1
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Qu A, Han B, Hua M, Wang C, Li T. SF3B4 downregulation restrains lung adenocarcinoma tumorigenesis via 5' alternative splicing of KAT2A. Sci Rep 2024; 14:30. [PMID: 38168564 PMCID: PMC10762244 DOI: 10.1038/s41598-023-50606-2] [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: 03/29/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Aberrant expression of splicing factors, including SF3B4, plays a vital role in lung adenocarcinoma (LUAD). However, the impact of SF3B4 in the progression of LUAD has not been studied well. Here, we demonstrated the effects of SF3B4 in LUAD via apoptosis, proliferation, migration assays, etc. Gene manipulations confirmed the role of SF3B4 via KAT2A. SF3B4 was found to promote LUAD growth. Further studies found that, upon SF3B4 knockdown in LUAD cells, an alternative splice site occurred at the 5'-UTR of KAT2A, which led to the downregulation of KAT2A at both RNA and protein levels. Furthermore, the decrease in KAT2A expression partially reversed the effect of SF3B4 in promoting tumorigenesis. The axis SF3B4/ KAT2A was identified as a significant player in LUAD progression, shedding light on the therapeutic development in LUAD.
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Affiliation(s)
- Ailin Qu
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Bo Han
- Department of Pathology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Mengmeng Hua
- Department of Oral and Maxillofacial Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Institute of Stomatology, Shandong University, Jinan, Shandong, China
| | - Chune Wang
- Department of Oral and Maxillofacial Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Institute of Stomatology, Shandong University, Jinan, Shandong, China
| | - Tao Li
- Department of Respiratory Diseases, Qilu Hospital of Shandong University, No. 107, Culture West Road, Jinan, China.
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2
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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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3
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Son JA, Weon JH, Baek GO, Ahn HR, Choi JY, Yoon MG, Cho HJ, Cheong JY, Eun JW, Kim SS. Circulating small extracellular vesicle-derived splicing factor 3b subunit 4 as a non-invasive diagnostic biomarker of early hepatocellular carcinoma. J Exp Clin Cancer Res 2023; 42:288. [PMID: 37899451 PMCID: PMC10614366 DOI: 10.1186/s13046-023-02867-y] [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: 05/25/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) accounts for a majority of primary liver cancer cases and related deaths. The purpose of this study was to assess the diagnostic value of splicing factor 3b subunit 4 (SF3B4) as a novel non-invasive biomarker for HCC and determine the association between SF3B4 expression and immune cell infiltration. METHODS An enzyme-linked immunosorbent assay (ELISA) was used to detect SF3B4 levels in plasma samples obtained from healthy controls (HCs) and patients with chronic hepatitis, liver cirrhosis, and HCC. The expression levels of autoantibodies that detect SF3B4 in the plasma samples of each group of patients were measured. Small extracellular vesicles (EVs) were isolated from patient sera, and the expression levels of EV-SF3B4 were measured using quantitative reverse transcription PCR. RESULTS ELISA results confirmed that the expression levels of SF3B4 proteins and autoantibodies in the plasma of patients with HCC were higher than those in HCs. However, their diagnostic performance was not better than that of alpha-fetoprotein (AFP). The mRNA expression of SF3B4 in serum EV increased but not in the buffy coat or serum of patients with HCC. Serum EV-SF3B4 displayed better diagnostic power than AFP for all stages of HCC (AUC = 0.968 vs. 0.816), including early-stage HCC (AUC = 0.960 vs. 0.842), and this was consistent in the external cohort. Single-cell RNA sequencing indicated that SF3B4 expression was correlated with myeloid-derived suppressor cells. The Tumor Immune Estimation Resource database reconfirmed the correlation between SF3B4 expression and immune cell infiltration in HCC. CONCLUSIONS SF3B4 may be associated with tumor immune infiltration in HCC, and EV-SF3B4 shows potential as a novel non-invasive diagnostic biomarker of HCC.
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Affiliation(s)
- Ju A Son
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Ji Hyang Weon
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Geum Ok Baek
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Hye Ri Ahn
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Ji Yi Choi
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Moon Gyeong Yoon
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Hyo Jung Cho
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jae Youn Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea.
| | - Soon Sun Kim
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea.
