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Cheng S, Zhou Z, Liu J, Li J, Wang Y, Xiao J, Luo Y. Landscape analysis of alternative splicing in kidney renal clear cell carcinoma and their clinical significance. Aging (Albany NY) 2024; 16:10016-10032. [PMID: 38862257 PMCID: PMC11210227 DOI: 10.18632/aging.205915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/25/2024] [Indexed: 06/13/2024]
Abstract
A growing number of studies reveal that alternative splicing (AS) is associated with tumorigenesis, progression, and metastasis. Systematic analysis of alternative splicing signatures in renal cancer is lacking. In our study, we investigated the AS landscape of kidney renal clear cell carcinoma (KIRC) and identified AS predictive model to improve the prognostic prediction of KIRC. We obtained clinical data and gene expression profiles of KIRC patients from the TCGA database to evaluate AS events. The calculation results for seven types of AS events indicated that 46276 AS events from 10577 genes were identified. Next, we applied Cox regression analysis to identify 5864 prognostic-associated AS events. We used the Metascape database to verify the potential pathways of prognostic-associated AS. Moreover, we constructed KIRC prediction systems with prognostic-associated AS events by the LASSO Cox regression model. AUCs demonstrated that these prediction systems had excellent prognostic accuracy simultaneously. We identified 34 prognostic associated splicing factors (SFs) and constructed homologous regulatory networks. Furthermore, in vitro experiments were performed to validate the favorable effect of SFs FMR1 in KIRC. In conclusion, we overviewed AS events in KIRC and identified AS-based prognostic models to assist the survival prediction of KIRC patients. Our study may provide a novel predictive signature to improve the prognostic prediction of KIRC, which might facilitate KIRC patient counseling and individualized management.
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Affiliation(s)
- Songtao Cheng
- Department of Urology, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zili Zhou
- Department of Gastrointestinal Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiannan Liu
- Department of Urology, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jun Li
- Department of Urology, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Wang
- Department of Urology, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiantao Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongwen Luo
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
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2
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Gimeno-Valiente F, López-Rodas G, Castillo J, Franco L. The Many Roads from Alternative Splicing to Cancer: Molecular Mechanisms Involving Driver Genes. Cancers (Basel) 2024; 16:2123. [PMID: 38893242 PMCID: PMC11171328 DOI: 10.3390/cancers16112123] [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: 05/05/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Cancer driver genes are either oncogenes or tumour suppressor genes that are classically activated or inactivated, respectively, by driver mutations. Alternative splicing-which produces various mature mRNAs and, eventually, protein variants from a single gene-may also result in driving neoplastic transformation because of the different and often opposed functions of the variants of driver genes. The present review analyses the different alternative splicing events that result in driving neoplastic transformation, with an emphasis on their molecular mechanisms. To do this, we collected a list of 568 gene drivers of cancer and revised the literature to select those involved in the alternative splicing of other genes as well as those in which its pre-mRNA is subject to alternative splicing, with the result, in both cases, of producing an oncogenic isoform. Thirty-one genes fall into the first category, which includes splicing factors and components of the spliceosome and splicing regulators. In the second category, namely that comprising driver genes in which alternative splicing produces the oncogenic isoform, 168 genes were found. Then, we grouped them according to the molecular mechanisms responsible for alternative splicing yielding oncogenic isoforms, namely, mutations in cis splicing-determining elements, other causes involving non-mutated cis elements, changes in splicing factors, and epigenetic and chromatin-related changes. The data given in the present review substantiate the idea that aberrant splicing may regulate the activation of proto-oncogenes or inactivation of tumour suppressor genes and details on the mechanisms involved are given for more than 40 driver genes.
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Affiliation(s)
- Francisco Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London WC1E 6DD, UK;
| | - Gerardo López-Rodas
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
| | - Josefa Castillo
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Luis Franco
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
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Zhou S, Cheng C, Liao YX, Wang L, Zeng JM, Zhou FF, Zhang XQ, Yang T. Epigenetic regulation of FOXI2 promotes clear cell renal cell carcinoma progression. Heliyon 2024; 10:e29218. [PMID: 38628758 PMCID: PMC11016964 DOI: 10.1016/j.heliyon.2024.e29218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
In recent decades, substantial advancements in epigenetics have unveiled a profound understanding of its mechanisms in tumorigenesis and have offered promising strategies for epigenetic therapy in cancer patients. In our study, through bioinformatics analysis, we discovered a significant downregulation and hypermethylation of FOXI2 in clear cell renal cell carcinoma (ccRCC), while the expression in chromophobe cell carcinoma (chRCC) exhibited the opposite trend. Moreover, we established a strong correlation between FOXI2 expression levels and the prognosis of ccRCC. Gene enrichment analysis and cell function experiments unequivocally demonstrate that FOXI2 possesses the capability to induce cell cycle arrest and inhibit cell proliferation. Our research findings demonstrate that the expression of FOXI2 in ccRCC is under the regulation of promoter hypermethylation. Furthermore, in vitro experiments have conclusively shown that the overexpression of FOXI2 induces cell cycle arrest and inhibits cell proliferation.
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Affiliation(s)
- Shuai Zhou
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Cong Cheng
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Yi xiang Liao
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Li Wang
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Jin min Zeng
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Fang fang Zhou
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Xiu qin Zhang
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Tao Yang
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
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Xu T, Li X, Zhao W, Wang X, Jin L, Feng Z, Li H, Zhang M, Tian Y, Hu G, Yue Y, Dai X, Shan C, Zhang W, Zhang C, Zhang Y. SF3B3-regulated mTOR alternative splicing promotes colorectal cancer progression and metastasis. J Exp Clin Cancer Res 2024; 43:126. [PMID: 38671459 PMCID: PMC11047005 DOI: 10.1186/s13046-024-03053-4] [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] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Aberrant alternative splicing (AS) is a pervasive event during colorectal cancer (CRC) development. SF3B3 is a splicing factor component of U2 small nuclear ribonucleoproteins which are crucial for early stages of spliceosome assembly. The role of SF3B3 in CRC remains unknown. METHODS SF3B3 expression in human CRCs was analyzed using publicly available CRC datasets, immunohistochemistry, qRT-PCR, and western blot. RNA-seq, RNA immunoprecipitation, and lipidomics were performed in SF3B3 knockdown or overexpressing CRC cell lines. CRC cell xenografts, patient-derived xenografts, patient-derived organoids, and orthotopic metastasis mouse models were utilized to determine the in vivo role of SF3B3 in CRC progression and metastasis. RESULTS SF3B3 was upregulated in CRC samples and associated with poor survival. Inhibition of SF3B3 by RNA silencing suppressed the proliferation and metastasis of CRC cells in vitro and in vivo, characterized by mitochondria injury, increased reactive oxygen species (ROS), and apoptosis. Mechanistically, silencing of SF3B3 increased mTOR exon-skipped splicing, leading to the suppression of lipogenesis via mTOR-SREBF1-FASN signaling. The combination of SF3B3 shRNAs and mTOR inhibitors showed synergistic antitumor activity in patient-derived CRC organoids and xenografts. Importantly, we identified SF3B3 as a critical regulator of mTOR splicing and autophagy in multiple cancers. CONCLUSIONS Our findings revealed that SF3B3 promoted CRC progression and metastasis by regulating mTOR alternative splicing and SREBF1-FASN-mediated lipogenesis, providing strong evidence to support SF3B3 as a druggable target for CRC therapy.
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Affiliation(s)
- Tong Xu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Xichuan Li
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300382, China
| | - Wennan Zhao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Xue Wang
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Leixin Jin
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, 30021, China
| | - Zhiqiang Feng
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, 30021, China
| | - Huixiang Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Mingzhe Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Yiqing Tian
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Ge Hu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Yuan Yue
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300382, China
| | - Xintong Dai
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, China
| | - Changliang Shan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, China
| | | | - Chunze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, 30021, China.
| | - Youcai Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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Chen C, Huang F, Li X, Liu L, Zhang J, Zhao J, Zhang W, Li H, Xu W, Qi Y, Wang Y. Identification of splicing factors signature predicting prognosis risk and the mechanistic roles of novel oncogenes in HNSCC. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167115. [PMID: 38458543 DOI: 10.1016/j.bbadis.2024.167115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 03/10/2024]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the most frequent subtype of head and neck cancer, generally with a poor prognosis and limited therapeutic options due to its highly heterogeneous malignancy. In this study, we screened functional splicing regulatory RNA binding proteins (RBPs) that were closely related with the prognosis of HNSCC patients and showed significant expression differences between HNSCC tumors and normal tissues. Based on this finding, we chose six candidate genes (HNRNPC, ZCRB1, RBM12B, SF3A2, SF3B3, and SRSF11) to generate a prognostic prediction model and validated the accuracy of the prognostic model for predicting patient survival outcomes. We found that the risk score predicted by our model can serve as an independent prognostic predictor. Notably, HNSCC tumors showing higher expression of SF3B3, HNRNPC, or ZCRB1 possessed higher risk scores in the discovered prediction model. The investigation of the underlying mechanism validated that knockdown of SF3B3, HNRNPC, and ZCRB1 separately induced a substantial impairment of HNSCC cell survival. Conversely, overexpression of each of the three genes promoted tumor cellular proliferation. High throughput RNA sequencing analysis revealed that changes in the expression of SF3B3 and HNRNPC remarkably affected alternative splicing of genes related to cell cycle regulation, whereas the depletion of ZCRB1 contributed to aberrant splicing events involving in DNA damage response. In addition, the prognostic prediction model's risk score was demonstrated to be related with the immune infiltration score. Particularly, SF3B3 has a negative correlation with CD8A expression. Therefore, our findings provide promising prognosis predictors and potential therapeutic targets for better treatment efficacy of HNSCC.
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Affiliation(s)
- Chaoqun Chen
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116023, China
| | - Fang Huang
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116023, China
| | - Xiaojie Li
- Department of Prosthodontics, College of Stomatology, Dalian Medical University, Dalian 116044, China
| | - Lin Liu
- Department of Otolaryngology Head and Neck Surgery, Dalian Friendship Hospital, Dalian 116001, China
| | - Jinrui Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Huizheng Li
- Department of Otolaryngology Head and Neck Surgery, Dalian Friendship Hospital, Dalian 116001, China.
| | - Wei Xu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China.
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China; Soochow University Cancer Institute, Suzhou, China.
| | - Yang Wang
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116023, China.
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6
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Arecco N, Mocavini I, Blanco E, Ballaré C, Libman E, Bonnal S, Irimia M, Di Croce L. Alternative splicing decouples local from global PRC2 activity. Mol Cell 2024; 84:1049-1061.e8. [PMID: 38452766 DOI: 10.1016/j.molcel.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 12/21/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024]
Abstract
The Polycomb repressive complex 2 (PRC2) mediates epigenetic maintenance of gene silencing in eukaryotes via methylation of histone H3 at lysine 27 (H3K27). Accessory factors define two distinct subtypes, PRC2.1 and PRC2.2, with different actions and chromatin-targeting mechanisms. The mechanisms orchestrating PRC2 assembly are not fully understood. Here, we report that alternative splicing (AS) of PRC2 core component SUZ12 generates an uncharacterized isoform SUZ12-S, which co-exists with the canonical SUZ12-L isoform in virtually all tissues and developmental stages. SUZ12-S drives PRC2.1 formation and favors PRC2 dimerization. While SUZ12-S is necessary and sufficient for the repression of target genes via promoter-proximal H3K27me3 deposition, SUZ12-L maintains global H3K27 methylation levels. Mouse embryonic stem cells (ESCs) lacking either isoform exit pluripotency more slowly and fail to acquire neuronal cell identity. Our findings reveal a physiological mechanism regulating PRC2 assembly and higher-order interactions in eutherians, with impacts on H3K27 methylation and gene repression.
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Affiliation(s)
- Niccolò Arecco
- Systems and Synthetic Biology Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain.
| | - Ivano Mocavini
- Genome Biology Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Enrique Blanco
- Genome Biology Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Cecilia Ballaré
- Genome Biology Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Elina Libman
- Systems and Synthetic Biology Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Sophie Bonnal
- Genome Biology Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Manuel Irimia
- Systems and Synthetic Biology Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain.
| | - Luciano Di Croce
- Genome Biology Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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7
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Temaj G, Chichiarelli S, Saha S, Telkoparan-Akillilar P, Nuhii N, Hadziselimovic R, Saso L. An intricate rewiring of cancer metabolism via alternative splicing. Biochem Pharmacol 2023; 217:115848. [PMID: 37813165 DOI: 10.1016/j.bcp.2023.115848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
All human genes undergo alternative splicing leading to the diversity of the proteins. However, in some cases, abnormal regulation of alternative splicing can result in diseases that trigger defects in metabolism, reduced apoptosis, increased proliferation, and progression in almost all tumor types. Metabolic dysregulations and immune dysfunctions are crucial factors in cancer. In this respect, alternative splicing in tumors could be a potential target for therapeutic cancer strategies. Dysregulation of alternative splicing during mRNA maturation promotes carcinogenesis and drug resistance in many cancer types. Alternative splicing (changing the target mRNA 3'UTR binding site) can result in a protein with altered drug affinity, ultimately leading to drug resistance.. Here, we will highlight the function of various alternative splicing factors, how it regulates the reprogramming of cancer cell metabolism, and their contribution to tumor initiation and proliferation. Also, we will discuss emerging therapeutics for treating tumors via abnormal alternative splicing. Finally, we will discuss the challenges associated with these therapeutic strategies for clinical applications.
