MUTYH Mutations Research Articles

Prevalence of Pathogenic Germline Mutations in Solid Tumor Predisposition Genes Detected By Tumor-Normal Whole Exome Sequencing Analysis Among Adults with Hematologic Malignancies

Background Approximately 7-10% of cancer patients have pathogenic germline variants (PGVs) in cancer predisposition genes. However, most studies to date have focused on PGVs in patients with solid tumors. Less is known about the prevalence of PGVs in patients with hematologic malignancies (HM). We investigated the prevalence of PGVs in 72 cancer predisposition genes in a cohort of HM cases from our tumor-normal whole exome sequencing (TN-WES) database. Methods We identified 363 unique HM patients with TN-WES performed at our lab (Sema4, Branford, CT) since 2020. Our analysis pipeline calls germline pathogenic/likely pathogenic variants (PGVs) in 72 cancer-predisposing genes (PGV-72) from normal tissue, predominantly buccal samples. These are reported clinically as secondary findings, with the patient's consent. Results The cohort (N=363) was comprised predominantly of patients with lymphoid malignancies (N=299, 82.4%), most commonly myeloma (N=222) and CLL/SLL (N=27). The most common myeloid malignancy was myelodysplastic syndrome (N=25). Of 363 unique HM patients with TN-WES, 33 (9.1%) were found to have PGVs in one of the PGV-72 genes. There was no significant difference between those with lymphoid and myeloid malignancies (8.0% vs. 14.1%, Fisher's exact p=0.15). Among patients with germline findings (N=33), the median age was 67 years (range 23-84). The most commonly mutated genes were APC (N=7), CHEK2 (N=7), MUTYH (N=6), and LZTR1 (N=4). LZTR1 and ATM PGVs were more common in patients with myeloid versus lymphoid malignancies (LZTR1: 4.7% vs 0.3%, p=0.02; ATM: 3.1% vs. 0%, p=0.03). Several founder mutations were identified: all APC variants were p.I1307K; four CHEK2 variants were p.T367Mfs*15 (c.100delC); five MUTYH variants were p.G396D. Two patients had more than one PGV: one patient with myeloma (APC p.I1307K and CHEK2 p.S428F) and one patient with CLL/SLL (CHEK2 p.T367Mfs*15 and HOXB13 p.G84E). One patient with myeloma had a BRCA2 p.S1982Rfs*22 germline variant. All PGVs were heterozygous, and none were associated with a somatic second hit. Conclusions The prevalence of PGVs in 72 cancer predisposition genes was approximately 9% in a set of patients with HM undergoing TN-WES. Most PGVs identified were associated with moderately increased risk for solid tumors. Many of the PGVs identified were founder mutations in APC, CHEK2, and MUTYH, likely reflecting the racial/ethnic composition of our cohort. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

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Gastrointestinal NursingVol. 20, No. 7 NewsNewsMelissa McAleesMelissa McAleesE-mail Address: [email protected] Twitter: @MfjMcaleesFreelance journalistSearch for more papers by this authorMelissa McAleesPublished Online:26 Oct 2022https://doi.org/10.12968/gasn.2022.20.7.10AboutSectionsView articleView Full TextPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareShare onFacebookTwitterLinked InEmail View article References Cancer Research UK. What is bowel cancer? 2022. https://www.cancerresearchuk.org/about-cancer/bowel-cancer/about-bowel-cancer (accessed 21 July 2022) Google ScholarRobinson PS, Thomas LE, Abascal F et al. Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells. Nat Commun. 2022; 13(1):3949. https://doi.org/10.1038/s41467-022-31341-0 Crossref, Google ScholarNursing Midwifery Council. International nurses now make up half of those joining the profession. 2022. https://tinyurl.com/f7vprwvh (accessed 21 July 2022) Google ScholarRoyal College of Nursing. Ministers must prioritise attracting the next generation of people to the profession, starting with fair pay, insists the RCN. 2022. https://tinyurl.com/epd4tn8p (accessed 21 July 2022) Google ScholarBowel Cancer UK. New #GetOnARoll campaign launched urging supermarkets to put bowel cancer symptoms on loo roll packaging. 2022. https://tinyurl.com/2taz8vj8 (accessed 21 July 2022) Google ScholarGastroenterology and Endoscopy News. Report from DDW ‘22: Colorectal polyp size often over-estimated. 2022. https://tinyurl.com/yby8xxtc (accessed 21 July 2022) Google ScholarGlobalData. Gut microbiome offers huge, unlocked potential for treating infectious diseases—including COVID-19, says GlobalData. 2022. https://tinyurl.com/yc4twsya (accessed 21 July 2022) Google ScholarBowel Cancer UK. A less invasive treatment approach for bowel cancer could save over £1 billion. 2022. https://tinyurl.com/4yr4n9kp (accessed 21 July 2022) Google Scholar FiguresReferencesRelatedDetails 2 September 2022Volume 20Issue 7ISSN (print): 1479-5248ISSN (online): 2052-2835 Metrics History Published online 26 October 2022 Published in print 2 September 2022 Information© MA Healthcare LimitedPDF download

