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Das NC, Gorai S, Gupta PSS, Panda SK, Rana MK, Mukherjee S. Immune targeting of filarial glutaredoxin through a multi-epitope peptide-based vaccine: A reverse vaccinology approach. Int Immunopharmacol 2024; 133:112120. [PMID: 38657497 DOI: 10.1016/j.intimp.2024.112120] [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: 01/14/2024] [Revised: 04/07/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
Despite the efforts of global programme to eliminate lymphatic filariasis (GPELF), the threat of lymphatic filariasis (LF) still looms over humanity in terms of long-term disabilities, and morbidities across the globe. In light of this situation, investigators have chosen to focus on the development of immunotherapeutics targeting the physiologically important filarial-specific proteins. Glutaredoxin (16.43 kDa) plays a pivotal role in filarial redox biology, serving as a vital contributor. In the context of the intra-host survival of filarial parasites, this antioxidant helps in mitigating the oxidative stress imposed by the host immune system. Given its significant contribution, the development of a vaccine targeting glutaredoxin holds promise as a new avenue for achieving a filaria-free world. Herein, multi-epitope-based vaccine was designed using advanced immunoinformatics approach. Initially, 4B-cell epitopes and 6 T-cell epitopes (4 MHC I and 2 MHC II) were identified from the 146 amino acid long sequence of glutaredoxin of the human filarid, Wuchereria bancrofti. Subsequent clustering of these epitopes with linker peptides finalized the vaccine structure. To boost TLR-mediated innate immunity, TLR-specific adjuvants were incorporated into the designed vaccine. After that, experimental analyses confirm the designed vaccine, Vac4 as anefficient ligand of human TLR5 to elicit protective innate immunity against filarial glutaredoxin. Immune simulation further demonstrated abundant levels of IgG and IgM as crucial contributors in triggering vaccine-induced adaptive responses in the recipients. Hence, to facilitate the validation of immunogenicity of the designed vaccine, Vac4 was cloned in silico in pET28a(+) expression vector for recombinant production. Taken together, our findings suggest that vaccine-mediated targeting of filarial glutaredoxin could be a future option for intervening LF on a global scale.
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Affiliation(s)
- Nabarun Chandra Das
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, West Bengal, India
| | - Sampa Gorai
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, West Bengal, India
| | - Parth Sarthi Sen Gupta
- School of Biosciences & Bioengineering, D. Y. Patil International University, Akurdi, Pune 411044, India
| | - Saroj Kumar Panda
- Department of Chemistry, Indian Institute of Science Education and Research, Berhampur, India
| | - Malay Kumar Rana
- Department of Chemistry, Indian Institute of Science Education and Research, Berhampur, India
| | - Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, West Bengal, India.
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Wade KJ, Suseno R, Kizer K, Williams J, Boquett J, Caillier S, Pollock NR, Renschen A, Santaniello A, Oksenberg JR, Norman PJ, Augusto DG, Hollenbach JA. MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.595060. [PMID: 38826378 PMCID: PMC11142050 DOI: 10.1101/2024.05.20.595060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short read de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target-capture short read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short read data. MHConstructor facilitates wide-spread access to high quality, alignment-free MHC sequence analysis.
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Affiliation(s)
- Kristen J. Wade
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Rayo Suseno
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Kerry Kizer
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jacqueline Williams
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Juliano Boquett
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Stacy Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Nicholas R. Pollock
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Adam Renschen
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Danillo G. Augusto
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, United States
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, 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
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3
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Irastorza-Azcarate I, Kukalev A, Kempfer R, Thieme CJ, Mastrobuoni G, Markowski J, Loof G, Sparks TM, Brookes E, Natarajan KN, Sauer S, Fisher AG, Nicodemi M, Ren B, Schwarz RF, Kempa S, Pombo A. Extensive folding variability between homologous chromosomes in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.591087. [PMID: 38766012 PMCID: PMC11100664 DOI: 10.1101/2024.05.08.591087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.
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Day G, Robb K, Oxley A, Telonis-Scott M, Ujvari B. Organisation and evolution of the major histocompatibility complex class I genes in cetaceans. iScience 2024; 27:109590. [PMID: 38632986 PMCID: PMC11022044 DOI: 10.1016/j.isci.2024.109590] [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: 04/26/2023] [Revised: 09/30/2023] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
A quarter of marine mammals are at risk of extinction, with disease and poor habitat quality contributing to population decline. Investigation of the Major Histocompatibility Complex (MHC) provides insight into species' capacity to respond to immune and environmental challenges. The eighteen available cetacean chromosome level genomes were used to annotate MHC Class I loci, and to reconstruct the phylogenetic relationship of the described loci. The highest number of loci was observed in the striped dolphin (Stenella coeruleoalba), while the least was observed in the pygmy sperm whale (Kogia breviceps) and rough toothed dolphin (Steno bredanensis). Of the species studied, Mysticetes had the most pseudogenes. Evolutionarily, MHC Class I diverged before the speciation of cetaceans. Yet, locus one was genomically and phylogenetically similar in many species, persisting over evolutionary time. This characterisation of MHC Class I in cetaceans lays the groundwork for future population genetics and MHC expression studies.
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Affiliation(s)
- Grace Day
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
- Marine Mammal Foundation, Melbourne 3194, VIC, Australia
| | - Kate Robb
- Marine Mammal Foundation, Melbourne 3194, VIC, Australia
| | - Andrew Oxley
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
| | - Marina Telonis-Scott
- School of Life and Environmental Sciences, Deakin University, Melbourne 3125, VIC, Australia
| | - Beata Ujvari
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
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Sheppard EC, Martin CA, Armstrong C, González-Quevedo C, Illera JC, Suh A, Spurgin LG, Richardson DS. Genotype-environment associations reveal genes potentially linked to avian malaria infection in populations of an endemic island bird. Mol Ecol 2024; 33:e17329. [PMID: 38533805 DOI: 10.1111/mec.17329] [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: 03/07/2023] [Revised: 01/29/2024] [Accepted: 03/01/2024] [Indexed: 03/28/2024]
Abstract
Patterns of pathogen prevalence are, at least partially, the result of coevolutionary host-pathogen interactions. Thus, exploring the distribution of host genetic variation in relation to infection by a pathogen within and across populations can provide important insights into mechanisms of host defence and adaptation. Here, we use a landscape genomics approach (Bayenv) in conjunction with genome-wide data (ddRADseq) to test for associations between avian malaria (Plasmodium) prevalence and host genetic variation across 13 populations of the island endemic Berthelot's pipit (Anthus berthelotii). Considerable and consistent spatial heterogeneity in malaria prevalence was observed among populations over a period of 15 years. The prevalence of malaria infection was also strongly positively correlated with pox (Avipoxvirus) prevalence. Multiple host loci showed significant associations with malaria prevalence after controlling for genome-wide neutral genetic structure. These sites were located near to or within genes linked to metabolism, stress response, transcriptional regulation, complement activity and the inflammatory response, many previously implicated in vertebrate responses to malarial infection. Our findings identify diverse genes - not just limited to the immune system - that may be involved in host protection against malaria and suggest that spatially variable pathogen pressure may be an important evolutionary driver of genetic divergence among wild animal populations, such as Berthelot's pipit. Furthermore, our data indicate that spatio-temporal variation in multiple different pathogens (e.g. malaria and pox in this case) may have to be studied together to develop a more holistic understanding of host pathogen-mediated evolution.
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Affiliation(s)
| | - Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Claire Armstrong
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | - Catalina González-Quevedo
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Grupo Ecología y Evolución de Vertebrados, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo, University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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Tebbe J, Havenstein K, Forcada J, Tiedemann R, Caspers B, Hoffman JI. No evidence for a role of MHC class II genotype in the chemical encoding of heterozygosity and relatedness in Antarctic fur seals. Proc Biol Sci 2024; 291:20232519. [PMID: 38503331 PMCID: PMC10950461 DOI: 10.1098/rspb.2023.2519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024] Open
Abstract
Despite decades of research, surprisingly little is known about the mechanism(s) by which an individual's genotype is encoded in odour. Many studies have focused on the role of the major histocompatibility complex (MHC) owing to its importance for survival and mate choice. However, the salience of MHC-mediated odours compared to chemicals influenced by the rest of the genome remains unclear, especially in wild populations where it is challenging to quantify and control for the effects of the genomic background. We addressed this issue in Antarctic fur seals by analysing skin swabs together with full-length MHC DQB II exon 2 sequences and data from 41 genome-wide distributed microsatellites. We did not find any effects of MHC relatedness on chemical similarity and there was also no relationship between MHC heterozygosity and chemical diversity. However, multilocus heterozygosity showed a significant positive association with chemical diversity, even after controlling for MHC heterozygosity. Our results appear to rule out a dominant role of the MHC in the chemical encoding of genetic information in a wild vertebrate population and highlight the need for genome-wide approaches to elucidate the mechanism(s) and specific genes underlying genotype-odour associations.