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Affiliation(s)
- Gazmend Temaj
- Faculty of Pharmacy, College UBT, 10000 Prishtina, Kosovo
| | - Silvia Chichiarelli
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, 00185 Rome, Italy.
| | - Sarmistha Saha
- Department of Biotechnology, GLA University, Mathura 00185, Uttar Pradesh, India
| | | | - Nexhibe Nuhii
- Department of Pharmacy, Faculty of Medical Sciences, State University of Tetovo, 1200 Tetovo, Macedonia
| | - Rifat Hadziselimovic
- Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", La Sapienza University, 00185 Rome, Italy.
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8
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Ahkin Chin Tai JK, Horzmann KA, Jenkins TL, Akoro IN, Stradtman S, Aryal UK, Freeman JL. Adverse developmental impacts in progeny of zebrafish exposed to the agricultural herbicide atrazine during embryogenesis. ENVIRONMENT INTERNATIONAL 2023; 180:108213. [PMID: 37774458 PMCID: PMC10613503 DOI: 10.1016/j.envint.2023.108213] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/01/2023]
Abstract
Atrazine (ATZ) is an herbicide commonly used on crops in the Midwestern US and other select global regions. The US Environmental Protection Agency ATZ regulatory limit is 3 parts per billion (ppb; µg/L), but this limit is often exceeded. ATZ has a long half-life, is a common contaminant of drinking water sources, and is indicated as an endocrine disrupting chemical in multiple species. The zebrafish was used to test the hypothesis that an embryonic parental ATZ exposure alters protein levels leading to modifications in morphology and behavior in developing progeny. Zebrafish embryos (F1) were collected from adults (F0) exposed to 0, 0.3, 3, or 30 ppb ATZ during embryogenesis. Differential proteomics, morphology, and behavior assays were completed with offspring aged 120 or 144 h with no additional chemical treatment. Proteomic analysis identified differential expression of proteins associated with neurological development and disease; and organ and organismal morphology, development, and injury, specifically the skeletomuscular system. Head length and ratio of head length to total length was significantly increased in the F1 of 0.3 and 30 ppb ATZ groups (p < 0.05). Based on molecular pathway alterations, further craniofacial morphology assessment found decreased distance for cartilaginous structures, decreased surface area and distance between saccular otoliths, and a more posteriorly positioned notochord (p < 0.05), indicating delayed ossification and skeletal growth. The visual motor response assay showed hyperactivity in progeny of the 30 ppb treatment group for distance moved and of the 0.3 and 30 ppb treatment groups for time spent moving (p < 0.05). Due to the changes in saccular otoliths, an acoustic startle assay was completed and showed decreased response in the 0.3 and 30 ppb treatments (p < 0.05). These findings suggest that a single embryonic parental exposure alters cellular pathways in their progeny that lead to perturbations in craniofacial development and behavior.
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Affiliation(s)
| | - Katharine A Horzmann
- School of Health Sciences, Purdue University, West Lafayette, IN, USA; Department of Pathobiology, Auburn University, Auburn, AL, USA
| | - Thomas L Jenkins
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Isabelle N Akoro
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | - Sydney Stradtman
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | - Uma K Aryal
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA; Bindley Bioscience Center, Discovery Park, Purdue University, West Lafayette, IN, USA
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9
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Hong Z, Chen X, Wang L, Zhou X, He H, Zou G, Liu Q, Wang Y. ROCK2-RNA interaction map reveals multiple biological mechanisms underlying tumor progression in renal cell carcinoma. Hum Cell 2023; 36:1790-1803. [PMID: 37418232 DOI: 10.1007/s13577-023-00947-x] [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: 03/12/2023] [Accepted: 06/24/2023] [Indexed: 07/08/2023]
Abstract
Renal cell carcinoma (RCC) is the most common form of kidney cancer in adults. Despite new therapeutic modalities, the outcomes for RCC patients remain unsatisfactory. Rho-associated coiled-coil forming protein kinase 2 (ROCK2) has previously been shown to be upregulated in RCC, and its expression was negatively correlated with patient survival. However, the precise molecular function of ROCK2 has remained unclear. Herein, using RNA-seq analysis of ROCK2 knockdown and control cells, we identified 464 differentially expressed genes, and 1287 alternative splicing events in 786-O RCC cells. Furthermore, mapping of iRIP-seq reads in 786-O cells showed a biased distribution at 5' UTR, intronic and intergenic regions. By comparing ROCK2-regulated alternative splicing and iRIP-seq data, we found 292 overlapping genes that are enriched in multiple tumorigenic pathways. Taken together, our work defined a complex ROCK2-RNA interaction map on a genomic scale in a human RCC cell line, which deepens our understanding of the molecular function of ROCK2 in cancer development.
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Affiliation(s)
- Zhengdong Hong
- Department of Urology Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xuexin Chen
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, 511436, China
| | - Lei Wang
- School of Pharmacy, Nanchang Medical College, Nanchang, China
- Jiangxi Health Vocational College, Nanchang, China
| | - Xiaocheng Zhou
- Department of Urology Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Haowei He
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, 511436, China
| | - Gaode Zou
- Department of Urology Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qingnan Liu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Yiqian Wang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, 511436, China.
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10
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Wang J, Weng Y, Li Y, Zhang Y, Zhou J, Tang J, Lin X, Guo Z, Zheng F, Yu G, Shao W, Hu H, Cai P, Wu S, Li H. The interplay between lncRNA NR_030777 and SF3B3 in neuronal damage caused by paraquat. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 255:114804. [PMID: 36948007 DOI: 10.1016/j.ecoenv.2023.114804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
Paraquat (PQ) has been widely acknowledged as an environmental risk factor for Parkinson's disease (PD). However, the interaction between splicing factor and long non-coding RNA (lncRNA) in the process of PQ-induced PD has rarely been studied. Based on previous research, this study focused on splicing factor 3 subunit 3 (SF3B3) and lncRNA NR_030777. After changing the target gene expression level by lentiviral transfection technology, the related gene expression was detected by western blot and qRT-PCR. The expression of SF3B3 protein was reduced in Neuro-2a cells after PQ exposure, and the reactive oxygen species (ROS) scavenger N-acetylcysteine prevented this decline. Knockdown of SF3B3 reduced the PQ-triggered NR_030777 expression increase, and overexpression of NR_030777 reduced the transcriptional and translational level of Sf3b3. Then, knockdown of SF3B3 exacerbated the PQ-induced decrease in cell viability and aggravated the reduction of tyrosine hydroxylase (TH) protein expression. Overexpressing SF3B3 reversed the reduction of TH expression caused by PQ. Moreover, after intervention with the autophagy inhibitor Bafilomycin A1, LC3B-II protein expression was further increased in Neuro-2a cells with the knockdown of SF3B3, indicating that autophagy was enhanced. In conclusion, PQ modulated the interplay between NR_030777 and SF3B3 through ROS production, thereby impairing autophagic flux and causing neuronal damage.
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Affiliation(s)
- Junxiang Wang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yali Weng
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yinhan Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yu Zhang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Jinfu Zhou
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Jianping Tang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Xinpei Lin
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Zhenkun Guo
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Key Lab of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Fuli Zheng
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Key Lab of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Guangxia Yu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Key Lab of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Wenya Shao
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Key Lab of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Hong Hu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Key Lab of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Ping Cai
- Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Siying Wu
- Key Lab of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Huangyuan Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Key Lab of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
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Mhatre A, Koroth J, Manjunath M, Kumar S S, Gawari R, Choudhary B. Multi-omics analysis of the Indian ovarian cancer cohort revealed histotype-specific mutation and gene expression patterns. Front Genet 2023; 14:1102114. [PMID: 37091785 PMCID: PMC10117685 DOI: 10.3389/fgene.2023.1102114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/22/2023] [Indexed: 04/08/2023] Open
Abstract
Introduction: In India, OVCa is women’s third most common and lethal cancer type, accounting for 6.7% of observed cancer incidences. The contribution of somatic mutations, aberrant expression of gene and splice forms in determining the cell fate, gene networks, tumour-specific variants, and the role of immune fraction infiltration have been proven essential in understanding tumorigenesis. However, their interplay in OVCa in a histotype-specific manner remains unclear in the Indian context. In the present study, we aimed to unravel the Indian population histotype-specific exome variants, differentially expressed gene modules, splice events and immune profiles of OVCa samples.Methods: We analysed 10 tumour samples across 4 ovarian cancer histotypes along with 2 normal patient samples. This included BCFtool utilities and CNVkit for exome, WGCNA and DESeq2 for obtaining differential module hub genes and dysregulated miRNA targets, CIBERSORTx for individual immune profiles and rMATS for tumour specific splice variants.Result: We identified population-specific novel mutations in Cancer Gene Census Tier1 and Tier2 genes. MUC16, MUC4, CIITA, and NCOR2 were among the most mutated genes, along with TP53. Transcriptome analysis showed significant overexpression of mutated genes MUC16, MUC4, and CIITA, whereas NCOR2 was downregulated. WGCNA revealed histotype-specific gene hubs and networks. Among the significant pathways, alteration in the immune system was one of the pathways, and immune profiling using CIBERSORTx revealed histotype-specific immune cell fraction. miRNA analysis revealed miR-200 family, miR-200a and miR-429 were upregulated in HGSOCs.Splice factor abrasion caused splicing perturbations, with the most abundant alternative splice event being exon skipping and the most spliced gene, SNHG17. Pathway analysis of spliced genes revealed translational elongation and Base excision repair as the pathways altered in OVCa.Conclusion: Integrated exome, transcriptome, and splicing patterns revealed different population-specific molecular signatures of ovarian cancer histotypes in the Indian Cohort.
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Affiliation(s)
- Anisha Mhatre
- Department of Biotechnology and Bioinformatics, Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Jinsha Koroth
- Department of Biotechnology and Bioinformatics, Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Meghana Manjunath
- Department of Biotechnology and Bioinformatics, Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
- Graduate Student Registered Under Manipal Academy of Higher Education, Manipal, Karnataka, India
| | | | - Ramesh Gawari
- Kidwai Cancer Institute of Oncology, Bangalore, India
| | - Bibha Choudhary
- Department of Biotechnology and Bioinformatics, Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
- *Correspondence: Bibha Choudhary,
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Novel long noncoding RNA LINC02820 augments TNF signaling pathway to remodel cytoskeleton and potentiate metastasis in esophageal squamous cell carcinoma. Cancer Gene Ther 2023; 30:375-387. [PMID: 36357564 PMCID: PMC9935391 DOI: 10.1038/s41417-022-00554-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common malignant tumors in China. However, there are no targets to treat ESCC because the molecular mechanism behind the cancer is still unclear. Here, we found a novel long noncoding RNA LINC02820 was upregulated in ESCC and associated with the ESCC clinicopathological stage. Through a series of functional experiments, we observed that LINC02820 only promoted the migration and invasion capabilities of ESCC cell lines. Mechanically, we found that LINC02820 may affect the cytoskeletal remodeling, interact with splice factor 3B subunit 3 (SF3B3), and cooperate with TNFα to amplify the NF-κB signaling pathway, which can lead to ESCC metastasis. Overall, our findings revealed that LINC02820 is a potential biomarker and therapeutic target for the diagnosis and treatment of ESCC.
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Chen T, Yang H, Liu P, Hamiti M, Zhang X, Xu Y, Quan W, Zhang Y, Yu W, Jiao L, Du T, Xi J, Yin B, Zhou W, Lu S, Peng X. Splicing factor SF3B3, a NS5-binding protein, restricts ZIKV infection by targeting GCH1. Virol Sin 2022; 38:222-232. [PMID: 36572150 PMCID: PMC10176263 DOI: 10.1016/j.virs.2022.12.005] [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] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Zika virus (ZIKV), a positive-sense single-stranded RNA virus, causes congenital ZIKV syndrome in children and Guillain-Barré Syndrome (GBS) in adults. ZIKV expresses nonstructural protein 5 (NS5), a large protein that is essential for viral replication. ZIKV NS5 confers the ability to evade interferon (IFN) signalling; however, the exact mechanism remains unclear. In this study, we employed affinity pull-down and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses and found that splicing factor 3b subunit 3 (SF3B3) is associated with the NS5-Flag pull-down complex through interaction with NS5. Functional assays showed that SF3B3 overexpression inhibited ZIKV replication by promoting IFN-stimulated gene (ISG) expression whereas silencing of SF3B3 inhibited expression of ISGs to promote ZIKV replication. GTP cyclohydrolase I (GCH1) is the first and rate-limiting enzyme in tetrahydrobiopterin (BH4) biosynthesis. NS5 upregulates the expression of GCH1 during ZIKV infection. And GCH1 marginally promoted ZIKV replication via the IFN pathway. Additionally, GCH1 expression is related to the regulation of SF3B3. Overexpression of the SF3B3 protein effectively reduced GCH1 protein levels, whereas SF3B3 knockdown increased its levels. These findings indicated that ZIKV NS5 binding protein SF3B3 contributed to the host immune response against ZIKV replication by modulating the expression of GCH1.
