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Yang J, Chen S, Ma F, Ding N, Mi S, Zhao Q, Xing Y, Yang T, Xing K, Yu Y, Wang C. Pathogen stimulations and immune cells synergistically affect the gene expression profile characteristics of porcine peripheral blood mononuclear cells. BMC Genomics 2024; 25:719. [PMID: 39054472 PMCID: PMC11270792 DOI: 10.1186/s12864-024-10603-9] [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: 02/07/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Pigs serve as a crucial source of protein in the human diet and play a fundamental role in ensuring food security. However, infectious diseases caused by bacteria or viruses are a major threat to effective global pig farming, jeopardizing human health. Peripheral blood mononuclear cells (PBMCs) are a mixture of immune cells that play crucial roles in immunity and disease resistance in pigs. Previous studies on the gene expression regulation patterns of PBMCs have concentrated on a single immune stimulus or immune cell subpopulation, which has limited our comprehensive understanding of the mechanisms of the pig immune response. RESULTS Here, we integrated and re-analyzed RNA-seq data published online for porcine PBMC stimulated by lipopolysaccharide (LPS), polyinosinic acid (PolyI:C), and various unknown microorganisms (EM). The results revealed that gene expression and its functional characterization are highly specific to the pathogen, identifying 603, 254, and 882 pathogen-specific genes and 38 shared genes, respectively. Notably, LPS and PolyI:C stimulation directly triggered inflammatory and immune-response pathways, while exposure to mixed microbes (EM) enhanced metabolic processes. These pathogen-specific genes were enriched in immune trait-associated quantitative trait loci (QTL) and eGenes in porcine immune tissues and were implicated in specific cell types. Furthermore, we discussed the roles of eQTLs rs3473322705 and rs1109431654 in regulating pathogen- and cell-specific genes CD300A and CD93, using cellular experiments. Additionally, by integrating genome-wide association studies datasets from 33 complex traits and diseases in humans, we found that pathogen-specific genes were significantly enriched for immune traits and metabolic diseases. CONCLUSIONS We systematically analyzed the gene expression profiles of the three stimulations and demonstrated pathogen-specific and cell-specific gene regulation across different stimulations in porcine PBMCs. These findings enhance our understanding of shared and distinct regulatory mechanisms of genetic variants in pig immune traits.
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Affiliation(s)
- Jinyan Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technologyn, China Agricultural University, Beijing, 100193, China
| | - Siqian Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technologyn, China Agricultural University, Beijing, 100193, China
| | - Fuping Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technologyn, China Agricultural University, Beijing, 100193, China
| | - Ning Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technologyn, China Agricultural University, Beijing, 100193, China
| | - Siyuan Mi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technologyn, China Agricultural University, Beijing, 100193, China
| | - Qingyao Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technologyn, China Agricultural University, Beijing, 100193, China
| | - Yue Xing
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technologyn, China Agricultural University, Beijing, 100193, China
| | - Ting Yang
- Dabei-Nong Science and Technology Group Co., Ltd, Beijing, 100080, China
| | - Kai Xing
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technologyn, China Agricultural University, Beijing, 100193, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technologyn, China Agricultural University, Beijing, 100193, China.
| | - Chuduan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technologyn, China Agricultural University, Beijing, 100193, China.
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2
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Kondo T, Okada Y, Shizuya S, Yamaguchi N, Hatakeyama S, Maruyama K. Neuroimmune modulation by tryptophan derivatives in neurological and inflammatory disorders. Eur J Cell Biol 2024; 103:151418. [PMID: 38729083 DOI: 10.1016/j.ejcb.2024.151418] [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: 12/25/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
The nervous and immune systems are highly developed, and each performs specialized physiological functions. However, they work together, and their dysfunction is associated with various diseases. Specialized molecules, such as neurotransmitters, cytokines, and more general metabolites, are essential for the appropriate regulation of both systems. Tryptophan, an essential amino acid, is converted into functional molecules such as serotonin and kynurenine, both of which play important roles in the nervous and immune systems. The role of kynurenine metabolites in neurodegenerative and psychiatric diseases has recently received particular attention. Recently, we found that hyperactivity of the kynurenine pathway is a critical risk factor for septic shock. In this review, we first outline neuroimmune interactions and tryptophan derivatives and then summarized the changes in tryptophan metabolism in neurological disorders. Finally, we discuss the potential of tryptophan derivatives as therapeutic targets for neuroimmune disorders.
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Affiliation(s)
- Takeshi Kondo
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Hokkaido 060-8636, Japan
| | - Yuka Okada
- Department of Ophthalmology, Wakayama Medical University School of Medicine, Wakayama 641-0012, Japan
| | - Saika Shizuya
- Department of Ophthalmology, Wakayama Medical University School of Medicine, Wakayama 641-0012, Japan
| | - Naoko Yamaguchi
- Department of Pharmacology, School of Medicine, Aichi Medical University, Aichi 480-1195, Japan
| | - Shigetsugu Hatakeyama
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Hokkaido 060-8636, Japan
| | - Kenta Maruyama
- Department of Pharmacology, School of Medicine, Aichi Medical University, Aichi 480-1195, Japan.
