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Ding X, Chen C, Zhao H, Dai B, Ye L, Song T, Huang S, Wang J, You T. Inhibiting SHP2 reduces glycolysis, promotes microglial M1 polarization, and alleviates secondary inflammation following spinal cord injury in a mouse model. Neural Regen Res 2025; 20:858-872. [PMID: 38886958 DOI: 10.4103/nrr.nrr-d-23-01925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 04/17/2024] [Indexed: 06/20/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202503000-00030/figure1/v/2024-06-17T092413Z/r/image-tiff Reducing the secondary inflammatory response, which is partly mediated by microglia, is a key focus in the treatment of spinal cord injury. Src homology 2-containing protein tyrosine phosphatase 2 (SHP2), encoded by PTPN11, is widely expressed in the human body and plays a role in inflammation through various mechanisms. Therefore, SHP2 is considered a potential target for the treatment of inflammation-related diseases. However, its role in secondary inflammation after spinal cord injury remains unclear. In this study, SHP2 was found to be abundantly expressed in microglia at the site of spinal cord injury. Inhibition of SHP2 expression using siRNA and SHP2 inhibitors attenuated the microglial inflammatory response in an in vitro lipopolysaccharide-induced model of inflammation. Notably, after treatment with SHP2 inhibitors, mice with spinal cord injury exhibited significantly improved hind limb locomotor function and reduced residual urine volume in the bladder. Subsequent in vitro experiments showed that, in microglia stimulated with lipopolysaccharide, inhibiting SHP2 expression promoted M2 polarization and inhibited M1 polarization. Finally, a co-culture experiment was conducted to assess the effect of microglia treated with SHP2 inhibitors on neuronal cells. The results demonstrated that inflammatory factors produced by microglia promoted neuronal apoptosis, while inhibiting SHP2 expression mitigated these effects. Collectively, our findings suggest that SHP2 enhances secondary inflammation and neuronal damage subsequent to spinal cord injury by modulating microglial phenotype. Therefore, inhibiting SHP2 alleviates the inflammatory response in mice with spinal cord injury and promotes functional recovery postinjury.
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Affiliation(s)
- Xintian Ding
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
- Department of Orthopedics, Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui Province, China
| | - Chun Chen
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Heng Zhao
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Bin Dai
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Lei Ye
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
- Department of Orthopedics, Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui Province, China
| | - Tao Song
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Shuai Huang
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Jia Wang
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Tao You
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
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Carrocci TJ, DeMario S, He K, Zeps NJ, Harkner CT, Chanfreau GF, Hoskins AA. Functional analysis of the zinc finger modules of the Saccharomyces cerevisiae splicing factor Luc7. RNA (NEW YORK, N.Y.) 2024; 30:1058-1069. [PMID: 38719745 PMCID: PMC11251517 DOI: 10.1261/rna.079956.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/14/2024] [Indexed: 05/21/2024]
Abstract
Identification of splice sites is a critical step in pre-messenger RNA (pre-mRNA) splicing because the definition of the exon/intron boundaries controls what nucleotides are incorporated into mature mRNAs. The intron boundary with the upstream exon is initially identified through interactions with the U1 small nuclear ribonucleoprotein (snRNP). This involves both base-pairing between the U1 snRNA and the pre-mRNA as well as snRNP proteins interacting with the 5' splice site (5'ss)/snRNA duplex. In yeast, this duplex is buttressed by two conserved protein factors, Yhc1 and Luc7. Luc7 has three human paralogs (LUC7L, LUC7L2, and LUC7L3), which play roles in alternative splicing. What domains of these paralogs promote splicing at particular sites is not yet clear. Here, we humanized the zinc finger (ZnF) domains of the yeast Luc7 protein in order to understand their roles in splice site selection using reporter assays, transcriptome analysis, and genetic interactions. Although we were unable to determine a function for the first ZnF domain, humanization of the second ZnF domain to mirror that found in LUC7L or LUC7L2 resulted in altered usage of nonconsensus 5'ss. In contrast, the corresponding ZnF domain of LUC7L3 could not support yeast viability. Further, humanization of Luc7 can suppress mutation of the ATPase Prp28, which is involved in U1 release and exchange for U6 at the 5'ss. Our work reveals a role for the second ZnF of Luc7 in splice site selection and suggests that different ZnF domains may have different ATPase requirements for release by Prp28.
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Affiliation(s)
- Tucker J Carrocci
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Samuel DeMario
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Kevin He
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Natalie J Zeps
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Cade T Harkner
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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3
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Chalivendra S, Shi S, Li X, Kuang Z, Giovinazzo J, Zhang L, Rossi J, Wang J, Saviola AJ, Welty R, Liu S, Vaeth KF, Zhou ZH, Hansen KC, Taliaferro JM, Zhao R. Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. RNA (NEW YORK, N.Y.) 2024; 30:1070-1088. [PMID: 38688558 PMCID: PMC11251525 DOI: 10.1261/rna.079917.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
The recognition of the 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand, the mechanism and regulation of 5' ss recognition, we selectively humanized components of the yeast U1 (yU1) snRNP to reveal the function of these components in 5' ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yU1 snRNA and the 5' ss RNA duplex. We replaced the zinc-finger (ZnF) domain of yeast U1C (yU1C) with its human counterpart, which resulted in a cold-sensitive growth phenotype and moderate splicing defects. We next added an auxin-inducible degron to yeast Luc7 (yLuc7) protein (to mimic the lack of Luc7Ls in human U1 snRNP). We found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of Prp40 and Snu71 (two other essential yU1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yU1 snRNP, and splicing plays a major role in the regulation of mitochondrial function in yeast.
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Affiliation(s)
- Subbaiah Chalivendra
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Shasha Shi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Zhiling Kuang
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Joseph Giovinazzo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - John Rossi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Robb Welty
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Katherine F Vaeth
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
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Tarannum M, Dinh K, Vergara J, Birch G, Abdulhamid YZ, Kaplan IE, Ay O, Maia A, Beaver O, Sheffer M, Shapiro R, Ali AK, Dong H, Ham JD, Bobilev E, James S, Cameron AB, Nguyen QD, Ganapathy S, Chayawatto C, Koreth J, Paweletz CP, Gokhale PC, Barbie DA, Matulonis UA, Soiffer RJ, Ritz J, Porter RL, Chen J, Romee R. CAR memory-like NK cells targeting the membrane proximal domain of mesothelin demonstrate promising activity in ovarian cancer. SCIENCE ADVANCES 2024; 10:eadn0881. [PMID: 38996027 PMCID: PMC11244547 DOI: 10.1126/sciadv.adn0881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 06/10/2024] [Indexed: 07/14/2024]
Abstract
Epithelial ovarian cancer (EOC) remains one of the most lethal gynecological cancers. Cytokine-induced memory-like (CIML) natural killer (NK) cells have shown promising results in preclinical and early-phase clinical trials. In the current study, CIML NK cells demonstrated superior antitumor responses against a panel of EOC cell lines, increased expression of activation receptors, and up-regulation of genes involved in cell cycle/proliferation and down-regulation of inhibitory/suppressive genes. CIML NK cells transduced with a chimeric antigen receptor (CAR) targeting the membrane-proximal domain of mesothelin (MSLN) further improved the antitumor responses against MSLN-expressing EOC cells and patient-derived xenograft tumor cells. CAR arming of the CIML NK cells subtanstially reduced their dysfunction in patient-derived ascites fluid with transcriptomic changes related to altered metabolism and tonic signaling as potential mechanisms. Lastly, the adoptive transfer of MSLN-CAR CIML NK cells demonstrated remarkable inhibition of tumor growth and prevented metastatic spread in xenograft mice, supporting their potential as an effective therapeutic strategy in EOC.
