Defect Recombination Research Articles

Abstract 5170: Novel dSTRIDE-HR assays can accurately assess DNA repair defects in human cancers and distinguish HR status of tumors

Abstract Accurate patient stratification is crucial for the successful application of targeted anti-cancer therapeutic approaches. It has been shown that PARP inhibitors are synthetic lethal with defective homologous recombination (HR) repair, with genes such as BRCA1 and BRCA2 identified as conferring therapy resistance or sensitivity, depending on their mutational status. Moreover, there is evidence of patient benefit of carboplatin-based therapy in HR deficient (HRD) tumors. With a growing emphasis on HRD in cancer treatment, efforts have been made to define the HRD phenotype. Nonetheless, the current approaches employed in the clinic, such as Next Generation Sequencing (NGS), HRD score or RAD51 assays have significant limitations and their interpretation can be unclear. To answer the need for a functional HR-specific biomarker, we have recently developed and introduced two new assays, called collectively dSTRIDE-HR. The assays are based on the STRIDE platform technology that enables direct and sensitive detection of single- or double-strand DNA breaks in situ in fixed cells. Novel dSTRIDE-HR explicitly detect double-strand DNA breaks localized in close proximity to RPA (dSTRIDE-RPA) or RAD51 (dSTRIDE-RAD51) proteins. The assays have been shown to be reliable reporters of HR activation in cellular models after exogenous DNA damage induction, yet their potential to predict HR status in an in vivo setting has not been tested so far. To assess the suitability of the dSTRIDE-HR assays for determining the HR status of patients’ tumor cells, we applied these assays in FFPE sections from biopsies derived from breast cancer patients with a different mutational status of BRCA1 and BRCA2 genes. The assays showed low dSTRIDE-RPA and dSTRIDE-RAD51 readouts in BRCA1/2 mutated tumors in comparison to wild type tumors, as well as a great concordance of readouts within a given genetic background. Additionally, the cell cycle analysis proved nearly twofold increase in foci numbers of dSTRIDE-RPA and dSTRIDE-RAD51 in G2/S phase. Our study unveils a potential of dSTRIDE-HR assays to become predictive biomarkers reporting on the status of HR repair in breast tumors, although more patient samples need to be tested to confirm initial findings. Citation Format: Monika Jarosz, Zsombor Prucsi, Franek Sierpowski, Karolina Stepien, Sophie Ostrowska-Paton, Szymon Koman, Nadeem Riaz, Simon Powell, Fresia Pareja, Edaise da Silva, Magdalena Kordon-Kiszala, Kamil Solarczyk. Novel dSTRIDE-HR assays can accurately assess DNA repair defects in human cancers and distinguish HR status of tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5170.

Abstract 2569: VEGFA gene expression is associated with cell proliferation, less immune cell infiltration, and worse survival, but better response to chemotherapy and immunotherapy

