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Liang X, Gong M, Wang Z, Wang J, Guo W, Cai A, Yang Z, Liu X, Xu F, Xiong W, Fu C, Wang X. LncRNA TubAR complexes with TUBB4A and TUBA1A to promote microtubule assembly and maintain myelination. Cell Discov 2024; 10:54. [PMID: 38769343 PMCID: PMC11106304 DOI: 10.1038/s41421-024-00667-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/13/2024] [Indexed: 05/22/2024] Open
Abstract
A long-standing hypothesis proposes that certain RNA(s) must exhibit structural roles in microtubule assembly. Here, we identify a long noncoding RNA (TubAR) that is highly expressed in cerebellum and forms RNA-protein complex with TUBB4A and TUBA1A, two tubulins clinically linked to cerebellar and myelination defects. TubAR knockdown in mouse cerebellum causes loss of oligodendrocytes and Purkinje cells, demyelination, and decreased locomotor activity. Biochemically, we establish the roles of TubAR in promoting TUBB4A-TUBA1A heterodimer formation and microtubule assembly. Intriguingly, different from the hypomyelination-causing mutations, the non-hypomyelination-causing mutation TUBB4A-R2G confers gain-of-function for an RNA-independent interaction with TUBA1A. Experimental use of R2G/A mutations restores TUBB4A-TUBA1A heterodimer formation, and rescues the neuronal cell death phenotype caused by TubAR knockdown. Together, we uncover TubAR as the long-elusive structural RNA for microtubule assembly and demonstrate how TubAR mediates microtubule assembly specifically from αβ-tubulin heterodimers, which is crucial for maintenance of cerebellar myelination and activity.
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Affiliation(s)
- Xiaolin Liang
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China
| | - Meng Gong
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhikai Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China
| | - Jie Wang
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Neuroscience and Brain Diseases, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Weiwei Guo
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Aoling Cai
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Zhenye Yang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China
| | - Xing Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China
| | - Fuqiang Xu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wei Xiong
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China.
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Chuanhai Fu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China.
| | - Xiangting Wang
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China.
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Dayal S, Chaubey D, Joshi DC, Ranmale S, Pillai B. Noncoding RNAs: Emerging regulators of behavioral complexity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1847. [PMID: 38702948 DOI: 10.1002/wrna.1847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 05/06/2024]
Abstract
The mammalian genome encodes thousands of non-coding RNAs (ncRNAs), ranging in size from about 20 nucleotides (microRNAs or miRNAs) to kilobases (long non-coding RNAs or lncRNAs). ncRNAs contribute to a layer of gene regulation that could explain the evolution of massive phenotypic complexity even as the number of protein-coding genes remains unaltered. We propose that low conservation, poor expression, and highly restricted spatiotemporal expression patterns-conventionally considered ncRNAs may affect behavior through direct, rapid, and often sustained regulation of gene expression at the transcriptional, post-transcriptional, or translational levels. Besides these direct roles, their effect during neurodevelopment may manifest as behavioral changes later in the organism's life, especially when exposed to environmental cues like stress and seasonal changes. The lncRNAs affect behavior through diverse mechanisms like sponging of miRNAs, recruitment of chromatin modifiers, and regulation of alternative splicing. We highlight the need for synthesis between rigorously designed behavioral paradigms in model organisms and the wide diversity of behaviors documented by ethologists through field studies on organisms exquisitely adapted to their environmental niche. Comparative genomics and the latest advancements in transcriptomics provide an unprecedented scope for merging field and lab studies on model and non-model organisms to shed light on the role of ncRNAs in driving the behavioral responses of individuals and groups. We touch upon the technical challenges and contentious issues that must be resolved to fully understand the role of ncRNAs in regulating complex behavioral traits. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Sanovar Dayal
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Divya Chaubey
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Dheeraj Chandra Joshi
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Samruddhi Ranmale
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Beena Pillai
