PMS2 Mutations Research Articles

Biallelic Mismatch Repair Deficiency in Children and Adolescents: A Review of Published and Unpublished Data from India—Need for an Indian Consortium

Abstract Introduction Biallelic mismatch repair deficiency or constitutional mismatch repair deficiency (CMMRD) is a rare and aggressive pediatric cancer predisposition syndrome that occurs as a result of homozygous (biallelic) pathogenic variants in mismatch repair genes. The primary malignancies that occur in CMMRD are mainly hematological and brain malignancies. Most published data are from the western populations and the Middle East. Data from India are limited to case reports. We performed an analysis to determine the prevalence of CMMRD in the Indian population. Materials and Methods All children aged less than 18 years with a diagnosis of CMMRD from various centers in India were included. CMMRD confirmed using genetic, molecular, and clinical criteria by an international consensus was included in the analysis. Literature search and data submitted by individual centers were reviewed. Results The analysis revealed that 22 children had genetically confirmed CMMRD. The median age of the cohort was 6.5 years, with a male predominance (male:female, 2:1). The classical phenotype of café-au-lait macules was observed in 72.7 % of subjects. The most common pathological variant was found in the PMS2 gene, which accounted for 77.3 % of children. Hematological malignancy (T cell acute lymphoblastic leukemia) was the most common primary malignancy in our study that occurred at a median age of 5 years (interquartile range 4–6 years) followed by brain tumors. The age at initial presentation for CMMRD with mutations in MSH2, MSH6, and PMS2 was 5.4, 4, and 7.5 years, respectively. Conclusion The diagnosis of CMMRD requires a high index of suspicion for the early diagnosis, management, surveillance, counseling, and testing of family members. The awareness about CMMRD in clinicians is important so that diagnosis is made early, and a second malignancy is detected and treated early. The need for an Indian consortium to determine the actual burden of the disease, genetic characteristics, and course of illness in our country has been emphasized.

PMS2 mutation spectra in Norway and risk of cancer for carriers of pathogenic variants

BackgroundIn Norway, we have offered testing of PMS2 since 2006, and have a large national cohort of carriers. The aim of this study was to describe all PMS2 variants identified, and to describe frequency, spectrum and penetrance of cancers in carriers of class 4/5 variants.MethodsAll detected PMS2 variants were collected from the diagnostic laboratories and reclassified according to ACMG criteria and gene specific guidelines. Data on variant, gender, cancer diagnosis, age at diagnosis, and age at last known follow-up was collected on all carriers of class 4/5 variants from electronic patient records. The Kaplan-Meier algorithm was used to calculate cumulative risk of any cancer, colorectal cancer and endometrial cancer.ResultsIn total, 220 different PMS2 variants were detected. Twenty nine class 4/5 variants were identified in 482 carriers. The most common pathogenic variant was the founder mutation c.989-1G > T, detected in 204 patients from 58 families. Eighty seven out of 482 (18.0%) had been diagnosed with colorectal cancer, 10 of these (11.8%) before 40 years. Cumulative risk at 70 years in our cohort was 34.7% for colorectal cancer and 26.1% for endometrial cancer.ConclusionsAfter 15 years of genetic testing, 29 different class 4/5 variants have been detected in Norway. Almost half of Norwegian PMS2 carriers have the founder variant 989-1G > T. Penetrance of colorectal cancer in our cohort was moderate but variable, as 11.5% of those diagnosed were younger than 40 years.

Long-term survivors in 976 supratentorial glioblastoma, IDH-wildtype patients.

Glioblastoma, isocitrate dehydrogenase (IDH)-wildtype is the most aggressive glioma with poor outcomes. The authors explored survival rates and factors associated with long-term survival in patients harboring a glioblastoma, IDH-wildtype. In an observational, retrospective, single-center study, the authors examined the medical records of 976 adults newly diagnosed with supratentorial glioblastomas, IDH-wildtype between January 2000 and January 2021. They analyzed clinical-, imaging-, and treatment-related factors associated with 2-year and 5-year survival. The median overall survival was 11.2 months (12.2 months for patients included after 2005 and the introduction of standard combined chemoradiotherapy). The median progression-free survival was 9.4 months (10.0 months for patients included after 2005). Overall, 17.6% of patients reached a 2-year overall survival, while 2.2% of patients reached a 5-year overall survival. Furthermore, 6.6% of patients survived 2 years without progression, while 1.1% of patients survived 5 years without progression. Two factors that were consistently associated with 2-year and 5-year survival were first-line oncological treatment with standard combined chemoradiotherapy and methylated O6-methylguanine-DNA methyltransferase promoter. Other factors that were significantly associated with 2-year or 5-year survival were age at diagnosis ≤ 60 years, headaches or signs of raised intracranial pressure at diagnosis, cortical contact of contrast enhancement, no contrast enhancement crossing the midline on initial imaging, total or subtotal tumor resection, and a second line of oncological treatment at recurrence. Within 21 cases of 5-year survival, 18 were confirmed to be glioblastomas, IDH-wildtype, and 7 of the 5-year survivors (38.9%) had additional genetic alterations: 3 cases had an FGFR mutation or fusion, 3 cases had a PIK3CA mutation, 1 case had a PTPN11 mutation, and 1 case had a PMS2 mutation in the context of constitutional mismatch repair deficiency syndrome. Five-year overall survival in patients with glioblastoma, IDH-wildtype is extremely low. Predictors of a longer survival are mostly treatment factors, emphasizing the importance of a complete oncological treatment plan, when achievable. Glioblastoma, IDH-wildtype 5-year survivors could be screened for actionable targets in case of recurrence.

Lynch Syndrome and Thyroid Nodules: A Single Center Experience.

