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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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Qi C, Ren H, Fan Y. Microglia specific alternative splicing alterations in multiple sclerosis. Aging (Albany NY) 2024; 16:11656-11667. [PMID: 39115871 PMCID: PMC11346782 DOI: 10.18632/aging.206045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 07/17/2024] [Indexed: 08/22/2024]
Abstract
Several aberrant alternative splicing (AS) events and their regulatory mechanisms are widely recognized in multiple sclerosis (MS). Yet the cell-type specific AS events have not been extensively examined. Here we assessed the diversity of AS events using web-based RNA-seq data of sorted CD15-CD11b+ microglia in white matter (WM) region from 10 patients with MS and 11 control subjects. The GSE111972 dataset was downloaded from GEO and ENA databases, aligned to the GRCh38 reference genome from ENSEMBL via STAR. rMATS was used to assess five types of AS events, alternative 3'SS (A3SS), alternative 5'SS (A5SS), skipped exon (SE), retained intron (RI) and mutually exclusive exons (MXE), followed by visualizing with rmats2sashimiplot and maser. Differential genes or transcripts were analyzed using the limma R package. Gene ontology (GO) analysis was performed with the clusterProfiler R package. 42,663 raw counts of AS events were identified and 132 significant AS events were retained based on the filtered criteria: 1) average coverage >10 and 2) delta percent spliced in (ΔPSI) >0.1. SE was the most common AS event (36.36%), followed by MXE events (32.58%), and RI (18.94%). Genes related to telomere maintenance and organization primarily underwent SE splicing, while genes associated with protein folding and mitochondrion organization were predominantly spliced in the MXE pattern. Conversely, genes experiencing RI were enriched in immune response and immunoglobulin production. In conclusion, we identified microglia-specific AS changes in the white matter of MS patients, which may shed light on novel pathological mechanisms underlying MS.
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Affiliation(s)
- Caiyun Qi
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Honglei Ren
- Department of Neurology, Tianjin Neurological Institute, Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Tianjin Medical University General Hospital, Tianjin, China
| | - Yong Fan
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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3
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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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Northrup V, Perez LJ, Edgett BA, Karakach T, Simpson JA, Brunt KR. Intron retention is a mechanism of erythropoietin regulation in brain cell models. Gene 2024; 898:148099. [PMID: 38128788 DOI: 10.1016/j.gene.2023.148099] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Intron retention is a mechanism of post-transcriptional gene regulation, including genes involved in erythropoiesis. Erythropoietin (EPO) is a hormone without evidence of intracellular vesicle storage that regulates erythropoiesis. We hypothesize that EPO uses intron retention as a mechanism of post-transcriptional regulation in response to hypoxia and ischemia. Cell models of hypoxia and ischemia for kidney, liver, and brain cells were examined for intron retention by real time quantitative PCR. EPO expression increased in most cells except for blood brain barrier and liver cells. The intron retained transcript ratio decreased in brain cells, except for Astrocytes, but showed no change in kidney or liver after 24 h of ischemia. The shift in intron ratio was maintained when using poly (A) enriched cDNA, suggesting that intron retention is not due to immature transcripts. The expression of EPO was elevated at variable time points amongst cell models with the intron ratio also changing over a time course of 2 to 16 h after ischemia. We conclude that intron retention is a mechanism regulating EPO expression in response to ischemia in a tissue specific manner.
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Affiliation(s)
- Victoria Northrup
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; Dalhousie Medicine New Brunswick, Saint John, New Brunswick, Canada; IMPART investigator team Canada
| | - Lester J Perez
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; Dalhousie Medicine New Brunswick, Saint John, New Brunswick, Canada; IMPART investigator team Canada
| | - Brittany A Edgett
- Department of Kinesiology, University of Calgary, Calgary, Alberta, Canada; IMPART investigator team Canada
| | - Tobias Karakach
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; IMPART investigator team Canada
| | - Jeremy A Simpson
- Department of Human and Nutritional Science, University of Guelph, Guelph, Ontario, Canada; IMPART investigator team Canada
| | - Keith R Brunt
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; Dalhousie Medicine New Brunswick, Saint John, New Brunswick, Canada; IMPART investigator team Canada.
