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Motamed-Gorji N, Khalil Y, Gonzalez-Robles C, Khan S, Mills P, Garcia-Moreno H, Ging H, Tariq A, Clayton PT, Giunti P. Elevated Bile Acid 3β,5α,6β-Trihydroxycholanoyl Glycine in a Subset of Adult Ataxias Including Niemann-Pick Type C. Antioxidants (Basel) 2024; 13:561. [PMID: 38790666 PMCID: PMC11117656 DOI: 10.3390/antiox13050561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Ataxia is a common neurological feature of Niemann-Pick disease type C (NPC). In this disease, unesterified cholesterol accumulates in lysosomes of the central nervous system and hepatic cells. Oxidation by reactive oxygen species produces oxysterols that can be metabolised to specific bile acids. These bile acids have been suggested as useful biomarkers to detect NPC. Concentrations of 3β,5α,6β-trihydroxycholanyl glycine (3β,5α,6β-triOH-Gly) and 3β,7β-dihydroxy-5-cholenyl glycine (3β,7β-diOH-Δ5-Gly) were measured in plasma of 184 adults with idiopathic ataxia. All patients were tested with whole genome sequencing containing hereditary ataxia panels, which include NPC1 and NPC2 mutations and other genetic causes of ataxia. Plasma 3β,5α,6β-triOH-Gly above normal (>90 nM) was found in 8 out of 184 patients. One patient was homozygous for the p.(Val1165Met) mutation in the NPC1 gene. The remaining seven included one patient with Friedreich's ataxia and three patients with autoimmune diseases. Oxidative stress is known to be increased in Friedreich's ataxia and in autoimmune diseases. Therefore, this subset of patients possibly shares a common mechanism that determines the increase of this bile acid. In a large cohort of adults with ataxia, plasma 3β,5α,6β-triOH-Gly was able to detect the one patient in the cohort with NPC1 disease, but also detected oxidation of cholesterol by ROS in other disorders. Plasma 3β,7β-diOH-Δ5-Gly is not a potential biomarker for NPC1.
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Affiliation(s)
- Nazgol Motamed-Gorji
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK (H.G.-M.)
| | - Youssef Khalil
- Inborn Errors of Metabolism, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK (P.M.)
| | - Cristina Gonzalez-Robles
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK (H.G.-M.)
| | - Shamsher Khan
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK (H.G.-M.)
| | - Philippa Mills
- Inborn Errors of Metabolism, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK (P.M.)
| | - Hector Garcia-Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK (H.G.-M.)
| | - Heather Ging
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK (H.G.-M.)
| | - Ambreen Tariq
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK (H.G.-M.)
| | - Peter T. Clayton
- Inborn Errors of Metabolism, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK (P.M.)
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK (H.G.-M.)
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Wójcik M, Plata-Babula A, Głowaczewska A, Sirek T, Orczyk A, Małecka M, Grabarek BO. Expression profile of mRNAs and miRNAs related to mitogen-activated kinases in HaCaT cell culture treated with lipopolysaccharide a and adalimumab. Cell Cycle 2024; 23:385-404. [PMID: 38557266 PMCID: PMC11174132 DOI: 10.1080/15384101.2024.2335051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Studies indicate that mitogen-activated protein kinases (MAPKs) exhibit activation and overexpression within psoriatic lesions. This study aimed to investigate alterations in the expression patterns of genes encoding MAPKs and microRNA (miRNA) molecules that potentially regulate their expression in human adult low-calcium high-temperature (HaCaT) keratinocytes when exposed to bacterial lipopolysaccharide A (LPS) and adalimumab. HaCaT cells underwent treatment with 1 µg/mL LPS for 8 hours, followed by treatment with 8 µg/mL adalimumab for 2, 8, or 24 hours. Untreated cells served as controls. The molecular analysis involved microarray, quantitative real-time polymerase chain reaction (RTqPCR), and enzyme-linked immunosorbent assay (ELISA) analyses. Changes in the expression profile of seven mRNAs: dual specificity phosphatase 1 (DUSP1), dual specificity phosphatase 3 (DUSP3), dual specificity phosphatase 4 (DUSP4), mitogen-activated protein kinase 9 (MAPK9), mitogen-activated protein kinase kinase kinase 2 (MAP3K2), mitogen-activated protein kinase kinase 2 (MAP2K2), and MAP kinase-activated protein kinase 2 (MAPKAPK2, also known as MK2) in cell culture exposed to LPS or LPS and the drug compared to the control. It was noted that miR-34a may potentially regulate the activity of DUSP1, DUSP3, and DUSP4, while miR-1275 is implicated in regulating MAPK9 expression. Additionally, miR-382 and miR-3188 are potential regulators of DUSP4 levels, and miR-200-5p is involved in regulating MAPKAPK2 and MAP3K2 levels. Thus, the analysis showed that these mRNA molecules and the proteins and miRNAs they encode appear to be useful molecular markers for monitoring the efficacy of adalimumab therapy.
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Affiliation(s)
- Michał Wójcik
- Collegium Medicum, WSB University, Dabrowa Gornicza, Poland
| | - Aleksandra Plata-Babula
- Department of Nursing and Maternity, High School of Strategic Planning in Dabrowa Gornicza, Dabrowa Gornicza, Poland
| | - Amelia Głowaczewska
- Faculty of Health Sciences, University of Applied Sciences in Nysa, Nysa, Poland
| | - Tomasz Sirek
- Department of Plastic Surgery, Faculty of Medicine, Academia of Silesia, Katowice, Poland
- Department of Plastic and Reconstructive Surgery, Hospital for Minimally Invasive and Reconstructive Surgery in Bielsko-Biała, Bielsko-Biala, Poland
| | - Aneta Orczyk
- Collegium Medicum, WSB University, Dabrowa Gornicza, Poland
| | - Mariola Małecka
- Faculty of Medicine, Uczelnia Medyczna im. Marii Skłodowskiej-Curie, Warszawa, Poland
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Zhang N, Ji C, Bao X, Peng X, Tang M, Yuan C. Uncovering potential new biomarkers and immune infiltration characteristics in primary Sjögren's syndrome by integrated bioinformatics analysis. Medicine (Baltimore) 2023; 102:e35534. [PMID: 37832090 PMCID: PMC10578719 DOI: 10.1097/md.0000000000035534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
Primary Sjögren's syndrome (pSS) is known as autoimmune disease characterized by damage to endocrine glands, such as the salivary and lacrimal glands. This study aimed to identify potential biomarkers for pSS using integrated bioinformatics analysis and explore the relationship between differentially expressed genes (DEGs) and immune infiltration. Three pSS datasets (GSE7451, GSE23117, and GSE40611) from the gene expression omnibus database were integrated. All the datasets were processed in R (version 4.0.3). A total of 16 immune cells and 13 immune functions were obtained. The top immune cell and immune function were "activated" dendritic cells and major histocompatibility complex class I. Correlation analysis showed the top correlation among 16 immune cells were B cells and tumor infiltrating lymphocytes, check-point and T cell co-stimulation, respectively. In comparisons of immune score, "activated" dendritic cells (.657 vs 594, P < .001), B cells (.492 vs 434, P = .004), macrophages (.631 vs 601, P = .010), inflammation-promoting (.545 vs 478, P < .001), Type I interferon Reponse (.728 vs 625, P < .001) and so on were higher in pSS than control group. In correlation analysis, the up-regulation of interferon induced protein with tetratricopeptide repeats 1 gene was strongly correlated with Type I interferon response with a correlation coefficient of .87. The receiver operating characteristic curve of 5 genes showed that the area under curve was.891. In the verification model, the area under curve was.881. In addition, disease ontology analysis supported the association between DEGs and pSS. In summary, pSS has a variety of DEGs in immune infiltration, which is worthy of the attention from clinicians.