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MESH Headings
- Mesothelin
- Humans
- Animals
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Female
- Mice
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Ovarian Neoplasms/immunology
- Ovarian Neoplasms/therapy
- Cell Line, Tumor
- Receptors, Chimeric Antigen/metabolism
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/genetics
- Xenograft Model Antitumor Assays
- GPI-Linked Proteins/metabolism
- GPI-Linked Proteins/genetics
- Immunotherapy, Adoptive/methods
- Carcinoma, Ovarian Epithelial/metabolism
- Carcinoma, Ovarian Epithelial/pathology
- Carcinoma, Ovarian Epithelial/immunology
- Carcinoma, Ovarian Epithelial/therapy
- Immunologic Memory
- Protein Domains
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Affiliation(s)
- Mubin Tarannum
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Khanhlinh Dinh
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Juliana Vergara
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Grace Birch
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yasmin Z Abdulhamid
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Isabel E Kaplan
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Oyku Ay
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Andreia Maia
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Owen Beaver
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Michal Sheffer
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Roman Shapiro
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alaa Kassim Ali
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Han Dong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - James Dongjoo Ham
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eden Bobilev
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Sydney James
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Amy B Cameron
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Suthakar Ganapathy
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chayapatou Chayawatto
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - John Koreth
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cloud P Paweletz
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Prafulla C Gokhale
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - David A Barbie
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Division of Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ursula A Matulonis
- Division of Gynecologic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Robert J Soiffer
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jerome Ritz
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Rebecca L Porter
- Division of Gynecologic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jianzhu Chen
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rizwan Romee
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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5
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Senn KA, Hoskins AA. Mechanisms and regulation of spliceosome-mediated pre-mRNA splicing in Saccharomyces cerevisiae. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1866. [PMID: 38972853 DOI: 10.1002/wrna.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 07/09/2024]
Abstract
Pre-mRNA splicing, the removal of introns and ligation of flanking exons, is a crucial step in eukaryotic gene expression. The spliceosome, a macromolecular complex made up of five small nuclear RNAs (snRNAs) and dozens of proteins, assembles on introns via a complex pathway before catalyzing the two transesterification reactions necessary for splicing. All of these steps have the potential to be highly regulated to ensure correct mRNA isoform production for proper cellular function. While Saccharomyces cerevisiae (yeast) has a limited set of intron-containing genes, many of these genes are highly expressed, resulting in a large number of transcripts in a cell being spliced. As a result, splicing regulation is of critical importance for yeast. Just as in humans, yeast splicing can be influenced by protein components of the splicing machinery, structures and properties of the pre-mRNA itself, or by the action of trans-acting factors. It is likely that further analysis of the mechanisms and pathways of splicing regulation in yeast can reveal general principles applicable to other eukaryotes. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Katherine Anne Senn
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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6
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Zhang Y, Yan H, Wei Y, Wei X. Decoding mitochondria's role in immunity and cancer therapy. Biochim Biophys Acta Rev Cancer 2024; 1879:189107. [PMID: 38734035 DOI: 10.1016/j.bbcan.2024.189107] [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: 02/08/2024] [Revised: 04/22/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024]
Abstract
The functions of mitochondria, including energy production and biomolecule synthesis, have been known for a long time. Given the rising incidence of cancer, the role of mitochondria in cancer has become increasingly popular. Activated by components released by mitochondria, various pathways interact with each other to induce immune responses to protect organisms from attack. However, mitochondria play dual roles in the progression of cancer. Abnormalities in proteins, which are the elementary structures of mitochondria, are closely linked with oncogenesis. Both the aberrant accumulation of intermediates and mutations in enzymes result in the generation and progression of cancer. Therefore, targeting mitochondria to treat cancer may be a new strategy. Several drugs aimed at inhibiting mutated enzymes and accumulated intermediates have been tested clinically. Here, we discuss the current understanding of mitochondria in cancer and the interactions between mitochondrial functions, immune responses, and oncogenesis. Furthermore, we discuss mitochondria as hopeful targets for cancer therapy, providing insights into the progression of future therapeutic strategies.
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Affiliation(s)
- Yu Zhang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan, PR China
| | - Hong Yan
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan, PR China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan, PR China.
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan, PR China.
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7
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Cao H, Li C, Sun X, Yang J, Li X, Yang G, Jin J, Shi X. Circular RNA circMYLK4 shifts energy metabolism from glycolysis to OXPHOS by binding to the calcium channel auxiliary subunit CACNA2D2. J Biol Chem 2024; 300:107426. [PMID: 38823637 PMCID: PMC11245919 DOI: 10.1016/j.jbc.2024.107426] [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: 01/17/2024] [Revised: 05/09/2024] [Accepted: 05/21/2024] [Indexed: 06/03/2024] Open
Abstract
Skeletal muscle is heterogeneous tissue, composed of fast-twitch fibers primarily relying on glycolysis and slow-twitch fibers primarily relying on oxidative phosphorylation. The relative expression and balance of glycolysis and oxidative phosphorylation in skeletal muscle are crucial for muscle growth and skeletal muscle metabolism. Here, we employed multi-omics approaches including transcriptomics, proteomics, phosphoproteomics, and metabolomics to unravel the role of circMYLK4, a differentially expressed circRNA in fast and slow-twitch muscle fibers, in muscle fiber metabolism. We discovered that circMYLK4 inhibits glycolysis and promotes mitochondrial oxidative phosphorylation. Mechanistically, circMYLK4 interacts with the voltage-gated calcium channel auxiliary subunit CACNA2D2, leading to the inhibition of Ca2+ release from the sarcoplasmic reticulum. The decrease in cytoplasmic Ca2+ concentration inhibits the expression of key enzymes, PHKB and PHKG1, involved in glycogen breakdown, thereby suppressing glycolysis. On the other hand, the increased fatty acid β-oxidation enhances the tricarboxylic acid cycle and mitochondrial oxidative phosphorylation. In general, circMYLK4 plays an indispensable role in maintaining the metabolic homeostasis of skeletal muscle.
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Affiliation(s)
- Haigang Cao
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chenchen Li
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaohui Sun
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jinjin Yang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiao Li
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Gongshe Yang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianjun Jin
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
| | - Xine Shi
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
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8
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Meisel JD, Wiesenthal PP, Mootha VK, Ruvkun G. CMTR-1 RNA methyltransferase mutations activate widespread expression of a dopaminergic neuron-specific mitochondrial complex I gene. Curr Biol 2024; 34:2728-2738.e6. [PMID: 38810637 PMCID: PMC11265314 DOI: 10.1016/j.cub.2024.04.079] [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: 06/11/2023] [Revised: 03/05/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
The mitochondrial proteome is comprised of approximately 1,100 proteins,1 all but 12 of which are encoded by the nuclear genome in C. elegans. The expression of nuclear-encoded mitochondrial proteins varies widely across cell lineages and metabolic states,2,3,4 but the factors that specify these programs are not known. Here, we identify mutations in two nuclear-localized mRNA processing proteins, CMTR1/CMTR-1 and SRRT/ARS2/SRRT-1, which we show act via the same mechanism to rescue the mitochondrial complex I mutant NDUFS2/gas-1(fc21). CMTR-1 is an FtsJ-family RNA methyltransferase that, in mammals, 2'-O-methylates the first nucleotide 3' to the mRNA CAP to promote RNA stability and translation5,6,7,8. The mutations isolated in cmtr-1 are dominant and lie exclusively in the regulatory G-patch domain. SRRT-1 is an RNA binding partner of the nuclear cap-binding complex and determines mRNA transcript fate.9 We show that cmtr-1 and srrt-1 mutations activate embryonic expression of NDUFS2/nduf-2.2, a paralog of NDUFS2/gas-1 normally expressed only in dopaminergic neurons, and that nduf-2.2 is necessary for the complex I rescue by the cmtr-1 G-patch mutant. Additionally, we find that loss of the cmtr-1 G-patch domain cause ectopic localization of CMTR-1 protein to processing bodies (P bodies), phase-separated organelles involved in mRNA storage and decay.10 P-body localization of the G-patch mutant CMTR-1 contributes to the rescue of the hyperoxia sensitivity of the NDUFS2/gas-1 mutant. This study suggests that mRNA methylation at P bodies may control nduf-2.2 gene expression, with broader implications for how the mitochondrial proteome is translationally remodeled in the face of tissue-specific metabolic requirements and stress.