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Affiliation(s)
- Tanxiu Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China; Department of Science and Education, Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Nanchang, 330029, China
| | - Hao Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Penghui Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Moliduer Hamiti
- The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xintian Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Yi Xu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Wenqi Quan
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Yong Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Wenhai Yu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Li Jiao
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Tingfu Du
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Juemin Xi
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Bin Yin
- The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Wei Zhou
- Department of Science and Education, Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Nanchang, 330029, China
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China.
| | - Xiaozhong Peng
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China; The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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14
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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15
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The splicing factor SF3B4 drives proliferation and invasion in cervical cancer by regulating SPAG5. Cell Death Discov 2022; 8:326. [PMID: 35853859 PMCID: PMC9296558 DOI: 10.1038/s41420-022-01120-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 12/24/2022] Open
Abstract
Regulation of alternative splicing (AS) by the splicing factor 3b (SF3B) family plays an essential role in cancer. However, the biological function of SF3B family members in cervical cancer (CC) needs to be further elucidated. In this study, we found that splicing factor 3b subunit 4 (SF3B4) was highly expressed in CC by bioinformatics analysis using cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) data from The Cancer Genome Atlas (TCGA). Then, we demonstrated that high expression of SF3B4 promoted proliferation and invasion abilities of CC cells in vitro and in vivo and that reduced expression of SF3B4 performed the opposite effect. Further RNA-seq and AS analysis showed that sperm-associated antigen 5 (SPAG5) was a downstream target gene of SF3B4. Interestingly, SPAG5 expression was decreased after SF3B4 knockdown because of retained introns (RIs) and reduced maturation of SPAG5 pre-mRNA. Importantly, SPAG5 deficiency impaired the oncogenic effects of SF3B4 overexpression on CC cells. In conclusion, SF3B4 promotes CC progression by regulating the effective splicing of SPAG5. SF3B4 could be a promising target for CC.
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Qiao Y, Shi Q, Yuan X, Ding J, Li X, Shen M, Huang S, Chen Z, Wang L, Zhao Y, He X. RNA binding protein RALY activates the cholesterol synthesis pathway through an MTA1 splicing switch in hepatocellular carcinoma. Cancer Lett 2022; 538:215711. [PMID: 35490918 DOI: 10.1016/j.canlet.2022.215711] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/15/2022]
Abstract
Alternative splicing is an important RNA processing event that contributes to RNA complexity and protein diversity in cancer. Accumulating evidence demonstrates the essential roles of some alternatively spliced genes in carcinogenesis. However, the potential roles of alternatively spliced genes in hepatocellular carcinoma (HCC) are still largely unknown. Here we showed that the HnRNP Associated with Lethal Yellow Protein Homolog (RALY) gene is upregulated and associated with poor outcomes in HCC patients. RALY acts as a tumor-promoting factor by cooperating with splicing factor 3b subunit 3 (SF3B3) and modulating the splicing switch of Metastasis Associated 1 (MTA1) from MTA-S to MTA1-L. Normally, MTA1-S inhibits cell proliferation by reducing the transcription of cholesterol synthesis genes. In HCC, RALY and SF3B3 cooperate to regulate the MTA1 splicing switch, leading to a reduction in the MTA1-S level, and alleviating the inhibitory effect of MTA1-S on cholesterol synthesis genes, thus promoting HCC cell proliferation. In conclusion, our results revealed that the RALY-SF3B3/MTA1/cholesterol synthesis pathway contributes essentially to hepatic carcinogenesis and could serve as a promising therapeutic target for HCC.
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Affiliation(s)
- Yejun Qiao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qili Shi
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xu Yuan
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jie Ding
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xinrong Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Mengting Shen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
| | - Zhiao Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
| | - Lu Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
| | - Yingjun Zhao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
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Lee K, Yu D, Hyung D, Cho SY, Park C. ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:466-482. [PMID: 35085775 PMCID: PMC9801047 DOI: 10.1016/j.gpb.2021.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 10/15/2021] [Accepted: 11/01/2021] [Indexed: 01/26/2023]
Abstract
Alternative splicing (AS) regulates biological processes governing phenotypes and diseases. Differential AS (DAS) gene test methods have been developed to investigate important exonic expression from high-throughput datasets. However, the DAS events extracted using statistical tests are insufficient to delineate relevant biological processes. In this study, we developed a novel application, Alternative Splicing Encyclopedia: Functional Interaction (ASpediaFI), to systemically identify DAS events and co-regulated genes and pathways. ASpediaFI establishes a heterogeneous interaction network of genes and their feature nodes (i.e., AS events and pathways) connected by co-expression or pathway gene set knowledge. Next, ASpediaFI explores the interaction network using the random walk with restart algorithm and interrogates the proximity from a query gene set. Finally, ASpediaFI extracts significant AS events, genes, and pathways. To evaluate the performance of our method, we simulated RNA sequencing (RNA-seq) datasets to consider various conditions of sequencing depth and sample size. The performance was compared with that of other methods. Additionally, we analyzed three public datasets of cancer patients or cell lines to evaluate how well ASpediaFI detects biologically relevant candidates. ASpediaFI exhibits strong performance in both simulated and public datasets. Our integrative approach reveals that DAS events that recognize a global co-expression network and relevant pathways determine the functional importance of spliced genes in the subnetwork. ASpediaFI is publicly available at https://bioconductor.org/packages/ASpediaFI.
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Han W, Fan B, Huang Y, Wang X, Zhang Z, Gu G, Liu Z. Construction and validation of a prognostic model of RNA binding proteins in clear cell renal carcinoma. BMC Nephrol 2022; 23:172. [PMID: 35513791 PMCID: PMC9069774 DOI: 10.1186/s12882-022-02801-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/25/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The dysfunction of RNA binding proteins (RBPs) is associated with various inflammation and cancer. The occurrence and progression of tumors are closely related to the abnormal expression of RBPs. There are few studies on RBPs in clear cell renal carcinoma (ccRCC), which allows us to explore the role of RBPs in ccRCC. METHODS We obtained the gene expression data and clinical data of ccRCC from the Cancer Genome Atlas (TCGA) database and extracted all the information of RBPs. We performed differential expression analysis of RBPs. Risk model were constructed based on the differentially expressed RBPs (DERBPs). The expression levels of model markers were examined by reverse transcription-quantitative PCR (RT-qPCR) and analyzed for model-clinical relevance. Finally, we mapped the model's nomograms to predict the 1, 3 and 5-year survival rates for ccRCC patients. RESULTS The results showed that the five-year survival rate for the high-risk group was 40.2% (95% CI = 0.313 ~ 0.518), while the five-year survival rate for the low-risk group was 84.3% (95% CI = 0.767 ~ 0.926). The ROC curves (AUC = 0.748) also showed that our model had stable predictive power. Further RT-qPCR results were in accordance with our analysis (p < 0.05). The results of the independent prognostic analysis showed that the model could be an independent prognostic factor for ccRCC. The results of the correlation analysis also demonstrated the good predictive ability of the model. CONCLUSION In summary, the 4-RBPs (EZH2, RPL22L1, RNASE2, U2AF1L4) risk model could be used as a prognostic indicator of ccRCC. Our study provides a possibility for predicting the survival of ccRCC.
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Affiliation(s)
- Wenkai Han
- Department of Clinical Medicine, Qingdao University, Qingdao, Shandong, 266000, China
| | - Bohao Fan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yongshen Huang
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Xiongbao Wang
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Zhao Zhang
- Department of Clinical Medicine, Qingdao University, Qingdao, Shandong, 266000, China.,Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Gangli Gu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China.
| | - Zhao Liu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China.
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Chen K, Xiao H, Zeng J, Yu G, Zhou H, Huang C, Yao W, Xiao W, Hu J, Guan W, Wu L, Huang J, Huang Q, Xu H, Ye Z. Correction: Alternative Splicing of EZH2 pre-mRNA by SF3B3 Contributes to the Tumorigenic Potential of Renal Cancer. Clin Cancer Res 2022; 28:1736. [PMID: 35419594 DOI: 10.1158/1078-0432.ccr-22-0563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Wang L, Zhou Y, Cao C, Lin S, Zhi W, Zhang D, Li J, Wei R, Jiang G, Xu H, Wang X, Xi L, Wu P. The exon 12-containing LHX6 isoforms promote cervical cancer cell proliferation by regulating the MAPK signaling pathway. Cancer Med 2022; 11:3657-3673. [PMID: 35384355 PMCID: PMC9554449 DOI: 10.1002/cam4.4734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 01/31/2022] [Accepted: 03/18/2022] [Indexed: 12/24/2022] Open
Abstract
LIM homeobox 6 (LHX6) has been reported to be downregulated and inhibits cell proliferation in various cancers. Alternative splicing of LHX6 leads to six annotated isoforms, which can be found in the NCBI database. However, the expression patterns and potential roles of these isoforms remain poorly characterized in cervical cancer. Here, we demonstrated that the LHX6 isoforms containing exon 12 (LHX6EX(+12) group) and isoforms lacking exon 12 (LHX6EX(-12) group) were differentially expressed in cervical tissue by qRT-PCR. The mRNA expression level of LHX6EX(+12) group was higher than that of LHX6EX(-12) group in cervical cancer tissue. Knockdown of LHX6EX(+12) group and all LHX6 isoforms (LHX6All group) inhibited cell growth, increased cell apoptosis, and induced cell cycle arrest from G0/G1 phase to S phase in vitro. Consistently, overexpression of the LHX6EX(+12) group promoted cervical cancer cell proliferation in vitro. In contrast, no significant differences in cell proliferation were found between LHX6EX(-12) isoform knockdown group and its control. RNA-sequencing suggested that the LHX6EX(+12) isoform group might exert its cancer-promoting effects in cervical cancer via regulating MAPK signaling pathway. Downregulation of the LHX6EX(+12) group significantly suppressed the phosphorylation of MRK, ERK, JNK, and P38 at the protein level. We also identified some unique biological processes and signaling pathways in which each isoform group might be involved. In summary, our results indicated that LHX6EX(+12) isoform group was the dominant oncogenic type of LHX6 in cervical cancer, which may be a new biomarker and a potential precise therapeutic target for cervical cancer in the future.
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Affiliation(s)
- Ling Wang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ying Zhou
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Canhui Cao
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Shitong Lin
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenhua Zhi
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Danya Zhang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jie Li
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Rui Wei
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guiying Jiang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hanjie Xu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xueqian Wang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ling Xi
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Peng Wu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Teng Z, Hao L, Yang R, Song J, Wang Z, Jiao Y, Fang J, Zheng S, Ma Z, Chen X, Liu S, Cheng Y. Key pituitary miRNAs mediate the expression of pig GHRHR splice variants by regulating splice factors. Int J Biol Macromol 2022; 208:208-218. [PMID: 35306020 DOI: 10.1016/j.ijbiomac.2022.03.070] [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: 01/13/2022] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 11/28/2022]
Abstract
The growth hormone releasing hormone receptor (GHRHR) is well documented in organism growth and its alternative splicing may generate multiple functional GHRHR splice variants (SVs). Our previous study has demonstrated the key pituitary miRNAs (let-7e and miR-328-5p) in pig regulated the expression of GHRHR SVs by directly targeting to them. And according to recent reports, the interplay between miRNA-based silencing of mRNAs and alternative splicing of pre-mRNAs is a crucial post-transcriptional mechanism. In this study, SF3B3 and CPSF4 were firstly excavated as the splice factors that involved in the formation of GHRHR SVs mediated by let-7e and miR-328-5p through the comparation of the expression relations of GHRHR SVs, let-7e/miR-328-5p and SF3B3/CPSF4 in pituitary tissues between Landrace pigs and BaMa pigs, as well as the prediction of the target relations of let-7e/miR-328-5p with SF3B3 and/or CPSF4. SF3B3 and CPSF4 targeted by let-7e and miR-328-5p were further verified by performing dual-luciferase reporter assays and detecting the expression of target transcripts. Then the RT-PCR, RT-qPCR and Western blot assays were used to confirm SF3B3 and CPSF4 were involved in the formation of the GHRHR SVs, and in this process, let-7e and miR-328-5p mediated GHRHR SVs by regulating SF3B3 and CPSF4. Finally, the target site of SF3B3 on pre-GHRHR was on the Exon 12 to Exon14, while CPSF4 acted on the other fragments of the pre-GHRHR, which were explored by dual-luciferase reporter system preliminarily. To the best of our knowledge, this paper is the first to report the miRNAs regulate GHRHR SVs indirectly by splice factors.
