1
|
Russell A, Wang W. The Rapidly Expanding Nexus of Immunoglobulin G N-Glycomics, Suboptimal Health Status, and Precision Medicine. EXPERIENTIA. SUPPLEMENTUM 2021; 112:545-564. [PMID: 34687022 DOI: 10.1007/978-3-030-76912-3_17] [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: 03/14/2023]
Abstract
Immunoglobulin G is a prevalent glycoprotein, whose downstream immune responses are partially mediated by the N-glycans within the fragment crystallisable domain. Collectively termed the N-glycome, it is considered a complex intermediate phenotype: an amalgamation of genetic predisposition, environmental exposure, and health behaviours over the life-course. Thus, the immunoglobulin G N-glycome may provide an indication of health status on the spectrum from health to disease and infirmary. Although variability exists within and between populations, composition of the immunoglobulin G N-glycome remains stable over short periods of time. This underscores the potential of harnessing the immunoglobulin G N-glycome as an ideal tool for preclinical disease risk prediction, stratification, and prognosis through the development of precise dynamic biomarkers.
Collapse
Affiliation(s)
- Alyce Russell
- Centre for Precision Health, Edith Cowan University, Joondalup, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Wei Wang
- Centre for Precision Health, Edith Cowan University, Joondalup, Australia.
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia.
| |
Collapse
|
2
|
Global discovery of lupus genetic risk variant allelic enhancer activity. Nat Commun 2021; 12:1611. [PMID: 33712590 PMCID: PMC7955039 DOI: 10.1038/s41467-021-21854-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we construct a massively parallel reporter assay (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into the Epstein-Barr virus-transformed B cell line GM12878 reveals 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. Comparison of MPRA results in GM12878 and Jurkat T cell lines highlights shared and unique allelic transcriptional regulatory mechanisms at SLE risk loci. In-depth analysis of allelic transcription factor (TF) binding at and around allelic variants identifies one class of TFs whose DNA-binding motif tends to be directly altered by the risk variant and a second class of TFs that bind allelically without direct alteration of their motif by the variant. Collectively, our approach provides a blueprint for the discovery of allelic gene regulation at risk loci for any disease and offers insight into the transcriptional regulatory mechanisms underlying SLE. Thousands of genetic variants have been associated with lupus, but causal variants and mechanisms are unknown. Here, the authors combine a massively parallel reporter assay with genome-wide ChIP experiments to identify risk variants with allelic enhancer activity mediated through transcription factor binding.
Collapse
|
3
|
Santarelli DM, Carroll AP, Cairns HM, Tooney PA, Cairns MJ. Schizophrenia-associated MicroRNA-Gene Interactions in the Dorsolateral Prefrontal Cortex. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 17:623-634. [PMID: 32006661 PMCID: PMC7212302 DOI: 10.1016/j.gpb.2019.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 10/01/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022]
Abstract
Schizophrenia-associated anomalies in gene expression in postmortem brain can be attributed to a combination of genetic and environmental influences. Given the small effect size of common variants, it is likely that we may only see the combined impact of some of these at the pathway level in small postmortem studies. At the gene level, however, there may be more impact from common environmental exposures mediated by influential epigenomic modifiers, such as microRNA (miRNA). We hypothesise that dysregulation of miRNAs and their alteration of gene expression have significant implications in the pathophysiology of schizophrenia. In this study, we integrate changes in cortical gene and miRNA expression to identify regulatory interactions and networks associated with the disorder. Gene expression analysis in post-mortem prefrontal dorsolateral cortex (BA 46) (n = 74 matched pairs of schizophrenia, schizoaffective, and control samples) was integrated with miRNA expression in the same cohort to identify gene-miRNA regulatory networks. A significant gene-miRNA interaction network was identified, including miR-92a, miR-495, and miR-134, which converged with differentially expressed genes in pathways involved in neurodevelopment and oligodendrocyte function. The capacity for miRNA to directly regulate gene expression through respective binding sites in BCL11A, PLP1, and SYT11 was also confirmed to support the biological relevance of this integrated network model. The observations in this study support the hypothesis that miRNA dysregulation is an important factor in the complex pathophysiology of schizophrenia.