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Affiliation(s)
- Joshua D Meisel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Presli P Wiesenthal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
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9
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Zhang X, Guo J, Shi X, Zhou X, Chen Q. LUC7L3 is a downstream factor of SRSF1 and prevents genomic instability. CELL INSIGHT 2024; 3:100170. [PMID: 38590928 PMCID: PMC10999515 DOI: 10.1016/j.cellin.2024.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024]
Abstract
The RNA-binding protein LUC7L3 is the human homolog of yeast U1 small nuclear RNA (snRNA)-related splicing factor Luc7p. While the primary function of LUC7L3 as an RNA-binding protein is believed to be involved in RNA metabolism, particularly in the splicing process, its exact role and other functions are still not fully understood. In this study, we aimed to elucidate the role of LUC7L3 and its impact on cell proliferation. Our study revealed that LUC7L3 depletion impairs cell proliferation compared to the other Luc7p paralogs, resulting in cell apoptosis and senescence. We explored the underlying mechanisms and found that LUC7L3 depletion leads to R-loop accumulation, DNA replication stress, and genome instability. Furthermore, we discovered that LUC7L3 depletion caused abnormalities in spindle assembly, leading to the formation of multinuclear cells. This was attributed to the dysregulation of protein translation of spindle-associated proteins. Additionally, we investigated the interplay between LUC7L3 and SRSF1 and identified SRSF1 as an upper stream regulator of LUC7L3, promoting the translation of LUC7L3 protein. These findings highlight the importance of LUC7L3 in maintaining genome stability and its relationship with SRSF1 in this regulatory pathway.
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Affiliation(s)
- Xiaqing Zhang
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Jing Guo
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Xin Shi
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Xin Zhou
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Qiang Chen
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
- Clinical Medical Research Center of Peritoneal Cancer of Wuhan, Wuhan, 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Province Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
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10
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Li K, Fan C, Chen J, Xu X, Lu C, Shao H, Xi Y. Role of oxidative stress-induced ferroptosis in cancer therapy. J Cell Mol Med 2024; 28:e18399. [PMID: 38757920 PMCID: PMC11100387 DOI: 10.1111/jcmm.18399] [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: 10/05/2023] [Revised: 02/06/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
Ferroptosis is a distinct mode of cell death, distinguishing itself from typical apoptosis by its reliance on the accumulation of iron ions and lipid peroxides. Cells manifest an imbalance between oxidative stress and antioxidant equilibrium during certain pathological contexts, such as tumours, resulting in oxidative stress. Notably, recent investigations propose that heightened intracellular reactive oxygen species (ROS) due to oxidative stress can heighten cellular susceptibility to ferroptosis inducers or expedite the onset of ferroptosis. Consequently, comprehending role of ROS in the initiation of ferroptosis has significance in elucidating disorders related to oxidative stress. Moreover, an exhaustive exploration into the mechanism and control of ferroptosis might offer novel targets for addressing specific tumour types. Within this context, our review delves into recent fundamental pathways and the molecular foundation of ferroptosis. Four classical ferroptotic molecular pathways are well characterized, namely, glutathione peroxidase 4-centred molecular pathway, nuclear factor erythroid 2-related factor 2 molecular pathway, mitochondrial molecular pathway, and mTOR-dependent autophagy pathway. Furthermore, we seek to elucidate the regulatory contributions enacted by ROS. Additionally, we provide an overview of targeted medications targeting four molecular pathways implicated in ferroptosis and their potential clinical applications. Here, we review the role of ROS and oxidative stress in ferroptosis, and we discuss opportunities to use ferroptosis as a new strategy for cancer therapy and point out the current challenges persisting within the domain of ROS-regulated anticancer drug research and development.
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Affiliation(s)
- Keqing Li
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science CenterNingbo UniversityNingboChina
| | - Chengjiang Fan
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science CenterNingbo UniversityNingboChina
| | - Jianing Chen
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science CenterNingbo UniversityNingboChina
| | - Xin Xu
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science CenterNingbo UniversityNingboChina
| | - Chuwei Lu
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science CenterNingbo UniversityNingboChina
| | - Hanjie Shao
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science CenterNingbo UniversityNingboChina
| | - Yang Xi
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science CenterNingbo UniversityNingboChina
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11
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Yue Q, Wang Z, Shen Y, Lan Y, Zhong X, Luo X, Yang T, Zhang M, Zuo B, Zeng T, Lu J, Wang Y, Liu B, Guo H. Histone H3K9 Lactylation Confers Temozolomide Resistance in Glioblastoma via LUC7L2-Mediated MLH1 Intron Retention. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309290. [PMID: 38477507 PMCID: PMC11109612 DOI: 10.1002/advs.202309290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/03/2024] [Indexed: 03/14/2024]
Abstract
Temozolomide (TMZ) resistance remains the major obstacle in the treatment of glioblastoma (GBM). Lactylation is a novel post-translational modification that is involved in various tumors. However, whether lactylation plays a role in GBM TMZ resistance remains unclear. Here it is found that histone H3K9 lactylation (H3K9la) confers TMZ resistance in GBM via LUC7L2-mediated intron 7 retention of MLH1. Mechanistically, lactylation is upregulated in recurrent GBM tissues and TMZ-resistant cells, and is mainly concentrated in histone H3K9. Combined multi-omics analysis, including CUT&Tag, SLAM-seq, and RNA-seq, reveals that H3K9 lactylation is significantly enriched in the LUC7L2 promoter and activates LUC7L2 transcription to promote its expression. LUC7L2 mediates intron 7 retention of MLH1 to reduce MLH1 expression, and thereby inhibit mismatch repair (MMR), ultimately leading to GBM TMZ resistance. Of note, it is identified that a clinical anti-epileptic drug, stiripentol, which can cross the blood-brain barrier and inhibit lactate dehydrogenase A/B (LDHA/B) activity, acts as a lactylation inhibitor and renders GBM cells more sensitive to TMZ in vitro and in vivo. These findings not only shed light on the mechanism of lactylation in GBM TMZ resistance but also provide a potential combined therapeutic strategy for clinical GBM treatment.
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Affiliation(s)
- Qu Yue
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Zhao Wang
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Yixiong Shen
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Yufei Lan
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Xiangyang Zhong
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Xin Luo
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Tao Yang
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Manqing Zhang
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Boming Zuo
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Tianci Zeng
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Jiankun Lu
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Yuankai Wang
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Boyang Liu
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
| | - Hongbo Guo
- Department of Neurosurgery CenterThe National Key Clinical SpecialtyThe Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular DiseaseGuangdong Provincial Key Laboratory on Brain Function Repair and RegenerationThe Neurosurgery Institute of Guangdong ProvinceZhujiang HospitalSouthern Medical UniversityGuangzhou510282China
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12
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Forman TE, Sajek MP, Larson ED, Mukherjee N, Fantauzzo KA. PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.587975. [PMID: 38617350 PMCID: PMC11014628 DOI: 10.1101/2024.04.03.587975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Signaling through the platelet-derived growth factor receptor alpha (PDGFRa) plays a critical role in craniofacial development, as mutations in PDGFRA are associated with cleft lip/palate in humans and Pdgfra mutant mouse models display varying degrees of facial clefting. Phosphatidylinositol 3-kinase (PI3K)/Akt is the primary effector of PDGFRα signaling during skeletal development in the mouse. We previously demonstrated that Akt phosphorylates the RNA-binding protein serine/arginine-rich splicing factor 3 (Srsf3) downstream of PI3K-mediated PDGFRa signaling in mouse embryonic palatal mesenchyme (MEPM) cells, leading to its nuclear translocation. We further showed that ablation of Srsf3 in the murine neural crest lineage results in severe midline facial clefting, due to defects in proliferation and survival of cranial neural crest cells, and widespread alternative RNA splicing (AS) changes. Here, we sought to determine the molecular mechanisms by which Srsf3 activity is regulated downstream of PDGFRa signaling to control AS of transcripts necessary for craniofacial development. We demonstrated via enhanced UV-crosslinking and immunoprecipitation (eCLIP) of MEPM cells that PDGF-AA stimulation leads to preferential binding of Srsf3 to exons and loss of binding to canonical Srsf3 CA-rich motifs. Through the analysis of complementary RNA-seq data, we showed that Srsf3 activity results in the preferential inclusion of exons with increased GC content and lower intron to exon length ratio. Moreover, we found that the subset of transcripts that are bound by Srsf3 and undergo AS upon PDGFRα signaling commonly encode regulators of PI3K signaling and early endosomal trafficking. Functional validation studies further confirmed that Srsf3 activity downstream of PDGFRα signaling leads to retention of the receptor in early endosomes and increases in downstream PI3K-mediated Akt signaling. Taken together, our findings reveal that growth factor-mediated phosphorylation of an RNA-binding protein underlies gene expression regulation necessary for mammalian craniofacial development.