Abstract Introduction: Vascular endothelial growth factor-A (VEGFA) is a well-known factor that induces angiogenesis, one of the hallmarks of cancer, which generates new blood vessels in the tumor microenvironment (TME) and provides conduit for cancer to metastasize. Interestingly, an anti-VEGFA drug (Avastin) failed to show benefit in clinical trials for breast cancer (BC). In this study we investigated the clinical relevance of VEGFA gene expression in BC. Methods: A total of 7336 BC patients from eight independent cohorts, TCGA (n= 1073), METABRIC (n= 1903), SCAN-B (GSE96058, n= 3069), GSE20194 (n=278), GSE34138 (n=178), GSE163882 (n=222), GSE25066 (n=508), and ISPY2 (GSE173839, n= 105) were analyzed. These cohorts were divided into high and low VEGFA gene expression groups using the median. Results: High VEGFA expression in BC was associated with worse overall survival in SCAN-B cohort which was validated in METABRIC cohort with overall, disease-specific, and disease-free survival (all p<0.02). VEGFA expression was higher in Triple Negative BC (TNBC) but was lower in BC with lymph node metastasis. High VEGFA BC was associated with significantly high intratumoral heterogeneity, homologous recombination defect, silent and non-silent mutations, and SNV neoantigens in TCGA, and was also associated with higher cell proliferation, evidenced by higher Nottingham histological grade, higher Ki67 gene expression, and enrichment of all the Hallmark cell proliferation-related gene sets: Mitotic spindle, G2M Checkpoint, E2F Targets, MYC Targets v1 and v2, and mTorC1 signaling, consistently, in SCAN-B, METABRIC, and TCGA cohorts. Reflecting its enhanced growth, high VEGFA expression was associated with less infiltration of fibroblasts and adipocytes (all p<0.05). Surprisingly, VEGFA expression did not enrich angiogenesis gene set in any of the cohorts, nor was related with infiltrations of blood or lymphatic vascular endothelial cells, besides pericytes. But high VEGFA BC was associated with significantly less infiltrations of anti-cancer immune cells; CD8, CD4, and dendritic cells were all significantly less, and T helper type 1 cells and regulatory T cells were significantly higher consistently in SCAN-B, METABRIC, and TCGA cohorts. VEGFA expression was significantly higher in BC that achieved pathological complete response after Anthracycline and Taxane based neoadjuvant therapy in both ER+/HER2- and TNBC subtypes in the GSE25066 cohort, and after immunotherapy in ER+/HER2- subtype, but not TNBC, in the ISPY2 clinical trial cohort. This was not validated in GSE20194, GSE34138, GSE163882 cohorts. Conclusion: Our research indicates that high VEGFA BC is associated with high cell proliferation, less immune cell infiltration, and worse survival, but better response to Anthracycline and Taxane based chemotherapy, and immunotherapy. Citation Format: Pia Sharma, Kohei Chida, Kenichi Hakamada, Kazuaki Takabe. VEGFA gene expression is associated with cell proliferation, less immune cell infiltration, and worse survival, but better response to chemotherapy and immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2569.

Abstract 3344: Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA binding proteins

Abstract Summary: Defects in homologous recombination DNA repair (HRD) both predispose to cancer development and produce therapeutic vulnerabilities, making it critical to define the spectrum of genetic events that cause HRD. However, we found that mutations in BRCA1/2 and other canonical HR genes only identified 10-20% of tumors that display genomic evidence of HRD. Using a networks-based approach, we discovered that over half of putative genes causing HRD originated outside of canonical DNA damage response genes, with a particular enrichment for RNA binding protein (RBP)-encoding genes. These putative drivers of HRD were experimentally validated, cross-validated in an independent cohort, and enriched in cancer-associated GWAS loci. Mechanistic studies indicate that some RBPs are recruited to sites of DNA damage to facilitate repair, whereas others control the expression of canonical HR genes. Overall, this study greatly expands the repertoire of known drivers of HRD, with implications for basic biology, genetic screening, and therapy stratification. Citation Format: Babita Kaundal, Daniel J. McGrail, Yang Li, Roger S. Smith, Bin Feng, Hui Dai, Limei Hu, Briana Dennehey, Sharad Awasthi, Marc L. Mendillo, Anil K. Sood, Gordon B. Mills, Shiaw-Yih Lin, S. Stephen Yi, Nidhi Sahni. Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA binding proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3344.

Abstract 2568: High infiltration of neurons was associated with lower cell proliferation and less immune response but not with response to treatments or survival in estrogen receptor-positive breast cancer

