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Xiao Y, Gao L, Zhao X, Zhao W, Mai L, Ma C, Han Y, Li X. Novel prognostic alternative splicing events in colorectal Cancer: Impact on immune infiltration and therapy response. Int Immunopharmacol 2024; 139:112603. [PMID: 39043103 DOI: 10.1016/j.intimp.2024.112603] [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: 01/15/2024] [Revised: 06/06/2024] [Accepted: 06/29/2024] [Indexed: 07/25/2024]
Abstract
OBJECTIVE This study aims to comprehensively analyze alternative splicing (AS) features in colorectal cancer (CRC) using integrative multi-omics and to elucidate their relationship with the CRC immune microenvironment. METHODS Transcriptomic data, clinical information, and Percent Spliced In (PSI) values of AS events for CRC patients were obtained from The Cancer Genome Atlas (TCGA) and TCGA SpliceSeq databases. Differentially expressed AS events were identified. Univariate Cox analysis was used to pinpoint prognosis-related AS events. A prognostic risk model was developed and validated using multivariate Cox analysis, patient survival analysis, and the area under the receiver operating characteristic (ROC) curve (AUC). Gene Set Enrichment Analysis (GSEA), immune infiltration, immunotherapy, chemotherapy sensitivity analyses, and regulatory relationships between AS events and splicing factors (SFs) were conducted. Single-cell sequencing was used to study the distribution of key factors. siRNA and overexpression vectors were utilized to silence/overexpress BCAS1 in CRC cells and evaluate their effects on cell growth, migration, and invasion. Furthermore, the interaction between BCAS1 and ANO7 pre-mRNA was investigated using RIP-PCR. RESULTS 82 prognosis-related AS events were identified in CRC patients. A 15-AS prognostic model was constructed, which correlated with immune cell infiltration and showed differences in immunotherapy and chemotherapy sensitivity. BCAS1 was identified as a potential regulator of the ANO7|58341|AT splicing event in CRC. Single-cell sequencing analysis revealed the distribution of BCAS1 and ANO7 in cancer stem cells. In vitro experiments demonstrated that overexpression of BCAS1 and silencing of ANO7 inhibit the proliferation, migration, and invasion of CRC cells. Moreover, BCAS1 suppresses the progression of CRC by modulating ANO7 alternative splicing. CONCLUSION This study provides new insights into the role of alternative splicing in colorectal cancer, particularly the potential regulatory action of BCAS1 on the ANO7|58341|AT splicing event. It also identifies the impact of alternative splicing on the tumor microenvironment and potential implications for immunotherapy, highlighting its relevance for the in-depth study and treatment of CRC.
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Affiliation(s)
- Yizhi Xiao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Liangqing Gao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Xiaojuan Zhao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Wang Zhao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Lei Mai
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Chengmin Ma
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Yanzhi Han
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China.
| | - Xiaofeng Li
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China.
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Sun S, Zhao B, Li J, Zhang X, Yao S, Bao Z, Cai J, Yang J, Chen Y, Wu X. Regulation of Hair Follicle Growth and Development by Different Alternative Spliceosomes of FGF5 in Rabbits. Genes (Basel) 2024; 15:409. [PMID: 38674344 PMCID: PMC11049220 DOI: 10.3390/genes15040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/23/2024] [Accepted: 03/24/2024] [Indexed: 04/28/2024] Open
Abstract
This study investigated the regulatory effect of alternative spliceosomes of the fibroblast growth factor 5 (FGF5) gene on hair follicle (HF) growth and development in rabbits. The FGF5 alternative spliceosomes (called FGF5-X1, FGF5-X2, FGF5-X3) were cloned. The overexpression vector and siRNA of spliceosomes were transfected into dermal papilla cells (DPCs) to analyze the regulatory effect on DPCs. The results revealed that FGF5-X2 and FGF5-X3 overexpression significantly decreased LEF1 mRNA expression (p < 0.01). FGF5-X1 overexpression significantly reduced CCND1 expression (p < 0.01). FGF5-X1 and FGF5-X2 possibly downregulated the expression level of FGF2 mRNA (p < 0.05), and FGF5-X3 significantly downregulated the expression level of FGF2 mRNA (p < 0.01). The FGF5 alternative spliceosomes significantly downregulated the BCL2 mRNA expression level in both cases (p < 0.01). FGF5-X1 and FGF5-X2 significantly increased TGFβ mRNA expression (p < 0.01). All three FGF5 alternative spliceosomes inhibited DPC proliferation. In conclusion, the expression profile of HF growth and development-related genes can be regulated by FGF5 alternative spliceosomes, inhibiting the proliferation of DPCs and has an influence on the regulation of HF growth in rabbits. This study provides insights to further investigate the mechanism of HF development in rabbits via FGF5 regulation.