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Affiliation(s)
- Jonas Tebbe
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
- Department of Behavioural Ecology, Bielefeld University, 33501 Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Katja Havenstein
- Unit of Evolutionary Biology / Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Ralph Tiedemann
- Unit of Evolutionary Biology / Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Barbara Caspers
- Department of Behavioural Ecology, Bielefeld University, 33501 Bielefeld, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany
| | - Joseph I. Hoffman
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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7
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Olayemi A, Schmid DW, Fleischer R, Wilhelm K, Heni AC, Mueller-Klein N, Haikukutu L, Fichet-Calvet E, Günther S, Sommer S. MHC-I alleles mediate clearance and antibody response to the zoonotic Lassa virus in Mastomys rodent reservoirs. PLoS Negl Trop Dis 2024; 18:e0011984. [PMID: 38421939 PMCID: PMC10903922 DOI: 10.1371/journal.pntd.0011984] [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: 04/18/2023] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
West African Mastomys rodents are the primary reservoir of the zoonotic Lassa virus (LASV). The virus causes haemorrhagic Lassa fever and considerable mortality in humans. To date, the role of Mastomys immunogenetics in resistance to, and persistence of, LASV infections is largely unknown. Here, we investigated the role of Major Histocompatibility Complex class I (MHC-I) on LASV infection status (i.e., active vs. cleared infection, determined via PCR and an immunofluorescence assay on IgG antibodies, respectively) in Mastomys natalensis and M. erythroleucus sampled within southwestern Nigeria. We identified more than 190 and 90 MHC-I alleles by Illumina high throughput-sequencing in M. natalensis and M. erythroleucus, respectively, with different MHC allele compositions and frequencies between LASV endemic and non-endemic sites. In M. natalensis, the MHC allele ManaMHC-I*006 was negatively associated with active infections (PCR-positive) and positively associated with cleared infections (IgG-positive) simultaneously, suggesting efficient immune responses that facilitate LASV clearance in animals carrying this allele. Contrarily, alleles ManaMHC-I*008 and ManaMHC-I*021 in M. natalensis, and MaerMHC-I*008 in M. erythroleucus, were positively associated with active infection, implying susceptibility. Alleles associated with susceptibility shared a glutamic acid at the positively selected codon 57, while ManaMHC-I*006 featured an arginine. There was no link between number of MHC alleles per Mastomys individual and LASV prevalence. Thus, specific alleles, but not MHC diversity per se, seem to mediate antibody responses to viremia. We conclude that co-evolution with LASV likely shaped the MHC-I diversity of the main LASV reservoirs in southwestern Nigeria, and that information on reservoir immunogenetics may hold insights into transmission dynamics and zoonotic spillover risks.
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Affiliation(s)
- Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Dominik Werner Schmid
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Ramona Fleischer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | | | - Nadine Mueller-Klein
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Lavinia Haikukutu
- Department of Wildlife Management, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Elisabeth Fichet-Calvet
- Department of Zoonoses Control, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Stephan Günther
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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Arbanasić H, Medrano-González L, Hrenar T, Mikelić A, Gomerčić T, Svetličić I, Pavlinec Ž, Đuras M, Galov A. Recent selection created distinctive variability patterns on MHC class II loci in three dolphin species from the Mediterranean Sea. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 150:105079. [PMID: 37832898 DOI: 10.1016/j.dci.2023.105079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
The major histocompatibility complex (MHC) includes highly polymorphic genes involved in antigen presentation, which is crucial for adaptive immune response. They represent fitness related genetic markers particularly informative for populations exposed to environmental challenges. Here we analyse the diversity and evolutionary traits of MHC class II DQA and DQB genes in the dolphins Stenella coeruleoalba and Grampus griseus from the Mediterranean Sea. We found substantial nucleotide and functional diversity, as well as strong evidence of balancing selection indicated by allele and supertype frequencies, Tajima's D statistics and dN/dS tests. The Risso's dolphin, considered the least abundant in the region, showed the effect of divergent allele advantage at the nucleotide and functional-peptide levels. An outstanding polymorphism was found in the striped dolphin, particularly intriguing in the DQA gene where the Ewens-Watterson test detected a selection sweep that occurred in recent history. We hypothesize that morbillivirus, which has recurrently invaded Mediterranean populations over the last decades, exerted the detected selective pressure.
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Affiliation(s)
- Haidi Arbanasić
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Luis Medrano-González
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.
| | - Tomica Hrenar
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Ana Mikelić
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Tomislav Gomerčić
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia.
| | - Ida Svetličić
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Željko Pavlinec
- Croatian Academy of Sciences and Arts, Trg Nikole Šubića Zrinskog 11, 10000, Zagreb, Croatia.
| | - Martina Đuras
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia.
| | - Ana Galov
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
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Sebastian A, Migalska M, Gaczorek T. AmpliSAS and AmpliHLA: Web Server and Local Tools for MHC Typing of Non-model Species and Human Using NGS Data. Methods Mol Biol 2024; 2809:37-66. [PMID: 38907889 DOI: 10.1007/978-1-0716-3874-3_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] [Indexed: 06/24/2024]
Abstract
AmpliSAS and AmpliHLA are tools for automatic genotyping of MHC genes from high-throughput sequencing data. AmpliSAS is designed specifically to analyze amplicon sequencing data from non-model species and it is able to perform de novo genotyping without any previous knowledge of the reference alleles. AmpliHLA is a human specific version; it performs HLA typing by comparing sequenced variants against human reference alleles from the IMGT/HLA database. Both tools are available in AmpliSAT web-server as well as scripts for local/server installation. Here we describe the installation and deployment of AmpliSAS and AmpliHLA Perl scripts and dependencies on a local or a server computer. We will show how to run them in the command line using as examples four genotyping protocols: the first two use amplicon sequencing data to genotype the MHC genes of a passerine bird and human respectively; the third and fourth present the HLA typing of a human cell line starting from RNA and exome sequencing data respectively.
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Affiliation(s)
| | - Magdalena Migalska
- Genomics and Experimental Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland.
| | - Tomasz Gaczorek
- Genomics and Experimental Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
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10
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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.
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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.)
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11
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Haikukutu L, Lyaku JR, Lyimo CM, Eiseb SJ, Makundi RH, Olayemi A, Wilhelm K, Müller-Klein N, Schmid DW, Fleischer R, Sommer S. Immunogenetics, sylvatic plague and its vectors: insights from the pathogen reservoir Mastomys natalensis in Tanzania. Immunogenetics 2023; 75:517-530. [PMID: 37853246 PMCID: PMC10651713 DOI: 10.1007/s00251-023-01323-7] [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: 06/14/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
Yersinia pestis is a historically important vector-borne pathogen causing plague in humans and other mammals. Contemporary zoonotic infections with Y. pestis still occur in sub-Saharan Africa, including Tanzania and Madagascar, but receive relatively little attention. Thus, the role of wildlife reservoirs in maintaining sylvatic plague and spillover risks to humans is largely unknown. The multimammate rodent Mastomys natalensis is the most abundant and widespread rodent in peri-domestic areas in Tanzania, where it plays a major role as a Y. pestis reservoir in endemic foci. Yet, how M. natalensis' immunogenetics contributes to the maintenance of plague has not been investigated to date. Here, we surveyed wild M. natalensis for Y. pestis vectors, i.e., fleas, and tested for the presence of antibodies against Y. pestis using enzyme-linked immunosorbent assays (ELISA) in areas known to be endemic or without previous records of Y. pestis in Tanzania. We characterized the allelic and functional (i.e., supertype) diversity of the major histocompatibility complex (MHC class II) of M. natalensis and investigated links to Y. pestis vectors and infections. We detected antibodies against Y. pestis in rodents inhabiting both endemic areas and areas considered non-endemic. Of the 111 nucleotide MHC alleles, only DRB*016 was associated with an increased infestation with the flea Xenopsylla. Surprisingly, we found no link between MHC alleles or supertypes and antibodies of Y. pestis. Our findings hint, however, at local adaptations towards Y. pestis vectors, an observation that more exhaustive sampling could unwind in the future.
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Affiliation(s)
- Lavinia Haikukutu
- Department of Wildlife Management, Sokoine University of Agriculture, Morogoro, Tanzania.
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany.
- Africa Centre of Excellence for Innovative Rodent Pest Management and Biosensor Technology Development, Sokoine University of Agriculture, Morogoro, Tanzania.
| | - Japhet R Lyaku
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Namibia, Windhoek, Namibia
| | - Charles M Lyimo
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture, Chuo Kikuu, Morogoro, Tanzania
| | - Seth J Eiseb
- Department of Environmental Sciences, University of Namibia, Windhoek, Namibia
| | - Rhodes H Makundi
- Africa Centre of Excellence for Innovative Rodent Pest Management and Biosensor Technology Development, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Ayodeji Olayemi
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Natural History Museum, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Nadine Müller-Klein
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Dominik W Schmid
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Ramona Fleischer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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12
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Lescroart J, Bonilla-Sánchez A, Napolitano C, Buitrago-Torres DL, Ramírez-Chaves HE, Pulido-Santacruz P, Murphy WJ, Svardal H, Eizirik E. Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus. Mol Biol Evol 2023; 40:msad255. [PMID: 37987559 PMCID: PMC10701098 DOI: 10.1093/molbev/msad255] [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: 08/31/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023] Open
Abstract
Even in the genomics era, the phylogeny of Neotropical small felids comprised in the genus Leopardus remains contentious. We used whole-genome resequencing data to construct a time-calibrated consensus phylogeny of this group, quantify phylogenomic discordance, test for interspecies introgression, and assess patterns of genetic diversity and demographic history. We infer that the Leopardus radiation started in the Early Pliocene as an initial speciation burst, followed by another in its subgenus Oncifelis during the Early Pleistocene. Our findings challenge the long-held notion that ocelot (Leopardus pardalis) and margay (L. wiedii) are sister species and instead indicate that margay is most closely related to the enigmatic Andean cat (L. jacobita), whose whole-genome data are reported here for the first time. In addition, we found that the newly sampled Andean tiger cat (L. tigrinus pardinoides) population from Colombia associates closely with Central American tiger cats (L. tigrinus oncilla). Genealogical discordance was largely attributable to incomplete lineage sorting, yet was augmented by strong gene flow between ocelot and the ancestral branch of Oncifelis, as well as between Geoffroy's cat (L. geoffroyi) and southern tiger cat (L. guttulus). Contrasting demographic trajectories have led to disparate levels of current genomic diversity, with a nearly tenfold difference in heterozygosity between Andean cat and ocelot, spanning the entire range of variability found in extant felids. Our analyses improved our understanding of the speciation history and diversity patterns in this felid radiation, and highlight the benefits to phylogenomic inference of embracing the many heterogeneous signals scattered across the genome.