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Affiliation(s)
- Naidan Zhang
- Department of Clinical Laboratory, Peoples Hospital of Deyang City, Deyang, China
| | - Chaixia Ji
- Department of Clinical Laboratory, Peoples Hospital of Deyang City, Deyang, China
| | - Xiao Bao
- Department of Rheumatology, Peoples Hospital of Deyang City, Deyang, China
| | - Xinyin Peng
- Chengdu University of Chinese Medicine, Chengdu, China
| | - Maoju Tang
- North Sichuan Medical College, Nanchong, China
| | - Chengliang Yuan
- Department of Clinical Laboratory, Peoples Hospital of Deyang City, Deyang, China
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Fidalgo M, Faria R, Carvalho C, Carvalheiras G, Mendonça D, Farinha F, da Silva BM, Vasconcelos C. Multiple autoimmune syndrome: Clinical, immunological and genotypic characterization. Eur J Intern Med 2023; 116:119-130. [PMID: 37385917 DOI: 10.1016/j.ejim.2023.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
INTRODUCTION The existence of subphenotypes common to several autoimmune diseases (AIDs) suggests a shared physiopathology - autoimmune tautology. Multiple Autoimmune Syndrome (MAS) - the coexistence of three or more AIDs in one person-, best illustrates that polyautoimmunity is more than a coincidence. OBJECTIVES Characterize and compare the monoautoimmune and MAS patients. Understand if clustering of AIDs leads to differences in disease severity, autoantibodies expression or genetic polymorphisms that could be markers for polyautoimmunity. METHODS Currently adult patients were selected from unit cohort. MAS was assumed when ≥3 AIDs were present. 343 patients were included after exclusion criteria: having two AIDs or undetermined diagnosis. Clinical and immunological data were collected from medical files. HLA-DRB1 was genotyped by PCR-SSP methodology and PTPN22(rs2476601) polymorphisms by TaqMan Real Time PCR. Data were analysed using Chi-Square, Fisher's exact tests and logistic regression. Odds ratios (OR) and 95% confidence intervals were calculated. RESULTS In comparison with control population: ELEVATED FREQUENCIES: HLA-DRB1*03 in study cohort (OR=3.68,p<0.001) and in monoautoimmune SLE (OR=2.79,p<0.001) and SjS (OR=8.27,p<0.001); HLA-DRB1*15 in monoautoimmune SjS (OR=2.39,p = 0.011); HLA-DRB1*16 in MAS SLE (OR=2.67,p = 0.031); PTPN22_T in all groups except monoautoimmune SjS and triple positive systemic MAS. DIMINISHED FREQUENCIES HLA-DRB1*11 in study cohort (OR=0.57,p = 0.013), in MAS SLE (OR=0.39,p = 0.031) and monoautoimmune SjS (OR=0.10,p = 0.005); HLA-DRB1*13 in study cohort (OR=0.52,p = 0.001) and in monoautoimmune SLE (OR=0.53,p = 0.009) and SjS (OR=0.38,p = 0.031); HLA-DRB1*14 in study cohort (OR=0.32,p = 0.013) and monoautoimmune SLE (OR=0.21,p = 0.021); SLE group: HLA-DRB1*07 frequency was higher in monoautoimmune patients (OR=0.43,p = 0.023). MAS patients had significantly more NPSLE (OR=2.99,p<0.001), subacute cutaneous lesions (OR=2.30,p = 0.037), muscle&tendon (OR=2.00,p = 0.045), and haematological (OR=3.18,p = 0.006) involvement and Raynaud's (OR=2.94,p<0.001). SjS group: MAS patients had more frequently cryoglobulins (OR=2.96,p = 0.030), low complement (OR=2.43,p = 0.030) and Raynaud's (OR=4.38,p<0.001); monoautoimmune patients had more parotid enlargement (OR=0.12,p<0.001). APS group: MAS patients had more non-thrombotic manifestations (OR=4.69,p = 0.020) and Raynaud's (OR=9.12,p<0.001). Triple positive systemic MAS (SLE+SjS+APS) had more frequently severe kidney involvement (OR=11.67,p = 0.021) and CNS thrombosis (OR=4.44,p = 0.009). Anti-U1RNP increased frequency was transversally attributable to MAS. CONCLUSIONS The coexistence of AIDs contributes to a more severe disease course. We confirmed previously established genetic risk and protection factors and suggest a new protective one - HLA-DRB1*14. HLA-DRB1*07 and anti-U1RNP could be markers for mono and polyautoimmunity, respectively; HLA-DRB1*13 could be a predictor for vascular risk in patients with multiple AIDs. PTPN22(rs2476601) polymorphism could be associated with less severe disease.