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Affiliation(s)
- Thomas E. Forman
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Marcin P. Sajek
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Eric D. Larson
- Department of Otolaryngology – Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Basic and Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neelanjan Mukherjee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katherine A. Fantauzzo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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13
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Wang Y, Xie Z, Kutschera E, Adams JI, Kadash-Edmondson KE, Xing Y. rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data. Nat Protoc 2024; 19:1083-1104. [PMID: 38396040 DOI: 10.1038/s41596-023-00944-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/02/2023] [Indexed: 02/25/2024]
Abstract
Pre-mRNA alternative splicing is a prevalent mechanism for diversifying eukaryotic transcriptomes and proteomes. Regulated alternative splicing plays a role in many biological processes, and dysregulated alternative splicing is a feature of many human diseases. Short-read RNA sequencing (RNA-seq) is now the standard approach for transcriptome-wide analysis of alternative splicing. Since 2011, our laboratory has developed and maintained Replicate Multivariate Analysis of Transcript Splicing (rMATS), a computational tool for discovering and quantifying alternative splicing events from RNA-seq data. Here we provide a protocol for the contemporary version of rMATS, rMATS-turbo, a fast and scalable re-implementation that maintains the statistical framework and user interface of the original rMATS software, while incorporating a revamped computational workflow with a substantial improvement in speed and data storage efficiency. The rMATS-turbo software scales up to massive RNA-seq datasets with tens of thousands of samples. To illustrate the utility of rMATS-turbo, we describe two representative application scenarios. First, we describe a broadly applicable two-group comparison to identify differential alternative splicing events between two sample groups, including both annotated and novel alternative splicing events. Second, we describe a quantitative analysis of alternative splicing in a large-scale RNA-seq dataset (~1,000 samples), including the discovery of alternative splicing events associated with distinct cell states. We detail the workflow and features of rMATS-turbo that enable efficient parallel processing and analysis of large-scale RNA-seq datasets on a compute cluster. We anticipate that this protocol will help the broad user base of rMATS-turbo make the best use of this software for studying alternative splicing in diverse biological systems.
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Affiliation(s)
- Yuanyuan Wang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zhijie Xie
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric Kutschera
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jenea I Adams
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn E Kadash-Edmondson
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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14
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Carrocci TJ, DeMario S, He K, Zeps NJ, Harkner CT, Chanfreau G, Hoskins AA. Functional Analysis of the Zinc Finger Modules of the S. cerevisiae Splicing Factor Luc7. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578419. [PMID: 38352541 PMCID: PMC10862913 DOI: 10.1101/2024.02.04.578419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Identification of splice sites is a critical step in pre-mRNA splicing since definition of the exon/intron boundaries controls what nucleotides are incorporated into mature mRNAs. The intron boundary with the upstream exon is initially identified through interactions with the U1 snRNP. This involves both base pairing between the U1 snRNA and the pre-mRNA as well as snRNP proteins interacting with the 5' splice site/snRNA duplex. In yeast, this duplex is buttressed by two conserved protein factors, Yhc1 and Luc7. Luc7 has three human paralogs (LUC7L, LUC7L2, and LUC7L3) which play roles in alternative splicing. What domains of these paralogs promote splicing at particular sites is not yet clear. Here, we humanized the zinc finger domains of the yeast Luc7 protein in order to understand their roles in splice site selection using reporter assays, transcriptome analysis, and genetic interactions. While we were unable to determine a function for the first zinc finger domain, humanization of the second zinc finger domain to mirror that found in LUC7L or LUC7L2 resulted in altered usage of nonconsensus 5' splice sites. In contrast, the corresponding zinc finger domain of LUC7L3 could not support yeast viability. Further, humanization of Luc7 can suppress mutation of the ATPase Prp28, which is involved in U1 release and exchange for U6 at the 5' splice site. Our work reveals a role for the second zinc finger of Luc7 in splice site selection and suggests that different zinc finger domains may have different ATPase requirements for release by Prp28.
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Affiliation(s)
- Tucker J. Carrocci
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Samuel DeMario
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin He
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Natalie J. Zeps
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cade T. Harkner
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Guillaume Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aaron A. Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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15
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Varineau JE, Calo E. A common cellular response to broad splicing perturbations is characterized by metabolic transcript downregulation driven by the Mdm2-p53 axis. Dis Model Mech 2024; 17:dmm050356. [PMID: 38426258 PMCID: PMC10924232 DOI: 10.1242/dmm.050356] [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: 06/16/2023] [Accepted: 01/09/2024] [Indexed: 03/02/2024] Open
Abstract
Disruptions in core cellular processes elicit stress responses that drive cell-state changes leading to organismal phenotypes. Perturbations in the splicing machinery cause widespread mis-splicing, resulting in p53-dependent cell-state changes that give rise to cell-type-specific phenotypes and disease. However, a unified framework for how cells respond to splicing perturbations, and how this response manifests itself in nuanced disease phenotypes, has yet to be established. Here, we show that a p53-stabilizing Mdm2 alternative splicing event and the resulting widespread downregulation of metabolic transcripts are common events that arise in response to various splicing perturbations in both cellular and organismal models. Together, our results classify a common cellular response to splicing perturbations, put forth a new mechanism behind the cell-type-specific phenotypes that arise when splicing is broadly disrupted, and lend insight into the pleiotropic nature of the effects of p53 stabilization in disease.
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Affiliation(s)
- Jade E. Varineau
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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16
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Jourdain AA, Wang F. Career pathways, part 13. Nat Metab 2024; 6:2-5. [PMID: 38233680 DOI: 10.1038/s42255-023-00954-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Affiliation(s)
- Alexis A Jourdain
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
| | - Feilong Wang
- Shanghai East Hospital, Tongji University, Shanghai, China.
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17
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Chalivendra S, Shi S, Li X, Kuang Z, Giovinazzo J, Zhang L, Rossi J, Saviola AJ, Wang J, Welty R, Liu S, Vaeth K, Zhou ZH, Hansen KC, Taliaferro JM, Zhao R. Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571893. [PMID: 38168357 PMCID: PMC10760170 DOI: 10.1101/2023.12.15.571893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The recognition of 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5' ss recognition, we selectively humanized components of the yeast U1 snRNP to reveal the function of these components in 5' ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yeast U1 (yU1) snRNA and the 5' ss RNA duplex. We replaced the Zinc-Finger (ZnF) domain of yU1C with its human counterpart, which resulted in cold-sensitive growth phenotype and moderate splicing defects. Next, we added an auxin-inducible degron to yLuc7 protein and found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of PRP40 and Snu71 (two other essential yeast U1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe 2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yeast U1 snRNP, and splicing plays a major role in the regulation of mitochondria function in yeast.
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18
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Fu C, Cao N, Zeng S, Zhu W, Fu X, Liu W, Fan S. Role of mitochondria in the regulation of ferroptosis and disease. Front Med (Lausanne) 2023; 10:1301822. [PMID: 38155662 PMCID: PMC10753798 DOI: 10.3389/fmed.2023.1301822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/09/2023] [Indexed: 12/30/2023] Open
Abstract
Ferroptosis is a distinctive form of iron-dependent cell death characterized by significant ultrastructural changes in mitochondria. Given the crucial involvement of mitochondria in various cellular processes such as reactive oxygen species production, energy metabolism, redox status, and iron metabolism, mounting evidence suggests a vital role of mitochondria in the regulation and execution of ferroptosis. Furthermore, there exists a strong correlation between ferroptosis and various diseases. In this review, we aim to summarize the mechanisms underlying the induction and defense of ferroptosis, emphasizing the influence of mitochondria on this intricate process. Additionally, we provide an overview of the role of ferroptosis in disease, particularly cancer, and elucidate the mechanisms by which drugs targeting mitochondria impact ferroptosis. By presenting a theoretical foundation and reference point, this review aims to contribute to both basic cell biology research and the investigation of clinically relevant diseases.
