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Vega-Benedetti AF, Porcedda C, Ercoli T, Fusco G, Burgaletto C, Pillai R, Palmas F, Cantone AF, Angius F, Solla P, De Simone A, Cantarella G, Giallongo C, Sogos V, Defazio G, Carta AR. Immune responses to oligomeric α-synuclein in Parkinson's disease peripheral blood mononuclear cells. J Neurol 2024:10.1007/s00415-024-12554-3. [PMID: 38985290 DOI: 10.1007/s00415-024-12554-3] [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: 03/01/2024] [Revised: 06/05/2024] [Accepted: 06/30/2024] [Indexed: 07/11/2024]
Abstract
Parkinson's disease displays clinical heterogeneity, presenting with motor and non-motor symptoms. Heterogeneous phenotypes, named brain-first and body-first, may reflect distinct α-synuclein pathology starting either in the central nervous system or in the periphery. The immune system plays a prominent role in the central and peripheral pathology, with misfolded α-synuclein being placed at the intersection between neurodegeneration and inflammation. Here, we characterized the inflammatory profile and immune-phenotype of peripheral blood mononuclear cells (PBMCs) from Parkinson's disease patients upon stimulation with α-synuclein monomer or oligomer, and investigated relationships of immune parameters with clinical scores of motor and non-motor symptoms. Freshly isolated PBMCs from 21 Parkinson's disease patients and 18 healthy subjects were exposed in vitro to α-synuclein species. Cytokine/chemokine release was measured in the culture supernatant by Multiplex Elisa. The immune-phenotype was studied by FACS-flow cytometry. Correlation analysis was computed between immune parameters and parkinsonian motor and non-motor scales. We found that Parkinson's disease patients exhibited a dysregulated PBMC-cytokine profile, which remained unaltered after exposure to α-synuclein species and correlated with both motor and non-motor severity, with a strong correlation observed with olfactory impairment. Exposure of PBMCs from healthy controls to α-synuclein monomer/oligomer increased the cytokine/chemokine release up to patient's values. Moreover, the PBMCs immune phenotype differed between patients and controls and revealed a prominent association of the Mos profile with olfactory impairment, and of NK profile with constipation. Results suggest that a deranged PBMC-immune profile may reflect distinct clinical subtypes and would fit with the recent classification of Parkinson's disease into peripheral-first versus brain-first phenotype.
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Affiliation(s)
| | - Clara Porcedda
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Tommaso Ercoli
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Giuliana Fusco
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Chiara Burgaletto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Rita Pillai
- Center for Research University Services-CeSAR, University of Cagliari, Cagliari, Italy
| | - Francesca Palmas
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Anna Flavia Cantone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Fabrizio Angius
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Paolo Solla
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Alfonso De Simone
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Giuseppina Cantarella
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Cesarina Giallongo
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, Catania, Italy
| | - Valeria Sogos
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Giovanni Defazio
- Department of Translational Biomedicine and Neuroscience, Aldo Moro University of Bari, Bari, Italy
| | - Anna R Carta
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy.
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Peris Sempere V, Luo G, Muñiz-Castrillo S, Pinto AL, Picard G, Rogemond V, Titulaer MJ, Finke C, Leypoldt F, Kuhlenbäumer G, Jones HF, Dale RC, Binks S, Irani SR, Bastiaansen AE, de Vries JM, de Bruijn MAAM, Roelen DL, Kim TJ, Chu K, Lee ST, Kanbayashi T, Pollock NR, Kichula KM, Mumme-Monheit A, Honnorat J, Norman PJ, Mignot E. HLA and KIR genetic association and NK cells in anti-NMDAR encephalitis. Front Immunol 2024; 15:1423149. [PMID: 39050850 PMCID: PMC11266021 DOI: 10.3389/fimmu.2024.1423149] [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: 04/25/2024] [Accepted: 06/06/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction Genetic predisposition to autoimmune encephalitis with antibodies against N-methyl-D-aspartate receptor (NMDAR) is poorly understood. Given the diversity of associated environmental factors (tumors, infections), we hypothesized that human leukocyte antigen (HLA) and killer-cell immunoglobulin-like receptors (KIR), two extremely polymorphic gene complexes key to the immune system, might be relevant for the genetic predisposition to anti-NMDAR encephalitis. Notably, KIR are chiefly expressed by Natural Killer (NK) cells, recognize distinct HLA class I allotypes and play a major role in anti-tumor and anti-infection responses. Methods We conducted a Genome Wide Association Study (GWAS) with subsequent control-matching using Principal Component Analysis (PCA) and HLA imputation, in a multi-ethnic cohort of anti-NMDAR encephalitis (n=479); KIR and HLA were further sequenced in a large subsample (n=323). PCA-controlled logistic regression was then conducted for carrier frequencies (HLA and KIR) and copy number variation (KIR). HLA-KIR interaction associations were also modeled. Additionally, single cell sequencing was conducted in peripheral blood mononuclear cells from 16 cases and 16 controls, NK cells were sorted and phenotyped. Results Anti-NMDAR encephalitis showed a weak HLA association with DRB1*01:01~DQA1*01:01~DQB1*05:01 (OR=1.57, 1.51, 1.45; respectively), and DRB1*11:01 (OR=1.60); these effects were stronger in European descendants and in patients without an underlying ovarian teratoma. More interestingly, we found increased copy number variation of KIR2DL5B (OR=1.72), principally due to an overrepresentation of KIR2DL5B*00201. Further, we identified two allele associations in framework genes, KIR2DL4*00103 (25.4% vs. 12.5% in controls, OR=1.98) and KIR3DL3*00302 (5.3% vs. 1.3%, OR=4.44). Notably, the ligands of these KIR2DL4 and KIR3DL3, respectively, HLA-G and HHLA2, are known to act as immune checkpoint with immunosuppressive functions. However, we did not find differences in specific KIR-HLA ligand interactions or HLA-G polymorphisms between cases and controls. Similarly, gene expression of CD56dim or CD56bright NK cells did not differ between cases and controls. Discussion Our observations for the first time suggest that the HLA-KIR axis might be involved in anti-NMDAR encephalitis. While the genetic risk conferred by the identified polymorphisms appears small, a role of this axis in the pathophysiology of this disease appears highly plausible and should be analyzed in future studies.
