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Yang BZ, Xiang B, Wang T, Ma S, Li CSR. Neurogenetic underpinnings of nicotine use severity: Integrating the brain transcriptomes and GWAS variants via network approaches. Psychiatry Res 2024; 334:115815. [PMID: 38422867 PMCID: PMC11017751 DOI: 10.1016/j.psychres.2024.115815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024]
Abstract
Our study focused on human brain transcriptomes and the genetic risks of cigarettes per day (CPD) to investigate the neurogenetic mechanisms of individual variation in nicotine use severity. We constructed whole-brain and intramodular region-specific coexpression networks using BrainSpan's transcriptomes, and the genomewide association studies identified risk variants of CPD, confirmed the associations between CPD and each gene set in the region-specific subnetworks using an independent dataset, and conducted bioinformatic analyses. Eight brain-region-specific coexpression subnetworks were identified in association with CPD: amygdala, hippocampus, medial prefrontal cortex (MPFC), orbitofrontal cortex (OPFC), dorsolateral prefrontal cortex, striatum, mediodorsal nucleus of the thalamus (MDTHAL), and primary motor cortex (M1C). Each gene set in the eight subnetworks was associated with CPD. We also identified three hub proteins encoded by GRIN2A in the amygdala, PMCA2 in the hippocampus, MPFC, OPFC, striatum, and MDTHAL, and SV2B in M1C. Intriguingly, the pancreatic secretion pathway appeared in all the significant protein interaction subnetworks, suggesting pleiotropic effects between cigarette smoking and pancreatic diseases. The three hub proteins and genes are implicated in stress response, drug memory, calcium homeostasis, and inhibitory control. These findings provide novel evidence of the neurogenetic underpinnings of smoking severity.
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Affiliation(s)
- Bao-Zhu Yang
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA.
| | - Bo Xiang
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China.
| | - Tingting Wang
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Shuangge Ma
- Department of Biostatistics, Yale University, New Haven, CT, USA
| | - Chiang-Shan R Li
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Wu Tsai Institute, Yale University, New Haven, CT, USA
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Ortiz GG, Torres-Mendoza BMG, Ramírez-Jirano J, Marquez-Pedroza J, Hernández-Cruz JJ, Mireles-Ramirez MA, Torres-Sánchez ED. Genetic Basis of Inflammatory Demyelinating Diseases of the Central Nervous System: Multiple Sclerosis and Neuromyelitis Optica Spectrum. Genes (Basel) 2023; 14:1319. [PMID: 37510224 PMCID: PMC10379341 DOI: 10.3390/genes14071319] [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: 05/10/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Demyelinating diseases alter myelin or the coating surrounding most nerve fibers in the central and peripheral nervous systems. The grouping of human central nervous system demyelinating disorders today includes multiple sclerosis (MS) and neuromyelitis optica spectrum disorders (NMOSD) as distinct disease categories. Each disease is caused by a complex combination of genetic and environmental variables, many involving an autoimmune response. Even though these conditions are fundamentally similar, research into genetic factors, their unique clinical manifestations, and lesion pathology has helped with differential diagnosis and disease pathogenesis knowledge. This review aims to synthesize the genetic approaches that explain the differential susceptibility between these diseases, explore the overlapping clinical features, and pathological findings, discuss existing and emerging hypotheses on the etiology of demyelination, and assess recent pathogenicity studies and their implications for human demyelination. This review presents critical information from previous studies on the disease, which asks several questions to understand the gaps in research in this field.
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Affiliation(s)
- Genaro Gabriel Ortiz
- Department of Philosophical and Methodological Disciplines and Service of Molecular Biology in Medicine Hospital, Civil University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
- Department of Neurology, High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44329, Jalisco, Mexico
| | - Blanca M G Torres-Mendoza
- Department of Philosophical and Methodological Disciplines and Service of Molecular Biology in Medicine Hospital, Civil University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
- Neurosciences Division, Western Biomedical Research Center, Mexican Social Security Institute (Instituto Mexicano del Seguro Social, IMSS), Guadalajara 44340, Jalisco, Mexico
| | - Javier Ramírez-Jirano
- Neurosciences Division, Western Biomedical Research Center, Mexican Social Security Institute (Instituto Mexicano del Seguro Social, IMSS), Guadalajara 44340, Jalisco, Mexico
| | - Jazmin Marquez-Pedroza
- Neurosciences Division, Western Biomedical Research Center, Mexican Social Security Institute (Instituto Mexicano del Seguro Social, IMSS), Guadalajara 44340, Jalisco, Mexico
- Coordination of Academic Activities, Western Biomedical Research Center, Mexican Social Security Institute (Instituto Mexicano del Seguro Social, IMSS), Guadalajara 44340, Jalisco, Mexico
| | - José J Hernández-Cruz
- Department of Neurology, High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44329, Jalisco, Mexico
| | - Mario A Mireles-Ramirez
- Department of Neurology, High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44329, Jalisco, Mexico
| | - Erandis D Torres-Sánchez
- Department of Medical and Life Sciences, University Center of la Cienega, University of Guadalajara, Ocotlan 47820, Jalisco, Mexico
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Abstract
From the first clinical trial by Dr. W.F. Anderson to the most recent US Food and Drug Administration-approved Luxturna (Spark Therapeutics, 2017) and Zolgensma (Novartis, 2019), gene therapy has revamped thinking and practice around cancer treatment and improved survival rates for adult and pediatric patients with genetic diseases. A major challenge to advancing gene therapies for a broader array of applications lies in safely delivering nucleic acids to their intended sites of action. Peptides offer unique potential to improve nucleic acid delivery based on their versatile and tunable interactions with biomolecules and cells. Cell-penetrating peptides and intracellular targeting peptides have received particular focus due to their promise for improving the delivery of gene therapies into cells. We highlight key examples of peptide-assisted, targeted gene delivery to cancer-specific signatures involved in tumor growth and subcellular organelle-targeting peptides, as well as emerging strategies to enhance peptide stability and bioavailability that will support long-term implementation.
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Affiliation(s)
- Sandeep Urandur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
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Gharibi T, Barpour N, Hosseini A, Mohammadzadeh A, Marofi F, Ebrahimi-Kalan A, Nejati-Koshki K, Abdollahpour-Alitappeh M, Safaei S, Baghbani E, Baradaran B. STA-21, a small molecule STAT3 inhibitor, ameliorates experimental autoimmune encephalomyelitis by altering Th-17/Treg balance. Int Immunopharmacol 2023; 119:110160. [PMID: 37080068 DOI: 10.1016/j.intimp.2023.110160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 04/22/2023]
Abstract
BACKGROUND Numerous studies have demonstrated the role of T helper (Th) 17 and T regulatory (reg) cells and pro-inflammatory and anti-inflammatory cytokines related to these cells in the pathogenesis of MS and its animal model, experimental autoimmune encephalomyelitis (EAE). STAT3 is one of the downstream signaling proteins of IL-23, IL-6, and IL-21 that are required for Th17 cells differentiation. STA-21 is a STAT3 inhibitor that functions by inhibiting STAT3 dimerization and binding to DNA impairing the expression of STAT3 target genes including, RORγt, IL-21 and IL-23R that are also required for Th17 cell differentiation. AIM In this study, we evaluated the effect of STA-21 on EAE Model and investigated how this small molecule can change Th17/Treg balance leading to amelioration of disease. METHODS After EAE induction and treatment with STA-21, its effects were assessed. Major assays were H&E and LFB staining, Flow cytometric analysis, Reverse transcription-PCR (RT-PCR), and ELISA. RESULTS STA-21 ameliorated the EAE severity and decreased the EAE inflammation and demyelination. It also decreased STAT3 phosphorylation, the proportion of Th17 cells and the protein level of IL-17. In contrast, the balance of Tregs and the level of anti-inflammatory cytokine, IL-10 increased in STA-21-treated mice. Moreover, STA-21 significantly decreased the expression of Th17 related transcription factors, RORɣt and IL-23R while FOXP3 expression associated with Treg differentiation was increased. CONCLUSION This study showed that STA-21 has therapeutic effects in EAE by reducing inflammation and shifting inflammatory immune responses to anti-inflammatory and can be used as a suitable treatment strategy for the treatment of EAE. The effectiveness of inhibiting or strengthening the functional cells of the immune system by these small molecules in terms of easy to access, simple construction and inexpensive expansion make them as a suitable tool for the treatment of inflammatory and autoimmune diseases.
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Affiliation(s)
- Tohid Gharibi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Neurosciences and Cognition, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nesa Barpour
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Neurosciences and Cognition, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Arezoo Hosseini
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Adel Mohammadzadeh
- Department of Immunology and Genetics, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Faroogh Marofi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abbas Ebrahimi-Kalan
- Department of Neurosciences and Cognition, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Kazem Nejati-Koshki
- Department of Immunology and Genetics, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Meghdad Abdollahpour-Alitappeh
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran; Department of Nursing, School of Nursing, Larestan University of Medical Sciences, Larestan, Iran
| | - Sahar Safaei
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Baghbani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Tabriz University of Medical Sciences, Tabriz, Iran.
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Nabirotchkin S, Bouaziz J, Glibert F, Mandel J, Foucquier J, Hajj R, Callizot N, Cholet N, Guedj M, Cohen D. Combinational Drug Repurposing from Genetic Networks Applied to Alzheimer’s Disease. J Alzheimers Dis 2022; 88:1585-1603. [DOI: 10.3233/jad-220120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: Human diseases are multi-factorial biological phenomena resulting from perturbations of numerous functional networks. The complex nature of human diseases explains frequently observed marginal or transitory efficacy of mono-therapeutic interventions. For this reason, combination therapy is being increasingly evaluated as a biologically plausible strategy for reversing disease state, fostering the development of dedicated methodological and experimental approaches. In parallel, genome-wide association studies (GWAS) provide a prominent opportunity for disclosing human-specific therapeutic targets and rational drug repurposing. Objective: In this context, our objective was to elaborate an integrated computational platform to accelerate discovery and experimental validation of synergistic combinations of repurposed drugs for treatment of common human diseases. Methods: The proposed approach combines adapted statistical analysis of GWAS data, pathway-based functional annotation of genetic findings using gene set enrichment technique, computational reconstruction of signaling networks enriched in disease-associated genes, selection of candidate repurposed drugs and proof-of-concept combinational experimental screening. Results: It enables robust identification of signaling pathways enriched in disease susceptibility loci. Therapeutic targeting of the disease-associated signaling networks provides a reliable way for rational drug repurposing and rapid development of synergistic drug combinations for common human diseases. Conclusion: Here we demonstrate the feasibility and efficacy of the proposed approach with an experiment application to Alzheimer’s disease.
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Krovi SH, Kuchroo VK. Activation pathways that drive CD4 + T cells to break tolerance in autoimmune diseases . Immunol Rev 2022; 307:161-190. [PMID: 35142369 PMCID: PMC9255211 DOI: 10.1111/imr.13071] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/11/2022]
Abstract
Autoimmune diseases are characterized by dysfunctional immune systems that misrecognize self as non-self and cause tissue destruction. Several cell types have been implicated in triggering and sustaining disease. Due to a strong association of major histocompatibility complex II (MHC-II) proteins with various autoimmune diseases, CD4+ T lymphocytes have been thoroughly investigated for their roles in dictating disease course. CD4+ T cell activation is a coordinated process that requires three distinct signals: Signal 1, which is mediated by antigen recognition on MHC-II molecules; Signal 2, which boosts signal 1 in a costimulatory manner; and Signal 3, which helps to differentiate the activated cells into functionally relevant subsets. These signals are disrupted during autoimmunity and prompt CD4+ T cells to break tolerance. Herein, we review our current understanding of how each of the three signals plays a role in three different autoimmune diseases and highlight the genetic polymorphisms that predispose individuals to autoimmunity. We also discuss the drawbacks of existing therapies and how they can be addressed to achieve lasting tolerance in patients.
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Affiliation(s)
- Sai Harsha Krovi
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Barkhane Z, Elmadi J, Satish Kumar L, Pugalenthi LS, Ahmad M, Reddy S. Multiple Sclerosis and Autoimmunity: A Veiled Relationship. Cureus 2022; 14:e24294. [PMID: 35607574 PMCID: PMC9123335 DOI: 10.7759/cureus.24294] [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] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune inflammatory illness that affects the central nervous system (CNS) when the body's immune system attacks its tissue. It is characterized by demyelination and varying degrees of axonal loss. This article has compiled various studies elaborating MS and other autoimmune diseases (ADs) co-occurrence. Several conditions that fall into this category, including type 1 diabetes (T1D), rheumatoid arthritis (RA), Guillain-Barre syndrome (GBS), myasthenia gravis (MG), and many others, are found in MS patients and their relatives, suggesting one or more common etiologic mechanisms, including genetic, environmental, and immunological factors, supporting the concept of a possible influence of poly-autoimmunity on MS and the rest of ADs, as well as providing a significant feature for early detection of the disease and also a potential treatment option by clinical neurologists.
