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Ding Y, Sun Y, Wang H, Zhao H, Yin R, Zhang M, Pan X, Zhu X. Atherosis-associated lnc_000048 activates PKR to enhance STAT1-mediated polarization of THP-1 macrophages to M1 phenotype. Neural Regen Res 2024; 19:2488-2498. [PMID: 38526285 PMCID: PMC11090429 DOI: 10.4103/nrr.nrr-d-23-01355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/12/2023] [Accepted: 01/20/2024] [Indexed: 03/26/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202419110-00029/figure1/v/2024-03-08T184507Z/r/image-tiff Our previous study has demonstrated that lnc_000048 is upregulated in large-artery atherosclerotic stroke and promotes atherosclerosis in ApoE-/- mice. However, little is known about the role of lnc_000048 in classically activated macrophage (M1) polarization. In this study, we established THP-1-derived testing state macrophages (M0), M1 macrophages, and alternately activated macrophages (M2). Real-time fluorescence quantitative PCR was used to verify the expression of marker genes and the expression of lnc_000048 in macrophages. Flow cytometry was used to detect phenotypic proteins (CD11b, CD38, CD80). We generated cell lines with lentivirus-mediated upregulation or downregulation of lnc_000048. Flow cytometry, western blot, and real-time fluorescence quantitative PCR results showed that down-regulation of lnc_000048 reduced M1 macrophage polarization and the inflammation response, while over-expression of lnc_000048 led to the opposite effect. Western blot results indicated that lnc_000048 enhanced the activation of the STAT1 pathway and mediated the M1 macrophage polarization. Moreover, catRAPID prediction, RNA-pull down, and mass spectrometry were used to identify and screen the protein kinase RNA-activated (PKR), then catRAPID and RPIseq were used to predict the binding ability of lnc_000048 to PKR. Immunofluorescence (IF)-RNA fluorescence in situ hybridization (FISH) double labeling was performed to verify the subcellular colocalization of lnc_000048 and PKR in the cytoplasm of M1 macrophage. We speculate that lnc_000048 may form stem-loop structure-specific binding and activate PKR by inducing its phosphorylation, leading to activation of STAT1 phosphorylation and thereby enhancing STAT1 pathway-mediated polarization of THP-1 macrophages to M1 and inflammatory factor expression. Taken together, these results reveal that the lnc_000048/PKR/STAT1 axis plays a crucial role in the polarization of M1 macrophages and may be a novel therapeutic target for atherosclerosis alleviation in stroke.
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Affiliation(s)
- Yuanyuan Ding
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Yu Sun
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Hongyan Wang
- Qingdao Cadre Health Care Service Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Hongqin Zhao
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Ruihua Yin
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Meng Zhang
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Xudong Pan
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Xiaoyan Zhu
- Department of Critical Care Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
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Xie S, Bao D, Xiao Y, Li H, Guo M, Dai B, Liu S, Huang J, Li M, Ding L, Meng Q, Lv CL, Distler JHW, Luo H, Zhu H. Alternative splicing and intron retention: Their profiles and roles in cutaneous fibrosis of systemic sclerosis. J Autoimmun 2024; 149:103306. [PMID: 39265192 DOI: 10.1016/j.jaut.2024.103306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/21/2024] [Accepted: 08/23/2024] [Indexed: 09/14/2024]
Abstract
BACKGROUND Alternative splicing (AS) and intron retention (IR) implicated in multiple pathophysiological processes, have rarely been reported in systemic sclerosis (SSc). METHODS We integrated bulk RNA-seq and 4D label-free mass spectrometry to perform a multi-omics analysis of AS and IR in SSc skin tissue and fibroblasts. RMATS and iREAD were used to identify AS and IR, which were validated by real-time PCR. Spearman correlation and the LASSO method were employed to assess correlations among clinical features, introns, splicing factors (regulators of AS) and proteins. FINDINGS AS profiles showed distinct alterations in SSc skin tissue, with the most pronounced changes occurring in IR. AS and IR were associated with total modified Rodnan skin score (mRSS) and local skin score. Upon TGF-β stimulation, fibroblasts exhibited significant alterations in IR profiles, affecting genes related to fibroblast proliferation and collagen fibril organization. A comprehensive integrated analysis of introns, exons, and proteome profiles revealed that IR exerted a negative impact on protein expression, with certain changes being under intronic control. RT-PCR confirmed the presence of intron and exon-derived sequences of CTTN, OGA, MED16 and PHYKPL. Additionally, notable changes were observed in the regulatory network of splicing factors in SSc skin tissues. These factors are also involved in fibrosis pathways and correlated with clinical features. CONCLUSION Totally, abnormal AS, IR profiles and splicing factors were identified in SSc, altered IRs and splicing factors participated in fibrosis-related pathways. IR exerted a negative impact on protein expression in TGF-β-stimulated fibroblasts. Clarification of the IR mechanisms will provide new insights into the pathophysiology of SSc.
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Affiliation(s)
- Shasha Xie
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ding Bao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yizhi Xiao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongdong Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Muyao Guo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bingying Dai
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Sijia Liu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jing Huang
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Muyuan Li
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Liqing Ding
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiming Meng
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chun-Liu Lv
- Department of Breast Tumor Plastic Surgery, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Jörg H W Distler
- Department of Rheumatology, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University, 40225, Düsseldorf, Germany; Hiller Research Center, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Hui Luo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Honglin Zhu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Tan C, Sim D, Zhen Y, Tian H, Koh J, Roca X. PRPF40A induces inclusion of exons in GC-rich regions important for human myeloid cell differentiation. Nucleic Acids Res 2024; 52:8800-8814. [PMID: 38943321 PMCID: PMC11347146 DOI: 10.1093/nar/gkae557] [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: 11/07/2023] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024] Open
Abstract
We characterized the regulatory mechanisms and role in human myeloid cell survival and differentiation of PRPF40A, a splicing factor lacking a canonical RNA Binding Domain. Upon PRPF40A knockdown, HL-60 cells displayed increased cell death, decreased proliferation and slight differentiation phenotype with upregulation of immune activation genes. Suggestive of both redundant and specific functions, cell death but not proliferation was rescued by overexpression of its paralog PRPF40B. Transcriptomic analysis revealed the predominant role of PRPF40A as an activator of cassette exon inclusion of functionally relevant splicing events. Mechanistically, the exons exclusively upregulated by PRPF40A are flanked by short and GC-rich introns which tend to localize to nuclear speckles in the nucleus center. These PRPF40A regulatory features are shared with other splicing regulators such as SRRM2, SON, PCBP1/2, and to a lesser extent TRA2B and SRSF2, as a part of a functional network that regulates splicing partly via co-localization in the nucleus.
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Affiliation(s)
- Cheryl Weiqi Tan
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Donald Yuhui Sim
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Yashu Zhen
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Haobo Tian
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Jace Koh
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
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Salz R, Vorsteveld EE, van der Made CI, Kersten S, Stemerdink M, Riepe TV, Hsieh TH, Mhlanga M, Netea MG, Volders PJ, Hoischen A, ’t Hoen PA. Multi-omic profiling of pathogen-stimulated primary immune cells. iScience 2024; 27:110471. [PMID: 39091463 PMCID: PMC11293528 DOI: 10.1016/j.isci.2024.110471] [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: 11/08/2023] [Revised: 04/23/2024] [Accepted: 07/04/2024] [Indexed: 08/04/2024] Open
Abstract
We performed long-read transcriptome and proteome profiling of pathogen-stimulated peripheral blood mononuclear cells (PBMCs) from healthy donors to discover new transcript and protein isoforms expressed during immune responses to diverse pathogens. Long-read transcriptome profiling reveals novel sequences and isoform switching induced upon pathogen stimulation, including transcripts that are difficult to detect using traditional short-read sequencing. Widespread loss of intron retention occurs as a common result of all pathogen stimulations. We highlight novel transcripts of NFKB1 and CASP1 that may indicate novel immunological mechanisms. RNA expression differences did not result in differences in the amounts of secreted proteins. Clustering analysis of secreted proteins revealed a correlation between chemokine (receptor) expression on the RNA and protein levels in C. albicans- and poly(I:C)-stimulated PBMCs. Isoform aware long-read sequencing of pathogen-stimulated immune cells highlights the potential of these methods to identify novel transcripts, revealing a more complex transcriptome landscape than previously appreciated.
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Affiliation(s)
- Renee Salz
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Emil E. Vorsteveld
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Caspar I. van der Made
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, 6525 GA Nijmegen, the Netherlands
| | - Simone Kersten
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Merel Stemerdink
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Tabea V. Riepe
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Tsung-han Hsieh
- Department of Cell Biology, Radboud University, 6500 HB Nijmegen, the Netherlands
| | - Musa Mhlanga
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Cell Biology, Radboud University, 6500 HB Nijmegen, the Netherlands
| | - Mihai G. Netea
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, 6525 GA Nijmegen, the Netherlands
| | - Pieter-Jan Volders
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Laboratory of Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium
| | - Alexander Hoischen
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, 6525 GA Nijmegen, the Netherlands
| | - Peter A.C. ’t Hoen
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
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Wang B, Li J, Song Y, Qin X, Lu X, Huang W, Peng C, Wei J, Huang D, Wang W. CLK2 Condensates Reorganize Nuclear Speckles and Induce Intron Retention. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2309588. [PMID: 39119950 DOI: 10.1002/advs.202309588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 07/28/2024] [Indexed: 08/10/2024]
Abstract
Intron retention (IR) constitutes a less explored form of alternative splicing, wherein introns are retained within mature mRNA transcripts. This investigation demonstrates that the cell division cycle (CDC)-like kinase 2 (CLK2) undergoes liquid-liquid phase separation (LLPS) within nuclear speckles in response to heat shock (HS). The formation of CLK2 condensates depends on the intrinsically disordered region (IDR) located within the N-terminal amino acids 1-148. Phosphorylation at residue T343 sustains CLK2 kinase activity and promotes overall autophosphorylation, which inhibits the LLPS activity of the IDR. These CLK2 condensates initiate the reorganization of nuclear speckles, transforming them into larger, rounded structures. Moreover, these condensates facilitate the recruitment of splicing factors into these compartments, restricting their access to mRNA for intron splicing and promoting the IR. The retained introns lead to the sequestration of transcripts within the nucleus. These findings extend to the realm of glioma stem cells (GSCs), where a physiological state mirroring HS stress inhibits T343 autophosphorylation, thereby inducing the formation of CLK2 condensates and subsequent IR. Notably, expressing the CLK2 condensates hampers the maintenance of GSCs. In conclusion, this research unveils a mechanism by which IR is propelled by CLK2 condensates, shedding light on its role in coping with cellular stress.
