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Liu C, Zhang L, Chen J, Gao Y. Targeted capture enrichment and sequencing identifies HLA variants associated with the severity of COVID-19. Genes Genomics 2023; 45:451-456. [PMID: 36574143 PMCID: PMC9793816 DOI: 10.1007/s13258-022-01358-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is currently a global pandemic. The pathogenesis of severe COVID-19 has been widely investigated, but it is still unclear. Human leukocyte antigen (HLA) plays a central role in immune response, and its variants might be related to COVID-19 progression and severity. OBJECTIVE To investigate the hypothesis that individual HLA variations could alter the course of COVID-19 and might be associated with the severity of COVID-19. METHODS In this study, we conducted an HLA targeted capture enrichment and sequencing of severe COVID-19 patients matched to mild cases. A total of 16 COVID-19 patients, confirmed by SARS-CoV-2 viral RNA polymerase-chain-reaction (PCR) test and chest computed tomography (CT) scan, were enrolled in this study. The HLA targeted capture enrichment and sequencing were conducted. HLA typing was performed by comparing contigs with IPD-IMGT/HLA Database. RESULTS In this study, 139 four-digit resolution HLA alleles were acquired. The results showed that HLA-DRB3*01:01 allele was significantly associated with the severity of COVID-19 (odds ratio [OR] = 27.64, 95% confidence interval [CI] = 1.35-560.50, P = 0.0064). And HLA-K*01:01 might be a potential risk factor for COVID-19 severity (OR = 0.11, 95% CI = 0.017-0.66, P = 0.019), but HLA-K*01:02 might be a protective factor (OR = 7.50, 95% CI = 1.48-37.92, P = 0.019). CONCLUSION Three non-classical HLA alleles, including HLA-DRB3*01:01, HLA-K*01:01, HLA-K*01:02 were identified to be associated with the severity of COVID-19 by comparing mild and severe patients. The current findings would be helpful for exploring the influence of HLA gene polymorphisms on the development and severity of COVID-19.
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Affiliation(s)
- Chuanmiao Liu
- Department of Infectious Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
- National Clinical Research Center for Infectious Diseases, First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
| | - Li Zhang
- Department of Infectious Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
- National Clinical Research Center for Infectious Diseases, First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
| | - Jiasheng Chen
- Department of Infectious Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
- National Clinical Research Center for Infectious Diseases, First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
| | - Yu Gao
- School of Life Science, Bengbu Medical College, Bengbu, China.
- Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, Bengbu, China.
- School of Life Science, Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, China.
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Nourié N, Nassereddine H, Mouawad S, Chebbou L, Ghaleb R, Abbas F, Azar H. Late antibody-mediated rejection in a kidney transplant recipient: COVID 19 induced? BMC Nephrol 2022; 23:91. [PMID: 35247969 PMCID: PMC8897769 DOI: 10.1186/s12882-022-02713-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/21/2022] [Indexed: 12/13/2022] Open
Abstract
Abstract
Background
Antibody-mediated rejection (AMR) was described in kidney transplant patients after viral infections, such as the cytomegalovirus. Very few cases were recently reported after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, probably in the context of lowering of immunosuppressive therapy. To date, no direct immunological link was proved to explain a connection between the coronavirus disease 19 (COVID-19) infection and antibody-mediated rejection (AMR) if it exists.
Case presentation
Here we try to find this association by presenting the case of a low immunological risk patient who presented, six years post-transplant, with c4d negative antibody mediated rejection due to an anti-HLA-C17 de novo donor specific antibody (DSA) after contracting the coronavirus disease 19.
The HLA-Cw17 activated the antibody-dependent cell-mediated cytotoxicity via the KIR2DS1 positive NK cells.
Discussion and conclusions
This case report may
prove a direct role for COVID-19 infection in AMRs in the kidney transplant
recipients, leading us to closely monitor kidney transplant recipients,
especially if they have “at-risk” donor antigens.