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Affiliation(s)
- Mariana Fidalgo
- Internal Medicine Resident, Clinical Internship at Unidade de Imunologia Clínica (2), Portugal.
| | - Raquel Faria
- Unidade de Imunologia Clínica, Centro Hospitalar do Porto, Portugal; Unit for Multidisciplinary Research in Biomedicine, Portugal
| | - Cláudia Carvalho
- Unit for Multidisciplinary Research in Biomedicine, Portugal; Laboratório de Imunogenética, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | | | - Denisa Mendonça
- Departamento de Estudos de Populações, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal; EpiUnit, Instituto de Saúde Pública, Universidade do Porto, Portugal
| | - Fátima Farinha
- Unidade de Imunologia Clínica, Centro Hospitalar do Porto, Portugal; Unit for Multidisciplinary Research in Biomedicine, Portugal
| | - Berta Martins da Silva
- Unit for Multidisciplinary Research in Biomedicine, Portugal; Laboratório de Imunogenética, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Carlos Vasconcelos
- Unidade de Imunologia Clínica, Centro Hospitalar do Porto, Portugal; Unit for Multidisciplinary Research in Biomedicine, Portugal
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Rajan S, Terman JR, Reisler E. MICAL-mediated oxidation of actin and its effects on cytoskeletal and cellular dynamics. Front Cell Dev Biol 2023; 11:1124202. [PMID: 36875759 PMCID: PMC9982024 DOI: 10.3389/fcell.2023.1124202] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Actin and its dynamic structural remodelings are involved in multiple cellular functions, including maintaining cell shape and integrity, cytokinesis, motility, navigation, and muscle contraction. Many actin-binding proteins regulate the cytoskeleton to facilitate these functions. Recently, actin's post-translational modifications (PTMs) and their importance to actin functions have gained increasing recognition. The MICAL family of proteins has emerged as important actin regulatory oxidation-reduction (Redox) enzymes, influencing actin's properties both in vitro and in vivo. MICALs specifically bind to actin filaments and selectively oxidize actin's methionine residues 44 and 47, which perturbs filaments' structure and leads to their disassembly. This review provides an overview of the MICALs and the impact of MICAL-mediated oxidation on actin's properties, including its assembly and disassembly, effects on other actin-binding proteins, and on cells and tissue systems.
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Affiliation(s)
- Sudeepa Rajan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jonathan R. Terman
- Departments of Neuroscience and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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Rojas M, Heuer LS, Zhang W, Chen YG, Ridgway WM. The long and winding road: From mouse linkage studies to a novel human therapeutic pathway in type 1 diabetes. Front Immunol 2022; 13:918837. [PMID: 35935980 PMCID: PMC9353112 DOI: 10.3389/fimmu.2022.918837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Autoimmunity involves a loss of immune tolerance to self-proteins due to a combination of genetic susceptibility and environmental provocation, which generates autoreactive T and B cells. Genetic susceptibility affects lymphocyte autoreactivity at the level of central tolerance (e.g., defective, or incomplete MHC-mediated negative selection of self-reactive T cells) and peripheral tolerance (e.g., failure of mechanisms to control circulating self-reactive T cells). T regulatory cell (Treg) mediated suppression is essential for controlling peripheral autoreactive T cells. Understanding the genetic control of Treg development and function and Treg interaction with T effector and other immune cells is thus a key goal of autoimmunity research. Herein, we will review immunogenetic control of tolerance in one of the classic models of autoimmunity, the non-obese diabetic (NOD) mouse model of autoimmune Type 1 diabetes (T1D). We review the long (and still evolving) elucidation of how one susceptibility gene, Cd137, (identified originally via linkage studies) affects both the immune response and its regulation in a highly complex fashion. The CD137 (present in both membrane and soluble forms) and the CD137 ligand (CD137L) both signal into a variety of immune cells (bi-directional signaling). The overall outcome of these multitudinous effects (either tolerance or autoimmunity) depends upon the balance between the regulatory signals (predominantly mediated by soluble CD137 via the CD137L pathway) and the effector signals (mediated by both membrane-bound CD137 and CD137L). This immune balance/homeostasis can be decisively affected by genetic (susceptibility vs. resistant alleles) and environmental factors (stimulation of soluble CD137 production). The discovery of the homeostatic immune effect of soluble CD137 on the CD137-CD137L system makes it a promising candidate for immunotherapy to restore tolerance in autoimmune diseases.
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Affiliation(s)
- Manuel Rojas
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
- School of Medicine and Health Sciences, Doctoral Program in Biological and Biomedical Sciences, Universidad del Rosario, Bogota, Colombia
| | - Luke S. Heuer
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
| | - Weici Zhang
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
| | - Yi-Guang Chen
- The Max McGee Research Center for Juvenile Diabetes, Children’s Research Institute of Children’s Wisconsin, Milwaukee, WI, United States
- Division of Endocrinology, Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, WI, United States
| | - William M. Ridgway
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
- *Correspondence: William M. Ridgway,
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Ordoñez-Cañizares MC, Mena-Vázquez N, Redondo-Rodriguez R, Manrique-Arija S, Jimenez-Núñez FG, Ureña-Garnica I, Fernández-Nebro A. Frequency of Polyautoimmunity in Patients With Rheumatoid Arthritis and Systemic Lupus Erythematosus. J Clin Rheumatol 2022; 28:e38-e43. [PMID: 32956154 DOI: 10.1097/rhu.0000000000001574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVE To describe the frequency of polyautoimmunity and multiple autoimmune syndrome in patients with rheumatoid arthritis (RA) and patients with systemic lupus erythematosus (SLE). PATIENTS AND METHODS This was a cross-sectional observational study of patients with RA, SLE, and controls without autoimmune rheumatic disease. Cases were those with RA according to the 2010 American College of Rheumatology/European League Against Rheumatism criteria and SLE according to the 2019 American College of Rheumatology/European League Against Rheumatism criteria, consecutively recruited in a rheumatology clinic. Controls were subjects with no rheumatic autoimmune disease (AIDs) recruited in the same area. Patients filled out a questionnaire on polyautoimmunity. Variables of interest were polyautoimmunity (RA or SLE with other AIDs), whereas secondary variables were rheumatic, skin, endocrine, digestive, and neurological AIDs. Multiple autoimmune syndrome is defined as the presence of 3 or more AIDs and a family history of AIDs. Statistical analyses performed were descriptive, bivariate, and multivariate (dependent variable: polyautoimmunity). RESULTS The study population comprised 109 patients with RA, 105 patients with SLE, and 88 controls. Polyautoimmunity was recorded in 15 patients with RA (13.8%), 43 with SLE (41%), and 2 controls (2.2%). The most frequent AID in RA was Sjögren syndrome (53.3%), followed by Hashimoto thyroiditis and psoriasis; the most frequent AIDs in SLE were Sjögren syndrome (55.8%) and antiphospholipid syndrome (30.2%), followed by Hashimoto thyroiditis. Obesity was associated with polyautoimmunity in RA (odds ratio [OR], 3.362; p = 0.034). In SLE, joint damage (OR, 2.282; p = 0.038) and anti-RNP antibodies (OR, 5.095; p = 0.028) were risk factors for polyautoimmunity, and hydroxychloroquine was a protective factor (OR, 0.190; p = 0.004). CONCLUSIONS Polyautoimmunity is frequent in RA and even more frequent in SLE. It was associated with obesity in RA and with joint damage and anti-RNP in SLE. Hydroxychloroquine was a protector.