Lynch syndrome (LS) is a genetic disease with increased risk of colorectal cancer and other malignancies. There are few reported cases of thyroid cancer in LS patients. The aim of this study is to investigate the presence of thyroid nodules in LS patients and to explore their association with the genetic features of the disease. A retrospective and descriptive analysis was conducted to include all LS patients followed at the CEMAD (Centro Malattie Apparato Digerente) of Fondazione Policlinico Universitario A. Gemelli IRCCS. The characteristics of LS disease, gene mutations, and previous history of thyroid disease were evaluated. Majority of patients underwent thyroid ultrasound (US), and nodule cytology was performed when needed. Of a total of 139 patients with LS, 110 patients were included in the study. A total of 103 patients (74%) underwent thyroid ultrasound examinations, and 7 patients (5%) had a previous history of thyroid disease (cancer or multinodular goiter). The mean age was 51.9 years. Thyroid nodules were found in 62 patients (60%) who underwent US, and 9 of them (14%) had suspicious features of malignancy, inducing a fine-needle aspiration biopsy. A cytologic analysis classified 7 of 9 cases (78%) as TIR2 and 2 (22%) as TIR3a. Between patients with nodular thyroid disease (single nodule, multinodular goiter, and cancer), most of them (25 patients, 36% of total) were carriers of the MSH6 mutation, while 22 (32%), 17 (24%), and 5 (7%) had MSH2, MLH1, and PMS2 mutations, respectively. A high prevalence of thyroid nodules was found in patients with LS, especially in MSH6-carrying patients. Performing at least one thyroid ultrasound examination is suggested for the detection of nodular thyroid disease in LS patients. Systematic investigations are needed to estimate their prevalence, features, and risk of malignant transformation.

HGG-01. DURABLE RESPONSE TO IMMUNOTHERAPY IN AN ADOLESCENT PATEINT WITH CONSTITUTIONAL MISMATCH REPAIR DEFICIENCY CMMRD AND SYNCHRONOUS THREE PRIMARY MALIGNANCIES

Abstract BACKGROUND Familial Cancer Syndrome FCS is of particular concern in Saudi Arabia due to the high rates of consanguinity. Constitutional mismatch repair deficiency Syndrome (CMMRD) is an autosomal recessive FCS with a wide spectrum of malignancies Caused by Biallelic germline mutations in one of 4 mismatch repair genes (MLH1, PMS2, MSH2, and MSH6). METHODS we report 13 yr. Saudi boy, previously healthy with multiple café-au-lait (CAL) macules, and Consanguineous parents with a positive family history of Malignancy. presented with progressive headache, vomiting, abdominal pain, weight loss, and microcytic anemia. MRI Brain showed a Large left hemispheric necrotic mass, MRI abdomen: Circumferential gastric body wall thickening Distal transverse colon intraluminal polypoid mass, and liver hypodense lesion. He had a Resection of the brain tumor and Upper GI endoscopy + colonoscopy with polypectomy: which showed an Ugly gastric ulcer, and multiple colonic polyps. RESULTS Brain tumor molecular pathology: Gliosarcoma WHO grade 4 with negative IHC expression in PMS2 protein, hypermutant tumor with somatic PMS2 ATRX, TP53, NFI, and PIK3R1 genes mutation. stomach biopsy confirmed invasive gastric adenocarcinoma and Colonic polyp biopsy: Tubulovillous adenoma. Genetic testing Detect pathogenic Biallelic germline PMS2 mutation. He received adjuvant focal Brain radiation therapy 59.4Gy/33 F concurrent with immunotherapy (PD-1) inhibitor Nivolumab. Follow-up Abdominal imaging showed excellent response to immunotherapy with no significant residual lesion. MRI of the brain showed surgical bed multi-cystic lesions with thick nodular enhancement suggestive either of radiation necrosis vs. progressions/pseudoprogression. repeated MRI confirmed further progression of the enhancing surgical cavity lesion which was unresectable. CTLA-4 Inhibitor ipilimumab was added to Nivolumab to optimize therapy. UpToDate our patient is clinically stable on Maintenance Nivolumab with no side effects. CONCLUSION Our case confirms immunotherapy’s efficacy for treating CMMRD-related cancers, which can improve survival while reducing toxicity from less effective conventional therapies.

Abstract PO2-20-10: Exceptional long-term disease control on pembrolizumab monotherapy in a patient with TMB-high PMS2-mutated MMR-deficient triple negative breast cancer brain metastasis

