scholarly journals Bioinformatic HLA Studies in the Context of SARS-CoV-2 Pandemic and Review on Association of HLA Alleles with Preexisting Medical Conditions

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Mina Mobini Kesheh ◽  
Sara Shavandi ◽  
Parastoo Hosseini ◽  
Rezvan Kakavand-Ghalehnoei ◽  
Hossein Keyvani

After the announcement of a new coronavirus in China in December 2019, which was then called SARS-CoV-2, this virus changed to a global concern and it was then declared as a pandemic by WHO. Human leukocyte antigen (HLA) alleles, which are one of the most polymorphic genes, play a pivotal role in both resistance and vulnerability of the body against viruses and other infections as well as chronic diseases. The association between HLA alleles and preexisting medical conditions such as cardiovascular diseases and diabetes mellitus is reported in various studies. In this review, we focused on the bioinformatic HLA studies to summarize the HLA alleles which responded to SARS-CoV-2 peptides and have been used to design vaccines. We also reviewed HLA alleles that are associated with comorbidities and might be related to the high mortality rate among COVID-19 patients. Since both genes and patients’ medical conditions play a key role in both severity of the disease and the mortality rate in COVID-19 patients, a better understanding of the connection between HLA alleles and SARS-CoV-2 can provide a wider perspective on the behavior of the virus. Such understanding can help scientists, especially in terms of protecting healthcare workers and designing effective vaccines.

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 951 ◽  
Author(s):  
Wolfram Hoetzenecker ◽  
Tarun Mehra ◽  
Ieva Saulite ◽  
Martin Glatz ◽  
Peter Schmid-Grendelmeier ◽  
...  

Toxic epidermal necrolysis (TEN) is a rare, life-threatening drug-induced skin disease with a mortality rate of approximately 30%. The clinical hallmark of TEN is a marked skin detachment caused by extensive keratinocyte cell death associated with mucosal involvement. The exact pathogenic mechanism of TEN is still uncertain. Recent advances in this field have led to the identification of several factors that might contribute to the induction of excessive apoptosis of keratinocytes. In addition, specific human leukocyte antigen types seem to be associated with certain drugs and the development of TEN. As well-controlled studies are lacking, patients are treated with various immunomodulators (e.g. intravenous immunoglobulin) in addition to the best supportive care.


2008 ◽  
Vol 68 (1) ◽  
pp. 107-109 ◽  
Author(s):  
K A Guthrie ◽  
N R Tishkevich ◽  
J L Nelson

Objectives:Some patients with rheumatoid arthritis (RA) lack RA-associated human leukocyte antigen (HLA) alleles. Prior studies investigated non-inherited maternal HLA alleles (NIMA) in RA risk with conflicting results.Methods:We examined NIMA in a large cohort of families from the North American Rheumatoid Arthritis Consortium (NARAC).Results:Among 620 patients with 1 or both parents having a HLA genotype, patients with RA informative for analysis included 176 without HLA-DRB1*04 and 86 without the HLA shared epitope (SE). The frequency of NIMA encoding HLA-DR4 or the SE was compared to the non-inherited paternal allele (NIPA). DR4-encoding NIMA vs NIPA revealed no significant difference (27% vs 20%). However, parity is known to modulate RA risk and analyses stratified by sex and age of onset showed significant variation among women. Interestingly, among women with onset <45 years DR4-encoding NIMA was increased compared to NIPA; among women ⩾45 years at onset the reverse was observed (31% vs 16% compared to 10% vs 60%, p = 0.008). DR4 encoding NIMA vs NIPA did not differ in men. The SE did not differ in men or women.Conclusions:Risk of RA was associated with HLA-DR4 encoding NIMA in younger-onset women but not in older-onset women or men. These observations could help explain conflicting prior results of NIMA in RA.


2019 ◽  
Vol 72 (1-2) ◽  
pp. 119-129 ◽  
Author(s):  
Kirsten Geneugelijk ◽  
Eric Spierings

AbstractHuman leukocyte antigen (HLA) mismatches between donors and recipients may lead to alloreactivity after solid organ transplantation. Over the last few decades, our knowledge of the complexity of the HLA system has dramatically increased, as numerous new HLA alleles have been identified. As a result, the likelihood of alloreactive responses towards HLA mismatches after solid organ transplantation cannot easily be assessed. Algorithms are promising solutions to estimate the risk for alloreactivity after solid organ transplantation. In this review, we show that the recently developed PIRCHE-II (Predicted Indirectly ReCognizable HLA Epitopes) algorithm can be used to minimize alloreactivity towards HLA mismatches. Together with the use of other algorithms and simulation approaches, the PIRCHE-II algorithm aims for a better estimated alloreactive risk for individual patients and eventually an improved graft survival after solid organ transplantation.