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Affiliation(s)
- Jonas Lescroart
- Department of Biology, University of Antwerp, Antwerp, Belgium
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Alejandra Bonilla-Sánchez
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Faculty of Exact and Natural Sciences, University of Antioquia, Medellín, Colombia
| | - Constanza Napolitano
- Department of Biological Sciences and Biodiversity, University of Los Lagos, Osorno, Chile
- Institute of Ecology and Biodiversity, Concepción, Chile
- Cape Horn International Center, Puerto Williams, Chile
- Andean Cat Alliance, Villa Carlos Paz, Argentina
| | - Diana L Buitrago-Torres
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Héctor E Ramírez-Chaves
- Department of Biological Sciences, University of Caldas, Manizales, Colombia
- Centro de Museos, Museo de Historia Natural, University of Caldas, Manizales, Colombia
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, Netherlands
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, Brazil
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13
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Clough J, Schwab S, Mikac K. Gut Microbiome Profiling of the Endangered Southern Greater Glider ( Petauroides volans) after the 2019-2020 Australian Megafire. Animals (Basel) 2023; 13:3583. [PMID: 38003202 PMCID: PMC10668662 DOI: 10.3390/ani13223583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Studying the gut microbiome can provide valuable insights into animal health and inform the conservation management of threatened wildlife. Gut microbiota play important roles in regulating mammalian host physiology, including digestion, energy metabolism and immunity. Dysbiosis can impair such physiological processes and compromise host health, so it is essential that the gut microbiome be considered in conservation planning. The southern greater glider (Petauroides volans) is an endangered arboreal marsupial that faced widespread habitat fragmentation and population declines following the 2019-2020 Australian bushfire season. This study details baseline data on the gut microbiome of this species. The V3-V4 region of the 16S rRNA gene was amplified from scats collected from individuals inhabiting burnt and unburnt sites across southeastern Australia and sequenced to determine bacterial community composition. Southern greater glider gut microbiomes were characterised by high relative abundances of Firmicutes and Bacteroidota, which is consistent with that reported for other marsupial herbivores. Significant differences in gut microbial diversity and community structure were detected among individuals from different geographic locations. Certain microbiota and functional orthologues were also found to be significantly differentially abundant between locations. The role of wildfire in shaping southern greater glider gut microbiomes was shown, with some significant differences in the diversity and abundance of microbiota detected between burnt and unburnt sites. Overall, this study details the first data on greater glider (Petauroides) gut microbiomes, laying the foundation for future studies to further explore relationships between microbial community structure, environmental stressors and host health.
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Affiliation(s)
- Jordyn Clough
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
| | - Sibylle Schwab
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Katarina Mikac
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
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14
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Dong PP, Wang RR, Abduriyim S. Diversity and evolution of the MHC class II DRB gene in the Capra sibirica experienced a demographic fluctuation in China. Sci Rep 2023; 13:19352. [PMID: 37935954 PMCID: PMC10630338 DOI: 10.1038/s41598-023-46717-5] [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: 08/17/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
The major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, and their proteins play a critical role in adaptive immunity for defense against a variety of pathogens. MHC diversity was lost in many species after experiencing a decline in size. To understand the variation and evolution of MHC genes in the Siberian ibex, Capra sibirica, which has undergone a population decline, we analyzed the variation of the second exon of MHC class II DRB genes in samples collected from five geographic localities in Xinjiang, China, that belong to three diverged mitochondrial clades. Consequently, we identified a total of 26 putative functional alleles (PFAs) with 260 bp in length from 43 individuals, and found one (for 27 individuals) to three (for 5 individuals) PFAs per individual, indicating the presence of one or two DRB loci per haploid genome. The Casi-DRB1*16 was the most frequently occurring PFA, Casi-DRB1*22 was found in only seven individuals, 14 PFAs occurred once, 7 PFAs twice, implying high frequency of rare PFAs. Interestingly, more than half (15) of the PFAs were specific to clade I, only two and three PFAs were specific to clades II and III, respectively. So, we assume that the polygamy and sexual segregation nature of this species likely contributed to the allelic diversity of DRB genes. Genetic diversity indices showed that PFAs of clade II were lower in nucleotide, amino acid, and supertype diversity compared to those of the other two clades. The pattern of allele sharing and FST values between the three clades was to some extent in agreement with the pattern observed in mitochondrial DNA divergence. In addition, recombination analyses revealed no evidence for significant signatures of recombination events. Alleles shared by clades III and the other two clades diverged 6 million years ago, and systematic neighbor grids showed Trans-species polymorphism. Together with the PAML and MEME analyses, the results indicated that the DRB gene in C. sibirica evolved under balancing and positive selection. However, by comparison, it can be clearly seen that different populations were under different selective pressures. Our results are valuable in understanding the diversity and evolution of the DRB gene in a mountain living C. sibirica and in making decisions on future long-term protection strategies.
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Affiliation(s)
- Pei-Pei Dong
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Rui-Rui Wang
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Shamshidin Abduriyim
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University, Shihezi, 832003, Xinjiang, China.
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15
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Prem P, Muneshwar KN, Agrawal S, Jaiswal A. The Impact of Increased Homozygosity on Human Fertility: A Comprehensive Review. Cureus 2023; 15:e49000. [PMID: 38111431 PMCID: PMC10726075 DOI: 10.7759/cureus.49000] [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: 10/29/2023] [Accepted: 11/18/2023] [Indexed: 12/20/2023] Open
Abstract
This comprehensive review explores the multifaceted relationship between increased homozygosity and human fertility, delving into the genetic, ethical, cultural, and public health dimensions of this complex phenomenon. Homozygosity, characterized by identical alleles at specific gene loci, can result from consanguineous marriages, genetic drift, and population isolation. The review highlights key findings, including the heightened risk of recessive genetic disorders, the implications for immune system diversity, and the influence on complex traits and diseases. It underscores the critical role of genetic counseling in addressing these consequences, considering the ethical implications, and respecting cultural practices. The delicate balance between genetic diversity and cultural norms is emphasized, calling for increased awareness and community engagement. Looking ahead, the review suggests emerging technologies, longitudinal studies, and interdisciplinary research as crucial avenues for further exploration, with the ultimate goal of informing effective public health policies and interventions that safeguard genetic diversity and cultural traditions for future generations.
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Affiliation(s)
- Pranjal Prem
- Community Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Komal N Muneshwar
- Community Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Suyash Agrawal
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Arpita Jaiswal
- Obstetrics and Gynaecology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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16
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Napolitano C, Sacristán I, Acuña F, Aguilar E, García S, López-Jara MJ, Cabello J, Hidalgo-Hermoso E, Poulin E, Grueber CE. Assessing micro-macroparasite selective pressures and anthropogenic disturbance as drivers of immune gene diversity in a Neotropical wild cat. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:166289. [PMID: 37591403 DOI: 10.1016/j.scitotenv.2023.166289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023]
Abstract
Anthropogenic environmental change is reducing available habitat for wild species, providing novel selection pressures such as infectious diseases and causing species to interact in new ways. The potential for emerging infectious diseases and zoonoses at the interface between humans, domestic animals, and wild species is a key global concern. In vertebrates, diversity at the major histocompatibility complex MHC is critical to disease resilience, and its study in wild populations provides insights into eco-evolutionary dynamics that human activities alter. In natural populations, variation at MHC loci is partly maintained by balancing selection, driven by pathogenic selective pressures. We hypothesize that MHC genetic diversity differs between guigna populations inhabiting human-dominated landscapes (higher pathogen pressures) versus more natural habitats (lower pathogen pressures). We predict that MHC diversity in guignas would be highest in human-dominated landscapes compared with continuous forest habitats. We also expected to find higher MHC diversity in guignas infected with micro and macro parasites (higher parasite load) versus non infected guignas. We characterized for the first time the genetic diversity at three MHC class I and II exons in 128 wild guignas (Leopardus guigna) across their distribution range in Chile (32-46° S) and Argentina, representing landscapes with varying levels of human disturbance. We integrated MHC sequence diversity with multiple measures of anthropogenic disturbance and both micro and macro parasite infection data. We also assessed signatures of positive selection acting on MHC genes. We found significantly higher MHC class I diversity in guignas inhabiting landscapes where houses were present, and with lower percentage of vegetation cover, and also in animals with more severe cardiorespiratory helminth infection (richness and intensity) and micro-macroparasite co-infection. This comprehensive, landscape-level assessment further enhances our knowledge on the evolutionary dynamics and adaptive potential of vertebrates in the face of emerging infectious disease threats and increasing anthropogenic impacts.
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Affiliation(s)
- Constanza Napolitano
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile; Institute of Ecology and Biodiversity (IEB), Concepción, Chile; Cape Horn International Center (CHIC), Puerto Williams, Chile.
| | - Irene Sacristán
- Universidad Andres Bello, Santiago, Chile; Animal Health Research Centre, National Institute for Agricultural and Food Research and Technology (INIA), Centro Superior de Investigaciones Científicas (CSIC), Valdeolmos, Madrid, Spain
| | - Francisca Acuña
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Emilio Aguilar
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Sebastián García
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - María José López-Jara
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Javier Cabello
- Chiloé Silvestre Center for the Conservation of Biodiversity, Ancud, Chile
| | | | - Elie Poulin
- Institute of Ecology and Biodiversity (IEB), Concepción, Chile; Millennium Institute of Biodiversity of Antarctic and Subantarctic Ecosystems and Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
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17
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Ziliotto M, Kulmann-Leal B, Kaminski VDL, Nunes GT, Riesgo RDS, Roman T, Schuch JB, Chies JAB. HLA-G*14 bp indel variant in autism spectrum disorder in a population from southern Brazil. J Neuroimmunol 2023; 383:578194. [PMID: 37683302 DOI: 10.1016/j.jneuroim.2023.578194] [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: 06/23/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Altered immune response during pregnancy has been associated with ASD susceptibility. HLA-G is expressed by the trophoblast at the maternal/fetal interface and induces allogenic tolerance toward the fetus. A 14-bp insertion in the HLA-G 3'UTR (rs371194629) was associated with reduced levels of HLA-G. We aimed to assess the influence of the HLA-G*14 bp indel variant in ASD susceptibility and symptomatology in a Brazilian admixed sample. The insertion genotype (14 bp+/14 bp+) was firstly associated with hetero aggression, but statistical significance was lost after correction (p = 0.035, pcorrected = 0.35). No association between the HLA-G variant and susceptibility to ASD or differential clinical manifestations were observed.
