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O'Connor AM, Hagenauer MH, Thew Forrester LC, Maras PM, Arakawa K, Hebda-Bauer EK, Khalil H, Richardson ER, Rob FI, Sannah Y, Watson SJ, Akil H. Adolescent environmental enrichment induces social resilience and alters neural gene expression in a selectively bred rodent model with anxious phenotype. Neurobiol Stress 2024; 31:100651. [PMID: 38933284 PMCID: PMC11201356 DOI: 10.1016/j.ynstr.2024.100651] [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: 10/04/2023] [Revised: 04/10/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Stress is a major influence on mental health status; the ways that individuals respond to or copes with stressors determine whether they are negatively affected in the future. Stress responses are established by an interplay between genetics, environment, and life experiences. Psychosocial stress is particularly impactful during adolescence, a critical period for the development of mood disorders. In this study we compared two established, selectively-bred Sprague Dawley rat lines, the "internalizing" bred Low Responder (bLR) line versus the "externalizing" bred High Responder (bHR) line, to investigate how genetic temperament and adolescent environment impact future responses to social interactions and psychosocial stress, and how these determinants of stress response interact. Male bLR and bHR rats were exposed to social and environmental enrichment in adolescence prior to experiencing social defeat and were then assessed for social interaction and anxiety-like behavior. Adolescent enrichment caused rats to display more social interaction, as well as nominally less social avoidance, less submission during defeat, and resilience to the effects of social stress on corticosterone, in a manner that seemed more notable in bLRs. For bHRs, enrichment also caused greater aggression during a neutral social encounter and nominally during defeat, and decreased anxiety-like behavior. To explore the neurobiology underlying the development of social resilience in the anxious phenotype bLRs, RNA-seq was conducted on the hippocampus and nucleus accumbens, two brain regions that mediate stress regulation and social behavior. Gene sets previously associated with stress, social behavior, aggression and exploratory activity were enriched with differential expression in both regions, with a particularly large effect on gene sets that regulate social behaviors. Our findings provide further evidence that adolescent enrichment can serve as an inoculating experience against future stressors. The ability to induce social resilience in a usually anxious line of animals by manipulating their environment has translational implications, as it underscores the feasibility of intervention strategies targeted at genetically vulnerable adolescent populations.
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Affiliation(s)
| | - Megan Hastings Hagenauer
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Liam Cannon Thew Forrester
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Pamela M. Maras
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Keiko Arakawa
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Elaine K. Hebda-Bauer
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Huzefa Khalil
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Evelyn R. Richardson
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Farizah I. Rob
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Yusra Sannah
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Stanley J. Watson
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Huda Akil
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
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O'Connor AM, Hagenauer MH, Forrester LCT, Maras PM, Arakawa K, Hebda-Bauer EK, Khalil H, Richardson ER, Rob FI, Sannah Y, Watson SJ, Akil H. Adolescent environmental enrichment induces social resilience and alters neural gene expression in a selectively bred rodent model with anxious phenotype. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.03.560702. [PMID: 38645129 PMCID: PMC11030238 DOI: 10.1101/2023.10.03.560702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Stress is a major influence on mental health status; the ways that individuals respond to or copes with stressors determine whether they are negatively affected in the future. Stress responses are established by an interplay between genetics, environment, and life experiences. Psychosocial stress is particularly impactful during adolescence, a critical period for the development of mood disorders. In this study we compared two established, selectively-bred Sprague Dawley rat lines, the "internalizing" bred Low Responder (bLR) line versus the "externalizing" bred High Responder (bHR) line, to investigate how genetic temperament and adolescent environment impact future responses to social interactions and psychosocial stress, and how these determinants of stress response interact. Male bLR and bHR rats were exposed to social and environmental enrichment in adolescence prior to experiencing social defeat and were then assessed for social interaction and anxiety-like behavior. Adolescent enrichment caused rats to display more social interaction, as well as nominally less social avoidance, less submission during defeat, and resilience to the effects of social stress on corticosterone, in a manner that seemed more notable in bLRs. For bHRs, enrichment also caused greater aggression during a neutral social encounter and nominally during defeat, and decreased anxiety-like behavior. To explore the neurobiology underlying the development of social resilience in the anxious phenotype bLRs, RNA-seq was conducted on the hippocampus and nucleus accumbens, two brain regions that mediate stress regulation and social behavior. Gene sets previously associated with stress, social behavior, aggression and exploratory activity were enriched with differential expression in both regions, with a particularly large effect on gene sets that regulate social behaviors. Our findings provide further evidence that adolescent enrichment can serve as an inoculating experience against future stressors. The ability to induce social resilience in a usually anxious line of animals by manipulating their environment has translational implications, as it underscores the feasibility of intervention strategies targeted at genetically vulnerable adolescent populations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Huda Akil
- Univ. of Michigan, Ann Arbor, MI, USA
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3
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Shegarfi H. Recognition of Listeria monocytogenes infection by natural killer cells: Towards a complete picture by experimental studies in rats. Innate Immun 2023; 29:110-121. [PMID: 37285590 PMCID: PMC10468624 DOI: 10.1177/17534259231178223] [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: 12/14/2022] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 06/09/2023] Open
Abstract
The study of cellular immune responses in animal disease models demands detailed knowledge of development, function, and regulation of immune cells, including natural killer (NK) cells. Listeria monocytogenes (LM) bacterium has been explored in a large area of research fields, including the host pathogen interaction. Although the importance role of NK cells in controlling the first phase of LM burden has been investigated, the interaction between NK cells and infected cells in details are far from being comprehended. From in vivo and in vitro experiments, we can drive several important pieces of knowledge that hopefully contribute to illuminating the intercommunication between LM-infected cells and NK cells. Experimental studies performed in rats revealed that certain NK cell ligands are influenced in LM-infected cells. These ligands include both classical- and non-classical MHC class I molecules and C-type lectin related (Clr) molecules that are ligands for Ly49- and NKR-P1 receptors respectively. Interaction between these receptors:ligands during LM infection, demonstrated stimulation of rat NK cells. Hence, these studies provided additional knowledge to the mechanisms NK cells utilise to recognise and respond to LM infection outlined in the current review.
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Zhao C, Chen S, Han Y, Zhang F, Ren M, Hu Q, Ye P, Li X, Jin E, Li S. Proteomic Analysis of Rat Duodenum Reveals the Modulatory Effect of Boron Supplementation on Immune Activity. Genes (Basel) 2023; 14:1560. [PMID: 37628612 PMCID: PMC10454175 DOI: 10.3390/genes14081560] [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: 06/14/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
The proper supplementation of boron, an essential trace element, can enhance animal immune function. We utilized the method of TMT peptide labeling in conjunction with LC-MS/MS quantitative proteomics for the purpose of examining the effects of boric acid on a rat model and analyzing proteins from the duodenum. In total, 5594 proteins were obtained from the 0, 10, and 320 mg/L boron treatment groups. Two hundred eighty-four proteins that exhibit differential expression were detected. Among the comparison, groups of 0 vs. 10 mg/L, 0 vs. 320 mg/L, and 10 vs. 320 mg/L of boron, 110, 32, and 179 proteins, respectively, demonstrated differential expression. The results revealed that these differential expression proteins (DEPs) mainly clustered into two profiles. GO annotations suggested that most of the DEPs played a role in the immune system process, in which 2'-5'-oligoadenylate synthetase-like, myxovirus resistance 1, myxovirus resistance 2, dynein cytoplasmic 1 intermediate chain 1, and coiled-coil domain containing 88B showed differential expression. The DEPs had demonstrated an augmentation in the signaling pathways, which primarily include phagosome, antigen processing, and presentation, as well as cell adhesion molecules (CAMs). Our study found that immune responses in the duodenum were enhanced by lower doses of boron and that this effect is likely mediated by changes in protein expression patterns in related signaling pathways. It offers an in-depth understanding of the underlying molecular mechanisms that lead to immune modulation in rats subjected to dietary boron treatment.
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Affiliation(s)
- Chunfang Zhao
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China; (C.Z.); (S.C.); (Y.H.); (F.Z.); (M.R.); (Q.H.); (P.Y.); (X.L.); (S.L.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China
| | - Shuqin Chen
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China; (C.Z.); (S.C.); (Y.H.); (F.Z.); (M.R.); (Q.H.); (P.Y.); (X.L.); (S.L.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China
| | - Yujiao Han
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China; (C.Z.); (S.C.); (Y.H.); (F.Z.); (M.R.); (Q.H.); (P.Y.); (X.L.); (S.L.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China
| | - Feng Zhang
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China; (C.Z.); (S.C.); (Y.H.); (F.Z.); (M.R.); (Q.H.); (P.Y.); (X.L.); (S.L.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China
| | - Man Ren
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China; (C.Z.); (S.C.); (Y.H.); (F.Z.); (M.R.); (Q.H.); (P.Y.); (X.L.); (S.L.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China
| | - Qianqian Hu
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China; (C.Z.); (S.C.); (Y.H.); (F.Z.); (M.R.); (Q.H.); (P.Y.); (X.L.); (S.L.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China
| | - Pengfei Ye
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China; (C.Z.); (S.C.); (Y.H.); (F.Z.); (M.R.); (Q.H.); (P.Y.); (X.L.); (S.L.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China
| | - Xiaojin Li
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China; (C.Z.); (S.C.); (Y.H.); (F.Z.); (M.R.); (Q.H.); (P.Y.); (X.L.); (S.L.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China
| | - Erhui Jin
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China; (C.Z.); (S.C.); (Y.H.); (F.Z.); (M.R.); (Q.H.); (P.Y.); (X.L.); (S.L.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China
| | - Shenghe Li
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China; (C.Z.); (S.C.); (Y.H.); (F.Z.); (M.R.); (Q.H.); (P.Y.); (X.L.); (S.L.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9 Donghua Road, Fengyang County, Chuzhou 233100, China
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Robertson JO, Bazeley P, Erzurum SC, Asosingh K. Single-cell transcriptomic profiling of microvascular endothelial cell heterogeneity in congenital diaphragmatic hernia. Sci Rep 2023; 13:9851. [PMID: 37330615 PMCID: PMC10276841 DOI: 10.1038/s41598-023-37050-y] [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: 03/10/2022] [Accepted: 06/15/2023] [Indexed: 06/19/2023] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a neonatal anomaly that includes pulmonary hypoplasia and hypertension. We hypothesized that microvascular endothelial cell (EC) heterogeneity is different in CDH lungs and related to lung underdevelopment and remodeling. To test this, we evaluated rat fetuses at E21.5 in a nitrofen model of CDH to compare lung transcriptomes among healthy controls (2HC), nitrofen-exposed controls (NC) and nitrofen-exposed subjects with CDH. Single-cell RNA sequencing with unbiased clustering revealed 3 distinct microvascular EC clusters: a general population (mvEC), a proliferative population and a population high in hemoglobin. Only the CDH mvEC cluster had a distinct inflammatory transcriptomic signature as compared to the 2HC and NC endothelial cells, e.g. greater activation and adhesion of inflammatory cells and production of reactive oxygen species. Furthermore, CDH mvECs had downregulated Ca4, Apln and Ednrb gene expression. Those genes are markers for ECs important to lung development, gas exchange and alveolar repair (mvCa4+). mvCa4+ ECs were reduced in CDH (2HC [22.6%], NC [13.1%] and CDH [5.3%], p < 0.0001). Overall, these findings identify transcriptionally distinct microvascular endothelial cell clusters in CDH, including the distinctly inflammatory mvEC cluster and the depleted group of mvCa4+ ECs, which together may contribute to pathogenesis.
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Affiliation(s)
- Jason O Robertson
- Department of Pediatric Surgery, Digestive Disease and Surgery Institute, Cleveland Clinic Children's, 9500 Euclid Avenue/A10, Cleveland, OH, 44195, USA.