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Affiliation(s)
- Zhaohui Teng
- College of Animal Science, Jilin University, Changchun, Jilin 130062, China
| | - Linlin Hao
- College of Animal Science, Jilin University, Changchun, Jilin 130062, China
| | - Rui Yang
- College of Animal Science, Jilin University, Changchun, Jilin 130062, China
| | - Jie Song
- College of Animal Science, Jilin University, Changchun, Jilin 130062, China
| | - Zhaoguo Wang
- College of Animal Science, Jilin University, Changchun, Jilin 130062, China
| | - Yingying Jiao
- College of Animal Science, Jilin University, Changchun, Jilin 130062, China
| | - Jiayuan Fang
- College of Animal Science, Jilin University, Changchun, Jilin 130062, China
| | - Shuo Zheng
- College of Animal Science, Jilin University, Changchun, Jilin 130062, China
| | - Ze Ma
- College of Animal Science, Jilin University, Changchun, Jilin 130062, China
| | - Xi Chen
- College of Animal Science, Jilin University, Changchun, Jilin 130062, China
| | - Songcai Liu
- College of Animal Science, Jilin University, Changchun, Jilin 130062, China
| | - Yunyun Cheng
- NHC Key Laboratory of Radiobiology, College of Public Health, Jilin University, Changchun 130021, China.
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22
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SF3B4 promotes ovarian cancer progression by regulating alternative splicing of RAD52. Cell Death Dis 2022; 13:179. [PMID: 35210412 PMCID: PMC8873359 DOI: 10.1038/s41419-022-04630-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 11/08/2022]
Abstract
Many studies have proven that splicing factors are crucial for human malignant tumor development. However, as a classical splicing factor, the expression of SF3B4 is not clear, and its biological function needs to be further clarified in ovarian cancer (OC). We determined that SF3B4 was obviously upregulated and its high expression was associated with poor prognosis in OC patients. In vitro and in vivo assays suggested that SF3B4 overexpression promoted OC cell proliferation and mobility, and downregulation of SF3B4 had the opposite effect. Further studies found that miR-509–3p decreased SF3B4 mRNA expression by binding to the 3’ -UTR of SF3B4 directly. Importantly, we revealed that RAD52 was a potential target of SF3B4 through alternative splicing events analysis. Loss of SF3B4 led to decreased expression of RAD52, owing to intron 8 retention and generation of premature termination codons. Moreover, decreased expression of RAD52 partially counteracted the tumor-promoting effect of SF3B4 overexpression. In conclusion, our results suggested that SF3B4, negatively regulated by miR-509–3p, promoted OC progression through effective splicing of RAD52. Therefore, SF3B4 may be a promising biomarker and effective therapeutic target for OC.
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Alternative Splicing, Epigenetic Modifications and Cancer: A Dangerous Triangle, or a Hopeful One? Cancers (Basel) 2022; 14:cancers14030560. [PMID: 35158828 PMCID: PMC8833605 DOI: 10.3390/cancers14030560] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Epigenetics studies the alteration of gene expression without changing DNA sequence and very often, epigenetic dysregulation causes cancer. Alternative splicing is a mechanism that results in the production of several mRNA isoforms from a single gene and aberrant splicing is also a frequent cause of cancer. The present review is built on the interrelations of epigenetics and alternative splicing. In an intuitive way, we say that epigenetic modifications and alternative splicing are at two vertices of a triangle, the third vertex being occupied by cancer. Interconnection between alternative splicing and epigenetic modifications occurs backward and forward and the mechanisms involved are widely reviewed. These connections also provide novel diagnostic or prognostic tools, which are listed. Finally, as epigenetic alterations are reversible and aberrant alternative splicing may be corrected, the therapeutic possibilities to break the triangle are discussed. Abstract The alteration of epigenetic modifications often causes cancer onset and development. In a similar way, aberrant alternative splicing may result in oncogenic products. These issues have often been individually reviewed, but there is a growing body of evidence for the interconnection of both causes of cancer. Actually, aberrant splicing may result from abnormal epigenetic signalization and epigenetic factors may be altered by alternative splicing. In this way, the interrelation between epigenetic marks and alternative splicing form the base of a triangle, while cancer may be placed at the vertex. The present review centers on the interconnections at the triangle base, i.e., between alternative splicing and epigenetic modifications, which may result in neoplastic transformations. The effects of different epigenetic factors, including DNA and histone modifications, the binding of non-coding RNAs and the alterations of chromatin organization on alternative splicing resulting in cancer are first considered. Other less-frequently considered questions, such as the epigenetic regulation of the splicing machinery, the aberrant splicing of epigenetic writers, readers and erasers, etc., are next reviewed in their connection with cancer. The knowledge of the above-mentioned relationships has allowed increasing the collection of biomarkers potentially useful as cancer diagnostic and/or prognostic tools. Finally, taking into account on one hand that epigenetic changes are reversible, and some epigenetic drugs already exist and, on the other hand, that drugs intended for reversing aberrations in alternative splicing, therapeutic possibilities for breaking the mentioned cancer-related triangle are discussed.
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Hu L, Yang K, Mai X, Wei J, Ma C. Depleted HDAC3 attenuates hyperuricemia-induced renal interstitial fibrosis via miR-19b-3p/SF3B3 axis. Cell Cycle 2022; 21:450-461. [PMID: 35025700 PMCID: PMC8942505 DOI: 10.1080/15384101.2021.1989899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Dysfunctional histone deacetylases (HDACs) elicit unrestrained fibrosis and damage to organs. With regard to the link between HDACs and fibrosis, this research is practiced to decipher the concrete mechanism of HDAC3 in hyperuricemia (HN)-induced renal interstitial fibrosis (RIF) from microRNA-19b-3p/splicing factor 3b subunit 3 (miR-19b-3p/SF3B3) axis.The HN model was established on rats to induce RIF by oral administration of adenine and potassium oxalate. HN rats were injected with miR-19b-3p- or HDAC3-related vectors to figure out their effects on RIF through detecting 24-h urine protein, uric acid (UA), blood urea nitrogen (BUN) and serum creatinine (Scr) contents and α-smooth muscle actin (α-SMA), transforming growth factor β1 (TGF-β1) and fibronectin (FN) contents in renal tissues and observing pathological damages and RIF index of renal tissues. HDAC3, miR-19b-3p and SF3B3 expression in renal tissues were tested, along with their interactions.Elevated HDAC3 and SF3B3 and reduced miR-19b-3p were displayed in renal tissues of HN rats. Suppressed HDAC3 or promoted miR-19b-3p relieved HN-induced RIF, as reflected by their inhibitory effects on 24 h urine protein, UA, BUN, Scr, α-SMA, TGF-β1, and FN contents and RIF index and their ameliorated effects on pathological damages of renal tissues. HDAC3 bound to the promoter of miR-19b-3p to regulate SF3B3. MiR-19b-3p depletion abrogated down-regulated HDAC3-induced effects on HN-induced RIF.It is delineated that depressed HDAC3 relives HN-induced RIF through restoring miR-19b-3p and knocking down SF3B3, replenishing the references for RIF curing.
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Affiliation(s)
- Langtao Hu
- Department of Nephrology, Hainan General Hospital, Haikou, China.,Department of Nephrology, Hainan Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Kai Yang
- Department of Nephrology, Hainan General Hospital, Haikou, China.,Department of Nephrology, Hainan Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Xing Mai
- Department of Nephrology, Hainan General Hospital, Haikou, China.,Department of Nephrology, Hainan Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Jiali Wei
- Department of Nephrology, Hainan General Hospital, Haikou, China.,Department of Nephrology, Hainan Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Chunyang Ma
- Department of Neurosurgery, First Affiliated Hospital of Hainan Medical College, Haikou, China
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Zhou Y, Yang Z, Zhang H, Li H, Zhang M, Wang H, Zhang M, Qiu P, Zhang R, Liu J. DNMT3A facilitates colorectal cancer progression via regulating DAB2IP mediated MEK/ERK activation. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166353. [DOI: 10.1016/j.bbadis.2022.166353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 12/16/2022]
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Zhang Y, Hua X, Shi H, Zhang L, Xiao H, Liang C. Systematic analyses of the role of prognostic and immunological EIF3A, a reader protein, in clear cell renal cell carcinoma. Cancer Cell Int 2021; 21:680. [PMID: 34923969 PMCID: PMC8684683 DOI: 10.1186/s12935-021-02364-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/24/2021] [Indexed: 02/08/2023] Open
Abstract
Background Eukaryotic initiation factor 3a (EIF3A), a “reader” protein for RNA methylation, has been found to be involved in promoting tumorigenesis in a variety of cancers. The impact of EIF3A in clear cell renal cell carcinoma (ccRCC) has yet to be reported. This study aimed to identify the prognostic value of EIF3A in ccRCC and investigate the relationship between EIF3A expression and immune infiltration. Methods We collected 29 m6A-related mRNA data and clinicopathological parameters from The Cancer Genome Atlas (TCGA) database. Logistic regression analyses were used to analyse the correlation between EIF3A expression and clinical characteristics. Immunohistochemistry (IHC) was applied to examine EIF3A levels in normal and ccRCC tissues. Univariate and multivariate analyses were conducted to recognize independent factors associated with overall survival (OS) and disease-free survival (DFS). The nomogram aimed to predict the 1-, 3- and 5-year survival probabilities. Gene set enrichment analysis (GSEA) was carried out to determine the potential functions and related signalling pathways of EIF3A expression. To investigate EIF3A of coexpressed genes, we used LinkedOmics, and the results were subjected to enrichment analysis. Simultaneously, LinkedOmics and STRING datasets were used to identify EIF3A coexpressed genes that were visualized via Cytoscape. Finally, we evaluated whether EIF3A expression correlated with the infiltration of immune cells and the expression of marker genes in ccRCC by Tumour Immune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA). Result EIF3A expression was significantly different between ccRCC tissues and normal tissues. EIF3A expression was correlated with poor prognostic clinicopathological factors, and K–M analyses revealed that low EIF3A expression was correlated with a poor prognosis. The results of univariate and multivariate analyses proved that EIF3A was a prognostic factor in ccRCC patients. GSEA results indicated that EIF3A high expression was enriched in the renal cell carcinoma pathway. EIF3A expression was significantly positively correlated with B cells, CD8 + T cells, CD4 + T cells, neutrophils, macrophages, and dendritic cells. Furthermore, EIF3A expression was associated with most marker genes of immune cells. Conclusions EIF3A could serve as a potential biomarker for prognostic and diagnostic stratification of ccRCC and is related to immune cell infiltrates. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02364-2.
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Affiliation(s)
- Yi Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, Anhui, China
| | - Xiaoliang Hua
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
| | - Haoqiang Shi
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, Anhui, China.,Institute of Urology, Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, Anhui, China.,Institute of Urology, Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Haibing Xiao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, Anhui, China. .,Institute of Urology, Anhui Medical University, Hefei, Anhui, China. .,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China.
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, Anhui, China. .,Institute of Urology, Anhui Medical University, Hefei, Anhui, China. .,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China.
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27
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Impact of alternative splicing on mechanisms of resistance to anticancer drugs. Biochem Pharmacol 2021; 193:114810. [PMID: 34673012 DOI: 10.1016/j.bcp.2021.114810] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022]
Abstract
A shared characteristic of many tumors is the lack of response to anticancer drugs. Multiple mechanisms of pharmacoresistance (MPRs) are involved in permitting cancer cells to overcome the effect of these agents. Pharmacoresistance can be primary (intrinsic) or secondary (acquired), i.e., triggered or enhanced in response to the treatment. Moreover, MPRs usually result in the lack of sensitivity to several agents, which accounts for diverse multidrug-resistant (MDR) phenotypes. MPRs are based on the dynamic expression of more than one hundred genes, constituting the so-called resistome. Alternative splicing (AS) during pre-mRNA maturation results in changes affecting proteins involved in the resistome. The resulting splicing variants (SVs) reduce the efficacy of anticancer drugs by lowering the intracellular levels of active agents, altering molecular targets, enhancing both DNA repair ability and defensive mechanism of tumors, inducing changes in the balance between pro-survival and pro-apoptosis signals, modifying interactions with the tumor microenvironment, and favoring malignant phenotypic transitions. Reasons accounting for cancer-associated aberrant splicing include mutations that create or disrupt splicing sites or splicing enhancers or silencers, abnormal expression of splicing factors, and impaired signaling pathways affecting the activity of the splicing machinery. Here we have reviewed the impact of AS on MPR in cancer cells.