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Affiliation(s)
- Cheng Fu
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Nan Cao
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Sen Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wenhui Zhu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xinliang Fu
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wenjun Liu
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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Gao Y, Long Q, Yang H, Hu Y, Xu Y, Tang C, Gu C, Yong S. Transcriptomics and metabolomics study in mouse kidney of the molecular mechanism underlying energy metabolism response to hypoxic stress in highland areas. Exp Ther Med 2023; 26:533. [PMID: 37869643 PMCID: PMC10587886 DOI: 10.3892/etm.2023.12232] [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: 05/15/2023] [Accepted: 08/25/2023] [Indexed: 10/24/2023] Open
Abstract
Exposure to hypoxia disrupts energy metabolism and induces inflammation. However, the pathways and mechanisms underlying energy metabolism disorders caused by hypoxic conditions remain unclear. In the present study, a hypoxic animal model was created and transcriptomic and non-targeted metabolomics techniques were applied to further investigate the pathways and mechanisms of hypoxia exposure that disrupt energy metabolism. Transcriptome results showed that 3,007 genes were significantly differentially expressed under hypoxic exposure, and Gene Ontology annotation analysis and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis showed that the differentially expressed genes (DEGs) were mainly involved in energy metabolism and were significantly enriched in the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS) pathway. The DEGs IDH3A, SUCLA2, and MDH2 in the TCA cycle and the DEGs NDUFA3, NDUFS7, UQCRC1, CYC1 and UQCRFS1 in the OXPHOS pathway were validated using mRNA and protein expression, and the results showed downregulation. The results of non-targeted metabolomics showed that 365 significant differential metabolites were identified under plateau hypoxia stress. KEGG enrichment analysis showed that the differential metabolites were mainly enriched in metabolic processes, such as energy, nucleotide and amino acid metabolism. Hypoxia exposure disrupted the TCA cycle and reduced the synthesis of amino acids and nucleotides by decreasing the concentration of cis-aconitate, α-ketoglutarate, NADH, NADPH and that of most amino acids, purines, and pyrimidines. Bioinformatics analysis was used to identify inflammatory genes related to hypoxia exposure and some of them were selected for verification. It was shown that the mRNA and protein expression levels of IL1B, IL12B, S100A8 and S100A9 in kidney tissues were upregulated under hypoxic exposure. The results suggest that hypoxia exposure inhibits the TCA cycle and the OXPHOS signalling pathway by inhibiting IDH3A, SUCLA2, MDH2, NDUFFA3, NDUFS7, UQCRC1, CYC1 and UQCRFS1, thereby suppressing energy metabolism, inducing amino acid and nucleotide deficiency and promoting inflammation, ultimately leading to kidney damage.
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Affiliation(s)
- Yujie Gao
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Qifu Long
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Hui Yang
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Ying Hu
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Yuzhen Xu
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Chaoqun Tang
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Cunlin Gu
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Sheng Yong
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
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20
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Zhao Y, Gao Q, Li B, Wang Y, Wang Y. Ferroptosis and its potential role in gestational diabetes mellitus: updated evidence from pathogenesis to therapy. Front Endocrinol (Lausanne) 2023; 14:1177547. [PMID: 37664858 PMCID: PMC10471987 DOI: 10.3389/fendo.2023.1177547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
Background Studies have demonstrated that high iron status is positively associated with gestational diabetes mellitus (GDM), implying that iron overload and ferroptosis play important roles in the development of GDM. The aim of this study was to explore effective therapeutic drugs from traditional Chinese medicine (TCM)formulas for the treatment of GDM based on ferroptosis. Methods In this study, the presence of ferroptosis in the placenta was verified through clinical and experimental data, and key genes were subsequently screened for association with ferroptosis in the development of GDM. The analysis was based on transcriptome sequencing of datasets combined with differentially expressed genes (DEGs) analysis and weighted gene correlation network analysis (WGCNA); functional enrichment analysis was also performed. A protein-protein interaction (PPI) network was constructed and pivotal genes were identified using Cytoscape. Finally, traditional Chinese medicine (TCM)formulas related to treating GDM were collected, then the proteins corresponding to the key genes were molecularly docked with the small molecular structures of clinically proven effective herbal tonics, and molecular dynamic simulations were performed to select the best candidates for pharmacological compounds. Results Elevated ferritin levels in patients with GDM were verified using clinical data. The presence of ferroptosis in placental tissues of patients with GDM was confirmed using electron microscopy and western blotting. Ninety-nine key genes with the highest correlation with ferroptosis were identified from DEGs and weighted gene co-expression network analysis (WGCNA). Analysis using the Kyoto Encyclopedia of Genes and Genomes demonstrated that the DEGs were primarily involved in the oxidative phosphorylation pathway. The key genes were further screened by PPI; two key genes, SF3B14 and BABAM1, were identified by combining the gene corresponding to protein structure and function, followed by molecular docking and molecular dynamic simulation. Coptis chinensis was proposed as the best candidate for herbal treatment at the molecular level. Conclusion This data revealed the presence of ferroptosis in patients with GDM and identified possible modulatory roles of ferroptosis-related genes involved in the molecular mechanisms of GDM, providing new insights into the pathogenesis of GDM, which also provided new directions for the systematic optimization of TCM formulas for the management and targeted treatment of GDM.
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Affiliation(s)
- Yan Zhao
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Qianqian Gao
- Department of Obstetrics, Weifang People’s Hospital, Weifang, ShanDong, China
| | - Baoxuan Li
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yang Wang
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yue Wang
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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21
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Sharifnia T, Wawer MJ, Goodale A, Lee Y, Kazachkova M, Dempster JM, Muller S, Levy J, Freed DM, Sommer J, Kalfon J, Vazquez F, Hahn WC, Root DE, Clemons PA, Schreiber SL. Mapping the landscape of genetic dependencies in chordoma. Nat Commun 2023; 14:1933. [PMID: 37024492 PMCID: PMC10079670 DOI: 10.1038/s41467-023-37593-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/21/2023] [Indexed: 04/08/2023] Open
Abstract
Identifying the spectrum of genes required for cancer cell survival can reveal essential cancer circuitry and therapeutic targets, but such a map remains incomplete for many cancer types. We apply genome-scale CRISPR-Cas9 loss-of-function screens to map the landscape of selectively essential genes in chordoma, a bone cancer with few validated targets. This approach confirms a known chordoma dependency, TBXT (T; brachyury), and identifies a range of additional dependencies, including PTPN11, ADAR, PRKRA, LUC7L2, SRRM2, SLC2A1, SLC7A5, FANCM, and THAP1. CDK6, SOX9, and EGFR, genes previously implicated in chordoma biology, are also recovered. We find genomic and transcriptomic features that predict specific dependencies, including interferon-stimulated gene expression, which correlates with ADAR dependence and is elevated in chordoma. Validating the therapeutic relevance of dependencies, small-molecule inhibitors of SHP2, encoded by PTPN11, have potent preclinical efficacy against chordoma. Our results generate an emerging map of chordoma dependencies to enable biological and therapeutic hypotheses.
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Affiliation(s)
- Tanaz Sharifnia
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - Mathias J Wawer
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Kojin Therapeutics, Boston, MA, 02210, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Yenarae Lee
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Mariya Kazachkova
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Sandrine Muller
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Joan Levy
- Chordoma Foundation, Durham, NC, 27702, USA
- Melanoma Research Alliance, Washington, D.C., 20005, USA
| | | | | | - Jérémie Kalfon
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Paul A Clemons
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Harvard University, Cambridge, MA, 02138, USA.
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22
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Rogalska ME, Vivori C, Valcárcel J. Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects. Nat Rev Genet 2023; 24:251-269. [PMID: 36526860 DOI: 10.1038/s41576-022-00556-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 12/23/2022]
Abstract
The removal of introns from mRNA precursors and its regulation by alternative splicing are key for eukaryotic gene expression and cellular function, as evidenced by the numerous pathologies induced or modified by splicing alterations. Major recent advances have been made in understanding the structures and functions of the splicing machinery, in the description and classification of physiological and pathological isoforms and in the development of the first therapies for genetic diseases based on modulation of splicing. Here, we review this progress and discuss important remaining challenges, including predicting splice sites from genomic sequences, understanding the variety of molecular mechanisms and logic of splicing regulation, and harnessing this knowledge for probing gene function and disease aetiology and for the design of novel therapeutic approaches.
