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Ko E, Kim Y, Shokoohi F, Mersha TB, Kang M. SPIN: sex-specific and pathway-based interpretable neural network for sexual dimorphism analysis. Brief Bioinform 2024; 25:bbae239. [PMID: 38807262 PMCID: PMC11133003 DOI: 10.1093/bib/bbae239] [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: 12/17/2023] [Revised: 03/29/2024] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
Sexual dimorphism in prevalence, severity and genetic susceptibility exists for most common diseases. However, most genetic and clinical outcome studies are designed in sex-combined framework considering sex as a covariate. Few sex-specific studies have analyzed males and females separately, which failed to identify gene-by-sex interaction. Here, we propose a novel unified biologically interpretable deep learning-based framework (named SPIN) for sexual dimorphism analysis. We demonstrate that SPIN significantly improved the C-index up to 23.6% in TCGA cancer datasets, and it was further validated using asthma datasets. In addition, SPIN identifies sex-specific and -shared risk loci that are often missed in previous sex-combined/-separate analysis. We also show that SPIN is interpretable for explaining how biological pathways contribute to sexual dimorphism and improve risk prediction in an individual level, which can result in the development of precision medicine tailored to a specific individual's characteristics.
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Affiliation(s)
- Euiseong Ko
- Department of Computer Science, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Youngsoon Kim
- Department of Information and Statistics and Department of Bio&Medical Bigdata (BK21 Four program), Gyeongsang National University, Jinju, Republic of Korea
| | - Farhad Shokoohi
- Department of Mathematical Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Tesfaye B Mersha
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, Las Vegas, NV, USA
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2
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Bertol BC, Debortoli G, Dias FC, de Araújo JNG, Maia LSM, de Almeida BS, de Figueiredo-Feitosa NL, de Freitas LCC, Castelli EC, Mendes-Junior CT, Silbiger VN, Maciel LMZ, Donadi EA. HLA-G Gene Variability Is Associated with Papillary Thyroid Carcinoma Morbidity and the HLA-G Protein Profile. Int J Mol Sci 2023; 24:12858. [PMID: 37629044 PMCID: PMC10454351 DOI: 10.3390/ijms241612858] [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: 07/16/2023] [Revised: 08/07/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Human leukocyte antigen (HLA)-G is an immune checkpoint molecule that is highly expressed in papillary thyroid carcinoma (PTC). The HLA-G gene presents several functional polymorphisms distributed across the coding and regulatory regions (5'URR: 5' upstream regulatory region and 3'UTR: 3' untranslated region) and some of them may impact HLA-G expression and human malignancy. To understand the contribution of the HLA-G genetic background in PTC, we studied the HLA-G gene variability in PTC patients in association with tumor morbidity, HLA-G tissue expression, and plasma soluble (sHLA-G) levels. We evaluated 185 PTC patients and 154 healthy controls. Polymorphic sites defining coding, regulatory and extended haplotypes were characterized by sequencing analyses. HLA-G tissue expression and plasma soluble HLA-G levels were evaluated by immunohistochemistry and ELISA, respectively. Compared to the controls, the G0104a(5'URR)G*01:04:04(coding)UTR-03(3'UTR) extended haplotype was underrepresented in the PTC patients, while G0104a(5'URR)G*01:04:01(coding)UTR-03(3'UTR) was less frequent in patients with metastatic and multifocal tumors. Decreased HLA-G tissue expression and undetectable plasma sHLA-G were associated with the G010102a(5'URR)G*01:01:02:01(coding)UTR-02(3'UTR) extended haplotype. We concluded that the HLA-G variability was associated with PTC development and morbidity, as well as the magnitude of the encoded protein expression at local and systemic levels.
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Affiliation(s)
- Bruna C. Bertol
- Postgraduate Program of Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Guilherme Debortoli
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada;
| | - Fabrício C. Dias
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (F.C.D.); (L.S.M.M.); (B.S.d.A.)
| | - Jéssica N. G. de Araújo
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal 59012-570, Brazil; (J.N.G.d.A.); (V.N.S.)
| | - Luana S. M. Maia
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (F.C.D.); (L.S.M.M.); (B.S.d.A.)
| | - Bibiana S. de Almeida
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (F.C.D.); (L.S.M.M.); (B.S.d.A.)
| | - Nathalie L. de Figueiredo-Feitosa
- Division of Endocrinology and Metabolism, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (N.L.d.F.-F.); (L.M.Z.M.)
| | - Luiz Carlos C. de Freitas
- Department of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Erick C. Castelli
- Department of Pathology, School of Medicine, São Paulo State University, Botucatu 18618-687, Brazil;
| | - Celso T. Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Vivian N. Silbiger
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal 59012-570, Brazil; (J.N.G.d.A.); (V.N.S.)
| | - Léa M. Z. Maciel
- Division of Endocrinology and Metabolism, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (N.L.d.F.-F.); (L.M.Z.M.)
| | - Eduardo A. Donadi
- Postgraduate Program of Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (F.C.D.); (L.S.M.M.); (B.S.d.A.)