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Göbel C, Schoof M, Holdhof D, Spohn M, Schüller U. SMARCA4 Loss and Mutated β-Catenin Induce Proliferative Lesions in the Murine Embryonic Cerebellum. J Neurosci 2024; 44:e1605232024. [PMID: 38383496 PMCID: PMC11007475 DOI: 10.1523/jneurosci.1605-23.2024] [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: 08/24/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Almost all medulloblastomas (MB) of the Wingless/Int-1 (WNT) type are characterized by hotspot mutations in CTNNB1, and mouse models have convincingly demonstrated the tumor-initiating role of these mutations. Additional alterations in SMARCA4 are detected in ∼20% of WNT MB, but their functional role is mostly unknown. We, therefore, amended previously described brain lipid binding protein (Blbp)-cre::Ctnnb1(ex3)fl/wt mice by the introduction of floxed Smarca4 alleles. Unexpectedly, mutated and thereby stabilized β-catenin on its own induced severe developmental phenotypes in male and female Blbp-cre::Ctnnb1(ex3)fl/wt mice in our hands, including a thinned cerebral cortex, hydrocephalus, missing cerebellar layering, and cell accumulations in the brainstem and cerebellum. An additional loss of SMARCA4 even resulted in prenatal death for most mice. Respective Blbp-cre::Ctnnb1(ex3)fl/wt::Smarca4fl/rec mutants (male and female) developed large proliferative lesions in the cerebellum evolving from E13.5 to E16.5. Histological and molecular analysis of these lesions by DNA methylation profiling and single-cell RNA sequencing suggested an origin in early undifferentiated SOX2-positive cerebellar progenitors. Furthermore, upregulated WNT signaling, altered actin/cytoskeleton organization, and reduced neuronal differentiation were evident in mutant cells. In vitro, cells harboring alterations in both Ctnnb1 and Smarca4 were negatively selected and did not show tumorigenic potential after transplantation in adult female recipient mice. However, in cerebellar explant cultures, mutant cells displayed significantly increased proliferation, suggesting an important role of the embryonic microenvironment in the development of lesions. Altogether, these results represent an important first step toward the unraveling of tumorigenic mechanisms induced by aberrant WNT signaling and SMARCA4 deficiency.
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Affiliation(s)
- Carolin Göbel
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Melanie Schoof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Michael Spohn
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
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Zhao J, Guo M, Yan Y, Wang Y, Zhao X, Yang J, Chen J, Chen C, Tang L, Zeng W, Liu Y, Qin M, Zhou Y, Xu L. The miR-7/EGFR axis controls the epithelial cell immunomodulation and regeneration and orchestrates the pathology in inflammatory bowel disease. J Adv Res 2024; 57:119-134. [PMID: 37094666 PMCID: PMC10918346 DOI: 10.1016/j.jare.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
INTRODUCTION The epithelial immunomodulation and regeneration are intrinsic critical events against inflammatory bowel disease (IBD). MiR-7 is well documented as a promising regulator in the development of various diseases including inflammatory diseases. OBJECTIVES This study aimed to assess the effect of miR-7 in intestinal epithelial cells (IECs) in IBD. METHODS MiR-7def mice were given dextran sulfate sodium (DSS) to induce enteritis model. The infiltration of inflammatory cells was measured by FCM and immunofluorescence assay. 5'deletion assay and EMSA assays were performed to study the regulatory mechanism of miR-7 expression in IECs. The inflammatory signals and the targets of miR-7 were analyzed by RNA-seq and FISH assay. IECs were isolated from miR-7def, miR-7oe and WT mice to identify the immunomodulation and regeneration capacity. IEC-specific miR-7 silencing expression vector was designed and administered by the tail vein into murine DSS-induced enteritis model to evaluate the pathological lesions of IBD. RESULTS We found miR-7 deficiency improved the pathological lesions of DSS-induced murine enteritis model, accompanied by elevated proliferation and enhanced transduction of NF-κB/AKT/ERK signals in colonic IECs, as well as decreased local infiltration of inflammatory cells. MiR-7 was dominantly upregulated in colonic IECs in colitis. Moreover, the transcription of pre-miR-7a-1, orchestrated by transcription factor C/EBPα, was a main resource of mature miR-7 in IECs. As for the mechanism, EGFR, a miR-7 target gene, was downregulated in colonic IECs in colitis model and Crohn's disease patients. Furthermore, miR-7 also controlled the proliferation and inflammatory-cytokine secretion of IECs in response to inflammatory-signals through EGFR/NF-κB/AKT/ERK pathway. Finally, IEC-specific miR-7 silencing promoted the proliferation and transduction of NF-κB pathway in IECs and alleviated the pathological damage of colitis. CONCLUSION Our results present the unknown role of miR-7/EGFR axis in IEC immunomodulation and regeneration in IBD and might provide clues for the application of miRNA-based therapeutic strategies in colonic diseases.