356P Biallelic MUTYH germline inactivation in patients with colon polyposis and subjects with sporadic colorectal cancer

MUTYH-associated polyposis (MAP) is a rare recessive condition typically characterized by the presence of 10-100 colorectal polyps and the elevated risk of colorectal cancer (CRC). CRCs arising in biallelic carriers of MUTYH mutation often contain KRAS G12C substitution and frequently arise without concomitant polyposis. This study included 74 consecutive patients with colon polyposis and 3486 consecutive patients with CRC referred to the N.N. Petrov Institute of Oncology (St. Petersburg, Russia) for molecular testing. Normal DNA obtained from subjects with polyposis was analyzed by NGS using custom panel for hereditary cancer genes. CRC patients were screened for recurrent MUTYH pathogenic alleles p.Y179C, p.R245H and p.G396D. The status of the remaining allele in MUTYH-heterozygous CRC cases was analyzed by Sanger sequencing. Biallelic MUTYH mutations were identified in 8/74 (11%) patients with polyposis. MAP was the second most common hereditary polyposis syndrome after familial adenomatous polyposis (47/74, 64%), with Peutz-Jeghers syndrome being in the third place (3/74, 5%). MUTYH biallelic alterations were detected in 9/3486 (0.3%) consecutive CRC patients. Somatic KRAS G12C substitution was observed in 223/3486 (6%) CRCs. Germ-line MUTYH inactivation was identified in 7/223 (3%) KRAS G12C-positive CRCs vs. 2/3253 (0.06%) patients without this mutation (p < 0.00001). Germ-line MUTYH biallelic mutations are significant contributors to the incidence of polyposis, while their impact in CRC morbidity is moderate. However, MUTYH gene analysis is highly feasible in CRC patients whose tumor harbors KRAS G12C substitution.

Real-World Evaluation of a Population Germline Genetic Screening Initiative for Family Medicine Patients.

Hereditary factors contribute to disease development and drug pharmacokinetics. The risk of hereditary disease development can be attenuated or eliminated by early screening or risk reducing interventions. The purpose of this study was to assess the clinical utility of germline medical exome sequencing in patients recruited from a family medicine clinic and compare the mutation frequency of hereditary predisposition genes to established general population frequencies. At the University of Kentucky, 205 family medicine patients underwent sequencing in a Clinical Laboratory Improvement Amendments of 1988-compliant laboratory to identify clinically actionable genomic findings. The study identified pathogenic or likely pathogenic genetic variants—classified according to the American College of Medical Genetics and Genomics variant classification guidelines—and actionable pharmacogenomic variants, as defined by the Clinical Pharmacogenetics Implementation Consortium. Test results for patients with pharmacogenomic variants and pathogenic or likely pathogenic variants were returned to the participant and enrolling physician. Hereditary disease predisposition gene mutations in APOB, BRCA2, MUTYH, CACNA1S, DSC2, KCNQ1, LDLR, SCN5A, or SDHB were identified in 6.3% (13/205) of the patients. Nine of 13 (69.2%) underwent subsequent clinical interventions. Pharmacogenomic variants were identified in 76.1% (156/205) of patients and included 4.9% (10/205) who were prescribed a medication that had pharmacogenomic implications. Family physicians changed medications for 1.5% (3/205) of patients to prevent toxicity. In this pilot study, we found that with systemic support, germline genetic screening initiatives were feasible and clinically beneficial in a primary care setting.

Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells

Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequence normal tissue DNAs from 10 individuals with MAP. Somatic base substitution mutation rates in intestinal epithelial cells were elevated 2 to 4-fold in all individuals, except for one showing a 31-fold increase, and were also increased in other tissues. The increased mutation burdens were of multiple mutational signatures characterised by C > A changes. Different mutation rates and signatures between individuals are likely due to different MUTYH mutations or additional inherited mutations in other BER pathway genes. The elevated base substitution rate in normal cells likely accounts for the predisposition to neoplasia in MAP. Despite ubiquitously elevated mutation rates, individuals with MAP do not display overt evidence of premature ageing. Thus, accumulation of somatic mutations may not be sufficient to cause the global organismal functional decline of ageing.

