1
|
Lyn Fortier A, Pritchard JK. The Primate Major Histocompatibility Complex: An Illustrative Example of Gene Family Evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.613318. [PMID: 39345418 PMCID: PMC11429698 DOI: 10.1101/2024.09.16.613318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Gene families are groups of evolutionarily-related genes. One large gene family that has experienced rapid evolution is the Major Histocompatibility Complex (MHC), whose proteins serve critical roles in innate and adaptive immunity. Across the ~60 million year history of the primates, some MHC genes have turned over completely, some have changed function, some have converged in function, and others have remained essentially unchanged. Past work has typically focused on identifying MHC alleles within particular species or comparing gene content, but more work is needed to understand the overall evolution of the gene family across species. Thus, despite the immunologic importance of the MHC and its peculiar evolutionary history, we lack a complete picture of MHC evolution in the primates. We readdress this question using sequences from dozens of MHC genes and pseudogenes spanning the entire primate order, building a comprehensive set of gene and allele trees with modern methods. Overall, we find that the Class I gene subfamily is evolving much more quickly than the Class II gene subfamily, with the exception of the Class II MHC-DRB genes. We also pay special attention to the often-ignored pseudogenes, which we use to reconstruct different events in the evolution of the Class I region. We find that despite the shared function of the MHC across species, different species employ different genes, haplotypes, and patterns of variation to achieve a successful immune response. Our trees and extensive literature review represent the most comprehensive look into MHC evolution to date.
Collapse
Affiliation(s)
- Alyssa Lyn Fortier
- Department of Biology, Stanford University, Stanford, CA USA
- Department of Genetics, Stanford University, Stanford, CA USA
| | - Jonathan K. Pritchard
- Department of Biology, Stanford University, Stanford, CA USA
- Department of Genetics, Stanford University, Stanford, CA USA
| |
Collapse
|
2
|
Al-kaabi M, Deshpande P, Firth M, Pavlos R, Chopra A, Basiri H, Currenti J, Alves E, Kalams S, Fellay J, Phillips E, Mallal S, John M, Gaudieri S. Epistatic interaction between ERAP2 and HLA modulates HIV-1 adaptation and disease outcome in an Australian population. PLoS Pathog 2024; 20:e1012359. [PMID: 38980912 PMCID: PMC11259285 DOI: 10.1371/journal.ppat.1012359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 07/19/2024] [Accepted: 06/19/2024] [Indexed: 07/11/2024] Open
Abstract
A strong genetic predictor of outcome following untreated HIV-1 infection is the carriage of specific alleles of human leukocyte antigens (HLAs) that present viral epitopes to T cells. Residual variation in outcome measures may be attributed, in part, to viral adaptation to HLA-restricted T cell responses. Variants of the endoplasmic reticulum aminopeptidases (ERAPs) influence the repertoire of T cell epitopes presented by HLA alleles as they trim pathogen-derived peptide precursors to optimal lengths for antigen presentation, along with other functions unrelated to antigen presentation. We investigated whether ERAP variants influence HLA-associated HIV-1 adaptation with demonstrable effects on overall HIV-1 disease outcome. Utilizing host and viral data of 249 West Australian individuals with HIV-1 subtype B infection, we identified a novel association between two linked ERAP2 single nucleotide polymorphisms (SNPs; rs2248374 and rs2549782) with plasma HIV RNA concentration (viral load) (P adjusted = 0.0024 for both SNPs). Greater HLA-associated HIV-1 adaptation in the HIV-1 Gag gene correlated significantly with higher viral load, lower CD4+ T cell count and proportion; P = 0.0103, P = 0.0061, P = 0.0061, respectively). When considered together, there was a significant interaction between the two ERAP2 SNPs and HLA-associated HIV-1 adaptation on viral load (P = 0.0111). In a comprehensive multivariate model, addition of ERAP2 haplotypes and HLA associated adaptation as an interaction term to known HLA and CCR5 determinants and demographic factors, increased the explanatory variance of population viral load from 17.67% to 45.1% in this dataset. These effects were not replicated in publicly available datasets with comparably sized cohorts, suggesting that any true global epistasis may be dependent on specific HLA-ERAP allelic combinations. Our data raises the possibility that ERAP2 variants may shape peptide repertoires presented to HLA class I-restricted T cells to modulate the degree of viral adaptation within individuals, in turn contributing to disease variability at the population level. Analyses of other populations and experimental studies, ideally with locally derived ERAP genotyping and HLA-specific viral adaptations are needed to elucidate this further.
Collapse
Affiliation(s)
- Marwah Al-kaabi
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Pooja Deshpande
- School of Human Sciences, University of Western Australia, Crawley, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Martin Firth
- School of Physics, Mathematics and Computing, Department of Mathematics and Statistics, University of Western Australia, Crawley, Australia
| | - Rebecca Pavlos
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Hamed Basiri
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Jennifer Currenti
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Eric Alves
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Spyros Kalams
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss HIV Cohort Study, Zurich, Switzerland
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Mina John
- School of Human Sciences, University of Western Australia, Crawley, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Australia
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| |
Collapse
|
3
|
Robinson J, Barker DJ, Marsh SGE. 25 years of the IPD-IMGT/HLA Database. HLA 2024; 103:e15549. [PMID: 38936817 DOI: 10.1111/tan.15549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/03/2024] [Accepted: 05/16/2024] [Indexed: 06/29/2024]
Abstract
Twenty-five years ago, in 1998, the HLA Informatics Group of the Anthony Nolan Research Institute released the IMGT/HLA Database. Since this time, this online resource has acted as the repository for the numerous variant sequences of HLA alleles named by the WHO Nomenclature Committee for Factors of the HLA System. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this work. During this time, the technology underlying HLA typing has undergone significant changes. Next generation sequencing (NGS) has superseded previous methodologies of HLA typing and can generate large amounts of high-resolution sequencing data. This has resulted in a drastic increase in the number and complexity of sequences submitted to the database. The challenge for the IPD-IMGT/HLA Database has been to maintain the highest standards of curation, while supporting the core set of tools and functionality to our users with increased numbers of submissions and sequences. Traditional methods of accessing and presenting data have been challenged and new methods utilising new computing technologies have had to be developed to keep pace and support a shifting user demographic.
Collapse
Affiliation(s)
- James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
| | - Dominic J Barker
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
| |
Collapse
|
4
|
Ohta R, Tanigawa Y, Suzuki Y, Kellis M, Morishita S. A polygenic score method boosted by non-additive models. Nat Commun 2024; 15:4433. [PMID: 38811555 DOI: 10.1038/s41467-024-48654-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
Dominance heritability in complex traits has received increasing recognition. However, most polygenic score (PGS) approaches do not incorporate non-additive effects. Here, we present GenoBoost, a flexible PGS modeling framework capable of considering both additive and non-additive effects, specifically focusing on genetic dominance. Building on statistical boosting theory, we derive provably optimal GenoBoost scores and provide its efficient implementation for analyzing large-scale cohorts. We benchmark it against seven commonly used PGS methods and demonstrate its competitive predictive performance. GenoBoost is ranked the best for four traits and second-best for three traits among twelve tested disease outcomes in UK Biobank. We reveal that GenoBoost improves prediction for autoimmune diseases by incorporating non-additive effects localized in the MHC locus and, more broadly, works best in less polygenic traits. We further demonstrate that GenoBoost can infer the mode of genetic inheritance without requiring prior knowledge. For example, GenoBoost finds non-zero genetic dominance effects for 602 of 900 selected genetic variants, resulting in 2.5% improvements in predicting psoriasis cases. Lastly, we show that GenoBoost can prioritize genetic loci with genetic dominance not previously reported in the GWAS catalog. Our results highlight the increased accuracy and biological insights from incorporating non-additive effects in PGS models.
Collapse
Affiliation(s)
- Rikifumi Ohta
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
| | - Yosuke Tanigawa
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Yuta Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
| |
Collapse
|
5
|
Hafeez M, Mc Donnell R, Colton A, Howe D, Denver D, Martin RC, Choi MY. Immune-Related Gene Profiles and Differential Expression in the Grey Garden Slug Deroceras reticulatum Infected with the Parasitic Nematode Phasmarhabditis hermaphrodita. INSECTS 2024; 15:311. [PMID: 38786867 PMCID: PMC11122010 DOI: 10.3390/insects15050311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
The grey garden slug (Deroceras reticulatum), a common terrestrial slug native to Europe with a global distribution including North America, is commonly considered the most severe slug pest in agriculture. The nematode Phasmarhabditis hermaphrodita, which has been used in the U.K. and Europe as a commercial biocontrol agent since 1994, has also recently been collected in Oregon and California and has long been considered a candidate biocontrol agent for slug management in the U.S. In this study, we report differential gene expressions in nematode-infected slugs using RNA-seq to identify slug immune-related genes against nematodes. Comparison of gene expression levels between the whole bodies of a nematode-infected slug (N-S) and an uninfected control slug (C-S) revealed that there were a total of 39,380 regulated unigenes, of which 3084 (3%) were upregulated and 6761 (6%) were downregulated at greater than 2-fold change (FC > 2) in the nematode-infected slug. To further investigate the biological functions of differentially expressed genes (DEGs), gene ontology (GO) and functional enrichment analysis were performed to map the DEGs to terms in the GO, eukaryotic ortholog groups of proteins (KOG) and Kyoto Encyclopedia of Genes and Genome Pathway (KEGG) databases. Among these DEGs, approximately 228 genes associated with immunity or immune-related pathways were upregulated 2-fold or more in the N-S compared to C-S. These genes include toll, Imd, JNK, scavenger receptors (SCRs), C-type lectins (CTLs), immunoglobulin-like domains, and JAK/STAT63 signaling pathways. From the RNA-seq results, we selected 18 genes and confirmed their expression levels by qRT-PCR. Our findings provide insights into the immune response of slugs during nematode infection. These studies provide fundamental information that will be valuable for the development of new methods of pest slug control using pathogenic nematodes in the field.
Collapse
Affiliation(s)
- Muhammad Hafeez
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330, USA;
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA;
| | - Rory Mc Donnell
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA; (R.M.D.); (A.C.)
| | - Andrew Colton
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA; (R.M.D.); (A.C.)
| | - Dana Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA; (D.H.); (D.D.)
| | - Dee Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA; (D.H.); (D.D.)
| | - Ruth C. Martin
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA;
| | - Man-Yeon Choi
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330, USA;
| |
Collapse
|
6
|
OBrien SJ. Legacy of a magic gene- CCR5-∆32: From discovery to clinical benefit in a generation. Proc Natl Acad Sci U S A 2024; 121:e2321907121. [PMID: 38457490 PMCID: PMC10962972 DOI: 10.1073/pnas.2321907121] [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: 12/14/2023] [Accepted: 01/22/2024] [Indexed: 03/10/2024] Open
Abstract
The discovery of the 32-bp deletion allele of the chemokine receptor gene CCR5 showed that homozygous carriers display near-complete resistance to HIV infection, irrespective of exposure. Algorithms of molecular evolutionary theory suggested that the CCR5-∆32 mutation occurred but once in the last millennium and rose by strong selective pressure relatively recently to a ~10% allele frequency in Europeans. Several lines of evidence support the hypothesis that CCR5-∆32 was selected due to its protective influence to resist Yersinia pestis, the agent of the Black Death/bubonic plague of the 14th century. Powerful anti-AIDS entry inhibitors targeting CCR5 were developed as a treatment for HIV patients, particularly those whose systems had developed resistance to powerful anti-retroviral therapies. Homozygous CCR5-∆32/∆32 stem cell transplant donors were used to produce HIV-cleared AIDS patients in at least five "cures" of HIV infection. CCR5 has also been implicated in regulating infection with Staphylococcus aureus, in recovery from stroke, and in ablation of the fatal graft versus host disease (GVHD) in cancer transplant patients. While homozygous CCR5-∆32/32 carriers block HIV infection, alternatively they display an increased risk for encephalomyelitis and death when infected with the West Nile virus.