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Affiliation(s)
- Vicente Peris Sempere
- Stanford Center for Sleep Science and Medicine, Stanford University, Palo Alto, CA, United States
| | - Guo Luo
- Stanford Center for Sleep Science and Medicine, Stanford University, Palo Alto, CA, United States
| | - Sergio Muñiz-Castrillo
- Stanford Center for Sleep Science and Medicine, Stanford University, Palo Alto, CA, United States
| | - Anne-Laurie Pinto
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, Lyon, France
| | - Géraldine Picard
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, Lyon, France
| | - Véronique Rogemond
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Carsten Finke
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Frank Leypoldt
- Department of Neurology, Christian-Albrechts-University/University Hospital Schleswig-Holstein, Kiel, Germany
- Neuroimmunology, Institute of Clinical Chemistry, University Hospital Schleswig-Holstein Kiel/Lübeck, Kiel, Germany
| | - Gregor Kuhlenbäumer
- Department of Neurology, Christian-Albrechts-University/University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Hannah F. Jones
- Starship Hospital, Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Russell C. Dale
- Kids Neuroscience Centre, Children’s Hospital at Westmead clinical school, University of Sydney, Sydney, NSW, Australia
| | - Sophie Binks
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Department of Neurology, John Radcliffe Hospital, Oxford, United Kingdom
| | - Sarosh R. Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Departments of Neurology and Neurosciences, Mayo Clinic, Jacksonville, FL, United States
| | | | - Juna M. de Vries
- Department of Neurology, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Dave L. Roelen
- Department of Immunogenetics and Transplantation Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Tae-Joon Kim
- Department of Neurology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Kon Chu
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soon-Tae Lee
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Nicholas R. Pollock
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Katherine M. Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Abigail Mumme-Monheit
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Jérôme Honnorat
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, Lyon, France
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Emmanuel Mignot
- Stanford Center for Sleep Science and Medicine, Stanford University, Palo Alto, CA, United States
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Marin WM, Augusto DG, Wade KJ, Hollenbach JA. High-throughput complement component 4 genomic sequence analysis with C4Investigator. HLA 2024; 103:e15273. [PMID: 37899688 PMCID: PMC11099535 DOI: 10.1111/tan.15273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/01/2023] [Accepted: 10/13/2023] [Indexed: 10/31/2023]
Abstract
The complement component 4 gene loci, composed of the C4A and C4B genes and located on chromosome 6, encodes for complement component 4 (C4) proteins, a key intermediate in the classical and lectin pathways of the complement system. The complement system is an important modulator of immune system activity and is also involved in the clearance of immune complexes and cellular debris. C4A and C4B gene loci exhibit copy number variation, with each composite gene varying between 0 and 5 copies per haplotype. C4A and C4B genes also vary in size depending on the presence of the human endogenous retrovirus (HERV) in intron 9, denoted by C4(L) for long-form and C4(S) for short-form, which affects expression and is found in both C4A and C4B. Additionally, human blood group antigens Rodgers and Chido are located on the C4 protein, with the Rodger epitope generally found on C4A protein, and the Chido epitope generally found on C4B protein. C4A and C4B copy number variation has been implicated in numerous autoimmune and pathogenic diseases. Despite the central role of C4 in immune function and regulation, high-throughput genomic sequence analysis of C4A and C4B variants has been impeded by the high degree of sequence similarity and complex genetic variation exhibited by these genes. To investigate C4 variation using genomic sequencing data, we have developed a novel bioinformatic pipeline for comprehensive, high-throughput characterization of human C4A and C4B sequences from short-read sequencing data, named C4Investigator. Using paired-end targeted or whole genome sequence data as input, C4Investigator determines the overall gene copy numbers, as well as C4A, C4B, C4(Rodger), C4(Ch), C4(L), and C4(S). Additionally, C4Ivestigator reports the full overall C4A and C4B aligned sequence, enabling nucleotide level analysis. To demonstrate the utility of this workflow we have analyzed C4A and C4B variation in the 1000 Genomes Project Data set, showing that these genes are highly poly-allelic with many variants that have the potential to impact C4 protein function.
