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Whole genome and RNA sequencing analyses for 254 Taiwanese hepatocellular carcinomas.
Chang, Ya-Sian; Tu, Siang-Jyun; Chen, Hong-Da; Chung, Chin-Chun; Hsu, Ming-Hon; Chou, Yu-Pao; Lee, Ya-Ting; Yen, Ju-Chen; Jeng, Long-Bin; Chang, Jan-Gowth.
Afiliación
  • Chang YS; Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan.
  • Tu SJ; Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan.
  • Chen HD; Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.
  • Chung CC; School of Medicine, China Medical University, Taichung, Taiwan.
  • Hsu MH; Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan.
  • Chou YP; Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan.
  • Lee YT; Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.
  • Yen JC; Center for Precision Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan.
  • Jeng LB; Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan.
  • Chang JG; Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.
Biomark Res ; 11(1): 68, 2023 Jul 04.
Article en En | MEDLINE | ID: mdl-37403120
ABSTRACT

BACKGROUND:

Comprehensive and integrative analysis of hepatocellular carcinoma (HCC) is important. In this study, we explored Taiwanese HCCs using multi-omics analyses.

METHODS:

We analyzed 254 HCCs by whole genome sequencing and total RNA sequencing, and then used bioinformatic tools to analyze genomic and transcriptomic alterations in coding and non-coding sequences to explore the clinical importance of each sequence.

RESULTS:

The frequencies of the five most commonly mutated cancer-related genes were TERT, TP53, CTNNB1, RB1, and ARID1A. Genetic alteration frequencies influenced the etiology of HCC; some alterations were also correlated with clinicopathological conditions. Many cancer-related genes had copy number alterations (CNAs) and structure variants (SVs) that changed according to etiology and exhibited potential associations with survival. We also identified several alterations in histone-related genes, HCC-related long non-coding RNAs, and non-coding driver genes that may contribute to the onset and progression of HCC. Transcriptomic analysis revealed that 229 differentially expressed and 148 novel alternative splicing (AS) genes, as well as the presence of fusion genes, were associated with patient survival. Moreover, somatic mutations, CNAs, and SVs were associated with immune checkpoint gene expression and tumor microenvironment. Finally, we identified relationships among AS, immune checkpoint gene expression and tumor microenvironment.

CONCLUSIONS:

This study shows that genomic alterations are associated with survival, including DNA-based and RNA-based data. Moreover, genomic alterations and their associations with immune checkpoint genes and the tumor microenvironment may provide novel insights for the diagnosis and treatment of HCC.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Biomark Res Año: 2023 Tipo del documento: Article País de afiliación: Taiwán

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Biomark Res Año: 2023 Tipo del documento: Article País de afiliación: Taiwán