2020 ◽  
Vol 245 (9) ◽  
pp. 815-822
Author(s):  
Kwesi Z Tandoh ◽  
Kwadwo A Kusi ◽  
Timothy N Archampong ◽  
Isaac Boamah ◽  
Osbourne Quaye

Chronic hepatitis B infection is an important medical problem in sub-Saharan Africa. With increasing concerns of dwindling access to needed care, increasing cost of treatment, and rising prevalence of dire outcomes like liver cirrhosis and hepatocellular cancer, the need to determine the genetic associations underpinning hepatitis B virus persistence or clearance in a population comes to the fore. Genetic association studies have suggested a variation in human leukocyte antigen alleles associated with hepatitis B virus outcome along geo-ethnic lines. We investigated the association of human leukocyte antigen alleles to hepatitis B virus outcome against this backdrop. We used targeted next generation sequencing to type the human leukocyte antigen class I and II alleles of 173 study participants. These comprised of 92 cases with chronic hepatitis B infection and 81 healthy controls with serological evidence of naturally cleared hepatitis B virus infection. We have identified human leukocyte antigen alleles associated with hepatitis B virus clearance and persistence for the first time in a Ghanaian population. The class 1 allele C*16:01 (odds ratio (OR) = 3.4, confidence interval (CI) = 1.6–7.0, P-value = 0.01) was associated with hepatitis B virus persistence. Four class I alleles and one class II allele: A*34:02 (OR = 0.1, CI = 0.04–0.2, P-value = 3.4e-05), A*74:01 (OR = 0.3, CI = 0.2–0.7, P-value = 0.0135), B*13:02 (OR = 0.04, CI = 0.01–0.2, P-value = 0.000172), C*08:04 (OR = 0.06, CI = 0.01–0.2, P-value = 7.83e-05), and DRB1*08:04 (OR = 0.2, CI = 0.03–0.27, P-value = 0.000252) were associated with hepatitis B virus clearance. Our data show that previously reported human leukocyte antigen alleles associations to hepatitis B virus outcome are not found in this Ghanaian study. This study has therefore identified human leukocyte antigen types that are associated with either hepatitis B virus persistence or clearance and highlights the importance of geo-ethnic pivoted studies in determining the genetic associations to acute hepatitis B virus infection outcome. Impact statement Genetic association studies can determine the effect size of gene loci on disease outcomes. In the arena of HBV infections, HLA alleles that associate with HBV outcomes can be used in clinical management decisions. This potential translational utility can shape the future management of HBV infections by identifying at-risk individuals and tailoring medical interventions accordingly. This precision medicine motif is currently only a nascent idea. However, it has stakes that may well override the current “wait and see” approach of clinical management of HBV infections. Here, we have identified HLA alleles associated with HBV outcome in a Ghanaian cohort. Our findings support the motif that HLA alleles associate with HBV outcome along geo-ethnic lines. This buttresses the need for further population pivoted studies. In the long term, our findings add to efforts towards the development of an HLA molecular-based algorithm for predicting HBV infection outcomes.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 3491-3491
Author(s):  
Basem M William ◽  
Tao Wang ◽  
Michael D Haagenson ◽  
Marcos J de Lima ◽  
Marcelo Anibal Fernandez-Vina ◽  
...  