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Affiliation(s)
- Bing Wang
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Jing Li
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yanyang Song
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Xuhui Qin
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Xia Lu
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Wei Huang
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Chentai Peng
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Jinxia Wei
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Donghui Huang
- Institute of Reproduction Health Research, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Wang
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
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Mehta P, Liu CSC, Sinha S, Mohite R, Arora S, Chattopadhyay P, Budhiraja S, Tarai B, Pandey R. Reduced protein-coding transcript diversity in severe dengue emphasises the role of alternative splicing. Life Sci Alliance 2024; 7:e202402683. [PMID: 38830771 PMCID: PMC11147948 DOI: 10.26508/lsa.202402683] [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: 02/28/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
Dengue fever, a neglected tropical arboviral disease, has emerged as a global health concern in the past decade. Necessitating a nuanced comprehension of the intricate dynamics of host-virus interactions influencing disease severity, we analysed transcriptomic patterns using bulk RNA-seq from 112 age- and gender-matched NS1 antigen-confirmed hospital-admitted dengue patients with varying severity. Severe cases exhibited reduced platelet count, increased lymphocytosis, and neutropenia, indicating a dysregulated immune response. Using bulk RNA-seq, our analysis revealed a minimal overlap between the differentially expressed gene and transcript isoform, with a distinct expression pattern across the disease severity. Severe patients showed enrichment in retained intron and nonsense-mediated decay transcript biotypes, suggesting altered splicing efficiency. Furthermore, an up-regulated programmed cell death, a haemolytic response, and an impaired interferon and antiviral response at the transcript level were observed. We also identified the potential involvement of the RBM39 gene among others in the innate immune response during dengue viral pathogenesis, warranting further investigation. These findings provide valuable insights into potential therapeutic targets, underscoring the importance of exploring transcriptomic landscapes between different disease sub-phenotypes in infectious diseases.
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Affiliation(s)
- Priyanka Mehta
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chinky Shiu Chen Liu
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Sristi Sinha
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Ramakant Mohite
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Smriti Arora
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Partha Chattopadhyay
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sandeep Budhiraja
- https://ror.org/00e7r7m66 Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Bansidhar Tarai
- https://ror.org/00e7r7m66 Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Rajesh Pandey
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Xiao Y, Xie S, Li HD, Liu Y, Zhang H, Zuo X, Zhu H, Li Y, Luo H. Characterised intron retention profiles in muscle tissue of idiopathic inflammatory myopathy subtypes. Ann Rheum Dis 2024; 83:901-914. [PMID: 38302260 DOI: 10.1136/ard-2023-225035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/23/2024] [Indexed: 02/03/2024]
Abstract
OBJECTIVES Idiopathic inflammatory myopathies (IIMs) are a group of heterogeneous autoimmune diseases. Intron retention (IR) serves as an important post-transcriptional and translational regulatory mechanism. This study aims to identify changes in IR profiles in IIM subtypes, investigating their influence on proteins and their correlations with clinical features. METHODS RNA sequencing and liquid chromatography-tandem mass spectrometry were performed on muscle tissues obtained from 174 patients with IIM and 19 controls, following QC procedures. GTFtools and iREAD software were used for IR identification. An analysis of differentially expressed IRs (DEIs), exons and proteins was carried out using edgeR or DEP. Functional analysis was performed with clusterProfiler, and SPIRON was used to assess splicing factors. RESULTS A total of 6783 IRs located in 3111 unique genes were identified in all IIM subtypes compared with controls. IIM subtype-specific DEIs were associated with the pathogenesis of respective IIM subtypes. Splicing factors YBX1 and HSPA2 exhibited the most changes in dermatomyositis and immune-mediated necrotising myopathy. Increased IR was associated with reduced protein expression. Some of the IIM-specific DEIs were correlated with clinical parameters (skin rash, MMT-8 scores and muscle enzymes) and muscle histopathological features (myofiber necrosis, regeneration and inflammation). IRs in IFIH1 and TRIM21 were strongly correlated with anti-MDA5+ antibody, while IRs in SRP14 were associated with anti-SRP+ antibody. CONCLUSION This study revealed distinct IRs and specific splicing factors associated with IIM subtypes, which might be contributing to the pathogenesis of IIM. We also emphasised the potential impact of IR on protein expression in IIM muscles.
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Affiliation(s)
- Yizhi Xiao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
| | - Shasha Xie
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
| | - Hong-Dong Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China PR
| | - Yanjuan Liu
- Institute of Emergency Medicine, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China PR
| | - Huali Zhang
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, China PR
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
| | - Honglin Zhu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
| | - Yisha Li
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
| | - Hui Luo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
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8
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Pinello N, Song R, Lee Q, Calonne E, Duan KL, Wong E, Tieng J, Mehravar M, Rong B, Lan F, Roediger B, Ma CJ, Yuan BF, Rasko JEJ, Larance M, Ye D, Fuks F, Wong JJL. Dynamic changes in RNA m 6A and 5 hmC influence gene expression programs during macrophage differentiation and polarisation. Cell Mol Life Sci 2024; 81:229. [PMID: 38780787 PMCID: PMC11116364 DOI: 10.1007/s00018-024-05261-9] [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: 02/06/2024] [Revised: 04/27/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
RNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications regulate the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear. While m6A has been widely studied, other RNA modifications, including 5 hmC, remain poorly characterised. We profiled m6A and 5 hmC epitranscriptomes, transcriptomes, translatomes and proteomes of monocytes and macrophages at rest and pro- and anti-inflammatory states. Transcriptome-wide mapping of m6A and 5 hmC reveals enrichment of m6A and/or 5 hmC on specific categories of transcripts essential for macrophage differentiation. Our analyses indicate that m6A and 5 hmC modifications are present in transcripts with critical functions in pro- and anti-inflammatory macrophages. Notably, we also discover the co-occurrence of m6A and 5 hmC on alternatively-spliced isoforms and/or opposing ends of the untranslated regions (UTR) of mRNAs with key roles in macrophage biology. In specific examples, RNA 5 hmC controls the decay of transcripts independently of m6A. This study provides (i) a comprehensive dataset to interrogate the role of RNA modifications in a plastic system (ii) a resource for exploring different layers of gene expression regulation in the context of human monocyte-to-macrophage differentiation and polarisation, (iii) new insights into RNA modifications as central regulators of effector cells in innate immunity.
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Affiliation(s)
- Natalia Pinello
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, 11400, Montevideo, Uruguay
| | - Renhua Song
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Quintin Lee
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Kun-Long Duan
- The Molecular and Cell Biology Lab, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Emilie Wong
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Jessica Tieng
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Majid Mehravar
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Bowen Rong
- Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ben Roediger
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Skin Inflammation Group, Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Autoimmunity, Transplantation and Inflammation (ATI) Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Cheng-Jie Ma
- School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Bi-Feng Yuan
- School of Public Health, Wuhan University, Wuhan, 430071, China
| | - John E J Rasko
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Gene and Stem Cell Therapy Program, Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, NSW, Australia
| | - Mark Larance
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Charles Perkins Centre, School of Medical Sciences, University of Sydney, Sydney, 2006, Australia
| | - Dan Ye
- The Molecular and Cell Biology Lab, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Justin J-L Wong
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.
- Charles Perkins Centre, School of Medical Sciences, University of Sydney, Sydney, 2006, Australia.
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9
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Castellano M, Blanco V, Calzi ML, Costa B, Witwer K, Hill M, Cayota A, Segovia M, Tosar JP. Ribonuclease activity undermines immune sensing of naked extracellular RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590771. [PMID: 38712104 PMCID: PMC11071435 DOI: 10.1101/2024.04.23.590771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The plasma membrane and the membrane of endosomal vesicles are considered physical barriers preventing extracellular RNA uptake. While naked RNA can be spontaneously internalized by certain cells types, functional delivery of naked RNA into the cytosol has been rarely observed. Here we show that extracellular ribonucleases, mainly derived from cell culture supplements, have so far hindered the study of extracellular RNA functionality. In the presence of active ribonuclease inhibitors (RI), naked bacterial RNA is pro-inflammatory when spiked in the media of dendritic cells and macrophages. In murine cells, this response mainly depends on the action of endosomal Toll-like receptors. However, we also show that naked RNA can perform endosomal escape and engage with cytosolic RNA sensors and ribosomes. For example, naked mRNAs encoding reporter proteins can be spontaneously internalized and translated by a variety of cell types, in an RI-dependent manner. In vivo, RI co-injection enhances the activation induced by naked extracellular RNA on splenic lymphocytes and myeloid-derived leukocytes. Furthermore, naked extracellular RNA is inherently pro-inflammatory in ribonuclease-poor compartments such as the peritoneal cavity. Overall, these results demonstrate that naked RNA is bioactive and does not need encapsulation inside synthetic or biological lipid vesicles for functional uptake, making a case for nonvesicular extracellular RNA-mediated intercellular communication.
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Affiliation(s)
- Mauricio Castellano
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
- Immunoregulation and Inflammation Laboratory, Institut Pasteur Montevideo, Uruguay
| | - Valentina Blanco
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
| | - Marco Li Calzi
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
| | - Bruno Costa
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
- Analytical Biochemistry Unit, School of Science, Universidad de la República, Uruguay
| | - Kenneth Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- EV Core Facility “EXCEL”, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marcelo Hill
- Immunoregulation and Inflammation Laboratory, Institut Pasteur Montevideo, Uruguay
- Academic Unit of Immunobiology, School of Medicine, Universidad de la República, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
- Hospital de Clínicas, Universidad de la República, Uruguay
| | - Mercedes Segovia
- Immunoregulation and Inflammation Laboratory, Institut Pasteur Montevideo, Uruguay
- Academic Unit of Immunobiology, School of Medicine, Universidad de la República, Uruguay
| | - Juan Pablo Tosar
- Functional Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
- Analytical Biochemistry Unit, School of Science, Universidad de la República, Uruguay
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10
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Scott HM, Smith MH, Coleman AK, Armijo KS, Chapman MJ, Apostalo SL, Wagner AR, Watson RO, Patrick KL. Serine/arginine-rich splicing factor 7 promotes the type I interferon response by activating Irf7 transcription. Cell Rep 2024; 43:113816. [PMID: 38393946 PMCID: PMC11056844 DOI: 10.1016/j.celrep.2024.113816] [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: 07/25/2023] [Revised: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Tight regulation of macrophage immune gene expression is required to fight infection without risking harmful inflammation. The contribution of RNA-binding proteins (RBPs) to shaping the macrophage response to pathogens remains poorly understood. Transcriptomic analysis reveals that a member of the serine/arginine-rich (SR) family of mRNA processing factors, SRSF7, is required for optimal expression of a cohort of interferon-stimulated genes in macrophages. Using genetic and biochemical assays, we discover that in addition to its canonical role in regulating alternative splicing, SRSF7 drives transcription of interferon regulatory transcription factor 7 (IRF7) to promote antiviral immunity. At the Irf7 promoter, SRSF7 maximizes STAT1 transcription factor binding and RNA polymerase II elongation via cooperation with the H4K20me1 histone methyltransferase KMT5a (SET8). These studies define a role for an SR protein in activating transcription and reveal an RBP-chromatin network that orchestrates macrophage antiviral gene expression.
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Affiliation(s)
- Haley M Scott
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Mackenzie H Smith
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Aja K Coleman
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Kaitlyn S Armijo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Morgan J Chapman
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Summer L Apostalo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Allison R Wagner
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Robert O Watson
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Kristin L Patrick
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA.