Collapse
Affiliation(s)
- Danielle M Santarelli
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
| | - Adam P Carroll
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
| | - Heath M Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
| | - Paul A Tooney
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia.
| |
Collapse
|
4
|
Sun J, Kranzler HR, Gelernter J, Bi J. A genome-wide association study of cocaine use disorder accounting for phenotypic heterogeneity and gene–environment interaction. J Psychiatry Neurosci 2020; 45:34-44. [PMID: 31490055 PMCID: PMC6919916 DOI: 10.1503/jpn.180098] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Phenotypic heterogeneity and complicated gene–environment interplay in etiology are among the primary factors that hinder the identification of genetic variants associated with cocaine use disorder. METHODS To detect novel genetic variants associated with cocaine use disorder, we derived disease traits with reduced phenotypic heterogeneity using cluster analysis of a study sample (n = 9965). We then used these traits in genome-wide association tests, performed separately for 2070 African Americans and 1570 European Americans, using a new mixed model that accounted for the moderating effects of 5 childhood environmental factors. We used an independent sample (918 African Americans, 1382 European Americans) for replication. RESULTS The cluster analysis yielded 5 cocaine use disorder subtypes, of which subtypes 4 (n = 3258) and 5 (n = 1916) comprised heavy cocaine users, had high heritability estimates (h2 = 0.66 and 0.64, respectively) and were used in association tests. Seven of the 13 identified genetic loci in the discovery phase were available in the replication sample. In African Americans, rs114492924 (discovery p = 1.23 × E−8), a single nucleotide polymorphism in LINC01411, was replicated in the replication sample (p = 3.63 × E−3). In a meta-analysis that combined the discovery and replication results, 3 loci in African Americans were significant genome-wide: rs10188036 in TRAK2 (p = 2.95 × E−8), del-1:15511771 in TMEM51 (p = 9.11 × E−10) and rs149843442 near LPHN2 (p = 3.50 × E−8). LIMITATIONS Lack of data prevented us from replicating 6 of the 13 identified loci. CONCLUSION Our results demonstrate the importance of considering phenotypic heterogeneity and gene–environment interplay in detecting genetic variations that contribute to cocaine use disorder, because new genetic loci have been identified using our novel analytic method.
Collapse
Affiliation(s)
- Jiangwen Sun
- From the Department of Computer Science and Engineering, University of Connecticut, School of Engineering, Storrs, CT (Sun, Bi); the University of Pennsylvania Perelman School of Medicine, Department of Psychiatry, Center for Studies of Addiction and Corporal Michael Crescenz VAMC, Philadelphia, PA (Kranzler); and the Yale University School of Medicine, Department of Psychiatry, Division of Human Genetics and Departments of Genetics and Neurobiology; and VA CT Healthcare Center, New Haven, CT (Gelernter)
| | - Henry R. Kranzler
- From the Department of Computer Science and Engineering, University of Connecticut, School of Engineering, Storrs, CT (Sun, Bi); the University of Pennsylvania Perelman School of Medicine, Department of Psychiatry, Center for Studies of Addiction and Corporal Michael Crescenz VAMC, Philadelphia, PA (Kranzler); and the Yale University School of Medicine, Department of Psychiatry, Division of Human Genetics and Departments of Genetics and Neurobiology; and VA CT Healthcare Center, New Haven, CT (Gelernter)
| | - Joel Gelernter
- From the Department of Computer Science and Engineering, University of Connecticut, School of Engineering, Storrs, CT (Sun, Bi); the University of Pennsylvania Perelman School of Medicine, Department of Psychiatry, Center for Studies of Addiction and Corporal Michael Crescenz VAMC, Philadelphia, PA (Kranzler); and the Yale University School of Medicine, Department of Psychiatry, Division of Human Genetics and Departments of Genetics and Neurobiology; and VA CT Healthcare Center, New Haven, CT (Gelernter)
| | - Jinbo Bi
- From the Department of Computer Science and Engineering, University of Connecticut, School of Engineering, Storrs, CT (Sun, Bi); the University of Pennsylvania Perelman School of Medicine, Department of Psychiatry, Center for Studies of Addiction and Corporal Michael Crescenz VAMC, Philadelphia, PA (Kranzler); and the Yale University School of Medicine, Department of Psychiatry, Division of Human Genetics and Departments of Genetics and Neurobiology; and VA CT Healthcare Center, New Haven, CT (Gelernter)
| |
Collapse
|
5
|
High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry. Nat Genet 2016; 48:323-30. [PMID: 26808113 PMCID: PMC4767573 DOI: 10.1038/ng.3496] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/23/2015] [Indexed: 01/04/2023]
Abstract
Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 × 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.
