Mutations In DNA Repair Genes Research Articles

Detection of Primary DNA Lesions by Transient Changes in Mating Behavior in Yeast Saccharomyces cerevisiae Using the Alpha-Test.

Spontaneous or induced DNA lesions can result in stable gene mutations and chromosomal aberrations due to their inaccurate repair, ultimately resulting in phenotype changes. Some DNA lesions per se may interfere with transcription, leading to temporary phenocopies of mutations. The direct impact of primary DNA lesions on phenotype before their removal by repair is not well understood. To address this question, we used the alpha-test, which allows for detecting various genetic events leading to temporary or hereditary changes in mating type α→a in heterothallic strains of yeast Saccharomyces cerevisiae. Here, we compared yeast strains carrying mutations in DNA repair genes, mismatch repair (pms1), base excision repair (ogg1), and homologous recombination repair (rad52), as well as mutagens causing specific DNA lesions (UV light and camptothecin). We found that double-strand breaks and UV-induced lesions have a stronger effect on the phenotype than mismatches and 8-oxoguanine. Moreover, the loss of the entire chromosome III leads to an immediate mating type switch α→a and does not prevent hybridization. We also evaluated the ability of primary DNA lesions to persist through the cell cycle by assessing the frequency of UV-induced inherited and non-inherited genetic changes in asynchronous cultures of a wild-type (wt) strain and in a cdc28-4 mutant arrested in the G1 phase. Our findings suggest that the phenotypic manifestation of primary DNA lesions depends on their type and the stage of the cell cycle in which it occurred.

The Clinical Significance of Genetic Variation in Ovarian Cancer.

Genetic variation is a well-known contributor to the onset and progression of cancer. The goal of this study is to provide a comprehensive examination of the nucleotide and chromosomal variation associated with the onset and progression of serous ovarian cancer. Using a variety of computational and statistical methods, we examine the exome sequence profiles of genetic variants present in the primary tumors of 432 ovarian cancer patient samples to compute: (1) the tumor mutational burden for all genes and (2) the chromosomal copy number alterations associated with the onset/progression of ovarian cancer. Tumor mutational burden is reduced in the late vs. early stages, with the highest levels being associated with loss-of-function mutations in DNA-repair genes. Nucleotide variation and copy number alterations associated with known cancer driver genes are selectively favored over ovarian cancer development. The results indicate that genetic variation is a significant contributor to the onset and progression of ovarian cancer. The measurement of the relative levels of genetic variation associated with individual ovarian cancer patient tumors may be a clinically valuable predictor of potential tumor aggressiveness and resistance to chemotherapy. Tumors found to be associated with high levels of genetic variation may help in the clinical identification of high-risk ovarian cancer patients who could benefit from more frequent monitoring.

Androgen receptor signaling mechanism in prostate cancer: resistance to antiandrogen therapy and association with DNA repair genes

Background. Metastatic castration-resistant prostate cancer remains a complex problem due to patients' previous treatments and limited selection of subsequent therapies. While 2nd generation antiandrogens are initially effective, resistance to them is not an exceptional event. Mechanisms depending on androgen receptor and independent of it have been described. A special focus is on mutations in DNA repair genes, particularly genes involved in homologous recombination repair (HRR) as a possible cause of somatic genetic abnormalities specifically in progressive metastatic disease. However, data on the effect of the HRR defect on the effectiveness of antiandrogen therapy for prostate cancer are very limited, which requires additional clinical studies.Aim. To evaluate the effect of clinical, morphological, molecular and genetic factors on the effectiveness of enzalutamide antiandrogen therapy in patients with prostate cancer and known mutations in DNA repair genes involved in HRR and mismatch repair.Materials and methods. The study was performed at the Clinical Oncological Dispensary No. 1 (Krasnodar). Retrospective analysis of clinical and morphological parameters of 54 patients with prostate cancer who received enzalutamide antiandrogen therapy and with known status of germ line and somatic mutations of HRR DNA repair genes (BRCA1, BRCA2, ATM, BARD, BRIP1, CDK12, CHEK1, CHEK2, PALB2, RAD51B, RAD51C, RAD54L, FANCL) and microsatellite instability in immunohistochemical determination of mismatch repair deficit was performed. Statistical analysis was performed using IBM SPSS Statistics v.22 software.Results and conclusion. In 17 of 54 patients, pathogenic germline and somatic mutations of HRR genes were detected: 7 mutations in BRCA2 gene, 4 - in CHEK2, 2 - in BRCA1, 2 - in CDK12, 1 - in BRIP1 and 1 - in ATM. It was shown that in the group of patients with metastatic castration-resistant prostate cancer, histological grade per the International Society of Urological Pathology (ISUP) G2 (total Gleason score 7 (3 + 4)) is significantly associated with the absence of HRR mutation, and grade G3 (total Gleason score 7 (4 + 3)) was associated with HRR mutations (р <0.05). Increase in prostate-specific antigen (PSA) level/biochemical progression 12-16 weeks after enzalutamide therapy start was significantly associated with metastatic castration-resistant prostate cancer without HRR mutations (р <0.05). In case of tumor response to enzalutamide therapy, decrease in PSA level did not depend on the age of disease onset, differentiation grade, primary advancement, previous docetaxel treatment, and presence of HRR mutation. Cox multivariate regression test showed that prescription of docetaxel before enzalutamide increased the risk of PSA-progression (hazard ratio (HR) 5.160; 95 % confidence interval (CI) 1.549-17.189; р = 0.008) and radiographic progression (HR 5.161; 95 % CI 1.550-17.187; р = 0.008). Progression risk decreased with increased level of PSA decrease 12-16 weeks after enzalutamide therapy start: for PSA decrease >30 % HR 0.150; 95 % CI 0.040-0.570; р = 0.005; for PSA decrease >50 % HR 0.039; 95 % CI 0.006-0.280; р = 0.001; for PSA decrease >90 % HR 0.116; 95 % CI 0.036-0.375; р = 0.000. Presence of HRR mutation, age <58 years, primary metastatic disease and poorly differentiated morphology did not affect duration without PSA-progression (p >0.05). Kaplan-Meier curves showed a trend towards increased time to development of castration resistance in the group of primary early cancer (Breslow р = 0.06; Tarone-Ware р = 0.062). Subgroup analysis showed that in the cohort of patients with castration-resistant prostate cancer (n = 48), absence of HRR mutation in patients who previously received docetaxel therapy increases time to PSA-progression compared to patients with mutations (log-rank р <0.05).