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11
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Pinello N, Song R, Lee Q, Calonne E, Larance M, Fuks F, Wong JJL. A multiomics dataset for the study of RNA modifications in human macrophage differentiation and polarisation. Sci Data 2024; 11:252. [PMID: 38418823 PMCID: PMC10902381 DOI: 10.1038/s41597-024-03076-8] [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: 09/26/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
RNA modifications have emerged as central regulators of gene expression programs. Amongst RNA modifications are N6-methyladenosine (m6A) and RNA 5-hydroxymethylcytosine (5hmC). While m6A is established as a versatile regulator of RNA metabolism, the functions of RNA 5hmC are unclear. Despite some evidence linking RNA modifications to immunity, their implications in gene expression control in macrophage development and functions remain unclear. Here we present a multi-omics dataset capturing different layers of the gene expression programs driving macrophage differentiation and polarisation. We obtained mRNA-Seq, m6A-IP-Seq, 5hmC-IP-Seq, Polyribo-Seq and LC-MS/MS data from monocytes and resting-, pro- and anti-inflammatory-like macrophages. We present technical validation showing high quality and correlation between samples for all datasets, and evidence of biological consistency of modelled macrophages at the transcriptomic, epitranscriptomic, translational and proteomic levels. This multi-omics dataset provides a resource for the study of RNA m6A and 5hmC in the context of macrophage biology and spans the gene expression process from transcripts to proteins.
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Affiliation(s)
- Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Quintin Lee
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mark Larance
- Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Camperdown, 2050, New South Wales, Australia
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.
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12
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Gómez-Montalvo J, de Obeso Fernández Del Valle A, De la Cruz Gutiérrez LF, Gonzalez-Meljem JM, Scheckhuber CQ. Replicative aging in yeast involves dynamic intron retention patterns associated with mRNA processing/export and protein ubiquitination. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:69-78. [PMID: 38414808 PMCID: PMC10897858 DOI: 10.15698/mic2024.02.816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 02/29/2024]
Abstract
Saccharomyces cerevisiae (baker's yeast) has yielded relevant insights into some of the basic mechanisms of organismal aging. Among these are genomic instability, oxidative stress, caloric restriction and mitochondrial dysfunction. Several genes are known to have an impact on the aging process, with corresponding mutants exhibiting short- or long-lived phenotypes. Research dedicated to unraveling the underlying cellular mechanisms can support the identification of conserved mechanisms of aging in other species. One of the hitherto less studied fields in yeast aging is how the organism regulates its gene expression at the transcriptional level. To our knowledge, we present the first investigation into alternative splicing, particularly intron retention, during replicative aging of S. cerevisiae. This was achieved by utilizing the IRFinder algorithm on a previously published RNA-seq data set by Janssens et al. (2015). In the present work, 44 differentially retained introns in 43 genes were identified during replicative aging. We found that genes with altered intron retention do not display significant changes in overall transcript levels. It was possible to functionally assign distinct groups of these genes to the cellular processes of mRNA processing and export (e.g., YRA1) in early and middle-aged yeast, and protein ubiquitination (e.g., UBC5) in older cells. In summary, our work uncovers a previously unexplored layer of the transcriptional program of yeast aging and, more generally, expands the knowledge on the occurrence of alternative splicing in baker's yeast.
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Affiliation(s)
- Jesús Gómez-Montalvo
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey, N.L., México
| | | | | | - Jose Mario Gonzalez-Meljem
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey, N.L., México
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13
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Dang E, Chen Y, Wang W, Zhang L, An N, Yin W, Yi J, Chen Y. A comparative study of platelet storage lesion in platelet-rich plasma under cryopreservation. Ann Hematol 2024; 103:631-643. [PMID: 38110587 DOI: 10.1007/s00277-023-05580-0] [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: 08/19/2023] [Accepted: 12/02/2023] [Indexed: 12/20/2023]
Abstract
Platelet-rich plasma (PRP) has significant potential for various applications and holds clinical value in regenerative medicine. Cryopreservation is used to extend the preservation period of PRP, facilitating its clinical application. However, the potential negative effects of long-term cryopreservation on platelet storage lesion are still uncertain. In this study, PRP was stored at - 30 °C or - 80 °C. Platelet count, apoptosis, reactive oxygen species (ROS) content, and CD62P expression were assessed on the 14th and 28th days. The study also evaluated platelet mitochondria morphology and function, serotonin (5-HT) secretion by platelets, and the inflammatory activating effect of cryopreserved platelets in PRP. The results showed that there were no significant differences in platelet count, the content of 5-HT, and inflammatory effects between fresh PRP and PRP cryopreserved at both - 30 °C and - 80 °C. However, there was an increase in ROS level, apoptosis, and CD62P level after cryopreservation at both temperatures. Additionally, the levels of ROS, apoptosis, and CD62P in platelets were similar after storage at - 30 °C and - 80 °C. The main difference observed was that the morphology and function of mitochondria were severely damaged after storage at - 30 °C, while they were less affected at - 80 °C. Based on these findings, it can be concluded that storing PRP at - 80 °C is more suitable for achieving a better therapeutic effect in clinical applications, but cryopreservation could not replace the current standard.
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Affiliation(s)
- E Dang
- Department of Transfusion Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yutong Chen
- Department of Transfusion Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Wenting Wang
- Department of Transfusion Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Lingling Zhang
- Department of Transfusion Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Ning An
- Department of Transfusion Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Wen Yin
- Department of Transfusion Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Jing Yi
- Department of Transfusion Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yaozhen Chen
- Department of Transfusion Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China.
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14
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Wong ACH, Wong JJL, Rasko JEJ, Schmitz U. SpliceWiz: interactive analysis and visualization of alternative splicing in R. Brief Bioinform 2023; 25:bbad468. [PMID: 38152981 PMCID: PMC10753292 DOI: 10.1093/bib/bbad468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/31/2023] [Accepted: 11/23/2023] [Indexed: 12/29/2023] Open
Abstract
Alternative splicing (AS) is a crucial mechanism for regulating gene expression and isoform diversity in eukaryotes. However, the analysis and visualization of AS events from RNA sequencing data remains challenging. Most tools require a certain level of computer literacy and the available means of visualizing AS events, such as coverage and sashimi plots, have limitations and can be misleading. To address these issues, we present SpliceWiz, an R package with an interactive Shiny interface that allows easy and efficient AS analysis and visualization at scale. A novel normalization algorithm is implemented to aggregate splicing levels within sample groups, thereby allowing group differences in splicing levels to be accurately visualized. The tool also offers downstream gene ontology enrichment analysis, highlighting ASEs belonging to functional pathways of interest. SpliceWiz is optimized for speed and efficiency and introduces a new file format for coverage data storage that is more efficient than BigWig. Alignment files are processed orders of magnitude faster than other R-based AS analysis tools and on par with command-line tools. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization. SpliceWiz is a Bioconductor package and is also available on GitHub (https://github.com/alexchwong/SpliceWiz).
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Affiliation(s)
- Alex C H Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, the University of Sydney, Camperdown, NSW 2050, Australia
- Epigenetics and RNA Biology Laboratory, School of Medical Sciences, Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Laboratory, School of Medical Sciences, Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, the University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Ulf Schmitz
- Biomedical Sciences and Molecular Biology, James Cook University, Townsville, QLD 4810, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4810, Australia
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15
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Kalomoiri M, Prakash CR, Lagström S, Hauschulz K, Ewing E, Shchetynsky K, Kular L, Needhamsen M, Jagodic M. Simultaneous detection of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing. Front Immunol 2023; 14:1251772. [PMID: 37691926 PMCID: PMC10484099 DOI: 10.3389/fimmu.2023.1251772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/02/2023] [Indexed: 09/12/2023] Open
Abstract
The Human Leukocyte Antigen (HLA) locus associates with a variety of complex diseases, particularly autoimmune and inflammatory conditions. The HLA-DR15 haplotype, for example, confers the major risk for developing Multiple Sclerosis in Caucasians, pinpointing an important role in the etiology of this chronic inflammatory disease of the central nervous system. In addition to the protein-coding variants that shape the functional HLA-antigen-T cell interaction, recent studies suggest that the levels of HLA molecule expression, that are epigenetically controlled, also play a role in disease development. However, deciphering the exact molecular mechanisms of the HLA association has been hampered by the tremendous genetic complexity of the locus and a lack of robust approaches to investigate it. Here, we developed a method to specifically enrich the genomic DNA from the HLA class II locus (chr6:32,426,802-34,167,129) and proximal promoters of 2,157 immune-relevant genes, utilizing the Agilent RNA-based SureSelect Methyl-Seq Capture related method, followed by sequencing to detect genetic and epigenetic variation. We demonstrated successful simultaneous detection of the genetic variation and quantification of DNA methylation levels in HLA locus. Moreover, by the detection of differentially methylated positions in promoters of immune-related genes, we identified relevant pathways following stimulation of cells. Taken together, we present a method that can be utilized to study the interplay between genetic variance and epigenetic regulation in the HLA class II region, potentially, in a wide disease context.
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Affiliation(s)
- Maria Kalomoiri
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chandana Rao Prakash
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sonja Lagström
- Diagnostics and Genomics Group, Agilent Technologies Sweden AB, Sundbyberg, Sweden
| | - Kai Hauschulz
- Diagnostics and Genomics Group, Agilent Technologies Deutschland GmbH, Waldbronn, Germany
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Klementy Shchetynsky
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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16
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Scott HM, Smith MH, Coleman AK, Apostalo SL, Wagner AR, Watson RO, Patrick KL. Serine arginine-rich splicing factor (SRSF7) cooperates with the histone methyltransferase KMT5a to promote the type I interferon response via transcriptional activation of IRF7. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540055. [PMID: 37503164 PMCID: PMC10369877 DOI: 10.1101/2023.05.09.540055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tight regulation of macrophage immune gene expression is required to fight infection without risking harmful inflammation. The contribution of RNA binding proteins (RBPs) to shaping the macrophage response to pathogens remains poorly understood. Transcriptomic analysis revealed that a member of the serine/arginine-rich (SR) family of mRNA processing factors, SRSF7, is required for optimal expression of a cohort of interferon stimulated genes (ISGs) in macrophages. Using genetic and biochemical assays, we discovered that in addition to its canonical role in regulating alternative splicing, SRSF7 drives transcription of interferon regulatory transcription factor 7 (IRF7) to promote antiviral immunity. At the Irf7 promoter, SRSF7 maximizes STAT1 transcription factor binding and RNA polymerase II elongation via cooperation with the H4K20me1 histone methyltransferase KMT5a (SET8). These studies define an unorthodox role for an SR protein in activating transcription and reveal an unappreciated RNA binding protein-chromatin network that orchestrates macrophage antiviral gene expression.
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17
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Feng Y, Chen Z, Xu Y, Han Y, Jia X, Wang Z, Zhang N, Lv W. The central inflammatory regulator IκBζ: induction, regulation and physiological functions. Front Immunol 2023; 14:1188253. [PMID: 37377955 PMCID: PMC10291074 DOI: 10.3389/fimmu.2023.1188253] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
IκBζ (encoded by NFKBIZ) is the most recently identified IkappaB family protein. As an atypical member of the IkappaB protein family, NFKBIZ has been the focus of recent studies because of its role in inflammation. Specifically, it is a key gene in the regulation of a variety of inflammatory factors in the NF-KB pathway, thereby affecting the progression of related diseases. In recent years, investigations into NFKBIZ have led to greater understanding of this gene. In this review, we summarize the induction of NFKBIZ and then elucidate its transcription, translation, molecular mechanism and physiological function. Finally, the roles played by NFKBIZ in psoriasis, cancer, kidney injury, autoimmune diseases and other diseases are described. NFKBIZ functions are universal and bidirectional, and therefore, this gene may exert a great influence on the regulation of inflammation and inflammation-related diseases.