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3
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Lando V, Calciano L, Minelli C, Bombieri C, Ferrari M, Malerba G, Margagliotti A, Murgia N, Nicolis M, Olivieri M, Potts J, Tardivo S, Accordini S. IL18 Gene Polymorphism Is Associated with Total IgE in Adult Subjects with Asthma. J Clin Med 2023; 12:3963. [PMID: 37373658 DOI: 10.3390/jcm12123963] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The allergic asthma phenotype is characterized by a T helper type 2 (Th2) immune response, based on Immunoglobulin E (IgE)-mediated type 1 hypersensitivity reactions. Total IgE is the sum of all IgE types produced by the human body and is used as a biomarker of inflammation in asthma. We analysed data collected in 143 asthma cases (median age 42.1 years) from the general Italian population (GEIRD survey; 2008-2010) to identify single nucleotide polymorphisms (SNPs) in candidate genes that are associated with total IgE in adult subjects with asthma. These patients reported respiratory symptoms in response to perennial allergens and provided data on 166 SNPs tagging 50 candidate genes or gene regions. Replication of the statistically significant results was performed in 842 asthma cases from other European countries (ECRHS II survey; 1998-2002). SNP rs549908 in interleukin 18 (IL18) gene was significantly associated with total IgE in GEIRD, and this result was replicated in ECRHS II. SNP rs1063320 in the human leukocyte antigen G (HLA-G) gene was identified in GEIRD, but this association was not replicated in ECRHS II. Further investigating IL18 and its biological pathways could be important for developing new therapeutic targets, due to its involvement in inflammatory response processes.
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Affiliation(s)
- Valentina Lando
- Unit of Epidemiology and Medical Statistics, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Lucia Calciano
- Unit of Epidemiology and Medical Statistics, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Cosetta Minelli
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - Cristina Bombieri
- Biology and Genetics Section, Department of Neuroscience, Biomedicine and Movement, University of Verona, 37134 Verona, Italy
| | - Marcello Ferrari
- Respiratory Diseases Section, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Giovanni Malerba
- Biology and Genetics Section, Department of Neuroscience, Biomedicine and Movement, University of Verona, 37134 Verona, Italy
| | - Antonino Margagliotti
- Unit of Epidemiology and Medical Statistics, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Nicola Murgia
- Department of Environmental and Prevention Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Morena Nicolis
- Unit of Hygiene and Preventive, Environmental and Occupational Medicine, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Mario Olivieri
- Unit of Occupational Medicine, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - James Potts
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - Stefano Tardivo
- Unit of Hygiene and Preventive, Environmental and Occupational Medicine, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Simone Accordini
- Unit of Epidemiology and Medical Statistics, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
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Zhang L, Qiu L, Wu J, Qi Y, Gao X, He C, Qi R, Wang H, Yao X, Zhu H, Li Y, Hao S, Lu Q, Long H, Lian S, Zhu W, Zhang H, Lai W, Su X, Lu R, Guo Z, Li J, Li M, Liu Q, Wang H, He L, Nong X, Li F, Li Y, Yao C, Xu J, Tang H, Wang D, Li Z, Yu H, Xiao S, An J, Pu X, Yu S, Zhang J, Chen X, Wang H, Huang W, Chen H, Xiao T. GWAS of Chronic Spontaneous Urticaria Reveals Genetic Overlap with Autoimmune Diseases, Not Atopic Diseases. J Invest Dermatol 2023; 143:67-77.e15. [PMID: 35933036 DOI: 10.1016/j.jid.2022.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 07/03/2022] [Accepted: 07/09/2022] [Indexed: 02/08/2023]
Abstract
Although chronic spontaneous urticaria (CSU) is a common disease, GWASs of CSU are lacking. We aimed to identify susceptibility SNPs by performing a GWAS in Chinese Han adults with CSU. The discovery cohort included 430 CSU cases and 482 healthy controls. The GWAS findings were validated in 800 CSU cases and 900 healthy controls. Genetic, functional enrichment, and bioinformatic analyses of genome-wide significant SNPs were performed to assess the association between CSU and autoimmunity or atopy. Five genome-wide significant SNPs were identified: rs434124/LILRA3, rs61986182/IGHG1/2, rs73075571/TDGF1, rs9378141/HLA-G, and rs3789612/PTPN22. The first four SNPs were in linkage disequilibrium with autoimmune-related diseases‒associated SNPs and were cis-expression quantitative trait loci in immune cells. The five SNPs-annotated genes were significantly enriched in immune processes. Higher polygenic risk scores and allele frequencies of rs3789612∗T, rs9378141∗C, and rs73075571∗G were significantly associated with autoimmune-related CSU phenotypes, including positive antithyroglobulin IgG, positive anti-FcεRIα IgG, total IgE <40 IU/ml, and positive antithyroid peroxidase IgG but not with atopic or allergic sensitized CSU phenotypes. This GWAS of CSU identifies five risk loci and reveals that CSU shares genetic overlap with autoimmune diseases and that genetic factors predisposing to CSU mainly manifest through associations with autoimmune traits.