Collapse
Affiliation(s)
- Stephen J. OBrien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Ft Lauderdale, FL33004
- Indiana University School of Public Health, Bloomington, IN47405
| |
Collapse
|
7
|
Zheng T, Roda G, Zabana Y, Escudero-Hernández C, Liu X, Chen Y, Camargo Tavares L, Bonfiglio F, Mellander MR, Janczewska I, Vigren L, Sjöberg K, Ohlsson B, Almer S, Halfvarson J, Miehlke S, Madisch A, Lieb W, Kupčinskas J, Weersma RK, Bujanda L, Julià A, Marsal S, Esteve M, Guagnozzi D, Fernández-Bañares F, Ferrer C, Peter I, Ludvigsson JF, Pardi D, Verhaegh B, Jonkers D, Pierik M, Münch A, Franke A, Bresso F, Khalili H, Colombel JF, D'Amato M. Human Leukocyte Antigen Signatures as Pathophysiological Discriminants of Microscopic Colitis Subtypes. J Crohns Colitis 2024; 18:349-359. [PMID: 37768647 DOI: 10.1093/ecco-jcc/jjad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/29/2023] [Accepted: 09/26/2023] [Indexed: 09/29/2023]
Abstract
BACKGROUND AND AIMS Microscopic colitis [MC] is currently regarded as an inflammatory bowel disease that manifests as two subtypes: collagenous colitis [CC] and lymphocytic colitis [LC]. Whether these represent a clinical continuum or distinct entities is, however, an open question. Genetic investigations may contribute important insight into their respective pathophysiologies. METHODS We conducted a genome-wide association study [GWAS] meta-analysis in 1498 CC, 373 LC patients, and 13 487 controls from Europe and the USA, combined with publicly available MC GWAS data from UK Biobank and FinnGen [2599 MC cases and 552 343 controls in total]. Human leukocyte antigen [HLA] alleles and polymorphic residues were imputed and tested for association, including conditional analyses for the identification of key causative variants and residues. Genetic correlations with other traits and diagnoses were also studied. RESULTS We detected strong HLA association with CC, and conditional analyses highlighted the DRB1*03:01 allele and its residues Y26, N77, and R74 as key to this association (best p = 1.4 × 10-23, odds ratio [OR] = 1.96). Nominally significant genetic correlations were detected between CC and pneumonia [rg = 0.77; p = 0.048] and oesophageal diseases [rg = 0.45, p = 0.023]. An additional locus was identified in MC GWAS analyses near the CLEC16A and RMI2 genes on chromosome 16 [rs35099084, p = 2.0 × 10-8, OR = 1.31]. No significant association was detected for LC. CONCLUSION Our results suggest CC and LC have distinct pathophysiological underpinnings, characterised by an HLA predisposing role only in CC. This challenges existing classifications, eventually calling for a re-evaluation of the utility of MC umbrella definitions.
Collapse
Affiliation(s)
- Tenghao Zheng
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giulia Roda
- Biostructures and Biosystems National Institute, Rome, Italy
| | - Yamile Zabana
- Gastroenterology Department, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
| | - Celia Escudero-Hernández
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Xingrong Liu
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ye Chen
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Ferdinando Bonfiglio
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Lina Vigren
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Klas Sjöberg
- Department of Clinical Sciences, Lund University, Skane University Hospital, Malmo, Sweden
| | - Bodil Ohlsson
- Department of Clinical Sciences, Lund University, Skane University Hospital, Malmo, Sweden
| | - Sven Almer
- Division of Gastroenterology, Department of Gastroenterology, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Orebro University Hospital, Örebro, Sweden
| | - Stephan Miehlke
- Centre for Digestive Diseases, Internal Medicine Centre Eppendorf, and Centre for Oesophageal Disorders, University Hospital Eppendorf, Hamburg, Germany
| | - Ahmed Madisch
- Department of Gastroenterology, CRH Clinic Siloah, Hannover, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Juozas Kupčinskas
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Luis Bujanda
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, Universidad del País Vasco, San Sebastian, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall d' Hebron Research Institute, Barcelona, Spain
| | - Sara Marsal
- Rheumatology Research Group, Vall d' Hebron Research Institute, Barcelona, Spain
| | - Maria Esteve
- Gastroenterology Department, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
| | - Danila Guagnozzi
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
- Department of Gastroenterology, Vall d'Hebron University Hospital, Neuro-Immuno-Gastroenterology Group, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Fernando Fernández-Bañares
- Gastroenterology Department, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
| | - Carmen Ferrer
- Pathology Department, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonas F Ludvigsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Darrell Pardi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Bas Verhaegh
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Daisy Jonkers
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Marieke Pierik
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Andreas Münch
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Gastroenterology and Hepatology, Linköping University, Linköping, Sweden
- Department of Health, Medicine, and Caring Sciences, Linköping University, Linköping, Sweden
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Francesca Bresso
- Division of Gastroenterology, Department of Gastroenterology, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jean-Frederic Colombel
- Dr Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mauro D'Amato
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Gastrointestinal Genetics Lab, CIC bioGUNE - BRTA, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Department of Medicine and Surgery, LUM University, Casamassima, Italy
| |
Collapse
|
8
|
Bowman J, Lynch VJ. Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582135. [PMID: 38463968 PMCID: PMC10925141 DOI: 10.1101/2024.02.27.582135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Elephants have emerged as a model system to study the evolution of body size and cancer resistance because, despite their immense size, they have a very low prevalence of cancer. Previous studies have found that duplication of tumor suppressors at least partly contributes to the evolution of anti-cancer cellular phenotypes in elephants. Still, many other mechanisms must have contributed to their augmented cancer resistance. Here, we use a suite of codon-based maximum-likelihood methods and a dataset of 13,310 protein-coding gene alignments from 261 Eutherian mammals to identify positively selected and rapidly evolving elephant genes. We found 496 genes (3.73% of alignments tested) with statistically significant evidence for positive selection and 660 genes (4.96% of alignments tested) that likely evolved rapidly in elephants. Positively selected and rapidly evolving genes are statistically enriched in gene ontology terms and biological pathways related to regulated cell death mechanisms, DNA damage repair, cell cycle regulation, epidermal growth factor receptor (EGFR) signaling, and immune functions, particularly neutrophil granules and degranulation. All of these biological factors are plausibly related to the evolution of cancer resistance. Thus, these positively selected and rapidly evolving genes are promising candidates for genes contributing to elephant-specific traits, including the evolution of molecular and cellular characteristics that enhance cancer resistance.
Collapse
Affiliation(s)
- Jacob Bowman
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, 14260, USA
| | - Vincent J. Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, 14260, USA
| |
Collapse
|
9
|
Salim B, Nakao R, Chatanga E, Marcuzzi O, Eissawi MA, Almathen F, Hanotte O, Giovambattista G. Exploring genetic diversity and variation of Ovar-DRB1 gene in Sudan Desert Sheep using targeted next-generation sequencing. BMC Genomics 2024; 25:160. [PMID: 38331741 PMCID: PMC10851530 DOI: 10.1186/s12864-024-10053-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
INTRODUCTION The Ovar-DRB1 gene, a crucial element of the Major Histocompatibility Complex (MHC) Class II region, initiates adaptive immunity by presenting antigens to T-cells. Genetic diversity in sheep, particularly in MHC Class II genes like Ovar-DRB1, directly influences the specturm of presented antigens impacting immune responses and disease susceptability. Understanding the allelic diversity of Ovar-DRB1 gene in Sudan Desert Sheep (SDS) is essential for uncovering the genetic basis of immune responses and disease resistance, given the the breeds significance in Sudan's unique environment. METHODS Utilizing Targeted Next-Generation Sequencing (NGS) we explore allelic diversity in Ovar-DRB1 gene within SDS. Successfully ampliying and and sequencing the second exon of this gene in 288 SDS samples representing six breeds provided a comprehensive allelic profile, enabling a detalied examination of the gene's genetic makeup. RESULTS We identifed forty-six alleles, including four previously unreported, enrichness the genetic diversity of SDS breeds. These alleles exhibiting non-uniform distribution, varying frequencies across breeds, indicating a breed-specific genetic landscape. Certain alleles, known and novel, show higher frequencies in specific populations, suggesting potential associations with adaptive immune responses. Identifying these alleles sets the stage for investigating their functional roles and implications for disease resistance. Genetic differentiation among SDS breeds, as indicated by FST values and clustering analyses, highlights a unique genetic makeup shaped by geographic and historical factors. These differentiation patterns among SDS breeds have broader implications for breed conservation and targeted breeding to enhance disease resistance in specific populations. CONCLUSION This study unveils Ovar-DRB1 gene allelic diversity in SDS breeds through targeted NGS and genetic analyses, revealing new alleles that underscore the breeds' unique genetic profile. Insights into the genetic factors governing immune responses and disease resistance emerge, promising for optimization of breeding strategies for enhanced livestock health in Sudan's unique environment.
Collapse
Affiliation(s)
- Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, Khartoum-North, Sudan.
- Camel Research Center, King Faisal University, Al-Hasa, Saudi Arabia.
| | - Ryo Nakao
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Elisha Chatanga
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Olivia Marcuzzi
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), La Plata, Argentina
| | | | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Guillermo Giovambattista
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), La Plata, Argentina
| |
Collapse
|
10
|
de Jong MJ, van Oosterhout C, Hoelzel AR, Janke A. Moderating the neutralist-selectionist debate: exactly which propositions are we debating, and which arguments are valid? Biol Rev Camb Philos Soc 2024; 99:23-55. [PMID: 37621151 DOI: 10.1111/brv.13010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation-random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist-selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?