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Cleveland Clinic Lerner Research Institute, Cleveland, 44195, USA
| | - Serpil C Erzurum
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, 44195, USA
| | - Kewal Asosingh
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, 44195, USA
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Allgood JE, Roballo KCS, Sparks BB, Bushman JS. The effects of graft source and orientation on outcomes after ablation of a branched peripheral nerve. Front Cell Neurosci 2022; 16:1055490. [PMID: 36451654 PMCID: PMC9701849 DOI: 10.3389/fncel.2022.1055490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/28/2022] [Indexed: 09/10/2024] Open
Abstract
Segmental peripheral nerve injuries (PNI) are the most common cause of enduring nervous system dysfunction. The peripheral nervous system (PNS) has an extensive and highly branching organization. While much is known about the factors that affect regeneration through sharp bisections and linear ablations of peripheral nerves, very little has been investigated or documented about PNIs that ablate branch points. Such injuries present additional complexity compared to linear segmental defects. This study compared outcomes following ablation of a branch point with branched grafts, specifically examining how graft source and orientation of the branched graft contributed to regeneration. The model system was Lewis rats that underwent a 2.5 cm ablation that started in the sciatic nerve trunk and included the peroneal/tibial branch point. Rats received grafts that were rat sciatic autograft, inbred sciatic allograft, and inbred femoral allograft, each of which was a branched graft of 2.5 cm. Allografts were obtained from Lewis rats, which is an inbred strain. Both branches of the sciatic grafts were mixed motor and sensory while the femoral grafts were smaller in diameter than sciatic grafts and one branch of the femoral graft is sensory and the other motor. All branched grafts were sutured into the defect in two orientations dictated by which branch in the graft was sutured to the tibial vs peroneal stumps in recipients. Outcome measures include compound muscle action potentials (CMAPs) and CatWalk gait analysis throughout the recovery period, with toluidine blue for intrinsic nerve morphometry and retrograde labeling conducted at the 36-week experimental end point. Results indicate that graft source and orientation does play a significant role earlier in the regenerative process but by 36 weeks all groups showed very similar indications of regeneration across multiple outcomes.
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Affiliation(s)
| | | | | | - Jared S. Bushman
- Division of Pharmaceutical Sciences, University of Wyoming, Laramie, WY, United States
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Card DC, Van Camp AG, Santonastaso T, Jensen-Seaman MI, Anthony NM, Edwards SV. Structure and evolution of the squamate major histocompatibility complex as revealed by two Anolis lizard genomes. Front Genet 2022; 13:979746. [PMID: 36425073 PMCID: PMC9679377 DOI: 10.3389/fgene.2022.979746] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/20/2022] [Indexed: 11/10/2022] Open
Abstract
The major histocompatibility complex (MHC) is an important genomic region for adaptive immunity and has long been studied in ecological and evolutionary contexts, such as disease resistance and mate and kin selection. The MHC has been investigated extensively in mammals and birds but far less so in squamate reptiles, the third major radiation of amniotes. We localized the core MHC genomic region in two squamate species, the green anole (Anolis carolinensis) and brown anole (A. sagrei), and provide the first detailed characterization of the squamate MHC, including the presence and ordering of known MHC genes in these species and comparative assessments of genomic structure and composition in MHC regions. We find that the Anolis MHC, located on chromosome 2 in both species, contains homologs of many previously-identified mammalian MHC genes in a single core MHC region. The repetitive element composition in anole MHC regions was similar to those observed in mammals but had important distinctions, such as higher proportions of DNA transposons. Moreover, longer introns and intergenic regions result in a much larger squamate MHC region (11.7 Mb and 24.6 Mb in the green and brown anole, respectively). Evolutionary analyses of MHC homologs of anoles and other representative amniotes uncovered generally monophyletic relationships between species-specific homologs and a loss of the peptide-binding domain exon 2 in one of two mhc2β gene homologs of each anole species. Signals of diversifying selection in each anole species was evident across codons of mhc1, many of which appear functionally relevant given known structures of this protein from the green anole, chicken, and human. Altogether, our investigation fills a major gap in understanding of amniote MHC diversity and evolution and provides an important foundation for future squamate-specific or vertebrate-wide investigations of the MHC.
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Affiliation(s)
- Daren C. Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
- *Correspondence: Daren C. Card,
| | - Andrew G. Van Camp
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
| | - Trenten Santonastaso
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
| | | | - Nicola M. Anthony
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
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Zhao C, Han Y, Wang C, Ren M, Hu Q, Gu Y, Ye P, Li S, Jin E. Transcriptome Profiling of Duodenum Reveals the Importance of Boron Supplementation in Modulating Immune Activities in Rats. Biol Trace Elem Res 2022; 200:3762-3773. [PMID: 34773147 DOI: 10.1007/s12011-021-02983-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/17/2021] [Indexed: 12/13/2022]
Abstract
As an essential trace element, appropriate boron supplementation can promote immune function of animals. To illustrate the effects of boron in a rat model, RNA-Seq was conducted for the RNA from duodenum after treatment with different concentration of boron in which boron was given in the form of boric acid. More than 47 million reads were obtained in 0, 10, and 320 mg/L boron (0, 57.21, and 1830.66 mg/L boric acid) treatment groups that produced 58 965 402, 48 607 328, and 46 760 660 clean reads, respectively. More than 95% of the clean reads were successfully matched to the rat reference genome and assembled to generate 32 662 transcripts. A total of 624 and 391 differentially expressed candidate genes (DEGs) were found between 0 vs.10 and 0 vs. 320 mg/L boron comparison groups. We also identified transcription start site, transcription terminal site, and skipped exons as the main alternative splicing events. GO annotations revealed most of DEGs were involved in the regulation of immune activity. The DEGs were enriched in influenza A, herpes simplex infection, cytosolic DNA-sensing pathway, and antigen processing and presentation signaling pathways. The expression levels of genes enriched in these signaling pathways indicate that lower doses of boron could achieve better effects on promoting immune response in the duodenum. These effects on the immune system appear to be mediated via altering the expression patterns of genes involved in the related signaling pathways in a dose-dependent pattern. These data provide more insights into the molecular mechanisms of immune regulation in rats in response to dietary boron treatment.
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Affiliation(s)
- Chunfang Zhao
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9, Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
| | - Yujiao Han
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9, Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
| | - Chenfang Wang
- College of Life and Health Science, Anhui Science and Technology University, No. 9, Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
| | - Man Ren
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9, Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
| | - Qianqian Hu
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9, Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
| | - Youfang Gu
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9, Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
| | - Pengfei Ye
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9, Donghua Road, Fengyang County, Chuzhou, Anhui Province, China
| | - Shenghe Li
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou, Anhui Province, China.
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9, Donghua Road, Fengyang County, Chuzhou, Anhui Province, China.
| | - Erhui Jin
- College of Animal Science, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang County, Chuzhou, Anhui Province, China.
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, No. 9, Donghua Road, Fengyang County, Chuzhou, Anhui Province, China.
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Machuka EM, Muigai AWT, Amimo JO, Domelevo Entfellner JB, Lekolool I, Abworo EO, Pelle R. Comparative Analysis of SLA-1, SLA-2, and DQB1 Genetic Diversity in Locally-Adapted Kenyan Pigs and Their Wild Relatives, Warthogs. Vet Sci 2021; 8:180. [PMID: 34564574 PMCID: PMC8473215 DOI: 10.3390/vetsci8090180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discriminating self and foreign antigens and initiating an immune response. Studies on SLA polymorphism have demonstrated associations between SLA allelic variants, immune response, and disease resistance. The SLA polymorphism is due to host-pathogen co-evolution resulting in improved adaptation to diverse environments making SLA a crucial genomic region for comparative diversity studies. Although locally-adapted African pigs have small body sizes, they possess increased resilience under harsh environmental conditions and robust immune systems with reported tolerance to some diseases, including African swine fever. However, data on the SLA diversity in these pigs are not available. We characterized the SLA of unrelated locally-adapted domestic pigs from Homa Bay, Kenya, alongside exotic pigs and warthogs. We undertook SLA comparative diversity of the functionally expressed SLA class I (SLA-1, SLA-2) and II (DQB1) repertoires in these three suids using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. Our data revealed higher genetic diversity in the locally-adapted pigs and warthogs compared to the exotic pigs. The nucleotide substitution rates were higher in the peptide-binding regions of the SLA-1, SLA-2, and DQB1 loci, indicative of adaptive evolution. We obtained high allele frequencies in the three SLA loci, including some breed-specific private alleles, which could guide breeders to increase their frequency through selection if confirmed to be associated with enhanced resilience. Our study contributes to the growing body of knowledge on genetic diversity in free-ranging animal populations in their natural environment, availing the first DQB1 gene data from locally-adapted Kenyan pigs.
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Affiliation(s)
- Eunice Magoma Machuka
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya;
- Institute for Basic Sciences Technology and Innovation (PAUSTI), Pan African University, Nairobi P.O. Box 62000-00200, Kenya
| | - Anne W. Thairu Muigai
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya;
| | - Joshua Oluoch Amimo
- Center for Food Animal Health, Department of Animal Sciences, 1680 Madison Avenue, The Ohio State University, Wooster, OH 44691, USA;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya;
| | - Isaac Lekolool
- Kenya Wildlife Services, Nairobi P.O. Box 40241-00100, Kenya;
| | - Edward Okoth Abworo
- Animal and Human Health Program, International Livestock Research Institute, Nairobi P.O. Box 30709-00100, Kenya;
| | - Roger Pelle
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya;
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10
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Bai Y, Lin W, Xu J, Song J, Yang D, Chen YE, Li L, Li Y, Wang Z, Zhang J. Improving the genome assembly of rabbits with long-read sequencing. Genomics 2021; 113:3216-3223. [PMID: 34051323 DOI: 10.1016/j.ygeno.2021.05.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
The European rabbit (Oryctolagus cuniculus) is important as a biomedical model given its unique features in immunity and metabolism. The current reference genome OryCun2.0 established with whole-genome shotgun sequencing was quite fragmented and had not been updated for ten years. In this work, we provided a new rabbit genome assembly UM_NZW_1.0 to improve OryCun2.0 by leveraging the contig lengths based on long-read sequencing and a wealth of available Illumina paired-end sequence data. UM_NZW_1.0 showed a remarkable increase of continuity compared with OryCun2.0, with 5 times longer contig N50 and approximately 75% gaps closed. Many of the closed gaps were overlapped with protein-coding genes or transcriptional features, resulting in an enhancement of gene annotations. In particular, UM_NZW_1.0 presented a more complete landscape of the MHC region and the IGH locus, therefore provided a valuable resource for future researches on rabbits.
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Affiliation(s)
- Yiqin Bai
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Weili Lin
- Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Dongshan Yang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Y Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Lin Li
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Yixue Li
- Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
| | - Zhen Wang
- Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Jifeng Zhang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, USA.