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A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population. PLoS Genet 2022; 18:e1010017. [PMID: 35108269 PMCID: PMC8843129 DOI: 10.1371/journal.pgen.1010017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 02/14/2022] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program. Slash pine is an important source of original timber and resin production on commercial forest plantations. It is necessary to implement precise breeding strategies to improve timber quality and resin yield. However, little is known about the species’ molecular genetic basis. Using a transcriptome dataset with sequencing from 240 individuals in the slash pine population, we combined multiple approaches (based on gene variation, expression variation and co-expression network) to dissect the genetic structure for slash pine major breeding traits. We found that the research population could be divided into three genetic groups with a mean heterozygosity of 0.2246. We also found that six genes with important functions in slash pine resin synthesis and timber formation through association studies. Four new SNPs associatation with the average ring width were also discovered. Our results provide new insights into the molecular genetic basis of important traits in slash pine and provide a comprehensive method for association analyses of conifer tree species with large genome.
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Shrestha V, Yobi A, Slaten ML, Chan YO, Holden S, Gyawali A, Flint-Garcia S, Lipka AE, Angelovici R. Multiomics approach reveals a role of translational machinery in shaping maize kernel amino acid composition. PLANT PHYSIOLOGY 2022; 188:111-133. [PMID: 34618082 PMCID: PMC8774818 DOI: 10.1093/plphys/kiab390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Maize (Zea mays) seeds are a good source of protein, despite being deficient in several essential amino acids. However, eliminating the highly abundant but poorly balanced seed storage proteins has revealed that the regulation of seed amino acids is complex and does not rely on only a handful of proteins. In this study, we used two complementary omics-based approaches to shed light on the genes and biological processes that underlie the regulation of seed amino acid composition. We first conducted a genome-wide association study to identify candidate genes involved in the natural variation of seed protein-bound amino acids. We then used weighted gene correlation network analysis to associate protein expression with seed amino acid composition dynamics during kernel development and maturation. We found that almost half of the proteome was significantly reduced during kernel development and maturation, including several translational machinery components such as ribosomal proteins, which strongly suggests translational reprogramming. The reduction was significantly associated with a decrease in several amino acids, including lysine and methionine, pointing to their role in shaping the seed amino acid composition. When we compared the candidate gene lists generated from both approaches, we found a nonrandom overlap of 80 genes. A functional analysis of these genes showed a tight interconnected cluster dominated by translational machinery genes, especially ribosomal proteins, further supporting the role of translation dynamics in shaping seed amino acid composition. These findings strongly suggest that seed biofortification strategies that target the translation machinery dynamics should be considered and explored further.
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Affiliation(s)
- Vivek Shrestha
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Abou Yobi
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Marianne L Slaten
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Yen On Chan
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Samuel Holden
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Abiskar Gyawali
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Sherry Flint-Garcia
- U.S. Department of Agriculture-Agricultural Research Service, Columbia, Missouri 65211, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, USA
| | - Ruthie Angelovici
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
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Capturing SNP Association across the NK Receptor and HLA Gene Regions in Multiple Sclerosis by Targeted Penalised Regression Models. Genes (Basel) 2021; 13:genes13010087. [PMID: 35052430 PMCID: PMC8774935 DOI: 10.3390/genes13010087] [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: 11/14/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022] Open
Abstract
Conventional genome-wide association studies (GWASs) of complex traits, such as Multiple Sclerosis (MS), are reliant on per-SNP p-values and are therefore heavily burdened by multiple testing correction. Thus, in order to detect more subtle alterations, ever increasing sample sizes are required, while ignoring potentially valuable information that is readily available in existing datasets. To overcome this, we used penalised regression incorporating elastic net with a stability selection method by iterative subsampling to detect the potential interaction of loci with MS risk. Through re-analysis of the ANZgene dataset (1617 cases and 1988 controls) and an IMSGC dataset as a replication cohort (1313 cases and 1458 controls), we identified new association signals for MS predisposition, including SNPs above and below conventional significance thresholds while targeting two natural killer receptor loci and the well-established HLA loci. For example, rs2844482 (98.1% iterations), otherwise ignored by conventional statistics (p = 0.673) in the same dataset, was independently strongly associated with MS in another GWAS that required more than 40 times the number of cases (~45 K). Further comparison of our hits to those present in a large-scale meta-analysis, confirmed that the majority of SNPs identified by the elastic net model reached conventional statistical GWAS thresholds (p < 5 × 10−8) in this much larger dataset. Moreover, we found that gene variants involved in oxidative stress, in addition to innate immunity, were associated with MS. Overall, this study highlights the benefit of using more advanced statistical methods to (re-)analyse subtle genetic variation among loci that have a biological basis for their contribution to disease risk.
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Fazia T, Marzanati D, Carotenuto AL, Beecham A, Hadjixenofontos A, McCauley JL, Saddi V, Piras M, Bernardinelli L, Gentilini D. Homozygosity Haplotype and Whole-Exome Sequencing Analysis to Identify Potentially Functional Rare Variants Involved in Multiple Sclerosis among Sardinian Families. Curr Issues Mol Biol 2021; 43:1778-1793. [PMID: 34889895 PMCID: PMC8929092 DOI: 10.3390/cimb43030125] [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: 09/22/2021] [Revised: 10/13/2021] [Accepted: 10/23/2021] [Indexed: 12/24/2022] Open
Abstract
Multiple Sclerosis (MS) is a complex multifactorial autoimmune disease, whose sex- and age-adjusted prevalence in Sardinia (Italy) is among the highest worldwide. To date, 233 loci were associated with MS and almost 20% of risk heritability is attributable to common genetic variants, but many low-frequency and rare variants remain to be discovered. Here, we aimed to contribute to the understanding of the genetic basis of MS by investigating potentially functional rare variants. To this end, we analyzed thirteen multiplex Sardinian families with Immunochip genotyping data. For five families, Whole Exome Sequencing (WES) data were also available. Firstly, we performed a non-parametric Homozygosity Haplotype analysis for identifying the Region from Common Ancestor (RCA). Then, on these potential disease-linked RCA, we searched for the presence of rare variants shared by the affected individuals by analyzing WES data. We found: (i) a variant (43181034 T > G) in the splicing region on exon 27 of CUL9; (ii) a variant (50245517 A > C) in the splicing region on exon 16 of ATP9A; (iii) a non-synonymous variant (43223539 A > C), on exon 9 of TTBK1; (iv) a non-synonymous variant (42976917 A > C) on exon 9 of PPP2R5D; and v) a variant (109859349-109859354) in 3'UTR of MYO16.
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Affiliation(s)
- Teresa Fazia
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (D.M.); (A.L.C.); (L.B.); (D.G.)
| | - Daria Marzanati
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (D.M.); (A.L.C.); (L.B.); (D.G.)
| | - Anna Laura Carotenuto
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (D.M.); (A.L.C.); (L.B.); (D.G.)
| | - Ashley Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (A.B.); (A.H.); (J.L.M.)
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, Miami, FL 33136, USA
| | - Athena Hadjixenofontos
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (A.B.); (A.H.); (J.L.M.)
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, Miami, FL 33136, USA
| | - Jacob L. McCauley
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (A.B.); (A.H.); (J.L.M.)
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, Miami, FL 33136, USA
| | - Valeria Saddi
- Divisione di Neurologia, Presidio Ospedaliero S. Francesco, ASL Numero 3 Nuoro, 08100 Nuoro, Italy; (V.S.); (M.P.)
| | - Marialuisa Piras
- Divisione di Neurologia, Presidio Ospedaliero S. Francesco, ASL Numero 3 Nuoro, 08100 Nuoro, Italy; (V.S.); (M.P.)
| | - Luisa Bernardinelli
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (D.M.); (A.L.C.); (L.B.); (D.G.)
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (D.M.); (A.L.C.); (L.B.); (D.G.)
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, 20095 Cusano Milanino, Italy
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Guglietti B, Sivasankar S, Mustafa S, Corrigan F, Collins-Praino LE. Fyn Kinase Activity and Its Role in Neurodegenerative Disease Pathology: a Potential Universal Target? Mol Neurobiol 2021; 58:5986-6005. [PMID: 34432266 DOI: 10.1007/s12035-021-02518-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022]
Abstract
Fyn is a non-receptor tyrosine kinase belonging to the Src family of kinases (SFKs) which has been implicated in several integral functions throughout the central nervous system (CNS), including myelination and synaptic transmission. More recently, Fyn dysfunction has been associated with pathological processes observed in neurodegenerative diseases, such as multiple sclerosis (MS), Alzheimer's disease (AD) and Parkinson's disease (PD). Neurodegenerative diseases are amongst the leading cause of death and disability worldwide and, due to the ageing population, prevalence is predicted to rise in the coming years. Symptoms across neurodegenerative diseases are both debilitating and degenerative in nature and, concerningly, there are currently no disease-modifying therapies to prevent their progression. As such, it is important to identify potential new therapeutic targets. This review will outline the role of Fyn in normal/homeostatic processes, as well as degenerative/pathological mechanisms associated with neurodegenerative diseases, such as demyelination, pathological protein aggregation, neuroinflammation and cognitive dysfunction.
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Affiliation(s)
- Bianca Guglietti
- Department of Medical Sciences, University of Adelaide, SG31, Helen Mayo South, Adelaide, SA, 5005, Australia
| | - Srisankavi Sivasankar
- Department of Medical Sciences, University of Adelaide, SG31, Helen Mayo South, Adelaide, SA, 5005, Australia
| | - Sanam Mustafa
- Department of Medical Sciences, University of Adelaide, SG31, Helen Mayo South, Adelaide, SA, 5005, Australia.,ARC Centre of Excellence for Nanoscale BioPhotonics, University of Adelaide, Adelaide, Australia
| | - Frances Corrigan
- Department of Medical Sciences, University of Adelaide, SG31, Helen Mayo South, Adelaide, SA, 5005, Australia
| | - Lyndsey E Collins-Praino
- Department of Medical Sciences, University of Adelaide, SG31, Helen Mayo South, Adelaide, SA, 5005, Australia. .,ARC Centre of Excellence for Nanoscale BioPhotonics, University of Adelaide, Adelaide, Australia.
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Woo MS, Ufer F, Rothammer N, Di Liberto G, Binkle L, Haferkamp U, Sonner JK, Engler JB, Hornig S, Bauer S, Wagner I, Egervari K, Raber J, Duvoisin RM, Pless O, Merkler D, Friese MA. Neuronal metabotropic glutamate receptor 8 protects against neurodegeneration in CNS inflammation. J Exp Med 2021; 218:e20201290. [PMID: 33661276 PMCID: PMC7938362 DOI: 10.1084/jem.20201290] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 12/17/2020] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system with continuous neuronal loss. Treatment of clinical progression remains challenging due to lack of insights into inflammation-induced neurodegenerative pathways. Here, we show that an imbalance in the neuronal receptor interactome is driving glutamate excitotoxicity in neurons of MS patients and identify the MS risk-associated metabotropic glutamate receptor 8 (GRM8) as a decisive modulator. Mechanistically, GRM8 activation counteracted neuronal cAMP accumulation, thereby directly desensitizing the inositol 1,4,5-trisphosphate receptor (IP3R). This profoundly limited glutamate-induced calcium release from the endoplasmic reticulum and subsequent cell death. Notably, we found Grm8-deficient neurons to be more prone to glutamate excitotoxicity, whereas pharmacological activation of GRM8 augmented neuroprotection in mouse and human neurons as well as in a preclinical mouse model of MS. Thus, we demonstrate that GRM8 conveys neuronal resilience to CNS inflammation and is a promising neuroprotective target with broad therapeutic implications.
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Affiliation(s)
- Marcel S. Woo
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Friederike Ufer
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Rothammer
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Giovanni Di Liberto
- Division of Clinical Pathology, Department of Pathology and Immunology, Geneva Faculty of Medicine, Geneva, Switzerland
| | - Lars Binkle
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Undine Haferkamp
- Fraunhofer Institute for Translational Medicine and Pharmacology, Hamburg, Germany
| | - Jana K. Sonner
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Jan Broder Engler
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Sönke Hornig
- Experimentelle Neuropädiatrie, Klinik für Kinder und Jugendmedizin, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Simone Bauer
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Ingrid Wagner
- Division of Clinical Pathology, Department of Pathology and Immunology, Geneva Faculty of Medicine, Geneva, Switzerland
| | - Kristof Egervari
- Division of Clinical Pathology, Department of Pathology and Immunology, Geneva Faculty of Medicine, Geneva, Switzerland
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR
- Department of Neurology, Oregon Health & Science University, Portland, OR
- Department of Radiation Medicine, Oregon Health & Science University, Portland, OR
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR
| | - Robert M. Duvoisin
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR
| | - Ole Pless
- Fraunhofer Institute for Translational Medicine and Pharmacology, Hamburg, Germany
| | - Doron Merkler
- Division of Clinical Pathology, Department of Pathology and Immunology, Geneva Faculty of Medicine, Geneva, Switzerland
| | - Manuel A. Friese
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
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14
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Cai R, Dong Y, Fang M, Fan Y, Cheng Z, Zhou Y, Gao J, Han F, Guo C, Ma X. Genome-Wide Association Identifies Risk Pathways for SAPHO Syndrome. Front Cell Dev Biol 2021; 9:643644. [PMID: 33816493 PMCID: PMC8012550 DOI: 10.3389/fcell.2021.643644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/18/2021] [Indexed: 11/13/2022] Open
Abstract
SAPHO syndrome is a rare chronic inflammatory disease which is characterized by the comprehensive manifestations of bone, joint, and skin. However, little is known about the pathogenesis of SAPHO syndrome. A genome-wide association study (GWAS) of 49 patients and 121 control subjects have primarily focused on identification of common genetic variants associated with SAPHO, the data were analyzed by classical multiple logistic regression. Later, GWAS findings were further validated using whole exome sequencing (WES) in 16 patients and 15 controls to identify potentially functional pathways involved in SAPHO pathogenesis. In general, 40588 SNPs in genomic regions were associated with P < 0.05 after filter process, only 9 SNPs meet the expected cut-off P-value, however, none of them had association with SAPHO syndrome based on published literatures. And then, 15 pathways were found involved in SAPHO pathogenesis, of them, 6 pathways including osteoclast differentiation, bacterial invasion of epithelial cells, et al., had strong association with skin, osteoarticular manifestations of SAPHO or inflammatory reaction based published research. This study identified aberrant osteoclast differentiation and other pathways were involved in SAPHO syndrome. This finding may give insight into the understanding of pathogenic genes of SAPHO and provide the basis for SAPHO research and treatment.