Abstract Introduction The brain is among the most common sites of breast cancer (BC) spread. Prognosis of BC brain metastasis (BCBM) differs by receptor subtype, with poorest median overall survival (OS) for triple-negative (TN) BCBM at under 5 months. Though treatment guidelines have evolved in recent years, most strategies have focused on local therapies including surgery and stereotactic radiotherapy (SRT), rather than on systemic agents. The 2020 FDA approval of pembrolizumab (pembro) for patients (pts) with metastatic high-tumor mutational burden (TMB-h, ≥ 10 mutations/megabase) solid tumors, agnostic of primary site, combined with clinical trials in melanoma reporting efficacy of immune checkpoint inhibitors (ICI) against BM, suggest a potential use of ICI for pts with TMB-h BCBM. Results of the TAPUR study supported modest therapeutic benefit of pembro for 28 pts with metastatic BC selected for TMB-h, with median OS of 30.6 weeks, but did not include pts with active BCBM. TMB-h is uncommon in BC, and further genomic signatures remain to be elucidated to identify pts with BCBM responsive to ICI. We present a remarkable case of a pt with Lynch Syndrome (LS) due to a germline PMS2 mutation, who developed TMB-h, mismatch repair (MMR)-deficient TN BCBM, and has maintained stable disease for over 6 years on pembro monotherapy. Case description A 62-y.o. woman underwent screening mammography that identified a right breast mass. Pt has a family history of a mother with uterine and pancreatic cancer, and father with bladder cancer. Biopsy confirmed invasive ductal carcinoma (IDC), grade 1 (G1), ER/PR-positive, HER2 score 0. She underwent partial mastectomy, axillary dissection, radiation, and received adjuvant anastrozole. Three years later, while still on anastrozole, she presented with a 6 cm right breast mass. Mastectomy disclosed G3, ER/PR-negative, HER2-positive (3+, Her2:CEP17 ratio 5.6) IDC. She received adjuvant chemotherapy (AC-T) and 1 year of trastuzumab. Seven years later, pt presented with headaches and word finding difficulties. MRI identified a 3.6 cm frontal mass, which biopsy revealed as TN BCBM. Systemic imaging ruled out distant metastases. Pt proceeded with SRT and exemestane (despite receptor staining ER- in case of a possible false negative result). Despite radiotherapy, pt had BCBM progression within the same year with the largest mass diameter grown to 4.8 cm. Resection (followed by SRT) identified the dominant histology as G3 TNBC. Following transition of care to our institution, germline testing revealed a pathogenic mutation in PMS2 (c943C >T). Tumor sequencing of the resected brain metastasis showed TMB of 48 and MMR deficiency. Therefore, systemic therapy with pembro monotherapy was initiated and maintained with good tolerability. Two years later, concern for progression from rising tumor markers led to addition of concurrent carboplatin/gemcitabine for 5 cycles. Imaging and tumor markers stabilized, and pt returned to pembro monotherapy. Today, 3 years later, and over 6.5 years after initial TN BCBM diagnosis, pt continues to have stable disease on pembro with an excellent performance status (ECOG 0) and no evidence of intracranial or extracranial progression. Discussion We document an exceptional case of prolonged benefit to pembro in a pt with TMB-h PMS2-mutated MMR-deficient TN BCBM. This case highlights two major pragmatic points to clinical practice; (i) the significance of germline testing in all pts with metastatic BC, and (ii) the impact of molecular testing of tumor tissue to identify rare alterations which may have dramatic effects on pt outcomes. Altogether, this case is a remarkable addition to growing evidence that TMB could be a biomarker for predicting response to ICI therapy and provides an example of ICI efficacy in the setting of BCBM. Further research on additional genomic, clinical, and pathologic features associated with ICI responsiveness is warranted for greater precision in BCBM management. Citation Format: Jaeyoon Cha, Albert Grinshpun, Lauren Buckley, Brian Alexander, Sara Tolaney, Nancy Lin. Exceptional long-term disease control on pembrolizumab monotherapy in a patient with TMB-high PMS2-mutated MMR-deficient triple negative breast cancer brain metastasis [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-20-10.

Abstract 5615: Functional analysis of variants of uncertain significance in the MSH6 mismatch repair gene

Abstract Lynch syndrome (LS) is a hereditary condition that increases patients’ lifetime risk of cancer, primarily colorectal cancer. LS is caused by germline mutations in mismatch repair (MMR) genes, MLH1, MSH2, MSH6, and PMS2. Identification and classification of these mutations is important in LS diagnosis for guiding treatment plans and preventative care for patients’ and their families. However, the consequences of some variants in these genes are not immediately obvious, granting them classification as variants of uncertain significance (VUS). Laboratory functional analysis to determine whether these variants disrupt MMR function in human cells can provide important evidence for understanding the pathogenicity of VUS and reclassifying them. Half of known variants in the MMR gene MSH6 are VUS and, thus, the goal of my project is to provide evidence for a subset of these variants to help provide evidence for reclassification for these variants. We are calibrating and validating functional assays for MSH6 variants, using known MSH6 pathogenic and benign controls. We will then test MSH6 VUS identified in patients as reported in the InSiGHT database, ClinVar database, and current literature. We are using CRISPR gene editing to recreate these variants in the endogenous MSH6 loci in human embryonic stem cells (hESC). Using these edited hESC lines we are examining the impact of the variants on RNA and protein stability, repair of DNA microsatellites, which is a hallmark of normal MMR function, and induction of the MMR-dependent DNA damage response. With this compilation of data, we will convert the results into a quantitative Odds of Pathogenicity value. This Odds of Pathogenicity score can be used by expert variant interpretation committees to help readily reclassify these variants and provide a clearer diagnosis for these suspected Lynch syndrome patients. Citation Format: Elizabeth Szabo, Emily Blackburn, Alexander Radecki, Abhijit Rath, Christopher Heinen. Functional analysis of variants of uncertain significance in the MSH6 mismatch repair gene [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 5615.

Abstract IA013: Unique metabolic changes in Lynch syndrome-associated endometrial cancer

Abstract Lynch syndrome-associated endometrial cancers (ECs) are defined by germline mutations in DNA mismatch repair genes, including MSH2, MSH6, PMS2, and MLH1. Lynch syndrome (LS) tumors have received increased attention in the therapeutic context as these tumors are microsatellite instable and often reflect increased immune cell infiltration and enhanced response to immunotherapy. However, relatively little attention has been paid to pathogenesis of LS ECs. Women with LS represent an at-risk population who could benefit from cancer interception strategies due to a 60% cumulative lifetime risk of developing EC. We developed a mouse model of MSH2 loss targeted to the uterus to evaluate EC pathogenesis, with the goal of elucidating mechanisms that alter disease penetrance for women with hereditary risk for EC development. Our Progesterone Receptor-Cre Msh2f lox/flox mice (abbreviated Msh2KO) develop ECs that closely mimic human EC. Whole transcriptome profiling of Msh2KO EC and Msh2KO normal endometrium compared to wild-type endometrium identified “Mitochondrial dysfunction” as a significantly altered pathway in Msh2 deficiency, prompting our in-depth evaluation of mitochondrial alterations in Msh2KO mice, MSH2-deficient cell lines, and LS-associated EC patient specimens. We will discuss the impact of MSH2 deficiency across multiple measures of mitochondrial content, integrity, function, and metabolomic analyses in ECs using preclinical models and human tissue studies. Overall, our studies reveal that MSH2-deficient EC is characterized by mitochondrial DNA damage, mitochondrial content reduction, and decreased mitochondrial function. In addition, decreased mitochondrial respiration for energy production facilitates metabolic reprogramming toward glycolysis. We are conducting further studies to define mechanisms underlying mitochondrial defects due to MSH2 loss and opportunities for intervention. Mitochondrial and metabolic aberrations could serve as novel biomarkers for EC development and targets for cancer prevention in women with LS. Citation Format: Melinda S. Yates. Unique metabolic changes in Lynch syndrome-associated endometrial cancer [abstract]. In: Proceedings of the AACR Special Conference on Endometrial Cancer: Transforming Care through Science; 2023 Nov 16-18; Boston, Massachusetts. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(5_Suppl):Abstract nr IA013.

