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Song F, Hou C, Huang Y, Liang J, Cai H, Tian G, Jiang Y, Wang Z, Hou J. Lactylome analyses suggest systematic lysine-lactylated substrates in oral squamous cell carcinoma under normoxia and hypoxia. Cell Signal 2024; 120:111228. [PMID: 38750680 DOI: 10.1016/j.cellsig.2024.111228] [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: 03/29/2024] [Revised: 05/05/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Cancer cells tend to live in hypoxic environment characterized by enhanced glycolysis and accumulation of lactate. Intracellular lactate is shown to drive a novel type of post-translational modification (PTM), lysine lactylation (Kla). Kla has been confirmed to affect the malignant progression of tumors such as hepatocellular carcinoma (HCC) and colon cancer, whereas the global lactylomic profiling of oral squamous cell carcinoma (OSCC) is unclear. Here, the integrative lactylome and proteome analyses by using liquid chromatography-tandem mass spectrometry (LC-MS/MS) identified 1011 Kla sites within 532 proteins and 1197 Kla sites within 608 proteins in SCC25 cells under normoxic and hypoxic environments, respectively. Among these lactylated proteins, histones accounted for only a small fraction, suggesting the presence of Kla modification of OSCC in a large number of non-histone proteins. Notably, Kla preferred to enrich in spliceosome, ribosome and glycolysis/gluconeogenesis pathway in both normoxic and hypoxic cultures. Compared with normoxia, 589 differential proteins with 898 differentially lactylated sites were detected under hypoxia, which were mainly associated with the glycolysis/gluconeogenesis pathway by KEGG analysis. Importantly, we verified the presence of lactylation modification in the spliceosomal proteins hnRNPA1, SF3A1, hnRNPU and SLU7, as well as in glycolytic enzyme PFKP. In addition, the differential alternative splicing analysis described the divergence of pre-mRNA splicing patterns in the presence or absence of sodium lactate and at different oxygen concentrations. Finally, a negative correlation between tissue Kla levels and the prognosis of OSCC patients was revealed by immunohistochemistry. Our study is the first report to elucidate the lactylome and its biological function in OSCC, which deepens our understanding of the mechanisms underlying OSCC progression and provides a novel strategy for targeted therapy for OSCC.
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Affiliation(s)
- Fan Song
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Chen Hou
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Yingzhao Huang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Jianfeng Liang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Hongshi Cai
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Guoli Tian
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Yaoqi Jiang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Ziyi Wang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Jinsong Hou
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China.
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2
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Wei C, Niu Y, Chen B, Wang Y, Cai H, Han R, Tian Y, Liu X, Guo W, Kang X, Li Z. Divergent Regulatory Roles of Transcriptional Variants of the Chicken LDB3 Gene in Muscle Shaping. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12240-12250. [PMID: 38764183 DOI: 10.1021/acs.jafc.4c00520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
LIM domain binding 3 (LDB3) serves as a striated muscle-specific Z-band alternatively spliced protein that plays an important role in mammalian skeletal muscle development, but its regulatory role and molecular mechanism in avian muscle development are still unclear. In this study, we reanalyzed RNA sequencing data sets of 1415 samples from 21 chicken tissues published in the NCBI GEO database. First, three variants (LDB3-X, LDB3-XN1, and LDB3-XN2) generated by alternative splicing of the LDB3 gene were identified in chicken skeletal muscle, among which LDB3-XN1 and LDB3-XN2 are novel variants. LDB3-X and LDB3-XN1 are derived from exon skipping in chicken skeletal muscle at the E18-D7 stage and share three LIM domains, but LDB3-XN2 lacks a LIM domain. Our results preliminarily suggest that the formation of three variants of LDB3 is regulated by RBM20. The three splice isomers have divergent functions in skeletal muscle according to in vitro and in vivo assays. Finally, we identified the mechanism by which different variants play different roles through interactions with IGF2BP1 and MYHC, which promote the proliferation and differentiation of chicken myoblasts, in turn regulating chicken myogenesis. In conclusion, this study revealed the divergent roles of three LDB3 variants in chicken myogenesis and muscle remodeling and demonstrated their regulatory mechanism through protein-protein interactions.