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11
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Cheng TC, Philip JL, Tabima DM, Kumari S, Yakubov B, Frump AL, Hacker TA, Bellofiore A, Li R, Sun X, Goss KN, Lahm T, Chesler NC. Estrogen receptor-α prevents right ventricular diastolic dysfunction and fibrosis in female rats. Am J Physiol Heart Circ Physiol 2020; 319:H1459-H1473. [PMID: 33064565 PMCID: PMC7792707 DOI: 10.1152/ajpheart.00247.2020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 12/24/2022]
Abstract
Although women are more susceptible to pulmonary arterial hypertension (PAH) than men, their right ventricular (RV) function is better preserved. Estrogen receptor-α (ERα) has been identified as a likely mediator for estrogen protection in the RV. However, the role of ERα in preserving RV function and remodeling during pressure overload remains poorly understood. We hypothesized that loss of functional ERα removes female protection from adverse remodeling and is permissive for the development of a maladapted RV phenotype. Male and female rats with a loss-of-function mutation in ERα (ERαMut) and wild-type (WT) littermates underwent RV pressure overload by pulmonary artery banding (PAB). At 10 wk post-PAB, WT and ERαMut demonstrated RV hypertrophy. Analysis of RV pressure waveforms demonstrated RV-pulmonary vascular uncoupling and diastolic dysfunction in female, but not male, ERαMut PAB rats. Similarly, female, but not male, ERαMut exhibited increased RV fibrosis, comprised primarily of thick collagen fibers. There was an increased protein expression ratio of TIMP metallopeptidase inhibitor 1 (Timp1) to matrix metalloproteinase 9 (Mmp9) in female ERαMut compared with WT PAB rats, suggesting less collagen degradation. RNA-sequencing in female WT and ERαMut RV revealed kallikrein-related peptidase 10 (Klk10) and Jun Proto-Oncogene (Jun) as possible mediators of female RV protection during PAB. In summary, ERα in females is protective against RV-pulmonary vascular uncoupling, diastolic dysfunction, and fibrosis in response to pressure overload. ERα appears to be dispensable for RV adaptation in males. ERα may be a mediator of superior RV adaptation in female patients with PAH.NEW & NOTEWORTHY Using a novel loss-of-function mutation in estrogen receptor-α (ERα), we demonstrate that female, but not male, ERα mutant rats display right ventricular (RV)-vascular uncoupling, diastolic dysfunction, and fibrosis following pressure overload, indicating a sex-dependent role of ERα in protecting against adverse RV remodeling. TIMP metallopeptidase inhibitor 1 (Timp1), matrix metalloproteinase 9 (Mmp9), kallikrein-related peptidase 10 (Klk10), and Jun Proto-Oncogene (Jun) were identified as potential mediators in ERα-regulated pathways in RV pressure overload.
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MESH Headings
- Animals
- Disease Models, Animal
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Female
- Fibrillar Collagens/metabolism
- Fibrosis
- Hypertrophy, Right Ventricular/metabolism
- Hypertrophy, Right Ventricular/pathology
- Hypertrophy, Right Ventricular/physiopathology
- Hypertrophy, Right Ventricular/prevention & control
- Kallikreins/genetics
- Kallikreins/metabolism
- Male
- Mitochondria, Heart/metabolism
- Mitochondria, Heart/pathology
- Mutation
- Myocardium/metabolism
- Myocardium/pathology
- Proto-Oncogene Proteins c-jun/genetics
- Proto-Oncogene Proteins c-jun/metabolism
- Rats, Mutant Strains
- Rats, Sprague-Dawley
- Sex Factors
- Signal Transduction
- Ventricular Dysfunction, Right/metabolism
- Ventricular Dysfunction, Right/pathology
- Ventricular Dysfunction, Right/physiopathology
- Ventricular Dysfunction, Right/prevention & control
- Ventricular Function, Right
- Ventricular Remodeling
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Affiliation(s)
- Tik-Chee Cheng
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Jennifer L Philip
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin
| | - Diana M Tabima
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Santosh Kumari
- Division of Allergy, Pulmonary and Critical Care Medicine, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - Bakhtiyor Yakubov
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Andrea L Frump
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Timothy A Hacker
- Cardiovascular Research Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Alessandro Bellofiore
- Department of Biomedical, Chemical and Materials Engineering, San Jose State University, San Jose, California
| | - Rongbo Li
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Xin Sun
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Kara N Goss
- Division of Allergy, Pulmonary and Critical Care Medicine, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - Tim Lahm
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Cellular and Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, Indiana
- Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, Indiana
| | - Naomi C Chesler
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
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12
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Topoisomerase IIβ targets DNA crossovers formed between distant homologous sites to induce chromatin opening. Sci Rep 2020; 10:18550. [PMID: 33122676 PMCID: PMC7596052 DOI: 10.1038/s41598-020-75004-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/09/2020] [Indexed: 11/08/2022] Open
Abstract
Type II DNA topoisomerases (topo II) flip the spatial positions of two DNA duplexes, called G- and T- segments, by a cleavage-passage-resealing mechanism. In living cells, these DNA segments can be derived from distant sites on the same chromosome. Due to lack of proper methodology, however, no direct evidence has been described so far. The beta isoform of topo II (topo IIβ) is essential for transcriptional regulation of genes expressed in the final stage of neuronal differentiation. Here we devise a genome-wide mapping technique (eTIP-seq) for topo IIβ target sites that can measure the genomic distance between G- and T-segments. It revealed that the enzyme operates in two distinctive modes, termed proximal strand passage (PSP) and distal strand passage (DSP). PSP sites are concentrated around transcription start sites, whereas DSP sites are heavily clustered in small number of hotspots. While PSP represent the conventional topo II targets that remove local torsional stresses, DSP sites have not been described previously. Most remarkably, DSP is driven by the pairing between homologous sequences or repeats located in a large distance. A model-building approach suggested that topo IIβ acts on crossovers to unknot the intertwined DSP sites, leading to chromatin decondensation.
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13
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Nilsson P, Solbakken MH, Schmid BV, Orr RJS, Lv R, Cui Y, Song Y, Zhang Y, Baalsrud HT, Tørresen OK, Stenseth NC, Yang R, Jakobsen KS, Easterday WR, Jentoft S. The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene. Genome Biol Evol 2020; 12:3832-3849. [PMID: 31971556 PMCID: PMC7046166 DOI: 10.1093/gbe/evaa008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
The great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious pathogens including the well-known plague bacterium (Yersinia pestis). Here, we present a continuous annotated genome assembly of the great gerbil, covering over 96% of the estimated 2.47-Gb genome. Taking advantage of the recent genome assemblies of the sand rat (Psammomys obesus) and the Mongolian gerbil (Meriones unguiculatus), comparative immunogenomic analyses reveal shared gene losses within TLR gene families (i.e., TLR8, TLR10, and the entire TLR11-subfamily) for Gerbillinae, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes as well as Leishmania and Leptospira epitopes, putatively leading to increased capability to withstand infections by these pathogens. Our study demonstrates the power of whole-genome sequencing combined with comparative genomic analyses to gain deeper insight into the immunogenomic landscape of the great gerbil and its close relatives.
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Affiliation(s)
- Pernille Nilsson
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Monica H Solbakken
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Boris V Schmid
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | | | - Ruichen Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujiang Zhang
- Xinjiang Center for Disease Control and Prevention, Urumqi, China
| | - Helle T Baalsrud
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - William Ryan Easterday
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
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14
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Nomenclature report on the major histocompatibility complex genes and alleles of the laboratory rat (Rattus norvegicus). Immunogenetics 2019; 72:5-8. [PMID: 31522238 DOI: 10.1007/s00251-019-01131-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/04/2019] [Indexed: 10/26/2022]
Abstract
The laboratory rat (Rattus norvegicus) has a long tradition as experimental animal in transplantation and autoimmunity research and, hence, there has been an inherent interest in its major histocompatibility complex (MHC), the RT1 complex. Available inbred rat strains and their derived RT1-congenic and intra-RT1 recombinant congenic strains were crucial for definition and characterization of RT1 genes and alleles and essentially advanced elucidation of the RT1 genomic organization in the past. The Immuno Polymorphism Database (IPD) harbors a section for rat MHC genes and alleles (IPD-MHC RT1) since 2005. The curator for IPD-MHC RT1 provides official designations for newly described genes and alleles of RT1. This is the first nomenclature report of RT1 genes and alleles that are currently included in IPD-MHC RT1.
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15
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Kitamura K, Buchholz BM, Abu-Elmagd K, Kalff JC, Schäfer N, von Websky MW. Chronic rejection after intestinal transplantation: A systematic review of experimental models. Transplant Rev (Orlando) 2019; 33:173-181. [DOI: 10.1016/j.trre.2019.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 01/28/2023]
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16
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Major histocompatibility complex class I diversity limits the repertoire of T cell receptors. Proc Natl Acad Sci U S A 2019; 116:5021-5026. [PMID: 30796191 DOI: 10.1073/pnas.1807864116] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Major histocompatibility complex (MHC) genes encode proteins that initiate adaptive immune responses through the presentation of foreign antigens to T cells. The high polymorphism found at these genes, thought to be promoted and maintained by pathogen-mediated selection, contrasts with the limited number of MHC loci found in most vertebrates. Although expressing many diverse MHC genes should broaden the range of detectable pathogens, it has been hypothesized to also cause deletion of larger fractions of self-reactive T cells, leading to a detrimental reduction of the T cell receptor (TCR) repertoire. However, a key prediction of this TCR depletion hypothesis, that the TCR repertoire should be inversely related to the individual MHC diversity, has never been tested. Here, using high-throughput sequencing and advanced sequencing error correction, we provide evidence of such an association in a rodent species with high interindividual variation in the number of expressed MHC molecules, the bank vole (Myodes glareolus). Higher individual diversity of MHC class I, but not class II, was associated with smaller TCR repertoires. Our results thus provide partial support for the TCR depletion model, while also highlighting the complex, potentially MHC class-specific mechanisms by which autoreactivity may trade off against evolutionary expansion of the MHC gene family.
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17
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Ballingall KT, Bontrop RE, Ellis SA, Grimholt U, Hammond JA, Ho CS, Kaufman J, Kennedy LJ, Maccari G, Miller D, Robinson J, Marsh SGE. Comparative MHC nomenclature: report from the ISAG/IUIS-VIC committee 2018. Immunogenetics 2018; 70:625-632. [PMID: 30039257 DOI: 10.1007/s00251-018-1073-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/13/2018] [Indexed: 12/24/2022]
Abstract
Significant progress has been made over the last decade in defining major histocompatibility complex (MHC) diversity at the nucleotide, allele, haplotype, diplotype, and population levels in many non-human species. Much of this progress has been driven by the increased availability and reduced costs associated with nucleotide sequencing technologies. This report provides an update on the activities of the comparative MHC nomenclature committee which is a standing committee of both the International Society for Animal Genetics (ISAG) and the International Union of Immunological Societies (IUIS) where it operates under the umbrella of the Veterinary Immunology Committee (VIC). A previous report from this committee in 2006 defined the role of the committee in providing guidance in the development of a standardized nomenclature for genes and alleles at MHC loci in non-human species. It described the establishment of the Immuno Polymorphism Database, IPD-MHC, which continues to provide public access to high quality MHC sequence data across a range of species. In this report, guidelines for the continued development of a universal MHC nomenclature framework are described, summarizing the continued development of each species section within the IPD-MHC project.
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Affiliation(s)
- Keith T Ballingall
- Moredun Research Institute, Midlothian, UK and Chair of the Comparative MHC Nomenclature Committee, Edinburgh, Scotland, UK.
| | | | | | | | | | | | | | - Lorna J Kennedy
- Centre for Integrated Genomic Medical Research, Manchester, UK
| | - Giuseppe Maccari
- The Pirbright Institute, Pirbright, Surrey, UK.,Anthony Nolan Research Institute, London, UK
| | - Donald Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - James Robinson
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
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18
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Shegarfi H, Kane KP, Nestvold J. Listeria monocytogenes infection enhances the interaction between rat non-classical MHC-Ib molecule and Ly49 receptors. Innate Immun 2018; 24:252-261. [PMID: 29792127 PMCID: PMC6830922 DOI: 10.1177/1753425918759589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Murine NK cell Ly49 receptors, functionally analogous to KIRs in humans recognize
MHC class I molecules and play a key role in controlling NK cell function. We
have previously shown that the paired activating Ly49s4 and inhibitory Ly49i4
receptors recognize undefined non-classical MHC-Ib ligands from the RT1-CE
region in rats. Here, the RT1-CE16 gene of the
RT1d haplotype was stably transfected into
the mouse RAW macrophage cell line, termed RAW-CE16d cells. Combining
RAW-CE16d cells with Ly49 expressing reporter cells demonstrated
Ly49i4 and Ly49s4 specificity for CE16d. The
Ly49s4/i4:CE16d interaction was confirmed by specific MHC-I
blocking monoclonal Abs. Further, we used our in vitro model to
study the effect of Listeria monocytogenes (LM) on
CE16d after infection. LM infection and IFN-γ stimulation both
led to enhanced CE16d expression on the surface of transfected
RAW-CE16d cells. Interestingly, the reporter cells displayed
increased response to LM-infected RAW-CE16d cells compared with
IFN-γ-treated RAW-CE16d cells, suggesting a fundamental difference
between these stimuli in supporting enhanced Ly49 recognition of
CE16d. Collectively, our data show that Ly49s4 and Ly49i4
recognize the non-classical RT1-CE16d molecule, which in turn is
up-regulated during LM infection and thereby may contribute to NK-mediated
responses against infected cells.