Abstract 5219: Frequency of germline mutations in Mexican children with cancer

Abstract Childhood cancer is a leading cause of death by disease in children from 5 -14 ages, for whom there are no prevention strategies. Due to early-age of diagnosis and short-time environmental factors exposition, increasing evidence suggests childhood cancer could have stronger association with germline alterations in predisposition cancer genes. It has been estimated that up to 30% all childhood cancer diagnosis may be caused by germline variants, but their frequency and distribution remain unclear. Elucidating the prevalence and role of germline mutations in the development of childhood cancer is crucial for understanding its bases, causes, cancer-risk reduction plan, surveillance, and treatment. Here, we present a pilot study on cancer children’s patients and their relatives. A total of 40 Mexican-mestizo children with any cancer diagnosis were recruited from several Institutions of Health in Mexico and a sample of saliva or blood was obtained. Whole Exome Sequencing was performed and bioinformatic analysis was carried out following GATK best practices for germline genetic variants. Additionally, we evaluated a risk selection tool for recognition of genetic predisposition in pediatric cancer patients. Pathogenic or likely-pathogenic genetic variants (mutations) were identified from the application of a filtering chain based on ACMG guidelines, and they were subsequently validated by Sanger sequencing. Germline mutations in MSH6, NF1, MUTYH, CDKN2A, CHEK2, DICER1, FANCA and SBDS genes were identified in 5/40 (12.5%) patients with cancer, only 3 of 5 index cases (60%) reported family history of cancer and all patients meet at least one criterion of the risk selection tool. Two patients were carriers of one mutation, while in three patients were identified 2 pathogenic variants. Additionally, we identified four nonsense candidate genetic variants on EWSR1, FANCL, EPCAM and HRAS genes and two pathogenic variants in non-cancer predisposition gene, ABCA4. Our results show for the first time a higher frequency (12.5%) of germline mutations in cancer predisposition genes in Mexican-mestizo children with cancer. The lack of family history in two carriers showed the need to establish standardized suspicion criteria for identification of children with higher risk of cancer who can benefitfrom genetic testing. Further characterization of additional genetic variants identified without clinical classification will be important to evaluate their real contribution, as well as the influence of environmental factors on de novo mutation promotion. Citation Format: Oscar Alonso Luna, Jorge Meléndez Zajgla, Marta Zapata Tarres, Luis Enrique Juárez Villegas, Elvia Cristina Mendoza Caamal, Elianeth Rey Helo, Socorro Aida Borges Yanez, Gabriela Elisa Mercado Celis, Rodrigo Barquera Lozano. Frequency of germline mutations in Mexican children with cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5219.

Concordance of hydrogen peroxide-induced 8-oxo-guanine patterns with two cancer mutation signatures of upper GI tract tumors.

Oxidative DNA damage has been linked to inflammation, cancer, and aging. Here, we have mapped two types of oxidative DNA damage, oxidized guanines produced by hydrogen peroxide and oxidized thymines created by potassium permanganate, at a single-base resolution. 8-Oxo-guanine occurs strictly dependent on the G/C sequence context and shows a pronounced peak at transcription start sites (TSSs). We determined the trinucleotide sequence pattern of guanine oxidation. This pattern shows high similarity to the cancer-associated single-base substitution signatures SBS18 and SBS36. SBS36 is found in colorectal cancers that carry mutations in MUTYH, encoding a repair enzyme that operates on 8-oxo-guanine mispairs. SBS18 is common in inflammation-associated upper gastrointestinal tract tumors including esophageal and gastric adenocarcinomas. Oxidized thymines induced by permanganate occur with a distinct dinucleotide specificity, 5′T-A/C, and are depleted at the TSS. Our data suggest that two cancer mutational signatures, SBS18 and SBS36, are caused by reactive oxygen species.

Genomic landscape of SMARCA4-deficient lung tumors by clinical RNA sequencing.

3118 Background: SMARCA4-deficient lung cancer is an undifferentiated lung cancer subtype associated with poor prognosis and morphological features that make them challenging to distinguish from sarcoma. These tumors are known to be resistant to standard of care surgery, radiation, and chemotherapy. Recent case reports suggest that these tumors might be resistant to immunotherapy. An assessment of the genomic and transcriptomic features of SMARCA4-deficient thoracic tumors may identify potential novel targets and treatment strategies for this new WHO lung cancer classification. Methods: We retrospectively analyzed de-identified NGS data from 8,484 thoracic formalin-fixed, paraffin-embedded tumor biopsies from lung cancer patients sequenced using the Tempus|xT solid tumor assay (DNA-seq of 595-648 genes at 500x coverage; whole-exome capture RNA-seq). Tumor-normal match sequencing was performed for all tumors, enabling the detection of incidental germline alterations across 46 genes. SMARCA4-deficiency was defined as tumors with a pathogenic or likely pathogenic SMARCA4 single nucleotide variant, insertion/deletion, or copy number alteration. Statistical significance was determined using Fisher's exact test and Wilcoxon rank-sum tests. Results: SMARCA4-deficiency was detected in 370 (4.4%) tumors, of which over 80% were stage III or IV. SMARCA4-deficient tumors included more male patients (63% vs 49%, p &lt; 0.001) and younger age at diagnosis (median 64 vs 68 years, p &lt; 0.001). There were more patients with high tumor mutational burden (TMB-H, ≥10 mutations per megabase) (34% vs 15%, p &lt; 0.001), and fewer patients with positive PD-L1 immunohistochemical staining (44% vs 54%, p = 0.009) compared to SMARCA4 wild-type tumors. Microsatellite instability status occurred at similar low frequencies across SMARCA4-deficient vs wild-type tumors (0.8% vs 0.5%, p = 0.5). SMARCA4-deficient tumors showed enrichment for somatic mutations in TP53 (71% vs 47%, q &lt; 0.001), STK11 (22% vs 6.8%, q &lt; 0.001), KEAP1 (15% vs 4.2%, q &lt; 0.001), and CDKN2A (15% vs 5.9%, q &lt; 0.001) compared to wild-type. Tumor normal-match sequencing identified incidental germline mutations in MUTYH (2.2%), ATM (1.1%), ATP7B (0.5%), and MSH6 (0.5%) for SMARCA4-deficient tumors. RNA-sequencing analysis confirmed reduced transcriptional expression of SMARCA4 (p &lt; 0.001), CD274 (PD-L1; p &lt; 0.001), TNFRSF18 (p &lt; 0.001), and TNFRSF4 (p = 0.035) in deficient tumors vs wild-type. Furthermore, SMARCA4-deficient tumors revealed reduced infiltration of CD4+ T cells (19% vs 22%, p &lt; 0.001). Conclusions: This study reveals the unique genomic and transcriptional characteristics of SMARCA4-deficient lung tumors. Further studies are needed to assess the impact of immunotherapies and targeted therapies among this patient population.