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4
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Choi S, Cho N, Kim EM, Kim KK. The role of alternative pre-mRNA splicing in cancer progression. Cancer Cell Int 2023; 23:249. [PMID: 37875914 PMCID: PMC10594706 DOI: 10.1186/s12935-023-03094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023] Open
Abstract
Alternative pre-mRNA splicing is a critical mechanism that generates multiple mRNA from a single gene, thereby increasing the diversity of the proteome. Recent research has highlighted the significance of specific splicing isoforms in cellular processes, particularly in regulating cell numbers. In this review, we examine the current understanding of the role of alternative splicing in controlling cancer cell growth and discuss specific splicing factors and isoforms and their molecular mechanisms in cancer progression. These isoforms have been found to intricately control signaling pathways crucial for cell cycle progression, proliferation, and apoptosis. Furthermore, studies have elucidated the characteristics and functional importance of splicing factors that influence cell numbers. Abnormal expression of oncogenic splicing isoforms and splicing factors, as well as disruptions in splicing caused by genetic mutations, have been implicated in the development and progression of tumors. Collectively, these findings provide valuable insights into the complex interplay between alternative splicing and cell proliferation, thereby suggesting the potential of alternative splicing as a therapeutic target for cancer.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea.
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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5
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Yang Z, Wang YX, Wen JK, Gao HT, Han ZW, Qi JC, Gu JF, Zhao CM, Zhang H, Shi B, Wang DD, Wang XL, Qu CB. SF3B4 promotes Twist1 expression and clear cell renal cell carcinoma progression by facilitating the export of KLF 16 mRNA from the nucleus to the cytoplasm. Cell Death Dis 2023; 14:26. [PMID: 36639679 PMCID: PMC9839716 DOI: 10.1038/s41419-022-05534-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
Splicing factor 3B subunit 4 (SF3B4) plays important functional roles not only in pre-mRNA splicing, but also in the regulation of transcription, translation, and cell signaling, and its dysregulation contributes to various diseases including Nager syndrome and tumorigenesis. However, the role of SF3B4 and underlying mechanisms in clear cell renal cell carcinoma (ccRCC) remain obscure. In the present study, we found that the expression of SF3B4 was significantly elevated in ccRCC tissues and negatively correlated with the overall survival of ccRCC patients. Upregulation of SF3B4 promotes migration and invasion of ccRCC cells in vitro and in vivo. The promoting effect of SF3B4 on cell migration and invasion is mediated by Twist1, a key transcription factor to mediate EMT. Interestingly, SF3B4, a component of the pre-mRNA spliceosome, is able to promote KLF16 expression by facilitating the transport of KLF16 mRNA into the cytoplasm. Mechanistically, SF3B4 promotes the export of KLF16 mRNA from the nucleus to the cytoplasm and thus enhances KLF16 expression, and in turn elevated KLF16 directly binds to the Twist1 promoter to activate its transcription, leading to EMT and ccRCC progression. Our findings provide evidence that the SF3B4-KLF16-Twist1 axis plays important functional roles in the development and progression of ccRCC, and manipulating this pathway may be a novel therapeutic target for the treatment of ccRCC.
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Affiliation(s)
- Zhan Yang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
- Molecular Biology Laboratory, Talent and Academic Exchange Center, The Second Hospital of Hebei Medical University, Shijiazhang, China
| | - Ya-Xuan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Jin-Kun Wen
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China
| | - Hai-Tao Gao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Zhen-Wei Han
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Jin-Chun Qi
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Jun-Fei Gu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chen-Ming Zhao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Hong Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Bei Shi
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Dan-Dan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Xiao-Lu Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chang-Bao Qu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
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6
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Kim H, Lee J, Jung SY, Yun HH, Ko JH, Lee JH. SF3B4 Depletion Retards the Growth of A549 Non-Small Cell Lung Cancer Cells via UBE4B-Mediated Regulation of p53/p21 and p27 Expression. Mol Cells 2022; 45:718-728. [PMID: 35996826 PMCID: PMC9589371 DOI: 10.14348/molcells.2022.0037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 11/27/2022] Open
Abstract
Splicing factor B subunit 4 (SF3B4), a component of the U2-pre-mRNA spliceosomal complex, contributes to tumorigenesis in several types of tumors. However, the oncogenic potential of SF3B4 in lung cancer has not yet been determined. The in vivo expression profiles of SF3B4 in non-small cell lung cancer (NSCLC) from publicly available data revealed a significant increase in SF3B4 expression in tumor tissues compared to that in normal tissues. The impact of SF3B4 deletion on the growth of NSCLC cells was determined using a siRNA strategy in A549 lung adenocarcinoma cells. SF3B4 silencing resulted in marked retardation of the A549 cell proliferation, accompanied by the accumulation of cells at the G0/G1 phase and increased expression of p27, p21, and p53. Double knockdown of SF3B4 and p53 resulted in the restoration of p21 expression and partial recovery of cell proliferation, indicating that the p53/p21 axis is involved, at least in part, in the SF3B4-mediated regulation of A549 cell proliferation. We also provided ubiquitination factor E4B (UBE4B) is essential for p53 accumulation after SF3B4 depletion based on followings. First, co-immunoprecipitation showed that SF3B4 interacts with UBE4B. Furthermore, UBE4B levels were decreased by SF3B4 depletion. UBE4B depletion, in turn, reproduced the outcome of SF3B4 depletion, including reduction of polyubiquitinated p53 levels, subsequent induction of p53/p21 and p27, and proliferation retardation. Collectively, our findings indicate the important role of SF3B4 in the regulation of A549 cell proliferation through the UBE4B/p53/p21 axis and p27, implicating the therapeutic strategies for NSCLC targeting SF3B4 and UBE4B.