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Affiliation(s)
- Marina Ziliotto
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Post Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Bruna Kulmann-Leal
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Post Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Valéria de Lima Kaminski
- Post Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Universidade Anhembi Morumbi, São José dos Campos, São Paulo, Brazil
| | - Guilherme Tyska Nunes
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Rudimar Dos Santos Riesgo
- Child Neurology Unit, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Tatiana Roman
- Laboratory of Psychiatric Genetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Jaqueline Bohrer Schuch
- Laboratory of Psychiatric Genetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Graduate Program in Psychiatry and Behavioral Sciences, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - José Artur Bogo Chies
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil.
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18
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Mullinax SR, Darby AM, Gupta A, Chan P, Smith BR, Unckless RL. A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.18.553899. [PMID: 37662279 PMCID: PMC10473621 DOI: 10.1101/2023.08.18.553899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales multiple alleles are maintained in populations. In this study, we focus on the Drosophila antimicrobial peptide Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab reared and wild caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous serine for diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general homozygous arginine flies have a longer lifespan after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.
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Affiliation(s)
- Sarah R. Mullinax
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Andrea M. Darby
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Anjali Gupta
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Patrick Chan
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Brittny R. Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Robert L. Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
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19
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Vasek MJ, Mueller SM, Fass SB, Deajon-Jackson JD, Liu Y, Crosby HW, Koester SK, Yi J, Li Q, Dougherty JD. Local translation in microglial processes is required for efficient phagocytosis. Nat Neurosci 2023; 26:1185-1195. [PMID: 37277487 PMCID: PMC10580685 DOI: 10.1038/s41593-023-01353-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/03/2023] [Indexed: 06/07/2023]
Abstract
Neurons, astrocytes and oligodendrocytes locally regulate protein translation within distal processes. Here, we tested whether there is regulated local translation within peripheral microglial processes (PeMPs) from mouse brain. We show that PeMPs contain ribosomes that engage in de novo protein synthesis, and these are associated with transcripts involved in pathogen defense, motility and phagocytosis. Using a live slice preparation, we further show that acute translation blockade impairs the formation of PeMP phagocytic cups, the localization of lysosomal proteins within them, and phagocytosis of apoptotic cells and pathogen-like particles. Finally, PeMPs severed from their somata exhibit and require de novo local protein synthesis to effectively surround pathogen-like particles. Collectively, these data argue for regulated local translation in PeMPs and indicate a need for new translation to support dynamic microglial functions.
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Affiliation(s)
- Michael J Vasek
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Shayna M Mueller
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Stuart B Fass
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jelani D Deajon-Jackson
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Haley W Crosby
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Sarah K Koester
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jiwon Yi
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, Saint Louis, MO, USA
| | - Qingyun Li
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA.
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20
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Lau Q, Igawa T, Kosch TA, Dharmayanthi AB, Berger L, Skerratt LF, Satta Y. Conserved Evolution of MHC Supertypes among Japanese Frogs Suggests Selection for Bd Resistance. Animals (Basel) 2023; 13:2121. [PMID: 37443920 DOI: 10.3390/ani13132121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
The chytrid fungus Batrachochytrium dendrobatidis (Bd) is a major threat to amphibians, yet there are no reports of major disease impacts in East Asian frogs. Genetic variation of the major histocompatibility complex (MHC) has been associated with resistance to Bd in frogs from East Asia and worldwide. Using transcriptomic data collated from 11 Japanese frog species (one individual per species), we isolated MHC class I and IIb sequences and validated using molecular cloning. We then compared MHC from Japanese frogs and other species worldwide, with varying Bd susceptibility. Supertyping analysis, which groups MHC alleles based on physicochemical properties of peptide binding sites, identified that all examined East Asian frogs contained at least one MHC-IIb allele belonging to supertype ST-1. This indicates that, despite the large divergence times between some Japanese frogs (up to 145 million years), particular functional properties in the peptide binding sites of MHC-II are conserved among East Asian frogs. Furthermore, preliminary analysis using NetMHCIIpan-4.0, which predicts potential Bd-peptide binding ability, suggests that MHC-IIb ST-1 and ST-2 have higher overall peptide binding ability than other supertypes, irrespective of whether the peptides are derived from Bd, other fungi, or bacteria. Our findings suggest that MHC-IIb among East Asian frogs may have co-evolved under the same selective pressure. Given that Bd originated in this region, it may be a major driver of MHC evolution in East Asian frogs.
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Affiliation(s)
- Quintin Lau
- Research Center for Integrative Evolutionary Science, Sokendai (The Graduate University for Advanced Studies), Hayama 240-0115, Japan
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Tiffany A Kosch
- One Health Research Group, Faculty of Science, University of Melbourne, Parkville 3010, Australia
| | - Anik B Dharmayanthi
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Bogor 16911, Indonesia
| | - Lee Berger
- One Health Research Group, Faculty of Science, University of Melbourne, Parkville 3010, Australia
| | - Lee F Skerratt
- One Health Research Group, Faculty of Science, University of Melbourne, Parkville 3010, Australia
| | - Yoko Satta
- Research Center for Integrative Evolutionary Science, Sokendai (The Graduate University for Advanced Studies), Hayama 240-0115, Japan
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21
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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: 0] [Impact Index Per Article: 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.
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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
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22
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Mashayekhi P, Omrani MD, Yassin Z, Dehghanifard A, Ashouri L, Aghabozorg Afjeh SS, Shabanzadeh Z. Influence of HLA-A, -B, -DR Polymorphisms on the Severity of COVID-19: A Case-Control Study in the Iranian Population. ARCHIVES OF IRANIAN MEDICINE 2023; 26:261-266. [PMID: 38301089 PMCID: PMC10685865 DOI: 10.34172/aim.2023.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 03/12/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND As an emerging pandemic disease, COVID-19 encompasses a spectrum of clinical diagnoses, from the common cold to severe respiratory syndrome. Considering the shreds of evidence demonstrating the relationship between human leukocyte antigen (HLA) allele diversity and infectious disease susceptibility, this study was conducted to determine the association of HLA alleles with COVID-19 severity in Iranian subjects. METHODS In this case-control study, a total of 200 unrelated individuals (consisting of 100 people with severe COVID-19 and an average age of 55.54 as the case group, and 100 patients with mild COVID-19 with an average age of 48.97 as the control group) were recruited, and HLA typing (Locus A, B, and DR) was performed using the Olerup sequence-specific oligonucleotide (SSO) HLA-typing kit. RESULTS Our results showed that HLA-A*11 and HLA-DRB1*14 alleles were more frequently observed in severe COVID-19 cases, while HLA-B*52 was more common in mild cases, which was in agreement with some previous studies. CONCLUSION Our results confirmed the evidence for the association of HLA alleles with COVID-19 outcomes. We found that HLA-A*11 and HLA-DRB1*14 alleles may be susceptibility factors for severe COVID-19, while HLA-B*52 may be a protective factor. These findings provide new insight into the pathogenesis of COVID-19 and help patient management.
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Affiliation(s)
- Parisa Mashayekhi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mir Davood Omrani
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeynab Yassin
- Antimicrobial resistance Research Center, Institute Of Immunology And Infectious Disease, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Dehghanifard
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Ashouri
- Antimicrobial resistance Research Center, Institute Of Immunology And Infectious Disease, Iran University of Medical Sciences, Tehran, Iran
| | | | - Zahra Shabanzadeh
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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23
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Rohrer SD, Jiménez-Uzcátegui G, Parker PG, Chubiz LM. Composition and function of the Galapagos penguin gut microbiome vary with age, location, and a putative bacterial pathogen. Sci Rep 2023; 13:5358. [PMID: 37005428 PMCID: PMC10067942 DOI: 10.1038/s41598-023-31826-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/17/2023] [Indexed: 04/04/2023] Open
Abstract
Microbial colonization plays a direct role in host health. Understanding the ecology of the resident microbial community for a given host species is thus an important step for detecting population vulnerabilities like disease. However, the idea of integrating microbiome research into conservation is still relatively new, and wild birds have received less attention in this field than mammals or domesticated animals. Here we examine the composition and function of the gut microbiome of the endangered Galapagos penguin (Spheniscus mendiculus) with the goals of characterizing the normal microbial community and resistome, identifying likely pathogens, and testing hypotheses of structuring forces for this community based on demographics, location, and infection status. We collected fecal samples from wild penguins in 2018 and performed 16S rRNA gene sequencing and whole genome sequencing (WGS) on extracted DNA. 16S sequencing revealed that the bacterial phyla Fusobacteria, Epsilonbacteraeota, Firmicutes, and Proteobacteria dominate the community. Functional pathways were computed from WGS data, showing genetic functional potential primarily focused on metabolism-amino acid metabolism, carbohydrate metabolism, and energy metabolism are the most well-represented functional groups. WGS samples were each screened for antimicrobial resistance, characterizing a resistome made up of nine antibiotic resistance genes. Samples were screened for potential enteric pathogens using virulence factors as indicators; Clostridium perfringens was revealed as a likely pathogen. Overall, three factors appear to be shaping the alpha and beta diversity of the microbial community: penguin developmental stage, sampling location, and C. perfringens. We found that juvenile penguins have significantly lower alpha diversity than adults based on three metrics, as well as significantly different beta diversity. Location effects are minimal, but one site has significantly lower Shannon diversity than the other primary sites. Finally, when samples were grouped by C. perfringens virulence factors, we found dramatic changes in beta diversity based on operational taxonomic units, protein families, and functional pathways. This study provides a baseline microbiome for an endangered species, implicates both penguin age and the presence of a potential bacterial pathogen as primary factors associated with microbial community variance, and reveals widespread antibiotic resistance genes across the population.
