1
|
Chen H, Wang X, Chang Z, Zhang J, Xie D. Genetic causal relationship between multiple immune cell phenotypes and Parkinson's disease: a two-sample bidirectional Mendelian randomization study. J Neurophysiol 2024; 131:1115-1125. [PMID: 38690999 DOI: 10.1152/jn.00481.2023] [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: 12/27/2023] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024] Open
Abstract
The exact etiology of Parkinson's disease (PD), a degenerative disease of the central nervous system, is unclear. It is currently believed that its main pathological basis is a decrease in dopamine concentration in the striatum of the brain. Although many researchers have previously focused on the critical role of the immune response in PD, there has been a lack of valid genetic evidence for a causal association between specific immune cell traits and phenotypes and PD. We employed Mendelian randomization (MR) as an analytical method to effectively assess genetic associations between exposure and outcome. Based on the largest Genome-Wide Association Study (GWAS) dataset to date, causal associations between multiple immune cell phenotypes and PD were validly assessed, controlling for confounding factors by using single-nucleotide polymorphisms (SNPs), which are genetic instrumental variables that are randomly assigned and not subject to any causality. By testing 731 immune cell phenotypes and their association with PD, the results of inverse variance weighting (IVW) analysis suggested that after Bonferroni correction multiple immune cell phenotypes had no statistically significant effect on PD. It is worth mentioning that some phenotypes with unadjusted P values (P < 0.05), including 40 immune phenotypes, that were located on the cDC panel, the Treg panel, the Maturation stages of T cell panel, the TBNK panel, the B cell panel, the Myeloid cell panel, and the Monocyte panel were considered to have nominal associations with PD. In addition, PD could have an effect on certain immunophenotypes located on the Myeloid cell panel and the Monocyte panel; the specific immunophenotypic results and statistical analysis values are shown in the text. The results of sensitivity analyses suggested that none of these observed the presence of horizontal pleiotropy. Our study identified a close link between immune cells and PD, and the results of this study provide ideas for the study of the immune mechanism of PD and the exploration of effective therapeutic means.NEW & NOTEWORTHY In this study, based on the GWAS Immunophenotyping Database, a Mendelian randomization approach was used to assess the genetic causal associations between 731 immunophenotypes and traits and Parkinson's disease (PD), which not only provides a reference for the immune response mechanism of PD but also provides ideas for exploring the effective diagnosis and treatment of PD.
Collapse
Affiliation(s)
- Hong Chen
- The First Clinical Medical College of Anhui University of Chinese Medicine, Hefei, China
| | - Xie Wang
- The First Clinical Medical College of Anhui University of Chinese Medicine, Hefei, China
| | - Ze Chang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Juan Zhang
- Department of Neurology, the First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, China
| | - Daojun Xie
- Department of Neurology, the First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, China
| |
Collapse
|
2
|
Navarro E, Efthymiou AG, Parks M, Riboldi GM, Vialle RA, Udine E, Muller BZ, Humphrey J, Allan A, Argyrou CC, Lopes KDP, Münch A, Raymond D, Sachdev R, Shanker VL, Miravite J, Katsnelson V, Leaver K, Frucht S, Bressman SB, Marcora E, Saunders-Pullman R, Goate A, Raj T. LRRK2 G2019S variant is associated with transcriptional changes in Parkinson's disease human myeloid cells under proinflammatory environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.594821. [PMID: 38854101 PMCID: PMC11160623 DOI: 10.1101/2024.05.27.594821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The G2019S mutation in the leucine-rich repeat kinase 2 (LRRK2) gene is a major risk factor for the development of Parkinson's disease (PD). LRRK2, although ubiquitously expressed, is highly abundant in cells of the innate immune system. Given the importance of central and peripheral immune cells in the development of PD, we sought to investigate the consequences of the G2019S mutation on microglial and monocyte transcriptome and function. We have generated large-scale transcriptomic profiles of isogenic human induced microglial cells (iMGLs) and patient derived monocytes carrying the G2019S mutation under baseline culture conditions and following exposure to the proinflammatory factors IFNγ and LPS. We demonstrate that the G2019S mutation exerts a profound impact on the transcriptomic profile of these myeloid cells, and describe corresponding functional differences in iMGLs. The G2019S mutation led to an upregulation in lipid metabolism and phagolysosomal pathway genes in untreated and LPS/IFNγ stimulated iMGLs, which was accompanied by an increased phagocytic capacity of myelin debris. We also identified dysregulation of cell cycle genes, with a downregulation of the E2F4 regulon. Transcriptomic characterization of human-derived monocytes carrying the G2019S mutation confirmed alteration in lipid metabolism associated genes. Altogether, these findings reveal the influence of G2019S on the dysregulation of the myeloid cell transcriptome under proinflammatory conditions.
Collapse
Affiliation(s)
- Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Instituto Universitario de Investigacion en Neuroquimica, Departamento de Bioquimica y Biologia Molecular, Facultad de Medicina, Universidad Complutense, Madrid, Spain
- Centro de Investigacion Biomedica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain
| | - Anastasia G. Efthymiou
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Madison Parks
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Giulietta M Riboldi
- The Marlene and Paolo Fresco Institute for Parkinson’s Disease and Movement Disorders, New York University Langone Health, New York, NY, USA
| | - Ricardo A. Vialle
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Rush Alzheimer’s Disease Center, Rush University Medical Center; Chicago, IL, 60612, USA
- Department of Neurological Sciences, Rush University Medical Center; Chicago, IL, 60612, USA
| | - Evan Udine
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Benjamin Z. Muller
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Amanda Allan
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Charlie Charalambos Argyrou
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Katia de Paiva Lopes
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Rush Alzheimer’s Disease Center, Rush University Medical Center; Chicago, IL, 60612, USA
- Department of Neurological Sciences, Rush University Medical Center; Chicago, IL, 60612, USA
| | - Alexandra Münch
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Deborah Raymond
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rivka Sachdev
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vicki L. Shanker
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joan Miravite
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Viktoryia Katsnelson
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katherine Leaver
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steve Frucht
- The Marlene and Paolo Fresco Institute for Parkinson’s Disease and Movement Disorders, New York University Langone Health, New York, NY, USA
| | - Susan B Bressman
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Rachel Saunders-Pullman
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison Goate
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| |
Collapse
|
3
|
Fujita M, Gao Z, Zeng L, McCabe C, White CC, Ng B, Green GS, Rozenblatt-Rosen O, Phillips D, Amir-Zilberstein L, Lee H, Pearse RV, Khan A, Vardarajan BN, Kiryluk K, Ye CJ, Klein HU, Wang G, Regev A, Habib N, Schneider JA, Wang Y, Young-Pearse T, Mostafavi S, Bennett DA, Menon V, De Jager PL. Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nat Genet 2024; 56:605-614. [PMID: 38514782 DOI: 10.1038/s41588-024-01685-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/08/2024] [Indexed: 03/23/2024]
Abstract
The relationship between genetic variation and gene expression in brain cell types and subtypes remains understudied. Here, we generated single-nucleus RNA sequencing data from the neocortex of 424 individuals of advanced age; we assessed the effect of genetic variants on RNA expression in cis (cis-expression quantitative trait loci) for seven cell types and 64 cell subtypes using 1.5 million transcriptomes. This effort identified 10,004 eGenes at the cell type level and 8,099 eGenes at the cell subtype level. Many eGenes are only detected within cell subtypes. A new variant influences APOE expression only in microglia and is associated with greater cerebral amyloid angiopathy but not Alzheimer's disease pathology, after adjusting for APOEε4, providing mechanistic insights into both pathologies. Furthermore, only a TMEM106B variant affects the proportion of cell subtypes. Integration of these results with genome-wide association studies highlighted the targeted cell type and probable causal gene within Alzheimer's disease, schizophrenia, educational attainment and Parkinson's disease loci.
Collapse
Affiliation(s)
- Masashi Fujita
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Zongmei Gao
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lu Zeng
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charles C White
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Bernard Ng
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Gilad Sahar Green
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | | | - Hyo Lee
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Atlas Khan
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Hans-Ulrich Klein
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Gao Wang
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Naomi Habib
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Tracy Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sara Mostafavi
- Department of Statistics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
4
|
Dressman D, Tasaki S, Yu L, Schneider J, Bennett DA, Elyaman W, Vardarajan B. Polygenic risk associated with Alzheimer's disease and other traits influences genes involved in T cell signaling and activation. Front Immunol 2024; 15:1337831. [PMID: 38590520 PMCID: PMC10999606 DOI: 10.3389/fimmu.2024.1337831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/22/2024] [Indexed: 04/10/2024] Open
Abstract
Introduction T cells, known for their ability to respond to an enormous variety of pathogens and other insults, are increasingly recognized as important mediators of pathology in neurodegeneration and other diseases. T cell gene expression phenotypes can be regulated by disease-associated genetic variants. Many complex diseases are better represented by polygenic risk than by individual variants. Methods We first compute a polygenic risk score (PRS) for Alzheimer's disease (AD) using genomic sequencing data from a cohort of Alzheimer's disease (AD) patients and age-matched controls, and validate the AD PRS against clinical metrics in our cohort. We then calculate the PRS for several autoimmune disease, neurological disorder, and immune function traits, and correlate these PRSs with T cell gene expression data from our cohort. We compare PRS-associated genes across traits and four T cell subtypes. Results Several genes and biological pathways associated with the PRS for these traits relate to key T cell functions. The PRS-associated gene signature generally correlates positively for traits within a particular category (autoimmune disease, neurological disease, immune function) with the exception of stroke. The trait-associated gene expression signature for autoimmune disease traits was polarized towards CD4+ T cell subtypes. Discussion Our findings show that polygenic risk for complex disease and immune function traits can have varying effects on T cell gene expression trends. Several PRS-associated genes are potential candidates for therapeutic modulation in T cells, and could be tested in in vitro applications using cells from patients bearing high or low polygenic risk for AD or other conditions.
Collapse
Affiliation(s)
- Dallin Dressman
- Department of Neurology, Columbia University, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
| | - Shinya Tasaki
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Lei Yu
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Julie Schneider
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
- Department of Pathology, Rush University Medical Center, Chicago, IL, United States
| | - David A. Bennett
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Wassim Elyaman
- Department of Neurology, Columbia University, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
| | - Badri Vardarajan
- Department of Neurology, Columbia University, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
- College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, The Gertrude H. Sergievsky Center, New York, NY, United States
| |
Collapse
|
5
|
Amini A, Esmaeili F, Golpich M. Possible role of lncRNAs in amelioration of Parkinson's disease symptoms by transplantation of dopaminergic cells. NPJ Parkinsons Dis 2024; 10:56. [PMID: 38472261 PMCID: PMC10933336 DOI: 10.1038/s41531-024-00661-x] [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: 09/19/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are biomarkers for diagnosis and treatment of Parkinson's disease (PD). Since dopaminergic cell transplantation is a clinical method to treat PD, this study investigated the effects of dopaminergic cell therapy on the expression of some lncRNAs and genes related to PD. In this study, Twenty-eight rats were randomly assigned to four experimental groups. The control group (Sal group) received saline injections. The Par group was a PD rat model with 6-hydroxydopamine (6-OHDA) injection in right striatum (ST). PD animals were transplanted by undifferentiated P19 stem cells (Par-E group), and P19-derived dopaminergic cells (Par-N group). Cell transplant effects were evaluated using behavioral tests (cylinder, open field, and rotarod tests), and histological methods (H&E and Nissl staining, and immunohistochemistry). Moreover, the expression of lncRNAs MALAT1, MEG3, and SNHG1, alongside specific neuronal (synaptophysin) and dopaminergic (tyrosine hydroxylase) markers was evaluated by qRT-PCR. Behavioral and histopathological examinations revealed that cell transplantation partially compensated dopaminergic cell degeneration in ST and substantia nigra (SN) of PD rats. The expression of MALAT1, SNHG1, and MEG3 was decreased in the ST of the Par group, while MEG3 and SNHG1 gene expression was increased in PBMC relative to the Sal group. In PBMC of the Par-N group, all three lncRNAs showed a reduction in their expression. Conversely, MALAT1 and SNHG1 expression was increased in ST tissue, while MEG3 gene expression was decreased compared to the Sal group. In conclusion, dopaminergic cell transplantation could change the lncRNAs expression. Furthermore, it partially improves symptoms in PD rats.
Collapse
Affiliation(s)
- A Amini
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - F Esmaeili
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - M Golpich
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| |
Collapse
|
6
|
Souquette A, Thomas PG. Variation in the basal immune state and implications for disease. eLife 2024; 13:e90091. [PMID: 38275224 PMCID: PMC10817719 DOI: 10.7554/elife.90091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/21/2024] [Indexed: 01/27/2024] Open
Abstract
Analysis of pre-existing immunity and its effects on acute infection often focus on memory responses associated with a prior infectious exposure. However, memory responses occur in the context of the overall immune state and leukocytes must interact with their microenvironment and other immune cells. Thus, it is important to also consider non-antigen-specific factors which shape the composite basal state and functional capacity of the immune system, termed here as I0 ('I naught'). In this review, we discuss the determinants of I0. Utilizing influenza virus as a model, we then consider the effect of I0 on susceptibility to infection and disease severity. Lastly, we outline a mathematical framework and demonstrate how researchers can build and tailor models to specific needs. Understanding how diverse factors uniquely and collectively impact immune competence will provide valuable insights into mechanisms of immune variation, aid in screening for high-risk populations, and promote the development of broadly applicable prophylactic and therapeutic treatments.