Abstract 4648: How inherited mutations affect single cells within the tumor microenvironment in breast tumors stratified by receptor status

Abstract The tumor microenvironment (TME) plays important roles in tumor progression, therapy response and patient survival. In this comprehensive study, we performed a detailed multiomic single cell analysis of breast cancers with inherited mutations in different genes (BRCA1, BRCA2, PALB2, ATM, CHEK2), and wild type mutation negative (WT) patients, stratified by hormone receptor status, to understand the relationship between inherited mutation and immunogenicity. Using spatial tissue multiplexing (PhenoCycler), single cell RNAseq (10X Genomics) and bulk RNAseq, we evaluated cellular markers within the TME associated with DNA damage as well as phenotypes with tumor suppressive (M1, CD8 T cells, NK cells) or tumor promotive (M2, Treg, CAF) properties. We developed a 43-plex antibody panel and characterized eight tissue microarrays containing 443 patient samples from mutation carriers (BRCA1: n=142, BRCA2: n=118, CHEK2: n=2, TP53: n=3, PALB2: n=7) and WT tumors (n=171). We addressed how the TME differs in mutation carriers versus WT tumors stratified by receptor status. To further investigate immune cell function (cytolytic function, exhaustion, immune checkpoint) as well as pathways involved in immune suppression and/or promotion, we performed scRNA sequencing using isolated single cells from fresh collected BC samples (WT ER: n=3, BRCA2 ER: n=1, CHEK2 ER: n=1, VUS ER: n=1) and bulk RNA (BRCA1: n=17, BRCA2: n=9). To determine immune cell (IC) frequency, we analyzed CD45+ cells detectable in each cohort and their co-expression of markers to determine specific phenotypes. Our data suggest that within BRCA mutation-associated BC, there are two groups: 1) with increased tumor infiltrating lymphocytes (TILs) including CD8+ cytotoxic T cells with high cytolytic function; and 2) with decreased TILs and cytolytic function. The frequency of CD8+ T cells is significantly decreased in breast cancers with BRCA2 mutations compared to BRCA1. Characterizing ER+ CHEK2 BC reveals T cell exhaustion compared to WT ER+ BC. Furthermore, preliminary scRNA results reveal increased fibroblast markers in ER+ CHEK2 and ER+ WT compared to ER+ BRCA2 tumors. Interestingly, cancer associated fibroblast (CAFs) markers (ACTA2, COL1A1, FAP, PDGFRA, PDGFRB, PDPN, THY1) as well as TAMs (CCL2, CD163, CD206, CD68, IL10, LOX, PLOD2, SIGLEC1) are increased in ER+ CHEK2 tumors compared to ER+ WT. These data could provide insights into how the TME associated with ER+ CHEK2 mutations might be driven by CAFs and TAMs with a frequency much higher than in ER+ WT. The detection of immune suppressive (Treg, M2) and immune promotive (M1) phenotypes differs in BRCA1 compared to BRCA2 mutated and WT TNBC. Our findings could decipher the role of DNA repair gene mutations and their effect on cells within the TME that might influence the design of treatment options in patients with inherited mutations based on their receptor status. Citation Format: Dana Pueschl, Derek A. Oldridge, Jonathan Belman, William Chandler, Anupma Nayak, Bradley Wubbenhorst, John Pluta, Michael Feldman, E. John Wherry, Heather Thorne, Georgia Chenevix-Trench, Kathleen Cuningham Foundation Consortium for Resea kConFab, Susan M. Domchek, Katherine L. Nathanson. How inherited mutations affect single cells within the tumor microenvironment in breast tumors stratified by receptor status. [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 4648.