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5
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Brase L, You SF, D'Oliveira Albanus R, Del-Aguila JL, Dai Y, Novotny BC, Soriano-Tarraga C, Dykstra T, Fernandez MV, Budde JP, Bergmann K, Morris JC, Bateman RJ, Perrin RJ, McDade E, Xiong C, Goate AM, Farlow M, Sutherland GT, Kipnis J, Karch CM, Benitez BA, Harari O. Single-nucleus RNA-sequencing of autosomal dominant Alzheimer disease and risk variant carriers. Nat Commun 2023; 14:2314. [PMID: 37085492 PMCID: PMC10121712 DOI: 10.1038/s41467-023-37437-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/15/2023] [Indexed: 04/23/2023] Open
Abstract
Genetic studies of Alzheimer disease (AD) have prioritized variants in genes related to the amyloid cascade, lipid metabolism, and neuroimmune modulation. However, the cell-specific effect of variants in these genes is not fully understood. Here, we perform single-nucleus RNA-sequencing (snRNA-seq) on nearly 300,000 nuclei from the parietal cortex of AD autosomal dominant (APP and PSEN1) and risk-modifying variant (APOE, TREM2 and MS4A) carriers. Within individual cell types, we capture genes commonly dysregulated across variant groups. However, specific transcriptional states are more prevalent within variant carriers. TREM2 oligodendrocytes show a dysregulated autophagy-lysosomal pathway, MS4A microglia have dysregulated complement cascade genes, and APOEε4 inhibitory neurons display signs of ferroptosis. All cell types have enriched states in autosomal dominant carriers. We leverage differential expression and single-nucleus ATAC-seq to map GWAS signals to effector cell types including the NCK2 signal to neurons in addition to the initially proposed microglia. Overall, our results provide insights into the transcriptional diversity resulting from AD genetic architecture and cellular heterogeneity. The data can be explored on the online browser ( http://web.hararilab.org/SNARE/ ).
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Affiliation(s)
- Logan Brase
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Shih-Feng You
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Ricardo D'Oliveira Albanus
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Yaoyi Dai
- Baylor College of Medicine, Houston, TX, USA
| | - Brenna C Novotny
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Carolina Soriano-Tarraga
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Taitea Dykstra
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - John P Budde
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - John C Morris
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Randall J Bateman
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Richard J Perrin
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Eric McDade
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Chengjie Xiong
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Alison M Goate
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martin Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Greg T Sutherland
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Jonathan Kipnis
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Bruno A Benitez
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
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Zuniga G, Levy S, Ramirez P, Mange JD, Gonzalez E, Gamez M, Frost B. Tau-induced deficits in nonsense-mediated mRNA decay contribute to neurodegeneration. Alzheimers Dement 2023; 19:405-420. [PMID: 35416419 PMCID: PMC9673995 DOI: 10.1002/alz.12653] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 01/26/2022] [Accepted: 02/17/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION While brains of patients with Alzheimer's disease and related tauopathies have evidence of altered RNA processing, we lack a mechanistic understanding of how altered RNA processing arises in these disorders and if such changes are causally linked to neurodegeneration. METHODS Using Drosophila melanogaster models of tauopathy, we find that overall activity of nonsense-mediated mRNA decay (NMD), a key RNA quality-control mechanism, is reduced. Genetic manipulation of NMD machinery significantly modifies tau-induced neurotoxicity, suggesting that deficits in NMD are causally linked to neurodegeneration. Mechanistically, we find that deficits in NMD are a consequence of aberrant RNA export and RNA accumulation within nuclear envelope invaginations in tauopathy. We identify a pharmacological activator of NMD that suppresses neurodegeneration in tau transgenic Drosophila, indicating that tau-induced deficits in RNA quality control are druggable. DISCUSSION Our studies suggest that NMD activators should be explored for their potential therapeutic value to patients with tauopathies.
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Affiliation(s)
- Gabrielle Zuniga
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Simon Levy
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Jasmine De Mange
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Elias Gonzalez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Maria Gamez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
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7
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David JK, Maden SK, Wood MA, Thompson RF, Nellore A. Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads. Genome Biol 2022; 23:240. [PMID: 36369064 PMCID: PMC9652823 DOI: 10.1186/s13059-022-02789-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is complicated by overlapping genes and transcripts as well as the presence of unprocessed or partially processed RNAs. RESULTS We compared introns detected by 8 tools using short RNA-seq reads with introns observed in long RNA-seq reads from the same biological specimens. We found significant disagreement among tools (Fleiss' [Formula: see text]) such that 47.7% of all detected intron retentions were not called by more than one tool. We also observed poor performance of all tools, with none achieving an F1-score greater than 0.26, and qualitatively different behaviors between general-purpose alternative splicing detection tools and tools confined to retained intron detection. CONCLUSIONS Short-read tools detect intron retention with poor recall and precision, calling into question the completeness and validity of a large percentage of putatively retained introns called by commonly used methods.