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Detecting Causal Variants in Mendelian Disorders Using Whole-Genome Sequencing. Methods Mol Biol 2021; 2243:1-25. [PMID: 33606250 DOI: 10.1007/978-1-0716-1103-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Increasingly affordable sequencing technologies are revolutionizing the field of genomic medicine. It is now feasible to interrogate all major classes of variation in an individual across the entire genome for less than $1000 USD. While the generation of patient sequence information using these technologies has become routine, the analysis and interpretation of this data remains the greatest obstacle to widespread clinical implementation. This chapter summarizes the steps to identify, annotate, and prioritize variant information required for clinical report generation. We discuss methods to detect each variant class and describe strategies to increase the likelihood of detecting causal variant(s) in Mendelian disease. Lastly, we describe a sample workflow for synthesizing large amount of genetic information into concise clinical reports.
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Bakshi D, Katoch A, Chakraborty S, Shah R, Sharma B, Bhat A, Verma S, Bhat GR, Nagpal A, Vaishnavi S, Goswami A, Kumar R. ANKLE1 as New Hotspot Mutation for Breast Cancer in Indian Population and Has a Role in DNA Damage and Repair in Mammalian Cells. Front Genet 2021; 11:609758. [PMID: 33584808 PMCID: PMC7873468 DOI: 10.3389/fgene.2020.609758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer has replaced cervical cancer as being the most common and having the highest mortality among women in India. ANKLE gene is conserved among organisms during evolutionary succession and is a member of LEM family proteins in lower metazoans and is involved in critical functions in the nuclear architecture, gene expression and cell signaling. ANKLE1 is the human orthologous of LEM-3 and is involved in DNA damage response and DNA repair. Whole Exome Sequencing (WES) of paired breast cancer samples was performed and ANKLE1 was found to be a new possible hotspot for predisposition of breast cancer. The mass array genotyping for breast cancer variant rs2363956 further confirmed the ANKLE1 association with the studied population of breast cancer. To elucidate the role of ANKLE1 in DNA damage, it was knocked down in MCF-7 breast cancer cell line and the expression of γH2AX was assessed. ANKLE1 knockdown cells displayed elevated levels of γ-H2AX foci in response to the cisplatin induced replication stress. The localization pattern of ANKLE1 further emphasized the role of ANKLE1 in DNA repair process. We observed that ANKLE1 is required for maintaining genomic stability and plays a role in DNA damage and repair process. These findings provided a molecular basis for the suspected role of ANKLE1 in human breast cancer and suggested an important role of this gene in controlling breast cancer development among women in India.
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Affiliation(s)
| | - Archana Katoch
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine (CSIR) Jammu, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Souneek Chakraborty
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine (CSIR) Jammu, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Ruchi Shah
- Shri Mata Vaishno Devi University, Katra, India
| | | | - Amrita Bhat
- Shri Mata Vaishno Devi University, Katra, India
| | | | | | | | | | - Anindya Goswami
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine (CSIR) Jammu, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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Amanat S, Requena T, Lopez-Escamez JA. A Systematic Review of Extreme Phenotype Strategies to Search for Rare Variants in Genetic Studies of Complex Disorders. Genes (Basel) 2020; 11:genes11090987. [PMID: 32854191 PMCID: PMC7564972 DOI: 10.3390/genes11090987] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022] Open
Abstract
Exome sequencing has been commonly used to characterize rare diseases by selecting multiplex families or singletons with an extreme phenotype (EP) and searching for rare variants in coding regions. The EP strategy covers both extreme ends of a disease spectrum and it has been also used to investigate the contribution of rare variants to the heritability of complex clinical traits. We conducted a systematic review to find evidence supporting the use of EP strategies in the search for rare variants in genetic studies of complex diseases and highlight the contribution of rare variations to the genetic structure of polygenic conditions. After assessing the quality of the retrieved records, we selected 19 genetic studies considering EPs to demonstrate genetic association. All studies successfully identified several rare or de novo variants, and many novel candidate genes were also identified by selecting an EP. There is enough evidence to support that the EP approach for patients with an early onset of a disease can contribute to the identification of rare variants in candidate genes or pathways involved in complex diseases. EP patients may contribute to a better understanding of the underlying genetic architecture of common heterogeneous disorders such as tinnitus or age-related hearing loss.
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Affiliation(s)
- Sana Amanat
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO—Centre for Genomics and Oncological Research—Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain;
| | - Teresa Requena
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK;
| | - Jose Antonio Lopez-Escamez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO—Centre for Genomics and Oncological Research—Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain;
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Universidad de Granada, 18016 Granada, Spain
- Department of Surgery, Division of Otolaryngology, Universidad de Granada, 18016 Granada, Spain
- Correspondence: ; Tel.: +34-958-715-500-160
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Field MA. Detecting pathogenic variants in autoimmune diseases using high-throughput sequencing. Immunol Cell Biol 2020; 99:146-156. [PMID: 32623783 PMCID: PMC7891608 DOI: 10.1111/imcb.12372] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022]
Abstract
Sequencing the first human genome in 2003 took 15 years and cost $2.7 billion. Advances in sequencing technologies have since decreased costs to the point where it is now feasible to resequence a whole human genome for $1000 in a single day. These advances have allowed the generation of huge volumes of high‐quality human sequence data used to construct increasingly large catalogs of both population‐level and disease‐causing variation. The existence of such databases, coupled with a high‐quality human reference genome, means we are able to interrogate and annotate all types of genetic variation and identify pathogenic variants for many diseases. Increasingly, sequencing‐based approaches are being used to elucidate the underlying genetic cause of autoimmune diseases, a group of roughly 80 polygenic diseases characterized by abnormal immune responses where healthy tissue is attacked. Although sequence data generation has become routine and affordable, significant challenges remain with no gold‐standard methodology to identify pathogenic variants currently available. This review examines the latest methodologies used to identify pathogenic variants in autoimmune diseases and considers available sequencing options and subsequent bioinformatic methodologies and strategies. The development of reliable and robust sequencing and analytic workflows to detect pathogenic variants is critical to realize the potential of precision medicine programs where patient variant information is used to inform clinical practice.