Collapse
Affiliation(s)
- Aisha Souquette
- Department of Immunology, St. Jude Children's Research HospitalMemphisUnited States
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research HospitalMemphisUnited States
| |
Collapse
|
7
|
Roussos P, Kosoy R, Fullard J, Bendl J, Kleopoulos S, Shao Z, Argyriou S, Mathur D, Vicari J, Ma Y, Humphrey J, Brophy E, Raj T, Katsel P, Voloudakis G, Lee D, Bennett D, Haroutunian V, Hoffman G. Alzheimer's disease transcriptional landscape in ex-vivo human microglia. RESEARCH SQUARE 2024:rs.3.rs-3851590. [PMID: 38343831 PMCID: PMC10854306 DOI: 10.21203/rs.3.rs-3851590/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Microglia are resident immune cells of the brain and are implicated in the etiology of Alzheimer's Disease (AD) and other diseases. Yet the cellular and molecular processes regulating their function throughout the course of the disease are poorly understood. Here, we present the transcriptional landscape of primary microglia from 189 human postmortem brains, including 58 healthy aging individuals and 131 with a range of disease phenotypes, including 63 patients representing the full spectrum of clinical and pathological severity of AD. We identified transcriptional changes associated with multiple AD phenotypes, capturing the severity of dementia and neuropathological lesions. Transcript-level analyses identified additional genes with heterogeneous isoform usage and AD phenotypes. We identified changes in gene-gene coordination in AD, dysregulation of co-expression modules, and disease subtypes with distinct gene expression. Taken together, these data further our understanding of the key role of microglia in AD biology and nominate candidates for therapeutic intervention.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yixuan Ma
- Icahn School of Medicine at Mount Sinai
| | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Kasela S, Aguet F, Kim-Hellmuth S, Brown BC, Nachun DC, Tracy RP, Durda P, Liu Y, Taylor KD, Johnson WC, Van Den Berg D, Gabriel S, Gupta N, Smith JD, Blackwell TW, Rotter JI, Ardlie KG, Manichaikul A, Rich SS, Barr RG, Lappalainen T. Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects. Am J Hum Genet 2024; 111:133-149. [PMID: 38181730 PMCID: PMC10806864 DOI: 10.1016/j.ajhg.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 01/07/2024] Open
Abstract
Bulk-tissue molecular quantitative trait loci (QTLs) have been the starting point for interpreting disease-associated variants, and context-specific QTLs show particular relevance for disease. Here, we present the results of mapping interaction QTLs (iQTLs) for cell type, age, and other phenotypic variables in multi-omic, longitudinal data from the blood of individuals of diverse ancestries. By modeling the interaction between genotype and estimated cell-type proportions, we demonstrate that cell-type iQTLs could be considered as proxies for cell-type-specific QTL effects, particularly for the most abundant cell type in the tissue. The interpretation of age iQTLs, however, warrants caution because the moderation effect of age on the genotype and molecular phenotype association could be mediated by changes in cell-type composition. Finally, we show that cell-type iQTLs contribute to cell-type-specific enrichment of diseases that, in combination with additional functional data, could guide future functional studies. Overall, this study highlights the use of iQTLs to gain insights into the context specificity of regulatory effects.
Collapse
Affiliation(s)
- Silva Kasela
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA.
| | | | - Sarah Kim-Hellmuth
- New York Genome Center, New York, NY, USA; Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany; Computational Health Center, Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Brielin C Brown
- New York Genome Center, New York, NY, USA; Data Science Institute, Columbia University, New York, NY, USA
| | - Daniel C Nachun
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Russell P Tracy
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Peter Durda
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Yongmei Liu
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - David Van Den Berg
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua D Smith
- Northwest Genomics Center, University of Washington, Seattle, WA, USA
| | - Thomas W Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - R Graham Barr
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA; Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| |
Collapse
|
9
|
Lopes KDP, Yu L, Shen X, Qiu Y, Tasaki S, Iatrou A, Beeri MS, Seyfried NT, Menon V, Wang Y, Schneider JA, Cantor H, Bennett DA. Associations of cortical SPP1 and ITGAX with cognition and common neuropathologies in older adults. Alzheimers Dement 2024; 20:525-537. [PMID: 37727065 PMCID: PMC10841499 DOI: 10.1002/alz.13474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/15/2023] [Accepted: 08/21/2023] [Indexed: 09/21/2023]
Abstract
INTRODUCTION The secreted phosphoprotein 1 (SPP1) gene expressed by CD11c+ cells is known to be associated with microglia activation and neuroinflammatory diseases. As most studies rely on mouse models, we investigated these genes and proteins in the cortical brain tissue of older adults and their role in Alzheimer's disease (AD) and related disorders. METHODS We leveraged protein measurements, single-nuclei, and RNASeq data from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) of over 1200 samples for association analysis. RESULTS Expression of SPP1 and its encoded protein osteopontin were associated with faster cognitive decline and greater odds of common neuropathologies. At single-cell resolution, integrin subunit alpha X (ITGAX) was highly expressed in microglia, where specific subpopulations were associated with AD and cerebral amyloid angiopathy. DISCUSSION The study provides evidence of SPP1 and ITGAX association with cognitive decline and common neuropathologies identifying a microglial subset associated with disease.
Collapse
Affiliation(s)
- Katia de Paiva Lopes
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Lei Yu
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Xianli Shen
- Department of Cancer Immunology and VirologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Yiguo Qiu
- Department of Cancer Immunology and VirologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
- Chongqing International Institute for ImmunologyChongqingChina
| | - Shinya Tasaki
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Artemis Iatrou
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
- Department of Psychiatry, McLean HospitalHarvard Medical SchoolBelmontMassachusettsUSA
| | - Michal Schnaider Beeri
- Joseph Sagol Neuroscience Center, Sheba Medical CenterRamat GanIsrael
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- The Herbert and Jackeline Krieger Klein Alzheimer's Research CenterRutgers Biomedical and Health Sciences, Rutgers UniversityNew JerseyUSA
| | - Nicholas T. Seyfried
- Goizueta Alzheimer's Disease Research Center, Department of Neurology and Department of BiochemistryEmory University School of MedicineAtlantaGeorgiaUSA
| | - Vilas Menon
- Center for Translational and Computational NeuroimmunologyDepartment of Neurology & Taub Institute for Research on Alzheimer's disease and the Aging BrainColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Yanling Wang
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Julie A. Schneider
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
- Department of PathologyRush University Medical CenterChicagoIllinoisUSA
| | - Harvey Cantor
- Department of Cancer Immunology and VirologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
| | - David A. Bennett
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| |
Collapse
|
10
|
Humphrey J, Brophy E, Kosoy R, Zeng B, Coccia E, Mattei D, Ravi A, Efthymiou AG, Navarro E, Muller BZ, Snijders GJLJ, Allan A, Münch A, Kitata RB, Kleopoulos SP, Argyriou S, Shao Z, Francoeur N, Tsai CF, Gritsenko MA, Monroe ME, Paurus VL, Weitz KK, Shi T, Sebra R, Liu T, de Witte LD, Goate AM, Bennett DA, Haroutunian V, Hoffman GE, Fullard JF, Roussos P, Raj T. Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.01.23299073. [PMID: 38076956 PMCID: PMC10705658 DOI: 10.1101/2023.12.01.23299073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Microglia, the innate immune cells of the central nervous system, have been genetically implicated in multiple neurodegenerative diseases. We previously mapped the genetic regulation of gene expression and mRNA splicing in human microglia, identifying several loci where common genetic variants in microglia-specific regulatory elements explain disease risk loci identified by GWAS. However, identifying genetic effects on splicing has been challenging due to the use of short sequencing reads to identify causal isoforms. Here we present the isoform-centric microglia genomic atlas (isoMiGA) which leverages the power of long-read RNA-seq to identify 35,879 novel microglia isoforms. We show that the novel microglia isoforms are involved in stimulation response and brain region specificity. We then quantified the expression of both known and novel isoforms in a multi-ethnic meta-analysis of 555 human microglia short-read RNA-seq samples from 391 donors, the largest to date, and found associations with genetic risk loci in Alzheimer's disease and Parkinson's disease. We nominate several loci that may act through complex changes in isoform and splice site usage.
Collapse
Affiliation(s)
- Jack Humphrey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erica Brophy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Biao Zeng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Elena Coccia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniele Mattei
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashvin Ravi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anastasia G. Efthymiou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elisa Navarro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Biochemistry and Molecular Biology, Faculty of Medicine (Universidad Complutense de Madrid), Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain
| | - Benjamin Z. Muller
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gijsje JLJ Snijders
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Amanda Allan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Münch
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Steven P Kleopoulos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Stathis Argyriou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Zhiping Shao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Nancy Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Vanessa L Paurus
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lot D. de Witte
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Alison M. Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Vahram Haroutunian
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Gabriel E. Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - John F. Fullard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
- Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Towfique Raj
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
11
|
Xu M, Liu Q, Bi R, Li Y, Li H, Kang WB, Yan Z, Zheng Q, Sun C, Ye M, Xiang BL, Luo XJ, Li M, Zhang DF, Yao YG. Coexistence of Multiple Functional Variants and Genes Underlies Genetic Risk Locus 11p11.2 of Alzheimer's Disease. Biol Psychiatry 2023; 94:743-759. [PMID: 37290560 DOI: 10.1016/j.biopsych.2023.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Genome-wide association studies have identified dozens of genetic risk loci for Alzheimer's disease (AD), yet the underlying causal variants and biological mechanisms remain elusive, especially for loci with complex linkage disequilibrium and regulation. METHODS To fully untangle the causal signal at a single locus, we performed a functional genomic study of 11p11.2 (the CELF1/SPI1 locus). Genome-wide association study signals at 11p11.2 were integrated with datasets of histone modification, open chromatin, and transcription factor binding to distill potentially functional variants (fVars). Their allelic regulatory activities were confirmed by allele imbalance, reporter assays, and base editing. Expressional quantitative trait loci and chromatin interaction data were incorporated to assign target genes to fVars. The relevance of these genes to AD was assessed by convergent functional genomics using bulk brain and single-cell transcriptomic, epigenomic, and proteomic datasets of patients with AD and control individuals, followed by cellular assays. RESULTS We found that 24 potential fVars, rather than a single variant, were responsible for the risk of 11p11.2. These fVars modulated transcription factor binding and regulated multiple genes by long-range chromatin interactions. Besides SPI1, convergent evidence indicated that 6 target genes (MTCH2, ACP2, NDUFS3, PSMC3, C1QTNF4, and MADD) of fVars were likely to be involved in AD development. Disruption of each gene led to cellular amyloid-β and phosphorylated tau changes, supporting the existence of multiple likely causal genes at 11p11.2. CONCLUSIONS Multiple variants and genes at 11p11.2 may contribute to AD risk. This finding provides new insights into the mechanistic and therapeutic challenges of AD.
Collapse
Affiliation(s)
- Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Qianjin Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Yu Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Hongli Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Wei-Bo Kang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zhongjiang Yan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Quanzhen Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Chunli Sun
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Maosen Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Bo-Lin Xiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| |
Collapse
|
12
|
Kang X, Ploner A, Roelstraete B, Ludvigsson JF, Wirdefeldt K. Risk of Parkinson's Disease in Celiac Disease: A Swedish Population-Based Study. Ann Neurol 2023; 94:911-916. [PMID: 37632335 DOI: 10.1002/ana.26780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023]
Abstract
Using a population-based matched cohort design, we assessed the association of celiac disease (CeD) with risk of PD by comparing patients with biopsy-confirmed CeD in Sweden to a biopsy-free population and their unaffected siblings, separately. No overall association was observed but CeD diagnosed before age 60 associated positively with incident diagnosis of PD (hazard ratio [HR] = 1.29; 95% confidence interval [CI]: 1.02-1.62), which was mainly attributed to the significantly elevated risk detected after 10-15 years since biopsy (HR = 1.68; 95% CI: 1.05-2.68). Our findings imply an increased vulnerability to long-term PD development among patients with CeD diagnosed before 60s. ANN NEUROL 2023;94:911-916.
Collapse
Affiliation(s)
- Xiaoying Kang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Bjorn Roelstraete
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jonas F Ludvigsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Pediatrics, Örebro University Hospital, Örebro, Sweden
| | - Karin Wirdefeldt
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
13
|
Andersen MS, Leikfoss IS, Brorson IS, Cappelletti C, Bettencourt C, Toft M, Pihlstrøm L. Epigenome-wide association study of peripheral immune cell populations in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:149. [PMID: 37903812 PMCID: PMC10616224 DOI: 10.1038/s41531-023-00594-x] [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: 06/13/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Understanding the contribution of immune mechanisms to Parkinson's disease pathogenesis is an important challenge, potentially of major therapeutic implications. To further elucidate the involvement of peripheral immune cells, we studied epigenome-wide DNA methylation in isolated populations of CD14+ monocytes, CD19+ B cells, CD4+ T cells, and CD8+ T cells from Parkinson's disease patients and healthy control participants. We included 25 patients with a maximum five years of disease duration and 25 controls, and isolated four immune cell populations from each fresh blood sample. Epigenome-wide DNA methylation profiles were generated from 186 samples using the Illumina MethylationEpic array and association with disease status was tested using linear regression models. We identified six differentially methylated CpGs in CD14+ monocytes and one in CD8 + T cells. Four differentially methylated regions were identified in monocytes, including a region upstream of RAB32, a gene that has been linked to LRRK2. Methylation upstream of RAB32 correlated negatively with mRNA expression, and RAB32 expression was upregulated in Parkinson's disease both in our samples and in summary statistics from a previous study. Our epigenome-wide association study of early Parkinson's disease provides evidence for methylation changes across different peripheral immune cell types, highlighting monocytes and the RAB32 locus. The findings were predominantly cell-type-specific, demonstrating the value of isolating purified cell populations for genomic studies.
Collapse
Affiliation(s)
- Maren Stolp Andersen
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | | | - Conceicao Bettencourt
- Department of Neurodegenerative Disease and Queen Square Brain Bank for Neurological Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
14
|
Matveeva N, Kiselev I, Baulina N, Semina E, Kakotkin V, Agapov M, Kulakova O, Favorova O. Shared genetic architecture of COVID-19 and Alzheimer's disease. Front Aging Neurosci 2023; 15:1287322. [PMID: 37927339 PMCID: PMC10625425 DOI: 10.3389/fnagi.2023.1287322] [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: 09/01/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
The severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and the сoronavirus disease 2019 (COVID-19) have become a global health threat. At the height of the pandemic, major efforts were focused on reducing COVID-19-associated morbidity and mortality. Now is the time to study the long-term effects of the pandemic, particularly cognitive impairment associated with long COVID. In recent years much attention has been paid to the possible relationship between COVID-19 and Alzheimer's disease, which is considered a main cause of age-related cognitive impairment. Genetic predisposition was shown for both COVID-19 and Alzheimer's disease. However, the analysis of the similarity of the genetic architecture of these diseases is usually limited to indicating a positive genetic correlation between them. In this review, we have described intrinsic linkages between COVID-19 and Alzheimer's disease, pointed out shared susceptibility genes that were previously identified in genome-wide association studies of both COVID-19 and Alzheimer's disease, and highlighted a panel of SNPs that includes candidate genetic risk markers of the long COVID-associated cognitive impairment.