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Affiliation(s)
- Hyungmin Kim
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Biomedicine & Health Sciences, Graduate School, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jeehan Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Soon-Young Jung
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Hye Hyeon Yun
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jeong-Heon Ko
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jeong-Hwa Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Biomedicine & Health Sciences, Graduate School, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
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7
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Ge S, Zhang Q, Yang X. GPAA1 promotes the proliferation, invasion and migration of hepatocellular carcinoma cells by binding to RNA‑binding protein SF3B4. Oncol Lett 2022; 23:160. [PMID: 35399327 PMCID: PMC8987926 DOI: 10.3892/ol.2022.13280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/13/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Song Ge
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Qiang Zhang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Xiaoyong Yang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
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8
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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: 8] [Impact Index Per Article: 4.0] [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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9
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Deng G, Luo Y, Zhang Y, Zhang J, He Z. Enabled homolog (ENAH) regulated by RNA binding protein splicing factor 3b subunit 4 (SF3B4) exacerbates the proliferation, invasion and migration of hepatocellular carcinoma cells via Notch signaling pathway. Bioengineered 2022; 13:2194-2206. [PMID: 35030977 PMCID: PMC8973836 DOI: 10.1080/21655979.2021.2023983] [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] [Indexed: 01/26/2023] Open
Abstract
Enabled homolog (ENAH) is an actin-binding protein that implicated in multiple malignant tumors. High ENAH expression has been verified to be associated with poor prognosis in hepatocellular carcinoma (HCC). We aimed to reveal the role of ENAH in HCC and the potential mechanism. ENAH expression in HCC tissues and the prognostic correlation were analyzed by GEPIA2 database. RT-qPCR and Western blot were used to test ENAH expression in HCC cells. Following ENAH silencing, cell proliferation was estimated by CCK-8 and colony formation assays. Transwell and wound healing assays were to assess cell invasion and migration. ENCORI database was to analyze the correlation between ENAH and splicing factor 3b subunit 4 (SF3B4) in HCC tissues, which was then verified by RIP and actinomycin D assay. Then, the expression of Notch signaling-related proteins was detected by Western blotting after ENAH knockdown. Afterward, Notch1 was overexpressed to validate whether ENAH impacted the biological events of HCC cells through mediating Notch signaling. Results revealed that ENAH expression was elevated in HCC tissues and cells and associated with poor prognosis. ENAH deficiency mitigated proliferation, invasion and migration of HCC cells. Mechanistically, ENAH was positively correlated with SF3B4 in HCC tissues. SF3B4 could bind to ENAH mRNA and stabilized ENAH. Besides, ENAH activated Notch signaling. Notch1 up-regulation reversed the influence of ENAH knockdown on biological events of HCC cells. Collectively, ENAH regulated by SF3B4 promoted the development of HCC through activating Notch signaling, which identified ENAH as a potent molecular target for HCC therapy and prognosis.