Collapse
Affiliation(s)
- Menno J de Jong
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
| | - Cock van Oosterhout
- Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse 9, Frankfurt am Main, 60438, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt am Main, 60325, Germany
| |
Collapse
|
11
|
Youk S, Kang M, Ahn B, Koo Y, Park C. Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human. Genes (Basel) 2023; 15:7. [PMID: 38275589 PMCID: PMC10815642 DOI: 10.3390/genes15010007] [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: 11/30/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Comparative analyses of MHC gene diversity and evolution across different species could offer valuable insights into the evolution of MHC genes. Intra- and inter-species sequence diversity and conservation of 12 classical major histocompatibility complex (MHC) class I genes from cattle, chimpanzees, pigs, and humans was analyzed using 20 representative allelic groups for each gene. The combined analysis of paralogous loci for each species revealed that intra-locus amino-acid sequence variations in the peptide-binding region (PBR) of MHC I genes did not differ significantly between species, ranging from 8.44% for SLA to 10.75% for BoLA class I genes. In contrast, intraspecies differences in the non-PBRs of these paralogous genes were more pronounced, varying from 4.59% for SLA to 16.89% for HLA. Interestingly, the Shannon diversity index and rate of nonsynonymous substitutions for PBR were significantly higher in SLA and BoLA than those in Patr and HLA. Analysis of peptide-binding pockets across all analyzed MHC class I genes of the four species indicated that pockets A and E showed the lowest and highest diversity, respectively. The estimated divergence times suggest that primate and artiodactyl MHC class I genes diverged 60.41 Mya, and BoLA and SLA genes diverged 35.34 Mya. These results offer new insights into the conservation and diversity of MHC class I genes in various mammalian species.
Collapse
Affiliation(s)
- Seungyeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Yangmo Koo
- Genetic & Breeding Department, Korea Animal Improvement Association, Seocho, Seoul 06668, Republic of Korea;
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| |
Collapse
|
12
|
Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. How chromosomal inversions reorient the evolutionary process. J Evol Biol 2023; 36:1761-1782. [PMID: 37942504 DOI: 10.1111/jeb.14242] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.
Collapse
Affiliation(s)
- Emma L Berdan
- Bioinformatics Core, Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Nicholas H Barton
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Roger Butlin
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Ecology and Evolutionary Biology, School of Bioscience, The University of Sheffield, Sheffield, UK
| | - Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Rui Faria
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Inês Fragata
- CHANGE - Global Change and Sustainability Institute/Animal Biology Department, cE3c - Center for Ecology, Evolution and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | | | - Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Martin Kapun
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- Central Research Laboratories, Natural History Museum of Vienna, Vienna, Austria
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Claire Mérot
- UMR 6553 Ecobio, Université de Rennes, OSUR, CNRS, Rennes, France
| | - Esra Durmaz Mitchell
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anja M Westram
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Stephen W Schaeffer
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kerstin Johannesson
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| |
Collapse
|
13
|
Nayak SS, Panigrahi M, Kumar H, Rajawat D, Sharma A, Bhushan B, Dutt T. Evidence for selective sweeps in the MHC gene repertoire of various cattle breeds. Anim Biotechnol 2023; 34:4167-4173. [PMID: 37039747 DOI: 10.1080/10495398.2023.2196317] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Major Histocompatibility Complex (MHC) genes are among the immune genes that have been extensively studied in vertebrates and are necessary for adaptive immunity. In the immunological response to infectious diseases, they play several significant roles. This research paper provides the selection signatures in the MHC region of the bovine genome as well as how certain genes related to innate immunity are undergoing a positive selective sweep. Here, we investigated signatures of historical selection on MHC genes in 15 different cattle populations and a total of 427 individuals. To identify the selection signatures, we have used three separate summary statistics. The findings show potential selection signatures in cattle from whom we isolated genes involved in the MHC. The most significant regions related to the bovine MHC are BOLA, non-classical MHC class I antigen (BOLA-NC1), Microneme protein 1 (MIC1) , Cluster of Differentiation 244 (CD244), Gap Junction Alpha-5 Protein (GJA5). It will be possible to gain new insight into immune system evolution by understanding the distinctive characteristics of MHC in cattle.
Collapse
Affiliation(s)
- Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| |
Collapse
|
14
|
Truong L, Matern BM, El-Lagta N, Mobegi FM, Askar M, Ogret Y, Oguz FS, Kwok J, D'Orsogna L, Martinez P, Petersdorf E, Tilanus MGJ, De Santis D. Report from the extended HLA-DPA1 ~ promoter ~ HLA-DPB1 haplotype of the 18th international HLA and immunogenetics workshop. HLA 2023; 102:690-706. [PMID: 37452528 DOI: 10.1111/tan.15155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/04/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
The primary goal of the HLA-DPA1 ~ promoter ~ HLA-DPB1 haplotype component of the 18th IHIWS was to characterise the extended haplotypes within the HLA-DP region and survey the extent of genetic diversity in this region across human populations. In this report, we analysed single-nucleotide polymorphisms (SNPs) in 255 subjects from 6 different cohorts. The results from the HLA-DP haplotype component have validated findings from the initial pilot study. SNPs in this region were inherited in strong linkage, particularly HLA-DPA1, SNP-linked promoter haplotypes and motifs in exon 2 of HLA-DPB1. We reported 17 SNP-linked haplotypes in the promoter region. Together with HLA-DPA1 and HLA-DPB1 alleles, they formed 74 distinct extended HLA-DP haplotypes in 438 sequences. We also observed the presence of region-specific alleles and promoter haplotypes. Our approach involved phasing extended SNPs including promoter SNPs, HLA-DPA1 and HLA-DPB1 alleles, in a 22 kb region, GRCh38/hg38 (chr6:33,064,111-33,086,679), followed by clustering of these SNPs as one extended haplotype. This hierarchical clustering revealed four major clades, suggesting that haplotypes within each clade may have diverged from a common ancestral haplotype and undergone similar evolutionary processes. The correlation between HLA-DPA1 and the promoter region raises questions about the role of HLA-DPA1 antigen in the heterodimer. This finding requires validation on a larger sample size specifically designed for anthropological analysis. Nevertheless, the results from this study highlight the clinical potential of selecting better-matched donors for patients awaiting haematopoietic stem cell transplants from genetically overlapping groups that share common ancestral haplotypes.
Collapse
Affiliation(s)
- Linh Truong
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Benedict M Matern
- Central Diagnostic Laboratory, University Medical Center Utrecht, Utrecht, Netherlands
| | - Naser El-Lagta
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Fredrick M Mobegi
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Medhat Askar
- QU Health Cluster & Department of Basic Sciences, College of Medicine, Qatar University, Doha, Qatar
| | - Yeliz Ogret
- Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Fatma S Oguz
- Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Janette Kwok
- Division of Transplantation and Immunogenetics, Queen Mary Hospital, Hong Kong, China
| | - Lloyd D'Orsogna
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Patricia Martinez
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Effie Petersdorf
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Marcel G J Tilanus
- School for Oncology and Reproduction, GROW, Maastricht University, Maastricht, Netherlands
| | - Dianne De Santis
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
- UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
| |
Collapse
|
15
|
Gowane GR, Sharma P, Kumar R, Misra SS, Alex R, Vohra V, Chhotaray S, Dass G, Chopra A, Kandalkar Y, Vijay V, Choudhary A, Magotra A, Rajendran R. Cross-population genetic analysis revealed genetic variation and selection in the Ovar-DRB1 gene of Indian sheep breeds. Anim Biotechnol 2023; 34:2928-2939. [PMID: 36153754 DOI: 10.1080/10495398.2022.2125404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
In sheep, MHC variability is studied widely to explore disease association. The aim of the current study was to explore the genetic diversity of Ovar-DRB diversity across sheep breeds of India. Here, Ovar-DRB1 locus was studied across 20 sheep breeds. DRB1 was amplified (301 bp) and sequenced using a PCR-sequence-based typing approach. Results revealed a high degree of heterozygosity across breeds (mean: 73.99%). Overall mean distance for DRB1 was highest in Sangamneri (0.18) and lowest in Madgyal sheep (0.10). There was a higher rate of transition, across breeds. Further, 39 alleles were isolated in different breeds, out of which 10 were new. To allow easy access and use of the immune-polymorphic database, an online database management system was launched (http://www.mhcdbms.in/). Nucleotide content across breeds for the DRB1 region revealed the richness of GC content (59.26%). Wu-Kabat index revealed vast genetic variation across peptide binding sites (PBS) of DRB1. Residues 6, 66, 69, 52, and 81, were polymorphic showing utility for antigen presentation. All breeds were under positive selection for DRB1 locus (dN > dS). Study revealed the importance of DRB locus diversity for beta chain specifically at PBS across sheep breeds of the Indian subcontinent and presented evidence of positive selection for DRB owing to its evolutionary significance.
Collapse
Affiliation(s)
- G R Gowane
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Priya Sharma
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Rajiv Kumar
- Animal Genetics & Breeding Division, ICAR-Central Sheep & Wool Research Institute, Avikanagar, India
| | - S S Misra
- Animal Genetics & Breeding Division, ICAR-Central Sheep & Wool Research Institute, Avikanagar, India
| | - Rani Alex
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - V Vohra
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Chhotaray
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Gopal Dass
- Animal Genetics & Breeding Division, ICAR-Central Institute for Research on Goats, Makhdoom, India
| | - Ashish Chopra
- Animal Genetics & Breeding Division, ICAR-Arid Region Campus, Central Sheep & Wool Research Institute Bikaner, Avikanagar, India
| | - Yogesh Kandalkar
- Deccani Sheep Breeding Unit, NWPSI at Mahatma Phule Krishi Vidyapith, Rahuri, India
| | - V Vijay
- Sonadi Seep Breeding Unit, NWPSI at Navaniya Maharana Pratap University of Agriculture and Technology, Udaipur, India
| | | | - Ankit Magotra
- Animal Genetics & Breeding Division, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - R Rajendran
- Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Theni, India
| |
Collapse
|
16
|
Logunova N, Kapina M, Kondratieva E, Apt A. The H2-A Class II molecule α/β-chain cis-mismatch severely affects cell surface expression, selection of conventional CD4 + T cells and protection against TB infection. Front Immunol 2023; 14:1183614. [PMID: 37426653 PMCID: PMC10324577 DOI: 10.3389/fimmu.2023.1183614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction To dissect the role of the part of the H2 complex comprised of the MHC-II genes in the control of tuberculosis (TB) infection, we previously established a panel of recombinant congenic mouse strains bearing different segments of the H2 j haplotype on the B6 (H2 b) genetic background. Fine genetic mapping, gene sequencing and assessment of TB phenotypes resulted in identification of the H2-Ab gene as a major factor of TB control. Methods We further narrowed the MHC-II H2 j interval by spotting a new recombination event, sequencing newly established DNA configuration and establishing a mouse strain B6.I-103 in which j/b recombination occurred within the coding sequence of the H2-Ab gene. Results Unexpectedly, a novel H2-Aα b/AβjE0 haplotype provided exclusively high susceptibility to TB challenge. Immunologic analysis revealed an altered CD4+ T-cell selection and maintenance in B6.I-103 mice, as well as seriously impaired expression of the H2-Aαb/Aβj molecule on the surface of antigen presenting cells. Unlike previously reported cases of Class II malfunctioning, the defective phenotype arose not from strong structural mutations, but from regular recombination events within the MHC-II recombination hot spot region. Discussion Our findings provide evidence that Class II α/β-chain cis-allelic mismatches created by regular genetic recombination may severely affect immune system functioning. This issue is discussed in the context of the MHC evolution.