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Affiliation(s)
- Chengjie Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yufang Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Bingjie Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanxing Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Wei Guo
- Departmentof Animal and Dairy Sciences, University of Wisconsin-Madison, 1933 Observatory Dr., Madison, Wisconsin 54706, United States
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
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3
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Perales S, Sigamani V, Rajasingh S, Gurusamy N, Bittel D, Czirok A, Radic M, Rajasingh J. scaRNA20 promotes pseudouridylatory modification of small nuclear snRNA U12 and improves cardiomyogenesis. Exp Cell Res 2024; 436:113961. [PMID: 38341080 PMCID: PMC10964393 DOI: 10.1016/j.yexcr.2024.113961] [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: 12/23/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
Non-coding RNAs, particularly small Cajal-body associated RNAs (scaRNAs), play a significant role in spliceosomal RNA modifications. While their involvement in ischemic myocardium regeneration is known, their role in cardiac development is unexplored. We investigated scaRNA20's role in iPSC differentiation into cardiomyocytes (iCMCs) via overexpression and knockdown assays. We measured scaRNA20-OE-iCMCs and scaRNA20-KD-iCMCs contractility using Particle Image Velocimetry (PIV), comparing them to control iCMCs. We explored scaRNA20's impact on alternative splicing via pseudouridylation (Ψ) of snRNA U12, analyzing its functional consequences in cardiac differentiation. scaRNA20-OE-iPSC differentiation increased beating colonies, upregulated cardiac-specific genes, activated TP53 and STAT3, and preserved contractility under hypoxia. Conversely, scaRNA20-KD-iCMCs exhibited poor differentiation and contractility. STAT3 inhibition in scaRNA20-OE-iPSCs hindered cardiac differentiation. RNA immunoprecipitation revealed increased Ψ at the 28th uridine of U12 RNA in scaRNA20-OE iCMCs. U12-KD iCMCs had reduced cardiac differentiation, which improved upon U12 RNA introduction. In summary, scaRNA20-OE in iPSCs enhances cardiomyogenesis, preserves iCMC function under hypoxia, and may have implications for ischemic myocardium regeneration.
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Affiliation(s)
- Selene Perales
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Vinoth Sigamani
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sheeja Rajasingh
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Narasimman Gurusamy
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Douglas Bittel
- Department of Biosciences, Kansas City University of Medicine and Biosciences, Kansas City, MO, USA
| | - Andras Czirok
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Marko Radic
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Johnson Rajasingh
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA; Department of Medicine-Cardiology, University of Tennessee Health Science Center, Memphis, TN, USA; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA.
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4
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Huang Y, Ping X, Cui Y, Yang H, Bao J, Yin Q, Ailifeire H, Shentu X. Glycolysis Aids in Human Lens Epithelial Cells' Adaptation to Hypoxia. Antioxidants (Basel) 2023; 12:1304. [PMID: 37372033 PMCID: PMC10295312 DOI: 10.3390/antiox12061304] [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: 05/06/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Hypoxic environments are known to trigger pathological damage in multiple cellular subtypes. Interestingly, the lens is a naturally hypoxic tissue, with glycolysis serving as its main source of energy. Hypoxia is essential for maintaining the long-term transparency of the lens in addition to avoiding nuclear cataracts. Herein, we explore the complex mechanisms by which lens epithelial cells adapt to hypoxic conditions while maintaining their normal growth and metabolic activity. Our data show that the glycolysis pathway is significantly upregulated during human lens epithelial (HLE) cells exposure to hypoxia. The inhibition of glycolysis under hypoxic conditions incited endoplasmic reticulum (ER) stress and reactive oxygen species (ROS) production in HLE cells, leading to cellular apoptosis. After ATP was replenished, the damage to the cells was not completely recovered, and ER stress, ROS production, and cell apoptosis still occurred. These results suggest that glycolysis not only performs energy metabolism in the process of HLE cells adapting to hypoxia, but also helps them continuously resist cell apoptosis caused by ER stress and ROS production. Furthermore, our proteomic atlas provides possible rescue mechanisms for cellular damage caused by hypoxia.
