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Laura Valle

Publications and source records attributed to Laura Valle.

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Integrating germline and tumor sequencing to improve hereditary cancer diagnosis and care.

A subset of cancers arises due to inherited germline pathogenic variants in specific genes, known as hereditary cancers. These genes typically include tumor suppressors, DNA repair and replication fidelity genes, and occasionally oncogenes. In most hereditary cancer syndromes, Knudson's two-hit hypothesis applies, where a second somatic event inactivates the remaining allele of a tumor suppressor or DNA repair gene, leading to tumorigenesis. Advancements in genome-wide sequencing have significantly enhanced our understanding of the mutational processes involved in hereditary cancers. In particular, the assessment of microsatellite instability (MSI), tumor mutational burden (TMB), and mutational signatures has emerged as a powerful tool for the identification of hereditary tumors. Tumors with high or ultra-high TMB often reflect underlying DNA repair deficiencies, while specific mutational signatures can pinpoint the defective pathway. These tumor mutational features are especially informative in syndromes involving mismatch repair (MMR), homologous recombination (HR), base excision repair (BER), nucleotide excision repair (NER), and polymerase proofreading. Moreover, tumor sequencing aids in the interpretation of germline variants, identifies somatic mosaicism, and helps differentiate hereditary from sporadic cancers. Additionally, tumor molecular features associated with DNA repair deficiencies offer insights into personalized therapies, such as the use of PARP inhibitors for BRCA1/2-deficient tumors and immune checkpoint inhibitors for MMR- and polymerase proofreading-deficient cancers. Tumor profiling also uncovers actionable mutations in oncogenes like RET and VHL, which can be targeted with specific therapies. This review explores the integration of tumor molecular features with germline genetic data to refine diagnosis, risk assessment, and therapeutic strategies in hereditary cancer.

Humans

Comparative Analysis of Somatic and Germline Polymerase Proofreading Deficiencies in Cancer: Molecular and Clinical Implications.

Polymerases ε and δ maintain genome integrity through exonuclease proofreading. Germline and somatic pathogenic variants (PVs) in the exonuclease domain (ED) of POLE and POLD1 impair proofreading, causing hypermutated tumors. Despite shared mutational features that make these tumors highly immunogenic, molecular and clinical distinctions between POLE and POLD1 mutations and between somatic and germline variants remain incompletely understood. We compared the molecular and clinical characteristics of POLE and POLD1 ED PVs (n = 31), assessing their location, pathogenicity, clinical phenotypes, mismatch repair (MMR) status, tumor mutational burden, and signatures. We analyzed 360 proofreading-deficient tumors (source: The Cancer Genome Atlas [TCGA] and Catalogue Of Somatic Mutations In Cancer [COSMIC]) and 70 families (249 individuals) with polymerase proofreading-associated polyposis. All germline and somatic PVs had high AlphaMissense scores (0.87-1) and clustered within or near Exo motifs. Recurrent, nonfounder germline PVs, POLE L424V and POLD1 S478N, showed low/modest REVEL scores. Somatic variants occurred mainly in endometrial cancers (75% of proofreading-deficient TCGA cancers), whereas colorectal cancer predominated in polymerase proofreading-associated polyposis (56% of carriers). Cancer risks and tumor spectra differed between POLE and POLD1 PV carriers. Aggressive hereditary phenotypes were linked to either specific POLE PVs (eg, S297F, V411L, P436R, M444K, A456P, and S461T) or the co-occurrence of germline ED PVs with germline MMR gene PVs. Distinct hypermutator profiles were confirmed for polymerase ε and polymerase δ proofreading deficiencies via unique mutational signatures (Polymerase ε: SBS10a/b, SBS28; Polymerase δ: SBS10c/d). Tumors with combined proofreading and MMR deficiencies had significantly higher tumor mutational burden and a shift in the associated mutational spectra. Unlike POLE, POLD1 ED PVs exhibited haplosufficiency, typically requiring a somatic second hit (eg, loss of heterozygosity) or MMR deficiency to drive hypermutation. In conclusion, differences between POLE and POLD1 and between somatic and germline mutations influence clinical presentation, mutagenic potential, and reliance on cooperating defects in tumorigenesis. These insights advance the understanding of proofreading-deficient cancers, with implications for diagnostics, genetic counseling, and precision oncology.