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Affiliation(s)
- Hamid Shegarfi
- 1 Atlantis Medical University College, Trondheimsveien 2, Oslo, Norway.,2 Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Kevin P Kane
- 3 Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Janne Nestvold
- 4 Department of Transplantation Medicine, Institute for Surgical Research, Oslo University Hospital, Oslo, Norway
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19
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Kaufman J. Unfinished Business: Evolution of the MHC and the Adaptive Immune System of Jawed Vertebrates. Annu Rev Immunol 2018; 36:383-409. [DOI: 10.1146/annurev-immunol-051116-052450] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB2 0ES, United Kingdom
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20
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Dai KZ, Ryan JC, Naper C, Vaage JT. Identification of MHC Class Ib Ligands for Stimulatory and Inhibitory Ly49 Receptors and Induction of Potent NK Cell Alloresponses in Rats. THE JOURNAL OF IMMUNOLOGY 2018. [PMID: 29531166 DOI: 10.4049/jimmunol.1701464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Early studies indicate that rats may have a repertoire of MHC class Ib-reactive Ly49 stimulatory receptors capable of mounting memory-like NK cell alloresponses. In this article, we provide molecular and functional evidence for this assumption. Pairs of Ly49 receptors with sequence similarities in the lectin-like domains, but with opposing signaling functions, showed specificity for ligands with class Ia-like structural features encoded from the first telomeric MHC class Ib gene cluster, RT1-CE, which is syntenic with the H2-D/H2-L/H2-Q cluster in mice. The activating Ly49s4 receptor and its inhibitory counterparts, Ly49i4 and Ly49i3, reacted with all allelic variants of RT1-U, whereas Ly49s5 and Ly49i5 were specific for RT1-Eu NK cell cytolytic responses were predictably activated and inhibited, and potent in vivo NK alloresponses were induced by repeated MHC class Ib alloimmunizations. Additional Ly49-class Ib interactions, including RT1-Cl with the Ly49s4/Ly49i4/Ly49i3 group of receptors, were characterized using overexpressed receptor/ligand pairs, in vitro functional assays, and limited mutational analyses. Obvious, as well as subtle, Ly49-class Ib interactions led to ligand-induced receptor calibration and NK subset expansions in vivo. Together, these studies suggest that in vivo NK alloresponses are controlled by pleomorphic Ly49-class Ib interactions, some of which may not be easily detectable in vitro.
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Affiliation(s)
- Ke-Zheng Dai
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - James C Ryan
- Department of Medicine, Veterans Affairs Medical Center, University of California, San Francisco, San Francisco, CA 94121; and
| | - Christian Naper
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - John T Vaage
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway; .,Department of Immunology, University of Oslo, 0424 Oslo, Norway
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21
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Yau ACY, Holmdahl R. Rheumatoid arthritis: identifying and characterising polymorphisms using rat models. Dis Model Mech 2017; 9:1111-1123. [PMID: 27736747 PMCID: PMC5087835 DOI: 10.1242/dmm.026435] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rheumatoid arthritis is a chronic inflammatory joint disorder characterised by erosive inflammation of the articular cartilage and by destruction of the synovial joints. It is regulated by both genetic and environmental factors, and, currently, there is no preventative treatment or cure for this disease. Genome-wide association studies have identified ∼100 new loci associated with rheumatoid arthritis, in addition to the already known locus within the major histocompatibility complex II region. However, together, these loci account for only a modest fraction of the genetic variance associated with this disease and very little is known about the pathogenic roles of most of the risk loci identified. Here, we discuss how rat models of rheumatoid arthritis are being used to detect quantitative trait loci that regulate different arthritic traits by genetic linkage analysis and to positionally clone the underlying causative genes using congenic strains. By isolating specific loci on a fixed genetic background, congenic strains overcome the challenges of genetic heterogeneity and environmental interactions associated with human studies. Most importantly, congenic strains allow functional experimental studies be performed to investigate the pathological consequences of natural genetic polymorphisms, as illustrated by the discovery of several major disease genes that contribute to arthritis in rats. We discuss how these advances have provided new biological insights into arthritis in humans.
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Affiliation(s)
- Anthony C Y Yau
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Rikard Holmdahl
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden Southern Medical University, Guangzhou 510515, China
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22
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Nonaka MI, Terado T, Kimura H, Nonaka M. Evolutionary analysis of two complement C4 genes: Ancient duplication and conservation during jawed vertebrate evolution. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 68:1-11. [PMID: 27840295 DOI: 10.1016/j.dci.2016.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/05/2016] [Accepted: 11/05/2016] [Indexed: 06/06/2023]
Abstract
The complement C4 is a thioester-containing protein, and a histidine (H) residue catalyzes the cleavage of the thioester to allow covalent binding to carbohydrates on target cells. Some mammalian and teleost species possess an additional isotype where the catalytic H is replaced by an aspartic acid (D), which binds preferentially to proteins. We found the two C4 isotypes in many other jawed vertebrates, including sharks and birds/reptiles. Phylogenetic analysis suggested that C4 gene duplication occurred in the early days of the jawed vertebrate evolution. The D-type C4 of bony fish except for mammals formed a cluster, termed D-lineage. The D-lineage genes were located in a syntenic region outside MHC, and evolved conservatively. Mammals lost the D-lineage before speciation, but D-type C4 was regenerated by recent gene duplication in some mammalian species or groups. Dual C4 molecules with different substrate specificities would have contributed to development of the antibody-dependent classical pathway.
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Affiliation(s)
- Mayumi I Nonaka
- Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Tokio Terado
- Department of Molecular Genetics in Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Hiroshi Kimura
- Department of Molecular Genetics in Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Masaru Nonaka
- Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Song Z, Xiong B, Zheng H, Manyande A, Guan X, Cao F, Ren L, Zhou Y, Ye D, Tian Y. STAT1 as a downstream mediator of ERK signaling contributes to bone cancer pain by regulating MHC II expression in spinal microglia. Brain Behav Immun 2017; 60:161-173. [PMID: 27742579 DOI: 10.1016/j.bbi.2016.10.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/08/2016] [Accepted: 10/10/2016] [Indexed: 01/05/2023] Open
Abstract
Major histocompatibility class II (MHC II)-specific activation of CD4+ T helper cells generates specific and persistent adaptive immunity against tumors. Emerging evidence demonstrates that MHC II is also involved in basic pain perception; however, little is known regarding its role in the development of cancer-induced bone pain (CIBP). In this study, we demonstrate that MHC II expression was markedly induced on the spinal microglia of CIBP rats in response to STAT1 phosphorylation. Mechanical allodynia was ameliorated by either pharmacological or genetic inhibition of MHC II upregulation, which was also attenuated by the inhibition of pSTAT1 and pERK but was deteriorated by intrathecal injection of IFNγ. Furthermore, inhibition of ERK signaling decreased the phosphorylation of STAT1, as well as the production of MHC II in vivo and in vitro. These findings suggest that STAT1 contributes to bone cancer pain as a downstream mediator of ERK signaling by regulating MHC II expression in spinal microglia.
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Affiliation(s)
- Zhenpeng Song
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Pain Medicine, Binzhou Medical University Hospital, Binzhou 256600, China
| | - Bingrui Xiong
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hua Zheng
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Anne Manyande
- School of Human and Social Sciences, University of West London, Middlesex TW8 9GA, UK
| | - Xuehai Guan
- Department of Anesthesiology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, China
| | - Fei Cao
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lifang Ren
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yaqun Zhou
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dawei Ye
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Yuke Tian
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Signatures of Crested Ibis MHC Revealed by Recombination Screening and Short-Reads Assembly Strategy. PLoS One 2016; 11:e0168744. [PMID: 27997612 PMCID: PMC5173252 DOI: 10.1371/journal.pone.0168744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 12/06/2016] [Indexed: 02/04/2023] Open
Abstract
Whole-genome shotgun (WGS) sequencing has become a routine method in genome research over the past decade. However, the assembly of highly polymorphic regions in WGS projects remains a challenge, especially for large genomes. Employing BAC library constructing, PCR screening and Sanger sequencing, traditional strategy is laborious and expensive, which hampers research on polymorphic genomic regions. As one of the most highly polymorphic regions, the major histocompatibility complex (MHC) plays a central role in the adaptive immunity of all jawed vertebrates. In this study, we introduced an efficient procedure based on recombination screening and short-reads assembly. With this procedure, we constructed a high quality 488-kb region of crested ibis MHC that consists of 3 superscaffolds and contains 50 genes. Our sequence showed comparable quality (97.29% identity) to traditional Sanger assembly, while the workload was reduced almost 7 times. Comparative study revealed distinctive features of crested ibis by exhibiting the COL11A2-BLA-BLB-BRD2 cluster and presenting both ADPRH and odorant receptor (OR) gene in the MHC region. Furthermore, the conservation of the BF-TAP1-TAP2 structure in crested ibis and other vertebrate lineages is interesting in light of the hypothesis that coevolution of functionally related genes in the primordial MHC is responsible for the appearance of the antigen presentation pathways at the birth of the adaptive immune system.
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Migalska M, Sebastian A, Konczal M, Kotlík P, Radwan J. De novo transcriptome assembly facilitates characterisation of fast-evolving gene families, MHC class I in the bank vole (Myodes glareolus). Heredity (Edinb) 2016; 118:348-357. [PMID: 27782121 DOI: 10.1038/hdy.2016.105] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/20/2016] [Indexed: 02/07/2023] Open
Abstract
The major histocompatibility complex (MHC) plays a central role in the adaptive immune response and is the most polymorphic gene family in vertebrates. Although high-throughput sequencing has increasingly been used for genotyping families of co-amplifying MHC genes, its potential to facilitate early steps in the characterisation of MHC variation in nonmodel organism has not been fully explored. In this study we evaluated the usefulness of de novo transcriptome assembly in characterisation of MHC sequence diversity. We found that although de novo transcriptome assembly of MHC I genes does not reconstruct sequences of individual alleles, it does allow the identification of conserved regions for PCR primer design. Using the newly designed primers, we characterised MHC I sequences in the bank vole. Phylogenetic analysis of the partial MHC I coding sequence (2-4 exons) of the bank vole revealed a lack of orthology to MHC I of other Cricetidae, consistent with the high gene turnover of this region. The diversity of expressed alleles was characterised using ultra-deep sequencing of the third exon that codes for the peptide-binding region of the MHC molecule. High allelic diversity was demonstrated, with 72 alleles found in 29 individuals. Interindividual variation in the number of expressed loci was found, with the number of alleles per individual ranging from 5 to 14. Strong signatures of positive selection were found for 8 amino acid sites, most of which are inferred to bind antigens in human MHC, indicating conservation of structure despite rapid sequence evolution.
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Affiliation(s)
- M Migalska
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - A Sebastian
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - M Konczal
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - P Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, Czech Republic
| | - J Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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Abstract
The concept of co-evolution (or co-adaptation) has a long history, but application at molecular levels (e.g., 'supergenes' in genetics) is more recent, with a consensus definition still developing. One interesting example is the chicken major histocompatibility complex (MHC). In contrast to typical mammals that have many class I and class I-like genes, only two classical class I genes, two CD1 genes and some non-classical Rfp-Y genes are known in chicken, and all are found on the microchromosome that bears the MHC. Rarity of recombination between the closely linked and polymorphic genes encoding classical class I and TAPs allows co-evolution, leading to a single dominantly expressed class I molecule in each MHC haplotype, with strong functional consequences in terms of resistance to infectious pathogens. Chicken tapasin is highly polymorphic, but co-evolution with TAP and class I genes remains unclear. T-cell receptors, natural killer (NK) cell receptors, and CD8 co-receptor genes are found on non-MHC chromosomes, with some evidence for co-evolution of surface residues and number of genes along the avian and mammalian lineages. Over even longer periods, co-evolution has been invoked to explain how the adaptive immune system of jawed vertebrates arose from closely linked receptor, ligand, and antigen-processing genes in the primordial MHC.