Abstract C086: NP1867, a potent, selective, covalent small molecule inhibitor of DNA Mismatch Repair (MMR) protein PMS2, functionally inhibits MMR in cells and elicits COSMIC mutational signatures consistent with MMR-deficient patient samples

Abstract Two complementary mechanisms safeguard genome fidelity during DNA replication: DNA polymerase proofreading and DNA mismatch repair (MMR). DNA polymerase proofreading or MMR deficiencies can occur independently or, more rarely, simultaneously; loss of function of either or both pathways leads to the accumulation of DNA mutations. Lynch Syndrome is caused by mono-allelic germline mutations in MMR genes MLH1, MSH2, MSH6 or PMS2. Gene expression from the wild-type allele elicits sufficient MMR activity until a second hit somatic mutation inactivates the wild-type allele leading to MMR deficiency (MMR-d). Constitutional mismatch repair deficiency (CMMRD) syndrome is an inherited early onset cancer predisposition syndrome resulting from biallelic germline mutations in MLH1, MSH2, MSH6 or PMS2. MMR-d cancers are commonly and typically characterized by accumulation of single nucleotide variants (SNVs) and insertions or deletions (indels) amongst repetitive DNA sequences - microsatellite instability (MSI); importantly, such mutations occur at higher rates in genetically unstable tumour cells under replicative stress than in normal cells. Cancers that harbour >40% microsatellite variations (positive for two or more of five clinically tested microsatellite markers) are described as MSI-high (MSI-H). Importantly, MMR-d, MSI-H tumours are now eligible for immune checkpoint therapy, irrespective of tissue type, providing substantial patient benefit and a major advance in cancer treatment. This clinical context is consistent with the hypothesis that MMR-d elicits an immunogenic state. However, there is an unmet need for chemical tools to explore the role of therapeutic MMR inhibition alongside immune checkpoint blockade. Here, for the first time, we demonstrate that NP1867 is a potent, selective small molecule inhibitor of the Gyrase, Hsp90, Histidine Kinase, MutL (GHKL) family endonuclease PMS1 Homolog 2, Mismatch Repair System Component (PMS2). We demonstrate by biochemical, biophysical, and protein-ligand X-ray crystallographic methods that NP1867 binds irreversibly to the ATP binding site of the N-terminal ATPase domain of PMS2. NP1867 displays potent binding to PMS2 in a NanoBRET cellular target engagement assay and inhibits MMR activity in cell-based assays of MMR-dependent DNA repair. NP1867 displays minimal off-target binding in broad biochemical screening panels including kinases and ATPases. Treatment of MMR-proficient, colorectal cancer cell lines with NP1867 increases tumour mutational burden and generates COSMIC mutational signatures consistent with MMR-d patient samples demonstrating, for the first time, that acute inhibition of PMS2 with a small molecule phenocopies the epigenetic silencing and/or genetic loss of MMR observed in patients. We characterise cell- and tissue-based target engagement, and in vivo pharmacokinetic and pharmacodynamic properties of NP1867 to inform optimal use by the research community for further exploring PMS2 and MMR function. Citation Format: Julian Blagg, Philippe Riou, Alexia Hervieu, Eleonora Piumatti, Giuseppe Rospo, Sasi Arunachalam, Bettina Meier, Sam Weeks, Maria Rodriguez, Kalpesh Parmar, Pradip Patel, Adam Peall, Paige Tongue, Tess McLaren, Robert Workman, Ruzica Bago, Stuart Robjohns, Rebecca Beaumont, Mike Briggs, Gareth Langley, Charles Nichols, David Clark, Paul Winship, Benoit Rousseau, Matthew Baker, Martin Drysdale, Giovanni Germano, Alberto Bardelli. NP1867, a potent, selective, covalent small molecule inhibitor of DNA Mismatch Repair (MMR) protein PMS2, functionally inhibits MMR in cells and elicits COSMIC mutational signatures consistent with MMR-deficient patient samples [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C086.

Routine Whole Genome Sequencing for All Children with Hematological Malignancies Defines a New Standard of Care - Data of the First 152 Cases from the NHS England Genomic Medicine Service

