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Das AS, Sherry EC, Vaughan RM, Henderson ML, Zieba J, Uhl KL, Koehn O, Bupp CP, Rajasekaran S, Li X, Chhetri SB, Nissim S, Williams CL, Prokop JW. The complex, dynamic SpliceOme of the small GTPase transcripts altered by technique, sex, genetics, tissue specificity, and RNA base editing. Front Cell Dev Biol 2022; 10:1033695. [PMID: 36467401 PMCID: PMC9714508 DOI: 10.3389/fcell.2022.1033695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/01/2022] [Indexed: 04/04/2024] Open
Abstract
The small GTPase family is well-studied in cancer and cellular physiology. With 162 annotated human genes, the family has a broad expression throughout cells of the body. Members of the family have multiple exons that require splicing. Yet, the role of splicing within the family has been underexplored. We have studied the splicing dynamics of small GTPases throughout 41,671 samples by integrating Nanopore and Illumina sequencing techniques. Within this work, we have made several discoveries. 1). Using the GTEx long read data of 92 samples, each small GTPase gene averages two transcripts, with 83 genes (51%) expressing two or more isoforms. 2). Cross-tissue analysis of GTEx from 17,382 samples shows 41 genes (25%) expressing two or more protein-coding isoforms. These include protein-changing transcripts in genes such as RHOA, RAB37, RAB40C, RAB4B, RAB5C, RHOC, RAB1A, RAN, RHEB, RAC1, and KRAS. 3). The isolation and library technique of the RNAseq influences the abundance of non-sense-mediated decay and retained intron transcripts of small GTPases, which are observed more often in genes than appreciated. 4). Analysis of 16,243 samples of "Blood PAXgene" identified seven genes (3.7%; RHOA, RAB40C, RAB4B, RAB37, RAB5B, RAB5C, RHOC) with two or more transcripts expressed as the major isoform (75% of the total gene), suggesting a role of genetics in altering splicing. 5). Rare (ARL6, RAB23, ARL13B, HRAS, NRAS) and common variants (GEM, RHOC, MRAS, RAB5B, RERG, ARL16) can influence splicing and have an impact on phenotypes and diseases. 6). Multiple genes (RAB9A, RAP2C, ARL4A, RAB3A, RAB26, RAB3C, RASL10A, RAB40B, and HRAS) have sex differences in transcript expression. 7). Several exons are included or excluded for small GTPase genes (RASEF, KRAS, RAC1, RHEB, ARL4A, RHOA, RAB30, RHOBTB1, ARL16, RAP1A) in one or more forms of cancer. 8). Ten transcripts are altered in hypoxia (SAR1B, IFT27, ARL14, RAB11A, RAB10, RAB38, RAN, RIT1, RAB9A) with RHOA identified to have a transient 3'UTR RNA base editing at a conserved site found in all of its transcripts. Overall, we show a remarkable and dynamic role of splicing within the small GTPase family that requires future explorations.
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Affiliation(s)
- Akansha S. Das
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Biology, Washington and Jefferson College, Washington, PA, United States
| | - Emily C. Sherry
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, United States
| | - Robert M. Vaughan
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Marian L. Henderson
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- The Department of Biology, Calvin University, Grand Rapids, MI, United States
| | - Jacob Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Genetics and Genome Sciences Program, BioMolecular Science, Michigan State University, East Lansing, MI, United States
| | - Katie L. Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Olivia Koehn
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Medical Genetics, Spectrum Health and Helen DeVos Children’s Hospital, Grand Rapids, MI, United States
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Pediatric Critical Care Medicine, Helen DeVos Children’s Hospital Spectrum Health, Grand Rapids, MI, United States
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Surya B. Chhetri
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MA, United States
| | - Sahar Nissim
- Genetics and Gastroenterology Divisions, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, United States
| | - Carol L. Williams
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Genetics and Genome Sciences Program, BioMolecular Science, Michigan State University, East Lansing, MI, United States
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
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Deng D, Qu Y, Sun L, Jia L, Bu J, Ye M, Chen Z, Geng Y, Zhou S, Fang B. Fuyuan Xingnao Decoction Promotes Angiogenesis Through the Rab1/AT1R Pathway in Diabetes Mellitus Complicated With Cerebral Infarction. Front Pharmacol 2021; 12:616165. [PMID: 33679398 PMCID: PMC7925884 DOI: 10.3389/fphar.2021.616165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Fuyuan Xingnao decoction (FYXN), a traditional Chinese formula comprised of seven herbs, has been utilized to treat diabetes mellitus complicated with cerebral infarction (DMCI) for years. Yet, its protective and regulatory mechanism is poorly understood. The aim of the study is to investigate the effects of FYXN on DMCI in vitro and in vivo, as well as its mechanism in angiogenesis. For in vivo experiments, FYXN was administered to DMCI rats with streptozotocin (STZ) injection-induced diabetes. Then middle cerebral artery occlusion (MCAO) was