, whereas 16 (34.8%) received primary ADT. There was a significant difference in overall survival between patients with adeno-NEPC and those with adeno-PCa (46.0 months vs. 65.0 months). There was also a significant difference in time from prostatectomy to biochemical recurrence between the groups of patients who underwent prostatectomy. Prostatectomy and normal lactate dehydrogenase levels were clinical factors that were significantly associated with better outcomes in patients with adeno-NEPC. Metastatic adeno-NEPC was associated with a higher programmed death ligand 1 (PD-L1) score (2–4) than localized PCa. The data showed that PD-L1 expression in adeno-NEPC may be negatively associated with that in CD8+ T cells.ConclusionsOur study revealed clinicopathological manifestations of adeno-NEPC and some possible predictive factors significantly associated with better outcomes in patients with adeno-NEPC. These findings might be beneficial in the development of diagnostic strategies and customized treatment plans.

TALASUR trial: a single arm phase II trial assessing efficacy and safety of TALazoparib and Avelumab as maintenance therapy in platinum-Sensitive metastatic or locally advanced URothelial carcinoma

BackgroundUrothelial carcinoma (UC) is the ninth most commonly diagnosed cancer worldwide, with a 3.8/1 male to female ratio. Platinum-based chemotherapy is the first line standard of care for fit patients with advanced UC. However, despite a response rate (RR) for approximately half of patients receiving standard chemotherapy, durable responses are rare (median progression-free progression (PFS) around 8 months). Recently, immune checkpoint inhibitors (ICI) have emerged as new therapeutic options. Among them, Avelumab, an anti-PD-L1 antibody, was assessed in maintenance treatment, demonstrating an overall survival improvement in the JAVELIN Bladder-100 phase III trial. These findings led to its approval as first line maintenance therapy for patients with locally advanced or metastatic UC who have not progressed on prior platinum-containing chemotherapy. However, disease progression as best response was noticed for 37% of patients under Avelumab as maintenance treatment.UC has targetable genomic alterations, including DNA damage repair (DDR) alterations. DDR deficiency is known to major sensitivity to both platinum-based chemotherapy and PD-1/PD-L1 blockade and the combination of ICI and PARP inhibitors showed promising results. It therefore warrants to assess the interest of combining ICI plus PARP inhibitors as maintenance treatment in UC patients.MethodsThe TALASUR trial is a single-arm multicenter phase 2 study aiming to assess the antitumor activity of the combination of Avelumab with Talazoparib among patients with locally advanced/metastatic UC in maintenance therapy after platinum-based chemotherapy.The primary objective is to determine the efficacy of the combination, assessed through PFS. Secondary objectives are as follows: safety profile of the association, objective response, duration of tumoral response, disease control rate, time to subsequent therapy, quality of life. A blood and tumor collections will be also constituted.Patient will receive the combination therapy of daily oral Talazoparib (1 mg/day) and intra-venous Avelumab 800 mg on days 1 and 15, in a 28-day cycle. Fifty patients will be enrolled.DiscussionTalazoparib with Avelumab combination may have additive activity when administrated jointly. We hypothesize that combination will increase the antitumor activity in UC first line maintenance setting with an acceptable safety profile.Trial registrationNCT04678362, registered December 21, 2020. Protocol version: Version 1.3 dated from 2020 09 11.

Molecular intrinsic subtypes, genomic, and immune landscapes of BRCA-proficient but HRD-high ER-positive/HER2-negative early breast cancers

PurposeThe vast majority of research studies that have described the links between DNA damage repair or homologous recombination deficiency (HRD) score, and tumor biology, have concerned either triple negative breast cancers or cancers with mutation of BRCA 1/2. We hypothesized that ER + /HER2- early breast tumors without BRCA 1/2 mutation could have high HRD score and aimed to describe their genomic, transcriptomic, and immune landscapes.Patients and methodsIn this study, we reported BRCA 1/2 mutational status, HRD score, and mutational signature 3 (S3) expression, in all early breast cancer (eBC) subtypes from the TCGA database, with a particular focus in ER + /HER2-. In this subtype, bioinformatics analyses of tumor transcriptomic, immune profile, and mutational landscape were performed, according to HRD status. Overall survival (OS), progression free-interval (PFI), and variables associated with outcome were also evaluated.ResultsAmong the 928 tumor samples analyzed, 46 harbored BRCA 1/2 mutations, and 606 were ER + /HER2- (of which 24 were BRCA 1/2 mutated). We found a subset of BRCA-proficient ER + /HER2— eBC, with high HRD score. These tumors displayed significantly different immune, mutational, and tumor molecular signatures landscapes, compared to BRCA-mutated and BRCA-proficient HRD-low tumors. Outcome did not significantly differ between these 3 groups, but biological factors associated with survival are not the same across the 3 entities.ConclusionThis study highlights possible novel biological differences among ER + /HER2- breast cancer related to HRD status. Our results could have important implications for translational research and/or the design of future clinical trials, but require prospective clinical evaluation.