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Affiliation(s)
- Malgorzata Ewa Rogalska
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Claudia Vivori
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- The Francis Crick Institute, London, UK
| | - Juan Valcárcel
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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23
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Ferroptosis, pyroptosis and necroptosis in acute respiratory distress syndrome. Cell Death Discov 2023; 9:91. [PMID: 36898986 PMCID: PMC10000361 DOI: 10.1038/s41420-023-01369-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 03/12/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) is an acute and uncontrolled pulmonary inflammation caused by various insults. Cell death is a critical mechanism in the pathogenesis of ARDS. Ferroptosis, a novel form of cell death defined as iron-mediated lipid peroxidation, has been shown to play a role in the pathogenesis of ARDS. Additionally, pyroptosis and necroptosis are also involved in the pathophysiological process of ARDS. The crosstalk among ferroptosis, pyroptosis, and necroptosis is getting increasing attention. Therefore, this review will mainly summarize the molecular mechanisms and central pathophysiological role of ferroptosis in ARDS. We will also discuss our understanding of pyroptosis and necroptosis as they pertain to the pathogenesis of ARDS. Furthermore, we also describe the pathological processes that engage crosstalk among ferroptosis, pyroptosis, and necroptosis. We consider that individual pathways of ferroptosis, pyroptosis, and necroptosis are highly interconnected and can compensate for one another to promote cell death.
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24
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Blanco-Fernandez J, Jourdain AA. Dead-Seq: Discovering Synthetic Lethal Interactions from Dead Cells Genomics. Methods Mol Biol 2023; 2661:329-342. [PMID: 37166646 DOI: 10.1007/978-1-0716-3171-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pooled genetic screens have revolutionized the field of functional genomics, yet perturbations that decrease fitness, such as those leading to synthetic lethality, have remained difficult to quantify at the genomic level. We and colleagues previously developed "death screening," a protocol based on the purification of dead cells in genetic screens, and used it to identify a set of genes necessary for mitochondrial gene expression, translation, and oxidative phosphorylation (OXPHOS), thus offering new possibilities for the diagnosis of mitochondrial disorders. Here, we describe Dead-Seq, a refined protocol for death screening that is compatible with most pooled screening protocols, including genome-wide CRISPR/Cas9 screening. Dead-Seq converts negative-selection screens into positive-selection screens and generates high-quality data directly from dead cells, at limited sequencing costs.
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Affiliation(s)
| | - Alexis A Jourdain
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
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25
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Liu Y, Sun Y, Guo Y, Shi X, Chen X, Feng W, Wu LL, Zhang J, Yu S, Wang Y, Shi Y. An Overview: The Diversified Role of Mitochondria in Cancer Metabolism. Int J Biol Sci 2023; 19:897-915. [PMID: 36778129 PMCID: PMC9910000 DOI: 10.7150/ijbs.81609] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 02/04/2023] Open
Abstract
Mitochondria are intracellular organelles involved in energy production, cell metabolism and cell signaling. They are essential not only in the process of ATP synthesis, lipid metabolism and nucleic acid metabolism, but also in tumor development and metastasis. Mutations in mtDNA are commonly found in cancer cells to promote the rewiring of bioenergetics and biosynthesis, various metabolites especially oncometabolites in mitochondria regulate tumor metabolism and progression. And mutation of enzymes in the TCA cycle leads to the unusual accumulation of certain metabolites and oncometabolites. Mitochondria have been demonstrated as the target for cancer treatment. Cancer cells rely on two main energy resources: oxidative phosphorylation (OXPHOS) and glycolysis. By manipulating OXPHOS genes or adjusting the metabolites production in mitochondria, tumor growth can be restrained. For example, enhanced complex I activity increases NAD+/NADH to prevent metastasis and progression of cancers. In this review, we discussed mitochondrial function in cancer cell metabolism and specially explored the unique role of mitochondria in cancer stem cells and the tumor microenvironment. Targeting the OXPHOS pathway and mitochondria-related metabolism emerging as a potential therapeutic strategy for various cancers.
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Affiliation(s)
- Yu'e Liu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yihong Sun
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yadong Guo
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoyun Shi
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Xi Chen
- Xi Chen, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wenfeng Feng
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Lei-Lei Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, 200433, Shanghai, China
| | - Jin Zhang
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, 39216, Jackson, Mississippi, USA
| | - Shibo Yu
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yi Wang
- Department of Critical Care Medicine, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yufeng Shi
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China.,Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai 200092, China
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26
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Chen M, Li M, Wei Y, Xue C, Chen M, Fei Y, Tan L, Luo Z, Cai K, Hu Y. ROS-activatable biomimetic interface mediates in-situ bioenergetic remodeling of osteogenic cells for osteoporotic bone repair. Biomaterials 2022; 291:121878. [DOI: 10.1016/j.biomaterials.2022.121878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/18/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
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27
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Jin P, Jiang J, Zhou L, Huang Z, Qin S, Chen H, Peng L, Zhang Z, Li B, Luo M, Zhang T, Ming H, Ding N, Li L, Xie N, Gao W, Zhang W, Nice EC, Wei Y, Huang C. Disrupting metformin adaptation of liver cancer cells by targeting the TOMM34/ATP5B axis. EMBO Mol Med 2022; 14:e16082. [PMID: 36321555 PMCID: PMC9728056 DOI: 10.15252/emmm.202216082] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 09/23/2022] [Accepted: 10/12/2022] [Indexed: 12/12/2022] Open
Abstract
Metformin, a well-known antidiabetic drug, has been repurposed for cancer treatment; however, recently observed drug resistance and tumor metastasis have questioned its further application. Here, we found that long-term metformin exposure led to metabolic adaptation of hepatocellular carcinoma (HCC) cells, which was characterized by an obvious epithelial-mesenchymal transition (EMT) phenotype and compensatory elevation of oxidative phosphorylation (OXPHOS). TOMM34, a translocase of the outer mitochondrial membrane, was upregulated to promote tumor metastasis in response to metformin-induced metabolic stress. Mechanistically, TOMM34 interacted with ATP5B to preserve F1 FO -ATPase activity, which conferred mitochondrial OXPHOS and ATP production. This metabolic preference for OXPHOS suggested a large requirement of energy supply by cancer cells to survive and spread in response to therapeutic stress. Notably, disturbing the interaction between TOMM34 and ATP5B using Gboxin, a specific OXPHOS inhibitor, increased sensitivity to metformin and suppressed tumor progression both in vitro and in vivo. Overall, this study demonstrates a molecular link of the TOMM34/ATP5B-ATP synthesis axis during metformin adaptation and provides promising therapeutic targets for metformin sensitization in cancer treatment.
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Affiliation(s)
- Ping Jin
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital and West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduChina
| | - Jingwen Jiang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital and West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduChina
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital and West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduChina
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital and West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduChina
| | - Siyuan Qin
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital and West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduChina
| | - Hai‐Ning Chen
- Colorectal Cancer Center, State Key Laboratory of Biotherapy and Cancer Center, West China HospitalSichuan UniversityChengduChina
| | - Liyuan Peng
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital and West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduChina
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital and West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduChina
| | - Bowen Li
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital and West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduChina
| | - Maochao Luo
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital and West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduChina
| | - Tingting Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital and West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduChina
| | - Hui Ming
- West China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengduChina
| | - Ning Ding
- School of Basic Medical SciencesChengdu University of Traditional Chinese MedicineChengduChina
| | - Lei Li
- School of Basic Medical SciencesChengdu University of Traditional Chinese MedicineChengduChina
| | - Na Xie
- West China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengduChina
| | - Wei Gao
- Clinical Genetics LaboratoryAffiliated Hospital & Clinical Medical College of Chengdu UniversityChengduChina
| | - Wei Zhang
- Mental Health Center and Psychiatric Laboratory, The State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Edouard C Nice
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVicAustralia
| | - Yuquan Wei
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital and West China School of Basic Medical Sciences and Forensic MedicineSichuan UniversityChengduChina
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28
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Jin P, Jiang J, Zhou L, Huang Z, Nice EC, Huang C, Fu L. Mitochondrial adaptation in cancer drug resistance: prevalence, mechanisms, and management. J Hematol Oncol 2022; 15:97. [PMID: 35851420 PMCID: PMC9290242 DOI: 10.1186/s13045-022-01313-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/29/2022] [Indexed: 02/08/2023] Open
Abstract
Drug resistance represents a major obstacle in cancer management, and the mechanisms underlying stress adaptation of cancer cells in response to therapy-induced hostile environment are largely unknown. As the central organelle for cellular energy supply, mitochondria can rapidly undergo dynamic changes and integrate cellular signaling pathways to provide bioenergetic and biosynthetic flexibility for cancer cells, which contributes to multiple aspects of tumor characteristics, including drug resistance. Therefore, targeting mitochondria for cancer therapy and overcoming drug resistance has attracted increasing attention for various types of cancer. Multiple mitochondrial adaptation processes, including mitochondrial dynamics, mitochondrial metabolism, and mitochondrial apoptotic regulatory machinery, have been demonstrated to be potential targets. However, recent increasing insights into mitochondria have revealed the complexity of mitochondrial structure and functions, the elusive functions of mitochondria in tumor biology, and the targeting inaccessibility of mitochondria, which have posed challenges for the clinical application of mitochondrial-based cancer therapeutic strategies. Therefore, discovery of both novel mitochondria-targeting agents and innovative mitochondria-targeting approaches is urgently required. Here, we review the most recent literature to summarize the molecular mechanisms underlying mitochondrial stress adaptation and their intricate connection with cancer drug resistance. In addition, an overview of the emerging strategies to target mitochondria for effectively overcoming chemoresistance is highlighted, with an emphasis on drug repositioning and mitochondrial drug delivery approaches, which may accelerate the application of mitochondria-targeting compounds for cancer therapy.