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Affiliation(s)
- Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.,John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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12
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Chuang HC, Tan TH. MAP4K Family Kinases and DUSP Family Phosphatases in T-Cell Signaling and Systemic Lupus Erythematosus. Cells 2019; 8:cells8111433. [PMID: 31766293 PMCID: PMC6912701 DOI: 10.3390/cells8111433] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022] Open
Abstract
T cells play a critical role in the pathogenesis of systemic lupus erythematosus (SLE), which is a severe autoimmune disease. In the past 60 years, only one new therapeutic agent with limited efficacy has been approved for SLE treatment; therefore, the development of early diagnostic biomarkers and therapeutic targets for SLE is desirable. Mitogen-activated protein kinase kinase kinase kinases (MAP4Ks) and dual-specificity phosphatases (DUSPs) are regulators of MAP kinases. Several MAP4Ks and DUSPs are involved in T-cell signaling and autoimmune responses. HPK1 (MAP4K1), DUSP22 (JKAP), and DUSP14 are negative regulators of T-cell activation. Consistently, HPK1 and DUSP22 are downregulated in the T cells of human SLE patients. In contrast, MAP4K3 (GLK) is a positive regulator of T-cell signaling and T-cell-mediated immune responses. MAP4K3 overexpression-induced RORγt–AhR complex specifically controls interleukin 17A (IL-17A) production in T cells, leading to autoimmune responses. Consistently, MAP4K3 and the RORγt–AhR complex are overexpressed in the T cells of human SLE patients, as are DUSP4 and DUSP23. In addition, DUSPs are also involved in either human autoimmune diseases (DUSP2, DUSP7, DUSP10, and DUSP12) or T-cell activation (DUSP1, DUSP5, and DUSP14). In this review, we summarize the MAP4Ks and DUSPs that are potential biomarkers and/or therapeutic targets for SLE.
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13
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Castro-Sánchez P, Aguilar-Sopeña O, Alegre-Gómez S, Ramirez-Munoz R, Roda-Navarro P. Regulation of CD4 + T Cell Signaling and Immunological Synapse by Protein Tyrosine Phosphatases: Molecular Mechanisms in Autoimmunity. Front Immunol 2019; 10:1447. [PMID: 31297117 PMCID: PMC6607956 DOI: 10.3389/fimmu.2019.01447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/10/2019] [Indexed: 12/13/2022] Open
Abstract
T cell activation and effector function is mediated by the formation of a long-lasting interaction established between T cells and antigen-presenting cells (APCs) called immunological synapse (IS). During T cell activation, different signaling molecules as well as the cytoskeleton and the endosomal compartment are polarized to the IS. This molecular dynamics is tightly regulated by phosphorylation networks, which are controlled by protein tyrosine phosphatases (PTPs). While some PTPs are known to be important regulators of adhesion, ligand discrimination or the stimulation threshold, there is still little information about the regulatory role of PTPs in cytoskeleton rearrangements and endosomal compartment dynamics. Besides, spatial and temporal regulation of PTPs and substrates at the IS is only barely known. Consistent with an important role of PTPs in T cell activation, multiple mutations as well as altered expression levels or dynamic behaviors have been associated with autoimmune diseases. However, the precise mechanism for the regulation of T cell activation and effector function by PTPs in health and autoimmunity is not fully understood. Herein, we review the current knowledge about the regulatory role of PTPs in CD4+ T cell activation, IS assembly and effector function. The potential molecular mechanisms mediating the action of these enzymes in autoimmune disorders are discussed.
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Affiliation(s)
- Patricia Castro-Sánchez
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain.,Health Research Institute '12 de Octubre (imas12)', Madrid, Spain
| | - Oscar Aguilar-Sopeña
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain.,Health Research Institute '12 de Octubre (imas12)', Madrid, Spain
| | - Sergio Alegre-Gómez
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain.,Health Research Institute '12 de Octubre (imas12)', Madrid, Spain
| | - Rocio Ramirez-Munoz
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain.,Health Research Institute '12 de Octubre (imas12)', Madrid, Spain
| | - Pedro Roda-Navarro
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain.,Health Research Institute '12 de Octubre (imas12)', Madrid, Spain
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Sereshki MMA, Almasi S, Behnam B, Semnani F. Autoimmune Haemolytic Anaemia and Multiple Autoimmune Syndrome. Eur J Case Rep Intern Med 2019; 6:001111. [PMID: 31157187 PMCID: PMC6542494 DOI: 10.12890/2019_001111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 12/02/2022] Open
Abstract
The presence of different autoimmune disorders in the same individual is called multiple autoimmune syndrome (MAS). One of these co-occurring conditions is autoimmune haemolytic anaemia (AIHA), which is characterized by the production of autoantibodies against red blood cells due to immune system malfunction and which results in severe tissue oxygenation disturbance. AIHA is not uncommon but occurs rarely in MAS; if it does, MAS is then classified as MAS type III. Herein, we describe a case of MAS type III including AIHA which was successfully treated with hydrocortisone with gradual resolution of symptoms.
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Affiliation(s)
- Mohammad Mahdi Adib Sereshki
- Department of Hematology and Medical Oncology, Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Simin Almasi
- Department of Rheumatology, Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Behdad Behnam
- Department of Internal Medicine, Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Farbod Semnani
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
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15
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Meng W, Adams MJ, Hebert HL, Deary IJ, McIntosh AM, Smith BH. A Genome-Wide Association Study Finds Genetic Associations with Broadly-Defined Headache in UK Biobank (N=223,773). EBioMedicine 2018; 28:180-186. [PMID: 29397368 PMCID: PMC5898025 DOI: 10.1016/j.ebiom.2018.01.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/20/2018] [Accepted: 01/20/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Headache is the most common neurological symptom and a leading cause of years lived with disability. We sought to identify the genetic variants associated with a broadly-defined headache phenotype in 223,773 subjects from the UK Biobank cohort. METHODS We defined headache based on a specific question answered by the UK Biobank participants. We performed a genome-wide association study of headache as a single entity, using 74,461 cases and 149,312 controls. RESULTS We identified 3343 SNPs which reached the genome-wide significance level of P<5×10-8. The SNPs were located in 28 loci, with the top SNP of rs11172113 in the LRP1 gene having a P value of 4.92×10-47. Of the 28 loci, 14 have previously been associated with migraine. Among 14 new loci, rs77804065 with a P value of 5.87×10-15 in the LINC02210-CRHR1 gene was the top SNP. Significant relationships between multiple brain tissues and genetic associations were identified through tissue expression analysis. We also identified significant positive genetic correlations between headache and many psychological traits. CONCLUSIONS Our results suggest that brain function is closely related to broadly-defined headache. In addition, we found that many psychological traits have genetic correlations with headache.