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Alaterre E, Vikova V, Kassambara A, Bruyer A, Robert N, Requirand G, Bret C, Herbaux C, Vincent L, Cartron G, Elemento O, Moreaux J. RNA-Sequencing-Based Transcriptomic Score with Prognostic and Theranostic Values in Multiple Myeloma. J Pers Med 2021; 11:jpm11100988. [PMID: 34683129 PMCID: PMC8541503 DOI: 10.3390/jpm11100988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 12/11/2022] Open
Abstract
Multiple myeloma (MM) is the second most frequent hematological cancer and is characterized by the clonal proliferation of malignant plasma cells. Genome-wide expression profiling (GEP) analysis with DNA microarrays has emerged as a powerful tool for biomedical research, generating a huge amount of data. Microarray analyses have improved our understanding of MM disease and have led to important clinical applications. In MM, GEP has been used to stratify patients, define risk, identify therapeutic targets, predict treatment response, and understand drug resistance. In this study, we built a gene risk score for 267 genes using RNA-seq data that demonstrated a prognostic value in two independent cohorts (n = 674 and n = 76) of newly diagnosed MM patients treated with high-dose Melphalan and autologous stem cell transplantation. High-risk patients were associated with the expression of genes involved in several major pathways implicated in MM pathophysiology, including interferon response, cell proliferation, hypoxia, IL-6 signaling pathway, stem cell genes, MYC, and epigenetic deregulation. The RNA-seq-based risk score was correlated with specific MM somatic mutation profiles and responses to targeted treatment including EZH2, MELK, TOPK/PBK, and Aurora kinase inhibitors, outlining potential utility for precision medicine strategies in MM.
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Affiliation(s)
- Elina Alaterre
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
| | - Veronika Vikova
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
| | - Alboukadel Kassambara
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
- Diag2Tec, 34395 Montpellier, France
| | - Angélique Bruyer
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
- Diag2Tec, 34395 Montpellier, France
| | - Nicolas Robert
- Department of Biological Hematology, CHU Montpellier, 34395 Montpellier, France; (N.R.); (G.R.)
| | - Guilhem Requirand
- Department of Biological Hematology, CHU Montpellier, 34395 Montpellier, France; (N.R.); (G.R.)
| | - Caroline Bret
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
- Department of Biological Hematology, CHU Montpellier, 34395 Montpellier, France; (N.R.); (G.R.)
- UFR de Médecine, University of Montpellier, 34003 Montpellier, France;
| | - Charles Herbaux
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
- UFR de Médecine, University of Montpellier, 34003 Montpellier, France;
- Department of Clinical Hematology, CHU Montpellier, 34395 Montpellier, France;
| | - Laure Vincent
- Department of Clinical Hematology, CHU Montpellier, 34395 Montpellier, France;
| | - Guillaume Cartron
- UFR de Médecine, University of Montpellier, 34003 Montpellier, France;
- Department of Clinical Hematology, CHU Montpellier, 34395 Montpellier, France;
- IGMM, UMR CNRS-UM 5535, 34090 Montpellier, France
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Jérôme Moreaux
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
- Department of Biological Hematology, CHU Montpellier, 34395 Montpellier, France; (N.R.); (G.R.)
- UFR de Médecine, University of Montpellier, 34003 Montpellier, France;
- IUF, Institut Universitaire de France, 75005 Paris, France
- Correspondence: ; Tel.: +33-(0)4-67-33-79-03
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Jin X, Liu L, Wu J, Jin X, Yu G, Jia L, Wang F, Shi M, Lu H, Liu J, Liu D, Yang J, Li H, Ni Y, Luo Q, Jia W, Wang W, Chen W. A multi-omics study delineates new molecular features and therapeutic targets for esophageal squamous cell carcinoma. Clin Transl Med 2021; 11:e538. [PMID: 34586744 PMCID: PMC8473482 DOI: 10.1002/ctm2.538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/16/2021] [Accepted: 08/02/2021] [Indexed: 12/13/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a major histological subtype of esophageal cancer with inferior prognosis. Here, we conducted comprehensive transcriptomic, proteomic, phosphoproteomic, and metabolomic characterization of human, treatment-naive ESCC and paired normal adjacent tissues (cohort 1, n = 24) in an effort to identify new molecular vulnerabilities for ESCC and potential therapeutic targets. Integrative analysis revealed a small group of genes that were related to the active posttranscriptional and posttranslational regulation of ESCC. By using proteomic, phosphoproteomic, and metabolomic data, networks of ESCC-related signaling and metabolic pathways that were closely linked to cancer etiology were unraveled. Notably, integrative analysis of proteomic and phosphoproteomic data pinpointed that certain pathways involved in RNA transcription, processing, and metabolism were stimulated in ESCC. Importantly, proteins with close linkage to ESCC prognosis were identified. By enrolling an ESCC patient cohort 2 (n = 41), three top-ranked prognostic proteins X-prolyl aminopeptidase 3 (XPNPEP3), bromodomain PHD finger transcription factor (BPTF), and fibrillarin (FBL) were verified to have increased expression in ESCC. Among these prognostic proteins, only FBL, a well-known nucleolar methyltransferase, was essential for ESCC cell growth in vitro and in vivo. Furthermore, a validation study using an ESCC patient cohort 3 (n = 100) demonstrated that high FBL expression predicted unfavorable patient survival. Finally, common cancer/testis antigens and established cancer drivers and kinases, all of which could direct therapeutic decisions, were characterized. Collectively, our multi-omics analyses delineated new molecular features associated with ESCC pathobiology involving epigenetic, posttranscriptional, posttranslational, and metabolic characteristics, and unveiled new molecular vulnerabilities with therapeutic potential for ESCC.
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Affiliation(s)
- Xing Jin
- Cancer InstituteLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Lei Liu
- Department of Thoracic SurgeryThe Affiliated Tumor Hospital of Nantong UniversityNantongChina
| | - Jia Wu
- Cancer InstituteLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Xiaoxia Jin
- Department of PathologyThe Affiliated Tumor Hospital of Nantong UniversityNantongChina
| | - Guanzhen Yu
- Cancer InstituteLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Lijun Jia
- Cancer InstituteLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Fengying Wang
- Cancer InstituteLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Minxin Shi
- Department of Thoracic SurgeryThe Affiliated Tumor Hospital of Nantong UniversityNantongChina
| | - Haimin Lu
- Department of Thoracic SurgeryThe Affiliated Tumor Hospital of Nantong UniversityNantongChina
| | - Jibin Liu
- Department of Thoracic SurgeryThe Affiliated Tumor Hospital of Nantong UniversityNantongChina
| | - Dan Liu
- Cancer InstituteLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Jing Yang
- Cancer InstituteLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Hua Li
- Bio‐ID CenterSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
| | - Yan Ni
- The Children's HospitalNational Clinical Research Center for Child HealthZhejiang University School of MedicineHangzhouChina
| | - Qin Luo
- Cancer InstituteLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Wei Jia
- Hong Kong Traditional Chinese Medicine Phenome Research CenterSchool of Chinese MedicineHong Kong Baptist UniversityKowloon TongHong KongChina
| | - Wei Wang
- Department of Thoracic SurgeryThe Affiliated Tumor Hospital of Nantong UniversityNantongChina
| | - Wen‐Lian Chen
- Cancer InstituteLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
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Wu T, Wang W, Wang Y, Yao M, Du L, Zhang X, Huang Y, Wang J, Yu H, Bian X. Comprehensive analysis of alternative splicing profiling reveals novel events associated with prognosis and the infiltration of immune cells in prostate cancer. Transl Androl Urol 2021; 10:3056-3068. [PMID: 34430408 PMCID: PMC8350246 DOI: 10.21037/tau-21-585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/16/2021] [Indexed: 11/17/2022] Open
Abstract
Background Alternative splicing (AS) is believed to play a vital role in tumor development. Therefore, comprehensive investigation of AS and its biological function in prostate cancer (PCa) is crucial. Methods The AS profiling of 489 patients with PCa was obtained from The Cancer Genome Atlas (TCGA) SpliceSeq database. Bioinformatics tools were used to describe splicing associations and build prognostic models. Unsupervised clustering of the determined prognostic AS events and the relationship with immune characteristics were also explored. Results In total, 20,723 AS events were detected and 2,805 were identified in PCa. In the regulatory networks, the data suggested a significant correlation between splicing factor (SF) expression and AS events. To stratify the progression risk of PCa patients, prognostic models were constructed using splicing patterns. Six AS events were screened out as independent prognostic factors for progression-free survival. Based on the gene features, we constructed the combined prognostic predictors model, and the receiver operating characteristic (ROC) curve for this model reached a high area under the ROC curve (AUC) of 0.729793, indicating a favorable ability to predict patient outcomes. Through unsupervised clustering analysis, the correlations between AS-based clusters and prognosis as well as immune characteristics were revealed. The correlation analysis on TIMER revealed the relationship between gene expression and immune cell infiltration. Conclusions This in-depth genome-wide analysis of the AS profiling in PCa revealed unique AS events associated with cancer progression and the infiltration of immune cells, with potential for predicting outcomes and therapeutic responses.
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Affiliation(s)
- Tianqi Wu
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Radiotherapy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenfeng Wang
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yanhao Wang
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Mengfei Yao
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Leilei Du
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xingming Zhang
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yongqiang Huang
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jianhua Wang
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Hongbo Yu
- Department of Urology, Affiliated Mingji Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaojie Bian
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
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31
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Lang X, Chen Z, Yang X, Yan Q, Xu M, Liu W, He Q, Zhang Y, Cheng W, Zhao W. Scutellarein induces apoptosis and inhibits proliferation, migration, and invasion in ovarian cancer via inhibition of EZH2/FOXO1 signaling. J Biochem Mol Toxicol 2021; 35:e22870. [PMID: 34350670 DOI: 10.1002/jbt.22870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 03/31/2021] [Accepted: 07/23/2021] [Indexed: 01/11/2023]
Abstract
Scutellarein, a flavone found in the perennial herb Scutellaria baicalensis, has antitumorigenic activity in multiple human cancers. However, whether scutellarein can attenuate ovarian cancer (OC) is unclear. This study investigated the effects of scutellarein in OC. In vitro cell viability was assessed using MTT assay whereas proliferation was assessed using 5-ethynyl-2'-deoxyuridine and colony formation assays. Cell apoptosis was detected by an Annexin V-fluorescein isothiocyanate/propidium iodide assay. Wound-healing and Transwell assays were used to determine cell migration and invasion. The differential expression of enhancer of zeste homolog 2 (EZH2) and forkhead box protein O1 (FOXO1) was measured by Quantitative real-time PCR and western blot analysis. We found that scutellarein inhibited viability, migration, invasion of A2780 and SKOV-3 cells, and reduced the expression of EZH2 in OC cells. In addition, FOXO1 was downregulated in OC tissues and cells and negatively regulated by EZH2. Also, scutellarein inhibited tumor growth and metastasis in vivo. In conclusion, scutellarein alleviates OC by the regulation of EZH2/FOXO1 signaling.
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Affiliation(s)
- Xiao Lang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Zheng Chen
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Xingyu Yang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Qi Yan
- Department of Obstetrics and Gynecology, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Manfei Xu
- Department of Obstetrics and Gynecology, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Wei Liu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Qin He
- Department of Obstetrics and Gynecology, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Yue Zhang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Weiwei Cheng
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Wenxia Zhao
- Department of Obstetrics and Gynecology, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
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32
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Mehterov N, Kazakova M, Sbirkov Y, Vladimirov B, Belev N, Yaneva G, Todorova K, Hayrabedyan S, Sarafian V. Alternative RNA Splicing-The Trojan Horse of Cancer Cells in Chemotherapy. Genes (Basel) 2021; 12:genes12071085. [PMID: 34356101 PMCID: PMC8306420 DOI: 10.3390/genes12071085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Almost all transcribed human genes undergo alternative RNA splicing, which increases the diversity of the coding and non-coding cellular landscape. The resultant gene products might have distinctly different and, in some cases, even opposite functions. Therefore, the abnormal regulation of alternative splicing plays a crucial role in malignant transformation, development, and progression, a fact supported by the distinct splicing profiles identified in both healthy and tumor cells. Drug resistance, resulting in treatment failure, still remains a major challenge for current cancer therapy. Furthermore, tumor cells often take advantage of aberrant RNA splicing to overcome the toxicity of the administered chemotherapeutic agents. Thus, deciphering the alternative RNA splicing variants in tumor cells would provide opportunities for designing novel therapeutics combating cancer more efficiently. In the present review, we provide a comprehensive outline of the recent findings in alternative splicing in the most common neoplasms, including lung, breast, prostate, head and neck, glioma, colon, and blood malignancies. Molecular mechanisms developed by cancer cells to promote oncogenesis as well as to evade anticancer drug treatment and the subsequent chemotherapy failure are also discussed. Taken together, these findings offer novel opportunities for future studies and the development of targeted therapy for cancer-specific splicing variants.
