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Guerri F, Junet V, Farrés J, Daura X. MMPred: a tool to predict peptide mimicry events in MHC class II recognition. Front Genet 2024; 15:1500684. [PMID: 39722794 PMCID: PMC11669352 DOI: 10.3389/fgene.2024.1500684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Accepted: 11/25/2024] [Indexed: 12/28/2024] Open
Abstract
We present MMPred, a software tool that integrates epitope prediction and sequence alignment algorithms to streamline the computational analysis of molecular mimicry events in autoimmune diseases. Starting with two protein or peptide sets (e.g., from human and SARS-CoV-2), MMPred facilitates the generation, investigation, and testing of mimicry hypotheses by providing epitope predictions specifically for MHC class II alleles, which are frequently implicated in autoimmunity. However, the tool is easily extendable to MHC class I predictions by incorporating pre-trained models from CNN-PepPred and NetMHCpan. To evaluate MMPred's ability to produce biologically meaningful insights, we conducted a comprehensive assessment involving i) predicting associations between known HLA class II human autoepitopes and microbial-peptide mimicry, ii) interpreting these predictions within a systems biology framework to identify potential functional links between the predicted autoantigens and pathophysiological pathways related to autoimmune diseases, and iii) analyzing illustrative cases in the context of SARS-CoV-2 infection and autoimmunity. MMPred code and user guide are made freely available at https://github.com/ComputBiol-IBB/MMPRED.
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Affiliation(s)
- Filippo Guerri
- Anaxomics Biotech, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Valentin Junet
- Anaxomics Biotech, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, Spain
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2
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Ferar K, Hall TO, Crawford DC, Rowley R, Satterfield BA, Li R, Gragert L, Karlson EW, de Andrade M, Kullo IJ, McCarty CA, Kho A, Hayes MG, Ritchie MD, Crane PK, Mirel DB, Carlson C, Connolly JJ, Hakonarson H, Crenshaw AT, Carrell D, Luo Y, Dikilitas O, Denny JC, Jarvik GP, Crosslin DR. Genetic variation in the human leukocyte antigen region confers susceptibility to Clostridioides difficile infection. Sci Rep 2023; 13:18532. [PMID: 37898691 PMCID: PMC10613277 DOI: 10.1038/s41598-023-45649-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 10/22/2023] [Indexed: 10/30/2023] Open
Abstract
Clostridioides difficile (C. diff.) infection (CDI) is a leading cause of hospital acquired diarrhea in North America and Europe and a major cause of morbidity and mortality. Known risk factors do not fully explain CDI susceptibility, and genetic susceptibility is suggested by the fact that some patients with colons that are colonized with C. diff. do not develop any infection while others develop severe or recurrent infections. To identify common genetic variants associated with CDI, we performed a genome-wide association analysis in 19,861 participants (1349 cases; 18,512 controls) from the Electronic Medical Records and Genomics (eMERGE) Network. Using logistic regression, we found strong evidence for genetic variation in the DRB locus of the MHC (HLA) II region that predisposes individuals to CDI (P > 1.0 × 10-14; OR 1.56). Altered transcriptional regulation in the HLA region may play a role in conferring susceptibility to this opportunistic enteric pathogen.
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Affiliation(s)
- Kathleen Ferar
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA.
| | - Taryn O Hall
- Optum Genomics, UnitedHealth Group, Minnetonka, MN, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Rongling Li
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Loren Gragert
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | | | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Catherine A McCarty
- University of Minnesota Medical School, Duluth, MN, USA
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - Abel Kho
- Divisions of General Internal Medicine and Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marylyn D Ritchie
- Department of Biochemistry and Molecular Biology, Center for Systems Genomics, Pennsylvania State University, University Park, PA, USA
| | - Paul K Crane
- Division of General Internal Medicine, University of Washington, Seattle, WA, USA
| | | | - Christopher Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - David Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Yuan Luo
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA.