Collapse
|
17
|
Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
Collapse
Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
| | | | | |
Collapse
|
18
|
Palmer WH, Norman PJ. The impact of HLA polymorphism on herpesvirus infection and disease. Immunogenetics 2023; 75:231-247. [PMID: 36595060 PMCID: PMC10205880 DOI: 10.1007/s00251-022-01288-z] [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: 08/18/2022] [Accepted: 11/24/2022] [Indexed: 01/04/2023]
Abstract
Human Leukocyte Antigens (HLA) are cell surface molecules, central in coordinating innate and adaptive immune responses, that are targets of strong diversifying natural selection by pathogens. Of these pathogens, human herpesviruses have a uniquely ancient relationship with our species, where coevolution likely has reciprocating impact on HLA and viral genomic diversity. Consistent with this notion, genetic variation at multiple HLA loci is strongly associated with modulating immunity to herpesvirus infection. Here, we synthesize published genetic associations of HLA with herpesvirus infection and disease, both from case/control and genome-wide association studies. We analyze genetic associations across the eight human herpesviruses and identify HLA alleles that are associated with diverse herpesvirus-related phenotypes. We find that whereas most HLA genetic associations are virus- or disease-specific, HLA-A*01 and HLA-A*02 allotypes may be more generally associated with immune susceptibility and control, respectively, across multiple herpesviruses. Connecting genetic association data with functional corroboration, we discuss mechanisms by which diverse HLA and cognate receptor allotypes direct variable immune responses during herpesvirus infection and pathogenesis. Together, this review examines the complexity of HLA-herpesvirus interactions driven by differential T cell and Natural Killer cell immune responses.
Collapse
Affiliation(s)
- William H. Palmer
- Department of Biomedical Informatics, University of Colorado, Aurora, CO USA
- Department of Immunology & Microbiology, University of Colorado, Aurora, CO USA
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado, Aurora, CO USA
- Department of Immunology & Microbiology, University of Colorado, Aurora, CO USA
| |
Collapse
|
19
|
Jia Y, Fu Q, Li B, Xu Y, Tariq A. Polymorphism analysis of major histocompatibility complex (MHC) DQB gene in the Asiatic black bear (Ursus thibetanus). MAMMAL RES 2023. [DOI: 10.1007/s13364-023-00685-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
|
20
|
Comparative transcriptome analyses of three Gentiana species provides signals for the molecular footprints of selection effects and the phylogenetic relationships. Mol Genet Genomics 2023; 298:399-411. [PMID: 36592219 DOI: 10.1007/s00438-022-01991-2] [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: 11/08/2021] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
Species in Gentiana section Cruciata are important alpine plants with a center of diversity and speciation in Qinghai-Tibet Plateau (QTP), and some of these species are sympatrically distributed in northeastern QTP. Studies on genome features and natural selection signatures of sympatric species in section Crucata have been impeded by a lack of genomic resources. Here, we showed transcript characterizations and molecular footprints of selection effects on G. straminea, G. dahurica and G. officinalis based on the comparative transcriptome. A total of 62.97 Gb clean reads were obtained with unigene numbers per species ranging from 141,819 to 236,408 after assembly. We found that these three species had similar distribution of functional categories in different databases, and key enzyme-encoding genes involved in the iridoids biosynthesis were also obtained. The selective pressure analyses indicated that most paired orthologs between these three species were subject to negative selection, and only a low proportion of the orthologs that underwent positive selection were detected. We found that some positive selected genes were involved in "catalytic activity", "metabolic process", "response to stimulus" and "response to stress". Besides, large numbers of SSR primer pairs with transferabilities were successfully designed based on the available transcriptome datasets of three Gentiana species. The phylogenetic relationships reconstructed based on 352 single-copy nuclear genes provided a rough phylogenetic framework for this genus and confirmed the monophyly of section Cruciata. Our study not only provides insights for the natural selection effects on sympatric Gentiana species, but also enhances future genetic breeding or evolutionary studies on Qinjiao species.
Collapse
|
21
|
Padgitt-Cobb LK, Pitra NJ, Matthews PD, Henning JA, Hendrix DA. An improved assembly of the "Cascade" hop ( Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family. HORTICULTURE RESEARCH 2023; 10:uhac281. [PMID: 36818366 PMCID: PMC9930403 DOI: 10.1093/hr/uhac281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/22/2022] [Indexed: 06/16/2023]
Abstract
We present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly were fragmented. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur. The chromosome-level assembly of Cascade was developed by scaffolding the previously reported Cascade assembly generated with PacBio long-read sequencing and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assessed molecular evolution in gene sequences, gene family expansion and contraction, and time of divergence from Cannabis sativa and other closely related plant species using Bayesian inference. We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the estimate for the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families. The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.
Collapse
Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Nicholi J Pitra
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
| | - Paul D Matthews
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
| | | | | |
Collapse
|
22
|
Lam DK, Frantz AC, Burke T, Geffen E, Sin SYW. Both selection and drift drive the spatial pattern of adaptive genetic variation in a wild mammal. Evolution 2023; 77:221-238. [PMID: 36626810 DOI: 10.1093/evolut/qpac014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 10/03/2022] [Accepted: 11/04/2022] [Indexed: 01/12/2023]
Abstract
The major histocompatibility complex (MHC) has been intensively studied for the relative effects of different evolutionary forces in recent decades. Pathogen-mediated balancing selection is generally thought to explain the high polymorphism observed in MHC genes, but it is still unclear to what extent MHC diversity is shaped by selection relative to neutral drift. In this study, we genotyped MHC class II DRB genes and 15 neutral microsatellite loci across 26 geographic populations of European badgers (Meles meles) covering most of their geographic range. By comparing variation of microsatellite and diversity of MHC at different levels, we demonstrate that both balancing selection and drift have shaped the evolution of MHC genes. When only MHC allelic identity was investigated, the spatial pattern of MHC variation was similar to that of microsatellites. By contrast, when functional aspects of the MHC diversity (e.g., immunological supertypes) were considered, balancing selection appears to decrease genetic structuring across populations. Our comprehensive sampling and analytical approach enable us to conclude that the likely mechanisms of selection are heterozygote advantage and/or rare-allele advantage. This study is a clear demonstration of how both balancing selection and genetic drift simultaneously affect the evolution of MHC genes in a widely distributed wild mammal.
Collapse
Affiliation(s)
- Derek Kong Lam
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Alain C Frantz
- Musée National d'Histoire Naturelle, Luxembourg, Luxembourg
| | - Terry Burke
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Eli Geffen
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
23
|
Durand A, Winkler CA, Vince N, Douillard V, Geffard E, Binns-Roemer E, Ng DK, Gourraud PA, Reidy K, Warady B, Furth S, Kopp JB, Kaskel FJ, Limou S. Identification of Novel Genetic Risk Factors for Focal Segmental Glomerulosclerosis in Children: Results From the Chronic Kidney Disease in Children (CKiD) Cohort. Am J Kidney Dis 2023; 81:635-646.e1. [PMID: 36623684 DOI: 10.1053/j.ajkd.2022.11.003] [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: 04/28/2022] [Accepted: 11/02/2022] [Indexed: 01/09/2023]
Abstract
RATIONALE & OBJECTIVE Focal segmental glomerulosclerosis (FSGS) is a major cause of pediatric nephrotic syndrome, and African Americans exhibit an increased risk for developing FSGS compared with other populations. Predisposing genetic factors have previously been described in adults. Here we performed genomic screening of primary FSGS in a pediatric African American population. STUDY DESIGN Prospective cohort with case-control genetic association study design. SETTING & PARTICIPANTS 140 African American children with chronic kidney disease from the Chronic Kidney Disease in Children (CKiD) cohort, including 32 cases with FSGS. PREDICTORS Over 680,000 common single-nucleotide polymorphisms (SNPs) were tested for association. We also ran a pathway enrichment analysis and a human leucocyte antigen (HLA)-focused association study. OUTCOME Primary biopsy-proven pediatric FSGS. ANALYTICAL APPROACH Multivariate logistic regression models. RESULTS The genome-wide association study revealed 169 SNPs from 14 independent loci significantly associated with FSGS (false discovery rate [FDR]<5%). We observed notable signals for genetic variants within the APOL1 (P=8.6×10-7; OR, 25.8 [95% CI, 7.1-94.0]), ALMS1 (P=1.3×10-7; 13.0% in FSGS cases vs 0% in controls), and FGFR4 (P=4.3×10-6; OR, 24.8 [95% CI, 6.3-97.7]) genes, all of which had previously been associated with adult FSGS, kidney function, or chronic kidney disease. We also highlighted novel, functionally relevant genes, including GRB2 (which encodes a slit diaphragm protein promoting podocyte structure through actin polymerization) and ITGB1 (which is linked to renal injuries). Our results suggest a major role for immune responses and antigen presentation in pediatric FSGS through (1) associations with SNPs in PTPRJ (or CD148, P=3.5×10-7), which plays a role in T-cell receptor signaling, (2) HLA-DRB1∗11:01 association (P=6.1×10-3; OR, 4.5 [95% CI, 1.5-13.0]), and (3) signaling pathway enrichment (P=1.3×10-6). LIMITATIONS Sample size and no independent replication cohort with genomic data readily available. CONCLUSIONS Our genetic study has identified functionally relevant risk factors and the importance of immune regulation for pediatric primary FSGS, which contributes to a better description of its molecular pathophysiological mechanisms.