Abstract Introduction: Psychological stress aggravates cancer cell biology which leads to cancer progression and metastasis through its influence on the sympathetic nervous system. Recently, infiltration of a local anesthetic lidocaine around a tumor prior to its removal was reported to lead to better survival in early-stage breast cancer (BC). Therefore, we hypothesized that neuron infiltration within the bulk tumor of BC could be associated with cancer aggressiveness and worse survival. Methods: A total of 5755 BC patients from five independent cohorts, including METABRIC (n=1903), SCAN-B (n=3273), GSE25066 (n=508), and ISPY2 (GSE173839; n=105), which have both clinical and transcriptomic data, were included in the study. The fraction of neuron infiltration was calculated using the xCell algorithm. Results: High neuron infiltration in BC was not associated with survival in either the METABRIC or SCAN-B cohorts. BC with high neuron infiltration had high expressions of neurotransmitter receptors: adrenergic receptor α1B and 2A, dopamine receptor D2, muscarinic acetylcholine receptor M3 and M4, and TAC1, which encodes TACR1, the receptor for substance P, but had lower expression of adrenergic receptor β2 and cholinergic acetylcholine receptor 1 and 10. Further, levels of neuron infiltration were highest in estrogen receptor-positive/HER2-negative (ER+/HER2-) among the subtypes and lower in tumors with lymph node metastasis, but was not associated with tumor size. Neuron infiltration was associated with higher AJCC staging in METABRIC, which was not validated in SCAN-B cohort. High neuron infiltration in BC was associated with reduced homologous recombination defects, mutation rate, and SNV neoantigen, and with less cell proliferation, evidenced by lower Nottingham histological grade and Ki67 gene expression, as well as less enrichment of Hallmark cell proliferation-related gene sets: E2F targets, G2M checkpoint, and Mitotic spindle. Despite its association with less cell proliferation, BC with high neuron infiltration was not associated with pathological complete response (pCR) in the GSE25066 cohort. High neuron infiltration in BC was associated with higher infiltration of lymph endovascular cells as well as less immune cell infiltration; CD8, CD4 memory, T-helper 1 and 2, dendritic cells, M1 and M2 macrophages, regulatory T cells, and B cells, lower cytolytic activity, and immune response; interferon-alpha and interferon-gamma and IL2 stat signaling. Despite this association, BC with high neuron infiltration was not associated with pCR after immunotherapy in the ISPY2 clinical trial cohort. Conclusion: BC with high infiltration of neurons was associated with lower cell proliferation and less immune response but not with response to systemic therapies or patient survival in ER+/HER2- subtype. Citation Format: Kohei Chida, Masanori Oshi, Arya Mariam Roy, Jun Arima, Pia Sharma, Itaru Endo, Kenichi Hakamada, Kazuaki Takabe. High infiltration of neurons was associated with lower cell proliferation and less immune response but not with response to treatments or survival in estrogen receptor-positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2568.

Abstract 4717: Small molecule modulation of PP2A selectively induces oncogenic cytotoxicity through chronic and irreversible integrated stress response

Abstract High-grade serous cancer (HGSC) is the most lethal gynecological malignancy and accounts for approximately 70% of all ovarian carcinomas. Despite recent advancements in drug discovery and a deeper understanding of the genetic mechanisms that drive HGSC oncogenesis, the mortality rate has remained stagnant over the past three decades, with a 5-year survival rate below 30%. Due to the prevalence of homologous recombination defects (HRD) in over 50% of HGSC tumors, the clinical management of patients harboring these genetic vulnerabilities has vastly relied on PARP inhibitors (PARPi). Nonetheless, about 80% of these patients ultimately relapse with refractory resistant and more aggressive disease, having no effective therapeutic alternatives currently available. Therefore, there is an urgent need for novel targeted therapies to be tailored towards the treatment of HGSC. Recently, we unveiled that 95% of HGSC tumors present with a widespread loss-of-heterozygosity in genes essential to form the tumor suppressor Protein Phosphatase 2A (PP2A) heterotrimer, second only to TP53. These deleterious alterations have been established to inhibit PP2A function, preventing it from counteracting oncogenic signatures that drive tumorigenesis. Our studies revealed that a Small Molecule Activator of PP2A (SMAP) synergizes with PARPi to induce synthetic lethality in HGSC cells while displaying favorable tolerability profiles in normal tissues. Mechanistically, SMAP activates distinct translational responses and stress signatures depending on the cellular context, driving selective oncogenic cytotoxicity through a chronic and irreversible integrated stress response (ISR), independent of PERK activation. In malignant contexts, SMAP-mediated activation of PP2A specifically drives the dephosphorylation of TFE3 to transcriptionally activate ATF4 and CHOP. Consequently, as cancer cells are incapable of activating adaptive homeostatic recovery mechanisms in response to SMAP, chronic ISR is induced, ultimately leading to cell death. Conversely, non-transformed cells leverage their intrinsic ISR plasticity to adapt, thereby restoring basal functions that allow cell survival under SMAP-mediated stress conditions. Collectively, our data highlights a new role of PP2A in HGSC and further underscore SMAP's selective cytotoxicity in cancer cells, independent of oncogenic genetic vulnerabilities or HRD profiles, by leveraging ISR plasticity and intrinsic adaptive homeostatic mechanisms. Thus, this class of PP2A modulators holds tremendous promise for broader therapeutic applications across diverse patient populations and tumor histological subtypes beyond HGSC, while mitigating standard-of-care therapy-associated toxicity. Citation Format: Rita A. Avelar, Riya Gupta, Grace Carvette, Felipe da Veiga Leprevost, Jose Colina, Jessica Teitel, Goutham Narla, Analisa DiFeo. Small molecule modulation of PP2A selectively induces oncogenic cytotoxicity through chronic and irreversible integrated stress response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4717.