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Affiliation(s)
- Wesley M. Marin
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Danillo G. Augusto
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, United States
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Kristen J. Wade
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States
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4
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Cardoso EM, Lourenço-Gomes V, Esgalhado AJ, Reste-Ferreira D, Oliveira N, Amaral AS, Martinho A, Gama JMR, Verde I, Lourenço O, Fonseca AM, Buchli R, Arosa FA. HLA-A23/HLA-A24 serotypes and dementia interaction in the elderly: Association with increased soluble HLA class I molecules in plasma. HLA 2023; 102:660-670. [PMID: 37400938 DOI: 10.1111/tan.15149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
MHC class I molecules regulate brain development and plasticity in mice and HLA class I molecules are associated with brain disorders in humans. We investigated the relationship between plasma-derived soluble human HLA class I molecules (sHLA class I), HLA class I serotypes and dementia. A cohort of HLA class I serotyped elderly subjects with no dementia/pre-dementia (NpD, n = 28), or with dementia (D, n = 28) was studied. Multivariate analysis was used to examine the influence of dementia and HLA class I serotype on sHLA class I levels, and to compare sHLA class I within four groups according to the presence or absence of HLA-A23/A24 and dementia. HLA-A23/A24 and dementia, but not age, significantly influenced the level of sHLA class I. Importantly, the concurrent presence of HLA-A23/A24 and dementia was associated with higher levels of sHLA class I (p < 0.001). This study has shown that the simultaneous presence of HLA-A23/HLA-A24 and dementia is associated with high levels of serum sHLA class I molecules. Thus, sHLA class I could be considered a biomarker of neurodegeneration in certain HLA class I carriers.
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Affiliation(s)
- Elsa M Cardoso
- ESS-IPG, School of Health Sciences, Polytechnic of Guarda, Guarda, Portugal
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
- FCS-UBI, Faculty of Health Sciences, University of Beira Interior, Covilhã, Portugal
| | | | - André J Esgalhado
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Débora Reste-Ferreira
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Nádia Oliveira
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Ana Saraiva Amaral
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - António Martinho
- Molecular Genetics Laboratory, Coimbra Blood and Transplantation Center, Coimbra, Portugal
| | - Jorge M R Gama
- Centre of Mathematics and Applications, Faculty of Sciences, University of Beira Interior, Covilhã, Portugal
| | - Ignácio Verde
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
- Centre of Mathematics and Applications, Faculty of Sciences, University of Beira Interior, Covilhã, Portugal
| | - Olga Lourenço
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
- FCS-UBI, Faculty of Health Sciences, University of Beira Interior, Covilhã, Portugal
| | - Ana M Fonseca
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
- FCS-UBI, Faculty of Health Sciences, University of Beira Interior, Covilhã, Portugal
| | - Rico Buchli
- Pure Protein LLC, Oklahoma City, Oklahoma, USA
| | - Fernando A Arosa
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
- FCS-UBI, Faculty of Health Sciences, University of Beira Interior, Covilhã, Portugal
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Marin WM, Augusto DG, Wade KJ, Hollenbach JA. High-throughput complement component 4 genomic sequence analysis with C4Investigator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549551. [PMID: 37503256 PMCID: PMC10370142 DOI: 10.1101/2023.07.18.549551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The complement component 4 gene locus, composed of the C4A and C4B genes and located on chromosome 6, encodes for C4 protein, a key intermediate in the classical and lectin pathways of the complement system. The complement system is an important modulator of immune system activity and is also involved in the clearance of immune complexes and cellular debris. The C4 gene locus exhibits copy number variation, with each composite gene varying between 0-5 copies per haplotype, C4 genes also vary in size depending on the presence of the HERV retrovirus in intron 9, denoted by C4(L) for long-form and C4(S) for short-form, which modulates expression and is found in both C4A and C4B. Additionally, human blood group antigens Rodgers and Chido are located on the C4 protein, with the Rodger epitope generally found on C4A protein, and the Chido epitope generally found on C4B protein. C4 copy number variation has been implicated in numerous autoimmune and pathogenic diseases. Despite the central role of C4 in immune function and regulation, high-throughput genomic sequence analysis of C4 variants has been impeded by the high degree of sequence similarity and complex genetic variation exhibited by these genes. To investigate C4 variation using genomic sequencing data, we have developed a novel bioinformatic pipeline for comprehensive, high-throughput characterization of human C4 sequence from short-read sequencing data, named C4Investigator. Using paired-end targeted or whole genome sequence data as input, C4Investigator determines gene copy number for overall C4, C4A, C4B, C4(Rodger), C4(Ch), C4(L), and C4(S), additionally, C4Ivestigator reports the full overall C4 aligned sequence, enabling nucleotide level analysis of C4. To demonstrate the utility of this workflow we have analyzed C4 variation in the 1000 Genomes Project Dataset, showing that the C4 genes are highly poly-allelic with many variants that have the potential to impact C4 protein function.