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Affiliation(s)
- Liming Zhang
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Li Qiu
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Jian Wu
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Yumeng Qi
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Xinghua Gao
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Chundi He
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Ruiqun Qi
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Hexiao Wang
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Xu Yao
- Department of Allergy and Rheumatology, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Hong Zhu
- Department of Allergy and Rheumatology, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Yuzhen Li
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Siyu Hao
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qianjin Lu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Hai Long
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Shi Lian
- Department of Dermatology, Xuan Wu Hospital Capital Medical Univerisity, Beijing, China
| | - Wei Zhu
- Department of Dermatology, Xuan Wu Hospital Capital Medical Univerisity, Beijing, China
| | - Haiping Zhang
- Department of Dermatology, Xuan Wu Hospital Capital Medical Univerisity, Beijing, China
| | - Wei Lai
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xiangyang Su
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Rongbiao Lu
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zaipei Guo
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, China
| | - Jingyi Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, China
| | - Quanzhong Liu
- Department of Dermatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Huiping Wang
- Department of Dermatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Li He
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiang Nong
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Fuqiu Li
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Yang Li
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Chunli Yao
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan Univeristy, Shanghai, China
| | - Hui Tang
- Department of Dermatology, Huashan Hospital, Fudan Univeristy, Shanghai, China
| | - Duoqin Wang
- Department of Dermatology, Huashan Hospital, Fudan Univeristy, Shanghai, China
| | - Zhenlu Li
- Department of Dermatology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Huiqian Yu
- Department of Dermatology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Shengxiang Xiao
- Department of Dermatology, The Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Jingang An
- Department of Dermatology, The Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Xiongming Pu
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang Key Laboratory of Dermatology Research (XJYS1707), Xinjiang, China
| | - Shirong Yu
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang Key Laboratory of Dermatology Research (XJYS1707), Xinjiang, China
| | - Jianzhong Zhang
- Department of Dermatology, Peking University People's Hospital, Beijing, China
| | - Xue Chen
- Department of Dermatology, Peking University People's Hospital, Beijing, China
| | - Haifeng Wang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC), Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC), Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Hongduo Chen
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Ting Xiao
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China.