Integrative analysis of metabolism subtypes and identification of prognostic metabolism-related genes for glioblastoma.

Increasing evidence has demonstrated that cancer cell metabolism is a critical factor in tumor development and progression; however, its role in glioblastoma (GBM) remains limited. In the present study, we classified GBM into three metabolism subtypes (MC1, MC2, and MC3) through cluster analysis of 153 GBM samples from the RNA-sequencing data of The Cancer Genome Atlas (TCGA) based on 2752 metabolism-related genes (MRGs). We further explored the prognostic value, metabolic signatures, immune infiltration, and immunotherapy sensitivity of the three metabolism subtypes. Moreover, the metabolism scoring model was established to quantify the different metabolic characteristics of the patients. Results showed that MC3, which is associated with a favorable survival outcome, had higher proportions of isocitrate dehydrogenase (IDH) mutations and lower tumor purity and proliferation. The MC1 subtype, which is associated with the worst prognosis, shows a higher number of segments and homologous recombination defects and significantly lower mRNA expression-based stemness index (mRNAsi) and epigenetic-regulation-based mRNAsi. The MC2 subtype has the highest T-cell exclusion score, indicating a high likelihood of immune escape. The results were validated using an independent dataset. Five MRGs (ACSL1, NDUFA2, CYP1B1, SLC11A1, and COX6B1) correlated with survival outcomes were identified based on metabolism-related co-expression module analysis. Laboratory-based validation tests further showed the expression of these MRGs in GBM tissues and how their expression influences cell function. The results provide a reference for developing clinical management approaches and treatments for GBM.

Performance optimization study of lead-free CsSnGeI3 based perovskite solar cell heterostructure with different inorganic electron transport layers: A numerical simulation approach

Perovskite solar cells (PSCs) are considered to be one of the most prominent candidates for its commercialization. The meteoric properties of the PSC have always astounded the researchers. Thus, in this perspective, the germanium-based PSCs are able to increase a sense of curiosity among photovoltaic (PV) researchers due to its superior stability and efficiency. In the present work, different combinations of the lead-free and non-toxic inorganic caesium tin-germanium (CsSnGeI3) based PSC structures have been studied using various electron transport layers (ETLs) (SnS2, TiO2, WS2, MoTe2 and ZnSe) and Mg–CuCrO2 as a hole transport layer due to its meteoric properties. For each ETL, the impact of material parameters including the thickness of the various layers, absorber acceptor density, donor density, absorber defect density, absorber radiative recombination and interfacial defect density are examined to study the cell performance (such as Voc, Jsc, FF, and PCE). Moreover, the role of operating temperature, shunt resistance and series resistance in analysing the cell performance has also been checked towards its practical applicability. The results show ZnSe as the best ETL in comparison to other inorganic ETLs for CsSnGeI3 based absorber with Mg–CuCrO2 as an HTL, used in this work resulting in a good cell performance with a power conversion efficiency (PCE) of 33.24%, Voc ∼ 1.36 V, Jsc ∼ 28.02 mA/cm2 and fill factor (FF) ∼ 86.79%. The proposed simulation work may pave the way for further design and optimization of Sn-based PSCs towards practical applications.

How BRCA and homologous recombination deficiency change therapeutic strategies in ovarian cancer: a review of literature.