Development of a Potent DNA Damaging Agent LP-284 for Treatment of Mantle Cell Lymphoma

Introduction: Mantle cell lymphoma (MCL) is a rare and aggressive type of non-Hodgkin lymphoma that is characterized by the hallmark t(11;14) translocation and subsequent deregulation of expression of the Cyclin D1 (CCND1) gene. Immunochemotherapy followed by autologous stem cell transplantation and/or maintenance therapy remains the most common frontline choice for eligible individuals. Additionally, the introduction of bruton's tyrosine kinase inhibitors (BTKi), anti-CD19 chimeric antigen receptor T-cell therapy, and targeted therapies have advanced the treatment of r/r (relapsed/refractory) MCL. Unfortunately, not all patients are eligible for these therapies and durable remission is rare. Alternative therapies with novel mechanisms of action and increased efficacy are urgently needed for MCL patients. LP-284 is a novel small molecule and DNA damaging agent being developed for the treatment of MCL. The DNA lesions induced by LP-284 are repaired by transcription-coupled DNA repair and can trigger apoptosis in tumors with DNA damage repair deficiencies. As LP-284 DNA lesions block transcription, we hypothesize that LP-284 directly starves transcriptionally addicted tumors such as those with actively transcribing onco-fusion genes such as CCND1. We previously reported that LP-284 shows nanomolar potency across 6 MCL cell lines, including cells resistant to BTKi, bortezomib (Btz.), and venetoclax. Here we report LP-284's efficacy in MCL xenograft mouse models and its ability to induce ATM and subsequent gamma-H2AX phosphorylation, transcriptomic response in MCL cell lines, and preliminary toxicological profile in dogs. Methods and Results: In JEKO1-derived MCL xenograft mice, LP-284 (2 or 4 mg/kg; i.v.) was tested to evaluate its survival benefits and efficacy compared to ibrutinib (Ibr.; 50mg/kg; oral) or Btz. (1 mg/kg; i.p.). LP-284 significantly (p< 0.001; n=7 or 8 per group) increased the overall survival of these mice from 20 days in the vehicle control group to 41 days (LP-284, 2 mg/kg) and 48 days (LP-284, 4 mg/kg). Additionally, LP-284 at either concentration showed significantly increased tumor growth inhibition (TGI) compared to Ibr. or Btz. At day 17 post treatment, 113% TGI was observed in the 4 mg/kg LP-284 arm and 63% TGI was observed in the 2 mg/kg LP-284 arm, whereas Ibr. or Btz. only resulted in 8% and 22% TGI, respectively. We also tested if LP-284 (4 mg/kg) could rescue tumors that grew after treatment of Ibr. or Btz. Our data showed that LP-284 treatment resulted in near complete TGI in tumors pretreated by and grew resistant to Ibr. or Btz. No tumor regrowth nor animal death was observed 15 days after the last dose of LP-284. Additionally, we performed western blot and RNAseq on JEKO1 and REC1 cells treated by LP-284 or the vehicle for 24 hours. LP-284 treatment resulted in increased phosphorylation of ATM and gamma-H2AX in JEKO1, indicating the formation of double-strand DNA breaks. Differential gene expression analysis indicated that LP-284 reduced the expression of CCND1 by ~2 fold and there was a significant down-regulation of the MYC pathway targets. The toxicological profile of LP-284 was evaluated in a non-GLP repeat-dose toxicity study in dogs. LP-284 was administered i.v. once a day on days 1, 8, and 15 and at 0.3, 0.6, or 1.2 mg/kg/doses. Adverse effects in body weight, clinical pathology and pathology were only observed at ≥0.6 mg/kg/dose. LP-284-related changes in hematology were noted at ≥0.3 mg/kg/dose. At the microscopic level, 0.3 mg/kg/dose LP-284-related hematological changes were considered non-adverse based on the small magnitude and no associated changes in clinical hematology compared with the control animals. Therefore, under the condition of this study, the No Observed Adverse Effect Level (NOAEL) was determined to be 0.3 mg/kg/dose. Conclusions: Taken together, our results demonstrated that LP-284 has significantly increased efficacy over Ibr., Btz., and vehicle treated MCL animal models. In addition, Ibr./Btz. resistance could be overcome by LP-284. We also demonstrated that LP-284 reduced the expression of the onco-fusion gene CCND1 and the MYC pathway, which are both genes and pathways implicated in MCL. LP-284's strong potency in in vivo MCL tumor models, novel mechanism of action, and the progress in toxicological studies are in favor of further development of LP-284 as a novel MCL therapy.