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Affiliation(s)
- Julianne K. David
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,Present Address: Base5 Genomics, Inc., Mountain View, CA USA
| | - Sean K. Maden
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,grid.21107.350000 0001 2171 9311Present Address: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Mary A. Wood
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.429936.30000 0004 5914 210XPortland VA Research Foundation, Portland, OR USA ,Present Address: Phase Genomics, Inc., Seattle, WA USA
| | - Reid F. Thompson
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,grid.484322.bDivision of Hospital and Specialty Medicine, VA Portland Healthcare System, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Radiation Medicine, Oregon Health & Science University, Portland, OR USA
| | - Abhinav Nellore
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Surgery, Oregon Health & Science University, Portland, OR USA
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8
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Santiago JA, Quinn JP, Potashkin JA. Sex-specific transcriptional rewiring in the brain of Alzheimer’s disease patients. Front Aging Neurosci 2022; 14:1009368. [PMID: 36389068 PMCID: PMC9659968 DOI: 10.3389/fnagi.2022.1009368] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/11/2022] [Indexed: 11/28/2022] Open
Abstract
Sex-specific differences may contribute to Alzheimer’s disease (AD) development. AD is more prevalent in women worldwide, and female sex has been suggested as a disease risk factor. Nevertheless, the molecular mechanisms underlying sex-biased differences in AD remain poorly characterized. To this end, we analyzed the transcriptional changes in the entorhinal cortex of symptomatic and asymptomatic AD patients stratified by sex. Co-expression network analysis implemented by SWItchMiner software identified sex-specific signatures of switch genes responsible for drastic transcriptional changes in the brain of AD and asymptomatic AD individuals. Pathway analysis of the switch genes revealed that morphine addiction, retrograde endocannabinoid signaling, and autophagy are associated with both females with AD (F-AD) and males with (M-AD). In contrast, nicotine addiction, cell adhesion molecules, oxytocin signaling, adipocytokine signaling, prolactin signaling, and alcoholism are uniquely associated with M-AD. Similarly, some of the unique pathways associated with F-AD switch genes are viral myocarditis, Hippo signaling pathway, endometrial cancer, insulin signaling, and PI3K-AKT signaling. Together these results reveal that there are many sex-specific pathways that may lead to AD. Approximately 20–30% of the elderly have an accumulation of amyloid beta in the brain, but show no cognitive deficit. Asymptomatic females (F-asymAD) and males (M-asymAD) both shared dysregulation of endocytosis. In contrast, pathways uniquely associated with F-asymAD switch genes are insulin secretion, progesterone-mediated oocyte maturation, axon guidance, renal cell carcinoma, and ErbB signaling pathway. Similarly, pathways uniquely associated with M-asymAD switch genes are fluid shear stress and atherosclerosis, FcγR mediated phagocytosis, and proteoglycans in cancer. These results reveal for the first time unique pathways associated with either disease progression or cognitive resilience in asymptomatic individuals. Additionally, we identified numerous sex-specific transcription factors and potential neurotoxic chemicals that may be involved in the pathogenesis of AD. Together these results reveal likely molecular drivers of sex differences in the brain of AD patients. Future molecular studies dissecting the functional role of these switch genes in driving sex differences in AD are warranted.
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Affiliation(s)
| | | | - Judith A. Potashkin
- Cellular and Molecular Pharmacology Department, Center for Neurodegenerative Diseases and Therapeutics, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
- *Correspondence: Judith A. Potashkin,
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9
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Mohammadi S, Mahmoudi J, Farajdokht F, Asadi M, Pirsarabi P, Kazeminiaei SF, Parvizpour S, Sadigh-Eteghad S. Polymorphisms of nicotinic acetylcholine receptors in Alzheimer’s disease: a systematic review and data analysis. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00357-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Objective
This study was conducted to accomplish a better insight into the impact of single nucleotide polymorphisms (SNPs) of nicotinic acetylcholine receptors (nAChR) at the risk of Alzheimer’s disease (AD) and their possible pathogenicity.
Methods
We carried out a systemic review of accessible studies. The case–control studies were assessed by an electronic search of international and local databases to identify relevant studies on SNPs relating to nAChR genes in AD. Two reviewers evaluated the inclusion/exclusion criteria, summarized, and analyzed the extracted data. We used odds ratios (ORs) with 95% confidence intervals (CIs) for reporting our data. Online databases were checked for possible pathogenicity of statistically significant SNPs. Also, online databases, including NCBI, NIH, ClinVar, RegulomeDB, and Ensemble, were used to analyze and identify structure and function, DNA features, and flank sequencing in SNPs.