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Affiliation(s)
| | | | | | | | | | | | | | - Xingchao Shentu
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, China
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5
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The VEGF/VEGFR Axis Revisited: Implications for Cancer Therapy. Int J Mol Sci 2022; 23:ijms232415585. [PMID: 36555234 PMCID: PMC9779738 DOI: 10.3390/ijms232415585] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The vascular endothelial growth factor (VEGF)/vascular endothelial growth factor receptor (VEGFR) axis is indispensable in the process of angiogenesis and has been implicated as a key driver of tumor vascularization. Consequently, several strategies that target VEGF and its cognate receptors, VEGFR-1 and VEGFR-2, have been designed to treat cancer. While therapies targeting full-length VEGF have resulted in an improvement in both overall survival and progression-free survival in various cancers, these benefits have been modest. In addition, the inhibition of VEGFRs is associated with undesirable off-target effects. Moreover, VEGF splice variants that modulate sprouting and non-sprouting angiogenesis have been identified in recent years. Cues within the tumor microenvironment determine the expression patterns of these variants. Noteworthy is that the mechanisms of action of these variants challenge the established norm of VEGF signaling. Furthermore, the aberrant expression of some of these variants has been observed in several cancers. Herein, developments in the understanding of the VEGF/VEGFR axis and the splice products of these molecules, as well as the environmental cues that regulate these variants are reviewed. Furthermore, strategies that incorporate the targeting of VEGF variants to enhance the effectiveness of antiangiogenic therapies in the clinical setting are discussed.
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Peciuliene I, Jakubauskiene E, Vilys L, Zinkeviciute R, Kvedaraviciute K, Kanopka A. Short-Term Hypoxia in Cells Induces Expression of Genes Which Are Enhanced in Stressed Cells. Genes (Basel) 2022; 13:genes13091596. [PMID: 36140764 PMCID: PMC9498350 DOI: 10.3390/genes13091596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/30/2022] Open
Abstract
All living organisms must respond to, and defend against, environmental stresses. Depending on the extent and severity of stress, cells try to alter their metabolism and adapt to a new state. Changes in alternative splicing of pre-mRNA are a crucial regulation mechanism through which cells are able to respond to a decrease in oxygen tension in the cellular environment. Currently, only limited data are available in the literature on how short-term hypoxia influences mRNA isoform formation. In this work, we discovered that expressions of the same genes that are activated during cellular stress are also activated in cells under short-term hypoxic conditions. Our results demonstrate that short-term hypoxia influences the splicing of genes associated with cell stress and apoptosis; however, the mRNA isoform formation patterns from the same pre-mRNAs in cells under short-term hypoxic conditions and prolonged hypoxia are different. Obtained data also show that short-term cellular hypoxia increases protein phosphatase but not protein kinase expression. Enhanced levels of protein phosphatase expression in cells are clearly important for changing mRNA isoform formation.
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Affiliation(s)
- Inga Peciuliene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, LT 10257 Vilnius, Lithuania
| | - Egle Jakubauskiene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, LT 10257 Vilnius, Lithuania
| | - Laurynas Vilys
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, LT 10257 Vilnius, Lithuania
| | - Ruta Zinkeviciute
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, LT 10257 Vilnius, Lithuania
| | - Kotryna Kvedaraviciute
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, LT 10257 Vilnius, Lithuania
| | - Arvydas Kanopka
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, LT 10257 Vilnius, Lithuania
- Correspondence: ; Tel.: +370-5-2602124
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7
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Bauer R, Meyer SP, Kloss KA, Guerrero Ruiz VM, Reuscher S, Zhou Y, Fuhrmann DC, Zarnack K, Schmid T, Brüne B. Functional RNA Dynamics Are Progressively Governed by RNA Destabilization during the Adaptation to Chronic Hypoxia. Int J Mol Sci 2022; 23:ijms23105824. [PMID: 35628634 PMCID: PMC9144826 DOI: 10.3390/ijms23105824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
Previous studies towards reduced oxygen availability have mostly focused on changes in total mRNA expression, neglecting underlying transcriptional and post-transcriptional events. Therefore, we generated a comprehensive overview of hypoxia-induced changes in total mRNA expression, global de novo transcription, and mRNA stability in monocytic THP-1 cells. Since hypoxic episodes often persist for prolonged periods, we further compared the adaptation to acute and chronic hypoxia. While total mRNA changes correlated well with enhanced transcription during short-term hypoxia, mRNA destabilization gained importance under chronic conditions. Reduced mRNA stability not only added to a compensatory attenuation of immune responses, but also, most notably, to the reduction in nuclear-encoded mRNAs associated with various mitochondrial functions. These changes may prevent the futile production of new mitochondria under conditions where mitochondria cannot exert their full metabolic function and are indeed actively removed by mitophagy. The post-transcriptional mode of regulation might further allow for the rapid recovery of mitochondrial capacities upon reoxygenation. Our results provide a comprehensive resource of functional mRNA expression dynamics and underlying transcriptional and post-transcriptional regulatory principles during the adaptation to hypoxia. Furthermore, we uncover that RNA stability regulation controls mitochondrial functions in the context of hypoxia.