EXTH-63. COMBINED INHIBITION OF TOP1 AND PARP: A NOVEL THERAPEUTIC STRATEGY FOR GBM WITH PTEN DEFICIENCY

Abstract BACKGROUND Glioblastoma (GBM) is the most aggressive and lethal type of brain tumor. Activation of PI3K/mTOR pathway along with the loss of its primary negative regulator, phosphatase and tensin homolog (PTEN), occurs in nearly 50% of GBM patients. As PTEN is known to promote DNA damage repair deficiency, here we investigated whether PTEN deficiency presents a vulnerability to a simultaneous induction of DNA damage and suppression of repair mechanisms by combining topoisomerase I (TOP1) and PARP inhibitors. METHODS We used patient-derived GBM cells and stem-like cells to determine response to LMP400 (Indotecan), a novel non-camptothecin TOP1 inhibitor, and the PARP inhibitors Olaparib or Niraparib. Treatment efficacy was also determined using cell viability, cell cycle, DNA damage, repair, and apoptosis assays in a pair of isogenic PTEN-null and PTEN-WT glioma cell lines derived from a genetically engineered mouse GBM model. RNAseq analysis was performed to identify treatment-induced dysregulated pathways. RESULTS PTEN-deficient cells are highly sensitive to LMP400 and PTEN rescue lessens sensitivity to the treatment. Combining LMP400 with PARP inhibitors, Olaparib or Niraparib, leads to synergistic cytotoxicity. LMP400/Niraparib combination induces G2/M cell cycle arrest, DNA damage, suppression of homologous recombination (HR)-related proteins and activation of caspase 3/7 activity significantly more in PTEN-null cells compared to isogenic PTEN-WT cells. Gene set enrichment analysis revealed suppression of cell cycle and DNA damage repair as well as activation of cell death pathways. Finally, CRISPR-Cas9 KO screening suggests that LMP400 is not likely to be a substrate for ABC transporters, suggesting the brain penetration and supporting the use in brain tumor patients. CONCLUSION Combined inhibition of TOP1 and PARP induces synergistic antiglioma effects selectively in PTEN-null glioblastoma cells, providing a strong scientific premise for a clinical trial of combined treatment with LMP400 and Niraparib in a subset of GBM with PTEN deficiency.

Somatic ARID1A mutation stratifies patients with gastric cancer to PD-1 blockade and adjuvant chemotherapy

BackgroundAT-rich interaction domain 1A (ARID1A) encodes a vital component of switch/sucrose non-fermentable chromatin-remodeling complex. Given its association with genomic instability, we conducted this study to determine whether ARID1A mutation status had an impact on therapeutic responsiveness in gastric cancer (GC), especially combinatory chemo-immunotherapy.MethodsWe retrospectively enrolled a total of 1162 patients from five independent cohorts. ZSHS Cohort and TCGA Cohort were designed to inform chemotherapeutic relevance and immunobiology of ARID1A-mutant GC based on tissue samples and sequencing data, respectively. MSKCC Cohort, mGC Cohort, and Melanoma Cohort were utilized to interrogate the predictive efficacy of ARID1A mutation to programmed cell death protein 1 (PD-1) blockade.ResultsARID1A mutation was enriched in EBV-positive, hypermutated-single nucleotide variant and microsatellite-unstable subtype GC, and was predictive of responsiveness to both fluorouracil-based chemotherapy and PD-1 blockade. Specifically, ARID1A mutation score was a highly sensitive indicator (91%) of response to pembrolizumab. Mechanistically, ARID1A mutation correlated with extensive DNA damage repair deficiency and immunogenic tumor microenvironment (TME) featured by elevated activated subsets of CD8+ T cells, CD4+ T cells, and NK cells. Type 17T helper cells were typically abundant in ARID1A-mutant GC and might be a precondition for chemosensitivity conferred by ARID1A mutation. Furthermore, ARID1A mutation indicated elevated expression of VEGFA and CLDN18, as well as over-representation of ERBB2 and FGFR2 signaling pathway.ConclusionsARID1A-mutant GC displayed immunogenic TME and might be a candidate for both monotherapy and the combination of frontline chemotherapy and PD-1 blockade.