Collapse
Affiliation(s)
- Natalia Matveeva
- Institute of Medicine and Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Laboratory of Medical Genomics, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan Kiselev
- Institute of Medicine and Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Laboratory of Medical Genomics, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Natalia Baulina
- Institute of Medicine and Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Laboratory of Medical Genomics, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina Semina
- Institute of Medicine and Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Viktor Kakotkin
- Institute of Medicine and Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Mikhail Agapov
- Institute of Medicine and Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Olga Kulakova
- Institute of Medicine and Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Laboratory of Medical Genomics, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Olga Favorova
- Institute of Medicine and Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Laboratory of Medical Genomics, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| |
Collapse
|
15
|
Xiao Q, Mears J, Nathan A, Ishigaki K, Baglaenko Y, Lim N, Cooney LA, Harris KM, Anderson MS, Fox DA, Smilek DE, Krueger JG, Raychaudhuri S. Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin. Nat Commun 2023; 14:6268. [PMID: 37805522 PMCID: PMC10560299 DOI: 10.1038/s41467-023-41984-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/25/2023] [Indexed: 10/09/2023] Open
Abstract
Psoriasis is a chronic, systemic inflammatory condition primarily affecting skin. While the role of the immune compartment (e.g., T cells) is well established, the changes in the skin compartment are more poorly understood. Using longitudinal skin biopsies (n = 375) from the "Psoriasis Treatment with Abatacept and Ustekinumab: A Study of Efficacy"(PAUSE) clinical trial (n = 101), we report 953 expression quantitative trait loci (eQTLs). Of those, 116 eQTLs have effect sizes that were modulated by local skin inflammation (eQTL interactions). By examining these eQTL genes (eGenes), we find that most are expressed in the skin tissue compartment, and a subset overlap with the NRF2 pathway. Indeed, the strongest eQTL interaction signal - rs1491377616-LCE3C - links a psoriasis risk locus with a gene specifically expressed in the epidermis. This eQTL study highlights the potential to use biospecimens from clinical trials to discover in vivo eQTL interactions with therapeutically relevant environmental variables.
Collapse
Affiliation(s)
- Qian Xiao
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph Mears
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan
| | - Yuriy Baglaenko
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noha Lim
- Immune Tolerance Network, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Laura A Cooney
- Immune Tolerance Network, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Internal Medicine and Clinical Autoimmunity Center of Excellence, University of Michigan, Ann Arbor, MI, USA
| | - Kristina M Harris
- Immune Tolerance Network, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Mark S Anderson
- Immune Tolerance Network, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - David A Fox
- Division of Rheumatology, Department of Internal Medicine and Clinical Autoimmunity Center of Excellence, University of Michigan, Ann Arbor, MI, USA
| | - Dawn E Smilek
- Immune Tolerance Network, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - James G Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK.
| |
Collapse
|
16
|
Dong X, Bai Y, Liao Z, Gritsch D, Liu X, Wang T, Borges-Monroy R, Ehrlich A, Serrano GE, Feany MB, Beach TG, Scherzer CR. Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease. Nat Commun 2023; 14:5327. [PMID: 37723137 PMCID: PMC10507039 DOI: 10.1038/s41467-023-40348-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 07/20/2023] [Indexed: 09/20/2023] Open
Abstract
Little is known about circular RNAs (circRNAs) in specific brain cells and human neuropsychiatric disease. Here, we systematically identify over 11,039 circRNAs expressed in vulnerable dopamine and pyramidal neurons laser-captured from 190 human brains and non-neuronal cells using ultra-deep, total RNA sequencing. 1526 and 3308 circRNAs are custom-tailored to the cell identity of dopamine and pyramidal neurons and enriched in synapse pathways. 29% of Parkinson's and 12% of Alzheimer's disease-associated genes produced validated circRNAs. circDNAJC6, which is transcribed from a juvenile-onset Parkinson's gene, is already dysregulated during prodromal, onset stages of common Parkinson's disease neuropathology. Globally, addiction-associated genes preferentially produce circRNAs in dopamine neurons, autism-associated genes in pyramidal neurons, and cancers in non-neuronal cells. This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA-regulated synaptic specialization in neuropsychiatric diseases.
Collapse
Affiliation(s)
- Xianjun Dong
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Genomics and Bioinformatics Hub, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Yunfei Bai
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- State Key Lab of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhixiang Liao
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - David Gritsch
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - Xiaoli Liu
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Department of Neurology, Zhejiang Hospital, Zhejiang, China
| | - Tao Wang
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Rebeca Borges-Monroy
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - Alyssa Ehrlich
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mel B Feany
- Departement of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Clemens R Scherzer
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA.
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
17
|
Hongyao HE, Chun JI, Xiaoyan G, Fangfang L, Jing Z, Lin Z, Pengxiang Z, Zengchun L. Associative gene networks reveal novel candidates important for ADHD and dyslexia comorbidity. BMC Med Genomics 2023; 16:208. [PMID: 37667328 PMCID: PMC10478365 DOI: 10.1186/s12920-023-01502-1] [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: 03/29/2022] [Accepted: 03/26/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Attention deficit hyperactivity disorder (ADHD) is commonly associated with developmental dyslexia (DD), which are both prevalent and complicated pediatric neurodevelopmental disorders that have a significant influence on children's learning and development. Clinically, the comorbidity incidence of DD and ADHD is between 25 and 48%. Children with DD and ADHD may have more severe cognitive deficiencies, a poorer level of schooling, and a higher risk of social and emotional management disorders. Furthermore, patients with this comorbidity are frequently treated for a single condition in clinical settings, and the therapeutic outcome is poor. The development of effective treatment approaches against these diseases is complicated by their comorbidity features. This is often a major problem in diagnosis and treatment. In this study, we developed bioinformatical methodology for the analysis of the comorbidity of these two diseases. As such, the search for candidate genes related to the comorbid conditions of ADHD and DD can help in elucidating the molecular mechanisms underlying the comorbid condition, and can also be useful for genotyping and identifying new drug targets. RESULTS Using the ANDSystem tool, the reconstruction and analysis of gene networks associated with ADHD and dyslexia was carried out. The gene network of ADHD included 599 genes/proteins and 148,978 interactions, while that of dyslexia included 167 genes/proteins and 27,083 interactions. When the ANDSystem and GeneCards data were combined, a total of 213 genes/proteins for ADHD and dyslexia were found. An approach for ranking genes implicated in the comorbid condition of the two diseases was proposed. The approach is based on ten criteria for ranking genes by their importance, including relevance scores of association between disease and genes, standard methods of gene prioritization, as well as original criteria that take into account the characteristics of an associative gene network and the presence of known polymorphisms in the analyzed genes. Among the top 20 genes with the highest priority DRD2, DRD4, CNTNAP2 and GRIN2B are mentioned in the literature as directly linked with the comorbidity of ADHD and dyslexia. According to the proposed approach, the genes OPRM1, CHRNA4 and SNCA had the highest priority in the development of comorbidity of these two diseases. Additionally, it was revealed that the most relevant genes are involved in biological processes related to signal transduction, positive regulation of transcription from RNA polymerase II promoters, chemical synaptic transmission, response to drugs, ion transmembrane transport, nervous system development, cell adhesion, and neuron migration. CONCLUSIONS The application of methods of reconstruction and analysis of gene networks is a powerful tool for studying the molecular mechanisms of comorbid conditions. The method put forth to rank genes by their importance for the comorbid condition of ADHD and dyslexia was employed to predict genes that play key roles in the development of the comorbid condition. The results can be utilized to plan experiments for the identification of novel candidate genes and search for novel pharmacological targets.
Collapse
Affiliation(s)
- H E Hongyao
- Medical College of Shihezi University, Shihezi, China
| | - J I Chun
- Medical College of Shihezi University, Shihezi, China
| | - Gao Xiaoyan
- Medical College of Shihezi University, Shihezi, China
| | - Liu Fangfang
- Medical College of Shihezi University, Shihezi, China
| | - Zhang Jing
- Medical College of Shihezi University, Shihezi, China
| | - Zhong Lin
- Medical College of Shihezi University, Shihezi, China
| | - Zuo Pengxiang
- Medical College of Shihezi University, Shihezi, China.
| | - Li Zengchun
- Medical College of Shihezi University, Shihezi, China.
| |
Collapse
|
18
|
Mettelman RC, Souquette A, Van de Velde LA, Vegesana K, Allen EK, Kackos CM, Trifkovic S, DeBeauchamp J, Wilson TL, St James DG, Menon SS, Wood T, Jelley L, Webby RJ, Huang QS, Thomas PG. Baseline innate and T cell populations are correlates of protection against symptomatic influenza virus infection independent of serology. Nat Immunol 2023; 24:1511-1526. [PMID: 37592015 PMCID: PMC10566627 DOI: 10.1038/s41590-023-01590-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/13/2023] [Indexed: 08/19/2023]
Abstract
Evidence suggests that innate and adaptive cellular responses mediate resistance to the influenza virus and confer protection after vaccination. However, few studies have resolved the contribution of cellular responses within the context of preexisting antibody titers. Here, we measured the peripheral immune profiles of 206 vaccinated or unvaccinated adults to determine how baseline variations in the cellular and humoral immune compartments contribute independently or synergistically to the risk of developing symptomatic influenza. Protection correlated with diverse and polyfunctional CD4+ and CD8+ T, circulating T follicular helper, T helper type 17, myeloid dendritic and CD16+ natural killer (NK) cell subsets. Conversely, increased susceptibility was predominantly attributed to nonspecific inflammatory populations, including γδ T cells and activated CD16- NK cells, as well as TNFα+ single-cytokine-producing CD8+ T cells. Multivariate and predictive modeling indicated that cellular subsets (1) work synergistically with humoral immunity to confer protection, (2) improve model performance over demographic and serologic factors alone and (3) comprise the most important predictive covariates. Together, these results demonstrate that preinfection peripheral cell composition improves the prediction of symptomatic influenza susceptibility over vaccination, demographics or serology alone.
Collapse
Affiliation(s)
- Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lee-Ann Van de Velde
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kasi Vegesana
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christina M Kackos
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sanja Trifkovic
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jennifer DeBeauchamp
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taylor L Wilson
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Microbiology, Immunology and Biochemistry, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Deryn G St James
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Microbiology, Immunology and Biochemistry, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Smrithi S Menon
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Timothy Wood
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand
| | - Lauren Jelley
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand
| | - Richard J Webby
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Q Sue Huang
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
19
|
McLaren PJ, Porreca I, Iaconis G, Mok HP, Mukhopadhyay S, Karakoc E, Cristinelli S, Pomilla C, Bartha I, Thorball CW, Tough RH, Angelino P, Kiar CS, Carstensen T, Fatumo S, Porter T, Jarvis I, Skarnes WC, Bassett A, DeGorter MK, Sathya Moorthy MP, Tuff JF, Kim EY, Walter M, Simons LM, Bashirova A, Buchbinder S, Carrington M, Cossarizza A, De Luca A, Goedert JJ, Goldstein DB, Haas DW, Herbeck JT, Johnson EO, Kaleebu P, Kilembe W, Kirk GD, Kootstra NA, Kral AH, Lambotte O, Luo M, Mallal S, Martinez-Picado J, Meyer L, Miro JM, Moodley P, Motala AA, Mullins JI, Nam K, Obel N, Pirie F, Plummer FA, Poli G, Price MA, Rauch A, Theodorou I, Trkola A, Walker BD, Winkler CA, Zagury JF, Montgomery SB, Ciuffi A, Hultquist JF, Wolinsky SM, Dougan G, Lever AML, Gurdasani D, Groom H, Sandhu MS, Fellay J. Africa-specific human genetic variation near CHD1L associates with HIV-1 load. Nature 2023; 620:1025-1030. [PMID: 37532928 PMCID: PMC10848312 DOI: 10.1038/s41586-023-06370-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/26/2023] [Indexed: 08/04/2023]
Abstract
HIV-1 remains a global health crisis1, highlighting the need to identify new targets for therapies. Here, given the disproportionate HIV-1 burden and marked human genome diversity in Africa2, we assessed the genetic determinants of control of set-point viral load in 3,879 people of African ancestries living with HIV-1 participating in the international collaboration for the genomics of HIV3. We identify a previously undescribed association signal on chromosome 1 where the peak variant associates with an approximately 0.3 log10-transformed copies per ml lower set-point viral load per minor allele copy and is specific to populations of African descent. The top associated variant is intergenic and lies between a long intergenic non-coding RNA (LINC00624) and the coding gene CHD1L, which encodes a helicase that is involved in DNA repair4. Infection assays in iPS cell-derived macrophages and other immortalized cell lines showed increased HIV-1 replication in CHD1L-knockdown and CHD1L-knockout cells. We provide evidence from population genetic studies that Africa-specific genetic variation near CHD1L associates with HIV replication in vivo. Although experimental studies suggest that CHD1L is able to limit HIV infection in some cell types in vitro, further investigation is required to understand the mechanisms underlying our observations, including any potential indirect effects of CHD1L on HIV spread in vivo that our cell-based assays cannot recapitulate.
Collapse
Affiliation(s)
- Paul J McLaren
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.
| | | | - Gennaro Iaconis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Hoi Ping Mok
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Subhankar Mukhopadhyay
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - István Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian W Thorball
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Riley H Tough
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Paolo Angelino
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Cher S Kiar
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Tommy Carstensen
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Department of Non-Communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Isobel Jarvis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Marianne K DeGorter
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mohana Prasad Sathya Moorthy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey F Tuff
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Eun-Young Kim
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Miriam Walter
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lacy M Simons
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea De Luca
- University Division of Infectious Diseases, Siena University Hospital, Siena, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - James J Goedert
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Eric O Johnson
- GenOmics and Translational Research Center and Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Alex H Kral
- Community Health Research Division, RTI International, Berkeley, CA, USA
| | - Olivier Lambotte
- Université Paris Saclay, Inserm UMR1184, CEA, Le Kremlin-Bicêtre, France
- APHP, Department of Clinical Immunology, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Vaccine and Therapeutics Laboratory, Medical and Scientific Affairs, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Simon Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Javier Martinez-Picado
- University of Vic-Central University of Catalonia, Vic, Spain
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Laurence Meyer
- INSERM U1018, Université Paris-Saclay, Le Kremlin Bicêtre, France
- AP-HP, Hôpital de Bicêtre, Département d'Épidémiologie, Le Kremlin Bicêtre, France
| | - José M Miro
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases Service, Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Pravi Moodley
- National Health Laboratory Service, South Africa and University of KwaZulu-Natal, Durban, South Africa
| | - Ayesha A Motala
- Department of Diabetes and Endocrinology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kireem Nam
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Niels Obel
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Guido Poli
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Matthew A Price
- International AIDS Vaccine Initiative, New York, NY, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ioannis Theodorou
- Laboratoire d'Immunologie, Hôpital Robert Debré Paris, Paris, France
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Frederick National Laboratory for Cancer Research and Cancer Innovative Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Judd F Hultquist
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Deepti Gurdasani
- Queen Mary University of London, London, UK
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Harriet Groom
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Manjinder S Sandhu
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK.