Background There is emerging evidence that whole genome sequencing (WGS) can benefit children with hematological malignancies, even when compared to extensive molecular assays. However, studies have been restricted to selected patient groups, and so there is a need to evaluate the feasibility and impact of WGS delivered as part of children's routine care. In England, following the 100k genome project, since early 2021 paired germline and tumor WGS has been made available to all children with a suspected malignancy via the nationalized Genomic Medicine Service. We set out to assess the real world impact of routine WGS, where sequential unselected children were sequenced, and results were used in clinical practice. Methods Clinical and diagnostic information was collected from all patients presenting to Great Ormond Street Hospital (GOSH) hematology department over a 2-year period. WGS findings were superimposed onto the center's standard of care (SOC) and WGS impact was evaluated. Results Between 1 January 2021 and 31 December 2022, 152 children with new diagnoses or relapsed disease had paired WGS, with an uptake rate of 83% (76/92) in the first year and (79/83) 95% in the second. Barriers to recruitment were clinicians not offering WGS (n=16) in year 1, and early death (n=2) or parents declining consent (n=2) in year 2. WGS was performed for all 20 diseases that were treated (Figure 1). Importantly, WGS matched all SOC findings by other genetic tests, including targeted DNA high throughput sequencing (HTS) and RNA-fusion panels. WGS revealed additional oncogenic drivers in 79/152 (52%) of patients, compared to all other genomic tests (including HTS and RNA-fusion panels). WGS aided diagnosis in 11% (17/152) of cases through picking up a novel lesion that defined the child's malignancy, and for 7% (10/152) of patients, it was able to place them into a new formal cytogenetic risk category. In 25/152 (17%) cases care was changed solely because of WGS (Figure 2), with a similar rate in year 1 (14%) and 2 (17%). In 3 cases of B-acute lymphoblastic leukemia (B-ALL) diagnostic testing failed to reveal a risk-defining lesion but WGS identified good risk variants (ETV6-RUNX1 and High Hyperdiploidy) allowing de-escalation of chemotherapy. IGH-DUX4 re-arrangements, solely picked up by WGS in 2 cases of B-ALL, led to 1 child not receiving escalated chemotherapy. In a child presenting with mixed phenotype leukemia, WGS alone revealed a KMT2A-USP2 fusion, which directed therapy, as well as providing an MRD marker. In 12 patients presenting with marrow failure (subsequently diagnosed with aplastic anemia or MDS), WGS was prioritized with a median turnaround time of 2 weeks. WGS was able to give an accelerated diagnosis, facilitating timely therapy. 9 children were found to have pathogenic germline variants. This included 2 cases of an accelerated diagnosis of expected mutations (e.g. an SBDS mutation). Other unexpected germline mutations (e.g. a TP53 mutation presenting with leukemia, and an incidental PMS2 mutation in the context of aplastic anemia), led to cascade testing for patients and their families, and tailored surveillance programs. WGS made 9 children eligible for novel therapeutics, including patients found to have a RAS pathway mutation solely by WGS, and patients who were hypermutated. Conclusion WGS can successfully be delivered as a nationalized genomics medicine service, for all children with suspected hematological malignancies. WGS can match conventional and advanced genomic diagnostics in a single assay, with obvious economic benefits of test consolidation. Beyond this, it delivers additional germline and somatic findings that aid diagnosis, offer therapeutic opportunities, and tangibly change the care patients and families receive. WGS has the additional benefit of future proofing diagnostic and research capabilities, as over time analysis pipelines can be modified and new variants added. For all children presenting with marrow failure, WGS was practice changing, providing all necessary read-outs, and facilitating timely therapy. In the case of the most common childhood malignancy, ALL, one test can replace all diagnostics, including IG/TCR MRD marker screening and pharmacogenomics for TPMT/NUDT15. With continued improvements in turnaround time, and reducing costs, we propose that WGS could feasibly replace multiple molecular diagnostic tests for pediatric hematological malignancies.

Genetic analysis of fundic gland‑type gastric adenocarcinoma.

This study aimed to analyze the molecular characteristics of gastric adenocarcinoma of the fundic-gland type (GAFG) and explore the possible mechanism of tumor development. Samples from 10 Chinese patients with GAFG were collected at the Peking University International Hospital and Liaocheng People's Hospital between January 2015 and March 2022. The nucleic acid sequence of Epstein Barr virus-encoded RNA (EBV-EBER) was detected by in situ hybridization. Genetic mutation information for GNAS, KRAS, NRAS, BRAF, PIK3CA, TP53, APC, CTNNB1, HER2, MLH1, MSH2, MSH6, and PMS2 was obtained by Next-Generation Sequencing, and the relevant literature was reviewed. A total of eight instances of missense mutations were detected, consisting of seven cases with GNAS mutations, two cases with KRAS mutations, and one case with a TP53 mutation. Additionally, two patients had simultaneous missense mutations in GNAS and KRAS. Nonsynonymous mutations in APC, CTNNB1, NRAS, BRAF, PIK3CA, HER2, MLH1, MSH2, MSH6, or PMS2 were not observed in any cases. In addition, all tumors were EBER-negative. GAFG exhibits diversity at the molecular level, and GNAS mutations are more common than KRAS mutations, TP53 mutations, and microsatellite instability. To date, no association between EBV/HER2 and GAFG has been found.

Recto-Sigmoid Synchronous Malignant Tumor with Lack of MLH1 and PMS2 Expression: Case Report and Literature Review

Abstract Background: Synchronous colorectal cancers are defined by the presence of at least two cancers (primary self-standing tumors) in the same time, in the same patient. In these conditions, the tumor with the maximum diameter has nomenclatures such as “primitive”, or “index”. The preoperative diagnosis of synchronous tumors is very important, as it can turn into metachronous tumors, which require a new surgical intervention. Case report: In the following, we report a case of a 54 year-old patient without any related oncological family history but with important cardiovascular comorbidities, who has been operated for stenotic synchronous cancer of the recto-sigmoid junction and middle rectum. During the initial work-up, no liver or peritoneal metastases were noted on the CT scan. The surgical intervention opted for was a recto-sigmoid laparoscopic with subtotal mesorectal excision followed by a termino-terminal mechanical stapled colorectal anastomosis. The histopathological examination showed both lesions to be moderately differentiated (G2) adenocarcinomas, with subserosal invasion in 2 of the 12 detected lymph nodes. Immunohistochemistry further revealed microsatellite instability, with MLH1 and PMS2 mutation. Conclusion: The literature review highlights certain particular aspects regarding the clinical, surgical and morphological management of such cases compared to cases with single tumor. The peculiarity of this case was laposcopic resection of the colon segment, and the microsatellite instability of the specimen, assessed by ancillary studies. Early preoperative diagnosis of synchronous tumors allows the selection of appropriate therapeutic management, depending on their location at the level of the affected colonic segments.