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Affiliation(s)
- Rebekka Bauer
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (R.B.); (S.P.M.); (V.M.G.R.); (D.C.F.); (B.B.)
| | - Sofie Patrizia Meyer
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (R.B.); (S.P.M.); (V.M.G.R.); (D.C.F.); (B.B.)
| | - Karolina Anna Kloss
- Faculty of Biological Sciences, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, 60438 Frankfurt, Germany; (K.A.K.); (S.R.); (Y.Z.)
| | - Vanesa Maria Guerrero Ruiz
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (R.B.); (S.P.M.); (V.M.G.R.); (D.C.F.); (B.B.)
| | - Samira Reuscher
- Faculty of Biological Sciences, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, 60438 Frankfurt, Germany; (K.A.K.); (S.R.); (Y.Z.)
| | - You Zhou
- Faculty of Biological Sciences, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, 60438 Frankfurt, Germany; (K.A.K.); (S.R.); (Y.Z.)
| | - Dominik Christian Fuhrmann
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (R.B.); (S.P.M.); (V.M.G.R.); (D.C.F.); (B.B.)
- German Cancer Consortium (DKTK), Partner Site Frankfurt, 60590 Frankfurt, Germany
| | - Kathi Zarnack
- Faculty of Biological Sciences, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, 60438 Frankfurt, Germany; (K.A.K.); (S.R.); (Y.Z.)
- Correspondence: (K.Z.); (T.S.)
| | - Tobias Schmid
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (R.B.); (S.P.M.); (V.M.G.R.); (D.C.F.); (B.B.)
- German Cancer Consortium (DKTK), Partner Site Frankfurt, 60590 Frankfurt, Germany
- Correspondence: (K.Z.); (T.S.)
| | - Bernhard Brüne
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (R.B.); (S.P.M.); (V.M.G.R.); (D.C.F.); (B.B.)
- German Cancer Consortium (DKTK), Partner Site Frankfurt, 60590 Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe-University Frankfurt, 60596 Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology, 60596 Frankfurt, Germany
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8
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Peng Q, Zhou Y, Oyang L, Wu N, Tang Y, Su M, Luo X, Wang Y, Sheng X, Ma J, Liao Q. Impacts and mechanisms of alternative mRNA splicing in cancer metabolism, immune response, and therapeutics. Mol Ther 2022; 30:1018-1035. [PMID: 34793975 PMCID: PMC8899522 DOI: 10.1016/j.ymthe.2021.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/29/2021] [Accepted: 11/11/2021] [Indexed: 02/08/2023] Open
Abstract
Alternative pre-mRNA splicing (AS) provides the potential to produce diversity at RNA and protein levels. Disruptions in the regulation of pre-mRNA splicing can lead to diseases. With the development of transcriptome and genome sequencing technology, increasing diseases have been identified to be associated with abnormal splicing of mRNAs. In tumors, abnormal alternative splicing frequently plays critical roles in cancer pathogenesis and may be considered as new biomarkers and therapeutic targets for cancer intervention. Metabolic abnormalities and immune disorders are important hallmarks of cancer. AS produces multiple different isoforms and diversifies protein expression, which is utilized by the immune and metabolic reprogramming systems to expand gene functions. The abnormal splicing events contributed to tumor progression, partially due to effects on immune response and metabolic reprogramming. Herein, we reviewed the vital role of alternative splicing in regulating cancer metabolism and immune response. We discussed how alternative splicing regulates metabolic reprogramming of cancer cells and antitumor immune response, and the possible strategies to targeting alternative splicing pathways or splicing-regulated metabolic pathway in the context of anticancer immunotherapy. Further, we highlighted the challenges and discuss the perspectives for RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Ying Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xiaowu Sheng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Jian Ma
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China.