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Affiliation(s)
- Yanpeng Feng
- Department of Neurosurgery & Pathophysiology, Institute of Neuroregeneration & Neurorehabilitation, Qingdao University, Qingdao, China
| | - Zhiyuan Chen
- Department of Neurosurgery & Pathophysiology, Institute of Neuroregeneration & Neurorehabilitation, Qingdao University, Qingdao, China
| | - Yi Xu
- Department of Neurosurgery & Pathophysiology, Institute of Neuroregeneration & Neurorehabilitation, Qingdao University, Qingdao, China
| | - Yuxuan Han
- Department of Neurosurgery & Pathophysiology, Institute of Neuroregeneration & Neurorehabilitation, Qingdao University, Qingdao, China
| | - Xiujuan Jia
- Department of Geriatrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zixuan Wang
- Department of Geriatrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Nannan Zhang
- Department of Geriatrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenjing Lv
- Department of Neurosurgery & Pathophysiology, Institute of Neuroregeneration & Neurorehabilitation, Qingdao University, Qingdao, China
- Department of Geriatrics, The Affiliated Hospital of Qingdao University, Qingdao, China
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18
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Zhang C, Wei S, Dai S, Li X, Wang H, Zhang H, Sun G, Shan B, Zhao L. The NR_109/FUBP1/c-Myc axis regulates TAM polarization and remodels the tumor microenvironment to promote cancer development. J Immunother Cancer 2023; 11:jitc-2022-006230. [PMID: 37217247 DOI: 10.1136/jitc-2022-006230] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Tumor-associated macrophages (TAMs) are a major component of the tumor microenvironment (TME) and exert an important role in tumor progression. Due to the heterogeneity and plasticity of TAMs, modulating the polarization states of TAMs is considered as a potential therapeutic strategy for tumors. Long noncoding RNAs (lncRNAs) have been implicated in various physiological and pathological processes, yet the underlying mechanism on how lncRNAs manipulate the polarization states of TAMs is still unclear and remains to be further investigated. METHODS Microarray analyses were employed to characterize the lncRNA profile involved in THP-1-induced M0, M1 and M2-like macrophage. Among those differentially expressed lncRNAs, NR_109 was further studied, for its function in M2-like macrophage polarization and the effects of the condition medium or macrophages mediated by NR_109 on tumor proliferation, metastasis and TME remodeling both in vitro and in vivo. Moreover, we revealed how NR_109 interacted with far upstream element-binding protein 1 (FUBP1) to regulate the protein stability through hindering ubiquitination modification by competitively binding with JVT-1. Finally, we examined sections of tumor patients to probe the correlation among the expression of NR_109 and related proteins, showing the clinical significance of NR_109. RESULTS We found that lncRNA NR_109 was highly expressed in M2-like macrophages. Knockdown NR_109 impeded IL-4 induced M2-like macrophage polarization and significantly reduced the activity of M2-like macrophages to support the proliferation and metastasis of tumor cells in vitro and in vivo. Mechanistically, NR_109 competed with JVT-1 to bind FUBP1 at its C-terminus domain, impeded the ubiquitin-mediated degradation of FUBP1, activated c-Myc transcription and thus promoted M2-like macrophages polarization. Meanwhile, as a transcription factor, c-Myc could bind to the promoter of NR_109 and enhance the transcription of NR_109. Clinically, high NR_109 expression was found in CD163+ TAMs from tumor tissues and was positively correlated with poor clinical stages of patients with gastric cancer and breast cancer. CONCLUSIONS Our work revealed for the first time that NR_109 exerted a crucial role in regulating the phenotype-remodeling and function of M2-like macrophages via a NR_109/FUBP1/c-Myc positive feedback loop. Thus, NR_109 has great translational potentials in the diagnosis, prognosis and immunotherapy of cancer.
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Affiliation(s)
- Cong Zhang
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Sisi Wei
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Suli Dai
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiaoya Li
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Huixia Wang
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hongtao Zhang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Guogui Sun
- Department of Hebei Key Laboratory of Medical-industrial Integration Precision Medicine, Affiliated Hospital, North China University of Science and Technology, Tangshan, China
| | - Baoen Shan
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lianmei Zhao
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
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19
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Wu S, Schmitz U. Single-cell and long-read sequencing to enhance modelling of splicing and cell-fate determination. Comput Struct Biotechnol J 2023; 21:2373-2380. [PMID: 37066125 PMCID: PMC10091034 DOI: 10.1016/j.csbj.2023.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Single-cell sequencing technologies have revolutionised the life sciences and biomedical research. Single-cell sequencing provides high-resolution data on cell heterogeneity, allowing high-fidelity cell type identification, and lineage tracking. Computational algorithms and mathematical models have been developed to make sense of the data, compensate for errors and simulate the biological processes, which has led to breakthroughs in our understanding of cell differentiation, cell-fate determination and tissue cell composition. The development of long-read (a.k.a. third-generation) sequencing technologies has produced powerful tools for investigating alternative splicing, isoform expression (at the RNA level), genome assembly and the detection of complex structural variants (at the DNA level). In this review, we provide an overview of the recent advancements in single-cell and long-read sequencing technologies, with a particular focus on the computational algorithms that help in correcting, analysing, and interpreting the resulting data. Additionally, we review some mathematical models that use single-cell and long-read sequencing data to study cell-fate determination and alternative splicing, respectively. Moreover, we highlight the emerging opportunities in modelling cell-fate determination that result from the combination of single-cell and long-read sequencing technologies.
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Affiliation(s)
- Siyuan Wu
- Department of Molecular & Cell Biology, James Cook University, Townsville 4811, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns 4870, Queensland, Australia
- School of Mathematics, Monash University, Melbourne 3800, Victoria, Australia
| | - Ulf Schmitz
- Department of Molecular & Cell Biology, James Cook University, Townsville 4811, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns 4870, Queensland, Australia
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20
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A Potential Therapy Using Antisense Oligonucleotides to Treat Autosomal Recessive Polycystic Kidney Disease. J Clin Med 2023; 12:jcm12041428. [PMID: 36835961 PMCID: PMC9966971 DOI: 10.3390/jcm12041428] [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: 12/27/2022] [Revised: 02/01/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
(1) Background: Autosomal recessive polycystic kidney disease (ARPKD) is a rare ciliopathy characterized by progressively enlarged kidneys with fusiform dilatation of the collecting ducts. Loss-of-function mutations in the PKHD1 gene, which encodes fibrocystin/polyductin, cause ARPKD; however, an efficient treatment method and drug for ARPKD have yet to be found. Antisense oligonucleotides (ASOs) are short special oligonucleotides which function to regulate gene expression and alter mRNA splicing. Several ASOs have been approved by the FDA for the treatment of genetic disorders, and many are progressing at present. We designed ASOs to verify whether ASOs mediate the correction of splicing further to treat ARPKD arising from splicing defects and explored them as a potential treatment option. (2) Methods: We screened 38 children with polycystic kidney disease for gene detection using whole-exome sequencing (WES) and targeted next-generation sequencing. Their clinical information was investigated and followed up. The PKHD1 variants were summarized and analyzed, and association analysis was carried out to analyze the relationship between genotype and phenotype. Various bioinformatics tools were used to predict pathogenicity. Hybrid minigene analysis was performed as part of the functional splicing analysis. Moreover, the de novo protein synthesis inhibitor cycloheximide was selected to verify the degraded pathway of abnormal pre-mRNAs. ASOs were designed to rescue aberrant splicing, and this was verified. (3) Results: Of the 11 patients with PKHD1 variants, all of them exhibited variable levels of complications of the liver and kidneys. We found that patients with truncating variants and variants in certain regions had a more severe phenotype. Two splicing variants of the PKHD1 genotypes were studied via the hybrid minigene assay: variants c.2141-3T>C and c.11174+5G>A. These cause aberrant splicing, and their strong pathogenicity was confirmed. We demonstrated that the abnormal pre-mRNAs produced from the variants escaped from the NMD pathway with the use of the de novo protein synthesis inhibitor cycloheximide. Moreover, we found that the splicing defects were rescued by using ASOs, which efficiently induced the exclusion of pseudoexons. (4) Conclusion: Patients with truncating variants and variants in certain regions had a more severe phenotype. ASOs are a potential drug for treating ARPKD patients harboring splicing mutations of the PKHD1 gene by correcting the splicing defects and increasing the expression of the normal PKHD1 gene.
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21
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Sengupta A, Dorn A, Jamshidi M, Schwob M, Hassan W, De Maddalena LL, Hugi A, Stucki AO, Dorn P, Marti TM, Wisser O, Stucki JD, Krebs T, Hobi N, Guenat OT. A multiplex inhalation platform to model in situ like aerosol delivery in a breathing lung-on-chip. Front Pharmacol 2023; 14:1114739. [PMID: 36959848 PMCID: PMC10029733 DOI: 10.3389/fphar.2023.1114739] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Prolonged exposure to environmental respirable toxicants can lead to the development and worsening of severe respiratory diseases such as asthma, chronic obstructive pulmonary disease (COPD) and fibrosis. The limited number of FDA-approved inhaled drugs for these serious lung conditions has led to a shift from in vivo towards the use of alternative in vitro human-relevant models to better predict the toxicity of inhaled particles in preclinical research. While there are several inhalation exposure models for the upper airways, the fragile and dynamic nature of the alveolar microenvironment has limited the development of reproducible exposure models for the distal lung. Here, we present a mechanistic approach using a new generation of exposure systems, the Cloud α AX12. This novel in vitro inhalation tool consists of a cloud-based exposure chamber (VITROCELL) that integrates the breathing AXLung-on-chip system (AlveoliX). The ultrathin and porous membrane of the AX12 plate was used to create a complex multicellular model that enables key physiological culture conditions: the air-liquid interface (ALI) and the three-dimensional cyclic stretch (CS). Human-relevant cellular models were established for a) the distal alveolar-capillary interface using primary cell-derived immortalized alveolar epithelial cells (AXiAECs), macrophages (THP-1) and endothelial (HLMVEC) cells, and b) the upper-airways using Calu3 cells. Primary human alveolar epithelial cells (AXhAEpCs) were used to validate the toxicity results obtained from the immortalized cell lines. To mimic in vivo relevant aerosol exposures with the Cloud α AX12, three different models were established using: a) titanium dioxide (TiO2) and zinc oxide nanoparticles b) polyhexamethylene guanidine a toxic chemical and c) an anti-inflammatory inhaled corticosteroid, fluticasone propionate (FL). Our results suggest an important synergistic effect on the air-blood barrier sensitivity, cytotoxicity and inflammation, when air-liquid interface and cyclic stretch culture conditions are combined. To the best of our knowledge, this is the first time that an in vitro inhalation exposure system for the distal lung has been described with a breathing lung-on-chip technology. The Cloud α AX12 model thus represents a state-of-the-art pre-clinical tool to study inhalation toxicity risks, drug safety and efficacy.