Results
Among all collected SNPs, rs4779978 and rs1827294 on CHRNA7, rs1044394 on CHRNA4, and rs1127314 on CHRNB2 showed statistically significant between AD cases and controls.
Conclusions
Some SNPs from the reviewed reports show evidence supporting their possible involvement in AD pathology. However, more comprehensive studies are necessary to identify the exact correlation and their role on the pathogenicity of disease.
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Truncated Tau caused by intron retention is enriched in Alzheimer's disease cortex and exhibits altered biochemical properties. Proc Natl Acad Sci U S A 2022; 119:e2204179119. [PMID: 36067305 PMCID: PMC9477417 DOI: 10.1073/pnas.2204179119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by the accumulation of amyloid-β plaques and Tau tangles in brain tissues. Recent studies indicate that aberrant splicing and increased level of intron retention is linked to AD pathogenesis. Bioinformatic analysis revealed increased retention of intron 11 at the Tau gene in AD female dorsal lateral prefrontal cortex as compared to healthy controls, an observation validated by quantitative polymerase chain reaction using different brain tissues. Retention of intron 11 introduces a premature stop codon, resulting in the production of truncated Tau11i protein. Probing with customized antibodies designed against amino acids encoded by intron 11 showed that Tau11i protein is more enriched in AD hippocampus, amygdala, parietal, temporal, and frontal lobe than in healthy controls. This indicates that Tau messenger RNA with the retained intron is translated in vivo instead of being subjected to nonsense-mediated decay. Compared to full-length Tau441 isoform, ectopically expressed Tau11i forms higher molecular weight species, is enriched in Sarkosyl-insoluble fraction, and exhibits greater protein stability in cycloheximide assay. Stably expressed Tau11i also shows weaker colocalization with α-tubulin of microtubule network in human mature cortical neurons as compared to Tau441. Endogenous Tau11i is enriched in Sarkosyl-insoluble fraction in AD hippocampus and forms aggregates that colocalize weakly with Tau4R fibril-like structure in AD temporal lobe. The elevated level of Tau11i protein in AD brain tissues tested, coupled with biochemical properties resembling pathological Tau species suggest that retention of intron 11 of Tau gene might be an early biomarker of AD pathology.
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11
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Li HD, Lin CX, Zheng J. GTFtools: a software package for analyzing various features of gene models. Bioinformatics 2022; 38:4806-4808. [PMID: 36000853 DOI: 10.1093/bioinformatics/btac561] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 07/30/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Gene-centric bioinformatics studies frequently involve calculation or extraction of various features of genes such as splice sites, promoters, independent introns, and untranslated regions (UTRs) through manipulation of gene models. Gene models are often annotated in gene transfer format (GTF) files. The features are essential for subsequent analysis such as intron retention detection, DNA-binding site identification, and computing splicing strength of splice sites. Some features such as independent introns and splice sites are not provided in existing resources including the commonly used BioMart database. A package that implements and integrates functions to analyze various features of genes will greatly ease routine analysis for related bioinformatics studies. However, to the best of our knowledge, such a package is not available yet. RESULTS In this work, we introduce GTFtools, a stand-alone command-line software that provides a set of functions to calculate various gene features, including splice sites, independent introns, transcription start sites (TSS)-flanking regions, UTRs, isoform coordination and length, different types of gene lengths, etc. It takes the ENSEMBL or GENCODE GTF files as input, and can be applied to both human and non-human gene models like the lab mouse. We compare the utilities of GTFtools with those of two related tools: Bedtools and BioMart. GTFtools is implemented in Python and not dependent on any third-party software, making it very easy to install and use. AVAILABILITY GTFtools is freely available at www.genemine.org/gtftools.php as well as pyPI and Bioconda.