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Affiliation(s)
- Sage D Rohrer
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, One University Blvd., St. Louis, MO, 63121, USA.
| | | | - Patricia G Parker
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, One University Blvd., St. Louis, MO, 63121, USA
- WildCare Institute, Saint Louis Zoo, One Government Drive, St. Louis, MO, 63110, USA
| | - Lon M Chubiz
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, One University Blvd., St. Louis, MO, 63121, USA
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24
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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]
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25
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Extensive MHC class IIβ diversity across multiple loci in the small-spotted catshark (Scyliorhinus canicula). Sci Rep 2023; 13:3837. [PMID: 36882519 PMCID: PMC9992475 DOI: 10.1038/s41598-023-30876-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
The major histocompatibility complex (MHC) is a multigene family responsible for pathogen detection, and initiation of adaptive immune responses. Duplication, natural selection, recombination, and their resulting high functional genetic diversity spread across several duplicated loci are the main hallmarks of the MHC. Although these features were described in several jawed vertebrate lineages, a detailed MHC IIβ characterization at the population level is still lacking for chondrichthyans (chimaeras, rays and sharks), i.e. the most basal lineage to possess an MHC-based adaptive immune system. We used the small-spotted catshark (Scyliorhinus canicula, Carcharhiniformes) as a case-study species to characterize MHC IIβ diversity using complementary molecular tools, including publicly available genome and transcriptome datasets, and a newly developed high-throughput Illumina sequencing protocol. We identified three MHC IIβ loci within the same genomic region, all of which are expressed in different tissues. Genetic screening of the exon 2 in 41 individuals of S. canicula from a single population revealed high levels of sequence diversity, evidence for positive selection, and footprints of recombination. Moreover, the results also suggest the presence of copy number variation in MHC IIβ genes. Thus, the small-spotted catshark exhibits characteristics of functional MHC IIβ genes typically observed in other jawed vertebrates.
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26
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Munir S, Rahman SB, Rehman S, Saba N, Mazhar K, Naluai ÅT. The Association of HLA Alleles and Haplotypes with Age of Disease Onset in Pakistani Psoriatic Patients. Int Arch Allergy Immunol 2023; 184:202-210. [PMID: 36382644 PMCID: PMC9932843 DOI: 10.1159/000527359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION The human leukocyte antigen (HLA) region on chromosome 6p21 is well known to carry the most important genetic factors in susceptibility to psoriasis. Different HLA alleles and haplotypes have been reported to be associated with psoriasis in different populations. Psoriasis has a variable age of onset and, based on this, it can be classified into two types; type I with age of onset before 40 years of age and type II with age of onset after 40 years of age. The objective of this study was to determine the association of HLA class I and class II alleles and haplotypes with disease and stratification using age of onset in Pakistani psoriatic patients. METHODS A group of 603 individuals (326 cases and 277 controls) were analyzed for HLA class I and II alleles and haplotype association by sequence specific PCR. The association was further analyzed according to the age of onset of the patients. RESULTS We found that HLA alleles B*57 and Cw*06:02, DQB1*03:03:02 are strongly associated with early onset psoriasis, while alleles B*15, DRB1*13:02 and DQB1*03:03:02 are associated with late-onset psoriasis. Cw*06:02 allele was not associated with late-onset psoriasis patients. Allele DQB1*03:03:02 had the highest odds ratio in all patients. We found a novel association specifically with late-onset psoriasis samples with the haplotype HLA-A*11; B*15; Cw*04; DRB1*15; DQB1*05 (Pc = 3.60 × 10-7). We also found strong association with previously reported extended haplotype EH-57.1: HLA-B*57; Cw*06:02; DRB1*07:01; DQB1*03:03:02 in all our patients (Pc = 8.34 × 10-07). CONCLUSION Our results show that different HLA class I and II alleles and haplotypes are associated with psoriasis at different age of onset. In this study, we have reported novel alleles and haplotype association with late-onset psoriasis. Our data confirm the previous strong associations with HLA alleles and haplotypes and also reports novel alleles and haplotype association in Pakistani psoriasis patients.
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Affiliation(s)
- Saeeda Munir
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan,
| | | | - Sadia Rehman
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Nusrat Saba
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Kehkashan Mazhar
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Åsa Torinsson Naluai
- Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden,*Åsa Torinsson Naluai,
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27
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Ameline C, Voegtli F, Andras J, Dexter E, Engelstädter J, Ebert D. Genetic slippage after sex maintains diversity for parasite resistance in a natural host population. SCIENCE ADVANCES 2022; 8:eabn0051. [PMID: 36399570 PMCID: PMC9674289 DOI: 10.1126/sciadv.abn0051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Although parasite-mediated selection is a major driver of host evolution, its influence on genetic variation for parasite resistance is not yet well understood. We monitored resistance in a large population of the planktonic crustacean Daphnia magna over 8 years, as it underwent yearly epidemics of the bacterial pathogen Pasteuria ramosa. We observed cyclic dynamics of resistance: Resistance increased throughout the epidemics, but susceptibility was restored each spring when hosts hatched from sexual resting stages. Host resting stages collected across the year showed that largely resistant host populations can produce susceptible sexual offspring. A genetic model of resistance developed for this host-parasite system, based on multiple loci and strong epistasis, is in partial agreement with our findings. Our results reveal that, despite strong selection for resistance in a natural host population, genetic slippage after sexual reproduction can be a strong factor for the maintenance of genetic diversity of host resistance.
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Affiliation(s)
- Camille Ameline
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Felix Voegtli
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Jason Andras
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Eric Dexter
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
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28
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Gupta SK, Osmanoglu Ö, Minocha R, Bandi SR, Bencurova E, Srivastava M, Dandekar T. Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information. Front Med (Lausanne) 2022; 9:1008527. [PMID: 36405591 PMCID: PMC9669072 DOI: 10.3389/fmed.2022.1008527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2023] Open
Abstract
Candida auris is a globally emerging fungal pathogen responsible for causing nosocomial outbreaks in healthcare associated settings. It is known to cause infection in all age groups and exhibits multi-drug resistance with high potential for horizontal transmission. Because of this reason combined with limited therapeutic choices available, C. auris infection has been acknowledged as a potential risk for causing a future pandemic, and thus seeking a promising strategy for its treatment is imperative. Here, we combined evolutionary information with reverse vaccinology approach to identify novel epitopes for vaccine design that could elicit CD4+ T-cell responses against C. auris. To this end, we extensively scanned the family of proteins encoded by C. auris genome. In addition, a pathogen may acquire substitutions in epitopes over a period of time which could cause its escape from the immune response thus rendering the vaccine ineffective. To lower this possibility in our design, we eliminated all rapidly evolving genes of C. auris with positive selection. We further employed highly conserved regions of multiple C. auris strains and identified two immunogenic and antigenic T-cell epitopes that could generate the most effective immune response against C. auris. The antigenicity scores of our predicted vaccine candidates were calculated as 0.85 and 1.88 where 0.5 is the threshold for prediction of fungal antigenic sequences. Based on our results, we conclude that our vaccine candidates have the potential to be successfully employed for the treatment of C. auris infection. However, in vivo experiments are imperative to further demonstrate the efficacy of our design.
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Affiliation(s)
- Shishir K. Gupta
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Evolutionary Genomics Group, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Özge Osmanoglu
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
| | - Rashmi Minocha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Sourish Reddy Bandi
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
| | - Mugdha Srivastava
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- BioComputing Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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29
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Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals. Sci Rep 2022; 12:17933. [PMID: 36289307 PMCID: PMC9606363 DOI: 10.1038/s41598-022-21658-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/29/2022] [Indexed: 01/20/2023] Open
Abstract
The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
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30
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Knoll A, Wijacki J, Plasil M, Burger PA, Horin P. Microsatellite markers of the major histocompatibility complex genomic region of domestic camels. Front Genet 2022; 13:1015288. [PMID: 36353100 PMCID: PMC9638106 DOI: 10.3389/fgene.2022.1015288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022] Open
Abstract
We identified and characterized 11 polymorphic microsatellite markers suitable for routine testing (three in the MHC class I sub-region, four in MHC class II and four in the MHC class III sub-region) of dromedaries and Bactrian camels. In total, 38 dromedaries and 33 Bactrian camels were genotyped, and interspecific differences were observed in the numbers of alleles and in allelic frequencies, as well as in the observed heterozygosity. These loci may be used as markers to study the adaptive genetic diversity of the MHC region in Old World camels.
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Affiliation(s)
- Ales Knoll
- Department of Animal Morphology, Physiology and Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czechia
| | - Jan Wijacki
- Department of Animal Morphology, Physiology and Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czechia
| | - Martin Plasil
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC-VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Pamela A. Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Petr Horin
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC-VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
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31
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Performance Comparison of Different Approaches in Genotyping MHC-DRB: The Contrast between Single-Locus and Multi-Locus Species. Animals (Basel) 2022; 12:ani12182452. [PMID: 36139311 PMCID: PMC9495155 DOI: 10.3390/ani12182452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Major histocompatibility complex (MHC) genes are widely recognised as valuable markers for wildlife genetic studies given their extreme polymorphism and functional importance in fitness-related traits. Newly developed genotyping methods, which rely on the use of next-generation sequencing (NGS), are gradually replacing traditional cloning and Sanger sequencing methods in MHC genotyping studies. Allele calling in NGS methods remains challenging due to extreme polymorphism and locus multiplication in the MHC coupled with allele amplification bias and the generation of artificial sequences. In this study, we compared the performance of molecular cloning with Illumina and Ion Torrent NGS sequencing in MHC-DRB genotyping of single-locus species (roe deer) and species with multiple DRB loci (red deer) in an attempt to adopt a reliable and straightforward method that does not require complex bioinformatic analyses. Our results show that all methods work similarly well in roe deer, but we demonstrate non-consistency in results across methods in red deer. With Illumina sequencing, we detected a maximum number of alleles in 10 red deer individuals (42), while other methods were somewhat less accurate as they scored 69–81% of alleles detected with Illumina sequencing.