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Affiliation(s)
- Nikolay Mehterov
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Maria Kazakova
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Yordan Sbirkov
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Boyan Vladimirov
- Department of Maxillofacial Surgery, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria;
| | - Nikolay Belev
- Medical Simulation and Training Center, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria;
| | - Galina Yaneva
- Department of Biology, Faculty of Pharmacy, Medical University of Varna, 9002 Varna, Bulgaria;
| | - Krassimira Todorova
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (K.T.); (S.H.)
| | - Soren Hayrabedyan
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (K.T.); (S.H.)
| | - Victoria Sarafian
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
- Correspondence: ; Tel.: +359-882-512-952
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Lin YH, Wu MH, Liu YC, Lyu PC, Yeh CT, Lin KH. LINC01348 suppresses hepatocellular carcinoma metastasis through inhibition of SF3B3-mediated EZH2 pre-mRNA splicing. Oncogene 2021; 40:4675-4685. [PMID: 34140643 DOI: 10.1038/s41388-021-01905-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 12/11/2022]
Abstract
Long non-coding RNAs (lncRNA) play crucial roles in hepatocellular carcinoma (HCC) progression. However, the specific functions of lncRNAs in alternative splicing (AS) and the metastatic cascade in liver cancer remain largely unclear. In this study, we identified a novel lncRNA, LINC01348, which was significantly downregulated in HCC and correlated with survival functions in HCC patients. Ectopic expression of LINC01348 induced marked inhibition of cell growth, and metastasis in vitro and in vivo. Conversely, these phenotypes were reversed upon knockdown of LINC01348. Mechanistically, LINC01348 complexed with splicing factor 3b subunit 3 (SF3B3) acted as a modulator of EZH2 pre-mRNA AS, and induced alterations in JNK/c-Jun activity and expression of Snail. Notably, C-terminal truncated HBx (Ct-HBx) negatively regulated LINC01348 through c-Jun signaling. Our data collectively highlight those novel regulatory associations involving LINC01348/SF3B3/EZH2/JNK/c-Jun/Snail are an important determinant of metastasis in HCC cells and support the potential utility of targeting LINC01348 as a therapeutic strategy for HCC.
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Affiliation(s)
- Yang-Hsiang Lin
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Meng-Han Wu
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Chung Liu
- Institute of Population Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Chau-Ting Yeh
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.
| | - Kwang-Huei Lin
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan.
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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Yazhini A, Sandhya S, Srinivasan N. Rewards of divergence in sequences, 3-D structures and dynamics of yeast and human spliceosome SF3b complexes. Curr Res Struct Biol 2021; 3:133-145. [PMID: 35028595 PMCID: PMC8714771 DOI: 10.1016/j.crstbi.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 12/21/2022] Open
Abstract
The evolution of homologous and functionally equivalent multiprotein assemblies is intriguing considering sequence divergence of constituent proteins. Here, we studied the implications of protein sequence divergence on the structure, dynamics and function of homologous yeast and human SF3b spliceosomal subcomplexes. Human and yeast SF3b comprise of 7 and 6 proteins respectively, with all yeast proteins homologous to their human counterparts at moderate sequence identity. SF3b6, an additional component in the human SF3b, interacts with the N-terminal extension of SF3b1 while the yeast homologue Hsh155 lacks the equivalent region. Through detailed homology studies, we show that SF3b6 is absent not only in yeast but in multiple lineages of eukaryotes implying that it is critical in specific organisms. We probed for the potential role of SF3b6 in the spliceosome assembled form through structural and flexibility analyses. By analysing normal modes derived from anisotropic network models of SF3b1, we demonstrate that when SF3b1 is bound to SF3b6, similarities in the magnitude of residue motions (0.86) and inter-residue correlated motions (0.94) with Hsh155 are significantly higher than when SF3b1 is considered in isolation (0.21 and 0.89 respectively). We observed that SF3b6 promotes functionally relevant 'open-to-close' transition in SF3b1 by enhancing concerted residue motions. Such motions are found to occur in the Hsh155 without SF3b6. The presence of SF3b6 influences motions of 16 residues that interact with U2 snRNA/branchpoint duplex and supports the participation of its interface residues in long-range communication in the SF3b1. These results advocate that SF3b6 potentially acts as an allosteric regulator of SF3b1 for BPS selection and might play a role in alternative splicing. Furthermore, we observe variability in the relative orientation of SF3b4 and in the local structure of three β-propeller domains of SF3b3 with reference to their yeast counterparts. Such differences influence the inter-protein interactions of SF3b between these two organisms. Together, our findings highlight features of SF3b evolution and suggests that the human SF3b may have evolved sophisticated mechanisms to fine tune its molecular function.
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Key Words
- Allostery
- BPS, branch-point sequence
- Bact, activated B spliceosome assembly
- Cryo-EM structure
- Cryo-EM, cryo-electron microscopy
- DOPE, discrete optimized protein energy
- NMA, normal mode analysis
- PDB, protein data bank
- Protein dynamics
- RMSD, root mean square deviation
- RRM, RNA recognition motif
- SF3b complex
- SF3b1
- SF3b1SF3b6−bound, SF3b1 bound to SF3b6
- SF3b1iso, SF3b1 in isolation
- SIP, square inner product
- Spliceosome
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Affiliation(s)
- Arangasamy Yazhini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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Gong Y, Liu Y, Wang T, Li Z, Gao L, Chen H, Shu Y, Li Y, Xu H, Zhou Z, Dai L. Age-Associated Proteomic Signatures and Potential Clinically Actionable Targets of Colorectal Cancer. Mol Cell Proteomics 2021; 20:100115. [PMID: 34129943 PMCID: PMC8441843 DOI: 10.1016/j.mcpro.2021.100115] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/04/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The occurrence and prevalence of colorectal cancer (CRC) is closely associated with age. More than 90% of patients with CRC are diagnosed after 50 years of age. However, CRC incidence of young individuals has been increasing since 1990s, whereas the overall CRC frequency is declining. Distinct overall survival rates between young and aged patients with CRC have been established. Tremendous efforts have been made to clarify the underlying mechanisms of age-dependent clinical differences, but it still remains elusive. Here, we performed proteomic profiling of 50 patients with CRC and revealed proteomic signatures of CRC across age groups. Gene set enrichment analysis showed that distinct age-dependent clinical outcomes might mainly attribute to varied MYC targets V1/V2, E2F targets and G2M checkpoint gene sets, which were associated with cancer cell proliferation, cell apoptosis, tumor growth, and tumor metastasis. Multiple linear regression analysis revealed a large number of functional proteins, such as NOP2, CSE1L, NHP2, NOC2L and CDK1, with adjusted expression significantly correlated with age (p < 0.05). Among them, NHP2 is a core component of the telomerase complex associated with age. High NHP2 expression predicted poor overall survival, with a more significant correlation in aged patients with CRC. Knockdown of NHP2 significantly suppressed cancer cell proliferation. In addition, we revealed some age-related potential clinically actionable targets, such as PSEN1, TSPO, and CDK1, which might be more suitable for patients with late-onset CRC. Collectively, this study identifies age-associated proteomic signatures and potential therapeutic targets of CRC and may help make a precise decision on CRC treatment. The proteomic signatures of early-onset CRC are disclosed. Alterations of some proteins between cancerous and normal tissues are age-correlated. NHP2, overexpressed in tumors especially in aged patients, predicts poor prognosis. Potential age-dependent druggable targets and their inhibitors are summarized.
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Affiliation(s)
- Yanqiu Gong
- Department of Gastrointestinal Surgery, National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yu Liu
- Department of Gastrointestinal Surgery, National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Tian Wang
- Life Science Mass Spectrometry Service Department, Thermo Fisher Scientific (China) Co, Chengdu, China
| | - Zhigui Li
- Department of Gastrointestinal Surgery, National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Li Gao
- Department of Gastrointestinal Surgery, National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Haining Chen
- Department of Gastrointestinal Surgery, National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yang Shu
- Department of Gastrointestinal Surgery, National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yuan Li
- Department of Gastrointestinal Surgery, National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Heng Xu
- Department of Gastrointestinal Surgery, National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Zongguang Zhou
- Department of Gastrointestinal Surgery, National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China.
| | - Lunzhi Dai
- Department of Gastrointestinal Surgery, National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China.
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36
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Zeng J, Xu H, Huang C, Sun Y, Xiao H, Yu G, Zhou H, Zhang Y, Yao W, Xiao W, Hu J, Wu L, Xing J, Wang T, Chen Z, Ye Z, Chen K. CD46 splice variant enhances translation of specific mRNAs linked to an aggressive tumor cell phenotype in bladder cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:140-153. [PMID: 33767911 PMCID: PMC7972933 DOI: 10.1016/j.omtn.2021.02.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/19/2021] [Indexed: 01/02/2023]
Abstract
CD46 is well known to be involved in diverse biological processes. Although several splice variants of CD46 have been identified, little is known about the contribution of alternative splicing to its tumorigenic functions. In this study, we found that exclusion of CD46 exon 13 is significantly increased in bladder cancer (BCa) samples. In BCa cell lines, enforced expression of CD46-CYT2 (exon 13-skipping isoform) promoted, and CD46-CYT1 (exon 13-containing isoform) attenuated, cell growth, migration, and tumorigenicity in a xenograft model. We also applied interaction proteomics to identify exhaustively the complexes containing the CYT1 or CYT2 domain in EJ-1 cells. 320 proteins were identified that interact with the CYT1 and/or CYT2 domain, and most of them are new interactors. Using an internal ribosome entry site (IRES)-dependent reporter system, we established that CD46 could regulate mRNA translation through an interaction with the translation machinery. We also identified heterogeneous nuclear ribonucleoprotein (hnRNP)A1 as a novel CYT2 binding partner, and this interaction facilitates the interaction of hnRNPA1 with IRES RNA to promote IRES-dependent translation of HIF1a and c-Myc. Strikingly, the splicing factor SRSF1 is highly correlated with CD46 exon 13 exclusion in clinical BCa samples. Taken together, our findings contribute to understanding the role of CD46 in BCa development.
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Affiliation(s)
- Jin Zeng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330000, P.R. China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
| | - Chunhua Huang
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, P.R. China
| | - Yi Sun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
| | - Haibing Xiao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
| | - Gan Yu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
| | - Hui Zhou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
| | - Yangjun Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
| | - Weimin Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
| | - Wei Xiao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
| | - Junhui Hu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Lily Wu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Jinchun Xing
- Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, P.R. China
| | - Tao Wang
- Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, P.R. China
| | - Zhiqiang Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
- Hubei Institute of Urology, Wuhan 430030, P.R. China
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Anwar T, Gonzalez ME, Kleer CG. Noncanonical Functions of the Polycomb Group Protein EZH2 in Breast Cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2021; 191:774-783. [PMID: 33556366 PMCID: PMC8127103 DOI: 10.1016/j.ajpath.2021.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/19/2021] [Indexed: 12/23/2022]
Abstract
Enhancer of Zeste Homologue 2 (EZH2) is the catalytic subunit of the polycomb repressive complex 2 (PRC2) that is critical for determining cell identity. An epigenetic writer, EZH2 has a well-defined role in transcriptional repression by depositing trimethyl marks on lysine 27 of histone H3. However, there is mounting evidence that histone methyltransferases like EZH2 exert histone methyltransferase-independent functions. The relevance of these functions to breast cancer progression and their regulatory mechanisms are only beginning to become understood. Here, we review the current understanding of EZH2 H3K27me3-independent, noncanonical, functions and their regulation in breast cancer.
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Affiliation(s)
- Talha Anwar
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Maria E Gonzalez
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Celina G Kleer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.
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Hu J, Cai D, Zhao Z, Zhong GC, Gong J. Suppression of Heterogeneous Nuclear Ribonucleoprotein C Inhibit Hepatocellular Carcinoma Proliferation, Migration, and Invasion via Ras/MAPK Signaling Pathway. Front Oncol 2021; 11:659676. [PMID: 33937074 PMCID: PMC8087488 DOI: 10.3389/fonc.2021.659676] [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: 01/28/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC), the most common malignant tumor, has high fatality and recurrence rates. Accumulating evidence shows that heterogeneous nuclear ribonucleoprotein C (HNRNPC), which is mainly involved in RNA splicing, export, and translation, promotes progression and metastasis of multiple tumor types; however, the effects of HNRNPC in HCC are unknown. In the present study, high levels of HNRNPC were detected in tumor tissues compared with para-tumor tissues by immunohistochemical and western blot assays. Furthermore, Cox proportional hazards regression models, the Kaplan–Meier method, and clinicopathologic features analysis showed that HNRNPC was not only an independent prognostic factor for both overall and disease-free survival in HCC but also a predictor of large tumor size and advanced tumor stage. Functional experiments revealed that silencing of HNRNPC not only led to arrest of more HCC cells at G0/G1 phase to inhibit their proliferation, but also suppressed EMT process to block their invasion, and migration in vitro; this was related to the Ras/MAPK signaling pathway. In addition, blocking of HCC cell proliferation regulated by HNRNPC silencing was observed in vivo. Finally, rescue tests showed that after recovery of Ras/MAPK signaling pathway activity by treatment with Ras agonists, the proliferation, migration, and invasion suppression of Huh-7 and Hep 3B cell lines caused by HNRNPC knockdown was partially reversed. Taken together, these results indicate that HNRNPC knockdown inhibits HCC cell proliferation, migration and invasion, in part via the Ras/MAPK signaling pathway. Thus, HNRNPC may have an important role in the progression of HCC and represents a promising biomarker for evaluation of prognosis and a potential therapeutic target in HCC patients.