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.
- Omnigen Biodata, Cambridge, UK.
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
20
|
Kasela S, Aguet F, Kim-Hellmuth S, Brown BC, Nachun DC, Tracy RP, Durda P, Liu Y, Taylor KD, Craig Johnson W, Berg DVD, Gabriel S, Gupta N, Smith JD, Blackwell TW, Rotter JI, Ardlie KG, Manichaikul A, Rich SS, Graham Barr R, Lappalainen T. Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546528. [PMID: 37425716 PMCID: PMC10326995 DOI: 10.1101/2023.06.26.546528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Bulk tissue molecular quantitative trait loci (QTLs) have been the starting point for interpreting disease-associated variants, while context-specific QTLs show particular relevance for disease. Here, we present the results of mapping interaction QTLs (iQTLs) for cell type, age, and other phenotypic variables in multi-omic, longitudinal data from blood of individuals of diverse ancestries. By modeling the interaction between genotype and estimated cell type proportions, we demonstrate that cell type iQTLs could be considered as proxies for cell type-specific QTL effects. The interpretation of age iQTLs, however, warrants caution as the moderation effect of age on the genotype and molecular phenotype association may be mediated by changes in cell type composition. Finally, we show that cell type iQTLs contribute to cell type-specific enrichment of diseases that, in combination with additional functional data, may guide future functional studies. Overall, this study highlights iQTLs to gain insights into the context-specificity of regulatory effects.
Collapse
Affiliation(s)
- Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Sarah Kim-Hellmuth
- New York Genome Center, New York, NY, USA
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
- Computational Health Center, Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Brielin C. Brown
- New York Genome Center, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
| | | | - Russell P. Tracy
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Peter Durda
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Yongmei Liu
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kent D. Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - David Van Den Berg
- Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | | | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua D. Smith
- Northwest Genomic Center, University of Washington, Seattle, WA, USA
| | - Thomas W. Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jerome I. Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Ani Manichaikul
- Center for Public health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Stephen S. Rich
- Center for Public health Genomics, University of Virginia, Charlottesville, VA, USA
| | - R. Graham Barr
- Epidemiology and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
21
|
Szelągowski A, Kozakiewicz M. A Glance at Biogenesis and Functionality of MicroRNAs and Their Role in the Neuropathogenesis of Parkinson's Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:7759053. [PMID: 37333462 PMCID: PMC10270766 DOI: 10.1155/2023/7759053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/11/2023] [Accepted: 05/20/2023] [Indexed: 06/20/2023]
Abstract
MicroRNAs (miRNAs) are short, noncoding RNA transcripts. Mammalian miRNA coding sequences are located in introns and exons of genes encoding various proteins. As the central nervous system is the largest source of miRNA transcripts in living organisms, miRNA molecules are an integral part of the regulation of epigenetic activity in physiological and pathological processes. Their activity depends on many proteins that act as processors, transporters, and chaperones. Many variants of Parkinson's disease have been directly linked to specific gene mutations which in pathological conditions are cumulated resulting in the progression of neurogenerative changes. These mutations can often coexist with specific miRNA dysregulation. Dysregulation of different extracellular miRNAs has been confirmed in many studies on the PD patients. It seems reasonable to conduct further research on the role of miRNAs in the pathogenesis of Parkinson's disease and their potential use in future therapies and diagnosis of the disease. This review presents the current state of knowledge about the biogenesis and functionality of miRNAs in the human genome and their role in the neuropathogenesis of Parkinson's disease (PD)-one of the most common neurodegenerative disorders. The article also describes the process of miRNA formation which can occur in two ways-the canonical and noncanonical one. However, the main focus was on miRNA's use in in vitro and in vivo studies in the context of pathophysiology, diagnosis, and treatment of PD. Some issues, especially those regarding the usefulness of miRNAs in PD's diagnostics and especially its treatment, require further research. More standardization efforts and clinical trials on miRNAs are needed.
Collapse
Affiliation(s)
- Adam Szelągowski
- Nicolaus Copernicus University in Toruń Ludwik Rydygier Collegium Medicum in Bydgoszcz, Faculty of Health Sciences, Department of Geriatrics, Bydgoszcz, Poland
| | - Mariusz Kozakiewicz
- Nicolaus Copernicus University in Toruń Ludwik Rydygier Collegium Medicum in Bydgoszcz, Faculty of Health Sciences, Department of Geriatrics, Bydgoszcz, Poland
| |
Collapse
|
22
|
Nott A, Holtman IR. Genetic insights into immune mechanisms of Alzheimer's and Parkinson's disease. Front Immunol 2023; 14:1168539. [PMID: 37359515 PMCID: PMC10285485 DOI: 10.3389/fimmu.2023.1168539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/17/2023] [Indexed: 06/28/2023] Open
Abstract
Microglia, the macrophages of the brain, are vital for brain homeostasis and have been implicated in a broad range of brain disorders. Neuroinflammation has gained traction as a possible therapeutic target for neurodegeneration, however, the precise function of microglia in specific neurodegenerative disorders is an ongoing area of research. Genetic studies offer valuable insights into understanding causality, rather than merely observing a correlation. Genome-wide association studies (GWAS) have identified many genetic loci that are linked to susceptibility to neurodegenerative disorders. (Post)-GWAS studies have determined that microglia likely play an important role in the development of Alzheimer's disease (AD) and Parkinson's disease (PD). The process of understanding how individual GWAS risk loci affect microglia function and mediate susceptibility is complex. A rapidly growing number of publications with genomic datasets and computational tools have formulated new hypotheses that guide the biological interpretation of AD and PD genetic risk. In this review, we discuss the key concepts and challenges in the post-GWAS interpretation of AD and PD GWAS risk alleles. Post-GWAS challenges include the identification of target cell (sub)type(s), causal variants, and target genes. Crucially, the prediction of GWAS-identified disease-risk cell types, variants and genes require validation and functional testing to understand the biological consequences within the pathology of the disorders. Many AD and PD risk genes are highly pleiotropic and perform multiple important functions that might not be equally relevant for the mechanisms by which GWAS risk alleles exert their effect(s). Ultimately, many GWAS risk alleles exert their effect by changing microglia function, thereby altering the pathophysiology of these disorders, and hence, we believe that modelling this context is crucial for a deepened understanding of these disorders.
Collapse
Affiliation(s)
- Alexi Nott
- Department of Brain Sciences, Imperial College London, London, United Kingdom
- UK Dementia Research Institute, Imperial College London, London, United Kingdom
| | - Inge R. Holtman
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| |
Collapse
|
23
|
Baltazar‐Soares M, Britton JR, Pinder A, Harrison AJ, Nunn AD, Quintella BR, Mateus CS, Bolland JD, Dodd JR, Almeida PR, Dominguez Almela V, Andreou D. Seascape genomics reveals limited dispersal and suggests spatially varying selection among European populations of sea lamprey ( Petromyzon marinus). Evol Appl 2023; 16:1169-1183. [PMID: 37360030 PMCID: PMC10286227 DOI: 10.1111/eva.13561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
Sea lamprey Petromyzon marinus is an anadromous and semelparous fish without homing behaviors. Despite being a freshwater, free-living organism for a large part of their life cycle, its adulthood is spent as a parasite of marine vertebrates. In their native European range, while it is well-established that sea lampreys comprise a single nearly-panmictic population, few studies have further explored the evolutionary history of natural populations. Here, we performed the first genome-wide characterization of sea lamprey's genetic diversity in their European natural range. The objectives were to investigate the connectivity among river basins and explore evolutionary processes mediating dispersal during the marine phase, with the sequencing of 186 individuals from 8 locations spanning the North Eastern Atlantic coast and the North Sea with double-digest RAD-sequencing, obtaining a total of 30,910 bi-allelic SNPs. Population genetic analyses reinforced the existence of a single metapopulation encompassing freshwater spawning sites within the North Eastern Atlantic and the North Sea, though the prevalence of private alleles at northern latitudes suggested some limits to the species' dispersal. Seascape genomics suggested a scenario where oxygen concentration and river runoffs impose spatially varying selection across their distribution range. Exploring associations with the abundance of potential hosts further suggested that hake and cod could also impose selective pressures, although the nature of such putative biotic interactions was unresolved. Overall, the identification of adaptive seascapes in a panmictic anadromous species could contribute to conservation practices by providing information for restoration activities to mitigate local extinctions on freshwater sites.
Collapse
Affiliation(s)
- Miguel Baltazar‐Soares
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
- MARE – Marine and Environmental Sciences CentreISPA – Instituto UniversitárioLisbonPortugal
- Department of BiologyUniversity of TurkuTurkuFinland
| | - J. Robert Britton
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Adrian Pinder
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Andrew J. Harrison
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Andrew D. Nunn
- University of HullHull International Fisheries InstituteHullUK
| | - Bernardo R. Quintella
- MARE—Marine and Environmental Sciences CentreUniversity of ÉvoraÉvoraPortugal
- Department of Animal BiologyFaculty of Sciences, University of LisbonLisbonPortugal
| | - Catarina S. Mateus
- MARE—Marine and Environmental Sciences CentreUniversity of ÉvoraÉvoraPortugal
| | | | - Jamie R. Dodd
- University of HullHull International Fisheries InstituteHullUK
| | - Pedro R. Almeida
- MARE—Marine and Environmental Sciences CentreUniversity of ÉvoraÉvoraPortugal
- Department of Biology, School of Sciences and TechnologyUniversity of ÉvoraÉvoraPortugal
| | - Victoria Dominguez Almela
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Demetra Andreou
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| |
Collapse
|
24
|
Zhong C, Wu C, Lin Y, Lin D. Refined expression quantitative trait locus analysis on adenocarcinoma at the gastroesophageal junction reveals susceptibility and prognostic markers. Front Genet 2023; 14:1180500. [PMID: 37265963 PMCID: PMC10230079 DOI: 10.3389/fgene.2023.1180500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/03/2023] [Indexed: 06/03/2023] Open
Abstract
Objectives: This study aimed to explore cell type level expression quantitative trait loci (eQTL) in adenocarcinoma at the gastroesophageal junction (ACGEJ) and identify susceptibility and prognosis markers. Methods: Whole-genome sequencing (WGS) was performed on 120 paired samples from Chinese ACGEJ patients. Germline mutations were detected by GATK tools. RNA sequencing (RNA-seq) data on ACGEJ samples were taken from our previous studies. Public single-cell RNA sequencing (scRNA-seq) data were used to produce the proportion of epithelial cells. Matrix eQTL and a linear mixed model were used to identify condition-specific cis-eQTLs. The R package coloc was used to perform co-localization analysis with the public data of genome-wide association studies (GWASs). Log-rank and Cox regression tests were used to identify survival-associated eQTL and genes. Functions of candidate risk loci were explored by experimental validation. Results: Refined eQTL analyses of paired ACGEJ samples were performed and 2,036 potential ACGEJ-specific eQTLs with East Asian specificity were identified in total. ACGEJ-gain eQTLs were enriched at promoter regions more than ACGEJ-loss eQTLs. rs658524 was identified as the top eQTL close to the transcription start site of its paired gene (CTSW). rs2240191-RASAL1, rs4236599-FOXP2, rs4947311-PSORS1C1, rs13134812-LOC391674, and rs17508585-CDK13-DT were identified as ACGEJ-specific susceptibility eQTLs. rs309483-LINC01355 was associated with the overall survival of ACGEJ patients. We explored functions of candidate eQTLs such as rs658524, rs309483, rs2240191, and rs4947311 by experimental validation. Conclusion: This study provides new risk loci for ACGEJ susceptibility and effective disease prognosis biomarkers.
Collapse
Affiliation(s)
- Ce Zhong
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Lin
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
25
|
Ye X, Zhang H, Li Q, Ren H, Xu X, Li X. Structural-Activity Relationship of Rare Ginsenosides from Red Ginseng in the Treatment of Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24108625. [PMID: 37239965 DOI: 10.3390/ijms24108625] [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: 04/24/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Rare ginsenosides are the major components of red ginseng. However, there has been little research into the relationship between the structure of ginsenosides and their anti-inflammatory activity. In this work, BV-2 cells induced by lipopolysaccharide (LPS) or nigericin, the anti-inflammatory activity of eight rare ginsenosides, and the target proteins expression of AD were compared. In addition, the Morris water maze test, HE staining, thioflavins staining, and urine metabonomics were used to evaluate the effect of Rh4 on AD mice. Our results showed that their configuration influences the anti-inflammatory activity of ginsenosides. Ginsenosides Rk1, Rg5, Rk3, and Rh4 have significant anti-inflammatory activity compared to ginsenosides S-Rh1, R-Rh1, S-Rg3, and R-Rg3. Ginsenosides S-Rh1 and S-Rg3 have more pronounced anti-inflammatory activity than ginsenosides R-Rh1 and R-Rg3, respectively. Furthermore, the two pairs of stereoisomeric ginsenosides can significantly reduce the level of NLRP3, caspase-1, and ASC in BV-2 cells. Interestingly, Rh4 can improve the learning ability of AD mice, improve cognitive impairment, reduce hippocampal neuronal apoptosis and Aβ deposition, and regulate AD-related pathways such as the tricarboxylic acid cycle and the sphingolipid metabolism. Our findings conclude that rare ginsenosides with a double bond have more anti-inflammatory activity than those without, and 20(S)-ginsenosides have more excellent anti-inflammatory activity than 20(R)-ginsenosides.