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Affiliation(s)
- Ruikun Cai
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
| | - Yichao Dong
- National Research Institute for Family Planning, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Mingxia Fang
- National Research Institute for Family Planning, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Yuxuan Fan
- National Research Institute for Family Planning, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Zian Cheng
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
| | - Yue Zhou
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
| | - Jianen Gao
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
| | - Feifei Han
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Changlong Guo
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
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15
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Blencowe M, Ahn IS, Saleem Z, Luk H, Cely I, Mäkinen VP, Zhao Y, Yang X. Gene networks and pathways for plasma lipid traits via multitissue multiomics systems analysis. J Lipid Res 2021; 62:100019. [PMID: 33561811 PMCID: PMC7873371 DOI: 10.1194/jlr.ra120000713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 12/04/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies (GWASs) have implicated ∼380 genetic loci for plasma lipid regulation. However, these loci only explain 17-27% of the trait variance, and a comprehensive understanding of the molecular mechanisms has not been achieved. In this study, we utilized an integrative genomics approach leveraging diverse genomic data from human populations to investigate whether genetic variants associated with various plasma lipid traits, namely, total cholesterol, high and low density lipoprotein cholesterol (HDL and LDL), and triglycerides, from GWASs were concentrated on specific parts of tissue-specific gene regulatory networks. In addition to the expected lipid metabolism pathways, gene subnetworks involved in "interferon signaling," "autoimmune/immune activation," "visual transduction," and "protein catabolism" were significantly associated with all lipid traits. In addition, we detected trait-specific subnetworks, including cadherin-associated subnetworks for LDL; glutathione metabolism for HDL; valine, leucine, and isoleucine biosynthesis for total cholesterol; and insulin signaling and complement pathways for triglyceride. Finally, by using gene-gene relations revealed by tissue-specific gene regulatory networks, we detected both known (e.g., APOH, APOA4, and ABCA1) and novel (e.g., F2 in adipose tissue) key regulator genes in these lipid-associated subnetworks. Knockdown of the F2 gene (coagulation factor II, thrombin) in 3T3-L1 and C3H10T1/2 adipocytes altered gene expression of Abcb11, Apoa5, Apof, Fabp1, Lipc, and Cd36; reduced intracellular adipocyte lipid content; and increased extracellular lipid content, supporting a link between adipose thrombin and lipid regulation. Our results shed light on the complex mechanisms underlying lipid metabolism and highlight potential novel targets for lipid regulation and lipid-associated diseases.
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Affiliation(s)
- Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA; Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - In Sook Ahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zara Saleem
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Helen Luk
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ingrid Cely
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ville-Petteri Mäkinen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA; South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA; Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA; Interdepartmental Program of Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA.
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16
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Wu L, Han L, Li Q, Wang G, Zhang H, Li L. Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future Crop Breeding. MOLECULAR PLANT 2021; 14:77-94. [PMID: 33340690 DOI: 10.1016/j.molp.2020.12.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 05/27/2023]
Abstract
The functional genes underlying phenotypic variation and their interactions represent "genetic mysteries". Understanding and utilizing these genetic mysteries are key solutions for mitigating the current threats to agriculture posed by population growth and individual food preferences. Due to advances in high-throughput multi-omics technologies, we are stepping into an Interactome Big Data era that is certain to revolutionize genetic research. In this article, we provide a brief overview of current strategies to explore genetic mysteries. We then introduce the methods for constructing and analyzing the Interactome Big Data and summarize currently available interactome resources. Next, we discuss how Interactome Big Data can be used as a versatile tool to dissect genetic mysteries. We propose an integrated strategy that could revolutionize genetic research by combining Interactome Big Data with machine learning, which involves mining information hidden in Big Data to identify the genetic models or networks that control various traits, and also provide a detailed procedure for systematic dissection of genetic mysteries,. Finally, we discuss three promising future breeding strategies utilizing the Interactome Big Data to improve crop yields and quality.
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Affiliation(s)
- Leiming Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongwei Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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17
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Caylak G, Tastan O, Cicek AE. Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection. J Comput Biol 2020; 28:365-377. [PMID: 33275856 DOI: 10.1089/cmb.2020.0429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies (GWAS) explain a fraction of the underlying heritability of genetic diseases. Investigating epistatic interactions between two or more loci help to close this gap. Unfortunately, the sheer number of loci combinations to process and hypotheses prohibit the process both computationally and statistically. Epistasis test prioritization algorithms rank likely epistatic single nucleotide polymorphism (SNP) pairs to limit the number of tests. However, they still suffer from very low precision. It was shown in the literature that selecting SNPs that are individually correlated with the phenotype and also diverse with respect to genomic location leads to better phenotype prediction due to genetic complementation. Here, we propose that an algorithm that pairs SNPs from such diverse regions and ranks them can improve prediction power. We propose an epistasis test prioritization algorithm that optimizes a submodular set function to select a diverse and complementary set of genomic regions that span the underlying genome. The SNP pairs from these regions are then further ranked w.r.t. their co-coverage of the case cohort. We compare our algorithm with the state of the art on three GWAS and show that (1) we substantially improve precision (from 0.003 to 0.652) while maintaining the significance of selected pairs, (2) decrease the number of tests by 25-fold, and (3) decrease the runtime by 4-fold. We also show that promoting SNPs from regulatory/coding regions improves the performance (up to 0.8). Potpourri is available at http:/ciceklab.cs.bilkent.edu.tr/potpourri.
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Affiliation(s)
- Gizem Caylak
- Computer Engineering Department, Bilkent University, Ankara, Turkey
| | - Oznur Tastan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - A Ercument Cicek
- Computer Engineering Department, Bilkent University, Ankara, Turkey
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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18
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Jiang S, Zhang CY, Tang L, Zhao LX, Chen HZ, Qiu Y. Integrated Genomic Analysis Revealed Associated Genes for Alzheimer's Disease in APOE4 Non-Carriers. Curr Alzheimer Res 2020; 16:753-763. [PMID: 31441725 DOI: 10.2174/1567205016666190823124724] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 07/14/2019] [Accepted: 08/08/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND APOE4 is the strongest genetic risk factor for late-onset Alzheimer's disease (LOAD). LOAD patients carrying or not carrying APOE4 manifest distinct clinico-pathological characteristics. APOE4 has been shown to play a critical role in the pathogenesis of AD by affecting various aspects of pathological processes. However, the pathogenesis involved in LOAD not-carrying APOE4 remains elusive. OBJECTIVE We aimed to identify the associated genes involved in LOAD not-carrying APOE4. METHODS An integrated genomic analysis of datasets of genome-wide association study, genome-wide expression profiling and genome-wide linkage scan and protein-protein interaction network construction were applied to identify associated gene clusters in APOE4 non-carriers. The role of one of hub gene of an APOE4 non-carrier-associated gene cluster in tau phosphorylation was studied by knockdown and western blot. RESULTS We identified 12 gene clusters associated with AD APOE4 non-carriers. The hub genes associated with AD in these clusters were MAPK8, POU2F1, XRCC1, PRKCG, EXOC6, VAMP4, SIRT1, MME, NOS1, ABCA1 and LDLR. The associated genes for APOE4 non-carriers were enriched in hereditary disorder, neurological disease and psychological disorders. Moreover, knockdown of PRKCG to reduce the expression of protein kinase Cγ isoform enhanced tau phosphorylation at Thr181 and Thr231 and the expression of glycogen synthase kinase 3β and cyclin-dependent kinase 5 in the presence of APOE3 but not APOE4. CONCLUSION The study provides new insight into the mechanism of distinct pathogenesis of LOAD not carrying APOE4 and prompts the functional exploration of identified genes based on APOE genotypes.
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Affiliation(s)
- Shan Jiang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Chun-Yun Zhang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ling Tang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lan-Xue Zhao
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hong-Zhuan Chen
- Institute of Interdisciplinary Integrative Biomedical Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201210, China
| | - Yu Qiu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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19
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Leal-Gutiérrez JD, Rezende FM, Reecy JM, Kramer LM, Peñagaricano F, Mateescu RG. Whole Genome Sequence Data Provides Novel Insights Into the Genetic Architecture of Meat Quality Traits in Beef. Front Genet 2020; 11:538640. [PMID: 33101375 PMCID: PMC7500205 DOI: 10.3389/fgene.2020.538640] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
Tenderness is a major quality attribute for fresh beef steaks in the United States, and meat quality traits in general are suitable candidates for genomic research. The objectives of the present analysis were to (1) perform genome-wide association (GWA) analysis for marbling, Warner-Bratzler shear force (WBSF), tenderness, and connective tissue using whole-genome data in an Angus population, (2) identify enriched pathways in each GWA analysis; (3) construct a protein-protein interaction network using the associated genes and (4) perform a μ-calpain proteolysis assessment for associated structural proteins. An Angus-sired population of 2,285 individuals was assessed. Animals were transported to a commercial packing plant and harvested at an average age of 457 ± 46 days. After 48 h postmortem, marbling was recorded by graders' visual appraisal. Two 2.54-cm steaks were sampled from each muscle for recording of WBSF, and tenderness, and connective tissue by a sensory panel. The relevance of additive effects on marbling, WBSF, tenderness, and connective tissue was evaluated on a genome-wide scale using a two-step mixed model-based approach in single-trait analysis. A tissue-restricted gene enrichment was performed for each GWA where all polymorphisms with an association p-value lower than 1 × 10-3 were included. The genes identified as associated were included in a protein-protein interaction network and a candidate structural protein assessment of proteolysis analyses. A total of 1,867, 3,181, 3,926, and 3,678 polymorphisms were significantly associated with marbling, WBSF, tenderness, and connective tissue, respectively. The associate region on BTA29 (36,432,655-44,313,046 bp) harbors 13 highly significant markers for meat quality traits. Enrichment for the GO term GO:0005634 (Nucleus), which includes transcription factors, was evident. The final protein-protein network included 431 interations between 349 genes. The 42 most important genes based on significance that encode structural proteins were included in a proteolysis analysis, and 81% of these proteins were potential μ-Calpain substrates. Overall, this comprehensive study unraveled genetic variants, genes and mechanisms of action responsible for the variation in meat quality traits. Our findings can provide opportunities for improving meat quality in beef cattle via marker-assisted selection.
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Affiliation(s)
| | - Fernanda M. Rezende
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - James M. Reecy
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Luke M. Kramer
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Raluca G. Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
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20
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Giussani P, Prinetti A, Tringali C. The role of Sphingolipids in myelination and myelin stability and their involvement in childhood and adult demyelinating disorders. J Neurochem 2020; 156:403-414. [PMID: 33448358 DOI: 10.1111/jnc.15133] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 01/02/2023]
Abstract
Multiple sclerosis (MS) represents the most common demyelinating disease affecting the central nervous system (CNS) in adults as well as in children. Furthermore, in children, in addition to acquired diseases such as MS, genetically inherited diseases significantly contribute to the incidence of demyelinating disorders. Some genetic defects lead to sphingolipid alterations that are able to elicit neurological symptoms. Sphingolipids are essential for brain development, and their aberrant functionality may thus contribute to demyelinating diseases such as MS. In particular, sphingolipidoses caused by deficits of sphingolipid-metabolizing enzymes, are often associated with demyelination. Sphingolipids are not only structural molecules but also bioactive molecules involved in the regulation of cellular events such as development of the nervous system, myelination and maintenance of myelin stability. Changes in the sphingolipid metabolism deeply affect plasma membrane organization. Thus, changes in myelin sphingolipid composition might crucially contribute to the phenotype of diseases characterized by demyelinalization. Here, we review key features of several sphingolipids such as ceramide/dihydroceramide, sphingosine/dihydrosphingosine, glucosylceramide and, galactosylceramide which act in myelin formation during rat brain development and in human brain demyelination during the pathogenesis of MS, suggesting that this knowledge could be useful in identifying targets for possible therapies.