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Affiliation(s)
- Arunima Sengupta
- Organs-on-Chip Technologies, ARTORG Center for Biomedical Engineering, University of Bern, Bern, Switzerland
| | - Aurélien Dorn
- Organs-on-Chip Technologies, ARTORG Center for Biomedical Engineering, University of Bern, Bern, Switzerland
- AlveoliX AG, Swiss Organs-on-Chip Innovation, Bern, Switzerland
| | - Mohammad Jamshidi
- Organs-on-Chip Technologies, ARTORG Center for Biomedical Engineering, University of Bern, Bern, Switzerland
| | - Magali Schwob
- Organs-on-Chip Technologies, ARTORG Center for Biomedical Engineering, University of Bern, Bern, Switzerland
| | - Widad Hassan
- Organs-on-Chip Technologies, ARTORG Center for Biomedical Engineering, University of Bern, Bern, Switzerland
| | | | - Andreas Hugi
- AlveoliX AG, Swiss Organs-on-Chip Innovation, Bern, Switzerland
| | - Andreas O. Stucki
- Organs-on-Chip Technologies, ARTORG Center for Biomedical Engineering, University of Bern, Bern, Switzerland
- *Correspondence: Andreas O. Stucki,
| | - Patrick Dorn
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Thomas M. Marti
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | | | | | - Nina Hobi
- AlveoliX AG, Swiss Organs-on-Chip Innovation, Bern, Switzerland
| | - Olivier T. Guenat
- Organs-on-Chip Technologies, ARTORG Center for Biomedical Engineering, University of Bern, Bern, Switzerland
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, Bern, Switzerland
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, Bern, Switzerland
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22
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Li X, Liu H. Expression and prognostic value of MIP-1α in neonatal acute respiratory distress syndrome. Am J Transl Res 2022; 14:7889-7897. [PMID: 36505316 PMCID: PMC9730077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/28/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To investigate the expression and prognostic value of macrophage inflammatory protein 1α (MIP-1α) in neonatal acute respiratory distress syndrome (NRDS). METHODS In this retrospective analysis, 96 newborns with NRDS in Affiliated Lianyungang Hospital of Xuzhou Medical University from January 2018 to June 2021 were included in the experimental group (EG), while the other 60 normal neonates were included as the control group (CG). The concentration of MIP-1α in umbilical cord blood was tested by Elisa method. The clinical value of MIP-1α in diagnosing NRDS was assessed via receiver operating characteristic (ROC) curve. According to the 28-day survival data, children were divided into a survival group and a death group. The prognostic factors were assessed by Cox regression analysis. The correlation between MIP-1α and IL-1β, IL-6, TNF-α, SNAPPE-II scores were evaluated by Pearson test. The relationship between the MIP-1α level and the severity of the disease was assessed. RESULTS The MIF-1α level in cord blood of children in the EG was dramatically higher than that in the CG (P<0.05). Besides, ROC curve further found that the area of MIF-1α under the curve of diagnosing NRSD was 0.949. MIF-1α was positively correlated with the levels of interleukin-1β (IL-1β), interleukin-6 (IL-6), tumor necrosis factor α (TNF-α) and SNAPPE-II score (P<0.001). With the increase of NRDS, the serum MIF-1α level increased, showing a positive association (P<0.05). Cox regression analysis revealed that the severity and MIF-1α level were independent prognostic factors of survival (P<0.001). The survival rate of children with MIF-1α <281.58 pg/mL as well as children with I-II grade was higher than those with MIF-1α >281.58 pg/mL as well as children with III-IV grade (P<0.05). CONCLUSION The increase of serum MIP-1α level is relevant to the condition and prognosis of NRDS children. The level of cord blood MIP-1α level is expected to become a potential outcome measure.
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23
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Petrova V, Song R, Nordström KJV, Walter J, Wong JJL, Armstrong N, Rasko JEJ, Schmitz U. Increased chromatin accessibility facilitates intron retention in specific cell differentiation states. Nucleic Acids Res 2022; 50:11563-11579. [PMID: 36354002 PMCID: PMC9723627 DOI: 10.1093/nar/gkac994] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022] Open
Abstract
Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including several cancers. Despite consistent reports demonstrating that intrinsic sequence features can help introns evade splicing, conflicting findings about cell type- or condition-specific IR regulation by trans-regulatory and epigenetic mechanisms demand an unbiased and systematic analysis of IR in a controlled experimental setting. We integrated matched mRNA sequencing (mRNA-Seq), whole-genome bisulfite sequencing (WGBS), nucleosome occupancy methylome sequencing (NOMe-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) data from primary human myeloid and lymphoid cells. Using these multi-omics data and machine learning, we trained two complementary models to determine the role of epigenetic factors in the regulation of IR in cells of the innate immune system. We show that increased chromatin accessibility, as revealed by nucleosome-free regions, contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. This study suggests an important role for chromatin architecture in IR regulation. With an increasing appreciation that pathogenic alterations are linked to RNA processing, our findings may provide useful insights for the development of novel therapeutic approaches that target aberrant splicing.
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Affiliation(s)
- Veronika Petrova
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | | | - Karl J V Nordström
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Jörn Walter
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Justin J L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Curtin University, Bentley, WA 6102, Australia
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24
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Mazille M, Buczak K, Scheiffele P, Mauger O. Stimulus-specific remodeling of the neuronal transcriptome through nuclear intron-retaining transcripts. EMBO J 2022; 41:e110192. [PMID: 36149731 DOI: 10.15252/embj.2021110192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 08/20/2022] [Accepted: 08/30/2022] [Indexed: 11/09/2022] Open
Abstract
The nuclear envelope has long been considered primarily a physical barrier separating nuclear and cytosolic contents. More recently, nuclear compartmentalization has been shown to have additional regulatory functions in controlling gene expression. A sizeable proportion of protein-coding mRNAs is more prevalent in the nucleus than in the cytosol, suggesting regulated mRNA trafficking to the cytosol, but the mechanisms underlying controlled nuclear mRNA retention remain unclear. Here, we provide a comprehensive map of the subcellular localization of mRNAs in mature mouse cortical neurons, and reveal that transcripts retained in the nucleus comprise the majority of stable intron-retaining mRNAs. Systematically probing the fate of nuclear transcripts upon neuronal stimulation, we found opposite effects on sub-populations of transcripts: while some are targeted for degradation, others complete splicing to generate fully mature mRNAs that are exported to the cytosol and mediate rapid increases in protein levels. Finally, different forms of stimulation mobilize distinct groups of intron-retaining transcripts, with this selectivity arising from the activation of specific signaling pathways. Overall, our findings uncover a cue-specific control of intron retention as a major regulator of acute remodeling of the neuronal transcriptome.
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Affiliation(s)
- Maxime Mazille
- Biozentrum of the University of Basel, Basel, Switzerland
| | | | | | - Oriane Mauger
- Biozentrum of the University of Basel, Basel, Switzerland
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25
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Ochsner SA, Pillich RT, Rawool D, Grethe JS, McKenna NJ. Transcriptional regulatory networks of circulating immune cells in type 1 diabetes: A community knowledgebase. iScience 2022; 25:104581. [PMID: 35832893 PMCID: PMC9272393 DOI: 10.1016/j.isci.2022.104581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 12/02/2022] Open
Abstract
Investigator-generated transcriptomic datasets interrogating circulating immune cell (CIC) gene expression in clinical type 1 diabetes (T1D) have underappreciated re-use value. Here, we repurposed these datasets to create an open science environment for the generation of hypotheses around CIC signaling pathways whose gain or loss of function contributes to T1D pathogenesis. We firstly computed sets of genes that were preferentially induced or repressed in T1D CICs and validated these against community benchmarks. We then inferred and validated signaling node networks regulating expression of these gene sets, as well as differentially expressed genes in the original underlying T1D case:control datasets. In a set of three use cases, we demonstrated how informed integration of these networks with complementary digital resources supports substantive, actionable hypotheses around signaling pathway dysfunction in T1D CICs. Finally, we developed a federated, cloud-based web resource that exposes the entire data matrix for unrestricted access and re-use by the research community. Re-use of transcriptomic type 1 diabetes (T1D) circulating immune cells (CICs) datasets We generated transcriptional regulatory networks for T1D CICs Use cases generate substantive hypotheses around signaling pathway dysfunction in T1D CICs Networks are freely accessible on the web for re-use by the research community
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Affiliation(s)
- Scott A. Ochsner
- Department of Molecular, Baylor College of Medicine, Houston, TX 77030, USA
- Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rudolf T. Pillich
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Deepali Rawool
- Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeffrey S. Grethe
- Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA
| | - Neil J. McKenna
- Department of Molecular, Baylor College of Medicine, Houston, TX 77030, USA
- Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Corresponding author
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26
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3’UTR-Seq analysis of chicken abdominal adipose tissue reveals widespread intron retention in 3’UTR and provides insight into molecular basis of feed efficiency. PLoS One 2022; 17:e0269534. [PMID: 35776773 PMCID: PMC9249230 DOI: 10.1371/journal.pone.0269534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 05/24/2022] [Indexed: 11/19/2022] Open
Abstract
Feed efficiency (FE) is an important trait in the broiler industry due to its direct correlation to efficient muscle growth instead of fat deposition. The present study characterized and compared gene expression profiles in abdominal fat from broiler chickens of different FE levels to enhance the understanding of FE biology. Specifically, traditional whole-transcript RNA-sequencing (RNA-seq) and 3’ UTR-sequencing (3’ UTR-seq) were applied to 22 and 61 samples, respectively. Overall, these two sequencing techniques shared a high correlation (0.76) between normalized counts, although 3’ UTR-seq showed a higher variance in sequencing and mapping performance statistics across samples and a lower rate of uniquely mapped reads. A higher percentage of 3’ UTR-seq reads mapped to introns suggested the frequent presence of cleavage sites in introns, thus warranting future research to study its regulatory function. Differential expression analysis identified 1198 differentially expressed genes (DEGs) between high FE (HFE) and intermediate FE (IFE) chickens with False Discovery Rate < 0.05 and fold change > 1.2. The processes that were significantly enriched by the DEGs included extracellular matrix remodeling and mechanisms impacting gene expression at the transcriptional and translational levels. Gene ontology enrichment analysis suggested that the divergence in fat deposition and FE in broiler chickens could be associated with peroxisome and lipid metabolism possibly regulated by G0/G1 switch gene 2 (G0S2).