Collapse
Affiliation(s)
- Xianwen Ye
- Centre of TCM Processing Research, Beijing University of Chinese Medicine, Beijing 102488, China
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
- Institute of Regulatory Science for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Haixia Zhang
- Centre of TCM Processing Research, Beijing University of Chinese Medicine, Beijing 102488, China
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Qian Li
- Centre of TCM Processing Research, Beijing University of Chinese Medicine, Beijing 102488, China
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Hongmin Ren
- Centre of TCM Processing Research, Beijing University of Chinese Medicine, Beijing 102488, China
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xinfang Xu
- Centre of TCM Processing Research, Beijing University of Chinese Medicine, Beijing 102488, China
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
- Institute of Regulatory Science for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xiangri Li
- Centre of TCM Processing Research, Beijing University of Chinese Medicine, Beijing 102488, China
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
- Institute of Regulatory Science for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 102488, China
| |
Collapse
|
26
|
Rizig M, Bandres-Ciga S, Makarious MB, Ojo O, Crea PW, Abiodun O, Levine KS, Abubakar S, Achoru C, Vitale D, Adeniji O, Agabi O, Koretsky MJ, Agulanna U, Hall DA, Akinyemi R, Xie T, Ali M, Shamim EA, Ani-Osheku I, Padmanaban M, Arigbodi O, Standaert DG, Bello A, Dean M, Erameh C, Elsayed I, Farombi T, Okunoye O, Fawale M, Billingsley KJ, Imarhiagbe F, Jerez PA, Iwuozo E, Baker B, Komolafe M, Malik L, Nwani P, Daida K, Nwazor E, Miano-Burkhardt A, Nyandaiti Y, Fang ZH, Obiabo Y, Kluss JH, Odeniyi O, Hernandez D, Odiase F, Tayebi N, Ojini F, Sidranksy E, Onwuegbuzie G, D’Souza AM, Osaigbovo G, Berhe B, Osemwegie N, Reed X, Oshinaike O, Leonard H, Otubogun F, Alvarado CX, Oyakhire S, Ozomma S, Samuel S, Taiwo F, Wahab K, Zubair Y, Iwaki H, Kim JJ, Morris HR, Hardy J, Nalls M, Heilbron K, Norcliffe-Kaufmann L, Blauwendraat C, Houlden H, Singleton A, Okubadejo N. Genome-wide Association Identifies Novel Etiological Insights Associated with Parkinson's Disease in African and African Admixed Populations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.05.23289529. [PMID: 37398408 PMCID: PMC10312852 DOI: 10.1101/2023.05.05.23289529] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background Understanding the genetic mechanisms underlying diseases in ancestrally diverse populations is a critical step towards the realization of the global application of precision medicine. The African and African admixed populations enable mapping of complex traits given their greater levels of genetic diversity, extensive population substructure, and distinct linkage disequilibrium patterns. Methods Here we perform a comprehensive genome-wide assessment of Parkinson's disease (PD) in 197,918 individuals (1,488 cases; 196,430 controls) of African and African admixed ancestry, characterizing population-specific risk, differential haplotype structure and admixture, coding and structural genetic variation and polygenic risk profiling. Findings We identified a novel common risk factor for PD and age at onset at the GBA1 locus (risk, rs3115534-G; OR=1.58, 95% CI = 1.37 - 1.80, P=2.397E-14; age at onset, BETA =-2.004, SE =0.57, P = 0.0005), that was found to be rare in non-African/African admixed populations. Downstream short- and long-read whole genome sequencing analyses did not reveal any coding or structural variant underlying the GWAS signal. However, we identified that this signal mediates PD risk via expression quantitative trait locus (eQTL) mechanisms. While previously identified GBA1 associated disease risk variants are coding mutations, here we suggest a novel functional mechanism consistent with a trend in decreasing glucocerebrosidase activity levels. Given the high population frequency of the underlying signal and the phenotypic characteristics of the homozygous carriers, we hypothesize that this variant may not cause Gaucher disease. Additionally, the prevalence of Gaucher's disease in Africa is low. Interpretation The present study identifies a novel African-ancestry genetic risk factor in GBA1 as a major mechanistic basis of PD in the African and African admixed populations. This striking result contrasts to previous work in Northern European populations, both in terms of mechanism and attributable risk. This finding highlights the importance of understanding population-specific genetic risk in complex diseases, a particularly crucial point as the field moves toward precision medicine in PD clinical trials and while recognizing the need for equitable inclusion of ancestrally diverse groups in such trials. Given the distinctive genetics of these underrepresented populations, their inclusion represents a valuable step towards insights into novel genetic determinants underlying PD etiology. This opens new avenues towards RNA-based and other therapeutic strategies aimed at reducing lifetime risk. Research in Context Evidence Before this Study Our current understanding of Parkinson's disease (PD) is disproportionately based on studying populations of European ancestry, leading to a significant gap in our knowledge about the genetics, clinical characteristics, and pathophysiology in underrepresented populations. This is particularly notable in individuals of African and African admixed ancestries. Over the last two decades, we have witnessed a revolution in the research area of complex genetic diseases. In the PD field, large-scale genome-wide association studies in the European, Asian, and Latin American populations have identified multiple risk loci associated with disease. These include 78 loci and 90 independent signals associated with PD risk in the European population, nine replicated loci and two novel population-specific signals in the Asian population, and a total of 11 novel loci recently nominated through multi-ancestry GWAS efforts.Nevertheless, the African and African admixed populations remain completely unexplored in the context of PD genetics. Added Value of this Study To address the lack of diversity in our research field, this study aimed to conduct the first genome-wide assessment of PD genetics in the African and African admixed populations. Here, we identified a genetic risk factor linked to PD etiology, dissected African-specific differences in risk and age at onset, characterized known genetic risk factors, and highlighted the utility of the African and African admixed risk haplotype substructure for future fine-mapping efforts. We identified a novel disease mechanism via expression changes consistent with decreased GBA1 activity levels. Future large scale single cell expression studies should investigate the neuronal populations in which expression differences are most prominent. This novel mechanism may hold promise for future efficient RNA-based therapeutic strategies such as antisense oligonucleotides or short interfering RNAs aimed at preventing and decreasing disease risk. We envisage that these data generated under the umbrella of the Global Parkinson's Genetics Program (GP2) will shed light on the molecular mechanisms involved in the disease process and might pave the way for future clinical trials and therapeutic interventions. This work represents a valuable resource in an underserved population, supporting pioneering research within GP2 and beyond. Deciphering causal and genetic risk factors in all these ancestries will help determine whether interventions, potential targets for disease modifying treatment, and prevention strategies that are being studied in the European populations are relevant to the African and African admixed populations. Implications of all the Available Evidence We nominate a novel signal impacting GBA1 as the major genetic risk factor for PD in the African and African admixed populations. The present study could inform future GBA1 clinical trials, improving patient stratification. In this regard, genetic testing can help to design trials likely to provide meaningful and actionable answers. It is our hope that these findings may ultimately have clinical utility for this underrepresented population.
Collapse
Affiliation(s)
- Mie Rizig
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London, WC1N 3BG, UK
| | - Sara Bandres-Ciga
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | - Mary B Makarious
- UCL Movement Disorders Centre, University College London, London, WC1N 3BG, UK
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Oluwadamilola Ojo
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
| | - Peter Wild Crea
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Kristin S Levine
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Data Tecnica International, Washington, DC, USA
| | - Sani Abubakar
- Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Charles Achoru
- Jos University Teaching Hospital, Jos, Plateau State, Nigeria
| | - Dan Vitale
- Data Tecnica International, Washington, DC, USA
| | | | - Osigwe Agabi
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
| | - Mathew J Koretsky
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | - Uchechi Agulanna
- Lagos University Teaching Hospital, Idi Araba, Lagos State, Nigeria
| | - Deborah A. Hall
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Rufus Akinyemi
- Neuroscience and Ageing Research Unit, Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Tao Xie
- Department of Neurology, University of Chicago Medicine, Chicago, Illinois, USA
| | - Mohammed Ali
- Federal Teaching Hospital Gombe, Gombe State, Nigeria
| | - Ejaz A. Shamim
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Kaiser Permanente Mid-Atlantic States, Largo, Maryland, USA
- MidAtlantic Permanente Research Institute, Rockville, Maryland, USA
| | | | - Mahesh Padmanaban
- Department of Neurology, University of Chicago Medicine, Chicago, Illinois, USA
| | | | - David G Standaert
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Abiodun Bello
- University of Ilorin Teaching Hospital, Ilorin, Kwara State, Nigeria
| | - Marissa Dean
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Cyril Erameh
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Inas Elsayed
- Faculty of Pharmacy, University of Gezira, Wadmadani, 20, Sudan
| | | | - Olaitan Okunoye
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Michael Fawale
- Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Kimberley J Billingsley
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Pilar Alvarez Jerez
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | | | - Breeana Baker
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | | | - Laksh Malik
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | - Paul Nwani
- Nnamdi Azikiwe University Teaching Hospital, Nnewi, Anambra State, Nigeria
| | - Kensuke Daida
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Ernest Nwazor
- Rivers State University Teaching Hospital, Port Harcourt, Rivers State, Nigeria
| | - Abigail Miano-Burkhardt
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Yakub Nyandaiti
- University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | - Zih-Hua Fang
- German Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany
| | - Yahaya Obiabo
- Federal University of Health Sciences, Otukpo, Benue State, Nigeria
| | - Jillian H. Kluss
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Nahid Tayebi
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Francis Ojini
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
| | - Ellen Sidranksy
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Andrea M. D’Souza
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Bahafta Berhe
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Xylena Reed
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | | | - Hampton Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Data Tecnica International, Washington, DC, USA
| | | | - Chelsea X Alvarado
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Data Tecnica International, Washington, DC, USA
| | | | - Simon Ozomma
- University of Calabar Teaching Hospital, Calabar, Cross River State, Nigeria
| | - Sarah Samuel
- University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | | | - Kolawole Wahab
- University of Ilorin Teaching Hospital, Ilorin, Kwara State, Nigeria
- University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Yusuf Zubair
- National Hospital, Abuja, Federal Capital Territory, Nigeria
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Data Tecnica International, Washington, DC, USA
| | - Jonggeol Jeffrey Kim
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Huw R Morris
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London, WC1N 3BG, UK
| | - John Hardy
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Mike Nalls
- Data Tecnica International, Washington, DC, USA
| | | | | | | | - Cornelis Blauwendraat
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Andrew Singleton
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Njideka Okubadejo
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
| |
Collapse
|
27
|
Strader S, West AB. The interplay between monocytes, α-synuclein and LRRK2 in Parkinson's disease. Biochem Soc Trans 2023; 51:747-758. [PMID: 37013975 PMCID: PMC11110874 DOI: 10.1042/bst20201091] [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: 01/29/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023]
Abstract
The accumulation of aggregated α-synuclein in susceptible neurons in the brain, together with robust activation of nearby myeloid cells, are pathological hallmarks of Parkinson's disease (PD). While microglia represent the dominant type of myeloid cell in the brain, recent genetic and whole-transcriptomic studies have implicated another type of myeloid cell, bone-marrow derived monocytes, in disease risk and progression. Monocytes in circulation harbor high concentrations of the PD-linked enzyme leucine-rich repeat kinase 2 (LRRK2) and respond to both intracellular and extracellular aggregated α-synuclein with a variety of strong pro-inflammatory responses. This review highlights recent findings from studies that functionally characterize monocytes in PD patients, monocytes that infiltrate into cerebrospinal fluid, and emerging analyses of whole myeloid cell populations in the PD-affected brain that include monocyte populations. Central controversies discussed include the relative contribution of monocytes acting in the periphery from those that might engraft in the brain to modify disease risk and progression. We conclude that further investigation into monocyte pathways and responses in PD, especially the discovery of additional markers, transcriptomic signatures, and functional classifications, that better distinguish monocyte lineages and responses in the brain from other types of myeloid cells may reveal points for therapeutic intervention, as well as a better understanding of ongoing inflammation associated with PD.
Collapse
Affiliation(s)
- Samuel Strader
- Duke Center for Neurodegeneration and Neurotherapeutics, Department of Pharmacology and Cancer Biology, Duke University, 3 Genome Court, Durham, 27710, North Carolina, U.S.A
| | - Andrew B. West
- Duke Center for Neurodegeneration and Neurotherapeutics, Department of Pharmacology and Cancer Biology, Duke University, 3 Genome Court, Durham, 27710, North Carolina, U.S.A
| |
Collapse
|
28
|
Zeng L, White CC, Bennett DA, Klein HU, De Jager PL. Genetic insights into the association between inflammatory bowel disease and Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.17.23286845. [PMID: 37131588 PMCID: PMC10153331 DOI: 10.1101/2023.04.17.23286845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Background Myeloid cells, including monocytes, macrophages, microglia, dendritic cells and neutrophils are a part of innate immunity, playing a major role in orchestrating innate and adaptive immune responses. Microglia are the resident myeloid cells of the central nervous system, and many Alzheimer's disease (AD) risk loci are found in or near genes that are highly or sometimes uniquely expressed in myeloid cells. Similarly, inflammatory bowel disease (IBD) loci are also enriched for genes expressed by myeloid cells. However, the extent to which there is overlap between the effects of AD and IBD susceptibility loci in myeloid cells remains poorly described, and the substantial IBD genetic maps may help to accelerate AD research. Methods Here, we leveraged summary statistics from large-scale genome-wide association studies (GWAS) to investigate the causal effect of IBD (including ulcerative colitis and Crohn's disease) variants on AD and AD endophenotypes. Microglia and monocyte expression Quantitative Trait Locus (eQTLs) were used to examine the functional consequences of IBD and AD risk variants enrichment in two different myeloid cell subtypes. Results Our results showed that, while PTK2B is implicated in both diseases and both sets of risk loci are enriched for myeloid genes, AD and IBD susceptibility loci largely implicate distinct sets of genes and pathways. AD loci are significantly more enriched for microglial eQTLs than IBD. We also found that genetically determined IBD is associated with a lower risk of AD, which may driven by a negative effect on the accumulation of neurofibrillary tangles (beta=-1.04, p=0.013). In addition, IBD displayed a significant positive genetic correlation with psychiatric disorders and multiple sclerosis, while AD showed a significant positive genetic correlation with amyotrophic lateral sclerosis. Conclusion To our knowledge, this is the first study to systematically contrast the genetic association between IBD and AD, our findings highlight a possible genetically protective effect of IBD on AD even if the majority of effects on myeloid cell gene expression by the two sets of disease variants are distinct. Thus, IBD myeloid studies may not help to accelerate AD functional studies, but our observation reinforces the role of myeloid cells in the accumulation of tau proteinopathy and provides a new avenue for discovering a protective factor.