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Affiliation(s)
- Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Ruan R, Ruan J, Wan XL, Zheng Y, Chen MM, Zheng JS, Wang D. Organization and characteristics of the major histocompatibility complex class II region in the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). Sci Rep 2016; 6:22471. [PMID: 26932528 PMCID: PMC4773811 DOI: 10.1038/srep22471] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 02/16/2016] [Indexed: 11/30/2022] Open
Abstract
Little is known about the major histocompatibility complex (MHC) in the genome of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) (YFP) or other cetaceans. In this study, a high-quality YFP bacterial artificial chromosome (BAC) library was constructed. We then determined the organization and characterization of YFP MHC class II region by screening the BAC library, followed by sequencing and assembly of positive BAC clones. The YFP MHC class II region consists of two segregated contigs (218,725 bp and 328,435 bp respectively) that include only eight expressed MHC class II genes, three pseudo MHC genes and twelve non-MHC genes. The YFP has fewer MHC class II genes than ruminants, showing locus reduction in DRB, DQA, DQB, and loss of DY. In addition, phylogenic and evolutionary analyses indicated that the DRB, DQA and DQB genes might have undergone birth-and-death evolution, whereas the DQB gene might have evolved under positive selection in cetaceans. These findings provide an essential foundation for future work, such as estimating MHC genetic variation in the YFP or other cetaceans. This work is the first report on the MHC class II region in cetaceans and offers valuable information for understanding the evolution of MHC genome in cetaceans.
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Affiliation(s)
- Rui Ruan
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jue Ruan
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong 518120, China
| | - Xiao-Ling Wan
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yang Zheng
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The University of Chinese Academy of Sciences, Beijing 100039, China
| | - Min-Min Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jin-Song Zheng
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ding Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Monzón-Casanova E, Rudolf R, Starick L, Müller I, Söllner C, Müller N, Westphal N, Miyoshi-Akiyama T, Uchiyama T, Berberich I, Walter L, Herrmann T. The Forgotten: Identification and Functional Characterization of MHC Class II Molecules H2-Eb2 and RT1-Db2. THE JOURNAL OF IMMUNOLOGY 2016; 196:988-99. [DOI: 10.4049/jimmunol.1403070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 12/01/2015] [Indexed: 11/19/2022]
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Yao FR, Wang HS, Guo Y, Zhao Y. The local effect of octreotide on mechanical pain sensitivity is more sensitive in DA rats than DA.1U rats. Clin Exp Pharmacol Physiol 2015; 43:213-20. [PMID: 26606866 DOI: 10.1111/1440-1681.12519] [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: 06/28/2015] [Revised: 11/14/2015] [Accepted: 11/19/2015] [Indexed: 11/29/2022]
Abstract
A recent study by the authors indicated that major histocompatibility complex (MHC) genes are associated with the differences in basal pain sensitivity and in formalin model between Dark-Agouti (DA) and novel congenic DA.1U rats, which have the same genetic background as DA rats except for the u alleles of MHC. The objective of the present study is to investigate whether there is a difference in the pristane-induced arthritis (PIA) model and local analgesic effect of octreotide (OCT) between DA and DA.1U rats. The hindpaw mechanical withdrawal threshold (MWT) and heat withdrawal latency (HWL) were observed. The C unit firings of the tibial nerve evoked by non-noxious and noxious toe movements were recorded by electrophysiological methods in normal and PIA models in DA and DA.1U rats before and after local OCT administration. The expression of somatostatin receptor 2A (SSTR2A) was observed by immunohistochemistry. The results demonstrate that DA rats have a higher mechanical sensitivity than DA.1U rats after PIA. Local OCT administration significantly elevated MWT in DA rats under normal and PIA sate, but not in DA.1U rats. The electrophysiological experiments showed OCT significantly attenuated the firings of C units evoked by non-noxious and noxious stimulation in DA rats more than those in DA.1U rats both in normal and PIA states. In addition, the expression of SSTR2A in the dorsal horn of the spinal cord was significantly higher in DA than in DA.1U rats. All of the findings suggest a higher local analgesic effect of OCT in DA rats than DA.1U rats, which might be associated with the MHC genes.
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Affiliation(s)
- Fan-Rong Yao
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Hui-Sheng Wang
- Department of Physiology and Pathophysiology, School of Basal Medical Science, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
| | - Yuan Guo
- Department of Physiology and Pathophysiology, School of Basal Medical Science, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
| | - Yan Zhao
- Department of Physiology and Pathophysiology, School of Basal Medical Science, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
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Siva Subramaniam N, Morgan EF, Wetherall JD, Stear MJ, Groth DM. A comprehensive mapping of the structure and gene organisation in the sheep MHC class I region. BMC Genomics 2015; 16:810. [PMID: 26480943 PMCID: PMC4613773 DOI: 10.1186/s12864-015-1992-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/06/2015] [Indexed: 11/13/2022] Open
Abstract
Background The major histocompatibility complex (MHC) is a chromosomal region that regulates immune responsiveness in vertebrates. This region is one of the most important for disease resistance because it has been associated with resistance or susceptibility to a wide variety of diseases and because the MHC often accounts for more of the variance than other loci. Selective breeding for disease resistance is becoming increasingly common in livestock industries, and it is important to determine how this will influence MHC polymorphism and resistance to diseases that are not targeted for selection. However, in sheep the order and sequence of the protein coding genes is controversial. Yet this information is needed to determine precisely how the MHC influences resistance and susceptibility to disease. Methods CHORI bacterial artificial chromosomes (BACs) known to contain sequences from the sheep MHC class I region were sub-cloned, and the clones partially sequenced. The resulting sequences were analysed and re-assembled to identify gene content and organisation within each BAC. The low resolution MHC class I physical map was then compared to the cattle reference genome, the Chinese Merino sheep MHC map published by Gao, et al. (2010) and the recently available sheep reference genome. Results Immune related class I genes are clustered into 3 blocks; beta, kappa and a novel block not previously identified in other organisms. The revised map is more similar to Bovidae maps than the previous sheep maps and also includes several genes previously not annotated in the Chinese Merino BAC assembly and others not currently annotated in the sheep reference chromosome 20. In particular, the organisation of nonclassical MHC class I genes is similar to that present in the cattle MHC. Sequence analysis and prediction of amino acid sequences of MHC class I classical and nonclassical genes was performed and it was observed that the map contained one classical and eight nonclassical genes together with three possible pseudogenes. Conclusions The comprehensive physical map of the sheep MHC class I region enhances our understanding of the genetic architecture of the class I MHC region in sheep and will facilitate future studies of MHC function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1992-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- N Siva Subramaniam
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
| | - E F Morgan
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
| | - J D Wetherall
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
| | - M J Stear
- Department of Animal Production and Public Health, Faculty of Veterinary Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK. .,Institute of Biodiversity, Animal Health and Comparative Medicine, Garscube Estate, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK.
| | - D M Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
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Guo Y, Yao FR, Cao DY, Li L, Wang HS, Xie W, Zhao Y. The major histocompatibility complex genes impact pain response in DA and DA.1U rats. Physiol Behav 2015; 147:30-7. [PMID: 25861730 DOI: 10.1016/j.physbeh.2015.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/13/2015] [Accepted: 04/04/2015] [Indexed: 12/29/2022]
Abstract
Our recent studies have shown that the difference in basal pain sensitivity to mechanical and thermal stimulation between Dark-Agouti (DA) rats and a novel congenic DA.1U rats is major histocompatibility complex (MHC) genes dependent. In the present study, we further used DA and DA.1U rats to investigate the role of MHC genes in formalin-induced pain model by behavioral, electrophysiological and immunohistochemical methods. Behavioral results showed biphasic nociceptive behaviors increased significantly following the intraplantar injection of formalin in the hindpaw of DA and DA.1U rats. The main nociceptive behaviors were lifting and licking, especially in DA rats (P<0.001 and P<0.01). The composite pain scores (CPS) in DA rats were significantly higher than those in DA.1U rats in both phases of the formalin test (P<0.01). Electrophysiological results also showed the biphasic increase in discharge rates of C and Aδ fibers of L5 dorsal root in the two strains, and the net change of the discharge rate of DA rats was significantly higher than that of DA.1U rats (P<0.05). The mechanical thresholds decreased after formalin injection in both strains (P<0.01), and the net change in the mechanical threshold in DA was greater than that in DA.1U rats (P<0.05). The expression of RT1-B, representation of MHC class II molecule, in laminae I-II of L4/5 spinal cord in DA rats was significantly higher than that in DA.1U rats in the respective experimental group (P<0.05). These results suggested that both DA and DA.1U rats exhibited nociceptive responses in formalin-induced pain model and DA rats were more sensitive to noxious chemical stimulus than DA.1U rats, indicating that MHC genes might contribute to the difference in pain sensitivity.
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Affiliation(s)
- Yuan Guo
- Department of Physiology and Pathophysiology, School of Basal Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China
| | - Fan-Rong Yao
- Department of Pharmacology and Toxicology in the Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Dong-Yuan Cao
- Research Center, Stomatological Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710004, PR China; Department of Neural and Pain Sciences, University of Maryland Dental School, 650 West, Baltimore Street, Baltimore, MD 21201, USA
| | - Li Li
- Department of Physiology and Pathophysiology, School of Basal Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China
| | - Hui-Sheng Wang
- Department of Physiology and Pathophysiology, School of Basal Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China
| | - Wen Xie
- Department of Physiology and Pathophysiology, School of Basal Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China
| | - Yan Zhao
- Department of Physiology and Pathophysiology, School of Basal Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China.
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32
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Chen LC, Lan H, Sun L, Deng YL, Tang KY, Wan QH. Genomic organization of the crested ibis MHC provides new insight into ancestral avian MHC structure. Sci Rep 2015; 5:7963. [PMID: 25608659 PMCID: PMC4302302 DOI: 10.1038/srep07963] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 12/31/2014] [Indexed: 01/06/2023] Open
Abstract
The major histocompatibility complex (MHC) plays an important role in immune response. Avian MHCs are not well characterized, only reporting highly compact Galliformes MHCs and extensively fragmented zebra finch MHC. We report the first genomic structure of an endangered Pelecaniformes (crested ibis) MHC containing 54 genes in three regions spanning ~500 kb. In contrast to the loose BG (26 loci within 265 kb) and Class I (11 within 150) genomic structures, the Core Region is condensed (17 within 85). Furthermore, this Region exhibits a COL11A2 gene, followed by four tandem MHC class II αβ dyads retaining two suites of anciently duplicated “αβ” lineages. Thus, the crested ibis MHC structure is entirely different from the known avian MHC architectures but similar to that of mammalian MHCs, suggesting that the fundamental structure of ancestral avian class II MHCs should be “COL11A2-IIαβ1-IIαβ2.” The gene structures, residue characteristics, and expression levels of the five class I genes reveal inter-locus functional divergence. However, phylogenetic analysis indicates that these five genes generate a well-supported intra-species clade, showing evidence for recent duplications. Our analyses suggest dramatic structural variation among avian MHC lineages, help elucidate avian MHC evolution, and provide a foundation for future conservation studies.