Collapse
Affiliation(s)
- Axelle Durand
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Cheryl A Winkler
- Basic Research Laboratory, Center for Cancer Research, Frederick National Laboratory, National Cancer Institute, Frederick, Maryland
| | - Nicolas Vince
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Venceslas Douillard
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Estelle Geffard
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Elizabeth Binns-Roemer
- Basic Research Laboratory, Center for Cancer Research, Frederick National Laboratory, National Cancer Institute, Frederick, Maryland
| | - Derek K Ng
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Pierre-Antoine Gourraud
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Kimberley Reidy
- Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, New York
| | | | - Susan Furth
- Children's Hospital of Pennsylvania, Philadelphia, Pennsylvania
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Frederick J Kaskel
- Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, New York
| | - Sophie Limou
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France.
| |
Collapse
|
24
|
Zhao M, Ma Y, Xin J, Cao C, Wang J. Detection of differential selection pressure and functional-specific sites in subunits of vertebrate neuronal nicotinic acetylcholine receptors. J Biomol Struct Dyn 2022; 40:13161-13170. [PMID: 34596010 DOI: 10.1080/07391102.2021.1982772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nicotinic acetylcholine receptors (nAChR) are made of subunits evolved from a common ancestor. Despite the similarity in their sequences and structures, the properties of these subunits vary significantly. Thus, identifying the evolution features and function-related sites specific to each subunit is essential for understanding the characteristics of the subunits and the receptors assembled by them. In this study, we examined the sequence features of the nine neuronal nAChRs subunits from representative vertebrate species. Analysis revealed that all the subunits were subject to strong purifying selection in evolution, and each was under a unique pattern of selection pressures. At the same time, the functional constraints were not uniform within each subunit, with different domains in the molecule being subject to different selection pressures. We also detected potential positive selection events in the subunits or subunit clusters, and identified the sites might be associated with the function specificity of each subunit. Furthermore, positive selection at some domains might contribute to the diversity of subunit function; for example, the β9 strand might be related to the agonist specificity of α subunit in heteromeric receptor and β4-β5 linker could be involved in Ca2+ permeability. Subunits α7, α4 and β2 subunits possess a strong adaptability in vertebrates. Our results highlighted the importance of tracking functional differentiation in protein sequence underlying functional properties of nAChRs. In summary, our work may provide clues on understanding the diversity and the function specificity of the nAChR subunits, as well as the receptors co-assembled by them.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mengwen Zhao
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Yuequn Ma
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Juncai Xin
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Changying Cao
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Ju Wang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| |
Collapse
|
25
|
Minias P, Palomar G, Dudek K, Babik W. Salamanders reveal novel trajectories of amphibian MHC evolution. Evolution 2022; 76:2436-2449. [PMID: 36000494 DOI: 10.1111/evo.14601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 07/06/2022] [Accepted: 07/29/2022] [Indexed: 01/22/2023]
Abstract
Genes of the major histocompatibility complex (MHC) code for immune proteins that are crucial for pathogen recognition in vertebrates. MHC research in nonmodel taxa has long been hampered by its genomic complexity that makes the locus-specific genotyping challenging. The recent progress in sequencing and genotyping methodologies allows an extensive phylogenetic coverage in studies of MHC evolution. Here, we analyzed the peptide-binding region of MHC class I (MHC-I) in 30 species of salamanders from six families representative of Urodela phylogeny. This extensive dataset revealed an extreme diversity of MHC-I in salamanders, both in terms of sequence diversity (about 3000 variants) and architecture (2-22 gene copies per species). The signal of positive selection was moderate and consistent between both peptide-binding domains, but varied greatly between genera. Positions of positively selected sites mostly coincided with human peptide-binding sites, suggesting similar structural properties of MHC-I molecules across distant vertebrate lineages. Finally, we provided evidence for the common intraexonic recombination at MHC-I and for the role of life history traits in the processes of MHC-I expansion/contraction. Our study revealed novel evolutionary trajectories of amphibian MHC and it contributes to the understanding of the mechanisms that generated extraordinary MHC diversity throughout vertebrate evolution.
Collapse
Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, 90-237, Poland
| | - Gemma Palomar
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, 30-387, Poland.,Parasitology Unit, Department of Biomedicine and Biotechnology, Faculty of Pharmacy, Universidad de Alcalá (UAH), Alcalá de Henares, Madrid, 28805, Spain
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, 30-387, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, 30-387, Poland
| |
Collapse
|
26
|
Oliveira MLG, Castelli EC, Veiga‐Castelli LC, Pereira ALE, Marcorin L, Carratto TMT, Souza AS, Andrade HS, Simões AL, Donadi EA, Courtin D, Sabbagh A, Giuliatti S, Mendes‐Junior CT. Genetic diversity of the
LILRB1
and
LILRB2
coding regions in an admixed Brazilian population sample. HLA 2022; 100:325-348. [DOI: 10.1111/tan.14725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/02/2022] [Accepted: 06/24/2022] [Indexed: 11/27/2022]
Affiliation(s)
| | - Erick C. Castelli
- Pathology Department, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Luciana C. Veiga‐Castelli
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Alison Luis E. Pereira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Thássia M. T. Carratto
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Andreia S. Souza
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Heloisa S. Andrade
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Aguinaldo L. Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Eduardo A. Donadi
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | | | | | - Silvana Giuliatti
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Celso Teixeira Mendes‐Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| |
Collapse
|
27
|
Dubois‐Mignon T, Monget P. Gene essentiality and variability: What is the link? A within‐ and between‐species perspective. Bioessays 2022; 44:e2200132. [DOI: 10.1002/bies.202200132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Tania Dubois‐Mignon
- Institut de Biologie de l’École Normale Supérieure Université PSL 46 rue d'Ulm Paris 75005 France
| | - Philippe Monget
- Physiologie de la Reproduction et des Comportements, Centre Val de Loire – UMR INRAE, CNRS, IFCE Université de Tours Nouzilly France
| |
Collapse
|
28
|
Klymus KE, Hrabik RA, Thompson NL, Cornman RS. Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas. PeerJ 2022; 10:e13954. [PMID: 36042859 PMCID: PMC9420404 DOI: 10.7717/peerj.13954] [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: 04/04/2022] [Accepted: 08/05/2022] [Indexed: 01/19/2023] Open
Abstract
Background The fathead minnow (Pimephales promelas) is a model species for toxicological research. A high-quality genome reference sequence is available, and genomic methods are increasingly used in toxicological studies of the species. However, phylogenetic relationships within the genus remain incompletely known and little population-genomic data are available for fathead minnow despite the potential effects of genetic background on toxicological responses. On the other hand, a wealth of extant samples is stored in museum collections that in principle allow fine-scale analysis of contemporary and historical genetic variation. Methods Here we use short-read shotgun resequencing to investigate sequence variation among and within Pimephales species. At the genus level, our objectives were to resolve phylogenetic relationships and identify genes with signatures of positive diversifying selection. At the species level, our objective was to evaluate the utility of archived-sample resequencing for detecting selective sweeps within fathead minnow, applied to a population introduced to the San Juan River of the southwestern United States sometime prior to 1950. Results We recovered well-supported but discordant phylogenetic topologies for nuclear and mitochondrial sequences that we hypothesize arose from mitochondrial transfer among species. The nuclear tree supported bluntnose minnow (P. notatus) as sister to fathead minnow, with the slim minnow (P. tenellus) and bullhead minnow (P. vigilax) more closely related to each other. Using multiple methods, we identified 11 genes that have diversified under positive selection within the genus. Within the San Juan River population, we identified selective-sweep regions overlapping several sets of related genes, including both genes that encode the giant sarcomere protein titin and the two genes encoding the MTORC1 complex, a key metabolic regulator. We also observed elevated polymorphism and reduced differentation among populations (FST) in genomic regions containing certain immune-gene clusters, similar to what has been reported in other taxa. Collectively, our data clarify evolutionary relationships and selective pressures within the genus and establish museum archives as a fruitful resource for characterizing genomic variation. We anticipate that large-scale resequencing will enable the detection of genetic variants associated with environmental toxicants such as heavy metals, high salinity, estrogens, and agrichemicals, which could be exploited as efficient biomarkers of exposure in natural populations.
Collapse
Affiliation(s)
- Katy E. Klymus
- U.S. Geological Survey, Columbia Ecological Research Center, Columbia, MO, USA
| | | | - Nathan L. Thompson
- U.S. Geological Survey, Columbia Ecological Research Center, Columbia, MO, USA
| | - Robert S. Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| |
Collapse
|
29
|
Cortazar-Chinarro M, Meurling S, Schroyens L, Siljestam M, Richter-Boix A, Laurila A, Höglund J. Major Histocompatibility Complex Variation and Haplotype Associated Survival in Response to Experimental Infection of Two Bd-GPL Strains Along a Latitudinal Gradient. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.915271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While both innate and adaptive immune system mechanisms have been implicated in resistance against the chytrid fungus Batrachochytrium dendrobatidis (Bd), studies on the role of specific MHC haplotypes on Bd infection are rare. Here, we studied variation in MHC Class IIB loci in the common toad Bufo bufo along a latitudinal gradient across Sweden. In general, Swedish toad populations had few MHC Class IIB haplotypes and MHC diversity declined from south (13 haplotypes) to the north (four haplotypes). The low diversity may compromise the ability of northern populations to fight emerging disease, such as Bd. In a laboratory experiment, we infected newly metamorphosed toads with two strains of the Global Pandemic Lineage of the fungus (Bd-GPL) and compared survival with sham controls. Bd-infected toads had lower survival compared to controls. Moreover, survival was dependent on the Bd-strain and northern toads had lower Bd-mediated survival than southern individuals. MHC diversity was lower in northern toads. All northern experimental animals were monomorphic for a single MHC haplotype, whereas we found seven different haplotypes in southern experimental animals. In southern toads, survival was dependent on both Bd-strain and MHC haplotype suggesting differential infection dynamics depending on both Bd-strain and host immune system characteristics.
Collapse
|
30
|
Mondal S, Mohamed Shafi K, Raizada A, Song H, Badigannavar AM, Sowdhamini R. Development of candidate gene-based markers and map-based cloning of a dominant rust resistance gene in cultivated groundnut (Arachis hypogaea L.). Gene 2022; 827:146474. [PMID: 35390447 DOI: 10.1016/j.gene.2022.146474] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/22/2022] [Accepted: 03/31/2022] [Indexed: 11/18/2022]
Abstract
A dominant rust resistance gene, VG 9514-Rgene was isolated through map-based cloning. Sequence analysis revealed non-synonymous mutations in the TIR, NBS and LRR region of the R-protein. Candidate gene-based markers from these SNPs revealed complete co-segregation of the isolated VG 9514-Rgene with rust resistance in a RIL population and confirmed their map position in between FRS 72 and SSR_GO340445 markers in arahy03 chromosome. Blastp search of VG 9514-Rprotein detected Arahy.T6DCA5 with >80.0% identity that localized at 142,544,745.0.142,549,184 in arahy03 chromosome. Ka/Ks calculation revealed that VG 9514-Rgene had undergone positive selection compared to four homologous genes in the groundnut genome. Homology based structure modelling of this R-protein revealed a typical consensus three-dimensional folding of TIR-NBS-LRR protein. Non-synonymous mutations in susceptible version of R-protein were mapped and found E268Q mutation in hhGRExE motif, Y309F in RNBS-A motif and I579T in MHD motif of NB-ARC domain are probable candidates for loss of function.
Collapse
Affiliation(s)
- Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, Maharashtra, India.
| | - K Mohamed Shafi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, Karnataka, India.
| | - Avi Raizada
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, Maharashtra, India
| | - Hui Song
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Anand M Badigannavar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, Maharashtra, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, Karnataka, India.
| |
Collapse
|
31
|
Soni V, Vos M, Eyre-Walker A. A new test suggests hundreds of amino acid polymorphisms in humans are subject to balancing selection. PLoS Biol 2022; 20:e3001645. [PMID: 35653351 PMCID: PMC9162324 DOI: 10.1371/journal.pbio.3001645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald–Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection.