Collapse
Affiliation(s)
- Lu Zeng
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer's disease and the Aging brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles C White
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer's disease and the Aging brain, Columbia University Irving Medical Center, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Hans-Ulrich Klein
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer's disease and the Aging brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer's disease and the Aging brain, Columbia University Irving Medical Center, New York, NY, USA
| |
Collapse
|
29
|
Zhuo Y, Li X, He Z, Lu M. Pathological mechanisms of neuroimmune response and multitarget disease-modifying therapies of mesenchymal stem cells in Parkinson's disease. Stem Cell Res Ther 2023; 14:80. [PMID: 37041580 PMCID: PMC10091615 DOI: 10.1186/s13287-023-03280-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 03/13/2023] [Indexed: 04/13/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disease characterized by the degeneration of dopaminergic neurons in the substantia nigra (SN); the etiology and pathological mechanism of the disease are still unclear. Recent studies have shown that the activation of a neuroimmune response plays a key role in the development of PD. Alpha-synuclein (α-Syn), the primary pathological marker of PD, can gather in the SN and trigger a neuroinflammatory response by activating microglia which can further activate the dopaminergic neuron's neuroimmune response mediated by reactive T cells through antigen presentation. It has been shown that adaptive immunity and antigen presentation processes are involved in the process of PD and further research on the neuroimmune response mechanism may open new methods for its prevention and therapy. While current therapeutic regimens are still focused on controlling clinical symptoms, applications such as immunoregulatory strategies can delay the symptoms and the process of neurodegeneration. In this review, we summarized the progression of the neuroimmune response in PD based on recent studies and focused on the use of mesenchymal stem cell (MSC) therapy and challenges as a strategy of disease-modifying therapy with multiple targets.
Collapse
Affiliation(s)
- Yi Zhuo
- Department of Neurosurgery, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, 410000, Hunan, China
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410006, Hunan, China
| | - Xuan Li
- Department of Neurosurgery, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, 410000, Hunan, China
| | - Zhengwen He
- Department of Neurosurgery, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, 410000, Hunan, China.
| | - Ming Lu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410006, Hunan, China.
- Hunan Provincial Key Laboratory of Neurorestoratology, The Second Affiliated Hospital (the 921st Hospital of PLA), Hunan Normal University, Changsha, 410003, Hunan, China.
| |
Collapse
|
30
|
Dong X, Bai Y, Liao Z, Gritsch D, Liu X, Wang T, Borges-Monroy R, Ehrlich A, Serano GE, Feany MB, Beach TG, Scherzer CR. Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535194. [PMID: 37066229 PMCID: PMC10103951 DOI: 10.1101/2023.04.01.535194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Little is known about circular RNAs (circRNAs) in specific brain cells and human neuropsychiatric disease. Here, we systematically identified over 11,039 circRNAs expressed in vulnerable dopamine and pyramidal neurons laser-captured from 190 human brains and non-neuronal cells using ultra-deep, total RNA sequencing. 1,526 and 3,308 circRNAs were custom-tailored to the cell identity of dopamine and pyramidal neurons and enriched in synapse pathways. 88% of Parkinson's and 80% of Alzheimer's disease-associated genes produced circRNAs. circDNAJC6, produced from a juvenile-onset Parkinson's gene, was already dysregulated during prodromal, onset stages of common Parkinson's disease neuropathology. Globally, addiction-associated genes preferentially produced circRNAs in dopamine neurons, autism-associated genes in pyramidal neurons, and cancers in non-neuronal cells. This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA- regulated synaptic specialization in neuropsychiatric diseases.
Collapse
Affiliation(s)
- Xianjun Dong
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Genomics and Bioinformatics Hub, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - Yunfei Bai
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhixiang Liao
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - David Gritsch
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - Xiaoli Liu
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Department of Neurology, Zhejiang Hospital, Zhejiang, China
| | - Tao Wang
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Rebeca Borges-Monroy
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - Alyssa Ehrlich
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mel B. Feany
- Departement of Pathology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Clemens R. Scherzer
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
31
|
Aschenbrenner AC, Bonaguro L. huva: A human variation analysis framework to predict gene perturbation from population-scale multi-omics data. STAR Protoc 2023; 4:102193. [PMID: 36964906 PMCID: PMC10050770 DOI: 10.1016/j.xpro.2023.102193] [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: 12/14/2022] [Revised: 01/29/2023] [Accepted: 03/02/2023] [Indexed: 03/26/2023] Open
Abstract
Variance of gene expression is intrinsic to any given natural population. Here, we present a protocol to analyze this variance using a conditional quasi loss- and gain-of-function approach. The huva (human variation) package takes advantage of population-scale multi-omics data to infer gene function and the relationship between phenotype and gene expression. We describe the steps for setting up the huva workspace, formatting datasets, performing huva experiments, and exporting data. For complete details on the use and execution of this protocol, please refer to Bonaguro et al. (2022).1.
Collapse
Affiliation(s)
- Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany.
| |
Collapse
|
32
|
Maszka P, Kwasniak-Butowska M, Cysewski D, Slawek J, Smolenski RT, Tomczyk M. Metabolomic Footprint of Disrupted Energetics and Amino Acid Metabolism in Neurodegenerative Diseases: Perspectives for Early Diagnosis and Monitoring of Therapy. Metabolites 2023; 13:metabo13030369. [PMID: 36984809 PMCID: PMC10057046 DOI: 10.3390/metabo13030369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
The prevalence of neurodegenerative diseases (NDs) is increasing due to the aging population and improved longevity. They are characterized by a range of pathological hallmarks, including protein aggregation, mitochondrial dysfunction, and oxidative stress. The aim of this review is to summarize the alterations in brain energy and amino acid metabolism in Alzheimer’s disease (AD), Parkinson’s disease (PD), and Huntington’s disease (HD). Based on our findings, we proposed a group of selected metabolites related to disturbed energy or mitochondrial metabolism as potential indicators or predictors of disease. We also discussed the hidden challenges of metabolomics studies in NDs and proposed future directions in this field. We concluded that biochemical parameters of brain energy metabolism disruption (obtained with metabolomics) may have potential application as a diagnostic tool for the diagnosis, prediction, and monitoring of the effectiveness of therapies for NDs. However, more studies are needed to determine the sensitivity of the proposed candidates. We suggested that the most valuable biomarkers for NDs studies could be groups of metabolites combined with other neuroimaging or molecular techniques. To attain clinically applicable results, the integration of metabolomics with other “omic” techniques might be required.
Collapse
Affiliation(s)
- Patrycja Maszka
- Department of Biochemistry, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Magdalena Kwasniak-Butowska
- Division of Neurological and Psychiatric Nursing, Medical University of Gdansk, 80-211 Gdansk, Poland
- Department of Neurology, St. Adalbert Hospital, 80-462 Gdansk, Poland
| | - Dominik Cysewski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Jaroslaw Slawek
- Division of Neurological and Psychiatric Nursing, Medical University of Gdansk, 80-211 Gdansk, Poland
- Department of Neurology, St. Adalbert Hospital, 80-462 Gdansk, Poland
| | - Ryszard T. Smolenski
- Department of Biochemistry, Medical University of Gdansk, 80-210 Gdansk, Poland
- Correspondence: (R.T.S.); (M.T.)
| | - Marta Tomczyk
- Department of Biochemistry, Medical University of Gdansk, 80-210 Gdansk, Poland
- Correspondence: (R.T.S.); (M.T.)
| |
Collapse
|
33
|
Kelly DE, Ramdas S, Ma R, Rawlings-Goss RA, Grant GR, Ranciaro A, Hirbo JB, Beggs W, Yeager M, Chanock S, Nyambo TB, Omar SA, Woldemeskel D, Belay G, Li H, Brown CD, Tishkoff SA. The genetic and evolutionary basis of gene expression variation in East Africans. Genome Biol 2023; 24:35. [PMID: 36829244 PMCID: PMC9951478 DOI: 10.1186/s13059-023-02874-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Mapping of quantitative trait loci (QTL) associated with molecular phenotypes is a powerful approach for identifying the genes and molecular mechanisms underlying human traits and diseases, though most studies have focused on individuals of European descent. While important progress has been made to study a greater diversity of human populations, many groups remain unstudied, particularly among indigenous populations within Africa. To better understand the genetics of gene regulation in East Africans, we perform expression and splicing QTL mapping in whole blood from a cohort of 162 diverse Africans from Ethiopia and Tanzania. We assess replication of these QTLs in cohorts of predominantly European ancestry and identify candidate genes under selection in human populations. RESULTS We find the gene regulatory architecture of African and non-African populations is broadly shared, though there is a considerable amount of variation at individual loci across populations. Comparing our analyses to an equivalently sized cohort of European Americans, we find that QTL mapping in Africans improves the detection of expression QTLs and fine-mapping of causal variation. Integrating our QTL scans with signatures of natural selection, we find several genes related to immunity and metabolism that are highly differentiated between Africans and non-Africans, as well as a gene associated with pigmentation. CONCLUSION Extending QTL mapping studies beyond European ancestry, particularly to diverse indigenous populations, is vital for a complete understanding of the genetic architecture of human traits and can reveal novel functional variation underlying human traits and disease.
Collapse
Affiliation(s)
- Derek E Kelly
- Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Shweta Ramdas
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Rong Ma
- Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Jibril B Hirbo
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - William Beggs
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Meredith Yeager
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Institutes of Health, Rockville, MD, USA
| | - Thomas B Nyambo
- Department of Biochemistry, Kampala International University in Tanzania, Dar Es Salaam, Tanzania
| | - Sabah A Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Dawit Woldemeskel
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Hongzhe Li
- Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher D Brown
- Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah A Tishkoff
- Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, USA.
| |
Collapse
|
34
|
Standaert DG, Harms AS, Childers GM, Webster JM. Disease mechanisms as subtypes: Inflammation in Parkinson disease and related disorders. HANDBOOK OF CLINICAL NEUROLOGY 2023; 193:95-106. [PMID: 36803825 DOI: 10.1016/b978-0-323-85555-6.00011-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Neuroinflammation is a core feature of Parkinson disease (PD) and related disorders. Inflammation is detectable early in PD and persists throughout the disease state. Both the innate and the adaptive arms of the immune system are engaged in both human PD as well as in animal models of the disease. The upstream causes of PD are likely multiple and complex, which makes targeting of disease-modifying therapies based on etiological factors difficult. Inflammation is a broadly shared common mechanism and likely makes an important contribution to progression in most patients with manifest symptoms. Development of treatments targeting neuroinflammation in PD will require an understanding of the specific immune mechanisms which are active, their relative effects on both injury and neurorestoration, as well as the role of key variables likely to modulate the immune response: age, sex, the nature of the proteinopathies present, and the presence of copathologies. Studies characterizing the specific state of immune response in individuals and groups of people affected by PD will be essential to the development of targeted disease-modifying immunotherapies.
Collapse
Affiliation(s)
- David G Standaert
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Ashley S Harms
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gabrielle M Childers
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jhodi M Webster
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States
| |
Collapse
|
35
|
Imbach KJ, Treadway NJ, Prahalad V, Kosters A, Arafat D, Duan M, Gergely T, Ponder LA, Chandrakasan S, Ghosn EEB, Prahalad S, Gibson G. Profiling the peripheral immune response to ex vivo TNF stimulation in untreated juvenile idiopathic arthritis using single cell RNA sequencing. Pediatr Rheumatol Online J 2023; 21:17. [PMID: 36793127 PMCID: PMC9929251 DOI: 10.1186/s12969-023-00787-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 01/08/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Juvenile Idiopathic Arthritis (JIA) is an autoimmune disease with a heterogenous clinical presentation and unpredictable response to available therapies. This personalized transcriptomics study sought proof-of-concept for single-cell RNA sequencing to characterize patient-specific immune profiles. METHODS Whole blood samples from six untreated children, newly diagnosed with JIA, and two healthy controls were cultured for 24 h with or without ex vivo TNF stimulation and subjected to scRNAseq to examine cellular populations and transcript expression in PBMCs. A novel analytical pipeline, scPool, was developed wherein cells are first pooled into pseudocells prior to expression analysis, facilitating variance partitioning of the effects of TNF stimulus, JIA disease status, and individual donor. RESULTS Seventeen robust immune cell-types were identified, the abundance of which was significantly affected by TNF stimulus, which resulted in notable elevation of memory CD8 + T-cells and NK56 cells, but down-regulation of naïve B-cell proportions. Memory CD8 + and CD4 + T-cells were also both reduced in the JIA cases relative to two controls. Significant differential expression responses to TNF stimulus were also characterized, with monocytes showing more transcriptional shifts than T-lymphocyte subsets, while the B-cell response was more limited. We also show that donor variability exceeds the small degree of possible intrinsic differentiation between JIA and control profiles. An incidental finding of interest was association of HLA-DQA2 and HLA-DRB5 expression with JIA status. CONCLUSIONS These results support the development of personalized immune-profiling combined with ex-vivo immune stimulation for evaluation of patient-specific modes of immune cell activity in autoimmune rheumatic disease.
Collapse
Affiliation(s)
- Kathleen J. Imbach
- grid.213917.f0000 0001 2097 4943Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Nicole J. Treadway
- grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30223 USA
| | - Vaishali Prahalad
- grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30223 USA
| | - Astrid Kosters
- grid.189967.80000 0001 0941 6502Lowance Center for Human Immunology, Division of Immunology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30223 USA
| | - Dalia Arafat
- grid.213917.f0000 0001 2097 4943Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Meixue Duan
- grid.213917.f0000 0001 2097 4943Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Talia Gergely
- grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30223 USA
| | - Lori A. Ponder
- grid.428158.20000 0004 0371 6071Center for Immunity and Applied Genomics, Children’s Healthcare of Atlanta, Atlanta, GA 30223 USA
| | - Shanmuganathan Chandrakasan
- grid.428158.20000 0004 0371 6071Center for Immunity and Applied Genomics, Children’s Healthcare of Atlanta, Atlanta, GA 30223 USA ,grid.189967.80000 0001 0941 6502Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30223 USA
| | - Eliver E. B. Ghosn
- grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30223 USA ,grid.189967.80000 0001 0941 6502Lowance Center for Human Immunology, Division of Immunology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30223 USA ,grid.428158.20000 0004 0371 6071Center for Immunity and Applied Genomics, Children’s Healthcare of Atlanta, Atlanta, GA 30223 USA
| | - Sampath Prahalad
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30223, USA. .,Center for Immunity and Applied Genomics, Children's Healthcare of Atlanta, Atlanta, GA, 30223, USA. .,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30223, USA.
| | - Greg Gibson
- grid.213917.f0000 0001 2097 4943Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA ,grid.428158.20000 0004 0371 6071Center for Immunity and Applied Genomics, Children’s Healthcare of Atlanta, Atlanta, GA 30223 USA
| |
Collapse
|
36
|
Aslanis I, Krokidis MG, Dimitrakopoulos GN, Vrahatis AG. Identifying Network Biomarkers for Alzheimer's Disease Using Single-Cell RNA Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:207-214. [PMID: 37525046 DOI: 10.1007/978-3-031-31978-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
System-level network-based approaches are an emerging field in the biomedical domain since biological networks can be used to analyze complicated biological processes and complex human disorders more efficiently. Network biomarkers are groups of interconnected molecular components causing perturbations in the entire network topology that can be used as indicators of pathogenic biological processes when studying a given disease. Although in the last years computational systems-based approaches have gained ground on the path to discovering new network biomarkers, in complex diseases like Alzheimer's disease (AD), this approach has still much to offer. Especially the adoption of single-cell RNA sequencing (scRNA-seq) has now become the dominant technology for the study of stochastic gene expression. Toward this orientation, we propose an R workflow that extracts disease-perturbed subpathways within a pathway network. We construct a gene-gene interaction network integrated with scRNA-seq expression profiles, and after network processing and pruning, the most active subnetworks are isolated from the entire network topology. The proposed methodology was applied on a real AD-based scRNA-seq data, providing already existing and new potential AD biomarkers in gene network context.