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Affiliation(s)
- Juanjuan Zhao
- School of Medicine, Guizhou University, Guiyang 550025, Guizhou, China; Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Mengmeng Guo
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Yaping Yan
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Ya Wang
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Xu Zhao
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Jing Yang
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Jing Chen
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Chao Chen
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Lin Tang
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Wenhuan Zeng
- Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Yiting Liu
- Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Ming Qin
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Ya Zhou
- Department of Medical Physics, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China
| | - Lin Xu
- School of Medicine, Guizhou University, Guiyang 550025, Guizhou, China; Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou Province, Guizhou, Zunyi 563000, China; Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, Guizhou 563000, China.
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Lu L, Shi Y, Wei B, Li W, Yu X, Zhao Y, Yu D, Sun M. YTHDF3 modulates the Cbln1 level by recruiting BTG2 and is implicated in the impaired cognition of prenatal hypoxia offspring. iScience 2024; 27:108703. [PMID: 38205248 PMCID: PMC10776956 DOI: 10.1016/j.isci.2023.108703] [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: 04/13/2023] [Revised: 09/22/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
The "Fetal Origins of Adult Disease (FOAD)" hypothesis holds that adverse factors during pregnancy can increase the risk of chronic diseases in offspring. Here, we investigated the effects of prenatal hypoxia (PH) on brain structure and function in adult offspring and explored the role of the N6-methyladenosine (m6A) pathway. The results suggest that abnormal cognition in PH offspring may be related to the dysregulation of the m6A pathway, specifically increased levels of YTHDF3 in the hippocampus. YTHDF3 interacts with BTG2 and is involved in the decay of Cbln1 mRNA, leading to the down-regulation of Cbln1 expression. Deficiency of Cbln1 may contribute to abnormal synaptic function, which in turn causes cognitive impairment in PH offspring. This study provides a scientific clues for understanding the mechanisms of impaired cognition in PH offspring and provides a theoretical basis for the treatment of cognitive impairment in offspring exposed to PH.
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Affiliation(s)
- Likui Lu
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yajun Shi
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China
| | - Bin Wei
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China
| | - Weisheng Li
- Department of Gynaecology, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, China
| | - Xi Yu
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China
| | - Yan Zhao
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China
| | - Dongyi Yu
- Center for Medical Genetics and Prenatal Diagnosis, Key Laboratory of Birth Defect Prevention and Genetic, Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
| | - Miao Sun
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China
- Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu Province, China
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Li X, Zhao Y, Kong H, Song C, Liu J, Xia J. Identification of region-specific splicing QTLs in human hippocampal tissue and its distinctive role in brain disorders. iScience 2023; 26:107958. [PMID: 37810239 PMCID: PMC10558811 DOI: 10.1016/j.isci.2023.107958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/28/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Alternative splicing (AS) regulation has an essential role in complex diseases. However, the AS profiles in the hippocampal (HIPPO) region of human brain are underexplored. Here, we investigated cis-acting sQTLs of HIPPO region in 264 samples and identified thousands of significant sQTLs. By enrichment analysis and functional characterization of these sQTLs, we found that the HIPPO sQTLs were enriched among histone-marked regions, transcription factors binding sites, RNA binding proteins sites, and brain disorders-associated loci. Comparative analyses with the dorsolateral prefrontal cortex revealed the importance of AS regulation in HIPPO (rg = 0.87). Furthermore, we performed a transcriptome-wide association study of Alzheimer's disease and identified 16 significant genes whose genetically regulated splicing levels may have a causal role in Alzheimer. Overall, our study improves our knowledge of the transcriptome gene regulation in the HIPPO region and provides novel insights into elucidating the pathogenesis of potential genes associated with brain disorders.