About 50% of High Grade Serous Ovarian Cancer exhibit a high degree of genomic instability due to mutation of genes involved in Homologous Recombination (HRD) and such defect accounts for synthetic lethality mechanism of PARP inhibitors (PARP-i). Several clinical trials have shown how BRCA and HRD mutational status profoundly affect first line chemotherapy as well as response to maintenance therapy with PARP-i, hence Progression Free Survival and Overall Survival. Consequently, there is urgent need for the development of increasingly reliable HRD tests, overcoming present limitations, as they play a key role in the diagnostic and therapeutic process as well as have a prognostic and predictive value. In this review we offer an overview of the state of the art regarding the actual knowledge about BRCA and HRD mutational status, the rationale of PARPi use and HRD testing (current and in development assays) and their implications in clinical practice and in the treatment decision process, in order to optimize and choose the best tailored therapy in patients with ovarian cancer.

Evolutions of microstructural defects in high-entropy carbide ceramics under ion irradiations at room temperature

This work studied and compared the evolutions of irradiation-induced microstructural defects in five high-entropy carbide ceramics (HECCs) at room temperature to reveal the irradiation resistances of HECCs and corresponding underlying mechanisms. The five HECCs exhibit high phase stabilities and no amorphization is observed up to 40 dpa. In-situ 800 keV Kr ion irradiation reveals similar evolutions of irradiation-induced defects. The densities of dislocation loops show non-monotonic variations, which reach the maximum at ∼ 2 dpa and then decrease due to the interactions with each other. In contrast, the sizes of dislocation loops increase monotonically with dose. (NbTaZrW)C exhibits the lowest defect densities and highest defect sizes, which is probably due to the high lattice distortion and its induced high defect recombination efficiencies. Based on the characterization results, it is deduced that the species of constituent elements play more important role in the defect behaviors than the number of constituent elements.

Abstract B114: Effect of spatial and temporal inter-tumoral heterogeneity on homologous recombination deficiency scores in high grade serous ovarian cancer

Abstract High-grade serous ovarian cancer (HGSC) is the most common and lethal subtype of ovarian cancer. Extensive genomic instability and heterogeneity are characteristics of HGSC, with near-ubiquitous TP53 loss-of-function mutations, defects in homologous recombination (HR) repair, and extensive copy number aberrations contributing to the vast genomic heterogeneity observed. Most patients relapse and acquire resistance to platinum or PARP inhibitor (PARPi)-based therapy. Diverse mechanisms leading to therapy resistance and lack of predictive biomarkers means that matching the best treatment options to patients is difficult. Testing tumors for HR-Deficiency (HRD) status is now a clinical test to predict PARPi sensitivity in HGSC. We aimed to determine the influence of spatial and temporal heterogeneity on HRD status in HGSC. Patients (n=59) at Hammersmith Hospital (HH) underwent maximal-effort upfront cytoreduction for advanced HGSC, had their tumor dissemination mapped and tumor biopsies collected (range 4-15). Paired relapse samples were collected for 10 patients. Tumor DNA was extracted (n=5 tumors per case, plus relapse), Illumina Human OmniExpress genotyping performed for 59 cases and whole genome sequencing (WGS; 30x depth) performed for 21 cases. Allele-specific copy number (CN) was quantified using ASCAT. Multi-site CN data was also accessed from two cohorts (GSE38787, GSE40546). Tumors that failed QC or had an aberrant cell fraction <0.3 were excluded. HR scores were estimated in each cohort using different genomic instability score (GIS) or mutational signature-based algorithms and relevant cut-offs were applied to determine HRD and HR-Proficient (HRP) tumors. Variations in HR scores were observed across the cohorts with a proportion of patients presenting with a mixed HR score, displaying both HRD and HRP scores in their tumors: HH cohort (20%, 11/54 patients); GSE38787 (17%, 4/24 patients); and GSE40546 (28%, 4/14 patients) using a scarHRD algorithm. In the HH cohort (n=45), we examined if mixed HR status was associated with survival and demonstrated that patients with HR-mixed or all HRP tumors had poorer progression-free (p=0.0052) and overall survival (p=0.00092) than patients with all HRD tumors. Applying different approaches to the HH WGS data (scarHRD, CHORD, >63 score cut-off), approximately 20% of patients demonstrated HR-mixed scores in their tumors in each approach. However, depending on the approach chosen to define HRD, different cases showed HR-mixed scores, 2/21 mixed cases overlapped between the different algorithms applied with tumors changing from HRD to HRP and vice versa depending on the approach applied. Differences in HR-deficiency/proficiency scores suggests that HR status may not be consistent across advanced disseminated HGSC, indicating that a single tumor biopsy may not accurately depict spatial HGSC tumor biology. HR score variations in different methods (GIS or mutational signatures) indicates that these tests are not analogous for defining HRD and thus PARPi suitability. Citation Format: Elizabeth L. Christie, Marc Lorentzen, Maiqi Liu, Nikki Burdett, Edward Curry, Chun Hei Kwok, Ahwan Pandey, Katherine Nixon, Jennifer Ploski, James J. Clark, Iain McNeish, David D.L. Bowtell, Jonathan Krell, Christina Fotopoulou, Paula Cunnea. Effect of spatial and temporal inter-tumoral heterogeneity on homologous recombination deficiency scores in high grade serous ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr B114.