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Affiliation(s)
- Hong-Dong Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China.,Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China
| | - Cui-Xiang Lin
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China.,Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China
| | - Jiantao Zheng
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China.,Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China
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12
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Distinct microglia alternative splicing in Alzheimer's disease. Aging (Albany NY) 2022; 14:6554-6566. [PMID: 36006403 PMCID: PMC9467408 DOI: 10.18632/aging.204223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022]
Abstract
Numerous alternative splicing (AS) events have been documented in Alzheimer's disease (AD). However, cell type-specific AS analysis is still lacking. We described AS events in the hippocampal microglia sorted by CD45 and CD11b from Aβ precursor protein (APP) and non-transgenic (Ntg) mice. GSE171195 dataset was downloaded from GEO database, aligned to GRCm39 genome. Skipped exon (SE), alternative 3'SS (A3SS), retained intron (RI), alternative 5'SS (A5SS), and mutually exclusive exons (MXE) were evaluated using rMATS and maser. Differential expressed genes or transcripts were analyzed via limma. Gene ontology and correlation analyses were performed with clusterProfiler and ggcorrplot R packages. 36,340 raw counts of AS were identified, and 95 significant AS events were eventually selected with strict criteria: (1) average coverage >5; (2) delta percent spliced in >0.1. SE was the most common AS events (68.42%), followed by A3SS and RI. Autophagy genes were mainly spliced in SE events, actin depolymerization genes spliced in A3SS events, while synaptic plasticity related genes were mainly spliced in RI pattern. These significant AS events may be regulated by dysregulated splicing factors in AD. In conclusion, we revealed microglia specific AS events in AD, and our study provides novel pathological mechanisms in the pathogenesis of AD.
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13
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Song L, Chen J, Lo CYZ, Guo Q, Feng J, Zhao XM. Impaired type I interferon signaling activity implicated in the peripheral blood transcriptome of preclinical Alzheimer's disease. EBioMedicine 2022; 82:104175. [PMID: 35863293 PMCID: PMC9304603 DOI: 10.1016/j.ebiom.2022.104175] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022] Open
Abstract
Background Subjective or objective subtle cognitive decline (SCD) is considered the preclinical manifestation of Alzheimer's disease (AD), which is a potentially crucial window for preventing or delaying the progression of the disease. Methods To explore the potential mechanism of disease progression and identify relevant biomarkers, we comprehensively assessed the peripheral blood transcriptomic alterations in SCD, covering lncRNA, mRNA, and miRNA. Findings Dysregulated protein-coding mRNA at both gene and isoform levels implicated impairment in the type I interferon signaling pathway in SCD. Specifically, this pathway was regulated by the transcription factor STAT1 and ncRNAs NRIR and has-miR-146a-5p. The miRNA-mRNA-lncRNA co-expression network revealed hub genes for the interferon module. Individuals with lower interferon signaling activity and lower expression of a hub gene STAT1 exhibited a higher conversion rate to mild cognitive impairment (MCI). Interpretation Our findings illustrated the down-regulation of interferon signaling activity would potentially increase the risk of disease progression and thus serve as a pre-disease biomarker. Funding This work was partly supported by National Key R&D Program of China (2020YFA0712403), National Natural Science Foundation of China (61932008), Shanghai Municipal Science and Technology Major Project (2018SHZDZX01), the 111 Project (No. B18015) of China, Greater Bay Area Institute of Precision Medicine (Guangzhou) (Grand No. IPM21C008), Natural Science Foundation of Shanghai (21ZR1403200), and Shanghai Center for Brain Science and Brain-Inspired Technology.
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14
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Lu Y, Yue D, Xie J, Cheng L, Wang X. Ontology Specific Alternative Splicing Changes in Alzheimer’s Disease. Front Genet 2022; 13:926049. [PMID: 35774499 PMCID: PMC9237535 DOI: 10.3389/fgene.2022.926049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/11/2022] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing (AS) is a common phenomenon and correlates with aging and aging-related disorders including Alzheimer’s disease (AD). We aimed to systematically characterize AS changes in the cerebral cortex of 9-month-old APP/PS1 mice. The GSE132177 dataset was downloaded from GEO and ENA databases, aligned to the GRCm39 reference genome from ENSEMBL via STAR. Alternative 3′SS (A3SS), alternative 5′SS (A5SS), skipped exon (SE), retained intron (RI), and mutually exclusive exons (MXE) AS events were evaluated using rMATS, rmats2sashimiplot, and maser. Differential genes or transcripts were analyzed using the limma R package. Gene ontology analysis was performed with the clusterProfiler R package. A total of 60,705 raw counts of AS were identified, and 113 significant AS events were finally selected in accordance with the selection criteria: 1) average coverage >10 and 2) delta percent spliced in (ΔPSI) >0.1. SE was the most abundant AS event (61.95%), and RI was the second most abundant AS type (13.27%), followed by A3SS (12.39%), thereafter A5SS and MXE comprised of 12.39%. Interestingly, genes that experienced SE were enriched in histone acetyltransferase (HAT) complex, while genes spliced by RI were enriched in autophagy and those which experienced A3SS were enriched in methyltransferase activity revealed by GO analysis. In conclusion, we revealed ontology specific AS changes in AD. Our analysis provides novel pathological mechanisms of AD.