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Affiliation(s)
- Guoming Deng
- The 2nd Department of Hepatobiliary Surgery, Meizhou People's Hospital, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Yufeng Luo
- The 2nd Department of Hepatobiliary Surgery, Meizhou People's Hospital, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Yaoming Zhang
- The 2nd Department of Hepatobiliary Surgery, Meizhou People's Hospital, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Jinfeng Zhang
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China.,The 3rd Department of Medical Oncology, Meizhou People's Hospital, Meizhou, China
| | - Zongyun He
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China.,The Department of Hepatology, Meizhou People's Hospital, Meizhou, China
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10
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Yazhini A, Srinivasan N, Sandhya S. Sequence Divergence and Functional Specializations of the Ancient Spliceosomal SF3b: Implications in Flexibility and Adaptations of the Multi-Protein Complex. Front Genet 2022; 12:747344. [PMID: 35082828 PMCID: PMC8785561 DOI: 10.3389/fgene.2021.747344] [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: 07/26/2021] [Accepted: 12/07/2021] [Indexed: 11/17/2022] Open
Abstract
Multi-protein assemblies are complex molecular systems that perform highly sophisticated biochemical functions in an orchestrated manner. They are subject to changes that are governed by the evolution of individual components. We performed a comparative analysis of the ancient and functionally conserved spliceosomal SF3b complex, to recognize molecular signatures that contribute to sequence divergence and functional specializations. For this, we recognized homologous sequences of individual SF3b proteins distributed across 10 supergroups of eukaryotes and identified all seven protein components of the complex in 578 eukaryotic species. Using sequence and structural analysis, we establish that proteins occurring on the surface of the SF3b complex harbor more sequence variation than the proteins that lie in the core. Further, we show through protein interface conservation patterns that the extent of conservation varies considerably between interacting partners. When we analyze phylogenetic distributions of individual components of the complex, we find that protein partners that are known to form independent subcomplexes are observed to share similar profiles, reaffirming the link between differential conservation of interface regions and their inter-dependence. When we extend our analysis to individual protein components of the complex, we find taxa-specific variability in molecular signatures of the proteins. These trends are discussed in the context of proline-rich motifs of SF3b4, functional and drug binding sites of SF3b1. Further, we report key protein-protein interactions between SF3b1 and SF3b6 whose presence is observed to be lineage-specific across eukaryotes. Together, our studies show the association of protein location within the complex and subcomplex formation patterns with the sequence conservation of SF3b proteins. In addition, our study underscores evolutionarily flexible elements that appear to confer adaptive features in individual components of the multi-protein SF3b complexes and may contribute to its functional adaptability.
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Affiliation(s)
- Arangasamy Yazhini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Biotechnology, Faculty of Life and Allied Health Sciences, M. S. Ramaiah University of Applied Sciences, Bengaluru, India
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11
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Prados-Carvajal R, Rodriguez-Real G, Gutierrez-Pozo G, Huertas P. CtIP -mediated alternative mRNA splicing finetunes the DNA damage response. RNA (NEW YORK, N.Y.) 2020; 27:rna.078519.120. [PMID: 33298529 PMCID: PMC7901839 DOI: 10.1261/rna.078519.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
In order to survive to the exposure of DNA damaging agents, cells activate a complex response that coordinates the cellular metabolism, cell cycle progression and DNA repair. Among many other events, recent evidence has described global changes in mRNA splicing in cells treated with genotoxic agents. Here, we explore further this DNA damage-dependent alternative splicing. Indeed, we show that both the splicing factor SF3B2 and the repair protein CtIP contribute to the global pattern of splicing both in cells treated or not to DNA damaging agents. Additionally, we focus on a specific DNA damage- and CtIP-dependent alternative splicing event of the helicase PIF1 and explore its relevance for the survival of cells upon exposure to ionizing radiation. Indeed, we described how the nuclear, active form of PIF1 is substituted by a splicing variant, named vPIF1, in a fashion that requires both the presence of DNA damage and CtIP. Interestingly, timely expression of vPIF1 is required for optimal survival to exposure to DNA damaging agents, but early expression of this isoform delays early events of the DNA damage response. On the contrary, expression of the full length PIF1 facilitates those early events, but increases the sensitivity to DNA damaging agents if the expression is maintained long-term.
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12
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Xiong F, Li S. SF3b4: A Versatile Player in Eukaryotic Cells. Front Cell Dev Biol 2020; 8:14. [PMID: 32083075 PMCID: PMC7002316 DOI: 10.3389/fcell.2020.00014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/10/2020] [Indexed: 01/16/2023] Open
Abstract
Spliceosomes are large protein-RNA complexes regulating pre-mRNA processing in eukaryotes. SF3b4 encodes a core subunit of the U2-type spliceosome, loss- or gain-of-function of which often associates with abnormal cell growth, leading to tumorigenesis. Homologs of SF3b4 in other phyla are also essential. In this review, we summarize recent findings on the function of SF3b4. Importantly, we highlight the versatile roles of SF3b4, not only as a component for pre-mRNA splicing, but also as a regulator for transcription, translation, and cell signaling. Recent studies of SF3b4 homologs in different species across evolution will facilitate a better understanding of human diseases caused by the malfunction of SF3b4, such as Nager syndrome (NS) and cancer, in the future.