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Affiliation(s)
- Wesley M. Marin
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Danillo G. Augusto
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, United States
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Kristen J. Wade
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States
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Mechanisms of Autoimmune Cell in DA Neuron Apoptosis of Parkinson's Disease: Recent Advancement. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7965433. [PMID: 36567855 PMCID: PMC9771667 DOI: 10.1155/2022/7965433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022]
Abstract
Parkinson's disease (PD) is a prevalent neurodegenerative disorder that manifests as motor and nonmotor symptoms due to the selective loss of midbrain DArgic (DA) neurons. More and more studies have shown that pathological reactions initiated by autoimmune cells play an essential role in the progression of PD. Autoimmune cells exist in the brain parenchyma, cerebrospinal fluid, and meninges; they are considered inducers of neuroinflammation and regulate the immune in the human brain in PD. For example, T cells can recognize α-synuclein presented by antigen-presenting cells to promote neuroinflammation. In addition, B cells will accelerate the apoptosis of DA neurons in the case of PD-related gene mutations. Activation of microglia and damage of DA neurons even form the self-degeneration cycle to deteriorate PD. Numerous autoimmune cells have been considered regulators of apoptosis, α-synuclein misfolding and aggregation, mitochondrial dysfunction, autophagy, and neuroinflammation of DA neurons in PD. The evidence is mounting that autoimmune cells promote DA neuron apoptosis. In this review, we discuss the current knowledge regarding the regulation and function of B cell, T cell, and microglia as well as NK cell in PD pathogenesis, focusing on DA neuron apoptosis to understand the disease better and propose potential target identification for the treatment in the early stages of PD. However, there are still some limitations in our work, for example, the specific mechanism of PD progression caused by autoimmune cells in mitochondrial dysfunction, ferroptosis, and autophagy has not been clarified in detail, which needs to be summarized in further work.
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Menees KB, Lee JK. New Insights and Implications of Natural Killer Cells in Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2022; 12:S83-S92. [PMID: 35570499 PMCID: PMC9535577 DOI: 10.3233/jpd-223212] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease and is characterized by the loss of dopaminergic neurons in the substantia nigra and the abnormal aggregation and accumulation of the alpha-synuclein (α-syn) protein into Lewy bodies. It is established that there is an association between inflammation and PD; however, the time course of the inflammatory process as well as the immune cells involved are still debated. Natural killer (NK) cells are innate lymphocytes with numerous functions including targeting and killing infected or malignant cells, antimicrobial defense, and resolving inflammation. NK cell subsets differ in their effector function capacities which are modulated by activating and inhibitory receptors expressed at the cell surface. Alterations in NK cell numbers and receptor expression have been reported in PD patients. Recently, NK cell numbers and frequency were shown to be altered in the periphery and in the central nervous system in a preclinical mouse model of PD. Moreover, NK cells have recently been shown to internalize and degrade α-syn aggregates and systemic NK cell depletion exacerbated synuclein pathology in a preclinical mouse model of PD, indicating a potential protective role of NK cells. Here, we review the inflammatory process in PD with a particular focus on alterations in NK cell numbers, phenotypes, and functions.
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Affiliation(s)
- Kelly B Menees
- Department of Physiology and Pharmacology, University of Georgia College of Veterinary Medicine, Athens, GA, USA
| | - Jae-Kyung Lee
- Department of Physiology and Pharmacology, University of Georgia College of Veterinary Medicine, Athens, GA, USA
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8
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Pollock NR, Harrison GF, Norman PJ. Immunogenomics of Killer Cell Immunoglobulin-Like Receptor (KIR) and HLA Class I: Coevolution and Consequences for Human Health. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:1763-1775. [PMID: 35561968 PMCID: PMC10038757 DOI: 10.1016/j.jaip.2022.04.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/12/2022]
Abstract
Interactions of killer cell immunoglobin-like receptors (KIR) with human leukocyte antigens (HLA) class I regulate effector functions of key cytotoxic cells of innate and adaptive immunity. The extreme diversity of this interaction is genetically determined, having evolved in the ever-changing environment of pathogen exposure. Diversity of KIR and HLA genes is further facilitated by their independent segregation on separate chromosomes. That fetal implantation relies on many of the same types of immune cells as infection control places certain constraints on the evolution of KIR interactions with HLA. Consequently, specific inherited combinations of receptors and ligands may predispose to specific immune-mediated diseases, including autoimmunity. Combinatorial diversity of KIR and HLA class I can also differentiate success rates of immunotherapy directed to these diseases. Progress toward both etiopathology and predicting response to therapy is being achieved through detailed characterization of the extent and consequences of the combinatorial diversity of KIR and HLA. Achieving these goals is more tractable with the development of integrated analyses of molecular evolution, function, and pathology that will establish guidelines for understanding and managing risks. Here, we present what is known about the coevolution of KIR with HLA class I and the impact of their complexity on immune function and homeostasis.
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Affiliation(s)
- Nicholas R Pollock
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo
| | - Genelle F Harrison
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo.
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Zhang L, Zhang Y, Fan D. Pathological Role of Natural Killer Cells in Parkinson's Disease: A Systematic Review. Front Aging Neurosci 2022; 14:890816. [PMID: 35663564 PMCID: PMC9157643 DOI: 10.3389/fnagi.2022.890816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson's disease (PD) is one of the common neurodegenerative diseases that is characterized by selective degeneration of dopaminergic neurons in the substantia nigra, and misfolding of α-synuclein into aggregates is thought to contribute to its pathology. Studies have shown that immune-inflammatory responses are involved in the development of PD and play an important role in α-synuclein scavenge. Natural killer (NK) cells are first responders in immune cells and can directly promote immune defense mechanisms by cytotoxicity and by secreting cytokines. Recent discoveries suggest that NK cells are increasingly recognized in the pathological features of PD. However, the mechanisms underlying it have not been fully understood. In this review, we systematically retrieved and evaluated published evidence about the functions of NK cells in PD. We find alterations in the number of NK cells and cytotoxicity during the progression of PD, and it seems that NK cells play a neuroprotective role in PD pathogenesis, which may further reveal novel targets for the management and treatment of PD.