Collapse
Affiliation(s)
- Vivak Soni
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn, United Kingdom
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- * E-mail:
| |
Collapse
|
32
|
Migalska M, Przesmycka K, Alsarraf M, Bajer A, Behnke-Borowczyk J, Grzybek M, Behnke JM, Radwan J. Long term patterns of association between MHC and helminth burdens in the bank vole support Red Queen dynamics. Mol Ecol 2022; 31:3400-3415. [PMID: 35510766 PMCID: PMC9325469 DOI: 10.1111/mec.16486] [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: 12/21/2021] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 11/28/2022]
Abstract
Major histocompatibility complex (MHC) genes encode proteins crucial for adaptive immunity of vertebrates. Negative frequency-dependent selection (NFDS), resulting from adaptation of parasites to common MHC types, has been hypothesized to maintain high, functionally relevant polymorphism of MHC, but demonstration of this relationship has remained elusive. In particular, differentiation of NFDS from fluctuating selection, resulting from changes in parasite communities in time and space (FS), has proved difficult in short-term studies. Here, we used temporal data, accumulated through long-term monitoring of helminths infecting bank voles (Myodes glareolus), to test specific predictions of NFDS on MHC class II. Data were collected in three, moderately genetically differentiated subpopulations in Poland, which were characterized by some stable spatiotemporal helminth communities but also events indicating introduction of new species and loss of others. We found a complex association between individual MHC diversity and species richness, where intermediate numbers of DRB supertypes correlated with lowest species richness, but the opposite was true for DQB supertypes - arguing against universal selection for immunogenetic optimality. We also showed that particular MHC supertypes explain a portion of the variance in prevalence and abundance of helminths, but this effect was subpopulation-specific, which is consistent with both NFDS and FS. Finally, in line with NFDS, we found that certain helminths that have recently colonized or spread in a given subpopulation, more frequently or intensely infected voles with MHC supertypes that have been common in the recent past. Overall, our results highlight complex spatial and temporal patterns of MHC-parasite associations, the latter being consistent with Red Queen coevolutionary dynamics.
Collapse
Affiliation(s)
- Magdalena Migalska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Karolina Przesmycka
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Mohammed Alsarraf
- Department of Eco-epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Anna Bajer
- Department of Eco-epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jolanta Behnke-Borowczyk
- Department of Forest Entomology and Pathology, Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 71c, 60-625, Poznań, Poland
| | - Maciej Grzybek
- Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Powstania Styczniowego 9B, 81-429, Gdynia, Poland
| | - Jerzy M Behnke
- School of Life Science, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Jacek Radwan
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| |
Collapse
|
33
|
Brackett NF, Davis BW, Adli M, Pomés A, Chapman MD. Evolutionary Biology and Gene Editing of Cat Allergen, Fel d 1. CRISPR J 2022; 5:213-223. [PMID: 35343817 DOI: 10.1089/crispr.2021.0101] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Allergy to domestic cat affects up to 15% of the population, and sensitization to cat allergen is associated with asthma. Despite the pervasiveness of cat allergic disease, current treatments have limited impact. Here, we present a bioinformatics analysis of the major cat allergen, Fel d 1, and demonstrate proof of principle for CRISPR gene editing of the allergen. Sequence and structural analyses of Fel d 1 from 50 domestic cats identified conserved coding regions in genes CH1 and CH2 suitable for CRISPR editing. Comparative analyses of Fel d 1 and orthologous sequences from eight exotic felid species determined relatively low-sequence identities for CH1 and CH2, and implied that the allergen may be nonessential for cats, given the apparent lack of evolutionary conservation. In vitro knockouts of domestic cat Fel d 1 using CRISPR-Cas9 yielded editing efficiencies of up to 55% and found no evidence of editing at predicted potential off-target sites. Taken together, our data indicate that Fel d 1 is both a rational and viable candidate for gene deletion, which may profoundly benefit cat allergy sufferers by removing the major allergen at the source.
Collapse
Affiliation(s)
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Mazhar Adli
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | | | | |
Collapse
|
34
|
Zhang LQ, Rozemuller E, Wang D, Liu XJ, Cai JP. Characterization of a novel HLA-A*11:335 allele resulting from a rare interlocus recombination involving HLA-A*11:01:01:01/126 and HLA-H*02:07/14/18 alleles with nanopore sequencing, in a volunteer from the China Marrow Donor Program. BMC Med Genomics 2022; 15:58. [PMID: 35296321 PMCID: PMC8925214 DOI: 10.1186/s12920-022-01176-1] [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: 05/02/2021] [Accepted: 02/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) in humans includes three classical class I loci (A, B, and C), which are important biomarkers for the transplantation of organs and hematopoietic stem cells. In the MHC, polymorphism is known to be extremely high while interlocus recombination is rare. We report a rare interlocus recombination between HLA-A and HLA-H, which was analyzed using next generation sequencing and nanopore sequencing. METHODS In the sample, the genotypes of HLA-A, B, C, DRB1, and DQB1 were firstly determined using the methods of sequence-specific primer, sequence-specific oligonucleotide, Sanger's sequencing, and NGS; however, HLA-A could not be phased. Nanopore sequencing was finally utilized to distinguish the sequence of the novel allele. RESULTS Finally, the novel HLA-A*11:335 allele was identified as an interlocus recombination involving HLA-A*11:01:01:01/126 and HLA-H*02:07/14/18 alleles; this was mainly achieved by nanopore sequencing. CONCLUSIONS The identification of the interlocus recombination indicated that nanopore sequencing can be helpful in the characterization of novel alleles with complex rearrangements. Interlocus recombination has been identified as one of the mechanisms involved in the generation of novel HLA alleles.
Collapse
Affiliation(s)
- Li-Qun Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, No. 1 DaHua Road, Dong Dan, Beijing, People's Republic of China
| | | | - Dan Wang
- Beijing BoFuRui Gene Diagnostic, LTD, Beijing, People's Republic of China
| | - Xiang-Jun Liu
- Beijing BoFuRui Gene Diagnostic, LTD, Beijing, People's Republic of China
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, No. 1 DaHua Road, Dong Dan, Beijing, People's Republic of China.
| |
Collapse
|
35
|
Tshabalala M, Mellet J, Vather K, Nelson D, Mohamed F, Christoffels A, Pepper MS. High Resolution HLA ∼A, ∼B, ∼C, ∼DRB1, ∼DQA1, and ∼DQB1 Diversity in South African Populations. Front Genet 2022; 13:711944. [PMID: 35309124 PMCID: PMC8931603 DOI: 10.3389/fgene.2022.711944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/17/2022] [Indexed: 01/10/2023] Open
Abstract
Background: Lack of HLA data in southern African populations hampers disease association studies and our understanding of genetic diversity in these populations. We aimed to determine HLA diversity in South African populations using high resolution HLA ∼A, ∼B, ∼C, ∼DRB1, ∼DQA1 and ∼DQB1 data, from 3005 previously typed individuals. Methods: We determined allele and haplotype frequencies, deviations from Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD) and neutrality test. South African HLA class I data was additionally compared to other global populations using non-metrical multidimensional scaling (NMDS), genetic distances and principal component analysis (PCA). Results: All loci strongly (p < 0.0001) deviated from HWE, coupled with excessive heterozygosity in most loci. Two of the three most frequent alleles, HLA ∼DQA1*05:02 (0.2584) and HLA ∼C*17:01 (0.1488) were previously reported in South African populations at lower frequencies. NMDS showed genetic distinctness of South African populations. Phylogenetic analysis and PCA clustered our current dataset with previous South African studies. Additionally, South Africans seem to be related to other sub-Saharan populations using HLA class I allele frequencies. Discussion and Conclusion: Despite the retrospective nature of the study, data missingness, the imbalance of sample sizes for each locus and haplotype pairs, and induced methodological difficulties, this study provides a unique and large HLA dataset of South Africans, which might be a useful resource to support anthropological studies, disease association studies, population based vaccine development and donor recruitment programs. We additionally provide simulated high resolution HLA class I data to augment the mixed resolution typing results generated from this study.
Collapse
Affiliation(s)
- Mqondisi Tshabalala
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Kuben Vather
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Derrick Nelson
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Fathima Mohamed
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Alan Christoffels
- SAMRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Michael S. Pepper
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- *Correspondence: Michael S. Pepper,
| |
Collapse
|
36
|
Ma C, Hu R, Costa C, Li J. Genetic Drift and Purifying Selection Shaped Mitochondrial Genome Variation in the High Royal Jelly-Producing Honeybee Strain (Apis mellifera ligustica). Front Genet 2022; 13:835967. [PMID: 35222549 PMCID: PMC8864236 DOI: 10.3389/fgene.2022.835967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/18/2022] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) are involved in cellular energy metabolism and have been shown to undergo adaptive evolution in organisms with increased energy-consuming activities. The genetically selected high royal jelly-producing bees (RJBs, Apis mellifera ligustica) in China can produce 10 times more royal jelly, a highly nutritional and functional food, relative to unselected Italian bees (ITBs). To test for potential adaptive evolution of RJB mitochondrial genes, we sequenced mitogenomes from 100 RJBs and 30 ITBs. Haplotype network and phylogenetic analysis indicate that RJBs and ITBs are not reciprocally monophyletic but mainly divided into the RJB- and ITB-dominant sublineages. The RJB-dominant sublineage proportion is 6-fold higher in RJBs (84/100) than in ITBs (4/30), which is mainly attributable to genetic drift rather than positive selection. The RJB-dominant sublineage exhibits a low genetic diversity due to purifying selection. Moreover, mitogenome abundance is not significantly different between RJBs and ITBs, thereby rejecting the association between mitogenome copy number and royal jelly-producing performance. Our findings demonstrate low genetic diversity levels of RJB mitogenomes and reveal genetic drift and purifying selection as potential forces driving RJB mitogenome evolution.
Collapse
Affiliation(s)
- Chuan Ma
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruoyang Hu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cecilia Costa
- CREA Research Centre for Agriculture and Environment, Bologna, Italy
| | - Jianke Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Jianke Li,
| |
Collapse
|
37
|
Ordoñez D, Bohórquez MD, Avendaño C, Patarroyo MA. Comparing Class II MHC DRB3 Diversity in Colombian Simmental and Simbrah Cattle Across Worldwide Bovine Populations. Front Genet 2022; 13:772885. [PMID: 35186024 PMCID: PMC8854852 DOI: 10.3389/fgene.2022.772885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/17/2022] [Indexed: 11/22/2022] Open
Abstract
The major histocompatibility complex (MHC) exerts great influence on responses to infectious diseases and vaccination due to its fundamental role in the adaptive immune system. Knowledge about MHC polymorphism distribution among breeds can provide insights into cattle evolution and diversification as well as population-based immune response variability, thus guiding further studies. Colombian Simmental and Simbrah cattle’s BoLA-DRB3 genetic diversity was compared to that of taurine and zebuine breeds worldwide to estimate functional diversity. High allele richness was observed for Simmental and Simbrah cattle; nevertheless, high homozygosity was associated with individual low sequence variability in both the β1 domain and the peptide binding region (PBR), thereby implying reduced MHC-presented peptide repertoire size. There were strong signals of positive selection acting on BoLA-DRB3 in all populations, some of which were poorly structured and displayed common alleles accounting for their high genetic similarity. PBR sequence correlation analysis suggested that, except for a few populations exhibiting some divergence at PBR, global diversity regarding potential MHC-presented peptide repertoire could be similar for the cattle populations analyzed here, which points to the retention of functional diversity in spite of the selective pressures imposed by breeding.