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Affiliation(s)
- Jiejun Hu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dong Cai
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhibo Zhao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guo-Chao Zhong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jianping Gong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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39
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Raspin K, FitzGerald LM, Marthick JR, Field MA, Malley RC, Banks A, Donovan S, Thomson RJ, Foley GR, Stanford JL, Dickinson JL. A rare variant in EZH2 is associated with prostate cancer risk. Int J Cancer 2021; 149:1089-1099. [PMID: 33821477 DOI: 10.1002/ijc.33584] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 11/11/2022]
Abstract
Prostate cancer (PrCa) is highly heritable, and although rare variants contribute significantly to PrCa risk, few have been identified to date. Herein, whole-genome sequencing was performed in a large PrCa family featuring multiple affected relatives spanning several generations. A rare, predicted splice site EZH2 variant, rs78589034 (G > A), was identified as segregating with disease in all but two individuals in the family, one of whom was affected with lymphoma and bowel cancer and a female relative. This variant was significantly associated with disease risk in combined familial and sporadic PrCa datasets (n = 1551; odds ratio [OR] = 3.55, P = 1.20 × 10-5 ). Transcriptome analysis was performed on prostate tumour needle biopsies available for two rare variant carriers and two wild-type cases. Although no allele-dependent differences were detected in EZH2 transcripts, a distinct differential gene expression signature was observed when comparing prostate tissue from the rare variant carriers with the wild-type samples. The gene expression signature comprised known downstream targets of EZH2 and included the top-ranked genes, DUSP1, FOS, JUNB and EGR1, which were subsequently validated by qPCR. These data provide evidence that rs78589034 is associated with increased PrCa risk in Tasmanian men and further, that this variant may be associated with perturbed EZH2 function in prostate tissue. Disrupted EZH2 function is a driver of tumourigenesis in several cancers, including prostate, and is of significant interest as a therapeutic target.
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Affiliation(s)
- Kelsie Raspin
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - James R Marthick
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Matt A Field
- Australian Institute of Tropical Health and Medicine and Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Roslyn C Malley
- Hobart Pathology, Hobart, Tasmania, Australia.,Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Annette Banks
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Russell J Thomson
- Centre for Research in Mathematics and Data Science, Western Sydney University, Sydney, New South Wales, Australia
| | - Georgea R Foley
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Janet L Stanford
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
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40
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Zhang D, Zhang W, Sun R, Huang Z. Novel insights into clear cell renal cell carcinoma prognosis by comprehensive characterization of aberrant alternative splicing signature: a study based on large-scale sequencing data. Bioengineered 2021; 12:1091-1110. [PMID: 33783315 PMCID: PMC8806224 DOI: 10.1080/21655979.2021.1906096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common type with poor prognosis in kidney tumor. Growing evidence has indicated that aberrant alternative splicing (AS) events are efficacious signatures for tumor prognosis prediction and therapeutic targets. However, the detailed roles of AS events in ccRCC are largely unknown. In our study, level 3 RNA-seq data was acquired from The Cancer Genome Atlas dataset and corresponding AS profiles were detected with the assistance of SpliceSeq software. A total of 2100 aberrant survival-associated AS events were identified via differential expression and univariate cox regression analysis. The final prognostic panel formed by 17 specific events was developed by stepwise least absolute shrinkage and selection operator (LASSO) penalty, with the area under curve (AUC) values of receiver operator characteristic (ROC) curves keeping above 0.7 spanning 1 year to 5 years. And the results from functional enrichment analyses are unanimous that autophagy could be a potential mechanism of splicing regulation in ccRCC. Furthermore, splicing regulatory network was constructed via Spearman correlation between splicing factors and AS events. Finally, unsupervised clustering analysis revealed three clusters with distinct survival patterns, and associated with specific clinicopathological phenotypes. In overall, we developed a robust and individualized predictive model based on large-scale sequencing data. The identified AS events and splicing network may be valuable in deciphering the crucial posttranscriptional mechanisms on tumorigenesis of ccRCC.
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Affiliation(s)
- Dong Zhang
- Department of Breast Surgery, Qilu Hospital, Shandong University, Jinan, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenjie Zhang
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of General Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Rui Sun
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China
| | - Zhongxian Huang
- Department of Urology, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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41
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Fan Z, Zhang Z, Piao C, Liu Z, Wang Z, Kong C. Genome-Wide Analyses of Prognostic and Therapeutic Alternative Splicing Signatures in Bladder Urothelial Carcinoma. Front Oncol 2021; 11:626858. [PMID: 33842332 PMCID: PMC8033158 DOI: 10.3389/fonc.2021.626858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/10/2021] [Indexed: 11/29/2022] Open
Abstract
Background Alternative splicing (AS) is an indispensable post-transcriptional modification applied during the maturation of mRNA, and AS defects have been associated with many cancers. This study was designed to thoroughly analyze AS events in bladder urothelial carcinoma (BLCA) at the genome-wide level. Methods We adopted a gap analysis to screen for significant differential AS events (DASEs) associated with BLCA. DASEs with prognostic value for OS and the disease-free interval (DFI) were identified by Cox analysis. In addition, a differential AS network and AS clusters were identified using unsupervised cluster analysis. We examined differences in the sensitivity to chemotherapy and immunotherapy between BLCA patients with high and low overall survival (OS) risk. Results An extensive number of DASEs (296) were found to be clinically relevant in BLCA. A prognosis model was established based prognostic value of OS and DFI. CUGBP elav-like family member 2 (CELF2) was identified as a hub splicing factor for AS networks. We also identified AS clusters associated with OS using unsupervised cluster analysis, and we predicted that the effects of cisplatin and gemcitabine chemotherapy would be different between high- and low-risk groups based on OS prognosis. Conclusion We completed a comprehensive analysis of AS events in BLCA at the genome-wide level. The present findings revealed that DASEs and splicing factors tended to impact BLCA patient survival and sensitivity to chemotherapy drugs, which may provide novel prospects for BLCA therapies.
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Affiliation(s)
- Zhongru Fan
- Department of Urology, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China
| | - Zhe Zhang
- Department of Urology, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China
| | - Chiyuan Piao
- Department of Urology, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China
| | - Zhuona Liu
- Department of Urology, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China
| | - Zeshu Wang
- Department of Urology, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China
| | - Chuize Kong
- Department of Urology, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China
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MicroRNA-214 enriched exosomes from human cerebral endothelial cells (hCEC) sensitize hepatocellular carcinoma to anti-cancer drugs. Oncotarget 2021; 12:185-198. [PMID: 33613846 PMCID: PMC7869574 DOI: 10.18632/oncotarget.27879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/19/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver tumor worldwide. Current medical therapy for HCC has limited efficacy. The present study tests the hypothesis that human cerebral endothelial cell-derived exosomes carrying elevated miR-214 (hCEC-Exo-214) can amplify the efficacy of anti-cancer drugs on HCC cells. Treatment of HepG2 and Hep3B cells with hCEC-Exo-214 in combination with anti-cancer agents, oxaliplatin or sorafenib, significantly reduced cancer cell viability and invasion compared with monotherapy with either drug. Additionally, the therapeutic effect of the combination therapy was detected in primary tumor cells derived from patients with HCC. The ability of hCEC-Exo-214 in sensitizing HCC cells to anti-cancer drugs was specific, in that combination therapy did not affect the viability and invasion of human liver epithelial cells and non-cancer primary cells. Furthermore, compared to monotherapy with oxaliplatin and sorafenib, hCEC-Exo-214 in combination with either drug substantially reduced protein levels of P-glycoprotein (P-gp) and splicing factor 3B subunit 3 (SF3B3) in HCC cells. P-gp and SF3B3 are among miR-214 target genes and are known to mediate drug resistance and cancer cell proliferation, respectively. In conclusion, the present in vitro study provides evidence that hCEC-Exo-214 significantly enhances the anti-tumor efficacy of oxaliplatin and sorafenib on HCC cells.
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Cai Y, Chen K, Cheng C, Xu Y, Cheng Q, Xu G, Wu Y, Wu Z. Prp19 Is an Independent Prognostic Marker and Promotes Neuroblastoma Metastasis by Regulating the Hippo-YAP Signaling Pathway. Front Oncol 2020; 10:575366. [PMID: 33224878 PMCID: PMC7667276 DOI: 10.3389/fonc.2020.575366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/19/2020] [Indexed: 01/06/2023] Open
Abstract
Pre-mRNA processing factor 19 (Prp19) was previously reported to be involved in tumor progression. However, Prp19 expression and its functions remain elusive in neuroblastoma. Here, we aim to identify the functions and mechanisms of Prp19 in neuroblastoma. Neuroblastic tumor tissue microarrays and two independent validation data sets indicate that Prp19 is associated with high-risk markers and bone marrow metastasis and serves as a prognostic marker for worse clinical outcomes with neuroblastoma. Gain- and loss-of-expression assays reveal that Prp19 promotes invasion, migration, and epithelial-mesenchymal transition (EMT) of neuroblastoma cells in vitro. Bioinformatics analysis of RNA-seq data shows that the expressions of YAP and its downstream genes are significantly inhibited after downregulation of Prp19. Prp19 and YAP expression in metastatic lymph nodes is higher than in situ neuroblastoma tissue. Further experiments show that Prp19 regulates YAP expression and consequently affects cell invasion, migration, and EMT in neuroblastoma by pre-mRNA splicing of YAP. In conclusion, our findings provide the first evidence that Prp19 is a potential therapeutic target and prognostic biomarker for patients with neuroblastoma.
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Affiliation(s)
- Yuanxia Cai
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Kai Chen
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Cheng Cheng
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Yonghu Xu
- Department of Pediatric Urology, Xinhua Hospital, National Key Clinical Specialty, Shanghai Top-Priority Clinical Center, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Qianqian Cheng
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Guofeng Xu
- Department of Pediatric Urology, Xinhua Hospital, National Key Clinical Specialty, Shanghai Top-Priority Clinical Center, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yeming Wu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China.,Department of Pediatric Surgery, Children's Hospital of Soochow University, Suzhou, China
| | - Zhixiang Wu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China.,Department of Pediatric Surgery, Children's Hospital of Soochow University, Suzhou, China
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Identification and Expression Pattern of EZH2 in Pig Developing Fetuses. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5315930. [PMID: 33083470 PMCID: PMC7557918 DOI: 10.1155/2020/5315930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/07/2020] [Accepted: 08/20/2020] [Indexed: 12/24/2022]
Abstract
The proper methylation status of histones is essential for appropriate cell lineage and organogenesis. EZH2, a methyltransferase catalyzing H3K27me3, has been abundantly studied in human and mouse embryonic development. The pig is an increasing important animal model for molecular study and pharmaceutical research. However, the transcript variant and temporal expression pattern of EZH2 in the middle and late porcine fetus are still unknown. Here, we identified the coding sequence of the EZH2 gene and characterized its expression pattern in fetal tissues of Duroc pigs at 65- and 90-day postcoitus (dpc). Our results showed that the coding sequence of EZH2 was 2241 bp, encoding 746 amino acids. There were 9 amino acid insertions and an amino acid substitution in this transcript compared with the validated reference sequence in NCBI. EZH2 was ubiquitously expressed in the fetal tissues of two time points with different expression levels. These results validated a different transcript in pigs and characterized its expression profile in fetal tissues of different gestation stages, which indicated that EZH2 played important roles during porcine embryonic development.
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45
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Wang X, Xie H, Ying Y, Chen D, Li J. Roles of N 6 -methyladenosine (m 6 A) RNA modifications in urological cancers. J Cell Mol Med 2020; 24:10302-10310. [PMID: 32808488 PMCID: PMC7521283 DOI: 10.1111/jcmm.15750] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/17/2020] [Accepted: 07/30/2020] [Indexed: 12/24/2022] Open
Abstract
Epigenetics has long been a hot topic in the field of scientific research. The scope of epigenetics usually includes chromatin remodelling, DNA methylation, histone modifications, non-coding RNAs and RNA modifications. In recent years, RNA modifications have emerged as important regulators in a variety of physiological processes and in disease progression, especially in human cancers. Among the various RNA modifications, m6 A is the most common. The function of m6 A modifications is mainly regulated by 3 types of proteins: m6 A methyltransferases (writers), m6 A demethylases (erasers) and m6 A-binding proteins (readers). In this review, we focus on RNA m6 A modification and its relationship with urological cancers, particularly focusing on its roles and potential clinical applications.