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Affiliation(s)
- Weihua Meng
- Division of Population Health Sciences, School of Medicine, University of Dundee, Dundee DD2 4BF, UK.
| | - Mark J Adams
- Division of Psychiatry, Edinburgh Medical School, University of Edinburgh, Edinburgh EH10 5HF, UK
| | - Harry L Hebert
- Division of Population Health Sciences, School of Medicine, University of Dundee, Dundee DD2 4BF, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Andrew M McIntosh
- Division of Psychiatry, Edinburgh Medical School, University of Edinburgh, Edinburgh EH10 5HF, UK; Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Blair H Smith
- Division of Population Health Sciences, School of Medicine, University of Dundee, Dundee DD2 4BF, UK
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16
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Pacheco Y, Barahona-Correa J, Monsalve DM, Acosta-Ampudia Y, Rojas M, Rodríguez Y, Saavedra J, Rodríguez-Jiménez M, Mantilla RD, Ramírez-Santana C, Molano-González N, Anaya JM. Cytokine and autoantibody clusters interaction in systemic lupus erythematosus. J Transl Med 2017; 15:239. [PMID: 29178890 PMCID: PMC5702157 DOI: 10.1186/s12967-017-1345-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/16/2017] [Indexed: 02/06/2023] Open
Abstract
Background Evidence supports the existence of different subphenotypes in systemic lupus erythematosus (SLE) and the pivotal role of cytokines and autoantibodies, which interact in a highly complex network. Thus, understanding how these complex nonlinear processes are connected and observed in real-life settings is a major challenge. Cluster approaches may assist in the identification of these subphenotypes, which represent such a phenomenon, and may contribute to the development of personalized medicine. Therefore, the relationship between autoantibody and cytokine clusters in SLE was analyzed. Methods This was an exploratory study in which 67 consecutive women with established SLE were assessed. Clinical characteristics including disease activity, a 14-autoantibody profile, and a panel of 15 serum cytokines were measured simultaneously. Mixed-cluster methodology and bivariate analyses were used to define autoantibody and cytokine clusters and to identify associations between them and related variables. Results First, three clusters of autoantibodies were defined: (1) neutral, (2) antiphospholipid antibodies (APLA)-dominant, and (3) anti-dsDNA/ENA-dominant. Second, eight cytokines showed levels above the threshold thus making possible to find 4 clusters: (1) neutral, (2) chemotactic, (3) G-CSF dominant, and (4) IFNα/Pro-inflammatory. Furthermore, the disease activity was associated with cytokine clusters, which, in turn, were associated with autoantibody clusters. Finally, when all biomarkers were included, three clusters were found: (1) neutral, (2) chemotactic/APLA, and (3) IFN/dsDNA, which were also associated with disease activity. Conclusion These results support the existence of three SLE cytokine-autoantibody driven subphenotypes. They encourage the practice of personalized medicine, and support proof-of-concept studies. Electronic supplementary material The online version of this article (10.1186/s12967-017-1345-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yovana Pacheco
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia
| | - Julián Barahona-Correa
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia
| | - Diana M Monsalve
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia
| | - Yeny Acosta-Ampudia
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia
| | - Manuel Rojas
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia
| | - Yhojan Rodríguez
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia
| | - Juliana Saavedra
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia
| | - Mónica Rodríguez-Jiménez
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia
| | - Rubén D Mantilla
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia
| | - Carolina Ramírez-Santana
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia
| | - Nicolás Molano-González
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA) School of Medicine and Health Sciences, Universidad del Rosario, Carrera 26 # 63B-51, Bogota, Colombia.
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17
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da Fonseca ACP, Mastronardi C, Johar A, Arcos-Burgos M, Paz-Filho G. Genetics of non-syndromic childhood obesity and the use of high-throughput DNA sequencing technologies. J Diabetes Complications 2017; 31:1549-1561. [PMID: 28735903 DOI: 10.1016/j.jdiacomp.2017.04.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Childhood obesity is a serious public health problem associated with the development of several chronic diseases, such as type 2 diabetes mellitus, dyslipidemia, and hypertension. The elevated prevalence of obesity is mostly due to inadequate diet and lifestyle, but it is also influenced by genetic factors. OBJECTIVES To review recent advances in the field of the genetics of obesity. We summarize the list of genes associated with the rare non-syndromic forms of obesity, and explain their function. Furthermore, we discuss the technologies that are available for the genetic diagnosis of obesity. RESULTS Several studies reported that single gene variants cause Mendelian forms of obesity, determined by mutations of major effect in single genes. Rare, non-syndromic forms of obesity are a result of loss-of-function mutations in genes that act on the development and function of the hypothalamus or the leptin-melanocortin pathway. These variants disrupt enzymes and receptors that play a role in energy homeostasis, resulting in severe early-onset obesity and endocrine dysfunctions. Different approaches and technologies have been used to understand the genetic background of obesity. Currently, whole genome and whole exome sequencing are important diagnostic tools to identify new genes and variants associated with severe obesity, but other approaches are also useful at individual or population levels, such as linkage analysis, candidate gene sequencing, chromosomal microarray analysis, and genome-wide association studies. CONCLUSIONS The understanding of the genetic causes of obesity and the usefulness and limitations of the genetic diagnostic approaches can contribute to the development of new personalized therapeutic targets against obesity.
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Affiliation(s)
| | - Claudio Mastronardi
- Institute of Translational Medicine, Universidad del Rosario, Bogota, Colombia
| | - Angad Johar
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Australia.
| | | | - Gilberto Paz-Filho
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Australia.
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18
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Bliddal S, Nielsen CH, Feldt-Rasmussen U. Recent advances in understanding autoimmune thyroid disease: the tallest tree in the forest of polyautoimmunity. F1000Res 2017; 6:1776. [PMID: 29043075 PMCID: PMC5621109 DOI: 10.12688/f1000research.11535.1] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/29/2017] [Indexed: 12/17/2022] Open
Abstract
Autoimmune thyroid disease (AITD) is often observed together with other autoimmune diseases. The coexistence of two or more autoimmune diseases in the same patient is referred to as polyautoimmunity, and AITD is the autoimmune disease most frequently involved. The occurrence of polyautoimmunity has led to the hypothesis that the affected patients suffer from a generalized dysregulation of their immune system. The present review summarizes recent discoveries unravelling the immunological mechanisms involved in autoimmunity, ranging from natural autoimmunity to disease-specific autoimmunity. Furthermore, the clinical grounds for considering AITD in a setting of polyautoimmunity are explored. A better understanding of these may pave the way for designing new treatment modalities targeting the underlying immune dysregulation when AITD appears in the context of polyautoimmunity.