Collapse
Affiliation(s)
- Ioannis Aslanis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece
| | - Marios G Krokidis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece
| | - Georgios N Dimitrakopoulos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece
| | - Aristidis G Vrahatis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece
| |
Collapse
|
37
|
Asante I, Louie S, Yassine HN. Uncovering mechanisms of brain inflammation in Alzheimer's disease with APOE4: Application of single cell-type lipidomics. Ann N Y Acad Sci 2022; 1518:84-105. [PMID: 36200578 PMCID: PMC10092192 DOI: 10.1111/nyas.14907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A chronic state of unresolved inflammation in Alzheimer's disease (AD) is intrinsically involved with the remodeling of brain lipids. This review highlights the effect of carrying the apolipoprotein E ε4 allele (APOE4) on various brain cell types in promoting an unresolved inflammatory state. Among its pleotropic effects on brain lipids, we focus on APOE4's activation of Ca2+ -dependent phospholipase A2 (cPLA2) and its effects on arachidonic acid, eicosapentaenoic acid, and docosahexaenoic acid signaling cascades in the brain. During the process of neurodegeneration, various brain cell types, such as astrocytes, microglia, and neurons, together with the neurovascular unit, develop distinct inflammatory phenotypes that impact their functions and have characteristic lipidomic fingerprints. We propose that lipidomic phenotyping of single cell-types harvested from brains differing by age, sex, disease severity stage, and dietary and genetic backgrounds can be employed to probe mechanisms of neurodegeneration. A better understanding of the brain cellular inflammatory/lipidomic response promises to guide the development of nutritional and drug interventions for AD dementia.
Collapse
Affiliation(s)
- Isaac Asante
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Stan Louie
- School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Hussein N Yassine
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
38
|
Differential compartmentalization of myeloid cell phenotypes and responses towards the CNS in Alzheimer's disease. Nat Commun 2022; 13:7210. [PMID: 36418303 PMCID: PMC9684147 DOI: 10.1038/s41467-022-34719-2] [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: 02/25/2022] [Accepted: 11/01/2022] [Indexed: 11/27/2022] Open
Abstract
Myeloid cells are suggested as an important player in Alzheimer´s disease (AD). However, its continuum of phenotypic and functional changes across different body compartments and their use as a biomarker in AD remains elusive. Here, we perform multiple state-of-the-art analyses to phenotypically and metabolically characterize immune cells between peripheral blood (n = 117), cerebrospinal fluid (CSF, n = 117), choroid plexus (CP, n = 13) and brain parenchyma (n = 13). We find that CSF cells increase expression of markers involved in inflammation, phagocytosis, and metabolism. Changes in phenotype of myeloid cells from AD patients are more pronounced in CP and brain parenchyma and upon in vitro stimulation, suggesting that AD-myeloid cells are more vulnerable to environmental changes. Our findings underscore the importance of myeloid cells in AD and the detailed characterization across body compartments may serve as a resource for future studies focusing on the assessment of these cells as biomarkers in AD.
Collapse
|
39
|
Bonaguro L, Schulte-Schrepping J, Carraro C, Sun LL, Reiz B, Gemünd I, Saglam A, Rahmouni S, Georges M, Arts P, Hoischen A, Joosten LA, van de Veerdonk FL, Netea MG, Händler K, Mukherjee S, Ulas T, Schultze JL, Aschenbrenner AC. Human variation in population-wide gene expression data predicts gene perturbation phenotype. iScience 2022; 25:105328. [PMID: 36310583 PMCID: PMC9614568 DOI: 10.1016/j.isci.2022.105328] [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: 03/02/2022] [Revised: 07/13/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022] Open
Abstract
Population-scale datasets of healthy individuals capture genetic and environmental factors influencing gene expression. The expression variance of a gene of interest (GOI) can be exploited to set up a quasi loss- or gain-of-function "in population" experiment. We describe here an approach, huva (human variation), taking advantage of population-scale multi-layered data to infer gene function and relationships between phenotypes and expression. Within a reference dataset, huva derives two experimental groups with LOW or HIGH expression of the GOI, enabling the subsequent comparison of their transcriptional profile and functional parameters. We demonstrate that this approach robustly identifies the phenotypic relevance of a GOI allowing the stratification of genes according to biological functions, and we generalize this concept to almost 16,000 genes in the human transcriptome. Additionally, we describe how huva predicts monocytes to be the major cell type in the pathophysiology of STAT1 mutations, evidence validated in a clinical cohort.
Collapse
Affiliation(s)
- Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Laura L. Sun
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | | | - Ioanna Gemünd
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, 3010 VIC, Australia
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
| | - Souad Rahmouni
- Unit of Animal Genomics, GIGA-Institute, University of Liège, 4000 Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-Institute, University of Liège, 4000 Liège, Belgium
| | - Peer Arts
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, 5000 SA, Australia
| | - Alexander Hoischen
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Leo A.B. Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Medical Genetics, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Frank L. van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Immunology and Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Kristian Händler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Sach Mukherjee
- Statistics and Machine Learning, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Anna C. Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| |
Collapse
|
40
|
Xu L, Li L, Pan C, Song J, Zhang C, Wu X, Hu F, Liu X, Zhang Z, Zhang Z. Erythropoietin signaling in peripheral macrophages is required for systemic β-amyloid clearance. EMBO J 2022; 41:e111038. [PMID: 36215698 PMCID: PMC9670197 DOI: 10.15252/embj.2022111038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 01/13/2023] Open
Abstract
Impaired clearance of beta-amyloid (Aβ) is a primary cause of sporadic Alzheimer's disease (AD). Aβ clearance in the periphery contributes to reducing brain Aβ levels and preventing Alzheimer's disease pathogenesis. We show here that erythropoietin (EPO) increases phagocytic activity, levels of Aβ-degrading enzymes, and Aβ clearance in peripheral macrophages via PPARγ. Erythropoietin is also shown to suppress Aβ-induced inflammatory responses. Deletion of EPO receptor in peripheral macrophages leads to increased peripheral and brain Aβ levels and exacerbates Alzheimer's-associated brain pathologies and behavioral deficits in AD-model mice. Moreover, erythropoietin signaling is impaired in peripheral macrophages of old AD-model mice. Exogenous erythropoietin normalizes impaired EPO signaling and dysregulated functions of peripheral macrophages in old AD-model mice, promotes systemic Aβ clearance, and alleviates disease progression. Erythropoietin treatment may represent a potential therapeutic approach for Alzheimer's disease.
Collapse
Affiliation(s)
- Lu Xu
- School of Basic Medical SciencesNanjing Medical UniversityNanjingChina
- Key Laboratory of Antibody Technique of Ministry of HealthNanjing Medical UniversityNanjingChina
- Department of Neurology, Sir Run Run HospitalNanjing Medical UniversityNanjingChina
| | - Lei Li
- School of Basic Medical SciencesNanjing Medical UniversityNanjingChina
| | - Cai‐Long Pan
- School of Basic Medical SciencesNanjing Medical UniversityNanjingChina
- Key Laboratory of Antibody Technique of Ministry of HealthNanjing Medical UniversityNanjingChina
| | - Jing‐Jing Song
- School of Basic Medical SciencesNanjing Medical UniversityNanjingChina
| | - Chen‐Yang Zhang
- School of Basic Medical SciencesNanjing Medical UniversityNanjingChina
| | - Xiang‐Hui Wu
- School of Basic Medical SciencesNanjing Medical UniversityNanjingChina
| | - Fan Hu
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Xue Liu
- School of Basic Medical SciencesNanjing Medical UniversityNanjingChina
| | - Zhiren Zhang
- Institute of ImmunologyArmy Medical UniversityChongqingChina
| | - Zhi‐Yuan Zhang
- School of Basic Medical SciencesNanjing Medical UniversityNanjingChina
- Key Laboratory of Antibody Technique of Ministry of HealthNanjing Medical UniversityNanjingChina
- Department of Neurology, Sir Run Run HospitalNanjing Medical UniversityNanjingChina
- Key Laboratory of Human Functional Genomics of Jiangsu ProvinceNanjing Medical UniversityNanjingChina
| |
Collapse
|
41
|
Romero-Molina C, Garretti F, Andrews SJ, Marcora E, Goate AM. Microglial efferocytosis: Diving into the Alzheimer's disease gene pool. Neuron 2022; 110:3513-3533. [PMID: 36327897 DOI: 10.1016/j.neuron.2022.10.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
Abstract
Genome-wide association studies and functional genomics studies have linked specific cell types, genes, and pathways to Alzheimer's disease (AD) risk. In particular, AD risk alleles primarily affect the abundance or structure, and thus the activity, of genes expressed in macrophages, strongly implicating microglia (the brain-resident macrophages) in the etiology of AD. These genes converge on pathways (endocytosis/phagocytosis, cholesterol metabolism, and immune response) with critical roles in core macrophage functions such as efferocytosis. Here, we review these pathways, highlighting relevant genes identified in the latest AD genetics and genomics studies, and describe how they may contribute to AD pathogenesis. Investigating the functional impact of AD-associated variants and genes in microglia is essential for elucidating disease risk mechanisms and developing effective therapeutic approaches.
Collapse
Affiliation(s)
- Carmen Romero-Molina
- Ronald M. Loeb Center for Alzheimer's Disease, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA; Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Garretti
- Ronald M. Loeb Center for Alzheimer's Disease, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA; Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shea J Andrews
- Ronald M. Loeb Center for Alzheimer's Disease, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA; Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Edoardo Marcora
- Ronald M. Loeb Center for Alzheimer's Disease, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA; Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Alison M Goate
- Ronald M. Loeb Center for Alzheimer's Disease, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA; Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
42
|
Dressman D, Buttrick T, Cimpean M, Bennett D, Menon V, Bradshaw EM, Vardarajan B, Elyaman W. Genotype-phenotype correlation of T-cell subtypes reveals senescent and cytotoxic genes in Alzheimer's disease. Hum Mol Genet 2022; 31:3355-3366. [PMID: 35640154 PMCID: PMC9523563 DOI: 10.1093/hmg/ddac126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022] Open
Abstract
Recent studies identifying expression quantitative trait loci (eQTLs) in immune cells have uncovered important links between disease risk alleles and gene expression trends in monocytes, T cells and other cell types. However, these studies are generally done with young, healthy subjects, limiting the utility of their findings for age-related conditions such as Alzheimer's disease (AD). We have performed RNA sequencing on four T-cell subsets in genome-wide genotyped and well-characterized AD subjects and age- and sex-matched controls from the Religious Orders Study/Memory and Aging Project. We correlated gene expression data with AD neuropathological traits and with single-nucleotide polymorphisms to detect eQTLs. We identified several significant genes involved in T-cell senescence and cytotoxicity, consistent with T-cell RNA sequencing studies in aged/AD cohorts. We identified unexpected eQTLs previously associated with neuropsychiatric disease traits. Finally, we discovered that pathways related to axon guidance and synaptic function were enriched among trans-eQTLs in coding regions of the genome. Our data strengthen the potential link between T-cell senescence and age-related neurodegenerative disease. In addition, our eQTL data suggest that T-cell phenotypes may influence neuropsychiatric disorders and can be influenced by genes involved in neurodevelopmental processes.
Collapse
Affiliation(s)
- Dallin Dressman
- Department of Pharmacology, Columbia University, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA
| | | | | | - David Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Vilas Menon
- Department of Neurology, Columbia University, New York, NY 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Elizabeth M Bradshaw
- Department of Neurology, Columbia University, New York, NY 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Badri Vardarajan
- Department of Neurology, Columbia University, New York, NY 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Wassim Elyaman
- Department of Neurology, Columbia University, New York, NY 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA
| |
Collapse
|
43
|
Pudjihartono M, Perry JK, Print C, O'Sullivan JM, Schierding W. Interpretation of the role of germline and somatic non-coding mutations in cancer: expression and chromatin conformation informed analysis. Clin Epigenetics 2022; 14:120. [PMID: 36171609 PMCID: PMC9520844 DOI: 10.1186/s13148-022-01342-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There has been extensive scrutiny of cancer driving mutations within the exome (especially amino acid altering mutations) as these are more likely to have a clear impact on protein functions, and thus on cell biology. However, this has come at the neglect of systematic identification of regulatory (non-coding) variants, which have recently been identified as putative somatic drivers and key germline risk factors for cancer development. Comprehensive understanding of non-coding mutations requires understanding their role in the disruption of regulatory elements, which then disrupt key biological functions such as gene expression. MAIN BODY We describe how advancements in sequencing technologies have led to the identification of a large number of non-coding mutations with uncharacterized biological significance. We summarize the strategies that have been developed to interpret and prioritize the biological mechanisms impacted by non-coding mutations, focusing on recent annotation of cancer non-coding variants utilizing chromatin states, eQTLs, and chromatin conformation data. CONCLUSION We believe that a better understanding of how to apply different regulatory data types into the study of non-coding mutations will enhance the discovery of novel mechanisms driving cancer.
Collapse
Affiliation(s)
| | - Jo K Perry
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Cris Print
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Australian Parkinson's Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
| |
Collapse
|
44
|
The Innate and Adaptive Immune Cells in Alzheimer’s and Parkinson’s Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1315248. [PMID: 36211819 PMCID: PMC9534688 DOI: 10.1155/2022/1315248] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/14/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common neurodegenerative disorders of the central nervous system (CNS). Increasing evidence supports the view that dysfunction of innate immune cells initiated by accumulated and misfolded proteins plays essential roles in the pathogenesis and progression of these diseases. The TLR family was found to be involved in the regulation of microglial function in the pathogenesis and progression of AD or PD, making it as double-edged sword in these diseases. Altered function of peripheral innate immune cells was found in AD and PD and thus contributed to the development and progression of AD and PD. Alteration of different subsets of T cells was found in the peripheral blood and CNS in AD and PD. The CNS-infiltrating T cells can exert both neuroprotective and neurotoxic effects in the pathogenesis and progression. Here, we review recent evidences for the roles of innate and adaptive immune cells in the pathogenesis and progression of AD and PD.