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Martins JO, Pagani F, Dezan MR, Oliveira VB, Conrado M, Ziza KC, Gualandro SFM, Langui DM, Bordin JO, Rocha V, Mendrone-Júnior A, Dinardo CL. Impact of HLA-G +3142C>G on the development of antibodies to blood group systems other than the Rh and Kell among sensitized patients with sickle cell disease. Transfus Apher Sci 2022; 61:103447. [PMID: 35487873 DOI: 10.1016/j.transci.2022.103447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Patients' inflammatory history is an important factor underlying red blood cell (RBC) alloimmunization, which is a frequent transfusion complication among individuals with sickle cell disease (SCD). HLA-G has been associated with different inflammatory and auto - immune diseases. Our goal was to verify whether the HLA-G + 3142 C>G and 14-bp Ins/Del variations are associated with RBC antibody development among SCD patients. METHODS This was a single-center case-control study. SCD patients were randomly selected for the study and divided into two groups: 'Alloimmunized' and 'Nonalloimmunized' depending on the presence of irregular antibodies. The 'Alloimmunized'group was further divided into two subgroups according to the presence of only antibodies against the Rh and Kell blood group systems or the existence of antibodies to antigens of the other blood group systems. RESULTS A total of 213 patients were included in the study (110 alloimmunized and 103 non-alloimmunized). The 'Alloimmunized' and 'Non-alloimmunized' groups did not differ statistically regarding the HLA-G + 14 bp Ins/Del ( p = 0.494) and + 3142 C>G ( p = 0.334). Individuals who had only antibodies against the Rh and Kell antigens had a frequency of HLA-G + 3142GG genotype almost twice as high compared to the groupwith antibodies against less immunogenic antigens ( p = 0.043). CONCLUSIONS The genotype frequency of HLA-G + 3142 C>G differs among alloimmunized SCD patients, depending on the presence of antibodies against low immunogenic RBC antigens. This highlights a possible role played by the HLA-G molecule in the RBC alloimmunization process.
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Affiliation(s)
| | - Flavia Pagani
- Fundação Pró-Sangue São Paulo Hemocenter, São Paulo, Brazil.
| | - Marcia R Dezan
- Fundação Pró-Sangue São Paulo Hemocenter, São Paulo, Brazil
| | | | - Marina Conrado
- Fundação Pró-Sangue São Paulo Hemocenter, São Paulo, Brazil
| | - Karen C Ziza
- Fundação Pró-Sangue São Paulo Hemocenter, São Paulo, Brazil
| | | | | | - José O Bordin
- Serviço de Hemoterapia da UNIFESP, São Paulo, Brazil
| | - Vanderson Rocha
- Serviço de Hemoterapia da UNIFESP, São Paulo, Brazil; Hematology Unit, University of São Paulo, School of Medicine, Brazil; Department of Hematology, Churchill Hospital, NHS BT, Oxford University, Oxford, United Kingdom
| | | | - Carla L Dinardo
- Serviço de Hemoterapia da UNIFESP, São Paulo, Brazil; Fundação Pró-Sangue São Paulo Hemocenter, São Paulo, Brazil; Institute of Tropical Medicine, University of São Paulo, School of Medicine, São Paulo, Brazil.
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Scavuzzi BM, van Drongelen V, Holoshitz J. HLA-G and the MHC Cusp Theory. Front Immunol 2022; 13:814967. [PMID: 35281038 PMCID: PMC8913506 DOI: 10.3389/fimmu.2022.814967] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/07/2022] [Indexed: 12/14/2022] Open
Abstract
Human leukocyte antigens (HLA) are significant genetic risk factors in a long list of diseases. However, the mechanisms underlying these associations remain elusive in many cases. The best-characterized function of classical major histocompatibility complex (MHC) antigens is to allow safe presentation of antigenic peptides via a self/non-self-discrimination process. Therefore, most hypotheses to date have posited that the observed associations between certain HLA molecules and human diseases involve antigen presentation (AP). However, these hypotheses often represent inconsistencies with current knowledge. To offer answers to the inconsistencies, a decade ago we have invoked the MHC Cusp theory, postulating that in addition to its main role in AP, the MHC codes for allele-specific molecules that act as ligands in a conformationally-conserved cusp-like fold, which upon interaction with cognate receptors can trigger MHC-associated diseases. In the ensuing years, we have provided empirical evidence that substantiates the theory in several HLA-Class II-associated autoimmune diseases. Notably, in a recent study we have demonstrated that HLA-DRB1 alleles known to protect against several autoimmune diseases encode a protective epitope at the cusp region, which activates anti-inflammatory signaling leading to transcriptional and functional modulatory effects. Relevant to the topic of this session, cusp ligands demonstrate several similarities to the functional effects of HLA-G. The overall goal of this opinion article is to delineate the parallels and distinctive features of the MHC Cusp theory with structural and functional aspects of HLA-G molecules.