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Affiliation(s)
- Le Zhang
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Peking University Health Science Center, Beijing, China
| | - Yingshuang Zhang
- Department of Neurology, Peking University Third Hospital, Beijing, China
- *Correspondence: Yingshuang Zhang
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- Dongsheng Fan
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10
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Hooshmand K, Halliday GM, Pineda SS, Sutherland GT, Guennewig B. Overlap between Central and Peripheral Transcriptomes in Parkinson’s Disease but Not Alzheimer’s Disease. Int J Mol Sci 2022; 23:ijms23095200. [PMID: 35563596 PMCID: PMC9104085 DOI: 10.3390/ijms23095200] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/20/2022] Open
Abstract
Most neurodegenerative disorders take decades to develop, and their early detection is challenged by confounding non-pathological ageing processes. Therefore, the discovery of genes and molecular pathways in both peripheral and brain tissues that are highly predictive of disease evolution is necessary. To find genes that influence Alzheimer’s disease (AD) and Parkinson’s disease (PD) pathogenesis, human RNA-Seq transcriptomic data from Brodmann Area 9 (BA9) of the dorsolateral prefrontal cortex (DLPFC), whole blood (WB), and peripheral blood mononuclear cells (PBMC) were analysed using a combination of differential gene expression and a random forest-based machine learning algorithm. The results suggest that there is little overlap between PD and AD, and the AD brain signature is unique mainly compared to blood-based samples. Moreover, the AD-BA9 was characterised by changes in ‘nervous system development’ with Myocyte-specific enhancer factor 2C (Mef2C), encoding a transcription factor that induces microglia activation, a prominent feature. The peripheral AD transcriptome was associated with alterations in ‘viral process’, and FYN, which has been previously shown to link amyloid-beta and tau, was the prominent feature. However, in the absence of any overlap with the central transcriptome, it is unclear whether peripheral FYN levels reflect AD severity or progression. In PD, central and peripheral signatures are characterised by anomalies in ‘exocytosis’ and specific genes related to the SNARE complex, including Vesicle-associated membrane protein 2 (VAMP2), Syntaxin 1A (STX1A), and p21-activated kinase 1 (PAK1). This is consistent with our current understanding of the physiological role of alpha-synuclein and how alpha-synuclein oligomers compromise vesicle docking and neurotransmission. Overall, the results describe distinct disease-specific pathomechanisms, both within the brain and peripherally, for the two most common neurodegenerative disorders.
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Affiliation(s)
- Kosar Hooshmand
- Brain and Mind Centre, Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW 2050, Australia; (K.H.); (G.M.H.); (S.S.P.)
| | - Glenda M. Halliday
- Brain and Mind Centre, Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW 2050, Australia; (K.H.); (G.M.H.); (S.S.P.)
| | - Sandy S. Pineda
- Brain and Mind Centre, Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW 2050, Australia; (K.H.); (G.M.H.); (S.S.P.)
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Greg T. Sutherland
- Charles Perkins Centre, Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW 2050, Australia;
| | - Boris Guennewig
- Brain and Mind Centre, Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW 2050, Australia; (K.H.); (G.M.H.); (S.S.P.)
- Correspondence:
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11
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Harrison GF, Leaton LA, Harrison EA, Kichula KM, Viken MK, Shortt J, Gignoux CR, Lie BA, Vukcevic D, Leslie S, Norman PJ. Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1. PLoS Comput Biol 2022; 18:e1009059. [PMID: 35192601 PMCID: PMC8896733 DOI: 10.1371/journal.pcbi.1009059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 03/04/2022] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Highly polymorphic interaction of KIR3DL1 and KIR3DS1 with HLA class I ligands modulates the effector functions of natural killer (NK) cells and some T cells. This genetically determined diversity affects severity of infections, immune-mediated diseases, and some cancers, and impacts the course of immunotherapies, including transplantation. KIR3DL1 is an inhibitory receptor, and KIR3DS1 is an activating receptor encoded by the KIR3DL1/S1 gene that has more than 200 diverse and divergent alleles. Determination of KIR3DL1/S1 genotypes for medical application is hampered by complex sequence and structural variation, requiring targeted approaches to generate and analyze high-resolution allele data. To overcome these obstacles, we developed and optimized a model for imputing KIR3DL1/S1 alleles at high-resolution from whole-genome SNP data. We designed the model to represent a substantial component of human genetic diversity. Our Global imputation model is effective at genotyping KIR3DL1/S1 alleles with an accuracy ranging from 88% in Africans to 97% in East Asians, with mean specificity of 99% and sensitivity of 95% for alleles >1% frequency. We used the established algorithm of the HIBAG program, in a modification named Pulling Out Natural killer cell Genomics (PONG). Because HIBAG was designed to impute HLA alleles also from whole-genome SNP data, PONG allows combinatorial diversity of KIR3DL1/S1 with HLA-A and -B to be analyzed using complementary techniques on a single data source. The use of PONG thus negates the need for targeted sequencing data in very large-scale association studies where such methods might not be tractable.