Collapse
|
6
|
The MARVEL domain protein Nce102 regulates actin organization and invasive growth of Candida albicans. mBio 2013; 4:e00723-13. [PMID: 24281718 PMCID: PMC3870249 DOI: 10.1128/mbio.00723-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Invasive growth of the fungal pathogen Candida albicans into tissues promotes disseminated infections in humans. The plasma membrane is essential for pathogenesis because this important barrier mediates morphogenesis and invasive growth, as well as secretion of virulence factors, cell wall synthesis, nutrient import, and other processes. Previous studies showed that the Sur7 tetraspan protein that localizes to MCC (membrane compartment occupied by Can1)/eisosome subdomains of the plasma membrane regulates a broad range of key functions, including cell wall synthesis, morphogenesis, and resistance to copper. Therefore, a distinct tetraspan protein found in MCC/eisosomes, Nce102, was investigated. Nce102 belongs to the MARVEL domain protein family, which is implicated in regulating membrane structure and function. Deletion of NCE102 did not cause the broad defects seen in sur7Δ cells. Instead, the nce102Δ mutant displayed a unique phenotype in that it was defective in forming hyphae and invading low concentrations of agar but could invade well in higher agar concentrations. This phenotype was likely due to a defect in actin organization that was observed by phalloidin staining. In support of this, the invasive growth defect of a bni1Δ mutant that mislocalizes actin due to lack of the Bni1 formin was also reversed at high agar concentrations. This suggests that a denser matrix provides a signal that compensates for the actin defects. The nce102Δ mutant displayed decreased virulence and formed abnormal hyphae in mice. These studies identify novel ways that Nce102 and the physical environment surrounding C. albicans regulate morphogenesis and pathogenesis. The plasma membrane promotes virulence of the human fungal pathogen Candida albicans by acting as a protective barrier around the cell and mediating dynamic activities, such as morphogenesis, cell wall synthesis, secretion of virulence factors, and nutrient uptake. To better understand how the plasma membrane contributes to virulence, we analyzed a set of eight genes encoding MARVEL family proteins that are predicted to function in membrane organization. Interestingly, deletion of one gene, NCE102, caused a strong defect in formation of invasive hyphal growth in vitro and decreased virulence in mice. The nce102Δ mutant cells showed defects in actin organization that underlie the morphogenesis defect, since mutation of a known regulator of actin organization caused a similar defect. These studies identify a novel way in which the plasma membrane regulates the actin cytoskeleton and contributes to pathogenesis.