Humans

Lynch Syndrome

CLINICAL CHARACTERISTICS: Lynch syndrome is characterized by an increased risk for colorectal cancer (CRC) and cancers of the endometrium, ovary, stomach, small bowel, urinary tract, biliary tract, prostate, brain (usually glioblastoma), skin (sebaceous adenomas, sebaceous epithelioma, sebaceous carcinomas, and keratoacanthomas), and pancreas. Cancer risks and age of onset vary depending on the associated gene. Several other cancer types have been reported to occur in individuals with Lynch syndrome (e.g., sarcomas, adrenocortical carcinoma). However, the data are not sufficient to demonstrate that the risk of developing these cancers is increased in individuals with Lynch syndrome. DIAGNOSIS/TESTING: The diagnosis of Lynch syndrome is established in a proband with a germline heterozygous pathogenic variant in MLH1, MSH2, MSH6, or PMS2 or a 3' EPCAM deletion identified by molecular genetic testing, or, rarely, constitutional inactivation of the MLH1 promotor due to methylation identified by DNA methylation analysis. MANAGEMENT: Treatment of manifestations: Polypectomy at the time of colonoscopy; referral to advanced endoscopist for lesions requiring advanced resection techniques; surgical resection of polyps when needed; individualized surgical management for colon cancer based on tumor location, stage, Lynch syndrome-associated gene, age, comorbidity, bowel function, anticipated quality of life, and risk of metachronous CRC; mismatch repair (MMR) testing, microsatellite instability (MSI) testing, and multidisciplinary evaluation for rectal cancer prior to treatment; consider immune checkpoint inhibitor therapy for metastatic or unresectable MMR-deficient or MSI-high tumors; other tumors are managed as in the general population. Prevention of primary manifestations: Risk-reducing hysterectomy with bilateral salpingo-oophorectomy can be considered after childbearing is completed. Prophylactic colectomy prior to the development of colon cancer is generally not recommended for individuals known to have Lynch syndrome because screening colonoscopy with polypectomy is an effective preventive measure. Aspirin therapy has been shown to decrease the risk for CRC in individuals with Lynch syndrome. Surveillance: Colonoscopy with removal of precancerous polyps with frequency and initial screening based on gene involved and family history; annual education for females regarding the symptoms of endometrial and ovarian cancers; consider transvaginal ultrasound examination and endometrial biopsy every one to two years beginning at age 30 to 35 years; consider upper endoscopy examination particularly for individuals with a family history of gastric cancer and those of Asian ancestry with frequency and initial screening based on gene involved and family history; biopsies should be evaluated for H pylori infections so that appropriate treatment can be given as needed; consider capsule endoscopy and small bowel enterography for distal small bowel cancers in symptomatic persons; consider urinalysis with urine cytology annually beginning between ages 30 and 35 years; consider pancreatic cancer screening in individuals with a family history of pancreatic cancer; follow population screening guidelines and maintain awareness for signs and symptoms of other cancers. Agents/circumstances to avoid: Obesity, physical inactivity, cigarette smoking, alcohol consumption, and type 2 diabetes may increase CRC risk in individuals with Lynch syndrome. Evaluation of relatives at risk: Molecular genetic testing for the familial Lynch syndrome-related pathogenic variant is recommended for all first-degree relatives (parents, sibs, and offspring) of an affected individual in order to identify as early as possible those who would benefit from surveillance, risk-reducing interventions, and other preventive measures. Testing for constitutional MLH1 hypermethylation is recommended for all first-degree relatives of individuals with Lynch syndrome caused by constitutional MLH1 methylation. GENETIC COUNSELING: Lynch syndrome caused by a heterozygous germline Lynch syndrome-related pathogenic variant (i.e., a pathogenic variant in MLH1, MSH2, MSH6, or PMS2 or a 3' EPCAM deletion) is inherited in an autosomal dominant manner. Individuals with Lynch syndrome caused by constitutional inactivation of MLH1 by methylation typically represent simplex cases, although affected individuals from a few families have been reported with inherited MLH1 promoter methylation. The majority of individuals with a heterozygous germline Lynch syndrome-related pathogenic variant inherited the pathogenic variant from a parent who may or may not have had cancer. Each child of an individual with Lynch syndrome has a 50% chance of inheriting the Lynch syndrome-related pathogenic variant and the related cancer risks. If the reproductive partner of an individual with Lynch syndrome has a germline heterozygous pathogenic variant in the same Lynch syndrome-related gene, offspring are at risk of inheriting biallelic pathogenic variants and having constitutional mismatch repair deficiency. Once a germline Lynch syndrome-related pathogenic variant has been identified in an affected family member, predictive testing for at-risk asymptomatic family members and prenatal/preimplantation genetic testing are possible.

Hereditary Non-Polyposis Colorectal Cancer (HNPCC)