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Zhang Y, Zhang X, Meng Y, Xu X, Zuo D. The role of glycolysis and lactate in the induction of tumor-associated macrophages immunosuppressive phenotype. Int Immunopharmacol 2022; 110:108994. [PMID: 35777265 DOI: 10.1016/j.intimp.2022.108994] [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: 01/21/2022] [Revised: 05/30/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022]
Abstract
Growing evidence highlights that glycolysis and tumor-derived lactate could skew tumor-associated macrophages (TAMs) toward an immunosuppressive phenotype. However, the updated research has not been systematically summarized yet. TAMs are educated by the tumor microenvironment (TME) and exert immunosuppressive functions and tumorigenic effects via multiple biological processes. It is well known that lactate generated by aerobic glycolysis is significantly accumulated in TME and promotes tumor progression in solid tumors. Moreover, some recent research demonstrated that glycolysis is activated in TAMs to support M2-like polarization, which is absolutely in contrast with the metabolic profile of M2 macrophages in inflammation. Notably, lactate produced by high levels of glycolysis is not only a metabolic by-product but also an oncometabolite. TAMs could access the biological information delivered by lactate and further enhance protumor functions such as immunosuppression and angiogenesis. Here, we outline the connection between glycolysis and TAM phenotype to elucidate the metabolic characteristics of TAMs. Further, insights into the specific molecular mechanisms of lactate-induced TAM polarization and potential therapeutic targets are summarized. We sought to discuss the reciprocal interaction between tumor cells and TAMs mediated by lactate, which will lay a foundation for the research aiming to elucidate the complex functions of TAMs.
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Affiliation(s)
- Yijia Zhang
- Department of Pharmacology, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Xue Zhang
- Department of Pharmacology, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Yuting Meng
- Department of Pharmacology, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Xiaobo Xu
- Department of Pharmacology, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Daiying Zuo
- Department of Pharmacology, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China.
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28
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Intron retention: importance, challenges, and opportunities. Trends Genet 2022; 38:789-792. [DOI: 10.1016/j.tig.2022.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 11/24/2022]
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29
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Schymik HS, Dahlem C, Barghash A, Kiemer AK. Comment on: The m6A Reader IGF2BP2 Regulates Macrophage Phenotypic Activation and Inflammatory Diseases by Stabilizing TSC1 and PPARγ. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104372. [PMID: 35038236 PMCID: PMC8922093 DOI: 10.1002/advs.202104372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/04/2021] [Indexed: 05/08/2023]
Abstract
Recently, first insights into the regulation and the role of the RNA-binding protein IMP2 in macrophage activation have been published by Wang et al. This study addresses differences in the regulation of IMP2 between the human and murine system. While the expression of IMP2 in anti-inflammatory macrophages is synchronous in mice and men, IMP2 expression is regulated differently in inflammatory macrophages.
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Affiliation(s)
- Hanna S. Schymik
- Department of PharmacyPharmaceutical BiologySaarland UniversitySaarbruecken66123Germany
| | - Charlotte Dahlem
- Department of PharmacyPharmaceutical BiologySaarland UniversitySaarbruecken66123Germany
| | - Ahmad Barghash
- School of Electrical Engineering and Information TechnologyGerman Jordanian UniversityAmman11180Jordan
| | - Alexandra K. Kiemer
- Department of PharmacyPharmaceutical BiologySaarland UniversitySaarbruecken66123Germany
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30
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Shah JS, Milevskiy MJG, Petrova V, Au AYM, Wong JJL, Visvader JE, Schmitz U, Rasko JEJ. Towards resolution of the intron retention paradox in breast cancer. Breast Cancer Res 2022; 24:100. [PMID: 36581993 PMCID: PMC9798573 DOI: 10.1186/s13058-022-01593-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/12/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND After many years of neglect in the field of alternative splicing, the importance of intron retention (IR) in cancer has come into focus following landmark discoveries of aberrant IR patterns in cancer. Many solid and liquid tumours are associated with drastic increases in IR, and such patterns have been pursued as both biomarkers and therapeutic targets. Paradoxically, breast cancer (BrCa) is the only tumour type in which IR is reduced compared to adjacent normal breast tissue. METHODS In this study, we have conducted a pan-cancer analysis of IR with emphasis on BrCa and its subtypes. We explored mechanisms that could cause aberrant and pathological IR and clarified why normal breast tissue has unusually high IR. RESULTS Strikingly, we found that aberrantly decreasing IR in BrCa can be largely attributed to normal breast tissue having the highest occurrence of IR events compared to other healthy tissues. Our analyses suggest that low numbers of IR events in breast tumours are associated with poor prognosis, particularly in the luminal B subtype. Interestingly, we found that IR frequencies negatively correlate with cell proliferation in BrCa cells, i.e. rapidly dividing tumour cells have the lowest number of IR events. Aberrant RNA-binding protein expression and changes in tissue composition are among the causes of aberrantly decreasing IR in BrCa. CONCLUSIONS Our results suggest that IR should be considered for therapeutic manipulation in BrCa patients with aberrantly low IR levels and that further work is needed to understand the cause and impact of high IR in other tumour types.
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Affiliation(s)
- Jaynish S. Shah
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia ,grid.1002.30000 0004 1936 7857Australian Centre for Blood Diseases, Central Clinical School, Monash University and Alfred Health, Melbourne, VIC Australia
| | - Michael J. G. Milevskiy
- grid.1042.70000 0004 0432 4889ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Veronika Petrova
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia
| | - Amy Y. M. Au
- grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia
| | - Justin J. L. Wong
- grid.1013.30000 0004 1936 834XEpigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050 Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Jane E. Visvader
- grid.1042.70000 0004 0432 4889ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Ulf Schmitz
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1011.10000 0004 0474 1797Department of Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 James Cook Drive, Townsville, QLD 4811 Australia ,grid.1011.10000 0004 0474 1797Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, 4878 Australia
| | - John E. J. Rasko
- grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Camperdown, Australia ,grid.413249.90000 0004 0385 0051Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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31
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Ren G, Juhl M, Peng Q, Fink T, Porsborg SR. Selection and validation of reference genes for qPCR analysis of differentiation and maturation of THP-1 cells into M1 macrophage-like cells. Immunol Cell Biol 2022; 100:822-829. [PMID: 36184577 PMCID: PMC9828170 DOI: 10.1111/imcb.12590] [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: 08/06/2022] [Revised: 09/19/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
For cell-based assays studying monocytes and macrophages, the immortalized monocyte cell line THP-1 is widely used and stimulated with phorbol 12-myristate 13-acetate, lipopolysaccharide (LPS) and/or interferon-γ (IFN-γ), after which it differentiates and polarizes into proinflammatory M1-like macrophages. For the quantification of this and the effect of different factors affecting these processes, the expression levels of various maturation markers are determined using reverse transcription-quantitative PCR. For this purpose, stably expressed reference genes are crucial. However, no studies evaluating the stability of reference genes in THP-1 cells stimulated with LPS and IFN-γ have been performed. Therefore, this paper describes the selection of the most used reference genes [RPL37A (ribosomal protein L37a), GAPDH (glyceraldehyde-3-phosphate dehydrogenase), UBC (ubiquitin C), B2M (0β2-microbulin), ACTB (β-actin) and PPIA (cyclophilin A)], the in silico primer design, the analysis and the validation of these in accordance with the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines and more recent recommendations for the validation of the stability of reference genes. Using the RefFinder platform, including the four most popular algorithms for reference gene validation, the Delta CT, BestKeeper, NormFinder and geNorm, we find the reference genes GAPDH and UBC to be the most stable. Furthermore, we demonstrate that the normalization of gene expression data using the least stable reference genes, ACTB and B2M, dramatically affects the interpretation of experimental data. Taken together, it is vital to validate the stability of reference genes under the specific experimental conditions used when utilizing the THP-1 monocyte model system.
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Affiliation(s)
- Guoqiang Ren
- Regenerative Medicine Group, Department of Health Science and TechnologyAalborg UniversityFredrik Bajers Vej 3B9220AalborgDenmark
| | - Morten Juhl
- Cardiology Stem Cell Centre, The Centre for Cardiac, Vascular, Pulmonary and Infectious DiseasesCopenhagen University Hospital RigshospitaletDenmark
| | - Qiuyue Peng
- Regenerative Medicine Group, Department of Health Science and TechnologyAalborg UniversityFredrik Bajers Vej 3B9220AalborgDenmark
| | - Trine Fink
- Regenerative Medicine Group, Department of Health Science and TechnologyAalborg UniversityFredrik Bajers Vej 3B9220AalborgDenmark
| | - Simone Riis Porsborg
- Regenerative Medicine Group, Department of Health Science and TechnologyAalborg UniversityFredrik Bajers Vej 3B9220AalborgDenmark
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32
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Song R, Tikoo S, Jain R, Pinello N, Au AY, Nagarajah R, Porse B, Rasko JEJ, Wong JJL. Dynamic intron retention modulates gene expression in the monocytic differentiation pathway. Immunology 2021; 165:274-286. [PMID: 34775600 DOI: 10.1111/imm.13435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/01/2022] Open
Abstract
Monocytes play a crucial role in maintaining homeostasis and mediating a successful innate immune response. They also act as central players in diverse pathological conditions, thus making them an attractive therapeutic target. Within the bone marrow, monocytes arise from a committed precursor termed cMoP (Common Monocyte Progenitor). However, molecular mechanisms that regulate the differentiation of cMoP to various monocytic subsets remain unclear. Herein, we purified murine myeloid precursors for deep poly-A enriched RNA sequencing to understand the role of alternative splicing in the development and differentiation of monocytes under homeostasis. Our analyses revealed intron retention to be the major alternative splicing mechanism involved in the monocyte differentiation cascade, especially in the differentiation of Ly6Chi monocytes to Ly6Clo monocytes. Furthermore, we found that the key genes regulated by intron retention in the differentiation of murine Ly6Chi to Ly6Clo monocytes were also conserved in humans. Our data highlight the unique role of intron retention in the regulation of the monocytic differentiation pathway.
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Affiliation(s)
- Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Shweta Tikoo
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Rohit Jain
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Amy Ym Au
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Rajini Nagarajah
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Bo Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.,Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - John E J Rasko
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
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33
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Lorenzi C, Barriere S, Arnold K, Luco RF, Oldfield AJ, Ritchie W. IRFinder-S: a comprehensive suite to discover and explore intron retention. Genome Biol 2021; 22:307. [PMID: 34749764 PMCID: PMC8573998 DOI: 10.1186/s13059-021-02515-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron retention events in multiple samples. Specifically, IRFinder-S allows a better identification of true intron retention events using a convolutional neural network, allows the sharing of intron retention results between labs, integrates a dynamic database to explore and contrast available samples, and provides a tested method to detect differential levels of intron retention.
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Affiliation(s)
- Claudio Lorenzi
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Sylvain Barriere
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Katharina Arnold
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Reini F Luco
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Andrew J Oldfield
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - William Ritchie
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France.
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34
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Nicolet BP, Zandhuis ND, Lattanzio VM, Wolkers MC. Sequence determinants as key regulators in gene expression of T cells. Immunol Rev 2021; 304:10-29. [PMID: 34486113 PMCID: PMC9292449 DOI: 10.1111/imr.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
T cell homeostasis, T cell differentiation, and T cell effector function rely on the constant fine-tuning of gene expression. To alter the T cell state, substantial remodeling of the proteome is required. This remodeling depends on the intricate interplay of regulatory mechanisms, including post-transcriptional gene regulation. In this review, we discuss how the sequence of a transcript influences these post-transcriptional events. In particular, we review how sequence determinants such as sequence conservation, GC content, and chemical modifications define the levels of the mRNA and the protein in a T cell. We describe the effect of different forms of alternative splicing on mRNA expression and protein production, and their effect on subcellular localization. In addition, we discuss the role of sequences and structures as binding hubs for miRNAs and RNA-binding proteins in T cells. The review thus highlights how the intimate interplay of post-transcriptional mechanisms dictate cellular fate decisions in T cells.