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Affiliation(s)
- Shaoning Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Xiyu Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Shuyu Yao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Zhiyuan Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Jiawei Cai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Jie Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
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Dery KJ, Wong Z, Wei M, Kupiec-Weglinski JW. Mechanistic Insights into Alternative Gene Splicing in Oxidative Stress and Tissue Injury. Antioxid Redox Signal 2023. [PMID: 37776178 DOI: 10.1089/ars.2023.0437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Significance: Oxidative stress (OS) and inflammation are inducers of tissue injury. Alternative splicing (AS) is an essential regulatory step for diversifying the eukaryotic proteome. Human diseases link AS to OS; however, the underlying mechanisms must be better understood. Recent Advances: Genome‑wide profiling studies identify new differentially expressed genes induced by OS-dependent ischemia/reperfusion injury. Overexpression of RNA-binding protein RBFOX1 protects against inflammation. Hypoxia-inducible factor-1α directs polypyrimidine tract binding protein 1 to regulate mouse carcinoembryonic antigen-related cell adhesion molecule 1 (Ceacam1) AS under OS conditions. Heterogeneous nuclear ribonucleoprotein L variant 1 contains an RGG/RG motif that coordinates with transcription factors to influence human CEACAM1 AS. Hypoxia intervention involving short interfering RNAs directed to long-noncoding RNA 260 polarizes M2 macrophages toward an anti-inflammatory phenotype and alleviates OS by inhibiting IL-28RA gene AS. Critical Issues: Protective mechanisms that eliminate reactive oxygen species (ROS) are important for resolving imbalances that lead to chronic inflammation. Defects in AS can cause ROS generation, cell death regulation, and the activation of innate and adaptive immune factors. We propose that AS pathways link redox regulation to the activation or suppression of the inflammatory response during cellular stress. Future Directions: Emergent studies using molecule-mediated RNA splicing are being conducted to exploit the immunogenicity of AS protein products. Deciphering the mechanisms that connect misspliced OS and pathologies should remain a priority. Controlled release of RNA directly into cells with clinical applications is needed as the demand for innovative nucleic acid delivery systems continues to be demonstrated.
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Affiliation(s)
- Kenneth J Dery
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Zeriel Wong
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Megan Wei
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jerzy W Kupiec-Weglinski
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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Li W, Zeng W, Zhang Y, Ma Z, Fang X, Han Y, Sun Y, Jin X, Ma L. A comparative metabolomics analysis of domestic yak ( Bos grunniens) milk with human breast milk. Front Vet Sci 2023; 10:1207950. [PMID: 37841471 PMCID: PMC10570732 DOI: 10.3389/fvets.2023.1207950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/08/2023] [Indexed: 10/17/2023] Open
Abstract
Yaks are tough animals living in Tibet's hypoxic stress environment. However, the metabolite composition of yak milk and its role in hypoxic stress tolerance remains largely unexplored. The similarities and differences between yak and human milk in hypoxic stress tolerance are also unclear. This study explored yak colostrum (YC) and yak mature milk (YMM) using GC-MS, and 354 metabolites were identified in yak milk. A comparative metabolomic analysis of yak and human milk metabolites showed that over 70% of metabolites were species-specific. Yak milk relies mainly on essential amino acids- arginine and essential branched-chain amino acids (BCAAs): L-isoleucine, L-leucine, and L-valine tolerate hypoxic stress. To slow hypoxic stress, human breast milk relies primarily on the neuroprotective effects of non-essential amino acids or derivates, such as citrulline, sarcosine, and creatine. In addition, metabolites related to hypoxic stress were significantly enriched in YC than in YMM. These results reveal the unique metabolite composition of yak and human milk and provide practical information for applying yak and human milk to hypoxic stress tolerance.
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Affiliation(s)
- Wenhao Li
- Institute of Animal Husbandry and Veterinary Science, Qinghai University, Xining, China
| | - Weike Zeng
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanping Zhang
- Institute of Animal Husbandry and Veterinary Science, Qinghai University, Xining, China
| | - Zhijie Ma
- Institute of Animal Husbandry and Veterinary Science, Qinghai University, Xining, China
| | - Xingyan Fang
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yingcang Han
- Institute of Animal Husbandry and Veterinary Science, Qinghai University, Xining, China
| | - Yonggang Sun
- Institute of Animal Husbandry and Veterinary Science, Qinghai University, Xining, China
| | - Xiayang Jin
- Institute of Animal Husbandry and Veterinary Science, Qinghai University, Xining, China
| | - Liuyin Ma
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
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