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Affiliation(s)
- Paola Giussani
- Department of Medical Biotechnology and Translational Medicine, Università di Milano, LITA Segrate, Segrate, Italy
| | - Alessandro Prinetti
- Department of Medical Biotechnology and Translational Medicine, Università di Milano, LITA Segrate, Segrate, Italy
| | - Cristina Tringali
- Department of Medical Biotechnology and Translational Medicine, Università di Milano, LITA Segrate, Segrate, Italy
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21
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Fyn Tyrosine Kinase as Harmonizing Factor in Neuronal Functions and Dysfunctions. Int J Mol Sci 2020; 21:ijms21124444. [PMID: 32580508 PMCID: PMC7352836 DOI: 10.3390/ijms21124444] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/25/2022] Open
Abstract
Fyn is a non-receptor or cytoplasmatic tyrosine kinase (TK) belonging to the Src family kinases (SFKs) involved in multiple transduction pathways in the central nervous system (CNS) including synaptic transmission, myelination, axon guidance, and oligodendrocyte formation. Almost one hundred years after the original description of Fyn, this protein continues to attract extreme interest because of its multiplicity of actions in the molecular signaling pathways underlying neurodevelopmental as well as neuropathologic events. This review highlights and summarizes the most relevant recent findings pertinent to the role that Fyn exerts in the brain, emphasizing aspects related to neurodevelopment and synaptic plasticity. Fyn is a common factor in healthy and diseased brains that targets different proteins and shapes different transduction signals according to the neurological conditions. We will primarily focus on Fyn-mediated signaling pathways involved in neuronal differentiation and plasticity that have been subjected to considerable attention lately, opening the fascinating scenario to target Fyn TK for the development of potential therapeutic interventions for the treatment of CNS injuries and certain neurodegenerative disorders like Alzheimer’s disease.
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22
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Åkerborg Ö, Spalinskas R, Pradhananga S, Anil A, Höjer P, Poujade FA, Folkersen L, Eriksson PP, Sahlén P. High-Resolution Regulatory Maps Connect Vascular Risk Variants to Disease-Related Pathways. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 12:e002353. [PMID: 30786239 PMCID: PMC8104016 DOI: 10.1161/circgen.118.002353] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Supplemental Digital Content is available in the text. Genetic variant landscape of coronary artery disease is dominated by noncoding variants among which many occur within putative enhancers regulating the expression levels of relevant genes. It is crucial to assign the genetic variants to their correct genes both to gain insights into perturbed functions and better assess the risk of disease.
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Affiliation(s)
- Örjan Åkerborg
- Science for Life Laboratory, Division of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden (Ö.Å., R.S., S.P., A.A., P.H., P.S.)
| | - Rapolas Spalinskas
- Science for Life Laboratory, Division of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden (Ö.Å., R.S., S.P., A.A., P.H., P.S.)
| | - Sailendra Pradhananga
- Science for Life Laboratory, Division of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden (Ö.Å., R.S., S.P., A.A., P.H., P.S.)
| | - Anandashankar Anil
- Science for Life Laboratory, Division of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden (Ö.Å., R.S., S.P., A.A., P.H., P.S.)
| | - Pontus Höjer
- Science for Life Laboratory, Division of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden (Ö.Å., R.S., S.P., A.A., P.H., P.S.)
| | - Flore-Anne Poujade
- Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden (F.-A.P., P.E.)
| | - Lasse Folkersen
- Department of Bioinformatics, Technical University of Denmark, Copenhagen, Denmark (L.F.)
| | - Professor Per Eriksson
- Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden (F.-A.P., P.E.)
| | - Pelin Sahlén
- Science for Life Laboratory, Division of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden (Ö.Å., R.S., S.P., A.A., P.H., P.S.)
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STAT3 signaling in myeloid cells promotes pathogenic myelin-specific T cell differentiation and autoimmune demyelination. Proc Natl Acad Sci U S A 2020; 117:5430-5441. [PMID: 32094172 PMCID: PMC7071888 DOI: 10.1073/pnas.1913997117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Myeloid lineage cells are suspected of having an integral role in pathophysiological processes of multiple sclerosis (MS), but the molecular mechanism(s) governing their effector function remains incompletely understood. We show that STAT3 is activated in myeloid cells near active MS lesions. Conditional deletion of Stat3 in myeloid cells abolished symptoms of experimental autoimmune encephalomyelitis (EAE) by suppressing the generation of pathogenic T cells. Functional and transcriptomic analyses of myeloid cells from wild-type and conditional knockout mice implicated antigen processing/presentation and inflammatory cytokine production as the mechanism underlying the effects of STAT3 deletion on impaired T cell activation. Our data indicate that targeting STAT3 in myeloid cells might be a viable treatment option for autoimmune demyelinating disease. Multiple sclerosis (MS) is an autoimmune inflammatory demyelinating disease of the central nervous system. Dysregulation of STAT3, a transcription factor pivotal to various cellular processes including Th17 cell differentiation, has been implicated in MS. Here, we report that STAT3 is activated in infiltrating monocytic cells near active MS lesions and that activation of STAT3 in myeloid cells is essential for leukocyte infiltration, neuroinflammation, and demyelination in experimental autoimmune encephalomyelitis (EAE). Genetic disruption of Stat3 in peripheral myeloid lineage cells abrogated EAE, which was associated with decreased antigen-specific T helper cell responses. Myeloid cells from immunized Stat3 mutant mice exhibited impaired antigen-presenting functions and were ineffective in driving encephalitogenic T cell differentiation. Single-cell transcriptome analyses of myeloid lineage cells from preclinical wild-type and mutant mice revealed that loss of myeloid STAT3 signaling disrupted antigen-dependent cross-activation of myeloid cells and T helper cells. This study identifies a previously unrecognized requisite for myeloid cell STAT3 in the activation of myelin-reactive T cells and suggests myeloid STAT3 as a potential therapeutic target for autoimmune demyelinating disease.
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24
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Faria do Valle Í. Recent advances in network medicine: From disease mechanisms to new treatment strategies. Mult Scler 2020; 26:609-615. [DOI: 10.1177/1352458519877002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Conventional reductionist approaches have guided most of our understanding in disease diagnostic and treatment. However, most diseases are not consequence of perturbations in a single protein or metabolite, but rather of the effect that these perturbations have in their cellular context. The emerging field of network medicine offers a set of tools to explore molecular networks and to retrieve insights about mechanisms of different diseases. The study of the protein interactome, the map of physical interactions among human proteins, revealed that disease proteins tend to interact with each other, linking diseases to well-defined interactome neighborhoods. These disease-associated neighborhoods have been defined as disease modules, and they can uncover the biological significance of genes identified by genetic studies, reveal molecular mechanisms that connect different phenotypes, and help identify new pharmacological strategies for disease treatment. Therefore, network medicine offers a framework in which the complexity of different aspects of multiple sclerosis can be explored in an integrative fashion, which can ultimately provide insights about disease mechanisms and treatment.
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Affiliation(s)
- Ítalo Faria do Valle
- Center for Complex Network Research, Department of Physics, Northeastern University, Boston, MA, USA/ Division of Population Health and Data Science, MAVERIC, Boston Veterans Affairs Medical Center, Boston, MA, USA
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25
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Escala-Garcia M, Abraham J, Andrulis IL, Anton-Culver H, Arndt V, Ashworth A, Auer PL, Auvinen P, Beckmann MW, Beesley J, Behrens S, Benitez J, Bermisheva M, Blomqvist C, Blot W, Bogdanova NV, Bojesen SE, Bolla MK, Børresen-Dale AL, Brauch H, Brenner H, Brucker SY, Burwinkel B, Caldas C, Canzian F, Chang-Claude J, Chanock SJ, Chin SF, Clarke CL, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Dennis J, Devilee P, Dunn JA, Dunning AM, Dwek M, Earl HM, Eccles DM, Eliassen AH, Ellberg C, Evans DG, Fasching PA, Figueroa J, Flyger H, Gago-Dominguez M, Gapstur SM, García-Closas M, García-Sáenz JA, Gaudet MM, George A, Giles GG, Goldgar DE, González-Neira A, Grip M, Guénel P, Guo Q, Haiman CA, Håkansson N, Hamann U, Harrington PA, Hiller L, Hooning MJ, Hopper JL, Howell A, Huang CS, Huang G, Hunter DJ, Jakubowska A, John EM, Kaaks R, Kapoor PM, Keeman R, Kitahara CM, Koppert LB, Kraft P, Kristensen VN, Lambrechts D, Le Marchand L, Lejbkowicz F, Lindblom A, Lubiński J, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Maurer T, Mavroudis D, Meindl A, Milne RL, Mulligan AM, Neuhausen SL, Nevanlinna H, Newman WG, Olshan AF, Olson JE, Olsson H, Orr N, Peterlongo P, Petridis C, Prentice RL, Presneau N, Punie K, Ramachandran D, Rennert G, Romero A, Sachchithananthan M, Saloustros E, Sawyer EJ, Schmutzler RK, Schwentner L, Scott C, Simard J, Sohn C, Southey MC, Swerdlow AJ, Tamimi RM, Tapper WJ, Teixeira MR, Terry MB, Thorne H, Tollenaar RAEM, Tomlinson I, Troester MA, Truong T, Turnbull C, Vachon CM, van der Kolk LE, Wang Q, Winqvist R, Wolk A, Yang XR, Ziogas A, Pharoah PDP, Hall P, Wessels LFA, Chenevix-Trench G, Bader GD, Dörk T, Easton DF, Canisius S, Schmidt MK. A network analysis to identify mediators of germline-driven differences in breast cancer prognosis. Nat Commun 2020; 11:312. [PMID: 31949161 PMCID: PMC6965101 DOI: 10.1038/s41467-019-14100-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 12/17/2019] [Indexed: 11/09/2022] Open
Abstract
Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based analysis studies ~7.3 million variants in 84,457 breast cancer patients in relation to breast cancer survival and confirms the results on 12,381 independent patients. Aggregating the prognostic effects of genetic variants across multiple genes, we identify four gene modules associated with survival in estrogen receptor (ER)-negative and one in ER-positive disease. The modules show biological enrichment for cancer-related processes such as G-alpha signaling, circadian clock, angiogenesis, and Rho-GTPases in apoptosis.
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Affiliation(s)
- Maria Escala-Garcia
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Jean Abraham
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
- Cambridge Breast Unit and NIHR Cambridge Biomedical Research Centre, University of Cambridge NHS Foundation Hospitals, Cambridge, UK
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Paul L Auer
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Päivi Auvinen
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Oncology, University of Eastern Finland, Kuopio, Finland
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Javier Benitez
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Oncology, Örebro University Hospital, Örebro, Sweden
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- iFIT-Cluster of Excellence, University of Tuebingen, Tuebingen, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Sara Y Brucker
- Department of Gynecology and Obstetrics, University of Tübingen, Tübingen, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Breast Cancer Programme, CRUK Cambridge Cancer Centre and NIHR Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Christine L Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Department of Oncology and Metabolism, Sheffield Institute for Nucleic Acids (SInFoNiA), University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Janet A Dunn
- Warwick Clinical Trials Unit, University of Warwick, Coventry, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Miriam Dwek
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Helena M Earl
- Cambridge Breast Unit and NIHR Cambridge Biomedical Research Centre, University of Cambridge NHS Foundation Hospitals, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Diana M Eccles
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Carolina Ellberg
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - D Gareth Evans
- Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Genomic Medicine, St Mary's Hospital, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Edinburgh, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - José A García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mia M Gaudet
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Angela George
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Anna González-Neira
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Pascal Guénel
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), University Paris-Saclay, INSERM, University Paris-Sud, Villejuif, France
| | - Qi Guo
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patricia A Harrington
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Louise Hiller
- Warwick Clinical Trials Unit, University of Warwick, Coventry, UK
| | - Maartje J Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Guanmengqian Huang
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Esther M John
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pooja Middha Kapoor
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Renske Keeman
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Linetta B Koppert
- Department of Surgical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Diether Lambrechts
- VIB, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Flavio Lejbkowicz
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Pathology, Imaging Center, Kuopio University Hospital, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano (INT), Milan, Italy
| | - Sara Margolin
- Department of Oncology, Sšdersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Sšdersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Maria Elena Martinez
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Tabea Maurer
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - William G Newman
- Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Genomic Medicine, St Mary's Hospital, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Andrew F Olshan
- Department of Epidemiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Nick Orr
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Ireland, UK
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM - the FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Christos Petridis
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Ross L Prentice
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nadege Presneau
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Kevin Punie
- Department of Oncology, Leuven Multidisciplinary Breast Center, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | | | - Gad Rennert
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | | | | | - Elinor J Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Lukas Schwentner
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Christopher Scott
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jacques Simard
- Genomics Center, Research Center, Centre Hospitalier Universitaire de Québec - Université Laval, Québec City, QC, Canada
| | - Christof Sohn
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Rulla M Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Heather Thorne
- Peter MacCallum Cancer Center, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Melissa A Troester
- Department of Epidemiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thérèse Truong
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), University Paris-Saclay, INSERM, University Paris-Sud, Villejuif, France
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Celine M Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Lizet E van der Kolk
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Robert Winqvist
- Biocenter Oulu, Cancer and Translational Medicine Research Unit, Laboratory of Cancer Genetics and Tumor Biology, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Argyrios Ziogas
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Sšdersjukhuset, Stockholm, Sweden
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Douglas F Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Sander Canisius
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
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Reworking GWAS Data to Understand the Role of Nongenetic Factors in MS Etiopathogenesis. Genes (Basel) 2020; 11:genes11010097. [PMID: 31947683 PMCID: PMC7017269 DOI: 10.3390/genes11010097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/03/2020] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified more than 200 multiple sclerosis (MS)-associated loci across the human genome over the last decade, suggesting complexity in the disease etiology. This complexity poses at least two challenges: the definition of an etiological model including the impact of nongenetic factors, and the clinical translation of genomic data that may be drivers for new druggable targets. We reviewed studies dealing with single genes of interest, to understand how MS-associated single nucleotide polymorphism (SNP) variants affect the expression and the function of those genes. We then surveyed studies on the bioinformatic reworking of genome-wide association studies (GWAS) data, with aggregate analyses of many GWAS loci, each contributing with a small effect to the overall disease predisposition. These investigations uncovered new information, especially when combined with nongenetic factors having possible roles in the disease etiology. In this context, the interactome approach, defined as “modules of genes whose products are known to physically interact with environmental or human factors with plausible relevance for MS pathogenesis”, will be reported in detail. For a future perspective, a polygenic risk score, defined as a cumulative risk derived from aggregating the contributions of many DNA variants associated with a complex trait, may be integrated with data on environmental factors affecting the disease risk or protection.