Pan-sarcoma analysis of DNA damage response pathway alterations and deficiency.

11548 Background: Alterations in DNA damage response (DDR) pathways contribute to genomic instability and malignant progression and have been shown to be of clinical significance in several carcinomas and solid tumors. While some studies have identified ostensibly pathogenic variations in known and novel cancer genes with implications for sarcoma risk and treatment opportunities, there is limited information regarding the role of DDR pathway alterations in sarcoma. We identified a gene alteration in ERCC2, a gene that codes for a DNA helicase in the nucleotide excision repair pathway, in a patient with multiply relapsed epithelioid sarcoma (ES), prompting an investigation of DDR pathway alterations in sarcoma samples using a global next-generation sequencing (NGS) platform. Methods: Sarcoma patient samples (N = 5310), representing 38 pediatric and adult histologic subtypes, underwent NGS of DNA (592 gene panel or whole exome) and RNA (whole transcriptome sequencing, N = 3612) at a CLIA-certified laboratory (Caris Life Sciences, Phoenix, AZ). A threshold of 10 mut/Mb was used to identify high tumor mutational burden (TMB-H). IHC was performed for PD-L1 (SP142; 2+|5% = positive). Homologous recombination deficiency (HRD) scores were calculated as a composite of loss of heterozygosity, telomeric allelic imbalance, and large-scale transitions, using a positive threshold of 42 (N = 2138). HRD score association with biomarker status was evaluated overall and in sarcoma subtypes. Results: A pathogenic DDR pathway mutation was noted in 842 (15.9%) of the total samples. ATRX was by far the most commonly altered DDR gene (10% of all samples), with mutations observed across 25 sarcoma subtypes (11 subtypes with &gt; 10% mutation rate: leiomyosarcoma [LMS], perivascular epithelioid cell tumor [PEComa], pleomorphic sarcoma [PLSARC], uterine sarcoma [OUSARC], osteosarcoma, spindle cell sarcoma, angiosarcoma, mesenchymal chondrosarcoma, sarcoma NOS, fibrosarcoma and ES). CHEK2, ATM, and MUTYH mutations were observed in 1-2% of sarcoma samples. More than 20 histologic subtypes showed distinct gene signatures with mutations occurring in &gt; 3% of the samples investigated. ERCC2 was mutated in 3% of ES and 6.5% in PEComa. Median HRD scores ranged between 20-58 across sarcoma subtypes. High rates of deficient HRD (HRDd ≥ 42) were observed in PLSARC (83.2%), OUSARC (73.7%), and dedifferentiated chondrosarcoma (71.4%), while low rates of HRDd were observed in Ewing sarcoma (0%) and clear cell sarcoma (10%). In the overall cohort, ERCC2, ATRX and BRCA2 were significantly associated with increased HRD scores (p = 0.01). Conclusions:DDR pathway alterations are present in numerous histologic subtypes of sarcoma. A more comprehensive analysis of individual histologic subtypes is in progress. Further research will evaluate the clinical implications of these known and novel mutations to guide risk stratification and potential therapeutic options.

Genomic alterations and evolution in patients with prostate cancer with histologic evidence of neuroendocrine differentiation.