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3
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Chapman C, Lucas RM, Ponsonby AL, Taylor B, Chapman C, Coulthard A, Dear K, Dwyer T, Kilpatrick T, Lucas R, McMichael T, Pender M, Ponsonby AL, Taylor B, Valery PC, van der Mei I, Williams D. Predictors of progression from a first demyelinating event to clinically definite multiple sclerosis. Brain Commun 2022; 4:fcac181. [PMID: 35891671 PMCID: PMC9308470 DOI: 10.1093/braincomms/fcac181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/07/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding the predictors of progression from a first to a second demyelinating event (and formerly, a diagnosis of clinically definite multiple sclerosis) is important clinically. Previous studies have focused on predictors within a single domain, e.g. radiological, lacking prospective data across multiple domains. We tested a comprehensive set of personal, environmental, neurological, MRI and genetic characteristics, considered together, as predictors of progression from a first demyelinating event to clinically definite multiple sclerosis. Participants were aged 18–59 years and had a first demyelinating event during the study recruitment period (1 November 2003–31 December 2006) for the Ausimmune Study (n = 216) and had follow-up data to 2–3 years post-initial interview. Detailed baseline data were available on a broad range of demographic and environmental factors, MRI, and genetic and viral studies. Follow-up data included confirmation of clinically definite multiple sclerosis (or not) and changes in environmental exposures during the follow-up period. We used multivariable logistic regression and Cox proportional hazards regression modelling to test predictors of, and time to, conversion to clinically definite multiple sclerosis. On review, one participant had an undiagnosed event prior to study recruitment and was excluded (n = 215). Data on progression to clinically definite multiple sclerosis were available for 91.2% (n = 196); 77% were diagnosed as clinically definite multiple sclerosis at follow-up. Mean (standard deviation) duration of follow-up was 2.7 (0.7) years. The set of predictors retained in the best predictive model for progression from a first demyelinating event to clinically definite multiple sclerosis were as follows: younger age at first demyelinating event [adjusted odds ratio (aOR) = 0.92, 95% confidence interval (CI) = 0.87–0.97, per additional year of age); being a smoker at baseline (versus not) (aOR = 2.55, 95% CI 0.85–7.69); lower sun exposure at age 6–18 years (aOR = 0.86, 95% CI 0.74–1.00, per 100 kJ/m2 increment in ultraviolet radiation dose), presence (versus absence) of infratentorial lesions on baseline magnetic resonance imaging (aOR = 7.41, 95% CI 2.08–26.41); and single nucleotide polymorphisms in human leukocyte antigen (HLA)-B (rs2523393, aOR = 0.25, 95% CI 0.09–0.68, for any G versus A:A), TNFRSF1A (rs1800693, aOR = 5.82, 95% CI 2.10–16.12, for any C versus T:T), and a vitamin D-binding protein gene (rs7041, aOR = 3.76, 95% CI 1.41–9.99, for any A versus C:C). The final model explained 36% of the variance. Predictors of more rapid progression to clinically definite multiple sclerosis (Cox proportional hazards regression) were similar. Genetic and magnetic resonance imaging characteristics as well as demographic and environmental factors predicted progression, and more rapid progression, from a first demyelinating event to a second event and clinically definite multiple sclerosis.
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Affiliation(s)
- Caron Chapman
- Barwon Health , PO Box 281, Geelong, VIC 3220 , Australia
| | - Robyn M Lucas
- National Centre for Epidemiology and Population Health, The Australian National University , Cnr Mills and Eggleston Roads, Canberra 2601 , Australia
| | - Anne-Louise Ponsonby
- The Florey Institute of Neuroscience and Mental Health , 30 Royal Pde, Parkville, VIC 3052 , Australia
| | - Bruce Taylor
- Menzies Institute for Medical Research, University of Tasmania , 17 Liverpool St, Hobart , Australia
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Li H, Lian G, Wang G, Yin Q, Su Z. A review of possible therapies for multiple sclerosis. Mol Cell Biochem 2021; 476:3261-3270. [PMID: 33886059 DOI: 10.1007/s11010-021-04119-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 02/23/2021] [Indexed: 01/22/2023]
Abstract
Multiple sclerosis (MS) is an autoimmune chronic inflammatory disease of the central nervous system with a wide range of symptoms, like executive function defect, cognitive dysfunction, blurred vision, decreased sensation, spasticity, fatigue, and other symptoms. This neurological disease is characterized by the destruction of the blood-brain barrier, loss of myelin, and damage to neurons. It is the result of immune cells crossing the blood-brain barrier into the central nervous system and attacking self-antigens. Heretofore, many treatments proved that they can retard the progression of the disease even though there is no cure. Therefore, treatments aimed at improving patients' quality of life and reducing adverse drug reactions and costs are essential. In this review, the treatment approaches to alleviate the progress of MS include the following: pharmacotherapy, antibody therapy, cell therapy, gene therapy, and surgery. The current treatment methods of MS are described in terms of the prevention of myelin shedding, the promotion of myelin regeneration, and the protection of neurons.
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Affiliation(s)
- Hui Li
- Hengyang Medical School, University of South China, Hengyang City, 421001, Hunan Province, China
| | - Gaojian Lian
- Hengyang Medical School, University of South China, Hengyang City, 421001, Hunan Province, China
| | - Guang Wang
- Hengyang Medical School, University of South China, Hengyang City, 421001, Hunan Province, China
| | - Qianmei Yin
- Hengyang Medical School, University of South China, Hengyang City, 421001, Hunan Province, China
| | - Zehong Su
- Hengyang Medical School, University of South China, Hengyang City, 421001, Hunan Province, China.
