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Chen KJ, Huang JH, Shih JH, Gu DL, Lee SS, Shen R, Hsu YH, Kung YC, Wu CY, Ho CM, Jen HW, Lee HY, Lang YD, Hsiao CH, Jou YS. Somatic A-to-I RNA-edited RHOA isoform 2 specific-R176G mutation promotes tumor progression in lung adenocarcinoma. Mol Carcinog 2023; 62:348-359. [PMID: 36453714 PMCID: PMC10107479 DOI: 10.1002/mc.23490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/06/2022] [Accepted: 11/20/2022] [Indexed: 12/04/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is the most common posttranscriptional editing to create somatic mutations and increase proteomic diversity. However, the functions of the edited mutations are largely underexplored. To identify novel targets in lung adenocarcinoma (LUAD), we conducted a genome-wide somatic A-to-I RNA editing analysis of 23 paired adjacent normal and LUAD transcriptomes and identified 26,280 events, including known nonsynonymous AZIN1-S367G and novel RHOAiso2 (RHOA isoform 2)-R176G, tubulin gamma complex associated protein 2 (TUBGCP2)-N211S, and RBMXL1-I40 M mutations. We validated the edited mutations in silico in multiple databases and in newly collected LUAD tissue pairs with the SEQUENOM MassARRAY® and TaqMan PCR Systems. We selected RHOAiso2-R176G due to its significant level, isoform-specificity, and being the most common somatic edited nonsynonymous mutation of RHOAiso2 to investigate its roles in LUAD tumorigenesis. RHOAiso2 is a ubiquitous but low-expression alternative spliced isoform received a unique Alu-rich exon at the 3' RHOA mRNA to become an editing RNA target, leading to somatic hypermutation and protein diversity. Interestingly, LUAD patients harboring the RHOAiso2-R176G mutation were associated with aberrant RHOA functions, cancer cell proliferation and migration, and poor clinical outcomes in transcriptome analysis. Mechanistically, RHOAiso2-R176G mutation-expressing LUAD cells potentiate RHOA-guanosine triphosphate (GTP) activity to phosphorylate ROCK1/2 effectors and enhance cell proliferation and migration in vitro and increase tumor growth in xenograft and systemic metastasis models in vivo. Taken together, the RHOAiso2-R176G mutation is a common somatic A-to-I edited mutation of the hypermutated RHOA isoform 2. It is an oncogenic and isoform-specific theranostic target that activates RHOA-GTP/p-ROCK1/2 signaling to promote tumor progression.
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Affiliation(s)
- Kuan-Ju Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jing-Hsiang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Department of Computer Science and Engineering, University of California at Santa Cruz, Santa Cruz, California, USA
| | - Jou-Ho Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - De-Leung Gu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Szu-Shuo Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Roger Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Yu-Hsuan Hsu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Ying-Chih Kung
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Cheng-Yen Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chun-Ming Ho
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsin-Wei Jen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsin-Yi Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yaw-Dong Lang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chen-Hao Hsiao
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.,Department of Surgery, Cheng Hsin General Hospital, Taipei, Taiwan
| | - Yuh-Shan Jou
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.,Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
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Duan Y, Dou S, Porath HT, Huang J, Eisenberg E, Lu J. A-to-I RNA editing in honeybees shows signals of adaptation and convergent evolution. iScience 2021; 24:101983. [PMID: 33458624 PMCID: PMC7797907 DOI: 10.1016/j.isci.2020.101983] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/18/2020] [Accepted: 12/17/2020] [Indexed: 12/27/2022] Open
Abstract
Social insects exhibit extensive phenotypic diversities among the genetically similar individuals, suggesting a role for the epigenetic regulations beyond the genome level. The ADAR-mediated adenosine-to-inosine (A-to-I) RNA editing, an evolutionarily conserved mechanism, facilitates adaptive evolution by expanding proteomic diversities. Here, we characterize the A-to-I RNA editome of honeybees (Apis mellifera), identifying 407 high-confidence A-to-I editing sites. Editing is most abundant in the heads and shows signatures for positive selection. Editing behavior differs between foragers and nurses, suggesting a role for editing in caste differentiation. Although only five sites are conserved between bees and flies, an unexpectedly large number of genes exhibit editing in both species, albeit at different locations, including the nonsynonymous auto-editing of Adar. This convergent evolution, where the same target genes independently acquire recoding events in distant diverged clades, together with the signals of adaptation observed in honeybees alone, further supports the notion of recoding being adaptive. Nonsynonymous editing sites in honeybees were under positive selection Differential editing may contribute to the phenotypic diversity between sub-castes Target genes acquire editing in different clades, suggesting convergent evolution
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Affiliation(s)
- Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Shengqian Dou
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Hagit T Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan 52900, Israel
| | - Jiaxing Huang
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
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