HGG-27. THE IMPACT OF MISMATCH REPAIR DEFICIENCY ON GLIOMAS IN CHILDREN, ADOLESCENTS, AND YOUNG ADULTS; A REPORT FROM THE IRRDC AND THE GLIOMA TASK FORCE

Abstract Mismatch repair deficiency (MMRD) is a pan-cancer mechanism resulting in universal hypermutation. MMRD-gliomas are resistant to chemoradiation but respond to immunotherapy. MMRD can occur somatically or be inherited as part of Lynch Syndrome (LS) or Constitutional Mismatch Repair Deficiency (CMMRD). However, the prevalence of MMRD in gliomas of children, adolescents, and young adults (CAYA), and impact of germline inheritance is unknown. We utilized functional genomic tools on population-based and validation cohorts from 3 large databases (Toronto, St-Jude and CBTN) to determine the prevalence, subgroup, and impact of germline mutations on MMRD-gliomas. Ongoing data on 998 pediatric-gliomas from Toronto reveals that MMRD is extremely rare in pediatric low-grade gliomas (PLGG) but common in pediatric high-grade gliomas (PHGG) (9%, p<0.0001). Similarly, data from St-Jude and CBTN (n=374) reveals that MMRD exists only in PHGG (8%). In both cohorts, MMRD-PHGG are enriched for RAS/MAPK, IDH, and TP53 mutations while pediatric-type fusions, BRAF-V600E and histone mutations are absent. In AYA-HGG (n=884), the most common groups include glioblastomas without chromosome-7/10 alterations (9%) and IDH1-astrocytomas, while MMRD is not present in IDH-oligodendrogliomas. All but 1 CAYA-MMRD-gliomas harbored germline MMR mutations. Data from the IRRDC on 174 patients reveal that LS is more common than CMMRD in gliomas, with the median age of onset 11 and 29 years in CMMRD and LS, respectively (p<0.001). Furthermore, CMMRD gliomas are commonly caused by germline PMS2 and MSH6 mutations, enriched for secondary polymerase mutations (60%, p<0.001), and exhibit ultra-hypermutation. In contrast, LS-gliomas are caused by MSH2 and MLH1 mutations, and enriched for IDH1 mutations (32%, p<0.025) with a lower mutational burden. Our data reveals high prevalence of MMRD in CAYA-HGG with alarming impact of germline predisposition. Specifically, unrecognized LS patients with AYA MMRD-HGG. These findings support universal screening for MMRD in HGG to identify patients for immunotherapy and surveillance.

Abstract B054: Inherited mutations of DNA damage repair genes in a racially diverse cohort of men with prostate cancer

Abstract Introduction: DNA damage repair genes (DDRGs) play an important role in genomic stability and mutations in DDRGs contribute to clinically significant prostate cancer (PCa). However, the association of germline mutations in DDRGs with PCa progression and therapeutic stratification remain to be defined in African American (AA) men. Our objective was to genomically profile all known DDRGs and provide ancestry specific findings, focusing on PCa patients with African ancestry. Methods: Germline mutations in all DDRGs (N=276) was evaluated by whole genome sequence (WGS) analysis of archived blood DNA samples from 600 PCa patients (300 AA and 300 CA) who underwent primary treatment at Walter Reed National Military Medical Center. The WGS mean coverage exceeded 37x. Principal Component Analysis using the Peddy program was conducted, and ancestry prediction was based on a machine learning approach using 1000G as reference. Variant frequencies in CPDR PCa patients were compared to variant frequencies available from the Exome Aggregation Consortium (ExAC) controls with no PCa. Data analysis approaches included single variant association, gene-based total frequency test and clinico-pathological associations for germline mutations. All statistical tests were two-sided, and FDR adjusted. FDR < 0.05 was set as significance threshold. Results: Comprehensive analysis of 276 DDRGs revealed that germline mutation (Pathogenic/Likely Pathogenic; P/LP) carrier rate was 23.5%, which is three times higher than reported before in both AA and CA men, due to our unbiased WGS approach. We found that only 13 of the 46 DDRGs identified with P/LP mutations were common to AA and CA men, demonstrating clear disparity along ancestry lines. Importantly, RAD family genes (RAD54L, RAD54B, RAD51), which are potentially targetable, as well as PMS2 and BRCA1, were among the most frequently mutated DDRGs in AA, but not in CA men. Germline mutations in RAD51 and PMS2 were enriched in AA cohort as compared to CA men (P 0.01 and 0.03 respectively), while germline mutations in FANCA were significantly enriched in CA cohort (P < 0.01). Pathway analysis showed that the HR pathway (with 15 mutations) was associated with faster disease progression to biochemical recurrence (BCR) (P <0.05), while the NHEJ pathway (with three mutations) was found to be marginally associated with metastasis (p <0.05). Additionally, we found that germline mutations in DDRGs was associated with shorter time to BCR (P <0.05) in AA patients, but not in CA men. Conclusion: Our findings highlight distinct DDRG germline mutation profile across AA and CA prostate cancer men. This may help refine patient stratification for specific targeted therapeutic options especially for under-studied AA men. Future replication studies in an independent patient cohort are warranted to validate our findings. Citation Format: Indu Kohaar, Xijun Zhang, Gregory Chesnut, Clifton Dalgard, Matthew D. Wilkerson, Gyorgy Petrovics. Inherited mutations of DNA damage repair genes in a racially diverse cohort of men with prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B054.

Molecular and immune profiling of TP53-mutated ovarian cancers with non-BRCA1/2 homologous recombination gene alterations.