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Angeloni B, Bigi R, Bellucci G, Mechelli R, Ballerini C, Romano C, Morena E, Pellicciari G, Reniè R, Rinaldi V, Buscarinu MC, Romano S, Ristori G, Salvetti M. A Case of Double Standard: Sex Differences in Multiple Sclerosis Risk Factors. Int J Mol Sci 2021; 22:ijms22073696. [PMID: 33918133 PMCID: PMC8037645 DOI: 10.3390/ijms22073696] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis is a complex, multifactorial, dysimmune disease prevalent in women. Its etiopathogenesis is extremely intricate, since each risk factor behaves as a variable that is interconnected with others. In order to understand these interactions, sex must be considered as a determining element, either in a protective or pathological sense, and not as one of many variables. In particular, sex seems to highly influence immune response at chromosomal, epigenetic, and hormonal levels. Environmental and genetic risk factors cannot be considered without sex, since sex-based immunological differences deeply affect disease onset, course, and prognosis. Understanding the mechanisms underlying sex-based differences is necessary in order to develop a more effective and personalized therapeutic approach.
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Affiliation(s)
- Benedetta Angeloni
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
| | - Rachele Bigi
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
- Correspondence: (R.B.); (G.R.)
| | - Gianmarco Bellucci
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
| | - Rosella Mechelli
- San Raffaele Roma Open University, 00166 Rome, Italy;
- Scientific Institute for Research, Hospitalization and Healthcare San Raffaele Pisana (IRCCS), 00166 Rome, Italy
| | - Chiara Ballerini
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
| | - Carmela Romano
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
| | - Emanuele Morena
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
| | - Giulia Pellicciari
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
| | - Roberta Reniè
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
| | - Virginia Rinaldi
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
| | - Maria Chiara Buscarinu
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
| | - Silvia Romano
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
| | - Giovanni Ristori
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
- Neuroimmunology Unit, Scientific Institute for Research, Hospitalization and Healthcare Fondazione Santa Lucia (IRCCS), 00179 Rome, Italy
- Correspondence: (R.B.); (G.R.)
| | - Marco Salvetti
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (B.A.); (G.B.); (C.B.); (C.R.); (E.M.); (G.P.); (R.R.); (V.R.); (M.C.B.); (S.R.); (M.S.)
- Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Istituto Neurologico Mediterraneo (INM) Neuromed, 86077 Pozzilli, Italy
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Bahrami T, Taheri M, Javadi S, Omrani MD, Karimipour M. Expression Analysis of Long Non-coding RNA Lnc-DC in HLA-DRB1*15:01-Negative Patients with Multiple Sclerosis: A Probable Cause for Gender Differences in Multiple Sclerosis Susceptibility? J Mol Neurosci 2020; 71:821-825. [PMID: 32951137 DOI: 10.1007/s12031-020-01704-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/07/2020] [Indexed: 11/29/2022]
Abstract
Multiple sclerosis is a disease that affects male and female patients differently. Several studies have been performed to explain the gender differences in MS susceptibility, but the genetic causes underlying gender differences remain unknown. The association between multiple sclerosis and the HLA-DRB1*15:01 haplotype has been confirmed to be female-specific. We hypothesized other immunological components such as lnc-DC may be gender-specific among multiple sclerosis patients, especially when MS patients are negative for the HLA-DRB1*15:01 allele. Therefore, the current study, considering the results of previous studies, aimed to evaluate the expression level of the lnc-DC gene in HLA-DRB1*15:01-negative female patients with relapsing remitting MS (RRMS). A total of 50 MS female patients and 50 female healthy controls were enrolled in this observational case-control study. HLA-DRB1*15:01, as a critical risk factor for MS, was ruled out in all patients. The peripheral blood mononuclear cells were obtained from all patients and total RNA was isolated and cDNA synthesis was carried out. The gene expression of lnc-DC was evaluated by real-time quantitative PCR. Our results have shown that lnc-DC expression level was significantly higher in total MS female patients compared with female controls (P = 0.0044). In addition, the correlation between lnc-DC with disease duration, EDSS, and age at onset did not reach a statistical significance in our study (r = 0.0336, P = 0.817; r = 0.0914, P = 0.5278 and r = 0.0743, P = 0.6083, respectively). Our results give further evidence that lnc-DC may play a gender-dependent role in MS pathogenesis.
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Affiliation(s)
- Tayyeb Bahrami
- Molecular Medicine Department, Biotechnology Research Center, Pasteure Institute of Iran, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sepehr Javadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Morteza Karimipour
- Molecular Medicine Department, Biotechnology Research Center, Pasteure Institute of Iran, Tehran, Iran
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