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9
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Kip AM, Valverde JM, Altelaar M, Heeren RMA, Hundscheid IHR, Dejong CHC, Olde Damink SWM, Balluff B, Lenaerts K. Combined Quantitative (Phospho)proteomics and Mass Spectrometry Imaging Reveal Temporal and Spatial Protein Changes in Human Intestinal Ischemia-Reperfusion. J Proteome Res 2021; 21:49-66. [PMID: 34874173 PMCID: PMC8750167 DOI: 10.1021/acs.jproteome.1c00447] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Intestinal ischemia–reperfusion
(IR) injury is a severe
clinical condition, and unraveling its pathophysiology is crucial
to improve therapeutic strategies and reduce the high morbidity and
mortality rates. Here, we studied the dynamic proteome and phosphoproteome
in the human intestine during ischemia and reperfusion, using liquid
chromatography-tandem mass spectrometry (LC-MS/MS) analysis to gain
quantitative information of thousands of proteins and phosphorylation
sites, as well as mass spectrometry imaging (MSI) to obtain spatial
information. We identified a significant decrease in abundance of
proteins related to intestinal absorption, microvillus, and cell junction,
whereas proteins involved in innate immunity, in particular the complement
cascade, and extracellular matrix organization increased in abundance
after IR. Differentially phosphorylated proteins were involved in
RNA splicing events and cytoskeletal and cell junction organization.
In addition, our analysis points to mitogen-activated protein kinase
(MAPK) and cyclin-dependent kinase (CDK) families to be active kinases
during IR. Finally, matrix-assisted laser desorption ionization time-of-flight
(MALDI-TOF) MSI presented peptide alterations in abundance and distribution,
which resulted, in combination with Fourier-transform ion cyclotron
resonance (FTICR) MSI and LC-MS/MS, in the annotation of proteins
related to RNA splicing, the complement cascade, and extracellular
matrix organization. This study expanded our understanding of the
molecular changes that occur during IR in the human intestine and
highlights the value of the complementary use of different MS-based
methodologies.
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Affiliation(s)
- Anna M Kip
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Juan Manuel Valverde
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Ron M A Heeren
- Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Inca H R Hundscheid
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Cornelis H C Dejong
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.,Department of General, Visceral- and Transplantation Surgery, RWTH Aachen University Hospital, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Steven W M Olde Damink
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.,Department of General, Visceral- and Transplantation Surgery, RWTH Aachen University Hospital, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Benjamin Balluff
- Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Kaatje Lenaerts
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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10
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LW1497, an Inhibitor of Malate Dehydrogenase, Suppresses TGF-β1-Induced Epithelial-Mesenchymal Transition in Lung Cancer Cells by Downregulating Slug. Antioxidants (Basel) 2021; 10:antiox10111674. [PMID: 34829545 PMCID: PMC8615288 DOI: 10.3390/antiox10111674] [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: 08/28/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 01/01/2023] Open
Abstract
LW1497 suppresses the expression of the hypoxia-inducing factor (HIF)-1α inhibiting malate dehydrogenase. Although hypoxia and HIF-1α are known to be important in cancer, LW1497 has not been therapeutically applied to cancer yet. Thus, we investigated the effect of LW1497 on the epithelial-mesenchymal transition (EMT) of lung cancer cells. A549 and H1299 lung cancer cells were induced to undergo via TGF-β1 treatment, resulting in the downregulation of E-cadherin and upregulation of N-cadherin and Vimentin concurrently with increases in the migration and invasion capacities of the cells. These effects of TGF-β1 were suppressed upon co-treatment of the cells with LW1497. An RNA-seq analysis revealed that LW1497 induced differential expression of genes related to hypoxia, RNA splicing, angiogenesis, cell migration, and metastasis in the A549 lung cancer cell lines. We confirmed the differential expression of Slug, an EMT-related transcription factor. Results from Western blotting and RT-PCR confirmed that LW1497 inhibited the expression of EMT markers and Slug. After orthotopically transplanting A549 cancer cells into mice, LW1497 was administered to examine whether the lung cancer progression was inhibited. We observed that LW1497 reduced the area of cancer. In addition, the results from immunohistochemical analyses showed that LW1497 downregulated EMT markers and Slug. In conclusion, LW1497 suppresses cancer progression through the inhibition of EMT by downregulating Slug.