Abstract Even in the modern era of targeted therapies, allo-HCT remains a strategy that offers a chance of extended survival in B-NHL who relapsed after, or are deemed ineligible for, autologous transplantation (auto-HCT). Moreover, it was shown that efficacy of auto-HCT in extending survival in patients with diffuse large B-cell lymphoma is limited in the post-rituximab era. The use of allo-HCT for salvage of relapsed/refractory B-NHL is likely to increase with the wide adoption of reduced intensity conditioning (RIC) since transplant-related mortality (TRM) is lower while preserving the benefit of graft vs lymphoma (GVL) effect. Further understanding of the factors likely to predict a more robust GVL response, and potentially better clinical outcomes, would be very useful in selecting patients with B-NHL who are likely to benefit from allo-HCT. Multiple prior studies have shown that the presence of certain human leukocyte antigen (HLA) alleles may be instrumental in modulating the outcomes of B-NHL after immunochemotherapy and/or allo-HCT. We hypothesized that certain HLA alleles may have superior ability to present antigens to cytotoxic T-cells or possibly modulate natural killer (NK) cell activity. We undertook a retrospective analysis of CIBMTR data to evaluate whether the presence of HLA-A2, HLA-C1C1, HLA-DRB1*01:01 or HLA-DRB1*13 alleles and HLA-A1+, HLA-A2- and HLA-B44- haplotypes were associated with outcomes of patients with relapsed/refractory B-NHL after transplantation from HLA-8/8 matched sibling (MRD) or unrelated (MUD) donors. The primary outcome was time to progression. Secondary outcomes included progression-free (PFS) and overall survival (OS), TRM, and incidence and severity of acute and chronic graft versus host disease (GVHD). Multivariate analyses were performed using Cox proportional hazards models adjusting for multiple disease and transplant related characteristics. HLA-A*02 was tested individually; HLA-DRB1*0101 and HLA-DRB1*13 were tested in 4 combinations; HLA-A1+/A2-, B44- vs. A2+ vs. neither. Because of multiple comparisons, p<0.01 is considered significant. The final analysis population was restricted to 1314 patients who received the first allo-HCT during the years of 1995-2012 for indolent (N=506), aggressive (N=514), and mantle (N=294) B-NHLs from MRD (N=708) or MUD (N=606) utilizing myeloablative; MA (N=636), RIC (N=434), non-myeloablative; NMA (N=196) or other (n=48) conditioning. The different HLA allele analysis groups were well-balanced for all disease, patient, transplant and donor characteristics. In multi-variate analysis, we have observed no significant association between any of the HLA alleles or combinations we tested with any of the primary or the secondary end-points. A power calculation suggested very large numbers would be needed to reach statistical significant based on the data analyzed so far. The marked heterogeneity of different lymphoma subtypes, conditioning regimens, donor choices, GVHD prophylaxis, supportive regimens or other center-related characteristics likely limited the ability to detect effects of differences in individual recipient HLA alleles. In conclusion, this study represents the largest reported series of allo-HCT outcomes of B-cell NHL patients based on HLA type. Further study of other variables will be required to delineate the immunologic impact of donor-host interactions on outcomes of allo-HCT for B-cell NHL. Disclosures No relevant conflicts of interest to declare.


2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Mette Dahl ◽  
Snezana Djurisic ◽  
Thomas Vauvert F. Hviid

Pregnancy is an immunological paradox, where fetal antigens encoded by polymorphic genes inherited from the father do not provoke a maternal immune response. The fetus is not rejected as it would be theorized according to principles of tissue transplantation. A major contribution to fetal tolerance is the human leukocyte antigen (HLA)-G, a nonclassical HLA protein displaying limited polymorphism, restricted tissue distribution, and a unique alternative splice pattern. HLA-G is primarily expressed in placenta and plays multifaceted roles during pregnancy, both as a soluble and a membrane-bound molecule. Its immunomodulatory functions involve interactions with different immune cells and possibly regulation of cell migration during placental development. Recent findings include HLA-G contributions from the father and the fetus itself. Much effort has been put into clarifying the role of HLA-G during pregnancy and pregnancy complications, such as preeclampsia, recurrent spontaneous abortions, and subfertility or infertility. This review aims to clarify the multifunctional role of HLA-G in pregnancy-related disorders by focusing on genetic variation, differences in mRNA stability betweenHLA-Galleles, differences in HLA-G isoform expression, and possible differences in functional activity. Furthermore, we highlight important observations regardingHLA-Ggenetics and expression in preeclampsia that future research should address.


2017 ◽  
Author(s):  
Antti Larjo ◽  
Robert Eveleigh ◽  
Elina Kilpeläinen ◽  
Tony Kwan ◽  
Tomi Pastinen ◽  
...  

AbstractThe human leukocyte antigen (HLA) genes code for proteins that play a central role in the function of the immune system by presenting peptide antigens to T cells. As HLA genes show extremely high genetic polymorphism, HLA typing on the allele level is demanding and is based on DNA sequencing. Determination of HLA alleles is warranted as many HLA alleles are major genetic factors that confer susceptibility to autoimmune diseases and is important for the matching of HLA alleles in transplantation. Here, we compared the accuracy of several published HLA-typing algorithms that are based on next generation sequencing (NGS) data. As genome screens are becoming increasingly routine in research, we wanted to test how well HLA alleles can be deduced from genome screens not designed for HLA typing. The accuracies were assessed using datasets consisting of NGS data produced using the ImmunoSEQ platform, including the full 4 Mbp HLA segment, from 94 stem cell transplantation patients and exome sequences from the 1000 Genomes collection. When used with the default settings none of the methods gave perfect results for all the genes and samples. However, we found that ensemble prediction of the results or modifications of the settings could be used to improve accuracy. Most of the algorithms did not perform very well for the exome-only data. The results indicate that the use of these algorithms for accurate HLA allele determination based on NGS data is not straightforward.


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