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Affiliation(s)
- Sofie Bliddal
- Department of Medical Endocrinology, Section 2132, Copenhagen University Hospital (Rigshospitalet), Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Claus Henrik Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, section 7521, Copenhagen University Hospital (Rigshospitalet), Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Ulla Feldt-Rasmussen
- Department of Medical Endocrinology, Section 2132, Copenhagen University Hospital (Rigshospitalet), Blegdamsvej 9, 2100 Copenhagen, Denmark
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Abstract
AIM To discuss the clinical characteristics of immune-related dry eye. METHODS Simple dry eye (SDE) group: we selected 224 patients of simple dry eye with no systemic lesions. Immune-related dry eye (IRDE) group: we selected 207 patients of dry eye complicated with immune system diseases, including 70 cases of Sjögren's syndrome (SS), 72 cases of systemic lupus erythematosus (SLE), and 65 cases of rheumatoid arthritis (RA). The classification of all patients was performed. The difference between the two groups was compared, including age, gender, ocular surface fluorescein staining and inflammatory reaction, tear breakup time (TBUT), Shirmer I test, confocal microscopy scan, and dry eye grading. RESULTS Compared with the SDE group, the patients of IRDE group were younger (P < 0.05). The female patients were significantly more than the male ones (P < 0.05). Corneal staining counts and ocular surface inflammation were significantly increased (P < 0.05). TBUT and Shirmer I test shortened significantly (P < 0.05). Corneal nerve fibers were less, and the number of local lymphocyte was significant increased. The number of dry eye patients in the moderate or above IRDE group was significantly increased (P < 0.05). CONCLUSIONS The dry eye symptom and sign and ocular surface inflammation of IRDE were significantly more severe than those of the SDE.
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20
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The autoimmune tautology. A summary of evidence. Joint Bone Spine 2017; 84:251-253. [DOI: 10.1016/j.jbspin.2016.11.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 11/30/2016] [Indexed: 11/19/2022]
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21
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Patel VI, Booth JL, Duggan ES, Cate S, White VL, Hutchings D, Kovats S, Burian DM, Dozmorov M, Metcalf JP. Transcriptional Classification and Functional Characterization of Human Airway Macrophage and Dendritic Cell Subsets. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 198:1183-1201. [PMID: 28031342 PMCID: PMC5262539 DOI: 10.4049/jimmunol.1600777] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 11/28/2016] [Indexed: 12/20/2022]
Abstract
The respiratory system is a complex network of many cell types, including subsets of macrophages and dendritic cells that work together to maintain steady-state respiration. Owing to limitations in acquiring cells from healthy human lung, these subsets remain poorly characterized transcriptionally and phenotypically. We set out to systematically identify these subsets in human airways by developing a schema of isolating large numbers of cells by whole-lung bronchoalveolar lavage. Six subsets of phagocytic APC (HLA-DR+) were consistently observed. Aside from alveolar macrophages, subsets of Langerin+, BDCA1-CD14+, BDCA1+CD14+, BDCA1+CD14-, and BDCA1-CD14- cells were identified. These subsets varied in their ability to internalize Escherichia coli, Staphylococcus aureus, and Bacillus anthracis particles. All subsets were more efficient at internalizing S. aureus and B. anthracis compared with E. coli Alveolar macrophages and CD14+ cells were overall more efficient at particle internalization compared with the four other populations. Subsets were further separated into two groups based on their inherent capacities to upregulate surface CD83, CD86, and CCR7 expression levels. Whole-genome transcriptional profiling revealed a clade of "true dendritic cells" consisting of Langerin+, BDCA1+CD14+, and BDCA1+CD14- cells. The dendritic cell clade was distinct from a macrophage/monocyte clade, as supported by higher mRNA expression levels of several dendritic cell-associated genes, including CD1, FLT3, CX3CR1, and CCR6 Each clade, and each member of both clades, was discerned by specific upregulated genes, which can serve as markers for future studies in healthy and diseased states.
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Affiliation(s)
- Vineet I Patel
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
- Pulmonary and Critical Care Division, Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - J Leland Booth
- Pulmonary and Critical Care Division, Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Elizabeth S Duggan
- Pulmonary and Critical Care Division, Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Steven Cate
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Vicky L White
- Office of Aviation Medicine, Federal Aviation Administration, Oklahoma City, OK 73169
| | | | - Susan Kovats
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104; and
| | - Dennis M Burian
- Office of Aviation Medicine, Federal Aviation Administration, Oklahoma City, OK 73169
| | - Mikhail Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298
| | - Jordan P Metcalf
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104;
- Pulmonary and Critical Care Division, Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
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Whole Exome Sequencing in Psoriasis Patients Contributes to Studies of Acitretin Treatment Difference. Int J Mol Sci 2017; 18:ijms18020295. [PMID: 28146080 PMCID: PMC5343831 DOI: 10.3390/ijms18020295] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/21/2017] [Accepted: 01/25/2017] [Indexed: 01/01/2023] Open
Abstract
Psoriasis vulgaris is an immune-mediated inflammatory skin disease. Although acitretin is a widely used synthetic retinoid for moderate to severe psoriasis, little is known about patients’ genetics in response to this drug. In this study, 179 patients were enrolled in either the discovery set (13 patients) or replication set (166 patients). The discovery set was sequenced by whole exome sequencing and sequential validation was conducted in the replication set by MassArray assays. Four SNPs (single nucleotide polymorphisms) (rs1105223T>C in CRB2, rs11086065A>G in ANKLE1, rs3821414T>C in ARHGEF3, rs1802073 T>G in SFRP4) were found to be significantly associated with acitretin response in either co-dominant or dominant models via multivariable logistic regression analysis, while CRB2 rs1105223CC (OR = 4.10, 95% CI = 1.46–11.5, p = 0.007) and ANKLE1 rs11086065AG/GG (OR = 2.76, 95% CI = 1.42–5.37, p = 0.003) were associated with no response to acitretin after 8-week treatment. Meanwhile, ARHGEF3 rs3821414CT/CC (OR = 0.25, 95% CI = 0.10–0.68, p = 0.006) and SFRP4 rs1802073GG/GT (OR = 2.40, 95% CI, 1.23–4.70, p = 0.011) were associated with a higher response rate. Four new genetic variations with potential influences on the response to acitretin were found in this study which may serve as genetic markers for acitretin in psoriasis patients.