Impact of an Expanded Definition of Family History on Outcomes of Active Surveillance for Prostate Cancer.

Despite family history being an established risk factor for prostate cancer, the role of a broader definition of family history inclusive of not just prostate cancer but other genetically related malignancies has not been investigated in the active surveillance population. Here, we evaluate the impact of an expanded definition of family history on active surveillance outcomes. Patients undergoing active surveillance for prostate cancer at Massachusetts General Hospital from 1997-2019 with detailed data available on family cancer history were identified. Primary outcome was biopsy progression-free survival, and secondary outcomes were treatment-free survival, adverse pathological features at prostatectomy, and biochemical recurrence after treatment. Statistical analyses were conducted using the Kaplan-Meier method and Cox regression. Among 855 evaluable patients, 300 (35.1%) patients had any family history of prostate cancer, and 95 (11.1%) had a family history of related malignancies suggestive of a hereditary cancer syndrome. Family history of prostate cancer alone was not associated with biopsy progression, whereas family history suggestive of a hereditary cancer syndrome was associated with a significantly increased risk of biopsy progression (HR 1.43, 95%CI 1.01-2.02), independent of other known clinicopathological risk factors in multivariable analysis. Similarly, family history suggestive of a hereditary cancer syndrome was associated with significantly lower treatment-free survival (HR 1.58, 95%CI 1.14-2.18) in multivariable analysis. No significant association was found between family history and adverse features on surgical pathology or biochemical recurrence. An expanded family history suggestive of a hereditary cancer syndrome is an independent predictor of biopsy progression during active surveillance. Men with such a family history may still be offered active surveillance but should be counseled regarding the higher risk of disease progression.

Abstract P5-12-05: Gestation and breast cancer in women with mutations in DNA repair genes: Is there any relationship?

Abstract Introduction: Women carrying mutations in reparative genes frequently ask about the safety of pregnancy or the use of fertility-promoting techniques. The evidence on gestation and breast cancer (BC), specifically in mutated BRCA, provides contradictory results1,3. On the one hand, there are studies that support the protective nature of pregnancy, while others show that gestation is a factor that promotes it1. Likewise, some point to differences in the association according to the type of mutation, BRCA1 or BRCA22. Objectives: To prove whether there is a relationship between pregnancy and BC in patients with mutations in DNA repair genes and to establish a solid knowledge base for counseling these patients in clinical practice. Patients and methods: We conducted an analytical, observational and retrospective study of 259 women with mutations in DNA repair genes, whether they had developed cancer or not, with different gestational histories in the Medical Oncology Service. The genes studied were: BRCA1and2, MUTYH, hMSH2, hMSH6,RAD51C,APC,CHECK2,ATM,PALB2,PTEN,BRIP1,ATM+RAD51D,BRCA1+NTHL1,CDKN2A,TP53,NF1,RAD51D. Results: The proportion of patients who develop cancer in the pregnant group is 46.9%. pregnant women is 46.9%, compared to 37.3% in nulliparous women ((χ²) =1.839, p= 0.171). We observed that the diagnosis of BC occurred before the age of 40 years in 40% of pregnant women, compared to 30% in nulliparous women. Likewise, we observed that from the third pregnancy onwards, the percentage of women suffering from BC is higher, with a peak in the fourth pregnancy (68.8% vs. 31.3%) (p=0.135) and that 51.3% of women whose first pregnancy was before the age of 30 years developed BC, compared to 38.6% in those whose first pregnancy was at a later age (X2=4.16, p=0.041). Finally, we observed that 80% of breast cancers developed after 10 years from the first birth. Conclusions: Considering our results, we cannot affirm that at present there is an association between gestation and BC in women with mutation in genes involved in DNA repair. Table: Cross table between cancer (Yes/No) and pregnancy (Yes/No) Citation Format: María López-herrero lópez, Cristina Morales Estévez, Ana Armenta Triviño, Maria Jose Contreras, Maria Gómez Aguilera, Beatriz Rodriguez Alonso, Ignacio Porras, Juan de la Haba-Rodríguez, Enrique Aranda Aguilar. Gestation and breast cancer in women with mutations in DNA repair genes: Is there any relationship? [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-12-05.

Internet-Based Germline Genetic Testing for Men With Metastatic Prostate Cancer.