5579 Background: Molecular alterations in homologous recombination (HR) pathway genes lead to HR deficiency (HRD) in ~50% of high grade serous ovarian carcinomas (HGSOC). The immune microenvironment of BRCA1/2-mutated HGSOC has been extensively characterized, in contrast to tumors with mutations in other HR genes. We evaluated a cohort of epithelial ovarian cancers (EOC) enriched for HGSOC and compared molecular and immune signatures of tumors with BRCA1/2 mutations ( BRCAm) to those with non-BRCA1/2 HR gene mutations (NBHRD). Methods: We characterized 173 EOC by comprehensive genomic and immune profiling (CGIP) using panel-based next-generation DNA (523 genes) and RNA sequencing (384 genes), respectively. We enriched for HGSOC by selecting for TP53 mutations and excluding tumors with non-serous histology or any mutation in POLE, MLH1, PMS2, MSH2, MSH6, or nucleotide excision repair genes. Tumors lacking BRCA1/2-mutations were classified as NBHRD if a reportable mutation was present in canonical HR genes. Mutational burden (TMB, mut/Mb) was estimated from detected SNV/indels. We calculated immune-related expression signatures, including tumor immunogenicity score (TIGS), cellular proliferation (CP), and cancer testis antigen burden (CTAB). PD-L1 expression was assessed by tumor proportion score (TPS) following 22C3 immunohistochemistry. Differences in TMB, TIGS, CP, CTAB, PD-L1 and gene expression rank were tested for using Wilcoxon rank-sum test. Results: Of 173 EOC, 84 cases had complete CGIP, including 11 (13%) BRCAm, 7 (8%) NBHRD (Table), and 66 (79%) lacking HR gene alterations. On average, NBHRD tumors harbored lower TMB (4.1±2.3 vs. 6.6±2.3 vs. p=0.03) and elevated TIGS (59.1±16.2 vs. 41.7±16.2 p=0.044) compared to BRCAm tumors. We found no difference in PD-L1 (p=0.21), CP (p=0.26), or CTAB (p=0.48). Expression changes were identified in 32 immune genes, of which 31 (97%) were substantially up-regulated (1.3-3.3 fold) in NBHRD compared to BRCAm tumors. Conclusions: Our findings showed our cohort of NBHRD tumors were more immunogenic but less mutagenic than BRCAm tumors, implying enhanced immunogenicity unrelated to neoantigen load. Given that immune checkpoint inhibitors have shown limited efficacy in ovarian cancer, our data suggest NBHRD tumors may have stronger and possibly distinct immune escape mechanisms compared to BRCAm tumors. [Table: see text]

Healthcare utilization among individuals diagnosed with lynch syndrome through a universal germline genetic testing program.

10603 Background: Most individuals with Lynch syndrome (LS) are unaware of their risk. Criteria-based testing will not close this gap as it fails to identify ~50% of mutation carriers. Universal germline testing (GT) for in oncology stands to identify more mutation carriers and advance cancer control. However, the clinical utility of universal germline testing is unknown. Methods: The enterprise-wide City of Hope INSPIRE study offers all consented patients GT for cancer susceptibility (155 genes) and actionable disorders (59 genes). We used an informatics approach to evaluate healthcare utilization for patients found to have MLH1, MSH2, MSH6, PMS2 or EPCAM mutations. We queried codified data elements in our electronic data warehouse before and after GT (post testing interval: 1-29 months). We binned care as possibly related/ not related to HBOC based on NCCN guidelines. Results: Of 10,814 patients who had GT, 80 (0.74%) had a pathogenic/ likely pathogenic mutation in either MLH1, MSH2, MSH6, PMS2 or a 3’ deletion of EPCAM. The demographic distribution of LS patients was: white (n = 51, 64%), Asian (n = 13, 16%), Hispanic (n = 19; 24%); female (n = 51, 64%); the mean age was 54 yrs. Eighty-six percent (n = 69) had cancer, including 45% with cancers associated with LS (colorectal 17%, endometrial 7%, ovarian 6%, esophageal/stomach 5%, bladder/urinary tract 5%, and prostate 5%) and 41% with cancers that are not associated with LS. Fifty-two percent of all LS patients had procedures, imaging, and/or therapy potentially related to their LS diagnosis. As expected, utilization of colonoscopy, EGD, MRCP/EUS, transvaginal ultrasound, and hysterectomy with bilateral salpingo-oophorectomy (HBSO) occurred both before and after testing for the cancer cohort, with the majority of utilization occurring after testing likely related to their Lynch syndrome diagnosis. Twelve (17%) cancer patients with Lynch syndrome received Immune Checkpoint Inhibitor therapies. In the unaffected cohort, rates of utilization were higher prior to testing for transvaginal ultrasound possibly because 2% underwent a HBSO after their diagnosis and no longer required endometrial surveillance. Rates of colonoscopy, EGD, and HBSO were all higher after GT. Conclusions: We found high levels of relevant healthcare utilization for Lynch syndrome gene mutation carriers in the context of universal GT. However, this initial informatics approach is limited because key information on prior GT and motivations for surgery (e.g., therapeutic vs prophylactic HBSO) are not adequately captured in codified data. Codified EHR queries will need to be augmented by text mining and/or manual chart review to fully capture care and assess the clinical utility of system-wide genetic care delivery interventions.