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Affiliation(s)
- Ping Jin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China
| | - Jingwen Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China.
| | - Li Fu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology and International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518060, Guangdong, People's Republic of China.
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29
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Cytogenetic and Genetic Abnormalities with Diagnostic Value in Myelodysplastic Syndromes (MDS): Focus on the Pre-Messenger RNA Splicing Process. Diagnostics (Basel) 2022; 12:diagnostics12071658. [PMID: 35885562 PMCID: PMC9320363 DOI: 10.3390/diagnostics12071658] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/19/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are considered to be diseases associated with splicing defects. A large number of genes involved in the pre-messenger RNA splicing process are mutated in MDS. Deletion of 5q and 7q are of diagnostic value, and those chromosome regions bear the numbers of splicing genes potentially deleted in del(5q) and del(7q)/-7 MDS. In this review, we present the splicing genes already known or suspected to be implicated in MDS pathogenesis. First, we focus on the splicing genes located on chromosome 5 (HNRNPA0, RBM27, RBM22, SLU7, DDX41), chromosome 7 (LUC7L2), and on the SF3B1 gene since both chromosome aberrations and the SF3B1 mutation are the only genetic abnormalities in splicing genes with clear diagnostic values. Then, we present and discuss other splicing genes that are showing a prognostic interest (SRSF2, U2AF1, ZRSR2, U2AF2, and PRPF8). Finally, we discuss the haploinsufficiency of splicing genes, especially from chromosomes 5 and 7, the important amplifier process of splicing defects, and the cumulative and synergistic effect of splicing genes defects in the MDS pathogenesis. At the time, when many authors suggest including the sequencing of some splicing genes to improve the diagnosis and the prognosis of MDS, a better understanding of these cooperative defects is needed.
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30
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Li S, Zhang S, Huang M, Hu H, Xie Y. U1RNP/lncRNA/Transcription Cycle Axis Promotes Tumorigenesis of Hepatocellular Carcinoma. Diagnostics (Basel) 2022; 12:1133. [PMID: 35626291 PMCID: PMC9139874 DOI: 10.3390/diagnostics12051133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/25/2022] [Accepted: 04/30/2022] [Indexed: 02/01/2023] Open
Abstract
As a component of the spliceosome, U1 small nuclear ribonucleoproteins (U1RNPs) play critical roles in RNA splicing, and recent studies have shown that U1RNPs could recruit long non-coding RNAs (lncRNAs) to chromatin which are involved in cancer development. However, the interplay of U1 snRNP, lncRNAs and downstream genes and signaling pathways are insufficiently understood in hepatocellular carcinoma (HCC). The expression of U1RNPs was found to be significantly higher in tumors than normal tissues in liver hepatocellular carcinomas of The Cancer Genome Atlas (TCGA-LIHC) dataset. LncRNAs with potential U1-binding sites (termed U1-lncRNAs) were found to be mostly located in the nucleus and their expression was higher in tumor than in normal tissues Bioinformatic analysis indicated that U1-lncRNAs worked with RNA-binding proteins and regulated the transcription cycle in HCC. A U1-lncRNA risk model was constructed using a TCGA dataset, and the AUCs of this risk model to predict 1-, 3- and 5-year overall survival were 0.82, 0.84 and 0.8, respectively. Furthermore, silencing of the small nuclear ribonucleoprotein D2 polypeptide (SNRPD2) resulted in impaired proliferation, G1/M cell cycle arrest and downregulation of transcription-cycle-related genes in HCC cell lines. Taken together, these results indicate that U1RNPs interact with lncRNAs and promote the transcription cycle process in HCC, which suggests that these could be novel biomarkers in the clinical management of HCC.
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Affiliation(s)
- Shun Li
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, No 58, Zhongshan Er Road, Guangzhou 510080, China; (S.L.); (M.H.)
| | - Shuaiyin Zhang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No 58, Zhongshan Er Road, Guangzhou 510080, China; (S.Z.); (H.H.)
| | - Mingle Huang
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, No 58, Zhongshan Er Road, Guangzhou 510080, China; (S.L.); (M.H.)
| | - Huanjing Hu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No 58, Zhongshan Er Road, Guangzhou 510080, China; (S.Z.); (H.H.)
| | - Yubin Xie
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No 58, Zhongshan Er Road, Guangzhou 510080, China; (S.Z.); (H.H.)
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Maremonti F, Meyer C, Linkermann A. Mechanisms and Models of Kidney Tubular Necrosis and Nephron Loss. J Am Soc Nephrol 2022; 33:472-486. [PMID: 35022311 PMCID: PMC8975069 DOI: 10.1681/asn.2021101293] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Understanding nephron loss is a primary strategy for preventing CKD progression. Death of renal tubular cells may occur by apoptosis during developmental and regenerative processes. However, during AKI, the transition of AKI to CKD, sepsis-associated AKI, and kidney transplantation ferroptosis and necroptosis, two pathways associated with the loss of plasma membrane integrity, kill renal cells. This necrotic type of cell death is associated with an inflammatory response, which is referred to as necroinflammation. Importantly, the necroinflammatory response to cells that die by necroptosis may be fundamentally different from the tissue response to ferroptosis. Although mechanisms of ferroptosis and necroptosis have recently been investigated in detail, the cell death propagation during tubular necrosis, although described morphologically, remains incompletely understood. Here, we argue that a molecular switch downstream of tubular necrosis determines nephron regeneration versus nephron loss. Unraveling the details of this "switch" must include the inflammatory response to tubular necrosis and regenerative signals potentially controlled by inflammatory cells, including the stimulation of myofibroblasts as the origin of fibrosis. Understanding in detail the molecular switch and the inflammatory responses to tubular necrosis can inform the discussion of therapeutic options.
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Affiliation(s)
- Francesca Maremonti
- Division of Nephrology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Claudia Meyer
- Division of Nephrology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Andreas Linkermann
- Division of Nephrology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany .,Biotechnology Center, Technical University of Dresden, Dresden, Germany
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Abstract
PURPOSE OF REVIEW Loss of chromosome 7 has long been associated with adverse-risk myeloid malignancy. In the last decade, CUX1 has been identified as a critical tumor suppressor gene (TSG) located within a commonly deleted segment of chromosome arm 7q. Additional genes encoded on 7q have also been identified as bona fide myeloid tumor suppressors, further implicating chromosome 7 deletions in disease pathogenesis. This review will discuss the clinical implications of del(7q) and CUX1 mutations, both in disease and clonal hematopoiesis, and synthesize recent literature on CUX1 and other chromosome 7 TSGs. RECENT FINDINGS Two major studies, including a new mouse model, have been published that support a role for CUX1 inactivation in the development of myeloid neoplasms. Additional recent studies describe the cellular and hematopoietic effects from loss of the 7q genes LUC7L2 and KMT2C/MLL3, and the implications of chromosome 7 deletions in clonal hematopoiesis. SUMMARY Mounting evidence supports CUX1 as being a key chromosome 7 TSG. As 7q encodes additional myeloid regulators and tumor suppressors, improved models of chromosome loss are needed to interrogate combinatorial loss of these critical 7q genes.