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Affiliation(s)
- Xiaoyan Li
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Yiran Zhao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Hui Kong
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Chengcheng Song
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Jie Liu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Junfeng Xia
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
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Fan T, Zhu M, Muhammad S, Xiao C, Li S, Tian H, Liu Y, Xue L, Zheng B, Li C, He J. H3K4me3-related lncRNAs signature and comprehensive analysis of H3K4me3 regulating tumor immunity in lung adenocarcinoma. Respir Res 2023; 24:122. [PMID: 37131252 PMCID: PMC10155324 DOI: 10.1186/s12931-023-02418-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/08/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUD The role of epigenetic modifications in tumorigenesis has been widely reported. However, the role and mechanism of H3K4me3 modification in lung adenocarcinoma (LUAD) are rarely reported systematically. We, therefore, sought to analyze the characteristics of LUAD associated with H3K4me3 modification, build an H3K4me3-lncRNAs score model to predict the prognosis of patients with LUAD and clarify the potential value of H3K4me3 in immunotherapy of LUAD. METHODS We evaluated H3K4me3-lncRNA patterns and H3K4me3-lncRNA scores of 477 LUAD samples based on 53 lncRNAs closely correlated to H3K4me3 regulators and comprehensive analyzed the role of these patterns in tumorigenesis and tumor immunity. Using Gene set variation analysis (GSVA), we systematically evaluated the H3K4me3 level of every sample and deeply analyzed the effect of H3K4me3 on the prognosis of LUAD. In addition, we included two independent immunotherapy cohorts to study the impact of high H3K4me3 score on the prognosis of patients. We also used an independent cohort with 52 matched paraffin specimens of LUAD to verify the impact of high H3K3me3 expression on the prognosis of patients. RESULTS We identified three H3K4me3-lncRNA patterns that exhibited specific immune characteristics. Characterized by immunosuppressive and increased TGFβ-mediated epithelial-mesenchymal transition (EMT), patients with high H3K4me3-lncRNA score had a poor overall survival and decreased H3K4me3 score. H3K4me3 score was significantly positively correlated with CD4+T-cell and CD8+T-cell activation, programmed cell death and immune checkpoints (ICs) expression, and was negatively correlated with MYC pathway, TP53 pathway, and cell proliferation. Patients with high H3K4me3 score showed elevated expression of ICs, potentiated CD4 T-cell and CD8 T-cell activation, increased programmed cell death, and suppressed cell proliferation and TGFβ-mediated EMT. Patients with high H3K4me3 score and high expression of CTLA4, ICOS, TIGIT, PDCD1LG2, IDO1, CD274, PDCD1, LAG3, or HAVCR2 had the best survival advantage. Two independent immunotherapy cohorts verified that patients with high H3K4me3 score showed an increased inflamed tumor microenvironment (TME) phenotype and enhanced anti-PD-1/L1 immunotherapy response. Immunohistochemistry (IHC) data from 52 matched paraffin specimens of LUAD confirmed that the protein level of H3K4me3 in tumor was significantly lower than that of paracancerous tissues and H3K4me3 brought significant survival benefits to patients with LUAD. CONCLUSIONS We build an H3K4me3-lncRNAs score model to predict the prognosis of patients with LUAD. More importantly, this study revealed characteristics of H3K4me3 modification in LUAD and clarified the important potential role of H3K4me3 on tumor immunotherapy and patients' survival.