Abstract 5236: Functional analysis of variants of uncertain significance of the MSH6 mismatch repair gene

Abstract Lynch syndrome (LS) is a hereditary condition that increases patients’ lifetime risk of cancer, primarily colorectal cancer. LS is caused by germline mutations in mismatch repair (MMR) genes, MLH1, MSH2, MSH6, and PMS2. Identification of these mutations is important in LS diagnosis in order to guide treatment plans and preventative care for patients’ and their families. However, the consequences of some variants in these genes are not immediately obvious, granting them classification as variants of uncertain significance (VUS). Half of known variants in the MMR gene MSH6 are VUS and, thus, the goal of my project is to provide evidence to help better determine their pathogenic significance. Laboratory functional analysis to determine whether these variants disrupt MMR function in human cells can provide such evidence toward this goal. We have previously used CRISPR gene editing to recreate variants in the endogenous loci for the MMR genes MSH2 and MLH1 in human embryonic stem cells (hESC) in order to test their effects on MMR function in a cellular environment. We will now use test whether this approach can be used to study MSH6 VUS. Using these edited hESC lines we are examining the impact of the variants on RNA and protein stability, repair of DNA microsatellites, which is a hallmark of normal MMR function, and induction of the MMR-dependent DNA damage response. Using a panel of known MSH6 pathogenic and benign controls, we will calibrate these functional assays in order to associate functional performance with likelihood of pathogenicity. We will next test a separate panel of known controls to validate these assays. Finally, we will examine up to 35 VUS. With this compilation of data, we will convert the results into a quantitative Odds of Pathogenicity value. This Odds of Pathogenicity score can be used by expert variant interpretation committees to help readily reclassify these variants, and provide a clearer diagnosis for these suspected Lynch syndrome patients. Citation Format: Elizabeth Szabo, Emily Blackburn, Patrick Pagano, Abhijit Rath, Christopher Heinen. Functional analysis of variants of uncertain significance of the MSH6 mismatch repair gene. [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 5236.

Mismatch repair-deficient glioma with spatially distinct IDH-mutant and IDH-wild type components arising in the setting of Lynch syndrome.

Pathogenic mutations in MLH1, MSH2, PMS2, and MSH6 compromise DNA mismatch repair mechanisms and in the heterozygous state result in Lynch syndrome, which is typified by a predisposition to endometrial, ovarian, colorectal, gastric, breast, hematologic, and soft tissue cancers. Rarely, germline pathogenic aberrations in these genes are associated with the development of primary central nervous system tumors. We present a report of an adult female with no prior cancer history who presented with a multicentric, infiltrative supratentorial glioma involving both the left anterior temporal horn and left precentral gyrus. Surgical treatment and neuropathological/molecular evaluation of these lesions revealed discordant isocitrate dehydrogenase (IDH) status and histologic grade at these spatially distinct disease sites. A frameshift alteration within the MLH1 gene (p.R217fs*12, c.648delT) was identified in both lesions and subsequently identified in germline testing of a blood sample, consistent with Lynch syndrome. Despite distinct histopathologic features and divergent IDH status of the patient's tumors, the molecular findings suggest that both sites of intracranial neoplasia may have developed as a consequence of underlying monoallelic germline mismatch repair deficiency. This case illustrates the importance of characterizing the genetic profile of multicentric gliomas and highlights the oncogenic potential of germline mismatch repair gene pathogenic alterations within central nervous system gliomas.

Endometrial Carcinomas With Subclonal Loss of Mismatch Repair Proteins: A Clinicopathologic and Genomic Study.

Subclonal loss of mismatch repair (MMR) proteins has been described in a small subset of endometrial carcinomas (ECs), but the genomic basis for this phenomenon has received limited attention. Herein, we retrospectively evaluated all ECs with MMR immunohistochemistry (n=285) for subclonal loss, and in those (n=6), performed a detailed clinicopathologic and genomic comparison of the MMR-deficient and MMR-proficient components. Three tumors were FIGO stage IA, and one each stage IB, II, and IIIC2. Patterns of subclonal loss were as follows: (1) 3 FIGO grade 1 endometrioid carcinomas with subclonal MLH1/PMS2, MLH1 promoter hypermethylation, and no MMR gene mutations; (2) POLE -mutated FIGO grade 3 endometrioid carcinoma with subclonal PMS2, and PMS2 and MSH6 mutations limited to the MMR-deficient component; (3) dedifferentiated carcinoma with subclonal MSH2/MSH6, as well as complete loss of MLH1/PMS2, MLH1 promoter hypermethylation, and PMS2 and MSH6 mutations in both components; (4) dedifferentiated carcinoma with subclonal MSH6, and somatic and germline MSH6 mutations in both components, but with a higher allele frequency in MMR-deficient foci. Recurrences occurred in 2 patients, one consisted of the MMR-proficient component from a FIGO 1 endometrioid carcinoma, while the other was from the MSH6 -mutated dedifferentiated endometrioid carcinoma. At the last follow-up (median: 44mo), 4 patients were alive and disease-free and 2 were alive with disease. In summary, subclonal MMR loss reflects subclonal and often complex genomic and epigenetic alterations, which may have therapeutic implications and therefore must be reported when present. In addition, subclonal loss can occur in both POLE -mutated and Lynch syndrome-associated ECs.

Exome sequencing in a Swedish family with PMS2 mutation with varying penetrance of colorectal cancer: investigating the presence of genetic risk modifiers in colorectal cancer risk.

Lynch syndrome is caused by germline mutations in the mismatch repair (MMR) genes, such as the PMS2 gene, and is characterised by a familial accumulation of colorectal cancer. The penetrance of cancer in PMS2 carriers is still not fully elucidated as a colorectal cancer risk has been shown to vary between PMS2 carriers, suggesting the presence of risk modifiers. Whole exome sequencing was performed in a Swedish family carrying a PMS2 missense mutation [c.2113G>A, p.(Glu705Lys)]. Thirteen genetic sequence variants were further selected and analysed in a case-control study (724 cases and 711 controls). The most interesting variant was an 18 bp deletion in gene BAG1. BAG1 has been linked to colorectal tumour progression with poor prognosis and is thought to promote colorectal tumour cell survival through increased NF-κB activity. We conclude the genetic architecture behind the incomplete penetrance of PMS2 is complicated and must be assessed in a genome wide manner using large families and multifactorial analysis.