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Start Over Author "Tao, Lin" Topic exome sequencing
3 results on '"Tao, Lin"'

1. A rare case of TFEB/6p21/VEGFA-amplified renal cell carcinoma diagnosed by whole-exome sequencing: clinicopathological and genetic feature report and literature review.

Author

Zhang R, Ding M, Zhu X, Li X, Hu Q, Tao L, Hu W, and Zou H

Subjects
Humans, Male, Middle Aged, Biomarkers, Tumor genetics, Carcinoma, Renal Cell genetics, Carcinoma, Renal Cell pathology, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors genetics, Kidney Neoplasms genetics, Kidney Neoplasms pathology, Exome Sequencing
Abstract

Background: TFEB/6p21/VEGFA-amplified renal cell carcinoma (RCC) is rare and difficult to diagnose, with diverse histological patterns and immunohistochemical and poorly defined molecular genetic characteristics., Case Presentation: We report a case of a 63-year-old male admitted in 2017 with complex histomorphology, three morphological features of clear cell, eosinophilic and papillary RCC and resembling areas of glomerular and tubular formation. The immunophenotype also showed a mixture of CD10 and P504s. RCC with a high suspicion of collision tumors was indicated according to the 2014 WHO classification system; no precise diagnosis was possible. The patient was diagnosed at a different hospital with poorly differentiated lung squamous cell carcinoma one year after RCC surgery. We exploited molecular technology advances to retrospectively investigate the patient's molecular genetic alterations by whole-exome sequencing. The results revealed a 6p21 amplification in VEGFA and TFEB gene acquisition absent in other RCC subtypes. Clear cell, papillary, chromophobe, TFE3-translocation, eosinophilic solid and cystic RCC were excluded. Strong TFEB and Melan-A protein positivity prompted rediagnosis as TFEB/6p21/VEGFA-amplified RCC as per 2022 WHO classification. TMB-L (low tumor mutational load), CCND3 gene acquisition and MRE11A and ATM gene deletion mutations indicated sensitivity to PD-1/PD-L1 inhibitor combinations and the FDA-approved targeted agents Niraparib (Grade C), Olaparib (Grade C), Rucaparib (Grade C) and Talazoparib (Class C). GO (Gene Ontology) and KEGG enrichment analyses revealed major mutations and abnormal CNVs in genes involved in biological processes such as the TGF-β, Hippo, E-cadherin, lysosomal biogenesis and autophagy signaling pathways, biofilm synthesis cell adhesion substance metabolism regulation and others. We compared TFEB/6p21/VEGFA-amplified with TFEB-translocated RCC; significant differences in disease onset age, histological patterns, pathological stages, clinical prognoses, and genetic characteristics were revealed., Conclusion: We clarified the patient's challenging diagnosis and discussed the clinicopathology, immunophenotype, differential diagnosis, and molecular genetic information regarding TFEB/6p21/VEGFA-amplified RCC via exome analysis and a literature review., (© 2024. The Author(s).)

Published
2024
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3. Exome sequencing analysis identifies frequent oligogenic involvement andFLNBvariants in adolescent idiopathic scoliosis

Author

Jun Ma, Tao Lin, Enjie Xu, Fu Yang, Jinghua Hu, Kai He, Jianquan Zhao, Shulun Liang, Rui Gao, Heng Jiang, Yichen Meng, Ce Wang, and Xuhui Zhou

Subjects
Male, 0301 basic medicine, Adolescent, Protein Conformation, Filamins, Idiopathic scoliosis, Disease, 030105 genetics & heredity, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Exome Sequencing, Genetics, Humans, Exome, Genetic Predisposition to Disease, FLNB, Genetic Testing, Child, Gene, Genetic Association Studies, Genetics (clinical), Exome sequencing, Complex Traits, Genetic heterogeneity, Proportional hazards model, Genetic Variation, Proteins, oligogenic, Penetrance, 030104 developmental biology, Scoliosis, adolescent idiopathic scoliosis, Female
Abstract

BackgroundAdolescent idiopathic scoliosis (AIS) is a genetically heterogeneous disease characterised by three-dimensional deformity of the spine in the absence of a congenital spinal anomaly or neurological musculoskeletal disorder. The clinical variability and incomplete penetrance of some genes linked with AIS indicate that this disease constitutes an oligogenic trait.ObjectiveWe aimed to explore the oligogenic nature of this disease and identify novel AIS genes.MethodsWe analysed rare damaging variants within AIS-associated genes by using exome sequencing in 40 AIS trios and 183 sporadic patients.ResultsMultiple variants within AIS-associated genes were identified in eight AIS trios, and five individuals harboured rare damaging variants in theFLNBgene. The patients showed more frequent oligogenicity than the controls. In the gene-based burden test, the top signal resided inFLNB. In functional studies, we found that the AIS-associatedFLNBvariants altered the protein’s conformation and subcellular localisation and its interaction with other proteins (TTC26 and OFD1) involved in AIS. The most compelling evidence of an oligogenic basis was that the number of rare damaging variants was recognised as an independent prognostic factor for curve progression in Cox regression analysis.ConclusionOur data indicate that AIS is an oligogenic disease and identifyFLNBas a susceptibility gene for AIS.

Published
2020

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