Abstract A115: DNA repair biomarkers to guide usage of combined PARP inhibitors and chemotherapy: A meta-analysis and systematic review

Abstract A115: DNA repair biomarkers to guide usage of combined PARP inhibitors and chemotherapy: A meta-analysis and systematic review

Somatic mutations in four novel genes contribute to homologous recombination deficiency in breast cancer: a real-world clinical tumor sequencing study.

Breast cancers involving mutations in homologous recombination (HR) genes, most commonly BRCA1 and BRCA2 (BRCA1/2), respond well to PARP inhibitors and platinum-based chemotherapy. However, except for these specific HR genes, it is not clear which other mutations contribute to homologous recombination defects (HRD). Here, we performed next-generation sequencing of tumor tissues and matched blood samples from 119 breast cancer patients using the OncoScreen Plus panel. Genomic mutation characteristics and HRD scores were analyzed. In the HR genes, we found that BRCA1/2 and PLAB2 mutations were related to HRD. HRD was also detected in a subset of patients without germline or somatic mutations in BRCA1/2, PLAB2, or other HR-related genes. Notably, LRP1B, NOTCH3, GATA2, and CARD11 (abbreviated as LNGC) mutations were associated with high HRD scores in breast cancer patients. Furthermore, functional experiments demonstrated that silencing CARD11 and GATA2 impairs HR repair efficiency and enhances the sensitivity of tumor cells to olaparib treatment. In summary, in the absence of mutations in the HR genes, the sensitivity of tumor cells to PARP inhibitors and platinum-based chemotherapy may be enhanced in a subset of breast cancer patients with LNGC somatic mutations.

Discovery and Proof of Concept of Potent Dual Polθ/PARP Inhibitors for Efficient Treatment of Homologous Recombination-Deficient Tumors.

DNA polymerase theta (Polθ) has recently emerged as a new attractive synthetic lethal target involved in DNA damage repair. Inactivating Polθ alone or in combination with PARP inhibitors has demonstrated substantial therapeutic potential against tumors with homologous recombination (HR) defects such as alternation of BRCA genes. Herein, we report the design and proof of concept of a highly potent dual Polθ/PARP inhibitor 25d, which exhibited low nanomolar inhibitory activities against both Polθ and PARP1. Compared to combination treatment, 25d demonstrated superior antitumor efficacy in both MDA-MB-436 cells and xenografts by inducing more DNA damage and apoptosis. Importantly, 25d retained sensitivity in PARP inhibitor-resistant MDA-MB-436 cells with 53BP1 defect. Altogether, these findings illustrate the potential advantages of 25d, a first-in-class dual Polθ/PARP inhibitor, over monotherapy in treating HR-deficient tumors, including those with acquired PARP inhibitor resistance.