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Affiliation(s)
- Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Daoyuan Yue
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiazhao Xie
- Department of Pathophysiology, Key Laboratory of Ministry of Education for Neurological Disorders, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Liming Cheng, ; Xiong Wang,
| | - Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Liming Cheng, ; Xiong Wang,
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15
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Reis MC, Patrun J, Ackl N, Winter P, Scheifele M, Danek A, Nolte D. A Severe Dementia Syndrome Caused by Intron Retention and Cryptic Splice Site Activation in STUB1 and Exacerbated by TBP Repeat Expansions. Front Mol Neurosci 2022; 15:878236. [PMID: 35493319 PMCID: PMC9048483 DOI: 10.3389/fnmol.2022.878236] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/08/2022] [Indexed: 11/23/2022] Open
Abstract
Heterozygous pathogenic variants in the STIP1 homologous and U-box containing protein 1 (STUB1) gene have been identified as causes of autosomal dominant inherited spinocerebellar ataxia type 48 (SCA48). SCA48 is characterized by an ataxic movement disorder that is often, but not always, accompanied by a cognitive affective syndrome. We report a severe early onset dementia syndrome that mimics frontotemporal dementia and is caused by the intronic splice donor variant c.524+1G>A in STUB1. Impaired splicing was demonstrated by RNA analysis and in minigene assays of mutated and wild-type constructs of STUB1. The most striking consequence of this splicing impairment was retention of intron 3 in STUB1, which led to an in-frame insertion of 63 amino acids (aa) (p.Arg175_Glu176ins63) into the highly conserved coiled-coil domain of its encoded protein, C-terminus of HSP70-interacting protein (CHIP). To a lesser extent, activation of two cryptic splice sites in intron 3 was observed. The almost exclusively used one, c.524+86, was not predicted by in silico programs. Variant c.524+86 caused a frameshift (p.Arg175fs*93) that resulted in a truncated protein and presumably impairs the C-terminal U-box of CHIP, which normally functions as an E3 ubiquitin ligase. The cryptic splice site c.524+99 was rarely used and led to an in-frame insertion of 33 aa (p.Arg175_Glu176ins33) that resulted in disruption of the coiled-coil domain, as has been previously postulated for complete intron 3 retention. We additionally detected repeat expansions in the range of reduced penetrance in the TATA box-binding protein (TBP) gene by excluding other genes associated with dementia syndromes. The repeat expansion was heterozygous in one patient but compound heterozygous in the more severely affected patient. Therefore, we concluded that the observed severe dementia syndrome has a digenic background, making STUB1 and TBP important candidate genes responsible for early onset dementia syndromes.
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Affiliation(s)
- Marlen Colleen Reis
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Julia Patrun
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Nibal Ackl
- Psychiatrische Dienste Thurgau, Münsterlingen, Switzerland
- Neurologische Klinik und Poliklinik, Klinikum der Universität München, Munich, Germany
| | - Pia Winter
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany
| | | | - Adrian Danek
- Neurologische Klinik und Poliklinik, Klinikum der Universität München, Munich, Germany
| | - Dagmar Nolte
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany
- *Correspondence: Dagmar Nolte,
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Lin CX, Li HD, Deng C, Liu W, Erhardt S, Wu FX, Zhao XM, Guan Y, Wang J, Wang D, Hu B, Wang J. An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease. Brief Bioinform 2022; 23:bbab522. [PMID: 34953465 PMCID: PMC8769916 DOI: 10.1093/bib/bbab522] [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: 08/06/2021] [Revised: 10/26/2021] [Accepted: 11/13/2021] [Indexed: 09/24/2024] Open
Abstract
Alzheimer's disease (AD) has a strong genetic predisposition. However, its risk genes remain incompletely identified. We developed an Alzheimer's brain gene network-based approach to predict AD-associated genes by leveraging the functional pattern of known AD-associated genes. Our constructed network outperformed existing networks in predicting AD genes. We then systematically validated the predictions using independent genetic, transcriptomic, proteomic data, neuropathological and clinical data. First, top-ranked genes were enriched in AD-associated pathways. Second, using external gene expression data from the Mount Sinai Brain Bank study, we found that the top-ranked genes were significantly associated with neuropathological and clinical traits, including the Consortium to Establish a Registry for Alzheimer's Disease score, Braak stage score and clinical dementia rating. The analysis of Alzheimer's brain single-cell RNA-seq data revealed cell-type-specific association of predicted genes with early pathology of AD. Third, by interrogating proteomic data in the Religious Orders Study and Memory and Aging Project and Baltimore Longitudinal Study of Aging studies, we observed a significant association of protein expression level with cognitive function and AD clinical severity. The network, method and predictions could become a valuable resource to advance the identification of risk genes for AD.