conducted and the cerebral cortex sections of the rats were obtained. The ultrastructure of cerebral microvessels and new vessel density of ischemic penumbra were evaluated by the transmission electron microscopy (TEM) assay and immunohistochemistry, respectively. Protein and mRNA expression levels of Rab1/AT1R in cortex were assayed by Western blotting and real-time fluorescence quantitative real-time polymerase chain reaction (RT-qPCR). In vitro, FYXN serum was produced in rats on the fourth day 2 h after the last FYXN administration. Green fluorescence was observed after transfection with lentivirus packaged Rab1-WT or siRNA for 24 h. The activity of brain microvascular endothelial cells (BMECs) treated with sera from these rats was tested by MTT assay and Transwell assays, respectively. The expression of AT1R on the cell membrane and endoplasmic reticulum of BMECs was evaluated by immunofluorescence staining. Protein expression levels of signaling molecules in the Rab1/AT1R pathways were also detected. Results showed that in vivo, FYXN treatment significantly intensified CD31 staining in the cortical areas and enhanced the mRNA and protein levels of AT1R, Ang II, Rab1a, Rab1b and VEGF expression in ischemic cerebral cortex tissues. In vitro, the expression levels of AT1R, Ang II, Rab1a, Rab1b and VEGF in the cerebral infarction model group were significantly higher than those in the control group, with further increases after administration of FYXN drug serum. FYXN promoted the proliferation and migration of BMECs by activating the Rab1/AT1R signaling pathway. In conclusion, FYXN exerts a protective effect against DMCI by promoting angiogenesis via the Rab1/AT1R pathway, which provides strong evidence for the therapeutic effect of FYXN on DMCI.
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Affiliation(s)
- Dong Deng
- Department of Emergency Medicine, LongHua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yao Qu
- Department of Emergency Medicine, LongHua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lihua Sun
- Department of Emergency Medicine, LongHua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Liyang Jia
- Department of Emergency Medicine, LongHua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jianhong Bu
- Department of Emergency Medicine, LongHua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Internal Medicine, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai, China
| | - Miaoqing Ye
- Department of Liver Disease, Shaanxi Provincial Hospital of Traditional Chinese Medicine, Xi'an, China
| | - Zhenyi Chen
- Department of Cardiology, the Second Clinical Medical College, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Yun Geng
- Department of Emergency Medicine, LongHua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shuang Zhou
- Department of Acupuncture and Massage College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bangjiang Fang
- Department of Emergency Medicine, LongHua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Xu H, Qian M, Zhao B, Wu C, Maskey N, Song H, Li D, Song J, Hua K, Fang L. Inhibition of RAB1A suppresses epithelial-mesenchymal transition and proliferation of triple-negative breast cancer cells. Oncol Rep 2017; 37:1619-1626. [PMID: 28184936 DOI: 10.3892/or.2017.5404] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/16/2017] [Indexed: 11/05/2022] Open
Abstract
RAB1A acts as an oncogene in various cancers, and emerging evidence has verified that RAB1A is an mTORC1 activator in hepatocellular and colorectal cancer, but the role of RAB1A in breast cancer remains unclear. In this investigation, RAB1A siRNA was successfully transfected in MDA-MB-231 and BT-549 human triple-negative breast cancer cells, and verified by real‑time quantitative polymerase chain reaction and western blotting. Then, MTT cell proliferation, colony formation, cell invasion and wound healing assays were performed to characterize the function of RAB1A in the breast cancer cell lines. Downregulation of RAB1A inhibited cellular growth, cell migration, cell invasion and cell epithelial-mesenchymal transition. Furthermore, compared with NC siRNA transfected cells, RAB1A siRNA transfected breast cancer cells inhibited the phosphorylation of S6K1, the effector molecular of mTORC1. Collectively, our data suggested that RAB1A acts as an oncogene by regulating cellular proliferation, growth, invasion and metastasis via activation of mTORC1 pathway in triple-negative breast cancer.
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Affiliation(s)
- Hui Xu
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
| | - Mingping Qian
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
| | - Bingkun Zhao
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
| | - Chenyang Wu
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
| | - Niraj Maskey
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
| | - Hongming Song
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
| | - Dengfeng Li
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
| | - Jialu Song
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
| | - Kaiyao Hua
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
| | - Lin Fang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
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