HLA in North Colombia Chimila Amerindians

Arnaiz‐Villena, Antonio; Palacio-Grüber, José; Juárez, Ignacio; Hernández, Ennio; Muñiz, Ester; Bayona, Brayan; Campos, Cristina; Nieto, Jorge Martínez-Pinna; Martin-Villa, José Manuel; Silvera, Carlos

doi:10.1016/j.humimm.2018.02.004

Cited by 7 publications

(3 citation statements)

References 6 publications

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“…The dataset of HLA I alleles used for epitope prediction included: (1) HLA-A, HLA-B and HLA-C alleles that presented the top ten highest frequencies in the Colombian general population (Dataset: Colombia-Bogotá). As well as, (2) the HLA-A, HLA-B and HLA-C alleles that exhibited the highest frequency for each of the eleven Colombian Amerindian groups with HLA I frequencies reported in the AFND [28], which coincided with the results of the literature search [29][30][31]. These Amerindian groups were: Arhuaco, Embera, Inga, Kogi, Chimila Norte, Wiwa Norte, Waunana, Wayyu, Zenú, Ticuna Arara, and Ticuna Tarapaca.…”

Section: Hlas Selection For Epitope Predictionsupporting

confidence: 69%

Bioinformatics Prediction of SARS-CoV-2 Epitopes as Vaccine Candidates for the Colombian Population

Montes-Grajales

Olívero-Verbel

2021

Vaccines

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Coronavirus disease (COVID-19) pandemic caused by the coronavirus SARS-CoV-2 represents an enormous challenge to global public health, with thousands of infections and deaths in over 200 countries worldwide. The purpose of this study was to identify SARS-CoV-2 epitopes with potential to interact in silico with the alleles of the human leukocyte antigen class I (HLA I) and class II (HLA II) commonly found in the Colombian population to promote both CD4 and CD8 immune responses against this virus. The generation and evaluation of the peptides in terms of HLA I and HLA II binding, immune response, toxicity and allergenicity were performed by using computer-aided tools, such as NetMHCpan 4.1, NetMHCIIpan 4.0, VaxiJem, ToxinPred and AllerTop. Furthermore, the interaction between the predicted epitopes with HLA I and HLA II proteins frequently found in the Colombian population was studied through molecular docking simulations in AutoDock Vina and interaction analysis in LigPlot+. One of the promising peptides proposed in this study is the HLA I epitope YQPYRVVVL, which displayed an estimated coverage of over 82% and 96% for the Colombian and worldwide population, respectively. These findings could be useful for the design of new epitope-vaccines that include Colombia among their population target.

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Section: Hlas Selection For Epitope Predictionsupporting

confidence: 69%

Bioinformatics Prediction of SARS-CoV-2 Epitopes as Vaccine Candidates for the Colombian Population

Montes-Grajales

Olívero-Verbel

2021

Vaccines

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“…Four of our 8 LFD alleles (A*68:16, A*68:23, B*35:09, DQB1*03:25) have been documented to date exclusively in South or Central American Native populations. In addition to the description of a respective unique occurrence in a Chilean Huiliche population ( 9 ), A*68:16 and A*68:23 were found in Chilean Mapuche ( 23 ) and in Chimila Amerindians of Colombia ( 49 ). Another study, whose results are not documented in AFND, reported the finding of allele A*68:23 in a cohort of n =559 Chileans from Santiago with a frequency of f >0.0125 ( 43 ).…”

Section: Discussionmentioning

confidence: 92%

HLA allele and haplotype frequencies of registered stem cell donors in Chile

Solloch,

Giani,

Pattillo Garnham

et al. 2023

Front. Immunol.

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Patients in need of hematopoietic stem cell transplantation often rely on unrelated stem cell donors matched in certain human leukocyte antigen (HLA) genes. Donor search is complicated by the extensive allelic variability of the HLA system. Therefore, large registries of potential donors are maintained in many countries worldwide. Population-specific HLA characteristics determine the registry benefits for patients and also the need for further regional donor recruitment. In this work, we analyzed HLA allele and haplotype frequencies of donors of DKMS Chile, the first Chilean donor registry, with self-assessed “non-Indigenous” (n=92,788) and “Mapuche” (n=1,993) ancestry. We identified HLA alleles that were distinctly more abundant in the Chilean subpopulations than in worldwide reference populations, four of them particularly characteristic for the Mapuche subpopulation, namely B*39:09g, B*35:09, DRB1*04:07g, and DRB1*16:02g. Both population subsamples carried haplotypes of both Native American and European origin at high frequencies, reflecting Chile’s complex history of admixture and immigration. Matching probability analysis revealed limited benefits for Chilean patients (both non-Indigenous and Mapuche) from donor registries of non-Chilean donors, thus indicating a need for ongoing significant donor recruitment efforts in Chile.