Collapse
|
7
|
Abstract
Sustained neuronal communication relies on the coordinated activity of multiple proteins that regulate synaptic vesicle biogenesis and cycling within the presynaptic terminal. Synaptogyrin and synaptophysin are conserved MARVEL domain-containing transmembrane proteins that are among the most abundant synaptic vesicle constituents, although their role in the synaptic vesicle cycle has remained elusive. To further investigate the function of these proteins, we generated and characterized a synaptogyrin (gyr)-null mutant in Drosophila, whose genome encodes a single synaptogyrin isoform and lacks a synaptophysin homolog. We demonstrate that Drosophila synaptogyrin plays a modulatory role in synaptic vesicle biogenesis at larval neuromuscular junctions. Drosophila lacking synaptogyrin are viable and fertile and have no overt deficits in motor function. However, ultrastructural analysis of gyr larvae revealed increased synaptic vesicle diameter and enhanced variability in the size of synaptic vesicles. In addition, the resolution of endocytic cisternae into synaptic vesicles in response to strong stimulation is defective in gyr mutants. Electrophysiological analysis demonstrated an increase in quantal size and a concomitant decrease in quantal content, suggesting functional consequences for transmission caused by the loss of synaptogyrin. Furthermore, high-frequency stimulation resulted in increased facilitation and a delay in recovery from synaptic depression, indicating that synaptic vesicle exo-endocytosis is abnormally regulated during intense stimulation conditions. These results suggest that synaptogyrin modulates the synaptic vesicle exo-endocytic cycle and is required for the proper biogenesis of synaptic vesicles at nerve terminals.
Collapse
|
8
|
Cacabelos R, Cacabelos P, Aliev G. Genomics of schizophrenia and pharmacogenomics of antipsychotic drugs. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ojpsych.2013.31008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
9
|
Löw C, Jegerschöld C, Kovermann M, Moberg P, Nordlund P. Optimisation of over-expression in E. coli and biophysical characterisation of human membrane protein synaptogyrin 1. PLoS One 2012; 7:e38244. [PMID: 22675529 PMCID: PMC3365889 DOI: 10.1371/journal.pone.0038244] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 05/02/2012] [Indexed: 11/25/2022] Open
Abstract
Progress in functional and structural studies of integral membrane proteins (IMPs) is lacking behind their soluble counterparts due to the great challenge in producing stable and homogeneous IMPs. Low natural abundance, toxicity when over-expressed and potential lipid requirements of IMPs are only a few reasons for the limited progress. Here, we describe an optimised workflow for the recombinant over-expression of the human tetraspan vesicle protein (TVP) synaptogyrin in Escherichia coli and its biophysical characterisation. TVPs are ubiquitous and abundant components of vesicles. They are believed to be involved in various aspects of the synaptic vesicle cycle, including vesicle biogenesis, exocytosis and endocytotic recycling. Even though TVPs are found in most cell types, high-resolution structural information for this class of membrane proteins is still missing. The optimisation of the N-terminal sequence of the gene together with the usage of the recently developed Lemo21(DE3) strain which allows the balancing of the translation with the membrane insertion rate led to a 50-fold increased expression rate compared to the classical BL21(DE3) strain. The protein was soluble and stable in a variety of mild detergents and multiple biophysical methods confirmed the folded state of the protein. Crosslinking experiments suggest an oligomeric architecture of at least four subunits. The protein stability is significantly improved in the presence of cholesteryl hemisuccinate as judged by differential light scattering. The approach described here can easily be adapted to other eukaryotic IMPs.
Collapse
Affiliation(s)
- Christian Löw
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (CL); (PN)
| | - Caroline Jegerschöld
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Michael Kovermann
- Institut für Physik, Biophysik, Martin-Luther-Universität Halle-Wittenberg, Saale, Germany
| | - Per Moberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pär Nordlund
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (CL); (PN)
| |
Collapse
|
10
|
Synaptogyrin-dependent modulation of synaptic neurotransmission in Caenorhabditis elegans. Neuroscience 2011; 190:75-88. [DOI: 10.1016/j.neuroscience.2011.05.069] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 05/20/2011] [Accepted: 05/28/2011] [Indexed: 01/31/2023]
|