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Affiliation(s)
- Benoit P. Nicolet
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Nordin D. Zandhuis
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - V. Maria Lattanzio
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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35
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The Expanding Role of Alternative Splicing in Vascular Smooth Muscle Cell Plasticity. Int J Mol Sci 2021; 22:ijms221910213. [PMID: 34638554 PMCID: PMC8508619 DOI: 10.3390/ijms221910213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/15/2021] [Accepted: 09/18/2021] [Indexed: 12/21/2022] Open
Abstract
Vascular smooth muscle cells (VSMCs) display extraordinary phenotypic plasticity. This allows them to differentiate or dedifferentiate, depending on environmental cues. The ability to ‘switch’ between a quiescent contractile phenotype to a highly proliferative synthetic state renders VSMCs as primary mediators of vascular repair and remodelling. When their plasticity is pathological, it can lead to cardiovascular diseases such as atherosclerosis and restenosis. Coinciding with significant technological and conceptual innovations in RNA biology, there has been a growing focus on the role of alternative splicing in VSMC gene expression regulation. Herein, we review how alternative splicing and its regulatory factors are involved in generating protein diversity and altering gene expression levels in VSMC plasticity. Moreover, we explore how recent advancements in the development of splicing-modulating therapies may be applied to VSMC-related pathologies.
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36
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Iampietro M, Dumont C, Mathieu C, Spanier J, Robert J, Charpenay A, Dupichaud S, Dhondt KP, Aurine N, Pelissier R, Ferren M, Mély S, Gerlier D, Kalinke U, Horvat B. Activation of cGAS/STING pathway upon paramyxovirus infection. iScience 2021; 24:102519. [PMID: 34142033 PMCID: PMC8188492 DOI: 10.1016/j.isci.2021.102519] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/02/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
During inflammatory diseases, cancer, and infection, the cGAS/STING pathway is known to recognize foreign or self-DNA in the cytosol and activate an innate immune response. Here, we report that negative-strand RNA paramyxoviruses, Nipah virus (NiV), and measles virus (MeV), can also trigger the cGAS/STING axis. Although mice deficient for MyD88, TRIF, and MAVS still moderately control NiV infection when compared with wild-type mice, additional STING deficiency resulted in 100% lethality, suggesting synergistic roles of these pathways in host protection. Moreover, deletion of cGAS or STING resulted in decreased type I interferon production with enhanced paramyxoviral infection in both human and murine cells. Finally, the phosphorylation and ubiquitination of STING, observed during viral infections, confirmed the activation of cGAS/STING pathway by NiV and MeV. Our data suggest that cGAS/STING activation is critical in controlling paramyxovirus infection and possibly represents attractive targets to develop countermeasures against severe disease induced by these pathogens.
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Affiliation(s)
- Mathieu Iampietro
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Claire Dumont
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Cyrille Mathieu
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Julia Spanier
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection research, a joint venture between the Hanover Medical School and the Helmholtz Centre for Infection Research, Hanover, Germany
| | - Jonathan Robert
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Aude Charpenay
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Sébastien Dupichaud
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Kévin P. Dhondt
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Noémie Aurine
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Rodolphe Pelissier
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Marion Ferren
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Stéphane Mély
- INSERM- Laboratoire P4 Jean Mérieux-21 Avenue Tony Garnier, 69365 Lyon, France
| | - Denis Gerlier
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection research, a joint venture between the Hanover Medical School and the Helmholtz Centre for Infection Research, Hanover, Germany
- Cluster of Excellence-Resolving Infection Susceptibility (RESIST), Hanover, Germany
| | - Branka Horvat
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
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37
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Li H, Funk CC, McFarland K, Dammer EB, Allen M, Carrasquillo MM, Levites Y, Chakrabarty P, Burgess JD, Wang X, Dickson D, Seyfried NT, Duong DM, Lah JJ, Younkin SG, Levey AI, Omenn GS, Ertekin‐Taner N, Golde TE, Price ND. Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer's disease. Alzheimers Dement 2021; 17:984-1004. [PMID: 33480174 PMCID: PMC8248162 DOI: 10.1002/alz.12254] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 10/08/2020] [Accepted: 10/17/2020] [Indexed: 12/21/2022]
Abstract
Intron retention (IR) has been implicated in the pathogenesis of complex diseases such as cancers; its association with Alzheimer's disease (AD) remains unexplored. We performed genome-wide analysis of IR through integrating genetic, transcriptomic, and proteomic data of AD subjects and mouse models from the Accelerating Medicines Partnership-Alzheimer's Disease project. We identified 4535 and 4086 IR events in 2173 human and 1736 mouse genes, respectively. Quantitation of IR enabled the identification of differentially expressed genes that conventional exon-level approaches did not reveal. There were significant correlations of intron expression within innate immune genes, like HMBOX1, with AD in humans. Peptides with a high probability of translation from intron-retained mRNAs were identified using mass spectrometry. Further, we established AD-specific intron expression Quantitative Trait Loci, and identified splicing-related genes that may regulate IR. Our analysis provides a novel resource for the search for new AD biomarkers and pathological mechanisms.
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Affiliation(s)
- Hong‐Dong Li
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangshaHunanP.R. China
- Institute for Systems BiologySeattleWashingtonUSA
| | - Cory C. Funk
- Institute for Systems BiologySeattleWashingtonUSA
| | - Karen McFarland
- Department of Neuroscience and NeurologyCenter for Translational Research in Neurodegenerative diseaseand McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Eric B. Dammer
- Department of BiochemistryEmory UniversityAtlantaGeorgiaUSA
| | - Mariet Allen
- Mayo ClinicDepartment ofNeuroscienceJacksonvilleFloridaUSA
| | | | - Yona Levites
- Department of Neuroscience and NeurologyCenter for Translational Research in Neurodegenerative diseaseand McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Paramita Chakrabarty
- Department of Neuroscience and NeurologyCenter for Translational Research in Neurodegenerative diseaseand McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
| | | | - Xue Wang
- Mayo ClinicDepartment of Health Sciences ResearchJacksonvilleFloridaUSA
| | - Dennis Dickson
- Mayo ClinicDepartment ofNeuroscienceJacksonvilleFloridaUSA
| | - Nicholas T. Seyfried
- Department of BiochemistryEmory UniversityAtlantaGeorgiaUSA
- Department of NeurologyEmory UniversityAtlantaGeorgiaUSA
| | - Duc M. Duong
- Department of BiochemistryEmory UniversityAtlantaGeorgiaUSA
| | - James J. Lah
- Department of NeurologyEmory UniversityAtlantaGeorgiaUSA
| | | | - Allan I. Levey
- Department of NeurologyEmory UniversityAtlantaGeorgiaUSA
| | - Gilbert S. Omenn
- Institute for Systems BiologySeattleWashingtonUSA
- Department of Computational Medicine and BioinformaticsUniversity of MichiganAnn ArborMichiganUSA
| | - Nilüfer Ertekin‐Taner
- Mayo ClinicDepartment ofNeuroscienceJacksonvilleFloridaUSA
- Mayo ClinicDepartment of NeurologyJacksonvilleFloridaUSA
| | - Todd E. Golde
- Department of Neuroscience and NeurologyCenter for Translational Research in Neurodegenerative diseaseand McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
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Ziff OJ, Taha DM, Crerar H, Clarke BE, Chakrabarti AM, Kelly G, Neeves J, Tyzack GE, Luscombe NM, Patani R. Reactive astrocytes in ALS display diminished intron retention. Nucleic Acids Res 2021; 49:3168-3184. [PMID: 33684213 PMCID: PMC8034657 DOI: 10.1093/nar/gkab115] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022] Open
Abstract
Reactive astrocytes are implicated in amyotrophic lateral sclerosis (ALS), although the mechanisms controlling reactive transformation are unknown. We show that decreased intron retention (IR) is common to human-induced pluripotent stem cell (hiPSC)-derived astrocytes carrying ALS-causing mutations in VCP, SOD1 and C9orf72. Notably, transcripts with decreased IR and increased expression are overrepresented in reactivity processes including cell adhesion, stress response and immune activation. This was recapitulated in public-datasets for (i) hiPSC-derived astrocytes stimulated with cytokines to undergo reactive transformation and (ii) in vivo astrocytes following selective deletion of TDP-43. We also re-examined public translatome sequencing (TRAP-seq) of astrocytes from a SOD1 mouse model, which revealed that transcripts upregulated in translation significantly overlap with transcripts exhibiting decreased IR. Using nucleocytoplasmic fractionation of VCP mutant astrocytes coupled with mRNA sequencing and proteomics, we identify that decreased IR in nuclear transcripts is associated with enhanced nonsense mediated decay and increased cytoplasmic expression of transcripts and proteins regulating reactive transformation. These findings are consistent with a molecular model for reactive transformation in astrocytes whereby poised nuclear reactivity-related IR transcripts are spliced, undergo nuclear-to-cytoplasmic translocation and translation. Our study therefore provides new insights into the molecular regulation of reactive transformation in astrocytes.
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Affiliation(s)
- Oliver J Ziff
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK
| | - Doaa M Taha
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21511, Egypt
| | - Hamish Crerar
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Benjamin E Clarke
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Anob M Chakrabarti
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jacob Neeves
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Giulia E Tyzack
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.,Okinawa Institute of Science & Technology Graduate University, Okinawa 904-0495, Japan
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK
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39
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Chen Z, Tao S, Zhu R, Tian S, Sun Y, Wang H, Yan R, Shao J, Zhang Y, Zhang J, Yao Z, Lu Q. Aberrant functional connectivity between the suprachiasmatic nucleus and the superior temporal gyrus: Bridging RORA gene polymorphism with diurnal mood variation in major depressive disorder. J Psychiatr Res 2021; 132:123-130. [PMID: 33091686 DOI: 10.1016/j.jpsychires.2020.09.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/24/2020] [Accepted: 09/30/2020] [Indexed: 10/23/2022]
Abstract
Diurnal mood variation (DMV), a common symptom of major depressive disorder (MDD), is associated with circadian related genes and dysregulation of the suprachiasmatic nucleus (SCN). Previous research confirmed that the RORA gene is involved in the regulation of circadian rhythms. In this study, we hypothesized that polymorphisms of RORA may affect DMV symptoms of MDD through functional changes in the SCN. A total of 208 patients diagnosed with depression and 120 control subjects were enrolled and underwent a resting-state functional magnetic resonance imaging (rs-fMRI). Blood samples were collected and genotyping of 9 RORA gene SNPs were performed using next-generation sequencing technology. Patients were categorized as an AA genotype or C allele carriers based on RORA rs72752802 polymorphism. SCN-seed functional connectivity (FC) was compared between the two groups and correlation with severity of DMV was analyzed. Finally, a mediation analysis was performed to further determine FC intermediary effects. We observed that rs72752802 was significantly associated with patients' DMV symptoms. C allele carriers of rs72752802 showed significantly decreased FC between the right SCN and right superior temporal gyrus (rSTG). This was also correlated with DMV symptoms. In addition, the rs72752802 SNP influenced DMV symptoms through intermediary effects of SCN-rSTG connectivity. The study presented here provides a neurological and genetic basis for understanding depressed patients experiencing DMV.