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Affiliation(s)
- Li-Cheng Chen
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Hong Lan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Li Sun
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yan-Li Deng
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Ke-Yi Tang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Qiu-Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
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33
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Pratheek BM, Nayak TK, Sahoo SS, Mohanty PK, Chattopadhyay S, Chakraborty NG, Chattopadhyay S. Mammalian non-classical major histocompatibility complex I and its receptors: Important contexts of gene, evolution, and immunity. INDIAN JOURNAL OF HUMAN GENETICS 2014; 20:129-41. [PMID: 25400340 PMCID: PMC4228563 DOI: 10.4103/0971-6866.142855] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The evolutionary conserved, less-polymorphic, nonclassical major histocompatibility complex (MHC) class I molecules: Qa-1 and its human homologue human leukocyte antigen-E (HLA-E) along with HLA-F, G and H cross-talk with the T-cell receptors and also interact with natural killer T-cells and other lymphocytes. Moreover, these nonclassical MHC molecules are known to interact with CD94/NKG2 heterodimeric receptors to induce immune responses and immune regulations. This dual role of Qa-1/HLA-E in terms of innate and adaptive immunity makes them more interesting. This review highlights the new updates of the mammalian nonclassical MHC-I molecules in terms of their gene organization, evolutionary perspective and their role in immunity.
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Affiliation(s)
- B M Pratheek
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | - Tapas K Nayak
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | - Subhransu S Sahoo
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | | | - Soma Chattopadhyay
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Ntiya G Chakraborty
- Department of Medicine, University of Connecticut Health Center, Farmington, USA
| | - Subhasis Chattopadhyay
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
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Scherman K, Råberg L, Westerdahl H. Positive selection on MHC class II DRB and DQB genes in the bank vole (Myodes glareolus). J Mol Evol 2014; 78:293-305. [PMID: 24748547 DOI: 10.1007/s00239-014-9618-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/30/2014] [Indexed: 10/25/2022]
Abstract
The major histocompatibility complex (MHC) class IIB genes show considerable sequence similarity between loci. The MHC class II DQB and DRB genes are known to exhibit a high level of polymorphism, most likely maintained by parasite-mediated selection. Studies of the MHC in wild rodents have focused on DRB, whilst DQB has been given much less attention. Here, we characterised DQB genes in Swedish bank voles Myodes glareolus, using full-length transcripts. We then designed primers that specifically amplify exon 2 from DRB (202 bp) and DQB (205 bp) and investigated molecular signatures of natural selection on DRB and DQB alleles. The presence of two separate gene clusters was confirmed using BLASTN and phylogenetic analysis, where our seven transcripts clustered according to either DQB or DRB homologues. These gene clusters were again confirmed on exon 2 data from 454-amplicon sequencing. Our DRB primers amplify a similar number of alleles per individual as previously published DRB primers, though our reads are longer. Traditional d N/d S analyses of DRB sequences in the bank vole have not found a conclusive signal of positive selection. Using a more advanced substitution model (the Kumar method) we found positive selection in the peptide binding region (PBR) of both DRB and DQB genes. Maximum likelihood models of codon substitutions detected positively selected sites located in the PBR of both DQB and DRB. Interestingly, these analyses detected at least twice as many positively selected sites in DQB than DRB, suggesting that DQB has been under stronger positive selection than DRB over evolutionary time.
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Affiliation(s)
- Kristin Scherman
- Department of Biology, MEMEG, Lund University, Sölvegatan 37, 223 62, Lund, Sweden,
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Tuncel J, Haag S, Yau ACY, Norin U, Baud A, Lönnblom E, Maratou K, Ytterberg AJ, Ekman D, Thordardottir S, Johannesson M, Gillett A, Stridh P, Jagodic M, Olsson T, Fernández-Teruel A, Zubarev RA, Mott R, Aitman TJ, Flint J, Holmdahl R. Natural polymorphisms in Tap2 influence negative selection and CD4∶CD8 lineage commitment in the rat. PLoS Genet 2014; 10:e1004151. [PMID: 24586191 PMCID: PMC3930506 DOI: 10.1371/journal.pgen.1004151] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 12/16/2013] [Indexed: 12/17/2022] Open
Abstract
Genetic variation in the major histocompatibility complex (MHC) affects CD4∶CD8 lineage commitment and MHC expression. However, the contribution of specific genes in this gene-dense region has not yet been resolved. Nor has it been established whether the same genes regulate MHC expression and T cell selection. Here, we assessed the impact of natural genetic variation on MHC expression and CD4∶CD8 lineage commitment using two genetic models in the rat. First, we mapped Quantitative Trait Loci (QTLs) associated with variation in MHC class I and II protein expression and the CD4∶CD8 T cell ratio in outbred Heterogeneous Stock rats. We identified 10 QTLs across the genome and found that QTLs for the individual traits colocalized within a region spanning the MHC. To identify the genes underlying these overlapping QTLs, we generated a large panel of MHC-recombinant congenic strains, and refined the QTLs to two adjacent intervals of ∼0.25 Mb in the MHC-I and II regions, respectively. An interaction between these intervals affected MHC class I expression as well as negative selection and lineage commitment of CD8 single-positive (SP) thymocytes. We mapped this effect to the transporter associated with antigen processing 2 (Tap2) in the MHC-II region and the classical MHC class I gene(s) (RT1-A) in the MHC-I region. This interaction was revealed by a recombination between RT1-A and Tap2, which occurred in 0.2% of the rats. Variants of Tap2 have previously been shown to influence the antigenicity of MHC class I molecules by altering the MHC class I ligandome. Our results show that a restricted peptide repertoire on MHC class I molecules leads to reduced negative selection of CD8SP cells. To our knowledge, this is the first study showing how a recombination between natural alleles of genes in the MHC influences lineage commitment of T cells. Peptides from degraded cytoplasmic proteins are transported via TAP into the endoplasmic reticulum for loading onto MHC class I molecules. TAP is encoded by Tap1 and Tap2, which in rodents are located close to the MHC class I genes. In the rat, genetic variation in Tap2 gives rise to two different transporters: a promiscuous A variant (TAP-A) and a more restrictive B variant (TAP-B). It has been proposed that the class I molecule in the DA rat (RT1-Aa) has co-evolved with TAP-A and it has been shown that RT1-Aa antigenicity is changed when co-expressed with TAP-B. To study the contribution of different allelic combinations of RT1-A and Tap2 to the variation in MHC expression and T cell selection, we generated DA rats with either congenic or background alleles in the RT1-A and Tap2 loci. We found increased numbers of mature CD8SP cells in the thymus of rats which co-expressed RT1-Aa and TAP-B. This increase of CD8 cells could be explained by reduced negative selection, but did not correlate with RT1-Aa expression levels on thymic antigen presenting cells. Thus, our results identify a crucial role of the TAP and the quality of the MHC class I repertoire in regulating T cell selection.
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Affiliation(s)
- Jonatan Tuncel
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (JT); (RH)
| | - Sabrina Haag
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anthony C. Y. Yau
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ulrika Norin
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Amelie Baud
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Erik Lönnblom
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Klio Maratou
- Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - A. Jimmy Ytterberg
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Stockholm, Sweden
- Medical Proteomics, Department of Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden and Science for Life Laboratory, Solna, Sweden
| | - Diana Ekman
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Soley Thordardottir
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Martina Johannesson
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alan Gillett
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | | | - Pernilla Stridh
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas Olsson
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Alberto Fernández-Teruel
- Medical Psychology Unit, Department of Psychiatry & Forensic Medicine, Institute of Neurosciences, School of Medicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Roman A. Zubarev
- Medical Proteomics, Department of Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden and Science for Life Laboratory, Solna, Sweden
| | - Richard Mott
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Timothy J. Aitman
- Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Jonathan Flint
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Rikard Holmdahl
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (JT); (RH)
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Jaratlerdsiri W, Isberg SR, Higgins DP, Miles LG, Gongora J. Selection and trans-species polymorphism of major histocompatibility complex class II genes in the order Crocodylia. PLoS One 2014; 9:e87534. [PMID: 24503938 PMCID: PMC3913596 DOI: 10.1371/journal.pone.0087534] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 12/30/2013] [Indexed: 12/26/2022] Open
Abstract
Major Histocompatibility Complex (MHC) class II genes encode for molecules that aid in the presentation of antigens to helper T cells. MHC characterisation within and between major vertebrate taxa has shed light on the evolutionary mechanisms shaping the diversity within this genomic region, though little characterisation has been performed within the Order Crocodylia. Here we investigate the extent and effect of selective pressures and trans-species polymorphism on MHC class II α and β evolution among 20 extant species of Crocodylia. Selection detection analyses showed that diversifying selection influenced MHC class II β diversity, whilst diversity within MHC class II α is the result of strong purifying selection. Comparison of translated sequences between species revealed the presence of twelve trans-species polymorphisms, some of which appear to be specific to the genera Crocodylus and Caiman. Phylogenetic reconstruction clustered MHC class II α sequences into two major clades representing the families Crocodilidae and Alligatoridae. However, no further subdivision within these clades was evident and, based on the observation that most MHC class II α sequences shared the same trans-species polymorphisms, it is possible that they correspond to the same gene lineage across species. In contrast, phylogenetic analyses of MHC class II β sequences showed a mixture of subclades containing sequences from Crocodilidae and/or Alligatoridae, illustrating orthologous relationships among those genes. Interestingly, two of the subclades containing sequences from both Crocodilidae and Alligatoridae shared specific trans-species polymorphisms, suggesting that they may belong to ancient lineages pre-dating the divergence of these two families from the common ancestor 85-90 million years ago. The results presented herein provide an immunogenetic resource that may be used to further assess MHC diversity and functionality in Crocodylia.
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Affiliation(s)
| | - Sally R. Isberg
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
- Centre for Crocodile Research, Noonamah, Northern Territory, Australia
| | - Damien P. Higgins
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Lee G. Miles
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jaime Gongora
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
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Díaz-Morán S, Palència M, Mont-Cardona C, Cañete T, Blázquez G, Martínez-Membrives E, López-Aumatell R, Sabariego M, Donaire R, Morón I, Torres C, Martínez-Conejero JA, Tobeña A, Esteban FJ, Fernández-Teruel A. Gene expression in hippocampus as a function of differential trait anxiety levels in genetically heterogeneous NIH-HS rats. Behav Brain Res 2013; 257:129-39. [PMID: 24095878 DOI: 10.1016/j.bbr.2013.09.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 09/20/2013] [Accepted: 09/23/2013] [Indexed: 02/07/2023]
Abstract
To identify genes involved in the development/expression of anxiety/fear, we analyzed the gene expression profile in the hippocampus of genetically heterogeneous NIH-HS rats. The NIH-HS rat stock is a unique genetic resource for the fine mapping of quantitative trait loci (QTLs) to very small genomic regions, due to the high amount of genetic recombinants accumulated along more than 50 breeding generations, and for the same reason it can be expected that those genetically heterogeneous rats should be especially useful for studying differential gene expression as a function of anxiety, fearfulness or other complex traits. We selected high- and low-anxious NIH-HS rats according to the number of avoidance responses they performed in a single 50-trial session of the two-way active avoidance task. Rats were also tested in unconditioned anxiety/fearfulness tests, i.e. the elevated zero-maze and a "novel-cage activity" test. Three weeks after behavioral testing, the hippocampus was dissected and prepared for the microarray study. There appeared 29 down-regulated and 37 up-regulated SNC-related genes (fold-change>|2.19|, FDR<0.05) in the "Low-anxious" vs. the "High-anxious" group. Regression analyses (stepwise) revealed that differential expression of some genes could be predictive of anxiety/fear responses. Among those genes for which the present results suggest a link with individual differences in trait anxiety, nine relevant genes (Avpr1b, Accn3, Cd74, Ltb, Nrg2, Oprdl1, Slc10a4, Slc5a7 and RT1-EC12), tested for validation through qRT-PCR, have either neuroendocrinological or neuroinmunological/inflammation-related functions, or have been related with the hippocampal cholinergic system, while some of them have also been involved in the modulation of anxiety or stress-related (neurobiological and behavioral) responses (i.e. Avpr1b, Oprdl1). The present work confirms the usefulness of NIH-HS rats as a good animal model for research on the neurogenetic basis or mechanisms involved in anxiety and/or fear, and suggest that some MHC-(neuroinmunological/inflammation)-related pathways, as well as the cholinergic system within the hippocampus, may play a role in shaping individual differences in trait anxiety.