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Affiliation(s)
- Cui-Xiang Lin
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China
- Hunan Provincial Key Lab of Bioinformatics, Central South University, Changsha, Hunan 410083, P. R. China
| | - Hong-Dong Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China
- Hunan Provincial Key Lab of Bioinformatics, Central South University, Changsha, Hunan 410083, P. R. China
| | - Chao Deng
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China
- Hunan Provincial Key Lab of Bioinformatics, Central South University, Changsha, Hunan 410083, P. R. China
| | - Weisheng Liu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China
- Hunan Provincial Key Lab of Bioinformatics, Central South University, Changsha, Hunan 410083, P. R. China
| | - Shannon Erhardt
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Fang-Xiang Wu
- Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SKS7N5A9, Canada
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics and Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Bin Hu
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, China
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China
- Hunan Provincial Key Lab of Bioinformatics, Central South University, Changsha, Hunan 410083, P. R. China
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17
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Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex. Brain Sci 2021; 12:brainsci12010047. [PMID: 35053791 PMCID: PMC8773923 DOI: 10.3390/brainsci12010047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 12/12/2022] Open
Abstract
Specific language impairment (SLI) is a common neurodevelopmental disorder (NDD) that displays high heritability estimates. Genetic studies have identified several loci, but the molecular basis of SLI remains unclear. With the aim to better understand the genetic architecture of SLI, we performed whole-exome sequencing (WES) in a single family (ID: 489; n = 11). We identified co-segregating rare variants in three new genes: BUD13, APLP2, and NDRG2. To determine the significance of these genes in SLI, we Sanger sequenced all coding regions of each gene in unrelated individuals with SLI (n = 175). We observed 13 additional rare variants in 18 unrelated individuals. Variants in BUD13 reached genome-wide significance (p-value < 0.01) upon comparison with similar variants in the 1000 Genomes Project, providing gene level evidence that BUD13 is involved in SLI. Additionally, five BUD13 variants showed cohesive variant level evidence of likely pathogenicity. Bud13 is a component of the retention and splicing (RES) complex. Additional supportive evidence from studies of an animal model (loss-of-function mutations in BUD13 caused a profound neural phenotype) and individuals with an NDD phenotype (carrying a CNV spanning BUD13), indicates BUD13 could be a target for investigation of the neural basis of language.
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18
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Conboy JG. A Deep Exon Cryptic Splice Site Promotes Aberrant Intron Retention in a Von Willebrand Disease Patient. Int J Mol Sci 2021; 22:13248. [PMID: 34948044 PMCID: PMC8706089 DOI: 10.3390/ijms222413248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/13/2022] Open
Abstract
A translationally silent single nucleotide mutation in exon 44 (E44) of the von Willebrand factor (VWF) gene is associated with inefficient removal of intron 44 in a von Willebrand disease (VWD) patient. This intron retention (IR) event was previously attributed to reordered E44 secondary structure that sequesters the normal splice donor site. We propose an alternative mechanism: the mutation introduces a cryptic splice donor site that interferes with the function of the annotated site to favor IR. We evaluated both models using minigene splicing reporters engineered to vary in secondary structure and/or cryptic splice site content. Analysis of splicing efficiency in transfected K562 cells suggested that the mutation-generated cryptic splice site in E44 was sufficient to induce substantial IR. Mutations predicted to vary secondary structure at the annotated site also had modest effects on IR and shifted the balance of residual splicing between the cryptic site and annotated site, supporting competition among the sites. Further studies demonstrated that introduction of cryptic splice donor motifs at other positions in E44 did not promote IR, indicating that interference with the annotated site is context dependent. We conclude that mutant deep exon splice sites can interfere with proper splicing by inducing IR.