Germline mutations in DNA repair genes are present in approximately 10% of men with metastatic prostate cancer (mPC), and guidelines recommend genetic germline testing. Notable barriers exist, including access to genetic counseling, insurance coverage, and out-of-pocket costs. The GENTleMEN study was designed to determine the feasibility of an Internet-based, patient-driven germline genetic testing approach for men with mPC. In this prospective cohort study, men with mPC provided informed consent via an Internet-based platform and completed a questionnaire including demographics and family cancer history. Supporting medical data were also collected. Genetic testing was performed using the Color Genomics 30-gene targeted panel of cancer predisposition genes on a mailed saliva sample. Men whose test results identified a germline pathogenic or likely pathogenic variant received results by phone or telehealth genetic counseling; other participants received results by email with an option for phone-based or telehealth genetic counseling. As of August 18, 2021, 816 eligible men were consented, of whom 68% (551) completed genetic testing, and 8.7% (48 of 551) were found to carry a pathogenic or likely pathogenic variant in a germline DNA repair gene: CHEK2 (17), BRCA2 (15), ATM (6), NBN1 (3), BRCA1 (2), PALB2 (2), PMS2 (2), and MSH6 (1). Participants were more likely to complete the testing process if they were non-Hispanic White, married, highly educated, or from a higher-income bracket. Here, we show the feasibility of delivering germline (inherited) genetic testing by a voluntary, patient-driven, Internet-based platform to men with mPC. Preliminary results show rates of germline DNA repair mutations, consistent with other cohorts. Although feasible for some, reduced steps for participation, more dedicated diverse outreach and participant support, and identification and addressing of additional barriers is needed to ensure equitable access and optimization.

DNA Damage and Its Role in Cancer Therapeutics.

DNA damage is a double-edged sword in cancer cells. On the one hand, DNA damage exacerbates gene mutation frequency and cancer risk. Mutations in key DNA repair genes, such as breast cancer 1 (BRCA1) and/or breast cancer 2 (BRCA2), induce genomic instability and promote tumorigenesis. On the other hand, the induction of DNA damage using chemical reagents or radiation kills cancer cells effectively. Cancer-burdening mutations in key DNA repair-related genes imply relatively high sensitivity to chemotherapy or radiotherapy because of reduced DNA repair efficiency. Therefore, designing specific inhibitors targeting key enzymes in the DNA repair pathway is an effective way to induce synthetic lethality with chemotherapy or radiotherapy in cancer therapeutics. This study reviews the general pathways involved in DNA repair in cancer cells and the potential proteins that could be targeted for cancer therapeutics.

Actionable genomic landscapes from a real-world cohort of urothelial carcinoma patients.

Recent targeted therapies for advanced and metastatic urothelial cancer have generated enthusiasm, but the actionable genomic landscape of early-stage disease remains largely unknown. Here, we utilized a large, real-world cohort to comprehensively investigate the incidence of genetic alterations with potential therapeutic implications at all stages of bladder cancer. We retrospectively analyzed next-generation sequencing (NGS) data from 1,562 bladder cancer patients (stages I-IV) with formalin-fixed, paraffin-embedded tumor biopsies sequenced using the Tempus xT solid tumor assay. Incidence of genetic alterations, tumor mutational burden (TMB), microsatellite instability (MSI), and PD-L1 status were assessed and stratified by bladder cancer stage. For patients with tumor-normal match sequencing (n=966), incidental germline alterations in 50 genes were assessed. The cohort was composed of 165 stage I-II, 211 stage III, and 1,186 stage IV tumors. TMB-high, PD-L1 positive, and MSI-high status were noted in 14%, 33%, and 0.7% of tumors, respectively, and were similar across stages. Alterations in fibroblast growth factor receptor (FGFR)2/3, homologous recombination repair genes, additional DNA repair gene mutations (ERCC2, RB1, FANCC), and NTRK fusions were detected at similar frequencies across disease stages. We identified a low rate of incidental germline mutations in all tumors (5.2%) and in specific genes: MUTYH (1.9%), BRCA2 (0.5%), and ATM (0.8%). Important subsets of patients demonstrate genetic alterations in potentially actionable molecular pathways at all stages. This analysis found minimal variability in these alterations across stages, providing rationale for early identification of genetic alterations and personalization of therapies at all stages for patients with bladder cancer.

Awareness of genetic risk for prostate cancer (PCa) in men from families with germline mutations in DNA-repair genes.