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Linkage and association analysis of ADHD endophenotypes in extended and multigenerational pedigrees from a genetic isolate. Mol Psychiatry 2016; 21:1434-40. [PMID: 26598068 PMCID: PMC4879118 DOI: 10.1038/mp.2015.172] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 07/02/2015] [Accepted: 08/05/2015] [Indexed: 12/16/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a heritable, chronic, neurodevelopmental disorder with serious long-term repercussions. Despite being one of the most common cognitive disorders, the clinical diagnosis of ADHD is based on subjective assessments of perceived behaviors. Endophenotypes (neurobiological markers that cosegregate and are associated with an illness) are thought to provide a more powerful and objective framework for revealing the underlying neurobiology than syndromic psychiatric classification. Here, we present the results of applying genetic linkage and association analyses to neuropsychological endophenotypes using microsatellite and single nucleotide polymorphisms. We found several new genetic regions linked and/or associated with these endophenotypes, and others previously associated to ADHD, for example, loci harbored in the LPHN3, FGF1, POLR2A, CHRNA4 and ANKFY1 genes. These findings, when compared with those linked and/or associated to ADHD, suggest that these endophenotypes lie on shared pathways. The genetic information provided by this study offers a novel and complementary method of assessing the genetic causes underpinning the susceptibility to behavioral conditions and may offer new insights on the neurobiology of the disorder.
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Anaya JM, Rojas-Villarraga A, Mantilla RD, Arcos-Burgos M, Sarmiento-Monroy JC. Polyautoimmunity in Sjögren Syndrome. Rheum Dis Clin North Am 2016; 42:457-72. [DOI: 10.1016/j.rdc.2016.03.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Johar A, Sarmiento-Monroy JC, Rojas-Villarraga A, Silva-Lara MF, Patel HR, Mantilla RD, Velez JI, Schulte KM, Mastronardi C, Arcos-Burgos M, Anaya JM. Definition of mutations in polyautoimmunity. J Autoimmun 2016; 72:65-72. [PMID: 27209085 DOI: 10.1016/j.jaut.2016.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/06/2016] [Accepted: 05/07/2016] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Familial autoimmunity and polyautoimmunity represent extreme phenotypes ideal for identifying major genomic variants contributing to autoimmunity. Whole exome sequencing (WES) and linkage analysis are well suited for this purpose due to its strong resolution upon familial segregation patterns of functional protein coding and splice variants. The primary objective of this study was to identify potentially autoimmune causative variants using WES data from extreme pedigrees segregating polyautoimmunity phenotypes. METHODS DNA of 47 individuals across 10 extreme pedigrees, ascertained from probands affected with polyautoimmunity and familial autoimmunity, were selected for WES. Variant calls were obtained through Genome Analysis Toolkit. Filtration and prioritization framework to identify mutation(s) were applied, and later implemented for genetic linkage analysis. Sanger sequencing corroborated variants with significant linkage. RESULTS Novel and mostly rare variants harbored in SRA1, MLL4, ABCB8, DHX34 and PLAUR showed significant linkage (LOD scores are >3.0). The strongest signal was in SRA1, with a LOD score of 5.48. Network analyses indicated that SRA1, PLAUR and ABCB8 contribute to regulation of apoptotic processes. CONCLUSIONS Novel and rare variants in genetic linkage with polyautoimmunity were identified throughout WES. Genes harboring these variants might be major players of autoimmunity.
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Affiliation(s)
- Angad Johar
- Genomics and Predictive Medicine, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology & Environment, The Australian National University, Canberra, ACT, Australia
| | - Juan C Sarmiento-Monroy
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | - Adriana Rojas-Villarraga
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | - Maria F Silva-Lara
- Genomics and Predictive Medicine, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology & Environment, The Australian National University, Canberra, ACT, Australia
| | - Hardip R Patel
- Genome Discovery Unit, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology & Environment, The Australian National University, Canberra, ACT, Australia
| | - Ruben D Mantilla
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | - Jorge I Velez
- Genomics and Predictive Medicine, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology & Environment, The Australian National University, Canberra, ACT, Australia
| | - Klaus-Martin Schulte
- Department of Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Claudio Mastronardi
- Genomics and Predictive Medicine, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology & Environment, The Australian National University, Canberra, ACT, Australia
| | - Mauricio Arcos-Burgos
- Genomics and Predictive Medicine, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology & Environment, The Australian National University, Canberra, ACT, Australia; Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia.
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia.
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Genetic Variants of Microtubule Actin Cross-linking Factor 1 (MACF1) Confer Risk for Parkinson’s Disease. Mol Neurobiol 2016; 54:2878-2888. [DOI: 10.1007/s12035-016-9861-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/17/2016] [Indexed: 01/12/2023]
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Braun J, Meixner A, Brachner A, Foisner R. The GIY-YIG Type Endonuclease Ankyrin Repeat and LEM Domain-Containing Protein 1 (ANKLE1) Is Dispensable for Mouse Hematopoiesis. PLoS One 2016; 11:e0152278. [PMID: 27010503 PMCID: PMC4807109 DOI: 10.1371/journal.pone.0152278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/12/2016] [Indexed: 01/01/2023] Open
Abstract
Ankyrin repeat and LEM-domain containing protein 1 (ANKLE1) is a GIY-YIG endonuclease with unknown functions, mainly expressed in mouse hematopoietic tissues. To test its potential role in hematopoiesis we generated Ankle1-deficient mice. Ankle1Δ/Δ mice are viable without any detectable phenotype in hematopoiesis. Neither hematopoietic progenitor cells, myeloid and lymphoid progenitors, nor B and T cell development in bone marrow, spleen and thymus, are affected in Ankle1Δ/Δ-mice. Similarly embryonic stress erythropoiesis in liver and adult erythropoiesis in bone marrow and spleen appear normal. To test whether ANKLE1, like the only other known GIY-YIG endonuclease in mammals, SLX1, may contribute to Holliday junction resolution during DNA repair, Ankle1-deficient cells were exposed to various DNA-damage inducing agents. However, lack of Ankle1 did not affect cell viability and, unlike depletion of Slx1, Ankle1-deficiency did not increase sister chromatid exchange in Bloom helicase-depleted cells. Altogether, we show that lack of Ankle1 does neither affect mouse hematopoiesis nor DNA damage repair in mouse embryonic fibroblasts, indicating a redundant or non-essential function of ANKLE1 in mouse.
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Affiliation(s)
- Juliane Braun
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Arabella Meixner
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Brachner
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Roland Foisner
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
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