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32
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Molecular Characterization of MHC Class I Alpha 1 and 2 Domains in Asian Seabass (Lates calcarifer). Int J Mol Sci 2022; 23:ijms231810688. [PMID: 36142628 PMCID: PMC9500968 DOI: 10.3390/ijms231810688] [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: 07/08/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
The Asian seabass is of importance both as a farmed and wild animal. With the emergence of infectious diseases, there is a need to understand and characterize the immune system. In humans, the highly polymorphic MHC class I (MHC-I) molecules play an important role in antigen presentation for the adaptive immune system. In the present study, we characterized a single MHC-I gene in Asian seabass (Lates calcarifer) by amplifying and sequencing the MHC-I alpha 1 and alpha 2 domains, followed by multi-sequence alignment analyses. The results indicated that the Asian seabass MHC-I α1 and α2 domain sequences showed an overall similarity within Asian seabass and retained the majority of the conserved binding residues of human leukocyte antigen-A2 (HLA-A2). Phylogenetic tree analysis revealed that the sequences belonged to the U lineage. Mapping the conserved binding residue positions on human HLA-A2 and grass carp crystal structure showed a high degree of similarity. In conclusion, the availability of MHC-I α1 and α2 sequences enhances the quality of MHC class I genetic information in Asian seabass, providing new tools to analyze fish immune responses to pathogen infections, and will be applicable in the study of the phylogeny and the evolution of antigen-specific receptors.
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Pagliuca S, Gurnari C, Rubio MT, Visconte V, Lenz TL. Individual HLA heterogeneity and its implications for cellular immune evasion in cancer and beyond. Front Immunol 2022; 13:944872. [PMID: 36131910 PMCID: PMC9483928 DOI: 10.3389/fimmu.2022.944872] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/17/2022] [Indexed: 01/07/2023] Open
Abstract
Structural and functional variability of human leukocyte antigen (HLA) is the foundation for competent adaptive immune responses against pathogen and tumor antigens as it assures the breadth of the presented immune-peptidome, theoretically sustaining an efficient and diverse T cell response. This variability is presumably the result of the continuous selection by pathogens, which over the course of evolution shaped the adaptive immune system favoring the assortment of a hyper-polymorphic HLA system able to elaborate efficient immune responses. Any genetic alteration affecting this diversity may lead to pathological processes, perturbing antigen presentation capabilities, T-cell reactivity and, to some extent, natural killer cell functionality. A highly variable germline HLA genotype can convey immunogenetic protection against infections, be associated with tumor surveillance or influence response to anti-neoplastic treatments. In contrast, somatic aberrations of HLA loci, rearranging the original germline configuration, theoretically decreasing its variability, can facilitate mechanisms of immune escape that promote tumor growth and immune resistance. The purpose of the present review is to provide a unified and up-to-date overview of the pathophysiological consequences related to the perturbations of the genomic heterogeneity of HLA complexes and their impact on human diseases, with a special focus on cancer.
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Affiliation(s)
- Simona Pagliuca
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH, United States
- Service d’hématologie Clinique, Hôpital Brabois, CHRU Nancy and CNRS UMR 7365 IMoPa, Biopole de l’Université de Loarraine, Vandoeuvre les Nancy, France
| | - Carmelo Gurnari
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH, United States
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Marie Thérèse Rubio
- Service d’hématologie Clinique, Hôpital Brabois, CHRU Nancy and CNRS UMR 7365 IMoPa, Biopole de l’Université de Loarraine, Vandoeuvre les Nancy, France
| | - Valeria Visconte
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH, United States
| | - Tobias L. Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
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Weyrich A, Guerrero-Altamirano TP, Yasar S, Czirják GÁ, Wachter B, Fickel J. First Steps towards the Development of Epigenetic Biomarkers in Female Cheetahs ( Acinonyx jubatus). LIFE (BASEL, SWITZERLAND) 2022; 12:life12060920. [PMID: 35743950 PMCID: PMC9225391 DOI: 10.3390/life12060920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Free-ranging cheetahs (Acinonyx jubatus) are generally healthy, whereas cheetahs under human care, such as those in zoological gardens, suffer from ill-defined infectious and degenerative pathologies. These differences are only partially explained by husbandry management programs because both groups share low genetic diversity. However, mounting evidence suggests that physiological differences between populations in different environments can be tracked down to differences in epigenetic signatures. Here, we identified differentially methylated regions (DMRs) between free-ranging cheetahs and conspecifics in zoological gardens and prospect putative links to pathways relevant to immunity, energy balance and homeostasis. Comparing epigenomic DNA methylation profiles obtained from peripheral blood mononuclear cells (PBMCs) from eight free-ranging female cheetahs from Namibia and seven female cheetahs living in zoological gardens within Europe, we identified DMRs of which 22 were hypermethylated and 23 hypomethylated. Hypermethylated regions in cheetahs under human care were located in the promoter region of a gene involved in host-pathogen interactions (KLC1) and in an intron of a transcription factor relevant for the development of pancreatic β-cells, liver, and kidney (GLIS3). The most canonical mechanism of DNA methylation in promoter regions is assumed to repress gene transcription. Taken together, this could indicate that hypermethylation at the promoter region of KLC1 is involved in the reduced immunity in cheetahs under human care. This approach can be generalized to characterize DNA methylation profiles in larger cheetah populations under human care with a more granular longitudinal data collection, which, in the future, could be used to monitor the early onset of pathologies, and ultimately translate into the development of biomarkers with prophylactic and/or therapeutic potential.
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Affiliation(s)
- Alexandra Weyrich
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (T.P.G.-A.); (S.Y.)
- Correspondence: (A.W.); (B.W.); (J.F.)
| | - Tania P. Guerrero-Altamirano
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (T.P.G.-A.); (S.Y.)
- Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Selma Yasar
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (T.P.G.-A.); (S.Y.)
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gábor Á. Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany;
| | - Bettina Wachter
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
- Correspondence: (A.W.); (B.W.); (J.F.)
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (T.P.G.-A.); (S.Y.)
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Correspondence: (A.W.); (B.W.); (J.F.)
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Moreno-Santillán DD, Machain-Williams C, Hernández-Montes G, Ortega J. Transcriptomic analysis elucidates evolution of the major histocompatibility complex class I in neotropical bats. J Mammal 2022. [DOI: 10.1093/jmammal/gyac052] [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
Abstract
The Order Chiroptera comprises more than 1,400 species, each with its evolutionary history and under unique selective pressures, among which are the host–pathogen interactions. Bats have coped with complex interactions with a broad spectrum of microbes throughout their evolutionary history, prompting the development of unique adaptations that allow them to co-exist with microbes with pathogenic potential more efficiently than other nonadapted species. In this sense, an extraordinary immune system with unique adaptations has been hypothesized in bats. To explore this, we focused on the major histocompatibility complex (MHC), which plays a crucial role in pathogen recognition and presentation to T cells to trigger the adaptive immune response. We analyzed MHC class I transcripts in five species, each from different families of New World bats. From RNA-seq data, we assembled a partial region of the MHC-I comprising the α1 and α2 domains, which are responsible for peptide binding and recognition. We described five putative functional variants, two of which have two independent insertions at the α2 domain. Our results suggest that this insertion appeared after the divergence of the order Chiroptera and may have an adaptive function in the defense against intracellular pathogens, providing evidence of positive selection and trans-specific polymorphism on the peptide-binding sites.
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Affiliation(s)
- Diana D Moreno-Santillán
- Department of Integrative Biology, University of California , Berkeley, California 94720-3200 , USA
| | - Carlos Machain-Williams
- Universidad Autónoma de Yucatán, Laboratorio de Arbovirología , Mérida, Yucatán 97000 , México
| | - Georgina Hernández-Montes
- Universidad Nacional Autónoma de México, Red de apoyo a la Investigación, Coordinación de la Investigación Científica entre Universidad y Red de Apoyo , Ciudad de México 14080 , México
| | - Jorge Ortega
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Departamento de Zoología, Posgrado en Ciencias Quimicobiológicas , Ciudad de México 11350 , México
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Attia MM, Soliman SM, Mahmoud MA, Salem MA. Oxidative stress markers, immune-regulating cytokines, and the pathological evaluation of sheep co-infected with Oestrus ovis and Coenuruscerebralis. Microb Pathog 2022; 169:105613. [PMID: 35705111 DOI: 10.1016/j.micpath.2022.105613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/18/2022]
Abstract
This study aimed to evaluate the immune response using the immune-regulating cytokines as (IL-1β; MHC-I and MHC-II) associated with co-infected sheep Oestrusovis and Coenurus cerebralisas well as oxidative stress markers (malondialdehyde "MDA" and nitric oxide "NO"). So; sheep samples from different regions in Egypt showed different neurological signs, were examined for detection of the cause of the nervous manifestations. Moreover, the O. ovis and C. cerebralis cysts were collected and identified using scanning electron microscopy. The brain tissues were evaluated for different immunological genes such as MHC-I, MHC-II, and Interleukin-1β activity using quantitative real-time PCR (qRT-PCR) techniques, where the infected sheep showed higher MHC-I gene expression (10-fold), higher MHC-II gene expression (peaked at 25-fold), and higher IL-1β gene expression (14-fold) than the control group. The MDA level was significantly increased. Also, stress marker (nitric oxide) levels were significantly higher in infectedsheep than in negative control one. During gross pathology, migrating larvae of O. ovis andC. cerebralis were noticed In such areas, hemorrhages and patches of clotted blood were noticed. cysts with prominent protoscolices were also observed and were attached to the caudal region near the cerebellum.