328 Background: Although one of the most important risk factors for prostate cancer (PCa) is a family history of the disease, there is a poor awareness of genetic risk. The aim of the current study is to investigate the awareness of genetic risk for PCa in men belonging to female families with germline variants in DNA-repair genes (DRGs). Methods: Data were extracted by a prospective observational study designed to select men with germline pathogenic variants (PVs) and offer them a dedicated PCa screening. The selection of probands was performed by genetic counseling and testing of male grade I relatives of female patients with a PVs. Male candidates were identified after reviewing the genealogical trees of all women who had received the diagnosis of breast and/or ovarian cancer and tested positive for a PVs. All the probands, 35-69 yrs old, who resulted positive for PVs were offered to participate to a specific PCa screening based on annually digital rectal examination (DRE), detection of PHI, which is a blood test including total PSA, free PSA, free/total PSA and -2proPSA, and multiparametric MRI. The primary outcome was the “willing to be tested”, defined as a proxy for male awareness of PCa risk. The secondary endpoint was the acceptance rate to be screened. Results: We reviewed the genealogical trees of breast/ovarian cancer female patients from January 2017 to December 2021 and we identified, over 1256 families, 139 positive cases for PVs in DRGs. Among 139 families, we identified 378 “healthy” 35-69 yrs old men, who were offered a genetic counseling, and if they agree a genetic testing. Overall 117/378 (31%) healthy males declared to be interested to be tested. Out of the 51 new tests (66 men already tested out of the study), we found 30 (58.8%) positive men. All the new positive tested men accepted to attend the PCa screening. Living in Northern Italy, having at least one child and higher (degree) level of education were the strongest predictors of willing for testing (p<0.01). Conclusions: Our data reveals a limited will to be tested, but all men tested positive for PVs accepted to participate to the PCa screening. These findings strongly support the urgent need to implement awareness of genetic risk for PCa.

TRIUMPH: Phase II trial of rucaparib monotherapy in patients with metastatic hormone-sensitive prostate cancer harboring germline DNA repair gene mutations.

190 Background: Androgen deprivation therapy (ADT) is the backbone of treatment for patients (pts) with metastatic prostate cancer (PCa), but many pts find this difficult to tolerate. Treatment with non-castrating regimens may avoid or delay the toxicities of hormonal therapy. The activity of PARP inhibitors (PARPi) in pts with homologous recombination DNA-repair (HRD) mutations (muts) and metastatic castration-resistant PCa has been established. We hypothesized here that the benefit of ARPi can be maintained in the absence of ADT in a biomarker-selected (HRD mutated) population with PCa. We designed a Phase 2 study in men with hormone-naïve, metastatic PCa who harbored a germline HRD mut treated with rucaparib monotherapy (without ADT). Methods: This was a multi-center, single arm Phase 2 study (NCT03413995) in men with asymptomatic hormone-sensitive metastatic PCa who received rucaparib 600mg by mouth daily. During consenting, pts were informed and had to opt out of ADT-based therapy. Pts must have had a germline mutation in an HRD gene on clinical-grade testing. The primary endpoint was confirmed PSA50 response rate. Key secondary endpoints included safety, objective response rate (ORR), and radiographic progression-free survival (rPFS). The trial was designed to detect a 25% absolute increase in PSA50 response from a null of 50%. Results: 12 pts were enrolled, 7 with BRCA1/2 and 5 with CHEK2 muts. The confirmed PSA50 response rate to rucaparib was 41.7% (N=5/12, 95% CI: 19.3-68.1%), which did not meet the pre-specified efficacy boundary to enroll additional patients to 2nd stage. In pts with measurable disease, the ORR was 60% (N=3/5, all with BRCA2). Median rPFS on rucaparib was 10.3 months (95% CI: 4.0 mo - NR). At the time of the interim analysis, 3 pts remained on study. The majority of adverse events (AE) were Grade ≤2 and expected. Translational studies are ongoing. Conclusions: Rucaparib can induce clinical responses in a biomarker-selected PCa population without concurrent ADT. However, the pre-specified threshold of PSA50 response was not met. Although durable responses were observed in a subset of pts, PARPi without ADT in metastatic hormone sensitive PCa will not be pursued. Clinical trial information: NCT03413995 . [Table: see text]

Immunogenomic Biomarkers and Validation in Lynch Syndrome.

Lynch syndrome (LS) is an inherited disorder in which affected individuals have a significantly higher-than-average risk of developing colorectal and non-colorectal cancers, often before the age of 50 years. In LS, mutations in DNA repair genes lead to a dysfunctional post-replication repair system. As a result, the unrepaired errors in coding regions of the genome produce novel proteins, called neoantigens. Neoantigens are recognised by the immune system as foreign and trigger an immune response. Due to the invasive nature of cancer screening tests, universal cancer screening guidelines unique for LS (primarily colonoscopy) are poorly adhered to by LS variant heterozygotes (LSVH). Currently, it is unclear whether immunogenomic components produced as a result of neoantigen formation can be used as novel biomarkers in LS. We hypothesise that: (i) LSVH produce measurable and dynamic immunogenomic components in blood, and (ii) these quantifiable immunogenomic components correlate with cancer onset and stage. Here, we discuss the feasibility to: (a) identify personalised novel immunogenomic biomarkers and (b) validate these biomarkers in various clinical scenarios in LSVH.

GWAS and functional studies suggest a role for altered DNA repair in the evolution of drug resistance in Mycobacterium tuberculosis.