5029 Background: The incidence of transformation to neuroendocrine prostate cancer (NEPC) has increased in castration resistant prostate cancer (CRPC) in parallel with treatment advances inhibiting androgen receptor signaling. The current understanding is that this occurs in ̃10-20% of CRPC cases. Missing is a determination of the timing of molecular events that drive the process. Methods: Under an IRB-approved protocol, retrospective annotation of all MSK-reviewed pathology reports was conducted for 1447 prostate cancer patients with MSK-IMPACT sequencing data. For patients with pathologically confirmed NEPC, the date of the first sample with unequivocally reported NEPC (described as “neuroendocrine carcinoma” or as having “neuroendocrine differentiation” or “neuroendocrine features”) was recorded. Patients with early signs of histologic transformation not specifically reported as NEPC (double negative prostate cancer or rare/focal staining for NE markers) were analyzed separately. Sequencing results were described by castration-status at collection (CRPC vs castration-sensitive) and, if applicable, the relationship to NEPC diagnosis (i.e. pre- vs post-NEPC). Genomic enrichment analysis was used to identify differentially altered genes between groups. Results: In total, 95 (6.6%) patients had pathologically confirmed NEPC during their disease course, from whom 150 samples with sequencing results were available: including 18 patients with matched pre- and post-NEPC samples. CRPC samples from patients with NEPC (n = 70) were significantly enriched for RB1 alterations (50% vs 12%, p &lt; 10-10, q &lt; 10-10). AR alterations were significantly enriched in CRPC samples from patients without NEPC (n = 380) (63% vs 21%, p &lt; 10-10, q &lt; 1.27*10-8). Further, alterations in numerous genes including TP53, AMER1, ARID5B, YAP1, SOX2, and NKX2.1 were enriched in NEPC patients at the 95% confidence interval (CI) without correction for repeat testing. Matched pre- and post-NEPC samples demonstrated that TP53 alterations in post-NEPC samples are detected in the majority of pre-NEPC samples (8 of 10 patients), but RB1 alterations in post-NEPC samples are detected in a minority of pre-NEPC samples (1 of 8 patients). 54 (3.7%) patients had evidence of early histologic transformation. CRPC samples from these patients (n = 29) were enriched for mutations in RB1, MAP2K2, MUTYH, and CTNNB1 at the 95% CI without correction. FOXA1 mutations were enriched in patients without transformation. Conclusions: RB1, consistent with previous findings, is enriched in NEPC. The inability to detect RB1 alterations in pre-NEPC samples supports divergent evolution, although technical limits of tissue panel sequencing make it difficult to rule out the presence of sub-clonal alterations. Further study of additional genes which contribute to histologic transformation and the development of NEPC is warranted.

Germline MUTYH mutations and high-grade gliomas: Novel evidence for a potential association.

There is growing body of evidence supporting the role of germline mutations in the pathogenesis of pediatric central nervous system (CNS) tumors, and the widespread use of next‐generation sequencing (NGS) panels facilitates their detection. Variants of the MUTYH gene are increasingly recognized as suspected germline background of various extraintestinal malignancies, besides their well‐characterized role in the polyposis syndrome associated with biallelic mutations. Using a multigene NGS panel (Illumina TruSight Oncology 500), we detected one H3 G34V‐ and one H3 K27M‐mutant pediatric high‐grade diffuse glioma, in association with c.1178G>A (p.G393D) and c.916C>T (p.R306C) MUTYH variants, respectively. Both MUTYH mutations were germline, heterozygous and inherited, according to the subsequent genetic testing of the patients and their first‐degree relatives. In the H3 K27M‐mutant glioma, amplifications affecting the 4q12 region were also detected, in association with KDR‐PDGFRA, KIT‐PDGFRA, and KDR‐CHIC2 fusions, previously unreported in this entity. Among 47 other CNS tumors of various histological types tested with the same NGS panel in our institution, only one adult glioblastoma harbored MUTYH mutation. Together with a single previous report, our data raises the possibility of an association between germline MUTYH mutations and CNS malignancies, particularly in pediatric histone H3‐mutant gliomas.

MUTYH-associated tumor syndrome: The other face of MAP.

MUTYH gene is involved in the base excision repair (BER) mechanism and its pathogenic alterations are associated with colorectal polyposis and cancer. MUTYH-associated polyposis (MAP) is a condition which is inherited in an autosomal recessive manner. MAP patients, beyond colorectal cancer (CRC), may develop other types of tumors, including duodenal, breast, ovarian, pancreatic, bladder and skin cancers. Carriers of biallelic MUTYH likely pathogenic/pathogenic variants exhibit a high lifetime risk of CRC, though cancer risk evidence becomes less clear when monoallelic carriers and extraintestinal tumors are considered. However, several studies recently reported an increased genetic susceptibility to cancer also for carriers of germline monoallelic MUTYH mutations. Moreover, experimental evidence highlighted the MUTYH involvement in many other biological functions. In future, MUTYH mutation carriers might benefit from new target therapies involving the use of PD-1 or KRAS inhibitors. Therefore, "MUTYH-associated tumor syndrome" might be the most appropriate term, due to the multiplicity of tumors observed in MAP patients and different biological contexts in which MUTYH acts as a "playmaker". In this Review, we will investigate the impact of germline mono- and biallelic MUTYH mutations on cancer risk, providing a proposal for clinical surveillance of mutation carriers.