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Affiliation(s)
- Marwa M Attia
- Department of Parasitology, Faculty of Veterinary Medicine, Cairo University, 12211, Giza, Egypt.
| | - Soliman M Soliman
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, 12211, Giza, Egypt
| | - Mahmoud A Mahmoud
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, PO.12211, Egypt
| | - Mai A Salem
- Department of Parasitology, Faculty of Veterinary Medicine, Cairo University, 12211, Giza, Egypt
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Awadi A, Suchentrunk F, Knauer F, Smith S, Tolesa Z, Ben Slimen H. Spatial diversity of MHC class II DRB exon2 sequences in North African cape hares (Lepus capensis): positive selection and climatic adaptation signals. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Human Leukocyte Antigen (HLA) System: Genetics and Association with Bacterial and Viral Infections. J Immunol Res 2022; 2022:9710376. [PMID: 35664353 PMCID: PMC9162874 DOI: 10.1155/2022/9710376] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/08/2022] [Indexed: 12/19/2022] Open
Abstract
The human leukocyte antigen (HLA) system is one of the most crucial host factors influencing disease progression in bacterial and viral infections. This review provides the basic concepts of the structure and function of HLA molecules in humans. Here, we highlight the main findings on the associations between HLA class I and class II alleles and susceptibility to important infectious diseases such as tuberculosis, leprosy, melioidosis, Staphylococcus aureus infection, human immunodeficiency virus infection, coronavirus disease 2019, hepatitis B, and hepatitis C in populations worldwide. Finally, we discuss challenges in HLA typing to predict disease outcomes in clinical implementation. Evaluation of the impact of HLA variants on the outcome of bacterial and viral infections would improve the understanding of pathogenesis and identify those at risk from infectious diseases in distinct populations and may improve the individual treatment.
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Mancilla-Morales MD, Velarde E, Contreras-Rodríguez A, Gómez-Lunar Z, Rosas-Rodríguez JA, Heras J, Soñanez-Organis JG, Ruiz EA. Characterization, Selection, and Trans-Species Polymorphism in the MHC Class II of Heermann’s Gull (Charadriiformes). Genes (Basel) 2022; 13:genes13050917. [PMID: 35627302 PMCID: PMC9140796 DOI: 10.3390/genes13050917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/16/2022] Open
Abstract
The major histocompatibility complex (MHC) enables vertebrates to cope with pathogens and maintain healthy populations, thus making it a unique set of loci for addressing ecology and evolutionary biology questions. The aim of our study was to examine the variability of Heermann’s Gull MHC class II (MHCIIB) and compare these loci with other Charadriiformes. Fifty-nine MHCIIB haplotypes were recovered from sixty-eight Heermann’s Gulls by cloning, of them, twelve were identified as putative true alleles, forty-five as unique alleles, and two as pseudogenes. Intra and interspecific relationships indicated at least two loci in Heermann’s Gull MHCIIB and trans-species polymorphism among Charadriiformes (coinciding with the documented evidence of two ancient avian MHCIIB lineages, except in the Charadriidae family). Additionally, sites under diversifying selection revealed a better match with peptide-binding sites inferred in birds than those described in humans. Despite the negative anthropogenic activity reported on Isla Rasa, Heermann’s Gull showed MHCIIB variability consistent with population expansion, possibly due to a sudden growth following conservation efforts. Duplication must play an essential role in shaping Charadriiformes MHCIIB variability, buffering selective pressures through balancing selection. These findings suggest that MHC copy number and protected islands can contribute to seabird conservation.
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Affiliation(s)
- Misael Daniel Mancilla-Morales
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
| | - Enriqueta Velarde
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Hidalgo 617, Colonia Río Jamapa, Boca del Rio, Veracruz CP 94290, Mexico;
| | - Araceli Contreras-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico; (A.C.-R.); (Z.G.-L.)
| | - Zulema Gómez-Lunar
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico; (A.C.-R.); (Z.G.-L.)
| | - Jesús A. Rosas-Rodríguez
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Lázaro Cárdenas del Río No. 100, Francisco Villa, Navojoa CP 85880, Mexico;
| | - Joseph Heras
- Departament of Biology, California State University, San Bernardino, 5500 University Parkway, San Bernardino, CA 92407, USA;
| | - José G. Soñanez-Organis
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Lázaro Cárdenas del Río No. 100, Francisco Villa, Navojoa CP 85880, Mexico;
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
| | - Enrico A. Ruiz
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
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Carlson KB, Wcisel DJ, Ackerman HD, Romanet J, Christiansen EF, Niemuth JN, Williams C, Breen M, Stoskopf MK, Dornburg A, Yoder JA. Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus baxteri. CONSERV GENET 2022; 23:669-681. [PMID: 37090205 PMCID: PMC10118071 DOI: 10.1007/s10592-022-01444-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Briefly considered extinct in the wild, the future of the Wyoming toad (Anaxyrus baxteri) continues to rely on captive breeding to supplement the wild population. Given its small natural geographic range and history of rapid population decline at least partly due to fungal disease, investigation of the diversity of key receptor families involved in the host immune response represents an important conservation need. Population decline may have reduced immunogenetic diversity sufficiently to increase the vulnerability of the species to infectious diseases. Here we use comparative transcriptomics to examine the diversity of toll-like receptors and major histocompatibility complex (MHC) sequences across three individual Wyoming toads. We find reduced diversity at MHC genes compared to bufonid species with a similar history of bottleneck events. Our data provide a foundation for future studies that seek to evaluate the genetic diversity of Wyoming toads, identify biomarkers for infectious disease outcomes, and guide breeding strategies to increase genomic variability and wild release successes.
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Affiliation(s)
- Kara B. Carlson
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Dustin J. Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Hayley D. Ackerman
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Jessica Romanet
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Emily F. Christiansen
- Environmental Medicine Consortium, North Carolina State University, Raleigh, NC, USA
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
- North Carolina Aquariums, Raleigh, NC, USA
| | - Jennifer N. Niemuth
- Environmental Medicine Consortium, North Carolina State University, Raleigh, NC, USA
| | - Christina Williams
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Michael K. Stoskopf
- Environmental Medicine Consortium, North Carolina State University, Raleigh, NC, USA
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC USA
| | - Jeffrey A. Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
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Plasil M, Futas J, Jelinek A, Burger PA, Horin P. Comparative Genomics of the Major Histocompatibility Complex (MHC) of Felids. Front Genet 2022; 13:829891. [PMID: 35309138 PMCID: PMC8924298 DOI: 10.3389/fgene.2022.829891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/15/2022] [Indexed: 12/25/2022] Open
Abstract
This review summarizes the current knowledge on the major histocompatibility complex (MHC) of the family Felidae. This family comprises an important domestic species, the cat, as well as a variety of free-living felids, including several endangered species. As such, the Felidae have the potential to be an informative model for studying different aspects of the biological functions of MHC genes, such as their role in disease mechanisms and adaptation to different environments, as well as the importance of genetic diversity for conservation issues in free-ranging or captive populations. Despite this potential, the current knowledge on the MHC in the family as a whole is fragmentary and based mostly on studies of the domestic cat and selected species of big cats. The overall structure of the domestic cat MHC is similar to other mammalian MHCs following the general scheme “centromere-MHC class I-MHC class III-MHC class II” with some differences in the gene contents. An unambiguously defined orthologue of the non-classical class I HLA-E gene has not been identified so far and the class II DQ and DP genes are missing or pseudogenized, respectively. A comparison with available genomes of other felids showed a generally high level of structural and sequence conservation of the MHC region. Very little and fragmentary information on in vitro and/or in vivo biological functions of felid MHC genes is available. So far, no association studies have indicated effects of MHC genetic diversity on a particular disease. No information is available on the role of MHC class I molecules in interactions with Natural Killer (NK) cell receptors or on the putative evolutionary interactions (co-evolution) of the underlying genes. A comparison of complex genomic regions encoding NK cell receptors (the Leukocyte Receptor Complex, LRC and the Natural Killer Cell Complex, NKC) in the available felid genomes showed a higher variability in the NKC compared to the LRC and the MHC regions. Studies of the genetic diversity of domestic cat populations and/or specific breeds have focused mainly on DRB genes. Not surprisingly, higher levels of MHC diversity were observed in stray cats compared to pure breeds, as evaluated by DRB sequencing as well as by MHC-linked microsatellite typing. Immunogenetic analysis in wild felids has only been performed on MHC class I and II loci in tigers, Namibian leopards and cheetahs. This information is important as part of current conservation tasks to assess the adaptive potential of endangered wild species at the human-wildlife interface, which will be essential for preserving biodiversity in a functional ecosystem.
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Affiliation(s)
- Martin Plasil
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Jan Futas
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - April Jelinek
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Pamela A. Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, VIA, Vienna, Austria
| | - Petr Horin
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
- *Correspondence: Petr Horin,
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Le QVC, Youk S, Choi M, Jeon H, Kim WI, Ho CS, Park C. Development of an Immortalized Porcine Fibroblast Cell Panel With Different Swine Leukocyte Antigen Genotypes. Front Genet 2022; 13:815328. [PMID: 35198008 PMCID: PMC8859410 DOI: 10.3389/fgene.2022.815328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
Immortalized cell lines are valuable resources to expand the molecular characterization of major histocompatibility complex genes and their presented antigens. We generated a panel of immortalized cell lines by transfecting human telomerase reverse transcriptase (hTERT) into primary fibroblast cells prepared from ear, fetal, and lung tissues of 10 pigs from five breeds and successfully cultured them for 30-45 passages. The cell growth characteristic of the immortalized fibroblasts was similar to that of primary fibroblast, which was unable to form colonies on soft agar. The genotypes of major swine leukocyte antigen (SLA) genes, including three classical class I (SLA-1, -2, and -3) and three class II genes (DQB1, DRB1, and DQA), were determined using high-resolution typing. A total of 58 alleles, including a novel allele for SLA-2, were identified. Each cell line was unique. A cell line derived from a National Institutes of Health miniature pig was homozygous across the six major SLA genes. The expression levels of SLA classical class I genes varied among the cell lines and were slightly upregulated in the immortalized compared to the primary cells based on semiquantitative reverse transcription polymerase chain reaction. The immortalized porcine fibroblast cell lines with diverse SLA haplotypes that were developed in this study have potential to be applied in studies regarding the molecular characteristics and genetic structure of SLA genes and epitope-major histocompatibility complex interactions in pigs.