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Affiliation(s)
- Genelle F. Harrison
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Laura Ann Leaton
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Erica A. Harrison
- Independent Researcher, Broomfield, Colorado, United States of America
| | - Katherine M. Kichula
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Marte K. Viken
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Jonathan Shortt
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Christopher R. Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Benedicte A. Lie
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Damjan Vukcevic
- School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia
| | - Stephen Leslie
- School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
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12
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Dubis J, Niepiekło-Miniewska W, Jędruchniewicz N, Sobczyński M, Witkiewicz W, Zapotoczny N, Kuśnierczyk P. Associations of Genes for Killer Cell Immunoglobulin-like Receptors and Their Human Leukocyte Antigen-A/B/C Ligands with Abdominal Aortic Aneurysm. Cells 2021; 10:cells10123357. [PMID: 34943866 PMCID: PMC8699266 DOI: 10.3390/cells10123357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/20/2021] [Accepted: 11/25/2021] [Indexed: 11/28/2022] Open
Abstract
Abdominal aortic aneurysm (AAA) is an immune-mediated disease with a genetic component. The multifactorial pathophysiology is not clear and there is still no pharmacotherapy to slow the growth of aneurysms. The signal integration of cell-surface KIRs (killer cell immunoglobulin-like receptors) with HLA (ligands, human leukocyte class I antigen molecules) modulates the activity of natural killer immune cells. The genetic diversity of the KIR/HLA system is associated with the risk of immune disorders. This study was a multivariate analysis of the association between genetic variants of KIRs, HLA ligands, clinical data and AAA formation. Genotyping was performed by single polymerase chain reaction with sequence-specific primers using commercial assays. Patients with HLA-A-Bw4 have a larger aneurysm by an average of 4 mm (p = 0.008). We observed a relationship between aneurysm diameter and BMI in patients with AAA and co-existing CAD; its shape was determined by the presence of HLA-A-Bw4. There was also a nearly 10% difference in KIR3DL1 allele frequency between the study and control groups. High expression of the cell surface receptor KIR3DL1 may protect, to some extent, against AAA. The presence of HLA-A-Bw4 may affect the rate of aneurysm growth and represents a potential regional pathogenetic risk of autoimmune injury to the aneurysmal aorta.
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Affiliation(s)
- Joanna Dubis
- Research and Development Centre, Regional Specialist Hospital, 51-124 Wroclaw, Poland;
- Correspondence: (J.D.); (P.K.)
| | - Wanda Niepiekło-Miniewska
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland;
| | | | - Maciej Sobczyński
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland;
| | - Wojciech Witkiewicz
- Department of Vascular Surgery, Regional Specialist Hospital in Wroclaw, 51-124 Wrocław, Poland; (W.W.); (N.Z.)
| | - Norbert Zapotoczny
- Department of Vascular Surgery, Regional Specialist Hospital in Wroclaw, 51-124 Wrocław, Poland; (W.W.); (N.Z.)
| | - Piotr Kuśnierczyk
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland;
- Correspondence: (J.D.); (P.K.)
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13
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Vargas LDB, Beltrame MH, Ho B, Marin WM, Dandekar R, Montero-Martín G, Fernández-Viña MA, Hurtado AM, Hill KR, Tsuneto LT, Hutz MH, Salzano FM, Petzl-Erler ML, Hollenbach JA, Augusto DG. Remarkably low KIR and HLA diversity in Amerindians reveals signatures of strong purifying selection shaping the centromeric KIR region. Mol Biol Evol 2021; 39:6388041. [PMID: 34633459 PMCID: PMC8763117 DOI: 10.1093/molbev/msab298] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The killer-cell immunoglobulin-like receptors (KIR) recognize human leukocyte antigen (HLA) molecules to regulate the cytotoxic and inflammatory responses of natural killer cells. KIR genes are encoded by a rapidly evolving gene family on chromosome 19 and present an unusual variation of presence and absence of genes and high allelic diversity. Although many studies have associated KIR polymorphism with susceptibility to several diseases over the last decades, the high-resolution allele-level haplotypes have only recently started to be described in populations. Here, we use a highly innovative custom next-generation sequencing method that provides a state-of-art characterization of KIR and HLA diversity in 706 individuals from eight unique South American populations: five Amerindian populations from Brazil (three Guarani and two Kaingang); one Amerindian population from Paraguay (Aché); and two urban populations from Southern Brazil (European and Japanese descendants from Curitiba). For the first time, we describe complete high-resolution KIR haplotypes in South American populations, exploring copy number, linkage disequilibrium, and KIR-HLA interactions. We show that all Amerindians analyzed to date exhibit the lowest numbers of KIR-HLA interactions among all described worldwide populations, and that 83-97% of their KIR-HLA interactions rely on a few HLA-C molecules. Using multiple approaches, we found signatures of strong purifying selection on the KIR centromeric region, which codes for the strongest NK cell educator receptors, possibly driven by the limited HLA diversity in these populations. Our study expands the current knowledge of KIR genetic diversity in populations to understand KIR-HLA coevolution and its impact on human health and survival.