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Affiliation(s)
| | - Vincent van Drongelen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Joseph Holoshitz
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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7
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Rebmann V, Schwich E, Michita RT, Grüntkemeier L, Bittner AK, Rohn H, Horn PA, Hoffmann O, Kimmig R, Kasimir-Bauer S. Systematic Evaluation of HLA-G 3'Untranslated Region Variants in Locally Advanced, Non-Metastatic Breast Cancer Patients: UTR-1, 2 or UTR-4 are Predictors for Therapy and Disease Outcome. Front Immunol 2022; 12:817132. [PMID: 35095919 PMCID: PMC8790528 DOI: 10.3389/fimmu.2021.817132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022] Open
Abstract
Despite major improvements in diagnostics and therapy in early as well as in locally advanced breast cancer (LABC), metastatic relapse occurs in about 20% of patients, often explained by early micro-metastatic spread into bone marrow by disseminated tumor cells (DTC). Although neoadjuvant chemotherapy (NACT) has been a successful tool to improve overall survival (OS), there is growing evidence that various environmental factors like the non-classical human leukocyte antigen-G (HLA-G) promotes cancer invasiveness and metastatic progression. HLA-G expression is associated with regulatory elements targeting certain single-nucleotide polymorphisms (SNP) in the HLA-G 3’ untranslated region (UTR), which arrange as haplotypes. Here, we systematically evaluated the impact of HLA-G 3’UTR polymorphisms on disease status, on the presence of DTC, on soluble HLA-G levels, and on therapy and disease outcome in non-metastatic LABC patients. Although haplotype frequencies were similar in patients (n = 142) and controls (n = 204), univariate analysis revealed that the UTR-7 haplotype was related to patients with low tumor burden, whereas UTR-4 was associated with tumor sizes >T1. Furthermore, UTR-4 was associated with the presence of DTC, but UTR-3 and UTR-7 were related to absence of DTC. Additionally, increased levels of soluble HLA-G molecules were found in patients carrying UTR-7. Regarding therapy and disease outcome, univariate and multivariate analysis highlighted UTR-1 or UTR-2 as a prognostic parameter indicative for a beneficial course of disease in terms of complete response towards NACT or progression-free survival (PFS). At variance, UTR-4 was an independent risk factor for a reduced OS besides already known parameters. Taken into account the most common HLA-G 3’UTR haplotypes (UTR-1–UTR-7, UTR-18), deduction of the UTR-1/2/4 haplotypes to specific SNPs revealed that the +3003C variant, unique for UTR-4, seemed to favor a detrimental disease outcome, while the +3187G and +3196G variants, unique for UTR-1 or UTR-2, were prognostic parameters for a beneficial course of disease. In conclusion, these data suggest that the HLA-G 3’UTR variants +3003C, +3187G, and +3196G are promising candidates for the prediction of therapy and disease outcome in LABC patients.
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Affiliation(s)
- Vera Rebmann
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Esther Schwich
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Rafael Tomoya Michita
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Medicine, Baylor College of Medicine (BCMC), Houston, TX, United States
| | - Lisa Grüntkemeier
- Department of Gynecology and Obstetrics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ann-Kathrin Bittner
- Department of Gynecology and Obstetrics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Hana Rohn
- Department of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Oliver Hoffmann
- Department of Gynecology and Obstetrics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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8
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Negrini S, Contini P, Murdaca G, Puppo F. HLA-G in Allergy: Does It Play an Immunoregulatory Role? Front Immunol 2022; 12:789684. [PMID: 35082780 PMCID: PMC8784385 DOI: 10.3389/fimmu.2021.789684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022] Open
Abstract
Allergy is an inflammatory process determined by a cascade of immune events characterized by T-helper 2 lymphocytes polarization leading to interleukin-4 upregulation, IgE secretion, and mast cell and eosinophil activation. HLA-G molecules, both in membrane-bound and in soluble forms, are known to play a key immunoregulatory role and their involvement in allergic diseases is supported by increasing literature data. HLA-G expression and secretion is specifically induced in peripheral blood mononuclear cells of allergic patients after in vitro incubation with the causal allergen. Elevated levels of soluble HLA-G molecules are detected in serum of patients with allergic rhinitis correlating with allergen-specific IgE levels, clinical severity, drug consumption and response to allergen-specific immunotherapy. HLA-G genetic polymorphisms confer susceptibility to allergic asthma development and high levels of soluble HLA-G molecules are found in plasma and bronchoalveolar lavage fluid of patients with allergic asthma correlating with allergen-specific IgE levels. Interestingly, allergic pregnant women have lower plasma sHLA-G levels than non-allergic women during the 3rd trimester of pregnancy and at delivery. Finally, in allergic patients with atopic dermatitis HLA-G molecules are expressed by T cells, monocytes-macrophages and Langerhans cells infiltrating the dermis. Although at present is difficult to completely define the role of HLA-G molecules in allergic diseases, it may be suggested that they are specifically expressed and secreted by immune cells during the allergic reaction in an attempt to suppress allergic inflammation.