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Affiliation(s)
| | - Megan E McNerney
- Department of Pathology
- Department of Pediatrics, Section of Hematology/Oncology
- The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA
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Abstract
In Eukarya, immature mRNA transcripts (pre-mRNA) often contain coding sequences, or exons, interleaved by non-coding sequences, or introns. Introns are removed upon splicing, and further regulation of the retained exons leads to alternatively spliced mRNA. The splicing reaction requires the stepwise assembly of the spliceosome, a macromolecular machine composed of small nuclear ribonucleoproteins (snRNPs). This review focuses on the early stage of spliceosome assembly, when U1 snRNP defines each intron 5’-splice site (5ʹss) in the pre-mRNA. We first introduce the splicing reaction and the impact of alternative splicing on gene expression regulation. Thereafter, we extensively discuss splicing descriptors that influence the 5ʹss selection by U1 snRNP, such as sequence determinants, and interactions mediated by U1-specific proteins or U1 small nuclear RNA (U1 snRNA). We also include examples of diseases that affect the 5ʹss selection by U1 snRNP, and discuss recent therapeutic advances that manipulate U1 snRNP 5ʹss selectivity with antisense oligonucleotides and small-molecule splicing switches.
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Affiliation(s)
- Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Cameron D Mackereth
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
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Ordureau A, Kraus F, Zhang J, An H, Park S, Ahfeldt T, Paulo JA, Harper JW. Temporal proteomics during neurogenesis reveals large-scale proteome and organelle remodeling via selective autophagy. Mol Cell 2021; 81:5082-5098.e11. [PMID: 34699746 DOI: 10.1016/j.molcel.2021.10.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/23/2021] [Accepted: 10/01/2021] [Indexed: 12/18/2022]
Abstract
Cell state changes are associated with proteome remodeling to serve newly emergent cell functions. Here, we show that NGN2-driven conversion of human embryonic stem cells to induced neurons (iNeurons) is associated with increased PINK1-independent mitophagic flux that is temporally correlated with metabolic reprogramming to support oxidative phosphorylation. Global multiplex proteomics during neurogenesis revealed large-scale remodeling of functional modules linked with pluripotency, mitochondrial metabolism, and proteostasis. Differentiation-dependent mitophagic flux required BNIP3L and its LC3-interacting region (LIR) motif, and BNIP3L also promoted mitophagy in dopaminergic neurons. Proteomic analysis of ATG12-/- iNeurons revealed accumulation of endoplasmic reticulum, Golgi, and mitochondria during differentiation, indicative of widespread organelle remodeling during neurogenesis. This work reveals broad organelle remodeling of membrane-bound organelles during NGN2-driven neurogenesis via autophagy, identifies BNIP3L's central role in programmed mitophagic flux, and provides a proteomic resource for elucidating how organelle remodeling and autophagy alter the proteome during changes in cell state.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| | - Felix Kraus
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Jiuchun Zhang
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Heeseon An
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Sookhee Park
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY 10029, USA; Department of Neurology at Mount Sinai, New York, NY 10029, USA; Department of Cell, Developmental and Regenerative Biology at Mount Sinai, New York, NY 10029, USA; Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute at Mount Sinai, New York, NY 10029, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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Nunes SC, Ramos C, Santos I, Mendes C, Silva F, Vicente JB, Pereira SA, Félix A, Gonçalves LG, Serpa J. Cysteine Boosts Fitness Under Hypoxia-Mimicked Conditions in Ovarian Cancer by Metabolic Reprogramming. Front Cell Dev Biol 2021; 9:722412. [PMID: 34458274 PMCID: PMC8386479 DOI: 10.3389/fcell.2021.722412] [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: 06/08/2021] [Accepted: 07/13/2021] [Indexed: 01/20/2023] Open
Abstract
Among gynecologic malignancies, ovarian cancer is the third most prevalent and the most common cause of death, especially due to diagnosis at an advanced stage together with resistance to therapy. As a solid tumor grows, cancer cells in the microenvironment are exposed to regions of hypoxia, a selective pressure prompting tumor progression and chemoresistance. We have previously shown that cysteine contributes to the adaptation to this hypoxic microenvironment, but the mechanisms by which cysteine protects ovarian cancer cells from hypoxia-induced death are still to be unveiled. Herein, we hypothesized that cysteine contribution relies on cellular metabolism reprogramming and energy production, being cysteine itself a metabolic source. Our results strongly supported a role of xCT symporter in energy production that requires cysteine metabolism instead of hydrogen sulfide (H2S) per se. Cysteine degradation depends on the action of the H2S-synthesizing enzymes cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE), and/or 3-mercaptopyruvate sulfurtransferase (MpST; together with cysteine aminotransferase, CAT). In normoxia, CBS and CSE inhibition had a mild impact on cysteine-sustained ATP production, pointing out the relevance of CAT + MpST pathway. However, in hypoxia, the concomitant inhibition of CBS and CSE had a stronger impact on ATP synthesis, thus also supporting a role of their hydrogen sulfide and/or cysteine persulfide-synthesizing activity in this stressful condition. However, the relative contributions of each of these enzymes (CBS/CSE/MpST) on cysteine-derived ATP synthesis under hypoxia remains unclear, due to the lack of specific inhibitors. Strikingly, NMR analysis strongly supported a role of cysteine in the whole cellular metabolism rewiring under hypoxia. Additionally, the use of cysteine to supply biosynthesis and bioenergetics was reinforced, bringing cysteine to the plateau of a main carbon sources in cancer. Collectively, this work supports that sulfur and carbon metabolism reprogramming underlies the adaptation to hypoxic microenvironment promoted by cysteine in ovarian cancer.
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Affiliation(s)
- Sofia C. Nunes
- Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisbon, Portugal
| | - Cristiano Ramos
- Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisbon, Portugal
| | - Inês Santos
- Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisbon, Portugal
| | - Cindy Mendes
- Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisbon, Portugal
| | - Fernanda Silva
- Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisbon, Portugal
| | - João B. Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia A. Pereira
- Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Ana Félix
- Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisbon, Portugal
| | - Luís G. Gonçalves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jacinta Serpa
- Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisbon, Portugal
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36
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Hoskins AA, Rhoads TW. When cells are down on their LUC7L2, alternative splicing rewires metabolism for OXPHOS. Mol Cell 2021; 81:1859-1860. [PMID: 33961773 DOI: 10.1016/j.molcel.2021.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Daniels et al. (2021) and Jourdain et al. (2021) identify LUC7L2 as a component of the U1 snRNP capable of reprogramming cellular metabolism through changes in alternative pre-mRNA splicing.
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Affiliation(s)
- Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Timothy W Rhoads
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
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37
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Daniels NJ, Hershberger CE, Gu X, Schueger C, DiPasquale WM, Brick J, Saunthararajah Y, Maciejewski JP, Padgett RA. Functional analyses of human LUC7-like proteins involved in splicing regulation and myeloid neoplasms. Cell Rep 2021; 35:108989. [PMID: 33852859 PMCID: PMC8078730 DOI: 10.1016/j.celrep.2021.108989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/12/2021] [Accepted: 03/23/2021] [Indexed: 02/06/2023] Open
Abstract
Vertebrates have evolved three paralogs, termed LUC7L, LUC7L2, and LUC7L3, of the essential yeast U1 small nuclear RNA (snRNA)-associated splicing factor Luc7p. We investigated the mechanistic and regulatory functions of these putative splicing factors, of which one (LUC7L2) is mutated or deleted in myeloid neoplasms. Protein interaction data show that all three proteins bind similar core but distinct regulatory splicing factors, probably mediated through their divergent arginine-serine-rich domains, which are not present in Luc7p. Knockdown of each factor reveals mostly unique sets of significantly dysregulated alternative splicing events dependent on their binding locations, which are largely non-overlapping. Notably, knockdown of LUC7L2 alone significantly upregulates the expression of multiple spliceosomal factors and downregulates glycolysis genes, possibly contributing to disease pathogenesis. RNA binding studies reveal that LUC7L2 and LUC7L3 crosslink to weak 5' splice sites and to the 5' end of U1 snRNA, establishing an evolutionarily conserved role in 5' splice site selection.
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Affiliation(s)
- Noah J Daniels
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Courtney E Hershberger
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaorong Gu
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Caroline Schueger
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - William M DiPasquale
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jonathan Brick
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Richard A Padgett
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
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