“It was a no-brainer”: A qualitative study of factors driving previvors’ decision-making when considering risk-reducing salpingectomy with delayed oophorectomy

ObjectivePrevivors are becoming more aware of the option of risk-reducing salpingectomy with delayed oophorectomy (RRS-DO) to mitigate their risk of ovarian cancer. In this qualitative study, we explored the clinical and non-clinical factors that impacted previvors’ decision-making to pursue RRS-DO as a risk reduction strategy. MethodsSemi-structured telephone interviews were conducted with previvors and transcribed verbatim. Using ATLAS.ti® software, two primary investigators interpreted data through thematic analysis. After coding four interviews, the investigators discussed discrepancies between codes with a moderator and resolved and refined code. The investigators applied the universal codebook to all interviews and revised the codebook using an iterative approach. Examining codes within and across interviews allowed for major themes and patterns to emerge. ResultsInterviews were conducted with seventeen previvors (ages 31–46). 6 (25%) previvors had a BRCA1 mutation, 7 (41%), a BRCA2 mutation, 3 (13%), a Lynch-related mutation, and 1 (6%), other (MUTYH mutation). At the time of interview, 12 previvors (71%) were planning (6) or had undergone (6) RRS-DO, 4 (23%) were planning (1) or had undergone (3) risk reducing salpingo-oophorectomy (RRSO), and 1 (6%) was undecided. Three major themes emerged: motivating factors for selecting surgical risk reduction option, barriers complicating surgical decision-making, and facilitating factors for surgical decision-making. RRS-DO-focused previvors prioritized avoiding menopause, and they also emphasized that self-advocacy and building rapport with providers facilitated their decision-making. ConclusionBy understanding previvors’ priorities and experiences, physicians can better partner with previvors as they navigate their ovarian cancer risk reduction journey. This will ultimately optimize shared decision-making.

A Case Report of CHEK2 and MUTYH Germline Mutations Associated With Cholangiocarcinoma in a Young Patient

Cholangiocarcinoma (CCA) is a major cause of primary liver carcinoma and has been associated with the penetrance of several germline mutations. We present a 31-year-old female evaluated for left upper quadrant pain and abnormal liver function tests. Ultrasound revealed a nodule in the liver, and biopsy showed intrahepatic adenocarcinoma. Germline testing was positive for two mutations: c.1100delC and c.1227_1228dupGG on the CHEK2 gene and the MUTYH gene, respectively. The patient was started on chemotherapy and tolerated it well. We aimed to demonstrate an association between CHEK2 and MUTYH mutations with CCA and highlight the importance of genetic testing for at-risk patients.

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

525 Background: 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 used real-world evidence to investigate differences between somatic and germline mutations in localized, early-stage urothelial cancers and advanced urothelial cancers. Methods: We retrospectively analyzed de-identified NGS data from 1,146 bladder cancer patients (stages I-IV) with formalin-fixed, paraffin-embedded tumor biopsies sequenced using the Tempus|xT solid tumor assay (DNA-seq of 595-648 genes at 500x coverage; whole-exome capture RNA-seq). For the subset of patients with tumor-normal match sequencing (n=758), additional incidental germline alterations in 46 different genes were assessed. Results: A total of 1,146 bladder cancer tumors were investigated: stage I-II (n=124), stage III (n=159), and stage IV (n=863)—summarized in Table. Tumor mutational burden (TMB) was calculated for 1,126 tumors, and TMB-high (TMB-H; ≥10 mutations per megabase) was similar across tumor stages. PD-L1 immunohistochemical staining was performed on 698 tumors, and no significant differences were observed. Microsatellite instability high (MSI-H) status was detected in only 2 (1.6%) stage I-II tumors and 8 (0.9%) stage IV tumors. Alterations—single nucleotide variants, insertions/deletions, and copy number variants—in FGFR2/3, homologous recombination repair genes (18 genes including BRCA1/2 and ATM), additional DNA repair gene mutations ( ERCC2, RB1, FANCC) and NTRK fusions were detected at similar frequencies across disease stages. In 758 patients with tumor/normal matched sequencing, we identified a low rate of incidental germline mutations in MUTYH (stage III, 1%; stage IV, 1.9%), BRCA2 (stages I-II, 1.2%; stage III, 1%; stage IV, 0.5%), BRIP1 (stages I-II, 1.2%), ATM (stage III, 1%; stage IV, 0.7%), MSH6 (stage III, 1%; stage IV, 0.2%), and TP53 (stage III, 1%; stage IV, 0.2%). Conclusions: Patients with bladder cancer have similar rates of potentially actionable mutations and genomic landscapes regardless of clinical disease stage. These findings provide a rationale for further investigating targeted therapies among early-stage bladder cancer patients.[Table: see text]

Abstract P2-09-14: Characteristics of TNBC patients carrying other than BRCA gene mutations