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A systems biology approach to identifying genetic factors affected by aging, lifestyle factors, and type 2 diabetes that influences Parkinson's disease progression. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Yuan S, Li H, Xie J, Sun X. Quantitative Trait Module-Based Genetic Analysis of Alzheimer's Disease. Int J Mol Sci 2019; 20:E5912. [PMID: 31775305 PMCID: PMC6928939 DOI: 10.3390/ijms20235912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 01/02/2023] Open
Abstract
The pathological features of Alzheimer's Disease (AD) first appear in the medial temporal lobe and then in other brain structures with the development of the disease. In this work, we investigated the association between genetic loci and subcortical structure volumes of AD on 393 samples in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Brain subcortical structures were clustered into modules using Pearson's correlation coefficient of volumes across all samples. Module volumes were used as quantitative traits to identify not only the main effect loci but also the interactive effect loci for each module. Thirty-five subcortical structures were clustered into five modules, each corresponding to a particular brain structure/area, including the limbic system (module I), the corpus callosum (module II), thalamus-cerebellum-brainstem-pallidum (module III), the basal ganglia neostriatum (module IV), and the ventricular system (module V). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results indicate that the gene annotations of the five modules were distinct, with few overlaps between different modules. We identified several main effect loci and interactive effect loci for each module. All these loci are related to the function of module structures and basic biological processes such as material transport and signal transduction.
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Affiliation(s)
| | | | | | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (S.Y.)
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29
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New and enlarging white matter lesions adjacent to the ventricle system and thalamic atrophy are independently associated with lateral ventricular enlargement in multiple sclerosis. J Neurol 2019; 267:192-202. [DOI: 10.1007/s00415-019-09565-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/28/2019] [Accepted: 09/30/2019] [Indexed: 01/03/2023]
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30
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Ming W, Xie H, Hu Z, Chen Y, Zhu Y, Bai Y, Liu H, Sun X, Liu Y, Gu W. Two Distinct Subtypes Revealed in Blood Transcriptome of Breast Cancer Patients With an Unsupervised Analysis. Front Oncol 2019; 9:985. [PMID: 31632916 PMCID: PMC6779774 DOI: 10.3389/fonc.2019.00985] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/16/2019] [Indexed: 12/16/2022] Open
Abstract
Background: Breast cancer (BC) is a highly heterogeneous cancer. The interaction between immune system and BC is complex, widespread yet unclear. In this study, we aimed to reveal the heterogeneity of host systemic immune response to BC and understand the possible mechanisms that may drive the heterogeneity using transcriptomic data from peripheral blood mononuclear cells (PBMCs). Methods: Transcriptome-wide gene expressions of PBMCs in 33 BC patients were generated by RNA sequencing. An unsupervised clustering algorithm was employed to discover PBMC transcriptome subtypes among BC patients. Association analysis between PBMC subtypes and age, clinical stage, abundance of immune cells, and other clinical factors was performed to understand the underlying biological processes that may drive this heterogeneity. Immune gene signature identification and in silico survival analysis were performed to investigate the potential clinical implications of these PBMC subtypes. The findings were validated using the whole blood transcriptomes of an independent cohort. Results: We observed that established BC subtypes were not associated with PBMC gene expression profiles. Instead, we discovered and validated two new BC subtypes using PBMC transcriptome, which have distinct immune cell proportions, especially for lymphocytes (P = 5.22 × 10-12) and neutrophils (P = 1.13 × 10-14). Enrichment analysis of differentially expressed genes revealed that these two subtypes had distinct patterns of immune responses, including osteoclast differentiation and interleukin-10 signaling pathway. We developed two immune gene signatures that can differentiate these two BC PBMC subtypes. Further analysis suggested they had the ability to predict the clinical outcome of BC patients. Conclusions: PBMC transcriptome profiles can classify BC patients into two distinct subtypes. These two subtypes are mainly shaped by different immune cell abundance, which may have implications on clinical outcomes.
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Affiliation(s)
- Wenlong Ming
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Hui Xie
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zixi Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yuanyuan Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yanhui Zhu
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yun Liu
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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Fitzgerald KC, Kim K, Smith MD, Aston SA, Fioravante N, Rothman AM, Krieger S, Cofield SS, Kimbrough DJ, Bhargava P, Saidha S, Whartenby KA, Green AJ, Mowry EM, Cutter GR, Lublin FD, Baranzini SE, De Jager PL, Calabresi PA. Early complement genes are associated with visual system degeneration in multiple sclerosis. Brain 2019; 142:2722-2736. [PMID: 31289819 PMCID: PMC6776113 DOI: 10.1093/brain/awz188] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/17/2019] [Accepted: 04/28/2019] [Indexed: 11/12/2022] Open
Abstract
Multiple sclerosis is a heterogeneous disease with an unpredictable course and a wide range of severity; some individuals rapidly progress to a disabled state whereas others experience only mild symptoms. Though genetic studies have identified variants that are associated with an increased risk of developing multiple sclerosis, no variants have been consistently associated with multiple sclerosis severity. In part, the lack of findings is related to inherent limitations of clinical rating scales; these scales are insensitive to early degenerative changes that underlie disease progression. Optical coherence tomography imaging of the retina and low-contrast letter acuity correlate with and predict clinical and imaging-based outcomes in multiple sclerosis. Therefore, they may serve as sensitive phenotypes to discover genetic predictors of disease course. We conducted a set of genome-wide association studies of longitudinal structural and functional visual pathway phenotypes in multiple sclerosis. First, we assessed genetic predictors of ganglion cell/inner plexiform layer atrophy in a discovery cohort of 374 patients with multiple sclerosis using mixed-effects models adjusting for age, sex, disease duration, optic neuritis and genetic ancestry and using a combination of single-variant and network-based analyses. For candidate variants identified in discovery, we conducted a similar set of analyses of ganglion cell/inner plexiform layer thinning in a replication cohort (n = 376). Second, we assessed genetic predictors of sustained loss of 5-letters in low-contrast letter acuity in discovery (n = 582) using multivariable-adjusted Cox proportional hazards models. We then evaluated candidate variants/pathways in a replication cohort. (n = 253). Results of both studies revealed novel subnetworks highly enriched for connected genes in early complement activation linked to measures of disease severity. Within these networks, C3 was the gene most strongly associated with ganglion cell/inner plexiform layer atrophy (P = 0.004) and C1QA and CR1 were top results in analysis of sustained low-contrast letter acuity loss. Namely, variant rs158772, linked to C1QA, and rs61822967, linked to CR1, were associated with 71% and 40% increases in risk of sustained LCLA loss, respectively, in meta-analysis pooling discovery and replication cohorts (rs158772: hazard ratio: 1.71; 95% confidence interval 1.30-2.25; P = 1.3 × 10-4; rs61822967: hazard ratio: 1.40; 95% confidence interval: 1.16-1.68; P = 4.1 × 10-4). In conclusion, early complement pathway gene variants were consistently associated with structural and functional measures of multiple sclerosis severity. These results from unbiased analyses are strongly supported by several prior reports that mechanistically implicated early complement factors in neurodegeneration.
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Affiliation(s)
| | - Kicheol Kim
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew D Smith
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sean A Aston
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nicholas Fioravante
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alissa M Rothman
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephen Krieger
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stacey S Cofield
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Pavan Bhargava
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shiv Saidha
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Katharine A Whartenby
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ari J Green
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
| | - Ellen M Mowry
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gary R Cutter
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Fred D Lublin
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sergio E Baranzini
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Peter A Calabresi
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Li KN, Zhang YY, Yu YN, Wu HL, Wang Z. Met-Controlled Allosteric Module of Neural Generation as A New Therapeutic Target in Rodent Brain Ischemia. Chin J Integr Med 2019; 27:896-904. [PMID: 31418133 DOI: 10.1007/s11655-019-3182-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2019] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To investigate a Met-controlled allosteric module (AM) of neural generation as a potential therapeutic target for brain ischemia. METHODS We selected Markov clustering algorithm (MCL) to mine functional modules in the related target networks. According to the topological similarity, one functional module was predicted in the modules of baicalin (BA), jasminoidin (JA), cholic acid (CA), compared with I/R model modules. This functional module included three genes: Inppl1, Met and Dapk3 (IMD). By gene ontology enrichment analysis, biological process related to this functional module was obtained. This functional module participated in generation of neurons. Western blotting was applied to present the compound-dependent regulation of IMD. Co-immunoprecipitation was used to reveal the relationship among the three members. We used IF to determine the number of newborn neurons between compound treatment group and ischemia/reperfusion group. The expressions of vascular endothelial growth factor (VEGF) and matrix metalloproteinase 9 (MMP-9) were supposed to show the changing circumstances for neural generation under cerebral ischemia. RESULTS Significant reduction in infarction volume and pathological changes were shown in the compound treatment groups compared with the I/R model group (P<0.05). Three nodes in one novel module of IMD were found to exert diverse compound-dependent ischemic-specific excitatory regulatory activities. An anti-ischemic excitatory allosteric module (AME) of generation of neurons (AME-GN) was validated successfully in vivo. Newborn neurons increased in BJC treatment group (P<0.05). The expression of VEGF and MMP-9 decreased in the compound treatment groups compared with the I/R model group (P<0.05). CONCLUSIONS AME demonstrates effectiveness of our pioneering approach to the discovery of therapeutic target. The novel approach for AM discovery in an effort to identify therapeutic targets holds the promise of accelerating elucidation of underlying pharmacological mechanisms in cerebral ischemia.
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Affiliation(s)
- Kang-Ning Li
- Department of Traditional Chinese Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Ying-Ying Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ya-Nan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Hong-Li Wu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Malekzadeh A, Leurs C, van Wieringen W, Steenwijk MD, Schoonheim MM, Amann M, Naegelin Y, Kuhle J, Killestein J, Teunissen CE. Plasma proteome in multiple sclerosis disease progression. Ann Clin Transl Neurol 2019; 6:1582-1594. [PMID: 31364818 PMCID: PMC7651845 DOI: 10.1002/acn3.771] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 02/28/2019] [Accepted: 03/07/2019] [Indexed: 01/01/2023] Open
Abstract
Background The pathophysiology of multiple sclerosis disease progression remains undetermined. The aim of this study was to identify differences in plasma proteome during different stages of MS disease progression. Methods We used a multiplex aptamer proteomics platform (Somalogic) for sensitive detection of 1129 proteins in plasma. MS patients were selected and categorized based on baseline and a 4‐year follow‐up EDSS (delta EDSS) scores; relapse‐onset (RO) slow progression (n = 31), RO with rapid progression (n = 29), primary progressive (n = 30), and healthy controls (n = 20). The relation of baseline plasma protein levels with delta EDSS and different MRI progression parameters were assessed using linear regression models. Results Regression analyses of plasma proteins with delta EDSS showed six significant associations. Strong associations were found for the proteins LGLAS8 (P = 7.64 × 10−5, q = 0.06), CCL3 (P = 0.0001, q = 0.06), and RGMA (P = 0.0005, q = 0.09). In addition, associations of plasma proteins were found with percentage brain volume for C3 (P = 2,08 × 10−9, q = 1,70 × 10−6), FGF9 (P = 3,42 × 10−9, q = 1,70 × 10−6), and EHMT2 (P = 0.0007, q = 0.01). Most of the significant markers were associated with cell‐cell and cell‐extracellular matrix adhesion, immune system communication, immune system activation, and complement pathways. Conclusions Our results revealed eight novel biomarkers related to clinical and radiological progression in MS. These results indicate that changes in immune system, complement pathway and ECM remodeling proteins contribute to MS progression and may therefore be further explored for use in prognosis of MS.