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Affiliation(s)
- Zhilu Chen
- Department of Psychiatry, the Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Shiwan Tao
- Department of Psychiatry, the Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Rongxin Zhu
- Department of Psychiatry, the Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Shui Tian
- School of Biological Sciences & Medical Engineering, Southeast University, Nanjing, 210096, China; Child Development and Learning Science, Key Laboratory of Ministry of Education, 210096, China
| | - Yurong Sun
- School of Biological Sciences & Medical Engineering, Southeast University, Nanjing, 210096, China; Child Development and Learning Science, Key Laboratory of Ministry of Education, 210096, China
| | - Huan Wang
- School of Biological Sciences & Medical Engineering, Southeast University, Nanjing, 210096, China; Child Development and Learning Science, Key Laboratory of Ministry of Education, 210096, China
| | - Rui Yan
- Department of Psychiatry, the Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China; Nanjing Brain Hospital, Medical School of Nanjing University, Nanjing, 210093, China
| | - Junneng Shao
- School of Biological Sciences & Medical Engineering, Southeast University, Nanjing, 210096, China; Child Development and Learning Science, Key Laboratory of Ministry of Education, 210096, China
| | - Yujie Zhang
- School of Biological Sciences & Medical Engineering, Southeast University, Nanjing, 210096, China; Child Development and Learning Science, Key Laboratory of Ministry of Education, 210096, China
| | - Jie Zhang
- Department of Psychiatry, the Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Zhijian Yao
- Department of Psychiatry, the Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China; School of Biological Sciences & Medical Engineering, Southeast University, Nanjing, 210096, China; Nanjing Brain Hospital, Medical School of Nanjing University, Nanjing, 210093, China.
| | - Qing Lu
- School of Biological Sciences & Medical Engineering, Southeast University, Nanjing, 210096, China; Child Development and Learning Science, Key Laboratory of Ministry of Education, 210096, China.
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40
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Schmitz U, Shah JS, Dhungel BP, Monteuuis G, Luu PL, Petrova V, Metierre C, Nair SS, Bailey CG, Saunders VA, Turhan AG, White DL, Branford S, Clark SJ, Hughes TP, Wong JJL, Rasko JE. Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients. Cancers (Basel) 2020; 12:cancers12123738. [PMID: 33322625 PMCID: PMC7764299 DOI: 10.3390/cancers12123738] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary This study provides new insights into the changing transcriptomic and epigenomic landscapes in chronic myeloid leukaemia (CML) patients who are receiving tyrosine kinase inhibitor (TKI) therapy (often life-long). Alternative splicing, vital for cellular homeostasis, is dysregulated in human cancers. Remarkably, we found abnormal splicing patterns despite molecular remission in peripheral blood cells of chronic-phase CML patients. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Abstract Vast transcriptomics and epigenomics changes are characteristic of human cancers, including leukaemia. At remission, we assume that these changes normalise so that omics-profiles resemble those of healthy individuals. However, an in-depth transcriptomic and epigenomic analysis of cancer remission has not been undertaken. A striking exemplar of targeted remission induction occurs in chronic myeloid leukaemia (CML) following tyrosine kinase inhibitor (TKI) therapy. Using RNA sequencing and whole-genome bisulfite sequencing, we profiled samples from chronic-phase CML patients at diagnosis and remission and compared these to healthy donors. Remarkably, our analyses revealed that abnormal splicing distinguishes remission samples from normal controls. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Most remarkable are the high intron retention (IR) levels that even exceed those observed in the diagnosis samples. Increased IR affects cell cycle regulators at diagnosis and splicing regulators at remission. We show that aberrant splicing in CML is associated with reduced expression of specific splicing factors, histone modifications and reduced DNA methylation. Our results provide novel insights into the changing transcriptomic and epigenomic landscapes of CML patients during remission. The conceptually unanticipated observation of widespread aberrant alternative splicing after remission induction warrants further exploration. These results have broad implications for studying CML relapse and treating minimal residual disease.
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Affiliation(s)
- Ulf Schmitz
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (U.S.); (V.P.)
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Jaynish S. Shah
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Bijay P. Dhungel
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Geoffray Monteuuis
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (P.-L.L.); (S.J.C.)
| | - Veronika Petrova
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (U.S.); (V.P.)
| | - Cynthia Metierre
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
| | - Shalima S. Nair
- Kinghorn Centre for Clinical Genomics Core Facility, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia;
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Charles G. Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Verity A. Saunders
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 50000, Australia; (V.A.S.); (D.L.W.)
| | - Ali G. Turhan
- APHP, Division of Hematology, Paris Sud University Hospitals and Inserm U935 INGESTEM Pluripotent Stem Cell Infrastructure 78 Rue du Général Leclerc, 94275 Le Kremlin Bicetre, France;
| | - Deborah L. White
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 50000, Australia; (V.A.S.); (D.L.W.)
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- Australasian Leukaemia and Lymphoma Group, Richmond, VIC 3121, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Susan Branford
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Susan J. Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (P.-L.L.); (S.J.C.)
- St Vincent’s Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Timothy P. Hughes
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- Australasian Leukaemia and Lymphoma Group, Richmond, VIC 3121, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
- Department of Haematology, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5001, Australia
| | - Justin J.-L. Wong
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E.J. Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- Correspondence: ; Tel.: +61-2-9565-6160
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Endoglin: An 'Accessory' Receptor Regulating Blood Cell Development and Inflammation. Int J Mol Sci 2020; 21:ijms21239247. [PMID: 33287465 PMCID: PMC7729465 DOI: 10.3390/ijms21239247] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Transforming growth factor-β1 (TGF-β1) is a pleiotropic factor sensed by most cells. It regulates a broad spectrum of cellular responses including hematopoiesis. In order to process TGF-β1-responses in time and space in an appropriate manner, there is a tight regulation of its signaling at diverse steps. The downstream signaling is mediated by type I and type II receptors and modulated by the ‘accessory’ receptor Endoglin also termed cluster of differentiation 105 (CD105). Endoglin was initially identified on pre-B leukemia cells but has received most attention due to its high expression on activated endothelial cells. In turn, Endoglin has been figured out as the causative factor for diseases associated with vascular dysfunction like hereditary hemorrhagic telangiectasia-1 (HHT-1), pre-eclampsia, and intrauterine growth restriction (IUPR). Because HHT patients often show signs of inflammation at vascular lesions, and loss of Endoglin in the myeloid lineage leads to spontaneous inflammation, it is speculated that Endoglin impacts inflammatory processes. In line, Endoglin is expressed on progenitor/precursor cells during hematopoiesis as well as on mature, differentiated cells of the innate and adaptive immune system. However, so far only pro-monocytes and macrophages have been in the focus of research, although Endoglin has been identified in many other immune system cell subsets. These findings imply a functional role of Endoglin in the maturation and function of immune cells. Aside the functional relevance of Endoglin in endothelial cells, CD105 is differentially expressed during hematopoiesis, arguing for a role of this receptor in the development of individual cell lineages. In addition, Endoglin expression is present on mature immune cells of the innate (i.e., macrophages and mast cells) and the adaptive (i.e., T-cells) immune system, further suggesting Endoglin as a factor that shapes immune responses. In this review, we summarize current knowledge on Endoglin expression and function in hematopoietic precursors and mature hematopoietic cells of different lineages.
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Monteuuis G, Schmitz U, Petrova V, Kearney PS, Rasko JEJ. Holding on to Junk Bonds: Intron Retention in Cancer and Therapy. Cancer Res 2020; 81:779-789. [PMID: 33046441 DOI: 10.1158/0008-5472.can-20-1943] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/16/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022]
Abstract
Intron retention (IR) in cancer was for a long time overlooked by the scientific community, as it was previously considered to be an artifact of a dysfunctional spliceosome. Technological advancements made in the last decade offer unique opportunities to explore the role of IR as a widespread phenomenon that contributes to the transcriptional diversity of many cancers. Numerous studies in cancer have shed light on dysregulation of cellular mechanisms that lead to aberrant and pathologic IR. IR is not merely a mechanism of gene regulation, but rather it can mediate cancer pathogenesis and therapeutic resistance in various human diseases. The burden of IR in cancer is governed by perturbations to mechanisms known to regulate this phenomenon and include epigenetic variation, mutations within the gene body, and splicing factor dysregulation. This review summarizes possible causes for aberrant IR and discusses the role of IR in therapy or as a consequence of disease treatment. As neoepitopes originating from retained introns can be presented on the cancer cell surface, the development of personalized cancer vaccines based on IR-derived neoepitopes should be considered. Ultimately, a deeper comprehension about the origins and consequences of aberrant IR may aid in the development of such personalized cancer vaccines.
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Affiliation(s)
- Geoffray Monteuuis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Sydney, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Veronika Petrova
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Sydney, Australia
| | - Padraic S Kearney
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia. .,Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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43
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Alharbi AB, Schmitz U, Marshall AD, Vanichkina D, Nagarajah R, Vellozzi M, Wong JJ, Bailey CG, Rasko JE. Ctcf haploinsufficiency mediates intron retention in a tissue-specific manner. RNA Biol 2020; 18:93-103. [PMID: 32816606 PMCID: PMC7834090 DOI: 10.1080/15476286.2020.1796052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
CTCF is a master regulator of gene transcription and chromatin organisation with occupancy at thousands of DNA target sites genome-wide. While CTCF is essential for cell survival, CTCF haploinsufficiency is associated with tumour development and hypermethylation. Increasing evidence demonstrates CTCF as a key player in several mechanisms regulating alternative splicing (AS), however, the genome-wide impact of Ctcf dosage on AS has not been investigated. We examined the effect of Ctcf haploinsufficiency on gene expression and AS in five tissues from Ctcf hemizygous (Ctcf+/-) mice. Reduced Ctcf levels caused distinct tissue-specific differences in gene expression and AS in all tissues. An increase in intron retention (IR) was observed in Ctcf+/- liver and kidney. In liver, this specifically impacted genes associated with cytoskeletal organisation, splicing and metabolism. Strikingly, most differentially retained introns were short, with a high GC content and enriched in Ctcf binding sites in their proximal upstream genomic region. This study provides new insights into the effects of CTCF haploinsufficiency on organ transcriptomes and the role of CTCF in AS regulation.
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Affiliation(s)
- Adel B Alharbi
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University , Makkah, Saudi Arabia
| | - Ulf Schmitz
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia
| | - Amy D Marshall
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Darya Vanichkina
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Sydney Informatics Hub, University of Sydney , Darlington, Australia
| | - Rajini Nagarajah
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Melissa Vellozzi
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Justin Jl Wong
- Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Charles G Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia
| | - John Ej Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Cell & Molecular Therapies, Royal Prince Alfred Hospital , Camperdown, Australia
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