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Affiliation(s)
- Luciana de Brito Vargas
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Marcia H Beltrame
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Brenda Ho
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Wesley M Marin
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ravi Dandekar
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Gonzalo Montero-Martín
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | | | - A Magdalena Hurtado
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287, USA
| | - Kim R Hill
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287, USA
| | - Luiza T Tsuneto
- Departamento de Análises Clínicas, Universidade Estadual de Maringá, Maringá, PR, 87020-900, Brazil
| | - Mara H Hutz
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Maria Luiza Petzl-Erler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Jill A Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158, USA
| | - Danillo G Augusto
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil.,Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
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14
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Aguiar VRC, Augusto DG, Castelli EC, Hollenbach JA, Meyer D, Nunes K, Petzl-Erler ML. An immunogenetic view of COVID-19. Genet Mol Biol 2021; 44:e20210036. [PMID: 34436508 PMCID: PMC8388242 DOI: 10.1590/1678-4685-gmb-2021-0036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023] Open
Abstract
Meeting the challenges brought by the COVID-19 pandemic requires an interdisciplinary approach. In this context, integrating knowledge of immune function with an understanding of how genetic variation influences the nature of immunity is a key challenge. Immunogenetics can help explain the heterogeneity of susceptibility and protection to the viral infection and disease progression. Here, we review the knowledge developed so far, discussing fundamental genes for triggering the innate and adaptive immune responses associated with a viral infection, especially with the SARS-CoV-2 mechanisms. We emphasize the role of the HLA and KIR genes, discussing what has been uncovered about their role in COVID-19 and addressing methodological challenges of studying these genes. Finally, we comment on questions that arise when studying admixed populations, highlighting the case of Brazil. We argue that the interplay between immunology and an understanding of genetic associations can provide an important contribution to our knowledge of COVID-19.
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Affiliation(s)
- Vitor R. C. Aguiar
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Danillo G. Augusto
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
- Universidade Federal do Paraná, Departamento de Genética, Curitiba,
PR, Brazil
| | - Erick C. Castelli
- Universidade Estadual Paulista, Faculdade de Medicina de Botucatu,
Departamento de Patologia, Botucatu, SP, Brazil
| | - Jill A. Hollenbach
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
| | - Diogo Meyer
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Kelly Nunes
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
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15
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Highlighting Immune System and Stress in Major Depressive Disorder, Parkinson's, and Alzheimer's Diseases, with a Connection with Serotonin. Int J Mol Sci 2021; 22:ijms22168525. [PMID: 34445231 PMCID: PMC8395198 DOI: 10.3390/ijms22168525] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 01/10/2023] Open
Abstract
There is recognition that both stress and immune responses are important factors in a variety of neurological disorders. Moreover, there is an important role of several neurotransmitters that connect these factors to several neurological diseases, with a special focus in this paper on serotonin. Accordingly, it is known that imbalances in stressors can promote a variety of neuropsychiatric or neurodegenerative pathologies. Here, we discuss some facts that link major depressive disorder, Alzheimer’s, and Parkinson’s to the stress and immune responses, as well as the connection between these responses and serotonergic signaling. These are important topics of investigation which may lead to new or better treatments, improving the life quality of patients that suffer from these conditions.
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16
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Marin WM, Dandekar R, Augusto DG, Yusufali T, Heyn B, Hofmann J, Lange V, Sauter J, Norman PJ, Hollenbach JA. High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING. PLoS Comput Biol 2021; 17:e1008904. [PMID: 34339413 PMCID: PMC8360517 DOI: 10.1371/journal.pcbi.1008904] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/12/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
The killer-cell immunoglobulin-like receptor (KIR) complex on chromosome 19 encodes receptors that modulate the activity of natural killer cells, and variation in these genes has been linked to infectious and autoimmune disease, as well as having bearing on pregnancy and transplant outcomes. The medical relevance and high variability of KIR genes makes short-read sequencing an attractive technology for interrogating the region, providing a high-throughput, high-fidelity sequencing method that is cost-effective. However, because this gene complex is characterized by extensive nucleotide polymorphism, structural variation including gene fusions and deletions, and a high level of homology between genes, its interrogation at high resolution has been thwarted by bioinformatic challenges, with most studies limited to examining presence or absence of specific genes. Here, we present the PING (Pushing Immunogenetics to the Next Generation) pipeline, which incorporates empirical data, novel alignment strategies and a custom alignment processing workflow to enable high-throughput KIR sequence analysis from short-read data. PING provides KIR gene copy number classification functionality for all KIR genes through use of a comprehensive alignment reference. The gene copy number determined per individual enables an innovative genotype determination workflow using genotype-matched references. Together, these methods address the challenges imposed by the structural complexity and overall homology of the KIR complex. To determine copy number and genotype determination accuracy, we applied PING to European and African validation cohorts and a synthetic dataset. PING demonstrated exceptional copy number determination performance across all datasets and robust genotype determination performance. Finally, an investigation into discordant genotypes for the synthetic dataset provides insight into misaligned reads, advancing our understanding in interpretation of short-read sequencing data in complex genomic regions. PING promises to support a new era of studies of KIR polymorphism, delivering high-resolution KIR genotypes that are highly accurate, enabling high-quality, high-throughput KIR genotyping for disease and population studies.