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Affiliation(s)
- Arjan Malekzadeh
- Department of Clinical Chemistry, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Cyra Leurs
- Department of Neurology, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Wessel van Wieringen
- Department of Mathematics, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Martijn D Steenwijk
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, MS Center Amsterdam, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Menno M Schoonheim
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, MS Center Amsterdam, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Michael Amann
- Division of Diagnostic and Interventional Neuroradiology, Department of Radiology and Nuclear Medicine, University Hospital Basel, Basel, Switzerland.,Medical Image Analysis Center (MIAC AG), Basel, Switzerland
| | - Yvonne Naegelin
- Department of Biomedicine and Clinical Research, University Hospital Basel, Basel, Switzerland
| | - Jens Kuhle
- Department of Biomedicine and Clinical Research, University Hospital Basel, Basel, Switzerland
| | - Joep Killestein
- Department of Neurology, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Department of Clinical Chemistry, Amsterdam University Medical Centre, Amsterdam, The Netherlands
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Foolad F, Khodagholi F, Javan M. Sirtuins in Multiple Sclerosis: The crossroad of neurodegeneration, autoimmunity and metabolism. Mult Scler Relat Disord 2019; 34:47-58. [PMID: 31228716 DOI: 10.1016/j.msard.2019.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/26/2019] [Accepted: 06/07/2019] [Indexed: 12/17/2022]
Abstract
Multiple Sclerosis (MS) is a challenging and disabling condition particularly in the secondary progressive (SP) phase of this disease. The available treatments cannot ameliorate or stop disease progression in this phase, and there is an urgent need to focus on effective therapies and the molecular pathways involved SPMS. Given the significant impact of neurodegeneration, autoimmunity and metabolic alterations in MS, focusing on the molecules that target these different pathways could help in finding new treatments. Sirtuins (SIRTs) are NAD+ dependent epigenetic and metabolic regulators, which have critical roles in the physiology of central nervous system, immune system and metabolism. Based on these facts, SIRTs are crucial candidates of therapeutic targets in MS and collecting the information related to MS disease for each SIRT individually is noteworthy and highlights the lack of investigation in each part. In this review we summarized the role of different sirtuins as key regulator in neurodegeneration, autoimmunity and metabolism pathways. We also clarify the rationale behind selecting SIRTs as therapeutic targets in MS disease by collecting the researches showing alteration of these proteins in human samples of MS patients and animal model of MS, and also the improvement of modeled animals after SIRT-directed treatments.
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Affiliation(s)
- Forough Foolad
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fariba Khodagholi
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Javan
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran; Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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Madireddy L, Patsopoulos NA, Cotsapas C, Bos SD, Beecham A, McCauley J, Kim K, Jia X, Santaniello A, Caillier SJ, Andlauer TFM, Barcellos LF, Berge T, Bernardinelli L, Martinelli-Boneschi F, Booth DR, Briggs F, Celius EG, Comabella M, Comi G, Cree BAC, D’Alfonso S, Dedham K, Duquette P, Dardiotis E, Esposito F, Fontaine B, Gasperi C, Goris A, Dubois B, Gourraud PA, Hadjigeorgiou G, Haines J, Hawkins C, Hemmer B, Hintzen R, Horakova D, Isobe N, Kalra S, Kira JI, Khalil M, Kockum I, Lill CM, Lincoln M, Luessi F, Martin R, Oturai A, Palotie A, Pericak-Vance MA, Henry R, Saarela J, Ivinson A, Olsson T, Taylor BV, Stewart GJ, Harbo HF, Compston A, Hauser SL, Hafler DA, Zipp F, De Jager P, Sawcer S, Oksenberg JR, Baranzini SE. A systems biology approach uncovers cell-specific gene regulatory effects of genetic associations in multiple sclerosis. Nat Commun 2019; 10:2236. [PMID: 31110181 PMCID: PMC6527683 DOI: 10.1038/s41467-019-09773-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/26/2019] [Indexed: 02/02/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 50,000 unique associations with common human traits. While this represents a substantial step forward, establishing the biology underlying these associations has proven extremely difficult. Even determining which cell types and which particular gene(s) are relevant continues to be a challenge. Here, we conduct a cell-specific pathway analysis of the latest GWAS in multiple sclerosis (MS), which had analyzed a total of 47,351 cases and 68,284 healthy controls and found more than 200 non-MHC genome-wide associations. Our analysis identifies pan immune cell as well as cell-specific susceptibility genes in T cells, B cells and monocytes. Finally, genotype-level data from 2,370 patients and 412 controls is used to compute intra-individual and cell-specific susceptibility pathways that offer a biological interpretation of the individual genetic risk to MS. This approach could be adopted in any other complex trait for which genome-wide data is available.
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Lee LYH, Loscalzo J. Network Medicine in Pathobiology. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:1311-1326. [PMID: 31014954 DOI: 10.1016/j.ajpath.2019.03.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/05/2019] [Indexed: 12/11/2022]
Abstract
The past decade has witnessed exponential growth in the generation of high-throughput human data across almost all known dimensions of biological systems. The discipline of network medicine has rapidly evolved in parallel, providing an unbiased, comprehensive biological framework through which to interrogate and integrate systematically these large-scale, multi-omic data to enhance our understanding of disease mechanisms and to design drugs that reflect a deep knowledge of molecular pathobiology. In this review, we discuss the key principles of network medicine and the human disease network and explore the latest applications of network medicine in this multi-omic era. We also highlight the current conceptual and technological challenges, which serve as exciting opportunities by which to improve and expand the network-based applications beyond the artificial boundaries of the current state of human pathobiology.
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Affiliation(s)
| | - Joseph Loscalzo
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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Leal-Gutiérrez JD, Elzo MA, Johnson DD, Hamblen H, Mateescu RG. Genome wide association and gene enrichment analysis reveal membrane anchoring and structural proteins associated with meat quality in beef. BMC Genomics 2019; 20:151. [PMID: 30791866 PMCID: PMC6385435 DOI: 10.1186/s12864-019-5518-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/07/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Meat quality related phenotypes are difficult and expensive to measure and predict but are ideal candidates for genomic selection if genetic markers that account for a worthwhile proportion of the phenotypic variation can be identified. The objectives of this study were: 1) to perform genome wide association analyses for Warner-Bratzler Shear Force (WBSF), marbling, cooking loss, tenderness, juiciness, connective tissue and flavor; 2) to determine enriched pathways present in each genome wide association analysis; and 3) to identify potential candidate genes with multiple quantitative trait loci (QTL) associated with meat quality. RESULTS The WBSF, marbling and cooking loss traits were measured in longissimus dorsi muscle from 672 steers. Out of these, 495 animals were used to measure tenderness, juiciness, connective tissue and flavor by a sensory panel. All animals were genotyped for 221,077 markers and included in a genome wide association analysis. A total number of 68 genomic regions covering 52 genes were identified using the whole genome association approach; 48% of these genes encode transmembrane proteins or membrane associated molecules. Two enrichment analysis were performed: a tissue restricted gene enrichment applying a correlation analysis between raw associated single nucleotide polymorphisms (SNPs) by trait, and a functional classification analysis performed using the DAVID Bioinformatic Resources 6.8 server. The tissue restricted gene enrichment approach identified eleven pathways including "Endoplasmic reticulum membrane" that influenced multiple traits simultaneously. The DAVID functional classification analysis uncovered eleven clusters related to transmembrane or structural proteins. A gene network was constructed where the number of raw associated uncorrelated SNPs for each gene across all traits was used as a weight. A multiple SNP association analysis was performed for the top five most connected genes in the gene-trait network. The gene network identified the EVC2, ANXA10 and PKHD1 genes as potentially harboring multiple QTLs. Polymorphisms identified in structural proteins can modulate two different processes with direct effect on meat quality: in vivo myocyte cytoskeletal organization and postmortem proteolysis. CONCLUSION The main result from the present analysis is the uncovering of several candidate genes associated with meat quality that have structural function in the skeletal muscle.
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Affiliation(s)
| | - Mauricio A. Elzo
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
| | - D. Dwain Johnson
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
| | - Heather Hamblen
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
| | - Raluca G. Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
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Li H, Chen L, Ma X, Cui P, Lang W, Hao J. Shared Gene Expression Between Multiple Sclerosis and Ischemic Stroke. Front Genet 2019; 9:598. [PMID: 30809253 PMCID: PMC6379658 DOI: 10.3389/fgene.2018.00598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/15/2018] [Indexed: 01/22/2023] Open
Abstract
Patients with multiple sclerosis (MS) appear to have an increased risk of ischemic stroke (IS). Although MS and IS have very different phenotypes, gene-based and pathway-based analyses of large-scale genome-wide association studies (GWAS) have increasingly enhanced our understanding of these two diseases. Whether there are common molecular mechanisms connecting MS and IS is still unclear. Here, we describe the outcome of gene-based test and pathway-based analysis of GWAS datasets that explored potential gene expression links between MS and IS. After identifying significant gene sets individually of MS and IS, we performed pathway-based analysis in four biological pathway databases (KEGG, PANTHER, REACTOME, and WikiPathways) and GO categories. We discovered that there were 9 shared pathways between MS and IS in KEGG, 2 in PANTHER, 14 in REACTOME, 1 in WikiPathways, and 194 in GO annotations (p < 0.05). These results provide an improved understanding about possible shared mechanisms and treatments strategies for MS and IS. They also provide some basis for further studies of how these two diseases are linked at the molecular level.
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Affiliation(s)
- He Li
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Lin Chen
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Xiaofeng Ma
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Pan Cui
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Wenjing Lang
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Junwei Hao
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
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40
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Pei G, Sun H, Dai Y, Liu X, Zhao Z, Jia P. Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics. BMC Genomics 2019; 20:79. [PMID: 30712509 PMCID: PMC6360716 DOI: 10.1186/s12864-018-5373-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background Genome-wide association studies (GWAS) have been successful in identifying disease-associated genetic variants. Recently, an increasing number of GWAS summary statistics have been made available to the research community, providing extensive repositories for studies of human complex diseases. In particular, cross-trait associations at the genetic level can be beneficial from large-scale GWAS summary statistics by using genetic variants that are associated with multiple traits. However, direct assessment of cross-trait associations using susceptibility loci has been challenging due to the complex genetic architectures in most diseases, calling for advantageous methods that could integrate functional interpretation and imply biological mechanisms. Results We developed an analytical framework for systematic integration of cross-trait associations. It incorporates two different approaches to detect enriched pathways and requires only summary statistics. We demonstrated the framework using 25 traits belonging to four phenotype groups. Our results revealed an average of 54 significantly associated pathways (ranged between 18 and 175) per trait. We further proved that pathway-based analysis provided increased power to estimate cross-trait associations compared to gene-level analysis. Based on Fisher’s Exact Test (FET), we identified a total of 24 (53) pairs of trait-trait association at adjusted pFET < 1 × 10− 3 (pFET < 0.01) among the 25 traits. Our trait-trait association network revealed not only many relationships among the traits within the same group but also novel relationships among traits from different groups, which warrants further investigation in future. Conclusions Our study revealed that risk variants for 25 different traits aggregated in particular biological pathways and that these pathways were frequently shared among traits. Our results confirmed known mechanisms and also suggested several novel insights into the etiology of multi-traits. Electronic supplementary material The online version of this article (10.1186/s12864-018-5373-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Hua Sun
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Xiaoming Liu
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. .,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA.
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Dardiotis E, Panayiotou E, Siokas V, Aloizou AM, Christodoulou K, Hadjisavvas A, Pantzaris M, Grigoriadis N, Hadjigeorgiou GM, Kyriakides T. Gene variants of adhesion molecules predispose to MS: A case-control study. NEUROLOGY-GENETICS 2019; 5:e304. [PMID: 30697591 PMCID: PMC6340332 DOI: 10.1212/nxg.0000000000000304] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/05/2018] [Indexed: 12/24/2022]
Abstract
Objective To examine the effect of variants in genes encoding molecules that are implicated in leukocyte trafficking into the CNS on the development of MS. Methods A total of 389 Greek MS cases and 336 controls were recruited by 3 MS centers in Cyprus and Greece. In total, 147 tagging single nucleotide polymorphisms across 9 genes encoding for P-selectin (SELP), integrins (ITGA4, ITGB1, and ITGB7), adhesion molecules (ICAM1, VCAM1, and MADCAM1), fibronectin 1 (FN1), and osteopontin (SPP1) were genotyped. The clinical end point of the study was diagnosis of MS according to the 2005 revised McDonald criteria. Permutation analysis was used for adjusting for multiple comparisons. Results Overall, 21 variants across SELP, ITGA4, ITGB1, ICAM1, VCAM1, MADCAM1, FN1, and SSP1 genes were each associated with MS (p perm < 0.05). The most significant were rs3917779 and rs2076074 (SELP), rs6721763 (ITGA4), and rs1250258 (FN1), all with a permutation p value of less than 1e-004. Conclusions The current study provides preliminary evidence that variants across genes encoding adhesion molecules, responsible for lymphocyte adhesion and trafficking within the CNS, are implicated in the risk of developing MS.