Abstract Triple-negative breast cancer (TNBC) represents approximately 10-20% of Breast Cancer (BC) diagnosed worldwide and in accordance with the current guideline it is defined by the absence of expression of the of expression of the estrogen receptor (ER&amp;lt;1%), progesterone receptor (PR&amp;lt;1%) and human epidermal growth factor 2-receptor (HER-2) amplification or overexpression. Up to 10-20% of TNBC patients (pts) are found to carry deleterious germline BRCA1/2 mutations and germline genetic testing is common practice in Modena Family Cancer Clinic (MFCC) since 1998. Many of the other genes involved in HR repair are now recognized to contribute to hereditary BC and/or ovarian cancer (OC) risk. Nowadays, the Italian Association of Medical Oncology (AIOM) guidelines recommend BRCA1/2 testing for patients meeting hereditary BC and/or OC or personal history of TNBC diagnosed before 60y while recommendations for testing of other genes are not fully established by National Guidelines. The aim of our study was to explore the high and moderate penetrance BC genes mutation rate in TNBC identified in the MFCC. Between 1998 and 2017, the MFCC offered BRCA1/2 genetic testing, while on January 2018, the Clinical Genomics Laboratory of the MFCC started to provide a Next Generation Sequencing (NGS) multigene panel (MGP) testing for 22 actionable genes (APC, ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM, MLH1, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53).For the purpose of our study, we retrospectively evaluated 274 TNBC patients underwent MGP testing in the last 42 months. In our study, 35 non-BRCA pathogenic or likely-pathogenic variant (PVs) were identified (12.8%). In details, we observed 16 PALB2 mutations (5.8%), 5 RAD51C/D mutations (1.8%), 3 ATM and MUTYH mutations (1.1%), 2 BRIP mutations (0.7%) and one mutation of PSM2, BARD1, CHECK2, TP53, NBN and PTEN genes (0.4%). Two pts carried 2 PVs together: BRCA and MUTYH, BRIP1 and TP53, respectively. Finally, 7 out of 34 pts (20.5%) were diagnosed at age &amp;gt;=60yThe majority of BC was diagnosed at an early stage. All TNBCs present ductal histotype, mostly with high proliferation rate and grading 3. Characteristics of tumors are shown in Table 1. In our cohort, PALB2 mutations were the most frequent PVs in non-BRCA genes, in line with several previous studies. Interesting, we identified RAD51C/D mutations as second PVs non-BRCA genes, in support of certain studies that suggest an association with an increased risk for TNBC and OC. In conclusion, our results support the MGP using, opening the question about the 60-year cut off for genetic testing in TNBC, regardless of family history. Table 1.Characteristics of TNBC tumors in patients carrying other than BRCA gene mutationsPALB2RAD51C/DATMMUTYHBRIPPMS2PTENNBNBARD1CHECK2TP53Number of patients165332111111Mean age at diagnosis (y)61.4 (44-94)48 (33-62)52.3 (49-54)44.3(40-50)42.5 (36-49)394958485036Ki 67 (%)&amp;lt;405(45.5%)01(50%)1 (50%)0011000&amp;gt;=406(54.5%)4(100%)1(50%)1 (50%)1(100%)100100unknown51111000011GradingG1-23 (25%)0000001000G39 (75%)4 (100%)3 (100%)3(100%)2(100%)110101Unknown41000000010Histotypeductal14 (100%)4(100%)3(100%)3(100%)2(100%)110111others00000001000unknown21000000000Stage at diagnosisI7 (63.6%)3 (60%)01 (100%)1 (100%)010000II4 (36.4%)1 (20%)2 (100%)00001000III01 (20%)000300000unknown50121000111 Citation Format: Laura Cortesi, Marta Venturelli, Angela Toss, Claudia Piombino, Elena Barbieri, Elisabetta Razzaboni, Luca Moscetti, Federico Piacentini, Claudia Omarini, Federica Domati, Massimo Dominici. Characteristics of TNBC patients carrying other than BRCA gene mutations [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-09-14.

New Perspectives on the Recurrent Monoallelic Germline Mutations of DNA Repair and Checkpoint Genes and Clinical Variability.

Background: Inherited cancers account for ∼10% of cancer cases. Many hereditary cancers are associated with mutations in DNA repair and checkpoint genes making their clinical surveillance important. Methods: We screened 900 patients using a comprehensive cancer gene panel with the following diagnoses: familial (n = 537, 59.6%), colorectal (n = 117, 13%), breast-ovarian (n = 215, 23.8%), endometrium (n = 12, 1.3%), gastric (n = 11, 1.2%), and thyroid (n = 8, 0.8%). Results: The most commonly mutated genes identified were ATM, MSH6, MUTYH, CHEK2, APC, MLH1, RAD50, PALB2, MSH2, CDH1, and PMS2. The most prevalent heterozygous was MUTYH: c.884C>T(P295L), which was predominant in the breast-ovarian group. Notably, the MUTYH, MSH6, and MSH2 variants showed a higher incidence of extracolonic malignancy. Among the DNA mismatch repair (MMR) genes, MSH6 mutations were the most common, followed by mutations in MLH1, MSH2, PMS2, and EPCAM. Conclusion: These findings offer a new perspective and suggest that, beyond ATM, CHEK2, and PALB2, patients with germline monoallelic mutations in MUTYH, MSH6, APC, CDH1, MHS2, and PMS2 may present with a hereditary breast-ovarian cancer phenotype. Continued developments in assessing and researching new variants of known cancer candidate genes will play an important role in improving individual risk prediction, therapy, and prognosis for familial cancers.

The Effect of Gene Mutations on Metastasis and Overall Survival in Metastatic and Nonmetastatic Colon Cancers.