Abstract B011: BRCA2 haploinsufficiency induces P53 degradation in primary mammary epithelial cells – a crucial early event in breast tumor promotion

Abstract The presence of heterozygous germline BRCA2 mutations is associated with an increased risk of breast and ovarian cancer. In order to design effective preventative strategies, it is critical to understand early tumor promoting events that the mammary epithelial cells undergo on their way to tumorigenesis. To investigate the impact of BRCA2 heterozygosity on tumor formation, we utilized primary BRCA2mut/+ mammary epithelial cells obtained from prophylactic breast tissue of women with BRCA2 mutations. Our findings indicate that BRCA2mut/+ cells display haploinsufficiency for repairing stalled replication forks and resolving RPA32 from these sites, indicative of impaired stalled fork repair. Moreover, they exhibit defects in RAD51 recruitment to double strand break sites indicating a defective homologous recombination dependent double strand break repair efficiency. BRCA2mut/+ cells also show increased sensitivity to both replication stress and double strand break-inducing agents. Interestingly, we find that BRCA2 heterozygous cells downregulate P53 protein levels when compared to BRCA2 wild type cells, and that this downregulation is MDM2-dependent. The decreased P53 levels appear to promote the survival of BRCA2 heterozygous cells under endogenous replication stress conditions. Notably, treatment with nutlin, a P53 protein stabilizer, leads to cell death in BRCA2 heterozygous cells but not in BRCA2 wildtype cells, highlighting the sensitivity of BRCA2 heterozygous cells to endogenous P53 protein levels. Moreover, complete loss of P53 in BRCA2 heterozygous cells results in rescue of sensitivity of these cells to both replication stress and double strand break inducing agents. Furthermore, whole genome sequencing analysis of BRCA2 heterozygous cells deleted for P53 reveal DNA mutational signatures similar to those observed in BRCA2 mutant tumors, implying that loss or downregulation of P53 is an early event driving tumorigenesis in the context of BRCA2 heterozygosity. In summary, our study uncovers the significance of BRCA2 haploinsufficiency in replication stress suppression and highlights the role of P53 loss in promoting BRCA2 heterozygosity-driven cancer. These findings contribute to a better understanding of the molecular mechanisms underlying BRCA2-associated tumorigenesis and may have implications for targeted preventative therapies in the future. Citation Format: Haohui Duan, Margaret Gillis, Deboral Dillon, Judy Garber, Shailja Pathania. BRCA2 haploinsufficiency induces P53 degradation in primary mammary epithelial cells – a crucial early event in breast tumor promotion [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B011.

Defective Homologous Recombination Repair By Up-Regulating Lnc-HZ10/Ahr Loop in Human Trophoblast Cells Induced Miscarriage.

Human trophoblast cells are crucial for healthy pregnancy. However, whether the defective homologous recombination (HR) repair of dsDNA break (DSB) in trophoblast cells may induce miscarriage is completely unknown. Moreover, the abundance of BRCA1 (a crucial protein for HR repair), its recruitment to DSB foci, and its epigenetic regulatory mechanisms, are also fully unexplored. In this work, it is identified that a novel lnc-HZ10, which is highly experssed in villous tissues of recurrent miscarriage (RM) vs their healthy control group, suppresses HR repair of DSB in trophoblast cell. Lnc-HZ10 and AhR (aryl hydrocarbon receptor) form a positive feedback loop. AhR acts as a transcription factor to promote lnc-HZ10 transcription. Meanwhile, lnc-HZ10 also increases AhR levels by suppressing its CUL4B-mediated ubiquitination degradation. Subsequently, AhR suppresses BRCA1 transcription; and lnc-HZ10 (mainly 1-447 nt) interacts with γ-H2AX; and thus, impairs its interactions with BRCA1. BPDE exposure may trigger this loop to suppress HR repair in trophoblast cells, possibly inducing miscarriage. Knockdown of murine Ahr efficiently recovers HR repair in placental tissues and alleviates miscarriage in a mouse miscarriage model. Therefore, it is suggested that AhR/lnc-HZ10/BRCA1 axis may be a promising target for alleviation of unexplained miscarriage.