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Affiliation(s)
- Sira Díaz-Morán
- Medical Psychology Unit, Department of Psychiatry & Forensic Medicine, Institute of Neurosciences, School of Medicine, Autonomous University of Barcelona, Barcelona, Spain
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Díaz-Morán S, Palència M, Mont-Cardona C, Cañete T, Blázquez G, Martínez-Membrives E, López-Aumatell R, Sabariego M, Donaire R, Morón I, Torres C, Martínez-Conejero JA, Tobeña A, Esteban FJ, Fernández-Teruel A. Gene expression in amygdala as a function of differential trait anxiety levels in genetically heterogeneous NIH-HS rats. Behav Brain Res 2013; 252:422-31. [PMID: 23777796 DOI: 10.1016/j.bbr.2013.05.066] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/07/2013] [Accepted: 05/10/2013] [Indexed: 12/12/2022]
Abstract
To identify genes involved in anxiety/fear traits, we analyzed the gene expression profile in the amygdala of genetically heterogeneous NIH-HS rats. The NIH-HS rat stock has revealed to be a unique genetic resource for the fine mapping of Quantitative Trait Loci (QTLs) to very small genomic regions, due to the high amount of genetic recombinants accumulated along more than 50 breeding generations, and for the same reason it can be expected that those genetically heterogeneous rats should be especially useful for studying differential gene expression as a function of anxiety-(or other)-related traits. We selected high- and low-anxious NIH-HS rats differing in their number of avoidances in a single 50-trial session of the two-way active avoidance task. Rats were also tested in unconditioned anxiety tests (e.g., elevated zero-maze). Three weeks after behavioural testing, the amygdala was dissected and prepared for the microarray study. There appeared 6 significantly down-regulated and 28 up-regulated genes (fold-change >|2|, FDR<0.05) between the low- and high-anxious groups, with central nervous system-related functions. Regression analyses (stepwise) revealed that differential expression of some genes could be predictive of anxiety/fear responses. Among those genes for which the present results suggest a link with individual differences in trait anxiety, six relevant genes were examined with qRT-PCR, four of which (Ucn3, Tacr3, H2-M9 and Arr3) were validated. Remarkably, some of them are characterized by sharing known functions related with hormonal HPA-axis responses to (and/or modulation of) stress, anxiety or fear, and putative involvement in related neurobehavioural functions. The results confirm the usefulness of NIH-HS rats as a good animal model for research on the neurogenetic basis of anxiety and fear, while suggesting the involvement of some neuropeptide/neuroendocrine pathways on the development of differential anxiety profiles.
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Affiliation(s)
- Sira Díaz-Morán
- Medical Psychology Unit, Department of Psychiatry & Forensic Medicine, Institute of Neurosciences, School of Medicine, Universidad Autónoma de Barcelona, Barcelona, Spain.
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Daws MR, Dai KZ, Zinöcker S, Naper C, Kveberg L, Hedrich HJ, Rolstad B, Vaage JT. Identification of an MHC class I ligand for the single member of a killer cell lectin-like receptor family, KLRH1. THE JOURNAL OF IMMUNOLOGY 2012; 189:5178-84. [PMID: 23100519 DOI: 10.4049/jimmunol.1201983] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Natural killer cells are able to recognize and kill target cells according to differences in MHC class I expression. In rodents, the Ly49 receptors are primarily responsible for this MHC differentiation. We previously described the cloning of a novel C-type lectin-like receptor, KLRH1, encoded in the NK complex adjacent to the Ly49 genes and expressed by subsets of NK and NKT cells. MHC influence on selection of KLRH1(+) NK cells in congenic strains suggested that KLRH1 may have an MHC ligand, although we were unable to identify any such ligand. In this study, we have used a sensitive reporter system and Fc fusion protein to demonstrate that KLRH1 binds specifically to the classical MHC class I molecule RT1-A2 of the RT1(n) haplotype. Cytolytic activity of KLRH1-transfected RNK-16 cells was also inhibited by target cells expressing RT1-A2(n). Thus, KLRH1 represents a novel family of MHC allele-specific inhibitory receptors expressed by NK cells.
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Affiliation(s)
- Michael R Daws
- Department of Anatomy, University of Oslo, 0317 Oslo, Norway.
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Tollenaere C, Ivanova S, Duplantier JM, Loiseau A, Rahalison L, Rahelinirina S, Brouat C. Contrasted patterns of selection on MHC-linked microsatellites in natural populations of the Malagasy plague reservoir. PLoS One 2012; 7:e32814. [PMID: 22403713 PMCID: PMC3293896 DOI: 10.1371/journal.pone.0032814] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 02/06/2012] [Indexed: 01/14/2023] Open
Abstract
Plague (Yersinia pestis infection) is a highly virulent rodent disease that persists in many natural ecosystems. The black rat (Rattus rattus) is the main host involved in the plague focus of the central highlands of Madagascar. Black rat populations from this area are highly resistant to plague, whereas those from areas in which the disease is absent (low altitude zones of Madagascar) are susceptible. Various lines of evidence suggest a role for the Major Histocompatibility Complex (MHC) in plague resistance. We therefore used the MHC region as a candidate for detecting signatures of plague-mediated selection in Malagasy black rats, by comparing population genetic structures for five MHC-linked microsatellites and neutral markers in two sampling designs. We first compared four pairs of populations, each pair including one population from the plague focus and one from the disease-free zone. Plague-mediated selection was expected to result in greater genetic differentiation between the two zones than expected under neutrality and this was observed for one MHC-class I-linked locus (D20Img2). For this marker as well as for four other MHC-linked loci, a geographic pattern of genetic structure was found at local scale within the plague focus. This pattern would be expected if plague selection pressures were spatially variable. Finally, another MHC-class I-linked locus (D20Rat21) showed evidences of balancing selection, but it seems more likely that this selection would be related to unknown pathogens more widely distributed in Madagascar than plague.
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Affiliation(s)
- Charlotte Tollenaere
- Institut de Recherche pour le Développement, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez, France
| | - Svilena Ivanova
- Institut de Recherche pour le Développement, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez, France
| | - Jean-Marc Duplantier
- Institut de Recherche pour le Développement, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez, France
| | - Anne Loiseau
- Institut National de la Recherche Agronomique, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez, France
| | - Lila Rahalison
- Institut Pasteur de Madagascar, Unité Peste, Antananarivo, Madagascar
| | | | - Carine Brouat
- Institut de Recherche pour le Développement, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez, France
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Naper C, Shegarfi H, Inngjerdingen M, Rolstad B. The role of natural killer cells in the defense against Listeria monocytogenes lessons from a rat model. J Innate Immun 2011; 3:289-97. [PMID: 21430356 DOI: 10.1159/000324143] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 01/10/2011] [Indexed: 01/22/2023] Open
Abstract
Ly49 receptors in rodents, like killer cell immunoglobulin-like receptors in humans, regulate natural killer (NK) cell activity. Although inhibitory Ly49 receptors clearly recognize classical major histocompatibility complex class I (MHC-I) molecules, the role for the activating Ly49 receptors has been less well understood. Here, we discuss recent data from a rat model for listeriosis. Rats depleted of NK cells, or more specifically the Ly49 receptor-bearing cells, showed increased bacterial loads in their spleen. Athymic nude rats with no functional T cells but increased numbers of Ly49-expressing NK cells were more resistant to infection, indicating a central role of NK cells in early immune defense against Listeria in this species. Listeria infection of macrophages or enteric epithelial cells led to upregulation of MHC-I, including nonclassical (Ib) molecules not regularly recognized by T cells. We have shown that activating Ly49 receptors are more efficiently stimulated when binding to upregulated class Ib antigens on infected cells. From this we postulate that activating Ly49 receptors may have a sentinel function in the early immune response against Listeria in detecting diseased cells 'flagged' by increased MHC-Ib expression.
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Affiliation(s)
- Christian Naper
- Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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Novota P, Zinöcker S, Norden J, Wang XN, Sviland L, Opitz L, Salinas-Riester G, Rolstad B, Dickinson AM, Walter L, Dressel R. Expression profiling of major histocompatibility and natural killer complex genes reveals candidates for controlling risk of graft versus host disease. PLoS One 2011; 6:e16582. [PMID: 21305040 PMCID: PMC3030590 DOI: 10.1371/journal.pone.0016582] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 12/23/2010] [Indexed: 12/23/2022] Open
Abstract
Background The major histocompatibility complex (MHC) is the most important genomic region that contributes to the risk of graft versus host disease (GVHD) after haematopoietic stem cell transplantation. Matching of MHC class I and II genes is essential for the success of transplantation. However, the MHC contains additional genes that also contribute to the risk of developing acute GVHD. It is difficult to identify these genes by genetic association studies alone due to linkage disequilibrium in this region. Therefore, we aimed to identify MHC genes and other genes involved in the pathophysiology of GVHD by mRNA expression profiling. Methodology/Principal Findings To reduce the complexity of the task, we used genetically well-defined rat inbred strains and a rat skin explant assay, an in-vitro-model of the graft versus host reaction (GVHR), to analyze the expression of MHC, natural killer complex (NKC), and other genes in cutaneous GVHR. We observed a statistically significant and strong up or down regulation of 11 MHC, 6 NKC, and 168 genes encoded in other genomic regions, i.e. 4.9%, 14.0%, and 2.6% of the tested genes respectively. The regulation of 7 selected MHC and 3 NKC genes was confirmed by quantitative real-time PCR and in independent skin explant assays. In addition, similar regulations of most of the selected genes were observed in GVHD-affected skin lesions of transplanted rats and in human skin explant assays. Conclusions/Significance We identified rat and human MHC and NKC genes that are regulated during GVHR in skin explant assays and could therefore serve as biomarkers for GVHD. Several of the respective human genes, including HLA-DMB, C2, AIF1, SPR1, UBD, and OLR1, are polymorphic. These candidates may therefore contribute to the genetic risk of GVHD in patients.
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Affiliation(s)
- Peter Novota
- Department of Cellular and Molecular Immunology, University of Göttingen, Göttingen, Germany
| | - Severin Zinöcker
- Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jean Norden
- Haematological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Xiao Nong Wang
- Haematological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Lisbet Sviland
- Department of Pathology, Haukeland Sykehus, Section of Pathology, Gades Institute, University of Bergen, Bergen, Norway
| | - Lennart Opitz
- Transcriptome Analysis Laboratory, University of Göttingen, Göttingen, Germany
| | | | - Bent Rolstad
- Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Anne M. Dickinson
- Haematological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Lutz Walter
- Department of Primate Genetics, German Primate Center, Göttingen, Germany
| | - Ralf Dressel
- Department of Cellular and Molecular Immunology, University of Göttingen, Göttingen, Germany
- * E-mail:
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Reikerås O, Sigurdsen UW, Shegarfi H. Impact of freezing on immunology and incorporation of bone allograft. J Orthop Res 2010; 28:1215-9. [PMID: 20196082 DOI: 10.1002/jor.21121] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
With an increasing clinical use of deep frozen allograft for bone reconstruction, it is important to understand the immunological and biological events of allograft incorporation. In this study, we have investigated the impact of deep freezing on immunology and biopotency for incorporation of bone allografts. Deep frozen bone grafts matched or mismatched for major histoscompatibilty complex (MHC) were implanted in an 8-mm segmental defect in the tibia in rats. The construct was stabilized with intramedullary nailing. The immune response was evaluated by determination of serum antibody against the grafts MHC molecules at day 1 and after 2 and 4 months. Incorporation of the graft was compared with fresh syngeneic grafts and assessed with the use of conventional radiography, biomechanical testing and measurement of bone mineral content and density after 4 months. The analyses revealed no antibody responses in the rats that received grafts from donors differing at histocompatibility loci, and at 4 months the frozen grafts showed an overall reconstruction that was not significantly different from the fresh grafts. This study indicates that in the long run there are no significant consequences; either immunological or biomechanical, of the use of deep frozen allogenous bone as compared to fresh autogenous bone grafts in this animal model.