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Affiliation(s)
- Simone Negrini
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Paola Contini
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Giuseppe Murdaca
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Francesco Puppo
- Department of Internal Medicine, University of Genoa, Genoa, Italy
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9
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Castelli EC, de Almeida BS, Muniz YCN, Silva NSB, Passos MRS, Souza AS, Page AE, Dyble M, Smith D, Aguileta G, Bertranpetit J, Migliano AB, Duarte YAO, Scliar MO, Wang J, Passos-Bueno MR, Naslavsky MS, Zatz M, Mendes-Junior CT, Donadi EA. HLA-G genetic diversity and evolutive aspects in worldwide populations. Sci Rep 2021; 11:23070. [PMID: 34845256 PMCID: PMC8629979 DOI: 10.1038/s41598-021-02106-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/01/2021] [Indexed: 12/15/2022] Open
Abstract
HLA-G is a promiscuous immune checkpoint molecule. The HLA-G gene presents substantial nucleotide variability in its regulatory regions. However, it encodes a limited number of proteins compared to classical HLA class I genes. We characterized the HLA-G genetic variability in 4640 individuals from 88 different population samples across the globe by using a state-of-the-art method to characterize polymorphisms and haplotypes from high-coverage next-generation sequencing data. We also provide insights regarding the HLA-G genetic diversity and a resource for future studies evaluating HLA-G polymorphisms in different populations and association studies. Despite the great haplotype variability, we demonstrated that: (1) most of the HLA-G polymorphisms are in introns and regulatory sequences, and these are the sites with evidence of balancing selection, (2) linkage disequilibrium is high throughout the gene, extending up to HLA-A, (3) there are few proteins frequently observed in worldwide populations, with lack of variation in residues associated with major HLA-G biological properties (dimer formation, interaction with leukocyte receptors). These observations corroborate the role of HLA-G as an immune checkpoint molecule rather than as an antigen-presenting molecule. Understanding HLA-G variability across populations is relevant for disease association and functional studies.
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Affiliation(s)
- Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil.
- Department of Pathology, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, CEP: 18618970, Brazil.
| | - Bibiana S de Almeida
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, CEP: 14049-900, Brazil
- Laboratório Multiusuário de Estudos em Biologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
| | - Yara C N Muniz
- Departamento de Biologia Celular, Embriologia e Genética, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
| | - Nayane S B Silva
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil
| | - Marília R S Passos
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil
| | - Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil
| | - Abigail E Page
- Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark Dyble
- Departament of Anthropology, University College London (UCL), London, UK
| | - Daniel Smith
- Bristol Medical School (PHS), University of Bristol, Bristol, UK
| | - Gabriela Aguileta
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaume Bertranpetit
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Andrea B Migliano
- Departament of Anthropology, Unversity of Zurich, Zurich, Switzerland
| | - Yeda A O Duarte
- Escola de Enfermagem e Faculdade de Saúde Pública, Universidade de São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Marília O Scliar
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Jaqueline Wang
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, State of São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, SP, Brazil
| | - Eduardo A Donadi
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, CEP: 14049-900, Brazil.
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10
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Arnaiz-Villena A, Juarez I, Suarez-Trujillo F, López-Nares A, Vaquero C, Palacio-Gruber J, Martin-Villa JM. HLA-G: Function, polymorphisms and pathology. Int J Immunogenet 2020; 48:172-192. [PMID: 33001562 DOI: 10.1111/iji.12513] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/04/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
Abstract
HLA-G immune modulatory genes and molecules are presently being studied by a widespread number of research groups. In the present study, we do not aim to be exhaustive since the number of manuscripts published every year is overwhelming. Instead, our aim is pointing out facts about HLA-G function, polymorphism and pathology that have been confirmed by several different researchers, together with exposing aspects that may have been overlooked or not sufficiently remarked in this productive field of study. On the other hand, we question whether performing mainly studies on HLA-G and disease associations is going to give a clear answer in the future, since 40 years of study of classical HLA molecules association with disease has still given no definite answer on this issue.
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Affiliation(s)
- Antonio Arnaiz-Villena
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Ignacio Juarez
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Fabio Suarez-Trujillo
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Adrián López-Nares
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Christian Vaquero
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Jose Palacio-Gruber
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Jose M Martin-Villa
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
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