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Affiliation(s)
- Feng Xiong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Sha Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China.,Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
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13
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Idris M, Harmston N, Petretto E, Madan B, Virshup DM. Broad regulation of gene isoform expression by Wnt signaling in cancer. RNA (NEW YORK, N.Y.) 2019; 25:1696-1713. [PMID: 31506381 PMCID: PMC6859862 DOI: 10.1261/rna.071506.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/06/2019] [Indexed: 05/08/2023]
Abstract
Differential gene isoform expression is a ubiquitous mechanism to enhance proteome diversity and maintain cell homeostasis. Mechanisms such as splicing that drive gene isoform variability are highly dynamic and responsive to changes in cell signaling pathways. Wnt/β-catenin signaling has profound effects on cell activity and cell fate and is known to modify several splicing events by altering the expression of individual splicing factors. However, a global assessment of how extensively Wnt signaling regulates splicing and other mechanisms that determine mRNA isoform composition in cancer is lacking. We used deep time-resolved RNA-seq in two independent in vivo Wnt-addicted tumor models during treatment with the potent Wnt inhibitor ETC-159 and examined Wnt regulated splicing events and splicing regulators. We found 1025 genes that underwent Wnt regulated variable exon usage leading to isoform expression changes. This was accompanied by extensive Wnt regulated changes in the expression of splicing regulators. Many of these Wnt regulated events were conserved in multiple human cancers, and many were linked to previously defined cancer-associated splicing quantitative trait loci. This suggests that the Wnt regulated splicing events are components of fundamental oncogenic processes. These findings demonstrate the wide-ranging effects of Wnt signaling on the isoform composition of the cell and provides an extensive resource of expression changes of splicing regulators and gene isoforms regulated by Wnt signaling.
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Affiliation(s)
- Muhammad Idris
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
| | - Nathan Harmston
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
- Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857
- Science Division, Yale-NUS College, Singapore, 138527
| | - Enrico Petretto
- Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857
| | - Babita Madan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
| | - David M Virshup
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina 27705, USA
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14
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Wu P, Jie W, Shang Q, Annan E, Jiang X, Hou C, Chen T, Guo X. DNA methylation in silkworm genome may provide insights into epigenetic regulation of response to Bombyx mori cypovirus infection. Sci Rep 2017; 7:16013. [PMID: 29167521 PMCID: PMC5700172 DOI: 10.1038/s41598-017-16357-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
DNA methylation is an important epigenetic modification that regulates a wide range of biological processes including immune response. However, information on the epigenetics-mediated immune mechanisms in insects is limited. Therefore, in this study, we examined transcriptomes and DNA methylomes in the fat body and midgut tissues of silkworm, Bombyx mori with or without B. mori cytoplasmic polyhedrosis virus (BmCPV) infection. The transcriptional profile and the genomic DNA methylation patterns in the midgut and fat body were tissue-specific and dynamically altered after BmCPV challenge. KEGG pathway analysis revealed that differentially methylated genes (DMGs) could be involved in pathways of RNA transport, RNA degradation, nucleotide excision repair, DNA replication, etc. 27 genes were shown to have both differential expression and differential methylation in the midgut and fat body of infected larvae, respectively, indicating that the BmCPV infection-induced expression changes of these genes could be mediated by variations in DNA methylation. BS-PCR validated the hypomethylation of G2/M phase-specific E3 ubiquitin-protein ligase-like gene in the BmCPV infected midgut. These results demonstrated that epigenetic regulation may play roles in host-virus interaction in silkworm and would be potential value for further studies on mechanism of BmCPV epithelial-specific infection and epigenetic regulation in the silkworm.
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Affiliation(s)
- Ping Wu
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Wencai Jie
- Beijing Genomics Institute (BGI), Shenzhen, Guangdong, China
| | - Qi Shang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Enoch Annan
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Xiaoxu Jiang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Chenxiang Hou
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Tao Chen
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Xijie Guo
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China.
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