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Affiliation(s)
- Wesley M. Marin
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | - Ravi Dandekar
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | - Danillo G. Augusto
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | - Tasneem Yusufali
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | | | | | | | | | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jill A. Hollenbach
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
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17
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Ahn R, Vukcevic D, Motyer A, Nititham J, Squire DM, Hollenbach JA, Norman PJ, Ellinghaus E, Nair RP, Tsoi LC, Oksenberg J, Foerster J, Lieb W, Weidinger S, Franke A, Elder JT, Jorgenson E, Leslie S, Liao W. Large-Scale Imputation of KIR Copy Number and HLA Alleles in North American and European Psoriasis Case-Control Cohorts Reveals Association of Inhibitory KIR2DL2 With Psoriasis. Front Immunol 2021; 12:684326. [PMID: 34177931 PMCID: PMC8231283 DOI: 10.3389/fimmu.2021.684326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
Killer cell immunoglobulin-like receptors (KIR) regulate immune responses in NK and CD8+ T cells via interaction with HLA ligands. KIR genes, including KIR2DS1, KIR3DL1, and KIR3DS1 have previously been implicated in psoriasis susceptibility. However, these previous studies were constrained to small sample sizes, in part due to the time and expense required for direct genotyping of KIR genes. Here, we implemented KIR*IMP to impute KIR copy number from single-nucleotide polymorphisms (SNPs) on chromosome 19 in the discovery cohort (n=11,912) from the PAGE consortium, University of California San Francisco, and the University of Dundee, and in a replication cohort (n=66,357) from Kaiser Permanente Northern California. Stratified multivariate logistic regression that accounted for patient ancestry and high-risk HLA alleles revealed that KIR2DL2 copy number was significantly associated with psoriasis in the discovery cohort (p ≤ 0.05). The KIR2DL2 copy number association was replicated in the Kaiser Permanente replication cohort. This is the first reported association of KIR2DL2 copy number with psoriasis and highlights the importance of KIR genetics in the pathogenesis of psoriasis.
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Affiliation(s)
- Richard Ahn
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Damjan Vukcevic
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
- Clinical Epidemiology and Biostatistics Unit, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Allan Motyer
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Joanne Nititham
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
| | - David McG. Squire
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Jill A. Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Paul J. Norman
- Division of Personalized Medicine, Department of Immunology and Microbiology, University of Colorado, San Francisco, CA, United States
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, United States
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Jorge Oksenberg
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - John Foerster
- College of Medicine, Dentistry, and Nursing, University of Dundee, Dundee, United Kingdom
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, University Hospital Schleswig Holstein, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - James T. Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
- Ann Arbor Veterans Affairs Hospital, Dermatology, Ann Arbor, MI, United States
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente, Oakland, CA, United States
| | - Stephen Leslie
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
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18
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Amorim LM, Augusto DG, Nemat-Gorgani N, Montero-Martin G, Marin WM, Shams H, Dandekar R, Caillier S, Parham P, Fernández-Viña MA, Oksenberg JR, Norman PJ, Hollenbach JA. High-Resolution Characterization of KIR Genes in a Large North American Cohort Reveals Novel Details of Structural and Sequence Diversity. Front Immunol 2021; 12:674778. [PMID: 34025673 PMCID: PMC8137979 DOI: 10.3389/fimmu.2021.674778] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
The KIR (killer-cell immunoglobulin-like receptor) region is characterized by structural variation and high sequence similarity among genes, imposing technical difficulties for analysis. We undertook the most comprehensive study to date of KIR genetic diversity in a large population sample, applying next-generation sequencing in 2,130 United States European-descendant individuals. Data were analyzed using our custom bioinformatics pipeline specifically designed to address technical obstacles in determining KIR genotypes. Precise gene copy number determination allowed us to identify a set of uncommon gene-content KIR haplotypes accounting for 5.2% of structural variation. In this cohort, KIR2DL4 is the framework gene that most varies in copy number (6.5% of all individuals). We identified phased high-resolution alleles in large multi-locus insertions and also likely founder haplotypes from which they were deleted. Additionally, we observed 250 alleles at 5-digit resolution, of which 90 have frequencies ≥1%. We found sequence patterns that were consistent with the presence of novel alleles in 398 (18.7%) individuals and contextualized multiple orphan dbSNPs within the KIR complex. We also identified a novel KIR2DL1 variant, Pro151Arg, and demonstrated by molecular dynamics that this substitution is predicted to affect interaction with HLA-C. No previous studies have fully explored the full range of structural and sequence variation of KIR as we present here. We demonstrate that pairing high-throughput sequencing with state-of-art computational tools in a large cohort permits exploration of all aspects of KIR variation including determination of population-level haplotype diversity, improving understanding of the KIR system, and providing an important reference for future studies.
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Affiliation(s)
- Leonardo M. Amorim
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Danillo G. Augusto
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
| | - Gonzalo Montero-Martin
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Wesley M. Marin
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Hengameh Shams
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Ravi Dandekar
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Stacy Caillier
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Peter Parham
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
| | | | - Jorge R. Oksenberg
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, CA, United States
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