Collapse
|
45
|
Gate D. New Perspectives on Immune Involvement in Parkinson’s Disease Pathogenesis. JOURNAL OF PARKINSON'S DISEASE 2022; 12:S5-S11. [PMID: 35811535 PMCID: PMC9535554 DOI: 10.3233/jpd-223240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Accumulating evidence implicates immune dysfunction in the etiology of Parkinson’s disease (PD). For instance, impaired cellular and humoral immune responses are emerging as established pathological hallmarks in PD. Further, in experimental models of PD, inflammatory cell activation and immune dysregulation are evident. Genetic and epidemiologic studies have drawn associations between autoimmune disease and PD. Distillation of these various lines of evidence indicates dysregulated immunogenetics as a primary risk factor for PD. This article will present novel perspectives on the association between genetic risk factors and immune processes in PD. The objective of this work is to synthesize the data surrounding the role of immunogenetics in PD to maximize the potential of targeting the immune system as a therapeutic modality.
Collapse
Affiliation(s)
- David Gate
- Department of Neurology, Northwestern University, Chicago, IL, USA
| |
Collapse
|
46
|
Gilchrist JJ, Auckland K, Parks T, Mentzer AJ, Goldblatt L, Naranbhai V, Band G, Rockett KA, Toure OB, Konate S, Sissoko S, Djimdé AA, Thera MA, Doumbo OK, Sow S, Floyd S, Pönnighaus JM, Warndorff DK, Crampin AC, Fine PEM, Fairfax BP, Hill AVS. Genome-wide association study of leprosy in Malawi and Mali. PLoS Pathog 2022; 18:e1010312. [PMID: 36121873 PMCID: PMC9624411 DOI: 10.1371/journal.ppat.1010312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 11/01/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022] Open
Abstract
Leprosy is a chronic infection of the skin and peripheral nerves caused by Mycobacterium leprae. Despite recent improvements in disease control, leprosy remains an important cause of infectious disability globally. Large-scale genetic association studies in Chinese, Vietnamese and Indian populations have identified over 30 susceptibility loci for leprosy. There is a significant burden of leprosy in Africa, however it is uncertain whether the findings of published genetic association studies are generalizable to African populations. To address this, we conducted a genome-wide association study (GWAS) of leprosy in Malawian (327 cases, 436 controls) and Malian (247 cases, 368 controls) individuals. In that analysis, we replicated four risk loci previously reported in China, Vietnam and India; MHC Class I and II, LACC1 and SLC29A3. We further identified a novel leprosy susceptibility locus at 10q24 (rs2015583; combined p = 8.81 × 10-9; OR = 0.51 [95% CI 0.40 - 0.64]). Using publicly-available data we characterise regulatory activity at this locus, identifying ACTR1A as a candidate mediator of leprosy risk. This locus shows evidence of recent positive selection and demonstrates pleiotropy with established risk loci for inflammatory bowel disease and childhood-onset asthma. A shared genetic architecture for leprosy and inflammatory bowel disease has been previously described. We expand on this, strengthening the hypothesis that selection pressure driven by leprosy has shaped the evolution of autoimmune and atopic disease in modern populations. More broadly, our data highlights the importance of defining the genetic architecture of disease across genetically diverse populations, and that disease insights derived from GWAS in one population may not translate to all affected populations.
Collapse
Affiliation(s)
- James J. Gilchrist
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Vivek Naranbhai
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kirk A. Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ousmane B. Toure
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Salimata Konate
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sibiri Sissoko
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye A. Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou A. Thera
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ogobara K. Doumbo
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Samba Sow
- Center for Vaccine Development, Bamako, Mali
| | - Sian Floyd
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jörg M. Pönnighaus
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - David K. Warndorff
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Amelia C. Crampin
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Paul E. M. Fine
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Benjamin P. Fairfax
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
| |
Collapse
|
47
|
Riboldi GM, Vialle RA, Navarro E, Udine E, de Paiva Lopes K, Humphrey J, Allan A, Parks M, Henderson B, Astudillo K, Argyrou C, Zhuang M, Sikder T, Oriol Narcis J, Kumar SD, Janssen W, Sowa A, Comi GP, Di Fonzo A, Crary JF, Frucht SJ, Raj T. Transcriptome deregulation of peripheral monocytes and whole blood in GBA-related Parkinson's disease. Mol Neurodegener 2022; 17:52. [PMID: 35978378 PMCID: PMC9386994 DOI: 10.1186/s13024-022-00554-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic mutations in beta-glucocerebrosidase (GBA) represent the major genetic risk factor for Parkinson's disease (PD). GBA participates in both the endo-lysosomal pathway and the immune response, two important mechanisms involved in the pathogenesis of PD. However, modifiers of GBA penetrance have not yet been fully elucidated. METHODS We characterized the transcriptomic profiles of circulating monocytes in a population of patients with PD and healthy controls (CTRL) with and without GBA variants (n = 23 PD/GBA, 13 CTRL/GBA, 56 PD, 66 CTRL) and whole blood (n = 616 PD, 362 CTRL, 127 PD/GBA, 165 CTRL/GBA). Differential expression analysis, pathway enrichment analysis, and outlier detection were performed. Ultrastructural characterization of isolated CD14+ monocytes in the four groups was also performed through electron microscopy. RESULTS We observed hundreds of differentially expressed genes and dysregulated pathways when comparing manifesting and non-manifesting GBA mutation carriers. Specifically, when compared to idiopathic PD, PD/GBA showed dysregulation in genes involved in alpha-synuclein degradation, aging and amyloid processing. Gene-based outlier analysis confirmed the involvement of lysosomal, membrane trafficking, and mitochondrial processing in manifesting compared to non-manifesting GBA-carriers, as also observed at the ultrastructural levels. Transcriptomic results were only partially replicated in an independent cohort of whole blood samples, suggesting cell-type specific changes. CONCLUSIONS Overall, our transcriptomic analysis of primary monocytes identified gene targets and biological processes that can help in understanding the pathogenic mechanisms associated with GBA mutations in the context of PD.
Collapse
Affiliation(s)
- Giulietta Maria Riboldi
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, 222 East 41st street, New York, NY, 10017, USA
| | - Ricardo A Vialle
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA.,Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA.,Department of Biochemistry and Molecular Biology (Universidad Complutense de Madrid) & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Evan Udine
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Katia de Paiva Lopes
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA.,Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Amanda Allan
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Madison Parks
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Brooklyn Henderson
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, 222 East 41st street, New York, NY, 10017, USA
| | - Kelly Astudillo
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, 222 East 41st street, New York, NY, 10017, USA
| | - Charalambos Argyrou
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Maojuan Zhuang
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Tamjeed Sikder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15th Floor, New York, NY, 10029, USA.,Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Room 9-22, New York, NY, 10029, USA
| | - J Oriol Narcis
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Shilpa Dilip Kumar
- Microscopy Core and Advanced Bioimaging Center at the Icahn School of Medicine at Mount Sinai Center, 1468 Madison Avenue, Room 18-250, New York, NY, 10029, USA
| | - William Janssen
- Microscopy Core and Advanced Bioimaging Center at the Icahn School of Medicine at Mount Sinai Center, 1468 Madison Avenue, Room 18-250, New York, NY, 10029, USA
| | - Allison Sowa
- Department of Pathology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15th Floor, New York, NY, 10029, USA
| | - Giacomo P Comi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy.,Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 35, 20122, Milano, MI, Italy
| | - Alessio Di Fonzo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy.,Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 35, 20122, Milano, MI, Italy
| | - John F Crary
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15th Floor, New York, NY, 10029, USA.,Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Room 9-22, New York, NY, 10029, USA
| | - Steven J Frucht
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, 222 East 41st street, New York, NY, 10017, USA
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA. .,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA. .,Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, ICAHN 10-70E, New York, NY, 10029-6574, USA.
| |
Collapse
|
48
|
Grotemeyer A, McFleder RL, Wu J, Wischhusen J, Ip CW. Neuroinflammation in Parkinson's Disease - Putative Pathomechanisms and Targets for Disease-Modification. Front Immunol 2022; 13:878771. [PMID: 35663989 PMCID: PMC9158130 DOI: 10.3389/fimmu.2022.878771] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/20/2022] [Indexed: 12/15/2022] Open
Abstract
Parkinson’s disease (PD) is a progressive and debilitating chronic disease that affects more than six million people worldwide, with rising prevalence. The hallmarks of PD are motor deficits, the spreading of pathological α-synuclein clusters in the central nervous system, and neuroinflammatory processes. PD is treated symptomatically, as no causally-acting drug or procedure has been successfully established for clinical use. Various pathways contributing to dopaminergic neuron loss in PD have been investigated and described to interact with the innate and adaptive immune system. We discuss the possible contribution of interconnected pathways related to the immune response, focusing on the pathophysiology and neurodegeneration of PD. In addition, we provide an overview of clinical trials targeting neuroinflammation in PD.
Collapse
Affiliation(s)
| | | | - Jingjing Wu
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany
| | - Jörg Wischhusen
- Section for Experimental Tumor Immunology, Department of Obstetrics and Gynecology, University Hospital of Würzburg, Würzburg, Germany
| | - Chi Wang Ip
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany
| |
Collapse
|
49
|
Gopinath A, Mackie P, Hashimi B, Buchanan AM, Smith AR, Bouchard R, Shaw G, Badov M, Saadatpour L, Gittis A, Ramirez-Zamora A, Okun MS, Streit WJ, Hashemi P, Khoshbouei H. DAT and TH expression marks human Parkinson's disease in peripheral immune cells. NPJ Parkinsons Dis 2022; 8:72. [PMID: 35672374 PMCID: PMC9174333 DOI: 10.1038/s41531-022-00333-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/11/2022] [Indexed: 12/26/2022] Open
Abstract
Parkinson's disease (PD) is marked by a loss of dopamine neurons, decreased dopamine transporter (DAT) and tyrosine hydroxylase (TH) expression. However, this validation approach cannot be used for diagnostic, drug effectiveness or investigational purposes in human patients because midbrain tissue is accessible postmortem. PD pathology affects both the central nervous and peripheral immune systems. Therefore, we immunophenotyped blood samples of PD patients for the presence of myeloid derived suppressor cells (MDSCs) and discovered that DAT+/TH+ monocytic MDSCs, but not granulocytic MDSCs are increased, suggesting a targeted immune response to PD. Because in peripheral immune cells DAT activity underlies an immune suppressive mechanism, we investigated whether expression levels of DAT and TH in the peripheral immune cells marks PD. We found drug naïve PD patients exhibit differential DAT+/TH+ expression in peripheral blood mononuclear cells (PBMCs) compared to aged/sex matched healthy subjects. While total PBMCs are not different between the groups, the percentage of DAT+/TH+ PBMCs was significantly higher in drug naïve PD patients compared to healthy controls irrespective of age, gender, disease duration, disease severity or treatment type. Importantly, treatment for PD negatively modulates DAT+/TH+ expressing PBMCs. Neither total nor the percentage of DAT+/TH+ PBMCs were altered in the Alzheimer's disease cohort. The mechanistic underpinning of this discovery in human PD was revealed when these findings were recapitulated in animal models of PD. The reverse translational experimental strategy revealed that alterations in dopaminergic markers in peripheral immune cells are due to the disease associated changes in the CNS. Our study demonstrates that the dopaminergic machinery on peripheral immune cells displays an association with human PD, with exciting implications in facilitating diagnosis and investigation of human PD pathophysiology.
Collapse
Affiliation(s)
- Adithya Gopinath
- Department of Neuroscience, University of Florida, Gainesville, FL, USA.
| | - Phillip Mackie
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Basil Hashimi
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | | | - Aidan R Smith
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | | | - Gerry Shaw
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
- EnCor Biotechnology, Inc, Gainesville, FL, USA
| | - Martin Badov
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Leila Saadatpour
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
- Department of Neurology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Aryn Gittis
- Carnegie Mellon University, Pittsburgh, PA, USA
| | - Adolfo Ramirez-Zamora
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, UF Health, Gainesville, FL, USA
| | - Michael S Okun
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, UF Health, Gainesville, FL, USA
| | - Wolfgang J Streit
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Parastoo Hashemi
- University of South Carolina, Columbia, SC, USA
- Department of Bioengineering, Imperial College, London, UK
| | - Habibeh Khoshbouei
- Department of Neuroscience, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
50
|
Oelen R, de Vries DH, Brugge H, Gordon MG, Vochteloo M, Ye CJ, Westra HJ, Franke L, van der Wijst MGP. Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure. Nat Commun 2022; 13:3267. [PMID: 35672358 PMCID: PMC9174272 DOI: 10.1038/s41467-022-30893-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 05/24/2022] [Indexed: 12/15/2022] Open
Abstract
The host's gene expression and gene regulatory response to pathogen exposure can be influenced by a combination of the host's genetic background, the type of and exposure time to pathogens. Here we provide a detailed dissection of this using single-cell RNA-sequencing of 1.3M peripheral blood mononuclear cells from 120 individuals, longitudinally exposed to three different pathogens. These analyses indicate that cell-type-specificity is a more prominent factor than pathogen-specificity regarding contexts that affect how genetics influences gene expression (i.e., eQTL) and co-expression (i.e., co-expression QTL). In monocytes, the strongest responder to pathogen stimulations, 71.4% of the genetic variants whose effect on gene expression is influenced by pathogen exposure (i.e., response QTL) also affect the co-expression between genes. This indicates widespread, context-specific changes in gene expression level and its regulation that are driven by genetics. Pathway analysis on the CLEC12A gene that exemplifies cell-type-, exposure-time- and genetic-background-dependent co-expression interactions, shows enrichment of the interferon (IFN) pathway specifically at 3-h post-exposure in monocytes. Similar genetic background-dependent association between IFN activity and CLEC12A co-expression patterns is confirmed in systemic lupus erythematosus by in silico analysis, which implies that CLEC12A might be an IFN-regulated gene. Altogether, this study highlights the importance of context for gaining a better understanding of the mechanisms of gene regulation in health and disease.
Collapse
Affiliation(s)
- Roy Oelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Dylan H de Vries
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Harm Brugge
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - M Grace Gordon
- Biological and Medical Informatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- UCSF Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Martijn Vochteloo
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Chun J Ye
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- UCSF Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| |
Collapse
|