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Michel Wolf J, Zingalli Bueno Pereira VR, Zanetti Ballardin Roncato PA, Castagna Wortmann A, Stumm GZ, Oliveira da Silva F, Lunge VR, Simon D. The HLA-G 14-bp insertion/deletion polymorphism is associated with chronic hepatitis B in Southern Brazil: A case-control study. Hum Immunol 2020; 81:79-84. [PMID: 31955869 DOI: 10.1016/j.humimm.2020.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/08/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022]
Abstract
There is growing evidence that the non-classical HLA-G has a role in the process of the immune response against pathogens, including HBV and HIV. Previous studies demonstrated that a 14-bp insertion/deletion (indel) polymorphism at 3'-untranslated region of HLA-G gene interferes in the mRNA stability and expression. The present study aimed to evaluate the association of the 14-bp indel polymorphism (rs371194629) with HBV infection in chronic hepatitis B (CHB) mono-infected and HBV/HIV co-infected patients from Southern Brazil. A total of 817 individuals were analyzed, including 357 CHB patients, 134 HBV/HIV co-infected patients and 326 healthy controls. The 14-bp indel polymorphism was analyzed by DNA amplification using PCR. Logistic regression models were performed to compute adjusted odds ratios (aORs) and 95% confidence intervals (95% CIs). To control for multiple comparisons, the Bonferroni correction was applied to the p-values. The 14-bp Ins allele was observed in 47.6% of the CHB mono-infected patients and in 41.6% of the controls (aOR = 1.33; 95% CI: 1.05-1.60; p = 0.02; pcorrected = 0.08). The results also showed that the 14-bp Ins/Ins genotype was present in 21.8% of the CHB mono-infected patients and in 12.9% of the controls (aOR = 1.91; 95% CI: 1.21-3.01; p < 0.01; pcorrected = 0.02). There was significant association between the 14-bp indel and CHB monoinfection, but not in HBV/HIV co-infection. In conclusion, the 14-bp indel polymorphism was associated with CHB in this specific population.
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Abstract
Human leukocyte antigens (HLAs) play various critical roles in both innate and adaptive immunity through processes such as presenting antigens to T cells and serving as ligands for receptors expressed on natural killer (NK) cells. Among the HLA class I family, the clinical significance and biological function of HLA-F have been the least investigated and have remained elusive for a long period of time. Previous studies have revealed that HLA-F expression might be involved in various physiological and pathological processes, such as pregnancy, viral infection, cancer, transplantation, and autoimmune diseases. However, recent data have shown that, akin to other HLA family members, HLA-F molecules can interact with both activating and inhibitory receptors on immune cells, such as NK cells, and can present a diverse panel of peptides. These important findings pave new avenues for investigations regarding the functions of HLA-F as an important immune regulatory molecule. In the present review, we summarize the studies on the role of HLA-F in immune modulation, with a special emphasis placed on the roles of HLA-F and KIR3DS1 interactions in viral infection.
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Affiliation(s)
- Aifen Lin
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Wei-Hua Yan
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
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Liu J, Ye Z, Mayer JG, Hoch BA, Green C, Rolak L, Cold C, Khor SS, Zheng X, Miyagawa T, Tokunaga K, Brilliant MH, Hebbring SJ. Phenome-wide association study maps new diseases to the human major histocompatibility complex region. J Med Genet 2016; 53:681-9. [PMID: 27287392 DOI: 10.1136/jmedgenet-2016-103867] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/19/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Over 160 disease phenotypes have been mapped to the major histocompatibility complex (MHC) region on chromosome 6 by genome-wide association study (GWAS), suggesting that the MHC region as a whole may be involved in the aetiology of many phenotypes, including unstudied diseases. The phenome-wide association study (PheWAS), a powerful and complementary approach to GWAS, has demonstrated its ability to discover and rediscover genetic associations. The objective of this study is to comprehensively investigate the MHC region by PheWAS to identify new phenotypes mapped to this genetically important region. METHODS In the current study, we systematically explored the MHC region using PheWAS to associate 2692 MHC-linked variants (minor allele frequency ≥0.01) with 6221 phenotypes in a cohort of 7481 subjects from the Marshfield Clinic Personalized Medicine Research Project. RESULTS Findings showed that expected associations previously identified by GWAS could be identified by PheWAS (eg, psoriasis, ankylosing spondylitis, type I diabetes and coeliac disease) with some having strong cross-phenotype associations potentially driven by pleiotropic effects. Importantly, novel associations with eight diseases not previously assessed by GWAS (eg, lichen planus) were also identified and replicated in an independent population. Many of these associated diseases appear to be immune-related disorders. Further assessment of these diseases in 16 484 Marshfield Clinic twins suggests that some of these diseases, including lichen planus, may have genetic aetiologies. CONCLUSIONS These results demonstrate that the PheWAS approach is a powerful and novel method to discover SNP-disease associations, and is ideal when characterising cross-phenotype associations, and further emphasise the importance of the MHC region in human health and disease.
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Affiliation(s)
- Jixia Liu
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
| | - Zhan Ye
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
| | - John G Mayer
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
| | - Brian A Hoch
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
| | - Clayton Green
- Department of Dermatology, Marshfield Clinic, Marshfield, Wisconsin, USA
| | - Loren Rolak
- Department of Neurology, Marshfield Clinic, Marshfield, Wisconsin, USA
| | - Christopher Cold
- Department of Pathology, Marshfield Clinic, Marshfield, Wisconsin, USA
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Taku Miyagawa
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan Sleep Disorders Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Murray H Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
| | - Scott J Hebbring
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
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