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Affiliation(s)
- Efthimios Dardiotis
- Cyprus Institute of Neurology and Genetics (E.D., E.P., K.C., A.H., M.P., T.K.), Nicosia; Department of Neurology, Laboratory of Neurogenetics (E.D., V.S., A.-M.A.), University of Thessaly, University Hospital of Larissa; Cyprus School of Molecular Medicine (E.P., K.C., A.H., T.K.), Nicosia; 2nd Department of Neurology (N.G.), AHEPA University Hospital, Aristotle University of Thessaloniki; and Department of Neurology (G.M.H.), Medical School, University of Cyprus, Nicosia, Greece
| | - Elena Panayiotou
- Cyprus Institute of Neurology and Genetics (E.D., E.P., K.C., A.H., M.P., T.K.), Nicosia; Department of Neurology, Laboratory of Neurogenetics (E.D., V.S., A.-M.A.), University of Thessaly, University Hospital of Larissa; Cyprus School of Molecular Medicine (E.P., K.C., A.H., T.K.), Nicosia; 2nd Department of Neurology (N.G.), AHEPA University Hospital, Aristotle University of Thessaloniki; and Department of Neurology (G.M.H.), Medical School, University of Cyprus, Nicosia, Greece
| | - Vasileios Siokas
- Cyprus Institute of Neurology and Genetics (E.D., E.P., K.C., A.H., M.P., T.K.), Nicosia; Department of Neurology, Laboratory of Neurogenetics (E.D., V.S., A.-M.A.), University of Thessaly, University Hospital of Larissa; Cyprus School of Molecular Medicine (E.P., K.C., A.H., T.K.), Nicosia; 2nd Department of Neurology (N.G.), AHEPA University Hospital, Aristotle University of Thessaloniki; and Department of Neurology (G.M.H.), Medical School, University of Cyprus, Nicosia, Greece
| | - Athina-Maria Aloizou
- Cyprus Institute of Neurology and Genetics (E.D., E.P., K.C., A.H., M.P., T.K.), Nicosia; Department of Neurology, Laboratory of Neurogenetics (E.D., V.S., A.-M.A.), University of Thessaly, University Hospital of Larissa; Cyprus School of Molecular Medicine (E.P., K.C., A.H., T.K.), Nicosia; 2nd Department of Neurology (N.G.), AHEPA University Hospital, Aristotle University of Thessaloniki; and Department of Neurology (G.M.H.), Medical School, University of Cyprus, Nicosia, Greece
| | - Kyproula Christodoulou
- Cyprus Institute of Neurology and Genetics (E.D., E.P., K.C., A.H., M.P., T.K.), Nicosia; Department of Neurology, Laboratory of Neurogenetics (E.D., V.S., A.-M.A.), University of Thessaly, University Hospital of Larissa; Cyprus School of Molecular Medicine (E.P., K.C., A.H., T.K.), Nicosia; 2nd Department of Neurology (N.G.), AHEPA University Hospital, Aristotle University of Thessaloniki; and Department of Neurology (G.M.H.), Medical School, University of Cyprus, Nicosia, Greece
| | - Andreas Hadjisavvas
- Cyprus Institute of Neurology and Genetics (E.D., E.P., K.C., A.H., M.P., T.K.), Nicosia; Department of Neurology, Laboratory of Neurogenetics (E.D., V.S., A.-M.A.), University of Thessaly, University Hospital of Larissa; Cyprus School of Molecular Medicine (E.P., K.C., A.H., T.K.), Nicosia; 2nd Department of Neurology (N.G.), AHEPA University Hospital, Aristotle University of Thessaloniki; and Department of Neurology (G.M.H.), Medical School, University of Cyprus, Nicosia, Greece
| | - Marios Pantzaris
- Cyprus Institute of Neurology and Genetics (E.D., E.P., K.C., A.H., M.P., T.K.), Nicosia; Department of Neurology, Laboratory of Neurogenetics (E.D., V.S., A.-M.A.), University of Thessaly, University Hospital of Larissa; Cyprus School of Molecular Medicine (E.P., K.C., A.H., T.K.), Nicosia; 2nd Department of Neurology (N.G.), AHEPA University Hospital, Aristotle University of Thessaloniki; and Department of Neurology (G.M.H.), Medical School, University of Cyprus, Nicosia, Greece
| | - Nikolaos Grigoriadis
- Cyprus Institute of Neurology and Genetics (E.D., E.P., K.C., A.H., M.P., T.K.), Nicosia; Department of Neurology, Laboratory of Neurogenetics (E.D., V.S., A.-M.A.), University of Thessaly, University Hospital of Larissa; Cyprus School of Molecular Medicine (E.P., K.C., A.H., T.K.), Nicosia; 2nd Department of Neurology (N.G.), AHEPA University Hospital, Aristotle University of Thessaloniki; and Department of Neurology (G.M.H.), Medical School, University of Cyprus, Nicosia, Greece
| | - Georgios M Hadjigeorgiou
- Cyprus Institute of Neurology and Genetics (E.D., E.P., K.C., A.H., M.P., T.K.), Nicosia; Department of Neurology, Laboratory of Neurogenetics (E.D., V.S., A.-M.A.), University of Thessaly, University Hospital of Larissa; Cyprus School of Molecular Medicine (E.P., K.C., A.H., T.K.), Nicosia; 2nd Department of Neurology (N.G.), AHEPA University Hospital, Aristotle University of Thessaloniki; and Department of Neurology (G.M.H.), Medical School, University of Cyprus, Nicosia, Greece
| | - Theodoros Kyriakides
- Cyprus Institute of Neurology and Genetics (E.D., E.P., K.C., A.H., M.P., T.K.), Nicosia; Department of Neurology, Laboratory of Neurogenetics (E.D., V.S., A.-M.A.), University of Thessaly, University Hospital of Larissa; Cyprus School of Molecular Medicine (E.P., K.C., A.H., T.K.), Nicosia; 2nd Department of Neurology (N.G.), AHEPA University Hospital, Aristotle University of Thessaloniki; and Department of Neurology (G.M.H.), Medical School, University of Cyprus, Nicosia, Greece
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Mitrovič M, Patsopoulos NA, Beecham AH, Dankowski T, Goris A, Dubois B, D’hooghe MB, Lemmens R, Van Damme P, Søndergaard HB, Sellebjerg F, Sorensen PS, Ullum H, Thørner LW, Werge T, Saarela J, Cournu-Rebeix I, Damotte V, Fontaine B, Guillot-Noel L, Lathrop M, Vukusik S, Gourraud PA, Andlauer TF, Pongratz V, Buck D, Gasperi C, Bayas A, Heesen C, Kümpfel T, Linker R, Paul F, Stangel M, Tackenberg B, Bergh FT, Warnke C, Wiendl H, Wildemann B, Zettl U, Ziemann U, Tumani H, Gold R, Grummel V, Hemmer B, Knier B, Lill CM, Luessi F, Dardiotis E, Agliardi C, Barizzone N, Mascia E, Bernardinelli L, Comi G, Cusi D, Esposito F, Ferrè L, Comi C, Galimberti D, Leone MA, Sorosina M, Mescheriakova J, Hintzen R, van Duijn C, Teunissen CE, Bos SD, Myhr KM, Celius EG, Lie BA, Spurkland A, Comabella M, Montalban X, Alfredsson L, Stridh P, Hillert J, Jagodic M, Piehl F, Jelčić I, Martin R, Sospedra M, Ban M, Hawkins C, Hysi P, Kalra S, Karpe F, Khadake J, Lachance G, Neville M, Santaniello A, Caillier SJ, Calabresi PA, Cree BA, Cross A, Davis MF, Haines JL, de Bakker PI, Delgado S, Dembele M, Edwards K, Fitzgerald KC, Hakonarson H, Konidari I, Lathi E, Manrique CP, Pericak-Vance MA, Piccio L, Schaefer C, McCabe C, Weiner H, Goldstein J, Olsson T, Hadjigeorgiou G, Taylor B, Tajouri L, Charlesworth J, Booth DR, Harbo HF, Ivinson AJ, Hauser SL, Compston A, Stewart G, Zipp F, Barcellos LF, Baranzini SE, Martinelli-Boneschi F, D’Alfonso S, Ziegler A, Oturai A, McCauley JL, Sawcer SJ, Oksenberg JR, De Jager PL, Kockum I, Hafler DA, Cotsapas C. Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk. Cell 2018; 175:1679-1687.e7. [PMID: 30343897 PMCID: PMC6269166 DOI: 10.1016/j.cell.2018.09.049] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/08/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022]
Abstract
Multiple sclerosis is a complex neurological disease, with ∼20% of risk heritability attributable to common genetic variants, including >230 identified by genome-wide association studies. Multiple strands of evidence suggest that much of the remaining heritability is also due to additive effects of common variants rather than epistasis between these variants or mutations exclusive to individual families. Here, we show in 68,379 cases and controls that up to 5% of this heritability is explained by low-frequency variation in gene coding sequence. We identify four novel genes driving MS risk independently of common-variant signals, highlighting key pathogenic roles for regulatory T cell homeostasis and regulation, IFNγ biology, and NFκB signaling. As low-frequency variants do not show substantial linkage disequilibrium with other variants, and as coding variants are more interpretable and experimentally tractable than non-coding variation, our discoveries constitute a rich resource for dissecting the pathobiology of MS.
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Hao T, Wang Q, Zhao L, Wu D, Wang E, Sun J. Analyzing of Molecular Networks for Human Diseases and Drug Discovery. Curr Top Med Chem 2018; 18:1007-1014. [PMID: 30101711 PMCID: PMC6174636 DOI: 10.2174/1568026618666180813143408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 06/22/2018] [Accepted: 07/03/2018] [Indexed: 01/11/2023]
Abstract
Molecular networks represent the interactions and relations of genes/proteins, and also encode molecular mechanisms of biological processes, development and diseases. Among the molecular networks, protein-protein Interaction Networks (PINs) have become effective platforms for uncovering the molecular mechanisms of diseases and drug discovery. PINs have been constructed for various organisms and utilized to solve many biological problems. In human, most proteins present their complex functions by interactions with other proteins, and the sum of these interactions represents the human protein interactome. Especially in the research on human disease and drugs, as an emerging tool, the PIN provides a platform to systematically explore the molecular complexities of specific diseases and the references for drug design. In this review, we summarized the commonly used approaches to aid disease research and drug discovery with PINs, including the network topological analysis, identification of novel pathways, drug targets and sub-network biomarkers for diseases. With the development of bioinformatic techniques and biological networks, PINs will play an increasingly important role in human disease research and drug discovery.
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Affiliation(s)
- Tong Hao
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Qian Wang
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Lingxuan Zhao
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Dan Wu
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Edwin Wang
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China.,University of Calgary Cumming School of Medicine, Calgary, Alberta T2N 4Z6, Canada
| | - Jinsheng Sun
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China.,Tianjin Bohai Fisheries Research Institute, Tianjin 300221, China
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Bove R, Chitnis T, Cree BA, Tintore M, Naegelin Y, Uitdehaag B, Kappos L, Khoury SJ, Montalban X, Hauser SL, Weiner HL. SUMMIT (Serially Unified Multicenter Multiple Sclerosis Investigation): creating a repository of deeply phenotyped contemporary multiple sclerosis cohorts. Mult Scler 2018; 24:1485-1498. [PMID: 28847219 PMCID: PMC5821573 DOI: 10.1177/1352458517726657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND There is a pressing need for robust longitudinal cohort studies in the modern treatment era of multiple sclerosis. OBJECTIVE Build a multiple sclerosis (MS) cohort repository to capture the variability of disability accumulation, as well as provide the depth of characterization (clinical, radiologic, genetic, biospecimens) required to adequately model and ultimately predict a patient's course. METHODS Serially Unified Multicenter Multiple Sclerosis Investigation (SUMMIT) is an international multi-center, prospectively enrolled cohort with over a decade of comprehensive follow-up on more than 1000 patients from two large North American academic MS Centers (Brigham and Women's Hospital (Comprehensive Longitudinal Investigation of Multiple Sclerosis at the Brigham and Women's Hospital (CLIMB; BWH)) and University of California, San Francisco (Expression/genomics, Proteomics, Imaging, and Clinical (EPIC))). It is bringing online more than 2500 patients from additional international MS Centers (Basel (Universitätsspital Basel (UHB)), VU University Medical Center MS Center Amsterdam (MSCA), Multiple Sclerosis Center of Catalonia-Vall d'Hebron Hospital (Barcelona clinically isolated syndrome (CIS) cohort), and American University of Beirut Medical Center (AUBMC-Multiple Sclerosis Interdisciplinary Research (AMIR)). RESULTS AND CONCLUSION We provide evidence for harmonization of two of the initial cohorts in terms of the characterization of demographics, disease, and treatment-related variables; demonstrate several proof-of-principle analyses examining genetic and radiologic predictors of disease progression; and discuss the steps involved in expanding SUMMIT into a repository accessible to the broader scientific community.