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11
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Ashok C, Ahuja N, Natua S, Mishra J, Samaiya A, Shukla S. E2F1 and epigenetic modifiers orchestrate breast cancer progression by regulating oxygen-dependent ESRP1 expression. Oncogenesis 2021; 10:58. [PMID: 34362878 PMCID: PMC8346533 DOI: 10.1038/s41389-021-00347-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Epithelial splicing regulatory protein 1 (ESRP1) is an RNA binding protein that governs the alternative splicing events related to epithelial phenotypes. ESRP1 contributes significantly at different stages of cancer progression. ESRP1 expression is substantially elevated in carcinoma in situ compared to the normal epithelium, whereas it is drastically ablated in cancer cells within hypoxic niches, which promotes epithelial to mesenchymal transition (EMT). Although a considerable body of research sought to understand the EMT-associated ESRP1 downregulation, the regulatory mechanisms underlying ESRP1 upregulation in primary tumors remained largely uncharted. This study seeks to unveil the regulatory mechanisms that spatiotemporally fine-tune the ESRP1 expression during breast carcinogenesis. Our results reveal that an elevated expression of transcription factor E2F1 and increased CpG hydroxymethylation of the E2F1 binding motif conjointly induce ESRP1 expression in breast carcinoma. However, E2F1 fails to upregulate ESRP1 despite its abundance in oxygen-deprived breast cancer cells. Mechanistically, impelled by the hypoxia-driven reduction of tet methylcytosine dioxygenase 3 (TET3) activity, CpG sites across the E2F1 binding motif lose the hydroxymethylation marks while gaining the de novo methyltransferase-elicited methylation marks. These two oxygen-sensitive epigenetic events work in concert to repel E2F1 from the ESRP1 promoter, thereby diminishing ESRP1 expression under hypoxia. Furthermore, E2F1 skews the cancer spliceome by upregulating splicing factor SRSF7 in hypoxic breast cancer cells. Our findings provide previously unreported mechanistic insights into the plastic nature of ESRP1 expression and insinuate important implications in therapeutics targeting breast cancer progression.
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Affiliation(s)
- Cheemala Ashok
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh India
| | - Neha Ahuja
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh India
| | - Subhashis Natua
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh India
| | - Jharna Mishra
- Department of Pathology, Bansal Hospital, Bhopal, Madhya Pradesh India
| | - Atul Samaiya
- Department of Surgical Oncology, Bansal Hospital, Bhopal, Madhya Pradesh India
| | - Sanjeev Shukla
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh India
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12
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Natua S, Dhamdhere SG, Mutnuru SA, Shukla S. Interplay within tumor microenvironment orchestrates neoplastic RNA metabolism and transcriptome diversity. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1676. [PMID: 34109748 DOI: 10.1002/wrna.1676] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/03/2021] [Accepted: 05/25/2021] [Indexed: 12/11/2022]
Abstract
The heterogeneous population of cancer cells within a tumor mass interacts intricately with the multifaceted aspects of the surrounding microenvironment. The reciprocal crosstalk between cancer cells and the tumor microenvironment (TME) shapes the cancer pathophysiome in a way that renders it uniquely suited for immune tolerance, angiogenesis, metastasis, and therapy resistance. This dynamic interaction involves a dramatic reconstruction of the transcriptomic landscape of tumors by altering the synthesis, modifications, stability, and processing of gene readouts. In this review, we categorically evaluate the influence of TME components, encompassing a myriad of resident and infiltrating cells, signaling molecules, extracellular vesicles, extracellular matrix, and blood vessels, in orchestrating the cancer-specific metabolism and diversity of both mRNA and noncoding RNA, including micro RNA, long noncoding RNA, circular RNA among others. We also highlight the transcriptomic adaptations in response to the physicochemical idiosyncrasies of TME, which include tumor hypoxia, extracellular acidosis, and osmotic stress. Finally, we provide a nuanced analysis of existing and prospective therapeutics targeting TME to ameliorate cancer-associated RNA metabolism, consequently thwarting the cancer progression. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Subhashis Natua
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Shruti Ganesh Dhamdhere
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Srinivas Abhishek Mutnuru
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
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