Objective:It is known that many genes are associated with colon cancer. We aimed to investigate the effect of gene mutations on metastasis and overall survival in metastatic and non metastatic colon cancers. Methods:A total of 50 patients with metastatic (n=25) and non metastatic (n=25) diagnosed with colon cancer between 2010 and 2018 were included in the study. APC, MUTYH, RAD50, MEN1, ATM, PALB2, NSH2, BRCA1, BRCA2, MLH1, BRIP1, TP53, PTEN, BARD1, MSH6, PMS2, NBN, and FAM175A gene mutations were evaluated using the next generation sequencing method. The effect of gene mutations on metastasis and overall survival were evaluated. Results:The mean age of patients with colon cancer without distant metastasis was 48.64±14.72 years and for patients with distance metases was 56.68±11.65. The mean survival time of colon cancer patients with distant organ metastasis after the metastasis date was 104.36±58.59 weeks. The presence of APC, MUTYH, and TP53 genetic mutations was observed with a higher rate in metastatic colon cancer (p<0.05). Conclusion:We showed that APC, MUTYH, and TP53 mutations are associated with distant organ metastasis.

'You cannot expect miracles to happen overnight': patience pays off when you wish to establish a new adrenocortical carcinoma cell line.

Growing attention is being paid to the association of adrenocortical carcinoma (ACC), a rare endocrine malignancy, to cancer predisposition syndromes caused by germline mutations in genes involved in the control of genome stability. Tumour cells with a defective DNA mismatch repair pathway have a high mutation burden, which results in the production of tumour-associated specific neoantigens and in an increase of the sensitivity to therapies that loosen the constraints of tumour attack by the immune system. The study by Landwehr et al. published in a recent issue of the European Journal of Endocrinology describes a patient with an aggressive ACC bearing a germline MUTYH mutation with loss of heterozygosity in the tumour and accumulation of 8-hydroxyguanine in its genomic DNA. The authors managed to establish a novel differentiated cell line from that tumour which bears the stigma of the defective DNA repair mechanism in its genome. The availability of this new cell model inside the expanding toolbox of the ACC cell lines will allow for novel experimental possibilities, in particular for the study of the tumour microenvironment and the response to immunotherapy.

Abstract 2079: Prediction of DDR and other mutation signatures using targeted panels for FFPE samples

Abstract Mutational processes can cause driver mutations and are considered the primary cause of tumorigenesis. Cosmic signatures classify environmental or intrinsic mutational processes. Identification of signatures including DNA Damage Response (DDR) signatures enables research into the origin of cancer mutagenesis and into treatment optimization. Typically, Mutation signatures are identified using Whole Genome Sequencing or Whole Exome Sequencing. We demonstrate signature prediction of mutation signatures with two amplification-based targeted panels, which have a high sequencing success rate for FFPE samples. ~2000 FFPE Samples from a pan-solid tumor cohort were sequenced with either of two AmpliSeq panels (OCAplus and OTMLA), sizes 1.4 Mb and 1.7 Mb, to optimize a method to identify mutation signatures. First, we identified somatic SNVs by filtering out likely population germline mutations, and used these to construct the single base change substitution (SBS) matrix. The COSMIC cancer signatures use properties of the whole genome: we normalized to extend signature detection to targeted panel data. We adjusted the mutation frequencies observed using the ratio of trinucleotide counts in the genome and the ratio in the panel. Next, we measured the cosine similarity between the normalized sample and the COSMIC signatures. We selected the signatures with a strong match (&amp;gt;0.7) to the normalized sample. We further impute the signatures using a reduced candidate set, to assess the signature fit in the sample and reduce false positives. These steps provide the optimized signatures. We detected optimized signatures in 33% of the samples. A single signature was detected in 9% of the samples, 2 signatures in 6%, and &amp;gt;2 signatures in 17% of the samples. ~3% of samples showed at least one MMR signatures (SBS6, SBS14, SBS15, SBS20, SBS21, SBS26 and SBS44). In all 10 OCAPlus samples with MMR signatures, we also detected mutation(s) in an MMR gene. APOBEC signatures, SBS2 and SBS13, were observed in 3% of samples sequenced with OCAPlus panel and TML panel. We found 3 samples showing HRR signature SBS3. We successfully identified the putative causal DDR mutation in a number of samples. For example, of 62 samples with NTHL1 mutations, 60 had NTHL1 related signature SBS30. A sample with MUTYH mutations was assigned the SBS36 signature. We sequenced matched Tumor/Normal pairs; in most cases, the tumor sample showed a stronger mutational signature, with their corresponding normal sample showing either no signature or a weaker matching signature. We assessed reproducibility of the mutational signature. Looking at duplicate and triplicate replicates, we found that replicates consistently displayed the same mutational signatures. We show identification of mutation signatures using targeted panels designed for FFPE samples. Citation Format: Fiona Hyland, Ajithavalli Chellappan, Chintan Vora, Shilpa Nair, Jagannath Patro, Ritika Raj, Rushikesh Kanap. Prediction of DDR and other mutation signatures using targeted panels for FFPE samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2079.