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Affiliation(s)
- Riley Bove
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Tanuja Chitnis
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bruce A.C. Cree
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mar Tintore
- Centre d’Esclerosi Mútiple de Catalunya (Cemcat), Barcelona, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Yvonne Naegelin
- Center for MS and Neuroimmunology, Universitätsspital Basel, Basel, Switzerland
| | - Bernard Uitdehaag
- MS Cetner Amsterdam, VU University Medical Center, Amsterdam, Netherlands
| | - Ludwig Kappos
- Center for MS and Neuroimmunology, Universitätsspital Basel, Basel, Switzerland
| | - Samia J. Khoury
- Nehme and Therese Tohme Multiple Sclerosis Center, American University of Beirut Medical Center, Beirut, Lebanon
| | - Xavier Montalban
- Centre d’Esclerosi Mútiple de Catalunya (Cemcat), Barcelona, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Stephen L. Hauser
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Howard L. Weiner
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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Yao X, Yan J, Liu K, Kim S, Nho K, Risacher SL, Greene CS, Moore JH, Saykin AJ, Shen L. Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules. Bioinformatics 2018; 33:3250-3257. [PMID: 28575147 DOI: 10.1093/bioinformatics/btx344] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/26/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Network-based genome-wide association studies (GWAS) aim to identify functional modules from biological networks that are enriched by top GWAS findings. Although gene functions are relevant to tissue context, most existing methods analyze tissue-free networks without reflecting phenotypic specificity. Results We propose a novel module identification framework for imaging genetic studies using the tissue-specific functional interaction network. Our method includes three steps: (i) re-prioritize imaging GWAS findings by applying machine learning methods to incorporate network topological information and enhance the connectivity among top genes; (ii) detect densely connected modules based on interactions among top re-prioritized genes; and (iii) identify phenotype-relevant modules enriched by top GWAS findings. We demonstrate our method on the GWAS of [18F]FDG-PET measures in the amygdala region using the imaging genetic data from the Alzheimer's Disease Neuroimaging Initiative, and map the GWAS results onto the amygdala-specific functional interaction network. The proposed network-based GWAS method can effectively detect densely connected modules enriched by top GWAS findings. Tissue-specific functional network can provide precise context to help explore the collective effects of genes with biologically meaningful interactions specific to the studied phenotype. Availability and implementation The R code and sample data are freely available at http://www.iu.edu/shenlab/tools/gwasmodule/. Contact shenli@iu.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiaohui Yao
- Department of BioHealth Informatics, Indiana University School of Informatics & Computing, Indianapolis, IN 46202, USA.,Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jingwen Yan
- Department of BioHealth Informatics, Indiana University School of Informatics & Computing, Indianapolis, IN 46202, USA.,Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kefei Liu
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sungeun Kim
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Electrical and Computer Engineering, SUNY Oswego, NY 13126, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Shannon L Risacher
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason H Moore
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Li Shen
- Department of BioHealth Informatics, Indiana University School of Informatics & Computing, Indianapolis, IN 46202, USA.,Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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46
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Farooqui A, Tazyeen S, Ahmed MM, Alam A, Ali S, Malik MZ, Ali S, Ishrat R. Assessment of the key regulatory genes and their Interologs for Turner Syndrome employing network approach. Sci Rep 2018; 8:10091. [PMID: 29973620 PMCID: PMC6031616 DOI: 10.1038/s41598-018-28375-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/15/2018] [Indexed: 12/13/2022] Open
Abstract
Turner Syndrome (TS) is a condition where several genes are affected but the molecular mechanism remains unknown. Identifying the genes that regulate the TS network is one of the main challenges in understanding its aetiology. Here, we studied the regulatory network from manually curated genes reported in the literature and identified essential proteins involved in TS. The power-law distribution analysis showed that TS network carries scale-free hierarchical fractal attributes. This organization of the network maintained the self-ruled constitution of nodes at various levels without having centrality-lethality control systems. Out of twenty-seven genes culminating into leading hubs in the network, we identified two key regulators (KRs) i.e. KDM6A and BDNF. These KRs serve as the backbone for all the network activities. Removal of KRs does not cause its breakdown, rather a change in the topological properties was observed. Since essential proteins are evolutionarily conserved, the orthologs of selected interacting proteins in C. elegans, cat and macaque monkey (lower to higher level organisms) were identified. We deciphered three important interologs i.e. KDM6A-WDR5, KDM6A-ASH2L and WDR5-ASH2L that form a triangular motif. In conclusion, these KRs and identified interologs are expected to regulate the TS network signifying their biological importance.
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Affiliation(s)
- Anam Farooqui
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Safia Tazyeen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Mohd Murshad Ahmed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Shahnawaz Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Md Zubbair Malik
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
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47
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Huang H, Zheng J, Shen N, Wang G, Zhou G, Fang Y, Lin J, Zhao J. Identification of pathways and genes associated with synovitis in osteoarthritis using bioinformatics analyses. Sci Rep 2018; 8:10050. [PMID: 29968759 PMCID: PMC6030156 DOI: 10.1038/s41598-018-28280-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/18/2018] [Indexed: 12/14/2022] Open
Abstract
Synovitis in osteoarthritis (OA) is a very common condition. However, its underlying mechanism is still not well understood. This study aimed to explore the molecular mechanisms of synovitis in OA. The gene expression profile GSE82107 (downloaded from the Gene Expression Omnibus database) included 10 synovial tissues of the OA patients and 7 synovial tissues of healthy people. Subsequently, differentially expressed gene (DEG) analysis, GO (gene ontology) enrichment analysis, pathway analysis, pathway network analysis, and gene signal network analysis were performed using Gene-Cloud of Biotechnology Information (GCBI). A total of 1,941 DEGs consisting of 1,471 upregulated genes and 470 downregulated genes were determined. Genes such as PSMG3, LRP12 MIA-RAB4B, ETHE1, SFXN1, DAZAP1, RABEP2, and C9orf16 were significantly regulated in synovitis of OA. In particular, the MAPK signalling pathway, apoptosis, and pathways in cancer played the most important roles in the pathway network. The relationships between these pathways were also analysed. Genes such as NRAS, SPHK2, FOS, CXCR4, PLD1, GNAI2, and PLA2G4F were strongly implicated in synovitis of OA. In summary, this study indicated that several molecular mechanisms were implicated in the development and progression of synovitis in OA, thus improving our understanding of OA and offering molecular targets for future therapeutic advances.
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Affiliation(s)
- Hui Huang
- Department of Orthopaedic Surgery, Jinling Hospital(Nanjing General Hospital of Nanjing Military Region), The First School of Clinical Medicine, Southern Medical University(Guangzhou), 305 East Zhongshan Road, Nanjing, 210002, Jiangsu Province, China.,Department of Orthopaedic Surgery, Hainan Provincial People's Hospital, Haikou, 570311, Hainan Province, China
| | - Jiaxuan Zheng
- Department of Orthopaedic Surgery, Hainan Provincial People's Hospital, Haikou, 570311, Hainan Province, China
| | - Ningjiang Shen
- Department of Orthopaedic Surgery, Hainan Provincial People's Hospital, Haikou, 570311, Hainan Province, China
| | - Guangji Wang
- Department of Orthopaedic Surgery, Hainan Provincial People's Hospital, Haikou, 570311, Hainan Province, China
| | - Gang Zhou
- Department of Orthopaedic Surgery, Hainan Provincial People's Hospital, Haikou, 570311, Hainan Province, China
| | - Yehan Fang
- Department of Orthopaedic Surgery, Hainan Provincial People's Hospital, Haikou, 570311, Hainan Province, China
| | - Jianping Lin
- Department of Orthopaedic Surgery, Hainan Provincial People's Hospital, Haikou, 570311, Hainan Province, China.
| | - Jianning Zhao
- Department of Orthopaedic Surgery, Jinling Hospital(Nanjing General Hospital of Nanjing Military Region), The First School of Clinical Medicine, Southern Medical University(Guangzhou), 305 East Zhongshan Road, Nanjing, 210002, Jiangsu Province, China.
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48
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Bidadi B, Liu D, Kalari KR, Rubner M, Hein A, Beckmann MW, Rack B, Janni W, Fasching PA, Weinshilboum RM, Wang L. Pathway-Based Analysis of Genome-Wide Association Data Identified SNPs in HMMR as Biomarker for Chemotherapy- Induced Neutropenia in Breast Cancer Patients. Front Pharmacol 2018; 9:158. [PMID: 29593529 PMCID: PMC5859084 DOI: 10.3389/fphar.2018.00158] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/13/2018] [Indexed: 12/14/2022] Open
Abstract
Neutropenia secondary to chemotherapy in breast cancer patients can be life-threatening and there are no biomarkers available to predict the risk of drug-induced neutropenia in those patients. We previously performed a genome-wide association study (GWAS) for neutropenia events in women with breast cancer who were treated with 5-fluorouracil, epirubicin and cyclophosphamide and recruited to the SUCCESS-A trial. A genome-wide significant single-nucleotide polymorphism (SNP) signal in the tumor necrosis factor superfamily member 13B (TNFSF13B) gene, encoding the cytokine B-cell activating factor (BAFF), was identified in that GWAS. Taking advantage of these existing GWAS data, in the present study we utilized a pathway-based analysis approach by leveraging knowledge of the pharmacokinetics and pharmacodynamics of drugs and breast cancer pathophysiology to identify additional SNPs/genes associated with the underlying etiology of chemotherapy-induced neutropenia. We identified three SNPs in the hyaluronan mediated motility receptor (HMMR) gene that were significantly associated with neutropenia (p < 1.0E-04). Those three SNPs were trans-expression quantitative trait loci for the expression of TNFSF13B (p < 1.0E-04). The minor allele of these HMMR SNPs was associated with a decreased TNFSF13B mRNA level. Additional functional studies performed with lymphoblastoid cell lines (LCLs) demonstrated that LCLs possessing the minor allele for the HMMR SNPs were more sensitive to drug treatment. Knock-down of TNFSF13B in LCLs and HL-60 promyelocytic cells and treatment of those cells with BAFF modulated the cell sensitivity to chemotherapy treatment. These results demonstrate that HMMR SNP-dependent cytotoxicity of these chemotherapeutic agents might be related to TNFSF13B expression level. In summary, utilizing a pathway-based approach for the analysis of GWAS data, we identified additional SNPs in the HMMR gene that were associated with neutropenia and also were correlated with TNFSF13B expression.
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Affiliation(s)
- Behzad Bidadi
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Krishna R Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Matthias Rubner
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Alexander Hein
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Brigitte Rack
- Department of Gynecology and Obstetrics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Janni
- Department of Gynecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
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Uppu S, Krishna A, Gopalan RP. A Review on Methods for Detecting SNP Interactions in High-Dimensional Genomic Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:599-612. [PMID: 28060710 DOI: 10.1109/tcbb.2016.2635125] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature. These interaction studies are mathematically challenging and computationally complex. These challenges have been addressed by a number of data mining and machine learning approaches. This paper reviews the current methods and the related software packages to detect the SNP interactions that contribute to diseases. The issues that need to be considered when developing these models are addressed in this review. The paper also reviews the achievements in data simulation to evaluate the performance of these models. Further, it discusses the future of SNP interaction analysis.
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50
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Pazhouhandeh M, Sahraian MA, Siadat SD, Fateh A, Vaziri F, Tabrizi F, Ajorloo F, Arshadi AK, Fatemi E, Piri Gavgani S, Mahboudi F, Rahimi Jamnani F. A systems medicine approach reveals disordered immune system and lipid metabolism in multiple sclerosis patients. Clin Exp Immunol 2018; 192:18-32. [PMID: 29194580 DOI: 10.1111/cei.13087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/19/2017] [Accepted: 11/20/2017] [Indexed: 02/06/2023] Open
Abstract
Identification of autoimmune processes and introduction of new autoantigens involved in the pathogenesis of multiple sclerosis (MS) can be helpful in the design of new drugs to prevent unresponsiveness and side effects in patients. To find significant changes, we evaluated the autoantibody repertoires in newly diagnosed relapsing-remitting MS patients (NDP) and those receiving disease-modifying therapy (RP). Through a random peptide phage library, a panel of NDP- and RP-specific peptides was identified, producing two protein data sets visualized using Gephi, based on protein--protein interactions in the STRING database. The top modules of NDP and RP networks were assessed using Enrichr. Based on the findings, a set of proteins, including ATP binding cassette subfamily C member 1 (ABCC1), neurogenic locus notch homologue protein 1 (NOTCH1), hepatocyte growth factor receptor (MET), RAF proto-oncogene serine/threonine-protein kinase (RAF1) and proto-oncogene vav (VAV1) was found in NDP and was involved in over-represented terms correlated with cell-mediated immunity and cancer. In contrast, transcription factor RelB (RELB), histone acetyltransferase p300 (EP300), acetyl-CoA carboxylase 2 (ACACB), adiponectin (ADIPOQ) and phosphoenolpyruvate carboxykinase 2 mitochondrial (PCK2) had major contributions to viral infections and lipid metabolism as significant events in RP. According to these findings, further research is required to demonstrate the pathogenic roles of such proteins and autoantibodies targeting them in MS and to develop therapeutic agents which can ameliorate disease severity.
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Affiliation(s)
- M Pazhouhandeh
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - M-A Sahraian
- MS Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - S D Siadat
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - A Fateh
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Vaziri
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Tabrizi
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Ajorloo
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Biology, Faculty of Science, Islamic Azad University, East Tehran Branch, Tehran, Iran
| | - A K Arshadi
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - E Fatemi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - S Piri Gavgani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Mahboudi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Rahimi Jamnani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
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