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Affiliation(s)
- John G Conboy
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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19
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Ma Y, Dammer EB, Felsky D, Duong DM, Klein HU, White CC, Zhou M, Logsdon BA, McCabe C, Xu J, Wang M, Wingo TS, Lah JJ, Zhang B, Schneider J, Allen M, Wang X, Ertekin-Taner N, Seyfried NT, Levey AI, Bennett DA, De Jager PL. Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue. Nat Commun 2021; 12:7035. [PMID: 34857756 PMCID: PMC8640037 DOI: 10.1038/s41467-021-27204-9] [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: 02/01/2020] [Accepted: 11/04/2021] [Indexed: 11/09/2022] Open
Abstract
RNA editing is a feature of RNA maturation resulting in the formation of transcripts whose sequence differs from the genome template. Brain RNA editing may be altered in Alzheimer's disease (AD). Here, we analyzed data from 1,865 brain samples covering 9 brain regions from 1,074 unrelated subjects on a transcriptome-wide scale to identify inter-regional differences in RNA editing. We expand the list of known brain editing events by identifying 58,761 previously unreported events. We note that only a small proportion of these editing events are found at the protein level in our proteome-wide validation effort. We also identified the occurrence of editing events associated with AD dementia, neuropathological measures and longitudinal cognitive decline in: SYT11, MCUR1, SOD2, ORAI2, HSDL2, PFKP, and GPRC5B. Thus, we present an extended reference set of brain RNA editing events, identify a subset that are found to be expressed at the protein level, and extend the narrative of transcriptomic perturbation in AD to RNA editing.
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Affiliation(s)
- Yiyi Ma
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th street, New York, NY, 10032, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th street, New York, NY, 10032, USA
| | - Charles C White
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge, MA, 02142, USA
| | - Maotian Zhou
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | | | - Cristin McCabe
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge, MA, 02142, USA
| | - Jishu Xu
- Rush Alzheimer's Disease Center, Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Thomas S Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Julie Schneider
- Rush Alzheimer's Disease Center, Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Mariet Allen
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL, 32224, USA
| | - Xue Wang
- Mayo Clinic Florida, Department of Health Sciences Research, Jacksonville, FL, 32224, USA
| | - Nilüfer Ertekin-Taner
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL, 32224, USA
- Mayo Clinic Florida, Department of Neurology, Jacksonville, FL, 32224, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th street, New York, NY, 10032, USA.
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge, MA, 02142, USA.
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20
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Bai B, Vanderwall D, Li Y, Wang X, Poudel S, Wang H, Dey KK, Chen PC, Yang K, Peng J. Proteomic landscape of Alzheimer's Disease: novel insights into pathogenesis and biomarker discovery. Mol Neurodegener 2021; 16:55. [PMID: 34384464 PMCID: PMC8359598 DOI: 10.1186/s13024-021-00474-z] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/18/2021] [Indexed: 12/15/2022] Open
Abstract
Mass spectrometry-based proteomics empowers deep profiling of proteome and protein posttranslational modifications (PTMs) in Alzheimer's disease (AD). Here we review the advances and limitations in historic and recent AD proteomic research. Complementary to genetic mapping, proteomic studies not only validate canonical amyloid and tau pathways, but also uncover novel components in broad protein networks, such as RNA splicing, development, immunity, membrane transport, lipid metabolism, synaptic function, and mitochondrial activity. Meta-analysis of seven deep datasets reveals 2,698 differentially expressed (DE) proteins in the landscape of AD brain proteome (n = 12,017 proteins/genes), covering 35 reported AD genes and risk loci. The DE proteins contain cellular markers enriched in neurons, microglia, astrocytes, oligodendrocytes, and epithelial cells, supporting the involvement of diverse cell types in AD pathology. We discuss the hypothesized protective or detrimental roles of selected DE proteins, emphasizing top proteins in "amyloidome" (all biomolecules in amyloid plaques) and disease progression. Comprehensive PTM analysis represents another layer of molecular events in AD. In particular, tau PTMs are correlated with disease stages and indicate the heterogeneity of individual AD patients. Moreover, the unprecedented proteomic coverage of biofluids, such as cerebrospinal fluid and serum, procures novel putative AD biomarkers through meta-analysis. Thus, proteomics-driven systems biology presents a new frontier to link genotype, proteotype, and phenotype, accelerating the development of improved AD models and treatment strategies.
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Affiliation(s)
- Bing Bai
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Current address: Center for Precision Medicine, Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu 210008 Nanjing, China
| | - David Vanderwall
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Yuxin Li
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Current address: Department of Biology, University of North Dakota, ND 58202 Grand Forks, USA
| | - Suresh Poudel
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Hong Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Kaushik Kumar Dey
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Ping-Chung Chen
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Ka Yang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
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21
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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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