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Affiliation(s)
- Tao Fan
- Department of Thoracic Surgery, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Mingchuang Zhu
- Department of Thoracic Surgery, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shan Muhammad
- Department of Thoracic Surgery, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chu Xiao
- Department of Thoracic Surgery, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shuofeng Li
- Department of Colorectal Surgery, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - He Tian
- Department of Thoracic Surgery, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yu Liu
- Department of Thoracic Surgery, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Liyan Xue
- Department of Pathology, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Bo Zheng
- Department of Pathology, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Chen HS, Wang J, Li HH, Wang X, Zhang SQ, Deng T, Li YK, Zou RS, Wang HJ, Zhu R, Xie WL, Zhao G, Wang F, Chen JG. Long noncoding RNA Gm2694 drives depressive-like behaviors in male mice by interacting with GRP78 to disrupt endoplasmic reticulum homeostasis. SCIENCE ADVANCES 2022; 8:eabn2496. [PMID: 36459549 PMCID: PMC10936050 DOI: 10.1126/sciadv.abn2496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 10/18/2022] [Indexed: 06/17/2023]
Abstract
Long noncoding RNAs (lncRNAs) are involved in various biological processes and implicated in the regulation of neuronal activity, but the potential role of lncRNAs in depression remains largely unknown. Here, we identified that lncRNA Gm2694 was increased in the medial prefrontal cortex (mPFC) of male mice subjected to chronic social defeat stress (CSDS). The down-regulation of Gm2694 in the mPFC alleviated CSDS-induced depressive-like behaviors through enhanced excitatory synaptic transmission. Furthermore, we found that Gm2694 preferentially interacted with the carboxyl-terminal domain of 78-kilodalton glucose-regulated protein (GRP78), which abrogated GRP78 function and disrupted endoplasmic reticulum homeostasis, resulting in a reduction of the surface expression of AMPA receptors (AMPARs). Overexpression of GRP78 in the mPFC promoted the surface expression of AMPARs and attenuated the CSDS-induced depressive-like behaviors of mice. Together, our results unraveled a previously unknown role of Gm2694 in regulating endoplasmic reticulum homeostasis and excitatory synaptic transmission in depression.
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Affiliation(s)
- Hong-Sheng Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
- The Research Center for Depression, Tongji Medical College, Huazhong University of Science, 430030 Wuhan, China
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, 430030 Wuhan, China
| | - Ji Wang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Hou-Hong Li
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Xiao Wang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Shao-Qi Zhang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Tan Deng
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Yu-Ke Li
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Ruo-Si Zou
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Hua-Jie Wang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Rui Zhu
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Wen-Long Xie
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Gang Zhao
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022 Wuhan, China
| | - Fang Wang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
- The Research Center for Depression, Tongji Medical College, Huazhong University of Science, 430030 Wuhan, China
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, 430030 Wuhan, China
- The Key Laboratory of Neurological Diseases (HUST), Ministry of Education of China, 430030 Wuhan, China
- Laboratory of Neuropsychiatric Diseases, The Institute of Brain Research, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Jian-Guo Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
- The Research Center for Depression, Tongji Medical College, Huazhong University of Science, 430030 Wuhan, China
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, 430030 Wuhan, China
- The Key Laboratory of Neurological Diseases (HUST), Ministry of Education of China, 430030 Wuhan, China
- Laboratory of Neuropsychiatric Diseases, The Institute of Brain Research, Huazhong University of Science and Technology, 430030 Wuhan, China
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Konina D, Sparber P, Viakhireva I, Filatova A, Skoblov M. Investigation of LINC00493/SMIM26 Gene Suggests Its Dual Functioning at mRNA and Protein Level. Int J Mol Sci 2021; 22:ijms22168477. [PMID: 34445188 PMCID: PMC8395196 DOI: 10.3390/ijms22168477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
The amount of human long noncoding RNA (lncRNA) genes is comparable to protein-coding; however, only a small number of lncRNAs are functionally annotated. Previously, it was shown that lncRNAs can participate in many key cellular processes, including regulation of gene expression at transcriptional and post-transcriptional levels. The lncRNA genes can contain small open reading frames (sORFs), and recent studies demonstrated that some of the resulting short proteins could play an important biological role. In the present study, we investigate the widely expressed lncRNA LINC00493. We determine the structure of the LINC00493 transcript, its cell localization and influence on cell physiology. Our data demonstrate that LINC00493 has an influence on cell viability in a cell-type-specific manner. Furthermore, it was recently shown that LINC00493 has a sORF that is translated into small protein SMIM26. The results of our knockdown and overexpression experiments suggest that both LINC00493/SMIM26 transcript and protein affect cell viability, but in the opposite manner.
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Affiliation(s)
- Daria Konina
- Moscow Institute of Physics and Technology, Phystech School of Biological and Medical Physics, 141701 Dolgoprudny, Russia
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
- Correspondence: (D.K.); (A.F.)
| | - Peter Sparber
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
| | - Iuliia Viakhireva
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
| | - Alexandra Filatova
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
- Correspondence: (D.K.); (A.F.)
| | - Mikhail Skoblov
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
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