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“…Remarkably, an important proportion of African MPA haplotypes were found, encompassing 11 out of 52 (21.1%) three-loci haplotypes previously described in high relative frequency in the following Black populations: A*30:02–C*08:02–B*14:02 in Brazil [Brazil Rio de Janeiro Black and Parda populations in reference ( 48 )], in Luo Tribe in Kenya (Nyanza Province) ( 79 ), and in South Africa ( 80 ); A*02:01–C*08:02–B*14:02 in Brazil [Barra Mansa Rio State Black in reference ( 48 )] and in Uganda Kampala population ( 81 ); A*23:01–C*06:02–B*45:01 in South Africa ( 82 ) and in Luo Tribe (Kenya) ( 79 ); A*23:01–C*18:01–B*81:01 in Costa Rica African-Caribbeans ( 67 ) and in Tanzania Massai population [defined in reference ( 48 )]; A*74:01–C*02:10–B*15:03 in Luo Tribe in Kenia ( 79 ) and in Amerindians from Colombia (North Chimila) ( 83 ); A*30:01–C*18:01–B*81:01 in Luo Tribe in Kenia ( 79 ) and in USA African Americans ( 84 ); A*74:01–C*04:01–B*53:01 in admixed population from Brazil (Vale do Ribera Quilombos) ( 77 ) and in Rio de Janeiro Parda (Brazil) [described in reference ( 48 )]; among others.…”

Section: Discussionmentioning

confidence: 99%

Honduras HIV cohort: HLA class I and CCR5-Δ32 profiles and their associations with HIV disease outcome

Valenzuela-Ponce,

Carbajal,

Soto-Nava

et al. 2023

Microbiol Spectr

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Human leukocyte antigen (HLA) polymorphisms represent the strongest genetic modifier of HIV disease progression. Diverse HLA distributions can lead to distinct HIV control landscapes at the population level. We aimed to describe HLA allele and haplotype frequencies (linkage disequilibrium, LD), CCR5-Δ32 frequency, and the impact of these variants on HIV disease outcome. HLA class I loci were typed at 4-digit resolution, and CCR5 variants were determined in 402 HIV clade B-infected, antiretroviral treatment-naïve individuals from Honduras. HLA LD was assessed using Fisher’s exact test. Using univariable and multivariable analyses, we evaluated HLA associations with HIV plasma viral load (pVL) and CD4 counts. We did not find any effect on HIV control between CCR5 genotypes. The previously defined HLA associations were found to be B*57:01/03 , B*42:01 , A*25:01 , and C*12:03 (protective) and B*53:01 and A*68:01 (risk). Consistent with our previous research in a Mesoamerican HIV cohort, Amerindian B*35:12 was associated with poor HIV control. Other HLA-HIV associations not previously described were C*03:04 and B*08:01 , which were associated with higher pVL. Overall, this first report highlights the immunogenetic uniqueness of the Honduras population that expresses Amerindian, Caucasian, and African HLA subtypes. These findings not only support this cohort as ideal for identifying HLA correlates of HIV control but also may improve future research regarding allotransplantation and disease association. IMPORTANCE We identify both canonical and novel human leukocyte antigen (HLA)-HIV associations, providing a first step toward improved understanding of HIV immune control among the understudied Honduras Mestizo population. Our results are relevant to understanding the protective or detrimental effects of HLA subtypes in Latin America because their unique HLA diversity poses challenges for designing vaccines against HIV and interpreting results from such vaccine trials. Likewise, the description of the HLA profile in an understudied population that shows a unique HLA immunogenetic background is not only relevant for HIV immunology but also relevant in population genetics, molecular anthropology, susceptibility to other infections, autoimmune diseases, and allograft transplantation.

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HLA in North Colombia Chimila Amerindians

Cited by 7 publications

References 6 publications

Bioinformatics Prediction of SARS-CoV-2 Epitopes as Vaccine Candidates for the Colombian Population

Bioinformatics Prediction of SARS-CoV-2 Epitopes as Vaccine Candidates for the Colombian Population

HLA allele and haplotype frequencies of registered stem cell donors in Chile

Honduras HIV cohort: HLA class I and CCR5-Δ32 profiles and their associations with HIV disease outcome

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