Collapse
Affiliation(s)
- Diego Ordoñez
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
- PhD Program in Tropical Health and Development, Universidad de Salamanca, Salamanca, Spain
| | - Michel David Bohórquez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- MSc Program in Microbiology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Catalina Avendaño
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Health Sciences Division, Main Campus, Universidad Santo Tomás, Bogotá, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- *Correspondence: Manuel Alfonso Patarroyo,
| |
Collapse
|
38
|
Abdel-Ghany SE, LaManna LM, Harroun HT, Maliga P, Sloan DB. Rapid sequence evolution is associated with genetic incompatibilities in the plastid Clp complex. PLANT MOLECULAR BIOLOGY 2022; 108:277-287. [PMID: 35039977 DOI: 10.1007/s11103-022-01241-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE Replacing the native clpP1 gene in the Nicotiana plastid genome with homologs from different donor species showed that the extent of genetic incompatibilities depended on the rate of sequence evolution. The plastid caseinolytic protease (Clp) complex plays essential roles in maintaining protein homeostasis and comprises both plastid-encoded and nuclear-encoded subunits. Despite the Clp complex being retained across green plants with highly conserved protein sequences in most species, examples of extremely accelerated amino acid substitution rates have been identified in numerous angiosperms. The causes of these accelerations have been the subject of extensive speculation but still remain unclear. To distinguish among prevailing hypotheses and begin to understand the functional consequences of rapid sequence divergence in Clp subunits, we used plastome transformation to replace the native clpP1 gene in tobacco (Nicotiana tabacum) with counterparts from another angiosperm genus (Silene) that exhibits a wide range in rates of Clp protein sequence evolution. We found that antibiotic-mediated selection could drive a transgenic clpP1 replacement from a slowly evolving donor species (S. latifolia) to homoplasmy but that clpP1 copies from Silene species with accelerated evolutionary rates remained heteroplasmic, meaning that they could not functionally replace the essential tobacco clpP1 gene. These results suggest that observed cases of rapid Clp sequence evolution are a source of epistatic incompatibilities that must be ameliorated by coevolutionary responses between plastid and nuclear subunits.
Collapse
Affiliation(s)
- Salah E Abdel-Ghany
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Lisa M LaManna
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Haleakala T Harroun
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Pal Maliga
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| |
Collapse
|
39
|
Huang W, Dicks KL, Hadfield JD, Johnston SE, Ballingall KT, Pemberton JM. Contemporary selection on MHC genes in a free-living ruminant population. Ecol Lett 2022; 25:828-838. [PMID: 35050541 PMCID: PMC9306867 DOI: 10.1111/ele.13957] [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: 06/01/2021] [Revised: 10/21/2021] [Accepted: 12/08/2021] [Indexed: 11/27/2022]
Abstract
Genes within the major histocompatibility complex (MHC) are the most variable identified in vertebrates. Pathogen-mediated selection is believed to be the main force maintaining MHC diversity. However, relatively few studies have demonstrated contemporary selection on MHC genes. Here, we examine associations between MHC variation and several fitness measurements including total fitness and five fitness components, in 3400 wild Soay sheep (Ovis aries) monitored between 1989 and 2012. In terms of total fitness, measured as lifetime breeding success of all individuals born, we found haplotypes named C and D were associated with decreased and increased male total fitness respectively. In terms of fitness components, juvenile survival was associated with haplotype divergence while individual haplotypes (C, D and F) were associated with adult fitness components. Consistent with the increased male total fitness, the rarest haplotype D has increased in frequency throughout the study period more than expected under neutral expectations. Our results demonstrate contemporary natural selection is acting on MHC class II genes in Soay sheep and the mode of selection on specific fitness components can be different mode from selection on total fitness.
Collapse
Affiliation(s)
- Wei Huang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Kara L Dicks
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Royal Zoological Society of Scotland, Edinburgh, UK
| | - Jarrod D Hadfield
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
40
|
Peng J, Svetec N, Zhao L. Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels. Mol Biol Evol 2021; 39:6456312. [PMID: 34878126 PMCID: PMC8789070 DOI: 10.1093/molbev/msab350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proteins are the building blocks for almost all the functions in cells. Understanding the molecular evolution of proteins and the forces that shape protein evolution is essential in understanding the basis of function and evolution. Previous studies have shown that adaptation frequently occurs at the protein surface, such as in genes involved in host–pathogen interactions. However, it remains unclear whether adaptive sites are distributed randomly or at regions associated with particular structural or functional characteristics across the genome, since many proteins lack structural or functional annotations. Here, we seek to tackle this question by combining large-scale bioinformatic prediction, structural analysis, phylogenetic inference, and population genomic analysis of Drosophila protein-coding genes. We found that protein sequence adaptation is more relevant to function-related rather than structure-related properties. Interestingly, intermolecular interactions contribute significantly to protein adaptation. We further showed that intermolecular interactions, such as physical interactions, may play a role in the coadaptation of fast-adaptive proteins. We found that strongly differentiated amino acids across geographic regions in protein-coding genes are mostly adaptive, which may contribute to the long-term adaptive evolution. This strongly indicates that a number of adaptive sites tend to be repeatedly mutated and selected throughout evolution in the past, present, and maybe future. Our results highlight the important roles of intermolecular interactions and coadaptation in the adaptive evolution of proteins both at the species and population levels.
Collapse
Affiliation(s)
- Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| |
Collapse
|
41
|
Douillard V, Castelli EC, Mack SJ, Hollenbach JA, Gourraud PA, Vince N, Limou S. Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research. Front Genet 2021; 12:774916. [PMID: 34925459 PMCID: PMC8677840 DOI: 10.3389/fgene.2021.774916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19|HLA & Immunogenetics Consortium.
Collapse
Affiliation(s)
- Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | | | - Steven J. Mack
- Division of Allergy, Immunology and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Department of Computer Sciences and Mathematics in Biology, Nantes, France
| |
Collapse
|
42
|
Huang W, Dicks KL, Ballingall KT, Johnston SE, Sparks AM, Watt K, Pilkington JG, Pemberton JM. Associations between MHC class II variation and phenotypic traits in a free-living sheep population. Mol Ecol 2021; 31:902-915. [PMID: 34748666 DOI: 10.1111/mec.16265] [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: 04/15/2021] [Revised: 10/22/2021] [Accepted: 11/03/2021] [Indexed: 01/03/2023]
Abstract
Pathogen-mediated selection (PMS) is thought to maintain the high level of allelic diversity observed in the major histocompatibility complex (MHC) class II genes. A comprehensive way to demonstrate contemporary selection is to examine associations between MHC variation and individual fitness. As individual fitness is hard to measure, many studies examine associations between MHC variation and phenotypic traits, including direct or indirect measures of adaptive immunity thought to contribute to fitness. Here, we tested associations between MHC class II variation and five phenotypic traits measured in free-living sheep captured in August: weight, strongyle faecal egg count, and plasma IgA, IgE and IgG immunoglobulin titres against the gastrointestinal nematode parasite Teladorsagia circumcincta. We found no association between MHC class II variation and weight or strongyle faecal egg count. We did, however, find associations between MHC class II variation and immunoglobulin levels which varied with isotype, age and sex. Our results suggest associations between MHC and phenotypic traits are more likely to be found for traits more closely associated with pathogen defence than integrative traits such as bodyweight and highlight the association between MHC variation and antibodies in wild populations.
Collapse
Affiliation(s)
- Wei Huang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Kara L Dicks
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Susan E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alexandra M Sparks
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,School of Biology, University of Leeds, Leeds, UK
| | - Kathryn Watt
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jill G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
43
|
Purohit D, Manu S, Ram MS, Sharma S, Patnaik HC, Deka PJ, Narayan G, Umapathy G. Genetic effects of long-term captive breeding on the endangered pygmy hog. PeerJ 2021; 9:e12212. [PMID: 34707930 PMCID: PMC8504462 DOI: 10.7717/peerj.12212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/05/2021] [Indexed: 01/02/2023] Open
Abstract
Long-term captive populations often accumulate genetic changes that are detrimental to their survival in the wild. Periodic genetic evaluation of captive populations is thus necessary to identify deleterious changes and minimize their impact through planned breeding. Pygmy hog (Porcula salvania) is an endangered species with a small population inhabiting the tall sub-Himalayan grasslands of Assam, India. A conservation breeding program of pygmy hog from six founders has produced a multi-generational captive population destined for reintroduction into the wild. However, the impact of conservation breeding on its genetic diversity remained undocumented. Here, we evaluate temporal genetic changes in 39 pygmy hogs from eight consecutive generations of a captive population using genome-wide SNPs, mitochondrial genomes, and MHC sequences, and explore the relationship between genetic diversity and reproductive success. We find that pygmy hog harbors a very low genome-wide heterozygosity (H) compared to other members of the Suidae family. However, within the captive population we find excess heterozygosity and a significant increase in H from the wild-caught founders to the individuals in subsequent generations due to the selective pairing strategy. The MHC and mitochondrial nucleotide diversities were lower in captive generations compared to the founders with a high prevalence of low-frequency MHC haplotypes and more unique mitochondrial genomes. Further, even though no signs of genetic inbreeding were observed from the estimates of individual inbreeding coefficient F and between individuals (FIS) in each generation, the kinship coefficient showed a slightly increasing trend in the recent generations, due to a relatively smaller non-random sample size compared to the entire captive population. Surprisingly, male pygmy hogs that had higher heterozygosity also showed lower breeding success. We briefly discuss the implications of our findings in the context of breeding management and recommend steps to minimize the genetic effects of long-term captive breeding.
Collapse
Affiliation(s)
| | - Shivakumara Manu
- CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Muthuvarmadam Subramanian Ram
- CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India.,CES, Indian Institute of Science, Bangalore, India
| | - Shradha Sharma
- CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Parag Jyoti Deka
- Aaranyak, Threatened Species Recovery Programme,, Beltola, Guwahati, India.,Durrell Wildlife Conservation Trust - Pygmy Hog Conservation Programme, Indira Nagar, Basistha, Guwahati, Assam, India
| | - Goutam Narayan
- EcoSystems-India, Rare & Endangered Species Conservation Unit, Beltola, Guwahati, India
| | | |
Collapse
|
44
|
Tamuri AU, Dos Reis M. A mutation-selection model of protein evolution under persistent positive selection. Mol Biol Evol 2021; 39:6409866. [PMID: 34694387 PMCID: PMC8760937 DOI: 10.1093/molbev/msab309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We use first principles of population genetics to model the evolution of proteins under persistent positive selection (PPS). PPS may occur when organisms are subjected to persistent environmental change, during adaptive radiations, or in host–pathogen interactions. Our mutation–selection model indicates protein evolution under PPS is an irreversible Markov process, and thus proteins under PPS show a strongly asymmetrical distribution of selection coefficients among amino acid substitutions. Our model shows the criteria ω>1 (where ω is the ratio of nonsynonymous over synonymous codon substitution rates) to detect positive selection is conservative and indeed arbitrary, because in real proteins many mutations are highly deleterious and are removed by selection even at positively selected sites. We use a penalized-likelihood implementation of the PPS model to successfully detect PPS in plant RuBisCO and influenza HA proteins. By directly estimating selection coefficients at protein sites, our inference procedure bypasses the need for using ω as a surrogate measure of selection and improves our ability to detect molecular adaptation in proteins.