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Affiliation(s)
- Quy Van Chanh Le
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - SeungYeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Munjeong Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Won-Il Kim
- College of Veterinary Medicine, Chonbuk National University, Iksan, South Korea
| | - Chak-Sum Ho
- Gift of Hope Organ & Tissue Donor Network, Itasca, IL, United States
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
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Bilderbeek RJC, Baranov MV, van den Bogaart G, Bianchi F. Transmembrane Helices Are an Over-Presented and Evolutionarily Conserved Source of Major Histocompatibility Complex Class I and II Epitopes. Front Immunol 2022; 12:763044. [PMID: 35087515 PMCID: PMC8787072 DOI: 10.3389/fimmu.2021.763044] [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: 08/23/2021] [Accepted: 12/02/2021] [Indexed: 11/28/2022] Open
Abstract
Cytolytic T cell responses are predicted to be biased towards membrane proteins. The peptide-binding grooves of most alleles of histocompatibility complex class I (MHC-I) are relatively hydrophobic, therefore peptide fragments derived from human transmembrane helices (TMHs) are predicted to be presented more often as would be expected based on their abundance in the proteome. However, the physiological reason of why membrane proteins might be over-presented is unclear. In this study, we show that the predicted over-presentation of TMH-derived peptides is general, as it is predicted for bacteria and viruses and for both MHC-I and MHC-II, and confirmed by re-analysis of epitope databases. Moreover, we show that TMHs are evolutionarily more conserved, because single nucleotide polymorphisms (SNPs) are present relatively less frequently in TMH-coding chromosomal regions compared to regions coding for extracellular and cytoplasmic protein regions. Thus, our findings suggest that both cytolytic and helper T cells are more tuned to respond to membrane proteins, because these are evolutionary more conserved. We speculate that TMHs are less prone to mutations that enable pathogens to evade T cell responses.
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Affiliation(s)
- Richèl J C Bilderbeek
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology (GBB) Institute, University of Groningen, Groningen, Netherlands
| | - Maksim V Baranov
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology (GBB) Institute, University of Groningen, Groningen, Netherlands
| | - Geert van den Bogaart
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology (GBB) Institute, University of Groningen, Groningen, Netherlands
| | - Frans Bianchi
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology (GBB) Institute, University of Groningen, Groningen, Netherlands
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Viluma A, Flagstad Ø, Åkesson M, Wikenros C, Sand H, Wabakken P, Ellegren H. Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population. Genome Res 2022; 32:449-458. [PMID: 35135873 PMCID: PMC8896455 DOI: 10.1101/gr.276070.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022]
Abstract
Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%–24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.
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Martin KR, Mansfield KL, Savage AE. Adaptive evolution of major histocompatibility complex class I immune genes and disease associations in coastal juvenile sea turtles. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211190. [PMID: 35154791 PMCID: PMC8825991 DOI: 10.1098/rsos.211190] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/06/2022] [Indexed: 05/12/2023]
Abstract
Characterizing polymorphism at the major histocompatibility complex (MHC) genes is key to understanding the vertebrate immune response to disease. Despite being globally afflicted by the infectious tumour disease fibropapillomatosis (FP), immunogenetic variation in sea turtles is minimally explored. We sequenced the α 1 peptide-binding region of MHC class I genes (162 bp) from 268 juvenile green (Chelonia mydas) and 88 loggerhead (Caretta caretta) sea turtles in Florida, USA. We recovered extensive variation (116 alleles) and trans-species polymorphism. Supertyping analysis uncovered three functional MHC supertypes corresponding to the three well-supported clades in the phylogeny. We found significant evidence of positive selection at seven amino acid sites in the class I exon. Random forest modelling and risk ratio analysis of Ch. mydas alleles uncovered one allele weakly associated with smooth FP tumour texture, which may be associated with disease outcome. Our study represents the first characterization of MHC class I diversity in Ch. mydas and the largest sample of sea turtles used to date in any study of adaptive genetic variation, revealing tremendous genetic variation and high adaptive potential to viral pathogen threats. The novel associations we identified between MHC diversity and FP outcomes in sea turtles further highlight the importance of evaluating genetic predictors of disease, including MHC and other functional markers.
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Affiliation(s)
- Katherine R. Martin
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
| | - Katherine L. Mansfield
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
| | - Anna E. Savage
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
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Köhnk S, Petros C, Lomas C, Riyad EM, Shameel I, Hawlitschek O, Stelfox M. Stowaways: Marine Leeches Infecting Olive Ridley Sea Turtles Entangled in Ghost Nets in Maldivian Waters. COMP PARASITOL 2021. [DOI: 10.1654/1525-2647-88.2.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Stephanie Köhnk
- Olive Ridley Project, Stone Moor Bottom, Padiham, BB12 7BW, U.K.; and University of Hamburg, Center of Natural History, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany (e-mail: )
| | - Claire Petros
- Olive Ridley Project, Stone Moor Bottom, Padiham, BB12 7BW, U.K. (e-mail: )
| | - Claire Lomas
- Olive Ridley Project, Stone Moor Bottom, Padiham, BB12 7BW, U.K. (e-mail: )
| | - Enas Mohamed Riyad
- Environmental Protection Agency, Handhuvaree Hingun, Malé, Republic of Maldives (e-mail: )
| | - Ibrahim Shameel
- Olive Ridley Project, Stone Moor Bottom, Padiham, BB12 7BW, U.K. (e-mail: )
| | - Oliver Hawlitschek
- University of Hamburg, Center of Natural History, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany (e-mail: )
| | - Martin Stelfox
- Olive Ridley Project, Stone Moor Bottom, Padiham, BB12 7BW, U.K.; and Aquatic Research Facility, Environment Sustainability Research Centre, College of Life and Natural Sciences, University of Derby, U.K. (e-mail: )
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Patra B, Panigrahi M, Kumar H, Kaisa K, Dutt T, Bhushan B. Molecular and phylogenetic analysis of MHC class I exons 7-8 in a variety of cattle and buffalo breeds. Anim Biotechnol 2021:1-7. [PMID: 34806546 DOI: 10.1080/10495398.2021.1999969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The present study was conducted on the MHC class I (BoLA-A/BuLA-A) gene in Sahiwal, Jersey, Hariana, and Tharparkar breeds of cattle and Murrah, Mehsana, and Bhadawari breeds of buffalo to study the polymorphism. Exons 7-8 of the MHC class I gene was first characterized for polymorphism study in buffalo and the results reveal that this gene has a higher level of nucleotide changes than the cattle. Genes were investigated for polymorphisms in 285 animals of cattle and buffalo breeds. Molecular characterization of the MHC class I (BoLa-A/Bula-A) gene reveals a higher degree of polymorphism at the nucleotide level in cattle and buffalo. Results revealed this region has a higher level of polymorphisms in buffalo as campared to the cattle. Alul restriction patterns were monomorphic except for three different patterns but it was able to illustrate the differences in buffalo and cattle. SSCP analysis of exons 7-8 showed remarkable differences in cattle and buffalo. Sequence analysis revealed more closeness of Murrah breed with crossbred and indigenous cattle than Holstein Friesian. Exon 8 had more deletion and stop codon as compared to exon 7. The investigation confirmed that MHC class I BoLa-A/Bula-A exons 7-8 is highly polymorphic in buffalo as compared to cattle.
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Affiliation(s)
- Biswanath Patra
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kaiho Kaisa
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
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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: 2] [Impact Index Per Article: 0.7] [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.
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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
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Bilgmann K, Armansin N, Ferchaud A, Normandeau E, Bernatchez L, Harcourt R, Ahonen H, Lowther A, Goldsworthy S, Stow A. Low effective population size in the genetically bottlenecked Australian sea lion is insufficient to maintain genetic variation. Anim Conserv 2021. [DOI: 10.1111/acv.12688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K. Bilgmann
- Department of Biological Sciences Macquarie University Sydney Australia
| | - N. Armansin
- Department of Biological Sciences Macquarie University Sydney Australia
| | - A.L. Ferchaud
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec QC Canada
| | - E. Normandeau
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec QC Canada
| | - L. Bernatchez
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec QC Canada
| | - R. Harcourt
- Department of Biological Sciences Macquarie University Sydney Australia
| | - H. Ahonen
- Department of Biological Sciences Macquarie University Sydney Australia
- Norwegian Polar Institute Tromsø Norway
| | | | - S.D. Goldsworthy
- South Australian Research and Development Institute Adelaide South Australia
| | - A. Stow
- Department of Biological Sciences Macquarie University Sydney Australia
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Cheng Y, Grueber C, Hogg CJ, Belov K. Improved high-throughput MHC typing for non-model species using long-read sequencing. Mol Ecol Resour 2021; 22:862-876. [PMID: 34551192 PMCID: PMC9293008 DOI: 10.1111/1755-0998.13511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/26/2021] [Accepted: 09/06/2021] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) plays a critical role in the vertebrate immune system. Accurate MHC typing is critical to understanding not only host fitness and disease susceptibility, but also the mechanisms underlying host‐pathogen co‐evolution. However, due to the high degree of gene duplication and diversification of MHC genes, it is often technically challenging to accurately characterise MHC genetic diversity in non‐model species. Here we conducted a systematic review to identify common issues associated with current widely used MHC typing approaches. Then to overcome these challenges, we developed a long‐read based MHC typing method along with a new analysis pipeline. Our approach enables the sequencing of fully phased MHC alleles spanning all key functional domains and the separation of highly similar alleles as well as the removal of technical artefacts such as PCR heteroduplexes and chimeras. Using this approach, we performed population‐scale MHC typing in the Tasmanian devil (Sarcophilus harrisii), revealing previously undiscovered MHC functional diversity in this endangered species. Our new method provides a better solution for addressing research questions that require high MHC typing accuracy. Since the method is not limited by species or the number of genes analysed, it will be applicable for studying not only the MHC but also other complex gene families.
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Affiliation(s)
- Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Catherine Grueber
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.,San Diego Zoo Wildlife Alliance, San Diego, California, USA
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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