The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-depth knowledge for timely diagnosis. We performed genome-wide association analysis using 2237 clinical strains of Mtb to identify novel genetic factors that evoke drug resistance. In addition to the known direct targets, we identified for the first time, a strong association between mutations in DNA repair genes and the multidrug-resistant phenotype. To evaluate the impact of variants identified in the clinical samples in the evolution of drug resistance, we utilized knockouts and complemented strains in Mycobacterium smegmatis and Mtb. Results show that variant mutations compromised the functions of MutY and UvrB. MutY variant showed enhanced survival compared with wild-type (Rv) when the Mtb strains were subjected to multiple rounds of ex vivo antibiotic stress. In an in vivo guinea pig infection model, the MutY variant outcompeted the wild-type strain. We show that novel variant mutations in the DNA repair genes collectively compromise their functions and contribute to better survival under antibiotic/host stress conditions.

The RUNX Family, a Novel Multifaceted Guardian of the Genome.

The DNA repair machinery exists to protect cells from daily genetic insults by orchestrating multiple intrinsic and extrinsic factors. One such factor recently identified is the Runt-related transcription factor (RUNX) family, a group of proteins that act as a master transcriptional regulator for multiple biological functions such as embryonic development, stem cell behaviors, and oncogenesis. A significant number of studies in the past decades have delineated the involvement of RUNX proteins in DNA repair. Alterations in RUNX genes cause organ failure and predisposition to cancers, as seen in patients carrying mutations in the other well-established DNA repair genes. Herein, we review the currently existing findings and provide new insights into transcriptional and non-transcriptional multifaceted regulation of DNA repair by RUNX family proteins.

Frequency of Pathogenic Germline Mutations in Early and Late Onset Familial Breast Cancer Patients Using Multi-Gene Panel Sequencing: An Egyptian Study.

Precision oncology has been increasingly used in clinical practice and rapidly evolving in the oncology field. Thus, this study was performed to assess the frequency of germline mutations in early and late onset familial breast cancer (BC) Egyptian patients using multi-gene panel sequencing to better understand the contribution of the inherited germline mutations in BC predisposition. Moreover, to determine the actionable deleterious mutations associated with familial BC that might be used as biomarker for early cancer detection. Whole blood samples were collected from 101 Egyptian patients selected for BC family history, in addition to 50 age-matched healthy controls. A QIAseq targeted DNA panel (human BC panel) was used to assess the frequency of germline mutations. A total of 58 patients (57.4%) out of 101 were found to have 27 deleterious germline mutations in 11 cancer susceptibility genes. Of them, 32 (31.6%) patients carried more than one pathogenic mutation and each one carried at least one pathogenic mutation. The major genes harboring the pathogenic mutations were: ATM, BRCA2, BRCA1, VHL, MSH6, APC, CHEK2, MSH2, MEN1, PALB2, and MUTYH. Thirty-one patients (30.6%) had BRCA2 mutations and twenty (19.8%) had BRCA1 mutations. Our results showed that exon 10 and exon 11 harbored 3 and 5 mutations, respectively, in BRCA1 and BRCA2 genes. Our analysis also revealed that the VHL gene significantly co-occurred with each of the BRCA2 gene (p = 0.003, event ratio 11/21), the MSH2 gene (p = 0.01, 4/10), the CHEK2 gene (p = 0.02, 4/11), and the MSH6 gene (p = 0.04, 4/12). In addition, the APC gene significantly co-occurred with the MSH2 gene (p = 0.01, 3/7). Furthermore, there was a significant mutually exclusive event between the APC gene and the ATM gene (p = 0.04, 1/36). Interestingly, we identified population specific germline mutations in genes showing potentials for targeted therapy to meet the need for incorporating precision oncology into clinical practice. For example, the mutations identified in the ATM, APC, and MSH2 genes. Multi-gene panel sequencing was used to detect the deleterious mutations associated with familial BC, which in turns mitigate the essential need for implementing next generation sequencing technologies in precision oncology to identify cancer predisposing genes. Moreover, identifying DNA repair gene mutations, with focus on non-BRCA genes, might serve as candidates for targeted therapy and will be increasingly used in precision oncology.

Prevalence of mutations in DNA repair genes in Russian patients with metastatic castration-resistant prostate cancer

Background. Prostate cancer is one of the most common malignant tumors in men. Tailored treatment approaches to metastatic castration-resistant prostate cancer based on identification of specific biomarkers have been introduced only recently. So far, the Food and Drug Administration has approved two drugs (olaparib and rucaparib) targeting the DNA repair genes.Aim. To assess the frequency of mutations in the DNA repair genes in the Russian population.Materials and methods. The article uses data from two centers (National Medical Research Radiological Center and A.I. Kryzhanovsky Krasnoyarsk Regional Clinical Oncological Dispensary) which included the largest numbers of patients in the largest Russian multicenter prospective trial ADAM. We performed genotyping of all valid tumor samples from 113 patients with metastatic castration-resistant prostate cancer to identify clinically significant mutations in the DNA repair genes.Results. Next-generation sequencing demonstrated that 27 patients (23.9 %) had clinically significant mutations in DNA repair genes were, including ATM in 6 (5.3 %), BRCA1 in 5 (4.4 %), BRCA2 in 4 (3.5 %), CDK12 in 3 (2.6 %), CHEK2 in 2 (1.8 %), PALB2 in 2 (1.8 %), BRIP1 in 2 (1.8 %), BARD1 in 1 (0.9 %), RAD51B in 1 (0.9 %), and RAD51C in 1 patient (0.9 %).Conclusion. Identification of mutations in the DNA repair genes should become a routine procedure, since a new treatment approach to metastatic castration-resistant prostate cancer is now being introduced.