Collapse
Affiliation(s)
- Asif U Tamuri
- Centre for Advanced Research Computing, University College London, Gower St, London, WC1E 6BT, UK.,EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Mario Dos Reis
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| |
Collapse
|
45
|
Jinam TA, Hosomichi K, Nakaoka H, Phipps ME, Saitou N, Inoue I. Allelic and haplotypic HLA diversity in indigenous Malaysian populations explored using Next Generation Sequencing. Hum Immunol 2021; 83:17-26. [PMID: 34615609 DOI: 10.1016/j.humimm.2021.09.005] [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: 05/22/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/04/2022]
Abstract
The heterogenous population of Malaysia includes more than 50 indigenous groups, and characterizing their HLA diversity would not only provide insights to their ancestry, but also on the effects of natural selection on their genome. We utilized hybridization-based sequence capture and short-read sequencing on the HLA region of 172 individuals representing seven indigenous groups in Malaysia (Jehai, Kintaq, Temiar, Mah Meri, Seletar, Temuan, Bidayuh). Allele and haplotype frequencies of HLA-A, -B, -C, -DRB1, -DQA1, -DQB1, -DPA1, and -DPB1 revealed several ancestry-informative markers. Using SNP-based heterozygosity and pairwise Fst, we observed signals of natural selection, particularly in HLA-A, -C and -DPB1 genes. Consequently, we showed the impact of natural selection on phylogenetic inference using HLA and non-HLA SNPs. We demonstrate the utility of Next Generation Sequencing for generating unambiguous, high-throughput, high-resolution HLA data that adds to our knowledge of HLA diversity and natural selection in indigenous minority groups.
Collapse
Affiliation(s)
- Timothy A Jinam
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan; Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan.
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, Tokyo, Japan
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan; Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| |
Collapse
|
46
|
Buckner JC, Jack KM, Melin AD, Schoof VAM, Gutiérrez-Espeleta GA, Lima MGM, Lynch JW. Major histocompatibility complex class II DR and DQ evolution and variation in wild capuchin monkey species (Cebinae). PLoS One 2021; 16:e0254604. [PMID: 34383779 PMCID: PMC8360539 DOI: 10.1371/journal.pone.0254604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/29/2021] [Indexed: 11/18/2022] Open
Abstract
The major histocompatibility complex (MHC) is an important gene complex contributing to adaptive immunity. Studies of platyrrhine MHC have focused on identifying experimental models of immune system function in the equivalent Human Leukocyte Antigen (HLA). These genes have thus been explored primarily in captive platyrrhine individuals from research colonies. However, investigations of standing MHC variation and evolution in wild populations are essential to understanding its role in immunity, sociality and ecology. Capuchins are a promising model group exhibiting the greatest habitat diversity, widest diet breadth and arguably the most social complexity among platyrrhines, together likely resulting in varied immunological challenges. We use high-throughput sequencing to characterize polymorphism in four Class II DR and DQ exons for the first time in seven capuchin species. We find evidence for at least three copies for DQ genes and at least five for DRB, with possible additional unrecovered diversity. Our data also reveal common genotypes that are inherited across our most widely sampled population, Cebus imitator in Sector Santa Rosa, Costa Rica. Notably, phylogenetic analyses reveal that platyrrhine DQA sequences form a monophyletic group to the exclusion of all Catarrhini sequences examined. This result is inconsistent with the trans-species hypothesis for MHC evolution across infraorders in Primates and provides further evidence for the independent origin of current MHC genetic diversity in Platyrrhini. Identical allele sharing across cebid species, and more rarely genera, however, does underscore the complexity of MHC gene evolution and the need for more comprehensive assessments of allelic diversity and genome structure.
Collapse
Affiliation(s)
- Janet C. Buckner
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States of America
- * E-mail: (JCB); (JWL)
| | - Katharine M. Jack
- Department of Anthropology, Tulane University, New Orleans, LA, United States of America
| | - Amanda D. Melin
- Department of Anthropology & Archaeology and Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Valérie A. M. Schoof
- Bilingual Biology Program, Glendon College, York University, Toronto, ON, Canada
| | | | - Marcela G. M. Lima
- Laboratory of Conservation Biogeography and Macroecology, Federal University of Pará, Belém, PA, Brazil
| | - Jessica W. Lynch
- Institute for Society and Genetics, University of California, Los Angeles, CA, United States of America
- Department of Anthropology, University of California, Los Angeles, CA, United States of America
- * E-mail: (JCB); (JWL)
| |
Collapse
|
47
|
Huang Y, Sun M, Zhuang L, He J. Molecular Phylogenetic Analysis of the AIG Family in Vertebrates. Genes (Basel) 2021; 12:genes12081190. [PMID: 34440364 PMCID: PMC8394805 DOI: 10.3390/genes12081190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 11/21/2022] Open
Abstract
Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.
Collapse
Affiliation(s)
- Yuqi Huang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Minghao Sun
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Lenan Zhuang
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China;
- Correspondence: (L.Z.); (J.H.); Tel.: +86-15-8361-28207 (L.Z.); +86-17-6818-74822 (J.H.)
| | - Jin He
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China;
- Correspondence: (L.Z.); (J.H.); Tel.: +86-15-8361-28207 (L.Z.); +86-17-6818-74822 (J.H.)
| |
Collapse
|
48
|
Shidhi PR, Biju VC, Anu S, Vipin CL, Deelip KR, Achuthsankar SN. Genome Characterization, Comparison and Phylogenetic Analysis of Complete Mitochondrial Genome of Evolvulus alsinoides Reveals Highly Rearranged Gene Order in Solanales. Life (Basel) 2021; 11:769. [PMID: 34440513 PMCID: PMC8398076 DOI: 10.3390/life11080769] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 11/23/2022] Open
Abstract
Mitogenome sequencing provides an understanding of the evolutionary mechanism of mitogenome formation, mechanisms driving plant gene order, genome structure, and migration sequences. Data on the mitochondrial genome for family Convolvulaceae members is lacking. E. alsinoides, also known as shankhpushpi, is an important medicinal plant under the family Convolvulaceae, widely used in the Ayurvedic system of medicine. We identified the mitogenome of E. alsinoides using the Illumina mate-pair sequencing platform, and annotated using bioinformatics approaches in the present study. The mitogenome of E. alsinoides was 344184 bp in length and comprised 46 unique coding genes, including 31 protein-coding genes (PCGs), 12 tRNA genes, and 3 rRNA genes. The secondary structure of tRNAs shows that all the tRNAs can be folded into canonical clover-leaf secondary structures, except three trnW, trnG, and trnC. Measurement of the skewness of the nucleotide composition showed that the AT and GC skew is positive, indicating higher A's and G's in the mitogenome of E. alsinoides. The Ka/Ks ratios of 11 protein-coding genes (atp1, ccmC, cob, cox1, rps19, rps12, nad3, nad9, atp9, rpl5, nad4L) were <1, indicating that these genes were under purifying selection. Synteny and gene order analysis were performed to identify homologous genes among the related species. Synteny blocks representing nine genes (nad9, nad2, ccmFc, nad1, nad4, nad5, matR, cox1, nad7) were observed in all the species of Solanales. Gene order comparison showed that a high level of gene rearrangement has occurred among all the species of Solanales. The mitogenome data obtained in the present study could be used as the Convolvulaceae family representative for future studies, as there is no complex taxonomic history associated with this plant.
Collapse
Affiliation(s)
- Pattayampadam Ramakrishnan Shidhi
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram 695581, India; (V.C.B.); (S.A.); (C.L.V.); (S.N.A.)
| | - Vadakkemukadiyil Chellappan Biju
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram 695581, India; (V.C.B.); (S.A.); (C.L.V.); (S.N.A.)
| | - Sasi Anu
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram 695581, India; (V.C.B.); (S.A.); (C.L.V.); (S.N.A.)
| | - Chandrasekharan Laila Vipin
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram 695581, India; (V.C.B.); (S.A.); (C.L.V.); (S.N.A.)
| | - Kumar Raveendran Deelip
- Campus Computing Facility (CCF) at the Central Laboratory for Instrumentation and Facilitation, University of Kerala, Thiruvananthapuram 695581, India;
| | - Sukumaran Nair Achuthsankar
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram 695581, India; (V.C.B.); (S.A.); (C.L.V.); (S.N.A.)
| |
Collapse
|
49
|
Kang M, Ahn B, Youk S, Cho HS, Choi M, Hong K, Do JT, Song H, Jiang H, Kennedy LJ, Park C. High Allelic Diversity of Dog Leukocyte Antigen Class II in East Asian Dogs: Identification of New Alleles and Haplotypes. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09560-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
50
|
Nunes K, Maia MHT, Dos Santos EJM, Dos Santos SEB, Guerreiro JF, Petzl-Erler ML, Bedoya G, Gallo C, Poletti G, Llop E, Tsuneto L, Bortolini MC, Rothhammer F, Single R, Ruiz-Linares A, Rocha J, Meyer D. How natural selection shapes genetic differentiation in the MHC region: A case study with Native Americans. Hum Immunol 2021; 82:523-531. [PMID: 33812704 PMCID: PMC8217218 DOI: 10.1016/j.humimm.2021.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 02/15/2021] [Accepted: 03/09/2021] [Indexed: 12/19/2022]
Abstract
The Human Leukocyte Antigen (HLA) loci are extremely well documented targets of balancing selection, yet few studies have explored how selection affects population differentiation at these loci. In the present study we investigate genetic differentiation at HLA genes by comparing differentiation at microsatellites distributed genomewide to those in the MHC region. Our study uses a sample of 494 individuals from 30 human populations, 28 of which are Native Americans, all of whom were typed for genomewide and MHC region microsatellites. We find greater differentiation in the MHC than in the remainder of the genome (FST-MHC = 0.130 and FST-Genomic = 0.087), and use a permutation approach to show that this difference is statistically significant, and not accounted for by confounding factors. This finding lies in the opposite direction to the expectation that balancing selection reduces population differentiation. We interpret our findings as evidence that selection favors different sets of alleles in distinct localities, leading to increased differentiation. Thus, balancing selection at HLA genes simultaneously increases intra-population polymorphism and inter-population differentiation in Native Americans.
Collapse
Affiliation(s)
- Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil.
| | | | | | | | | | | | - Gabriel Bedoya
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Giovanni Poletti
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Elena Llop
- Instituto de Ciencias Biomédicas, Faculdad de Medicina, Universidade de Chile, Santiago, Chile
| | - Luiza Tsuneto
- Departamento de Ciências Básicas da Saúde, Universidade Estadual de Maringá, Maringá, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Richard Single
- Department of Mathematics and Statistics, University of Vermont, Burlington, VT, USA
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200433, China; D Aix-Marseille University, CNRS, EFS, ADES, Marseille 13007, France
| | - Jorge Rocha
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal; CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal.
| | - Diogo Meyer
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil.
| |
Collapse
|