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Affiliation(s)
- Xiao Wang
- Department of Urology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiyun Xie
- Department of Urology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yufan Ying
- Department of Urology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Danni Chen
- Department of Radiation Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiangfeng Li
- Department of Urology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Sun Y, Zou J, Ouyang W, Chen K. Identification of PDE7B as a Potential Core Gene Involved in the Metastasis of Clear Cell Renal Cell Carcinoma. Cancer Manag Res 2020; 12:5701-5712. [PMID: 32765073 PMCID: PMC7367933 DOI: 10.2147/cmar.s259192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
Background Metastasis is the main cause of treatment failure in various cancer, including ccRCC. However, the key genes involved in ccRCC metastasis remain largely unknown. Purpose The identification of the aberrant gene expression patterns associated with metastatic traits is of great clinical significance. The aim of this study was to investigate the clinical significance and function of PDE7B in ccRCC. Materials and Methods Expression profiling data for patient-matched primary and metastatic ccRCC tumors were obtained from GEO Dataset. Limma package was used to identify differentially expressed genes (DEGs) between the metastatic and the primary groups. Gene Ontology, Kyoto Encyclopedia of Genes Genomes (KEGG), and PPI network analysis were used to study the interacting activities and the interconnection of the DEGs. CCK-8 assays and Transwell assays were performed to detect the proliferation and migration of renal cancer cells. Results We obtained 163 DEGs, including 132 that were upregulated and 31 that were downregulated in metastatic ccRCC tissues. Both Gene Ontology function and KEGG pathway analysis showed that DEGs were involved in extracellular matrix (ECM) organization and cell adhesion. After utilizing PPI network to explore the interconnection among the DEGs, 22 genes were selected as the hub genes. Subsequently, survival analysis revealed that seven hub genes (SFN, NKX2-1, HP, MAPT, EPHA4, KCNAB1, and PDE7B) were significantly associated with overall survival disease-specific survival, and progression-free interval in ccRCC. Moreover, the low expression of PDE7B was found in clinical ccRCC samples and correlated with TNM stage and histologic grade. We further showed that knockdown of PDE7B increased cell growth and migration of renal cancer cells. Conclusion Our results implicated that PDE7B may play a key role in the development of metastatic RCC.
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Affiliation(s)
- Yi Sun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China.,Hubei Institute of Urology, Wuhan 430030, People's Republic of China
| | - Junxia Zou
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Wei Ouyang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China.,Hubei Institute of Urology, Wuhan 430030, People's Republic of China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China.,Hubei Institute of Urology, Wuhan 430030, People's Republic of China
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47
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Sun G, Zhou H, Chen K, Zeng J, Zhang Y, Yan L, Yao W, Hu J, Wang T, Xing J, Xiao K, Wu L, Ye Z, Xu H. HnRNP A1 - mediated alternative splicing of CCDC50 contributes to cancer progression of clear cell renal cell carcinoma via ZNF395. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:116. [PMID: 32560659 PMCID: PMC7304168 DOI: 10.1186/s13046-020-01606-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/28/2020] [Indexed: 01/26/2023]
Abstract
BACKGROUND Aberrant alternative splicing events play critical roles in carcinogenesis and progression of many cancers, while sparse studies regarding to alternative splicing are available for clear cell renal cell carcinoma (ccRCC). We identified that alternative splicing of coiled-coil domain containing 50 (CCDC50) was dysregulated in ccRCC, whereas the clinical significance of this splicing event and its splicing regulation mechanisms were still elusive. METHODS Bioinformatic algorithm was utilized to identify significant exon skipping events in ccRCC via exon sequencing data from The Cancer Genome Atlas. Semi-quantitative real-time polymerase chain reaction and western blot were used to validate the aberrant expression of different transcripts in renal cancer tissues, cell lines and corresponding noncancerous controls. Short hairpin RNA targeting CCDC50 and overexpressing plasmids for each transcript were introduced into ccRCC cell lines, followed by a series of in vitro and in vivo functional experiments. Moreover, a panel of splicing factors were identified and their roles on splicing regulation of CCDC50 precursor mRNA (pre-mRNA) were studied. Furthermore, RNAseq data were analyzed to elucidate downstream molecules of CCDC50. Two-way analysis of variance and unpaired Student t test were used in statistical analysis. RESULTS Pre-mRNA of CCDC50 generated two transcripts, full-length transcript (CCDC50-FL) and truncated transcript (CCDC50-S) with exon 6 skipped. CCDC50-S was overexpressed in ccRCC tissues and cell lines compared to noncancerous counterparts, but CCDC50-FL was only detected in noncancerous tissues and normal renal epithelial cells. Higher percent spliced-in index was associated with better survival in ccRCC patients. In vitro and in vivo functional experiments indicated that CCDC50-S transcript promoted the proliferation, migration, invasion and tumorigenesis of ccRCC, while CCDC50-FL exerted opposite tumor suppressive functions. Besides, we identified that heterogeneous nuclear ribonucleoprotein A1 (HnRNP A1) could promote the skipping of exon 6, which resulted in higher portion of CCDC50-S and oncogenic transformation. Moreover, zinc finger protein 395 (ZNF395) was identified as a downstream protein of CCDC50-S, and the interaction initiated oncogenic pathways which were involved in ccRCC progression. CONCLUSIONS Aberrant alternative splicing of CCDC50 is regulated by HnRNP A1 in ccRCC. This splicing event contributes to cancer progression through the downstream pathway involving ZNF395.
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Affiliation(s)
- Guoliang Sun
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Hui Zhou
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Ke Chen
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Jin Zeng
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Yangjun Zhang
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Libin Yan
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Weimin Yao
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Junhui Hu
- Hubei Institute of Urology, Wuhan, 430030 P.R. China ,grid.19006.3e0000 0000 9632 6718Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095 USA
| | - Tao Wang
- grid.412625.6Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen, 361000 P.R. China
| | - Jinchun Xing
- grid.412625.6Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen, 361000 P.R. China
| | - Kefeng Xiao
- Department of Urology, The People’s Hospital of Shenzhen City, Shenzhen, 518000 P.R. China
| | - Lily Wu
- grid.19006.3e0000 0000 9632 6718Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095 USA
| | - Zhangqun Ye
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China. .,Hubei Institute of Urology, Wuhan, 430030, P.R. China.
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Wu J, Li L, Zhang Y, Zhu J. Decreased miR-124 contributes to the epithelial-mesenchymal transition phenotype formation of lung adenocarcinoma cells via targeting enhancer of zeste homolog 2. Pathol Res Pract 2020; 216:152976. [PMID: 32370988 DOI: 10.1016/j.prp.2020.152976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 01/09/2023]
Abstract
INTRODUCTION MiR-124, a tumor suppressor, is involved in regulating various cellular processes. The purpose of this study was to investigate the possible function of miR-124 in LA (lung adenocarcinoma) cells. AIMS MiR-124 expression levels in the 54 pairs of LA tissues (and corresponding non-tumor tissues) obtained at the Sixth People's Hospital of Yancheng City and in LA cells were assessed by qRT-PCR. Colony formation assay, wound healing assay, transwell assays, attachment/detachment, western blotting and immunofluorescence assays were performed to assess the function of miR-124 on proliferation, migration and epithelial-to-mesenchymal (EMT) phenotypes in LA cells in vitro. Enhancer of zeste homolog 2 (EZH2) is identified as a target of miR-124 by bioinformatics analysis and luciferase reporter assays. Rescue assays were applied to verify the relationship between miR-124 and EZH2. RESULTS MiR-124 was down-regulated in LA tissues (compared to adjacent non-tumor tissues), and was down-regulated in 3 out of 4 lung cancer cell lines compared to immortalized, non-tumorigenic bronchial epithelial cells. Forced expression of miR-124 significantly suppressed tumor cell proliferation, migration and inhibited the EMT process. On the contrary, deletion of miR-124 could obviously promote cell proliferation, migration and facilitate the formation of EMT phenotype. Bioinformatics analysis and luciferase reporter assays confirmed that EZH2 was a target gene of miR-124 and was negatively correlated with the level of miR-124 in cancer tissues. CONCLUSION Our current study suggested that miR-124 was a tumor suppressor in LA, and miR-124 was associated with LA cell EMT phenotype formation via targeting EZH2.
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Affiliation(s)
- Jian Wu
- Department of Medical Oncology, The Sixth People's Hospital of Yancheng City, No. 66 Tingzhong Road, Yancheng, Jiangsu, 224000, China
| | - Lingling Li
- Department of Medical Oncology, The Sixth People's Hospital of Yancheng City, No. 66 Tingzhong Road, Yancheng, Jiangsu, 224000, China
| | - Yi Zhang
- Department of Oncology, Jimin Hospital, Shanghai, 200052, China
| | - Jianjun Zhu
- Department of Medical Oncology, The Sixth People's Hospital of Yancheng City, No. 66 Tingzhong Road, Yancheng, Jiangsu, 224000, China.
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49
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Xu N, Ke ZB, Lin XD, Lin F, Chen SH, Wu YP, Chen YH, Wei Y, Zheng QS. Identification of survival-associated alternative splicing events and signatures in adrenocortical carcinoma based on TCGA SpliceSeq data. Aging (Albany NY) 2020; 12:4996-5009. [PMID: 32217810 PMCID: PMC7138552 DOI: 10.18632/aging.102924] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/02/2020] [Indexed: 12/17/2022]
Abstract
Objective: To explore the correlations among alternative splicing (AS), splicing factors (SF) and survival outcome in adrenocortical carcinoma (ACC) patients. Results: A total of 92 ACC patients were included. Univariate analysis identified 3919 AS events significantly associated with overall survival. Lasso method followed by multivariate analysis revealed that the prognostic capacity of these survival-related AS events is satisfactory. Interestingly, we found that the area under the curve (AUC) of AA, AD, AP and RI were more than 0.9, indicating that these four types of AS were of great significance. Independent prognostic analysis showed that only the risk score was the independent risk factor of ACC survival. Finally, we constructed an interesting interaction network between AS and SF. Conclusions: This is the first and most comprehensive study to explore the aberrant AS variants in ACC, which might provide novel insights into molecular mechanism of ACC. Methods: The transcriptome data, clinical information and Percent Spliced In (PSI) values of the ACC were obtained from TCGA database and TCGA SpliceSeq data portal. Lasso method and uni/multivariate Cox regression analysis were used to identify survival-related AS events and develop multi-AS-based signatures. The relationship between AS events and SFs was also investigated.
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Affiliation(s)
- Ning Xu
- Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Zhi-Bin Ke
- Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Xiao-Dan Lin
- Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Fei Lin
- Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Shao-Hao Chen
- Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Yu-Peng Wu
- Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Ye-Hui Chen
- Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Yong Wei
- Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Qing-Shui Zheng
- Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
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50
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Huang R, Li Z, Li C, Wang G, Yan P, Peng L, Wang J, Zhu X, Hu P, Zhang J, Chang Z, Huang Z, Cheng L, Zhang J. Germ Cell-Specific Gene 1-Like Protein Regulated by Splicing Factor CUGBP Elav-Like Family Member 5 and Primary Bile Acid Biosynthesis are Prognostic in Glioblastoma Multiforme. Front Genet 2020; 10:1380. [PMID: 32117422 PMCID: PMC7010853 DOI: 10.3389/fgene.2019.01380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
Background Alternative splicing (AS) modifies 92-94% human genes, abnormal splicing events might relate to tumor development and invasion. Glioblastoma Multiforme (GBM) is a fatal, invasive, and malignant tumor in nervous system. The recurrence and development leads to poor prognosis. However, few studies have focused on AS in GBM. Methods RNA-seq and Alternative splicing events (ASEs) data of GBM samples were downloaded from The Cancer Genome Atlas (TCGA) and TCGASpliceSeq databases, respectively. Firstly, the Cox regression analysis was utilized to identify the overall survival splicing events (OS-SEs). Secondly, a multivariable model was applied to access the prognostic value of risk score. Then, we constructed a co-expressed network between splicing factors (SFs) and overall survival alternative splicing events (OS-SEs). Additionally, to explore the relationship between the potential prognostic signaling pathways and OS-SEs, we constructed a network between these pathways and OS-SEs. Ultimately, to better explain the results, validations from multi-dimension platforms were applied. Results In the first step, 1,062 OS-SEs were selected by Cox regression. Then, 11 OS-SEs were integrated in a multivariate model by Lasso regression. The area under the curve (AUC) of receiver operator characteristic (ROC) curve was 0.861. In addition, the risk score generated from the multivariate model was confirmed to be an independent prognostic factor (P < 0.001). What's more, in the network of SFs and ASEs, CELF5 significantly regulated GSG1L|35696|AP and GSG1L|35698|AP (P < 0.001, R = 0.511 and = -0.492). Additionally, GSG1L|35696|AP (P = 0.006) and GSG1L|35698|AP (P = 0.007) showed a significant relationship with cancer status. Eventually, KEGG pathways related to prognosis of GBM were selected by GSVA. The primary bile acid synthesis (P < 0.001, R = 0.420) was the significant pathway co-expressed with Germ Cell-Specific Gene 1-Like Protein (GSG1L). Conclusions Based on the comprehensive bioinformatics analysis, we proposed that aberrant splicing factor CUGBP Elav-like family member 5 (CELF5) significantly, positively and negatively, regulated ASE of GSG1L, and the primary bile acid synthesis pathway might play an important role in tumorigenesis and prognosis of GBM.
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Affiliation(s)
- Runzhi Huang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China
| | - Zhenyu Li
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Chen Li
- Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China
| | - Guanghua Wang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li Peng
- Shanghai Key Laboratory of Meteorology and Health, Shanghai, China
| | - Jiaqi Wang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Xiaolong Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Peng Hu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junfang Zhang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Zhengyan Chang
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liming Cheng
- Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China
| | - Jie Zhang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
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