Complex molecular profile of DNA repair genes in epithelial ovarian carcinoma patients with different sensitivity to platinum-based therapy.

Epithelial ovarian carcinoma (EOC) is known for high mortality due to diagnosis at advanced stages and frequent therapy resistance. Previous findings suggested that the DNA repair system is involved in the therapeutic response of cancer patients and DNA repair genes are promising targets for novel therapies. This study aimed to address complex inter-relations among gene expression levels, methylation profiles, and somatic mutations in DNA repair genes and EOC prognosis and therapy resistance status. We found significant associations of DUT expression with the presence of peritoneal metastases in EOC patients. The high-grade serous EOC subtype was enriched with TP53 mutations compared to other subtypes. Furthermore, somatic mutations in XPC and PRKDC were significantly associated with worse overall survival of EOC patients, and higher FAAP20 expression in platinum-resistant than platinum-sensitive patients was observed. We found higher methylation of RAD50 in platinum-resistant than in platinum-sensitive patients. Somatic mutations in BRCA1 and RAD9A were significantly associated with higher RBBP8 methylation in platinum-sensitive compared to platinum-resistant EOC patients. In conclusion, we discovered associations of several candidate genes from the DNA repair pathway with the prognosis and platinum resistance status of EOC patients, which deserve further validation as potential predictive biomarkers.

Clinical and molecular characterization of Xeroderma pigmentosum in Moroccan population: a case series of 40 patients

BackgroundXeroderma pigmentosum (XP) is a rare autosomal recessive skin disorder characterized by hyperpigmentation, premature skin aging, ocular and cutaneous photosensitivity with increased risk of skin tumors. XP is caused by mutations in DNA repair genes that protect cells from UV-induced DNA damage. The current study aims to investigate, on clinical and genetic basis, Moroccan XP patients. We explored by direct sequencing the involvement of the prevalent XPA and XPC genes mutations: nonsense mutation (c.682C>T, p.Arg228X) and a two-base-pair (2 bp) deletion (c.1643 1644delTG or p.Val548Ala fsX25), respectively, in 40 index cases from 37 unrelated families in Moroccan population.ResultsEarly skin and ocular manifestations were detected with high rate of malignancy. Cutaneous lesions progressed to malignant skin tumor in 70% of cases. Ocular tumors were also observed in 11 patients including BCC in eight cases, SCC in three cases and melanoma in four cases. Among the 40 patients, there were 20 homozygous cases for the 2 bp deletion in the XPC gene and 9 homozygous cases carrying the nonsense XPA mutation.ConclusionThese findings obtained in the present study revealed that the XPC gene mutation (c.1643 1644delTG, p.Val548AlafsX25) is the major cause of Xeroderma pigmentosum in our population. The c.682C>T (p.Arg228X) mutation is relatively associated with moderate phenotype in XP group A Moroccan families. This result will also contribute to improving the molecular diagnosis of XP disease and will have a significant impact on improving the care of Moroccan patients and their relatives.

Extranodal Marginal Zone Lymphomas Show Recurrent Mutations in DNA Repair Genes, Cancer-Associated Proliferative Signaling and NOTCH1 Signaling Pathways, Regardless of Anatomic Site