Minimizing the diffusivity difference between vacancies and interstitials in multi-principal element alloys

Interstitial atoms usually diffuse much faster than vacancies, which is often the root cause for the ineffective recombination of point defects in metals under irradiation. Here, via ab initio modeling of single-defect diffusion behavior in the equiatomic NiCoCrFe(Pd) alloy, we demonstrate an alloy design strategy that can reduce the diffusivity difference between the two types of point defects. The two diffusivities become almost equal after substituting the NiCoCrFe base alloy with Pd. The underlying mechanism is that Pd, with a much larger atomic size (hence larger compressibility) than the rest of the constituents, not only heightens the activation energy barrier (Ea) for interstitial motion by narrowing the diffusion channels but simultaneously also reduces Ea for vacancies due to less energy penalty required for bond length change between the initial and the saddle states. Our findings have a broad implication that the dynamics of point defects can be manipulated by taking advantage of the atomic size disparity, to facilitate point-defect annihilation that suppresses void formation and swelling, thereby improving radiation tolerance.

Nested loops explain low irradiation-induced swelling rate

In the quest of radiation and oxidation-resistant materials for the fuel claddings of nuclear power stations, chromium (Cr) emerges as a good candidate. It shows a significantly lower irradiation-induced swelling rate of nearly an order magnitude lower than other body-centered cubic materials, such as W and Fe. This phenomenon indicates that there is an unsuspected aspect, beyond the crystal structure that affects the swelling of materials. To understand it, the structure and distribution of irradiation-induced dislocation loops in Cr were investigated after ion irradiation at 550 ℃ from 0.1 to 15 dpa. It appears that after irradiation Cr exhibits nested loops, either vacancy-type loops called ‘trough’ or interstitial-type loops called ‘island’, which are composed of a large dislocation loop containing multiple small and coplanar loops with inverse nature. Our results indicate that the nested trough and island dislocation loops stem from the 1D migration of dislocation loops. This loop formation mechanism is an alternative mechanism of recombination and annihilation of point defects, which in turn can explain the low swelling rate in Cr. This mechanism provides a new insight into the irradiation-induced swelling rate of metals.

Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions

Linking clinical multi-omics with mechanistic studies may improve the understanding of rare cancers. We leverage two precision oncology programs to investigate rhabdomyosarcoma with FUS/EWSR1-TFCP2 fusions, an orphan malignancy without effective therapies. All tumors exhibit outlier ALK expression, partly accompanied by intragenic deletions and aberrant splicing resulting in ALK variants that are oncogenic and sensitive to ALK inhibitors. Additionally, recurrent CKDN2A/MTAP co-deletions provide a rationale for PRMT5-targeted therapies. Functional studies show that FUS-TFCP2 blocks myogenic differentiation, induces transcription of ALK and truncated TERT, and inhibits DNA repair. Unlike other fusion-driven sarcomas, TFCP2-rearranged tumors exhibit genomic instability and signs of defective homologous recombination. DNA methylation profiling demonstrates a close relationship with undifferentiated sarcomas. In two patients, sarcoma was preceded by benign lesions carrying FUS-TFCP2, indicating stepwise sarcomagenesis. This study illustrates the potential of linking precision oncology with preclinical research to gain insight into the classification, pathogenesis, and therapeutic vulnerabilities of rare cancers.

Effect of gamma-rays on recombination dynamics and defect concentration in a wide bandgap perovskite

Effect of gamma-rays on recombination dynamics and defect concentration in a wide bandgap perovskite

Solar power conversion: CuI hole transport layer and Ba3NCl3 absorber enable advanced solar cell technology boosting efficiency over 30.

Researchers are becoming more interested in novel barium-nitride-chloride (Ba3NCl3) hybrid perovskite solar cells (HPSCs) due to their remarkable semiconductor properties. An electron transport layer (ETL) built from TiO2 and a hole transport layer (HTL) made of CuI have been studied in Ba3NCl3-based single junction photovoltaic cells in a variety of variations. Through extensive numerical analysis using SCAPS-1D simulation software, we investigated elements such as layer thickness, defect density, doping concentration, interface defect density, carrier concentration, generation, recombination, temperature, series and shunt resistance, open circuit voltage (V OC), short circuit current (J SC), fill factor (FF), and power conversion efficiency (PCE). The study found that the HTL CuI design reached the highest PCE at 30.47% with a V OC of 1.0649 V, a J SC of 38.2609 mA cm-2, and an FF of 74.78%. These findings offer useful data and a practical plan for producing inexpensive, Ba3NCl3-based thin-film solar cells.