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Affiliation(s)
- Olav Reikerås
- Faculty Division Rikshospitalet, Department of Orthopaedics, University of Oslo, N-0027 Oslo, Norway.
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Gao J, Liu K, Liu H, Blair HT, Li G, Chen C, Tan P, Ma RZ. A complete DNA sequence map of the ovine major histocompatibility complex. BMC Genomics 2010; 11:466. [PMID: 20698968 PMCID: PMC3091662 DOI: 10.1186/1471-2164-11-466] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 08/10/2010] [Indexed: 11/30/2022] Open
Abstract
Background The ovine Major Histocompatibility Complex (MHC) harbors clusters of genes involved in overall resistance/susceptibility of an animal to infectious pathogens. However, only a limited number of ovine MHC genes have been identified and no adequate sequence information is available, as compared to those of swine and bovine. We previously constructed a BAC clone-based physical map that covers entire class I, class II and class III region of ovine MHC. Here we describe the assembling of a complete DNA sequence map for the ovine MHC by shotgun sequencing of 26 overlapping BAC clones. Results DNA shotgun sequencing generated approximately 8-fold genome equivalent data that were successfully assembled into a finished sequence map of the ovine MHC. The sequence map spans approximately 2,434,000 nucleotides in length, covering almost all of the MHC loci currently known in the sheep and cattle. Gene annotation resulted in the identification of 177 protein-coding genes/ORFs, among which 145 were not previously reported in the sheep, and 10 were ovine species specific, absent in cattle or other mammals. A comparative sequence analyses among human, sheep and cattle revealed a high conservation in the MHC structure and loci order except for the class II, which were divided into IIa and IIb subregions in the sheep and cattle, separated by a large piece of non-MHC autosome of approximately 18.5 Mb. In addition, a total of 18 non-protein-coding microRNAs were predicted in the ovine MHC region for the first time. Conclusion An ovine MHC DNA sequence map was successfully assembled by shotgun sequencing of 26 overlapping BAC clone. This makes the sheep the second ruminant species for which the complete MHC sequence information is available for evolution and functional studies, following that of the bovine. The results of the comparative analysis support a hypothesis that an inversion of the ancestral chromosome containing the MHC has shaped the MHC structures of ruminants, as we currently observed in the sheep and cattle. Identification of relative large numbers of microRNAs in the ovine MHC region helps to provide evidence that microRNAs are actively involved in the regulation of MHC gene expression and function.
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Affiliation(s)
- Jianfeng Gao
- School of Life Sciences, Shihezi University, Xinjiang 832007, China
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Strandberg LS, Ambrosi A, Jagodic M, Dzikaite V, Janson P, Khademi M, Salomonsson S, Ottosson L, Klauninger R, Adén U, Sonesson SE, Sunnerhagen M, de Graaf KL, Kuchroo VK, Achour A, Winqvist O, Olsson T, Wahren-Herlenius M. Maternal MHC regulates generation of pathogenic antibodies and fetal MHC-encoded genes determine susceptibility in congenital heart block. THE JOURNAL OF IMMUNOLOGY 2010; 185:3574-82. [PMID: 20696861 DOI: 10.4049/jimmunol.1001396] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Congenital heart block develops in fetuses of anti-Ro52 Ab-positive women. A recurrence rate of 20%, despite the persistence of maternal autoantibodies, indicates that there are additional, yet unidentified, factors critical for development of congenital heart block. In this study, we demonstrate that besides the maternal MHC controlling Ab specificity, fetal MHC-encoded genes influence fetal susceptibility to congenital heart block. Using MHC congenic rat strains, we show that heart block develops in rat pups of three strains carrying MHC haplotype RT1(av1) (DA, PVG.AV1, and LEW.AV1) after maternal Ro52 immunization, but not in LEW rats (RT1(l)). Different anti-Ro52 Ab fine specificities were generated in RT1(av1) versus RT1(l) animals. Maternal and fetal influence was determined in an F(2) cross between LEW.AV1 and LEW strains, which revealed higher susceptibility in RT1(l) than RT1(av1) pups once pathogenic Ro52 Abs were present. This was further confirmed in that RT1(l) pups more frequently developed heart block than RT1(av1) pups after passive transfer of RT1(av1) anti-Ro52 sera. Our findings show that generation of pathogenic Ro52 Abs is restricted by maternal MHC, whereas the fetal MHC locus regulates susceptibility and determines the fetal disease outcome in anti-Ro52-positive pregnancies.
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Affiliation(s)
- Linn S Strandberg
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
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46
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Gómez D, Conejeros P, Marshall SH, Consuegra S. MHC evolution in three salmonid species: a comparison between class II alpha and beta genes. Immunogenetics 2010; 62:531-42. [PMID: 20521040 DOI: 10.1007/s00251-010-0456-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 05/15/2010] [Indexed: 11/26/2022]
Abstract
The genes of the major histocompatibility complex (MHC) are amongst the most variable in vertebrates and represent some of the best candidates to study processes of adaptive evolution. However, despite the number of studies available, most of the information on the structure and function of these genes come from studies in mammals and birds in which the MHC class I and II genes are tightly linked and class II alpha exhibits low variability in many cases. Teleost fishes are among the most primitive vertebrates with MHC and represent good organisms for the study of MHC evolution because their class I and class II loci are not physically linked, allowing for independent evolution of both classes of genes. We have compared the diversity and molecular mechanisms of evolution of classical MH class II alpha and class II beta loci in farm populations of three salmonid species: Oncorhynchus kisutch, Oncorhynchus mykiss and Salmo salar. We found single classical class II loci and high polymorphism at both class II alpha and beta genes in the three species. Mechanisms of evolution were common for both class II genes, with recombination and point mutation involved in generating diversity and positive selection acting on the peptide-binding residues. These results suggest that the maintenance of variability at the class IIalpha gene could be a mechanism to increase diversity in the MHC class II in salmonids in order to compensate for the expression of one single classical locus and to respond to a wider array of parasites.
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Affiliation(s)
- Daniela Gómez
- Instituto de Biología, Facultad de Ciencias Básicas y Matemáticas, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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Guo Y, Yao F, Lu S, Cao DY, Reed WR, Zhao Y. The major histocompatibility complex genes are associated with basal pain sensitivity differences between Dark-Agouti and novel congenic DA.1U rats. Life Sci 2010; 86:972-8. [DOI: 10.1016/j.lfs.2010.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 03/17/2010] [Accepted: 05/07/2010] [Indexed: 11/24/2022]
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Lenz TL, Wells K, Pfeiffer M, Sommer S. Diverse MHC IIB allele repertoire increases parasite resistance and body condition in the Long-tailed giant rat (Leopoldamys sabanus). BMC Evol Biol 2009; 9:269. [PMID: 19930637 PMCID: PMC2788554 DOI: 10.1186/1471-2148-9-269] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 11/23/2009] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Genes of the major histocompatibility complex (MHC) code for key functions in the adaptive immune response of vertebrates and most of them show exceptionally high polymorphism. This polymorphism has been associated with the selection by diverse and changing parasite communities. We analysed MHC class IIB diversity, gastrointestinal parasite load and body condition in the wild ranging tropical rat Leopoldamys sabanus (Thomas, 1887) under natural selection conditions in a highly variable rainforest environment in Borneo to explore the mechanisms that maintain these high levels of genetic polymorphism. RESULTS Allelic diversity was determined via SSCP and sequencing, and parasite screening was done through non-invasive faecal egg count. The detected alleles showed expected high levels of polymorphism and balancing selection. Besides a clear advantage for more diverse MHC genotypes in terms of number of alleles, reflected in better body condition and resistance against helminth infection, our data also suggested a positive effect of MHC allele divergence within an individual on these parameters. CONCLUSION In accordance with the heterozygote advantage hypothesis, this study provides evidence for an advantage of more diverse MHC genotypes. More specifically, the potential negative relation between individual allele divergence and number of parasite species is in line with the 'divergent allele advantage' hypothesis.
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Affiliation(s)
- Tobias L Lenz
- Department of Animal Ecology and Animal Conservation, University of Hamburg, 20146 Hamburg, Germany
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Konstans Wells
- Institute of Experimental Ecology, University of Ulm, 89069 Ulm, Germany
| | - Martin Pfeiffer
- Institute of Experimental Ecology, University of Ulm, 89069 Ulm, Germany
| | - Simone Sommer
- Department of Animal Ecology and Animal Conservation, University of Hamburg, 20146 Hamburg, Germany
- Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Postfach 601103, D-10252 Berlin, Germany
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49
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Averdam A, Petersen B, Rosner C, Neff J, Roos C, Eberle M, Aujard F, Münch C, Schempp W, Carrington M, Shiina T, Inoko H, Knaust F, Coggill P, Sehra H, Beck S, Abi-Rached L, Reinhardt R, Walter L. A novel system of polymorphic and diverse NK cell receptors in primates. PLoS Genet 2009; 5:e1000688. [PMID: 19834558 PMCID: PMC2757895 DOI: 10.1371/journal.pgen.1000688] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 09/17/2009] [Indexed: 11/21/2022] Open
Abstract
There are two main classes of natural killer (NK) cell receptors in mammals, the killer cell immunoglobulin-like receptors (KIR) and the structurally unrelated killer cell lectin-like receptors (KLR). While KIR represent the most diverse group of NK receptors in all primates studied to date, including humans, apes, and Old and New World monkeys, KLR represent the functional equivalent in rodents. Here, we report a first digression from this rule in lemurs, where the KLR (CD94/NKG2) rather than KIR constitute the most diverse group of NK cell receptors. We demonstrate that natural selection contributed to such diversification in lemurs and particularly targeted KLR residues interacting with the peptide presented by MHC class I ligands. We further show that lemurs lack a strict ortholog or functional equivalent of MHC-E, the ligands of non-polymorphic KLR in "higher" primates. Our data support the existence of a hitherto unknown system of polymorphic and diverse NK cell receptors in primates and of combinatorial diversity as a novel mechanism to increase NK cell receptor repertoire.
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Affiliation(s)
- Anne Averdam
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
| | - Beatrix Petersen
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
| | - Cornelia Rosner
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
| | - Jennifer Neff
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
| | - Christian Roos
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
- Gene Bank of Primates, German Primate Centre, Göttingen, Germany
| | - Manfred Eberle
- Department of Behavioural Ecology and Sociobiology, German Primate Centre, Göttingen, Germany
| | - Fabienne Aujard
- Adaptive Mechanisms and Evolution, UMR CNRS/MNHN 7179, Brunoy, France
| | - Claudia Münch
- Institute for Human Genetics, University of Freiburg, Freiburg, Germany
| | - Werner Schempp
- Institute for Human Genetics, University of Freiburg, Freiburg, Germany
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | | | | | - Florian Knaust
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Penny Coggill
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Stephan Beck
- University College London Cancer Institute, University College London, London, United Kingdom
| | - Laurent Abi-Rached
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Lutz Walter
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
- Gene Bank of Primates, German Primate Centre, Göttingen, Germany
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de Bellocq JG, Leirs H. Complementary DNA sequences encoding the multimammate rat MHC class II DQ alpha and beta chains and cross-species sequence comparison in rodents. TISSUE ANTIGENS 2009; 74:233-237. [PMID: 19691639 DOI: 10.1111/j.1399-0039.2009.01305.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sequences of the complete open reading frame (ORF) for rodents major histocompatibility complex (MHC) class II genes are rare. Multimammate rat (Mastomys natalensis) complementary DNA (cDNA) encoding the alpha and beta chains of MHC class II DQ gene was cloned from a rapid amplifications of cDNA Emds (RACE) cDNA library. The ORFs consist of 801 and 771 bp encoding 266 and 256 amino acid residues for DQB and DQA, respectively. The genomic structure of Mana-DQ genes is globally analogous to that described for other rodents except for the insertion of a serine residue in the signal peptide of Mana-DQB, which is unique among known rodents.
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Affiliation(s)
- J Goüy de Bellocq
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, Antwerp, Belgium.
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