Extranodal marginal zone lymphomas (EMZL) are usually indolent B cell lymphomas arising in acquired mucosa-associated lymphoid tissue (MALT) as a result of chronic antigen stimulation from infection or autoimmune processes. EMZLs occurring at different MALT sites have shared and unique genetic events including site-associated chromosomal structural changes and mutations. While large scale genetic analyses of EMZL are lacking, previous small studies have shown that EMZL often show activation of NF-κB through chronic stimulation of the B cell receptor and other cooperating genetic events that include somatic mutations, most frequently in TNFAIP3. Here, we report the largest whole exome sequencing (WES) and copy number (CN) analysis to date in EMZL. Formalin-fixed paraffin-embedded (FFPE) samples of EMZL were collected as part of the Atlas of Blood Cancer Genomes (ABCG) consortium. All cases underwent central pathology review by expert hematopathologists and diagnoses were confirmed as defined by the 2016 WHO classification. We defined global CN gains and losses at log2 fold change value of ±0.3, a value used by many CN tools. DNA and RNA WES were performed using the Illumina platform and DNA and RNA reads aligned to the GRCh38 genome and transcriptome, respectively. Exonic variants were identified and filtered using normal samples and population-based databases to identify putative driver mutations which were then aggregated at the gene level. Mutational analysis was done on samples that passed quality filtering. 225 unique diagnostic specimens were collected from 24 academic hematopathology departments. Cases originated from North America (USA and Canada, 86%), Europe (8%), and Asia (Singapore and China, 6%). 72 tumors were excluded due to inadequate mean coverage related to size of the biopsy or its quality. CN analysis and WES to identify non-silent mutations was performed in 153 unique EMZL including ocular adnexal (31), stomach (26), lung (23), salivary gland (23), and other extranodal locations (50). Average patient age was 63 years (range 53-71 years), female: male ratio of 1.6. Mutation calls identified 718 variants (613 missense mutations and 105 truncating mutations) across 59 putative driver genes detected in ≥5% cases across all the anatomic locations. Among the most commonly mutated genes, we detected genes previously reported to be altered by targeted sequencing in EMZL (e.g., SPEN (12%), TNFAIP3 (A20) (8%), CREBBP (8%), TBL1XR1 (7%), and others) confirming our filtering strategy. A total of 44 focal CN alterations (24 gains and 20 CN losses) were detected for our set of recurrently mutated genes. Global CN gains included chromosome 3 (6%), 6p (7%), 8 (3%), 12 (4%), and 18 (5%) and losses in 21p (10%). Previously described tumor suppressor genes such as TNFAIP3 showed a typical pattern of alterations consisting of CN losses (6q23.3 deletion in 6%) and/or mostly truncating mutations (8%). Combining DNA mutations and CN alterations, the number of genetic lesions per tumor sample in the 59 putative driver genes ranged from 1 to 21, with an average load of 4.9 aberrations per case, consistent with previous genetic studies in other types of MZL lymphoma. The most frequent mutations across all sites were IGLL5 (22%), KMT2C (15%), KMT2D (14%), SPEN (12%), PRDM2 (11%), and NCOR1 (10%). Analysis using Elsevier Pathway Collection, BioPlanet 2019 and Go Biological Process 2021 revealed adjusted statistically significant enrichment of aberrations in genes in NOTCH signaling, DNA repair, cancer-associated sustaining of proliferative signaling, cancer associated histone methylation and positive regulation of transcription, by DNA-templated (GO:0045893) and RNA polymerase II (GO:0045944). Many of the mutated genes were previously not reported in EMZL. Some of the mutations were shared by tumors at different anatomic locations while some were more unique. Mutations in TET2, previous reported as specific for thyroid EMZL, were also detected in ocular adnexa, gastric and salivary gland MZL. Mutations in PTPRD, previously suggested as specific for NMZL, were detected also in EMZL. Overall, this analysis of a large number of samples from different anatomic locations further refines the mutational landscape in EMZL and provides novel clues on pathogenesis. More detailed analyses of mutations, CN variations and RNA expression will be presented at the meeting.

Abstract A024: Prognostic effects of different TP53 mutations in pancreatic ductal adenocarcinoma

Abstract Approximately, 70% of pancreatic ductal adenocarcinomas (PDACs) have mutations in the TP53 gene; however, it is still unknown if gain- or loss- of function mutations in TP53 provide differential prognostic value to guide therapy. To fill this gap, we assessed the potential effect of wild-type, missense (gain-of-function) and truncating (loss-of-function) TP53 mutations in patient survival, in two independent clinical cohorts (The Cancer Genome Atlas cohort=141, and the Memorial Sloan Kettering–Integrated Mutation Profiling of Actionable Cancer Targets cohort=376 PDACs). We employed multivariable Cox proportional hazards regression models adjusting for patient demographic (age at diagnosis, sex, race/ethnicity) and tumor characteristics (presence of distant metastasis at diagnosis). Additionally, we conducted stratified analyses by the status of “druggable” (DNA repair gene mutations) and other driver mutations (SMAD4 and CDKN2A genes). We found that PDACs with missense TP53 mutations were associated with a worse patient survival compared to tumors with wild-typeTP53 (HR = 1.47, 95% CI: 1.00-2.17; p=0.051). Similarly, patients with truncating mutations in TP53 had a trend to worse OS (HR=1.11, 95% CI, 0.70-1.76; p=0.654) compared to patients with wild-type TP53, however, these associations were not significant. Furthermore, we found that mutations in DNA repair genes, SMAD4 and CDKN2A genes did not show any prognostic value. Our findings suggest that molecular characterization of specific TP53 mutations may help to determine differences in patient prognosis and potentially guide future clinical management of patients. Citation Format: Carlos M. Mejia Arbelaez, Xining Shan, Tseng Robert, Marie E. Robert, Xiaomei Ma, Luisa F. Escobar-Hoyos. Prognostic effects of different TP53 mutations in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A024.