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3
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McMinds R, Jiang RHY, Adapa SR, Cornelius Ruhs E, Munds RA, Leiding JW, Downs CJ, Martin LB. Bacterial sepsis triggers stronger transcriptomic immune responses in larger primates. Proc Biol Sci 2024; 291:20240535. [PMID: 38917861 DOI: 10.1098/rspb.2024.0535] [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: 08/15/2023] [Accepted: 04/05/2024] [Indexed: 06/27/2024] Open
Abstract
Empirical data relating body mass to immune defence against infections remain limited. Although the metabolic theory of ecology predicts that larger organisms would have weaker immune responses, recent studies have suggested that the opposite may be true. These discoveries have led to the safety factor hypothesis, which proposes that larger organisms have evolved stronger immune defences because they carry greater risks of exposure to pathogens and parasites. In this study, we simulated sepsis by exposing blood from nine primate species to a bacterial lipopolysaccharide (LPS), measured the relative expression of immune and other genes using RNAseq, and fitted phylogenetic models to determine how gene expression was related to body mass. In contrast to non-immune-annotated genes, we discovered hypermetric scaling in the LPS-induced expression of innate immune genes, such that large primates had a disproportionately greater increase in gene expression of immune genes compared to small primates. Hypermetric immune gene expression appears to support the safety factor hypothesis, though this pattern may represent a balanced evolutionary mechanism to compensate for lower per-transcript immunological effectiveness. This study contributes to the growing body of immune allometry research, highlighting its importance in understanding the complex interplay between body size and immunity over evolutionary timescales.
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Affiliation(s)
- Ryan McMinds
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
- USF Genomics Program, University of South Florida College of Public Health , Tampa, FL, USA
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
- USF Genomics Program, University of South Florida College of Public Health , Tampa, FL, USA
| | - Swamy R Adapa
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
- USF Genomics Program, University of South Florida College of Public Health , Tampa, FL, USA
| | - Emily Cornelius Ruhs
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
- Department of Ecology and Evolution, University of Chicago , Chicago, IL, USA
- Grainger Bioinformatics Center, Field Museum of Natural History , Chicago, IL, USA
| | - Rachel A Munds
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
| | - Jennifer W Leiding
- Division of Allergy and Immunology, Department of Pediatrics, Johns Hopkins Medicine , St Petersburg, FL, USA
- Institute for Clinical and Translational Research, Johns Hopkins All Children's Hospital , St Petersburg, FL, USA
| | - Cynthia J Downs
- Department of Environmental Biology, SUNY College of Environmental Science and Forestry , Syracuse, NY, USA
| | - Lynn B Martin
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
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4
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Lanz-Mendoza H, Gálvez D, Contreras-Garduño J. The plasticity of immune memory in invertebrates. J Exp Biol 2024; 227:jeb246158. [PMID: 38449328 DOI: 10.1242/jeb.246158] [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] [Indexed: 03/08/2024]
Abstract
Whether specific immune protection after initial pathogen exposure (immune memory) occurs in invertebrates has long been uncertain. The absence of antibodies, B-cells and T-cells, and the short lifespans of invertebrates led to the hypothesis that immune memory does not occur in these organisms. However, research in the past two decades has supported the existence of immune memory in several invertebrate groups, including Ctenophora, Cnidaria, Nematoda, Mollusca and Arthropoda. Interestingly, some studies have demonstrated immune memory that is specific to the parasite strain. Nonetheless, other work does not provide support for immune memory in invertebrates or offers only partial support. Moreover, the expected biphasic immune response, a characteristic of adaptive immune memory in vertebrates, varies within and between invertebrate species. This variation may be attributed to the influence of biotic or abiotic factors, particularly parasites, on the outcome of immune memory. Despite its critical importance for survival, the role of phenotypic plasticity in immune memory has not been systematically examined in the past two decades. Additionally, the features of immune responses occurring in diverse environments have yet to be fully characterized.
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Affiliation(s)
- Humberto Lanz-Mendoza
- Centro de Investigaciones sobre Enfermedades Infecciosas, INSP, 62100 Cuernavaca, Morelos, Mexico
| | - Dumas Gálvez
- Coiba Scientific Station, City of Knowledge, Calle Gustavo Lara, Boulevard 145B, Clayton 0843-01853, Panama
- Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Estafeta universitaria, Avenida Simón Bolívar, 0824, Panama
- Sistema Nacional de Investigación, Edificio 205, Ciudad del Saber, 0816-02852, Panama
| | - Jorge Contreras-Garduño
- Escuela Nacional de Estudios Superiores, Unidad Morelia, UNAM, 58190 Morelia, Mexico
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
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5
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Zhou SO, Arunkumar R, Irfan A, Ding SD, Leitão AB, Jiggins FM. The evolution of constitutively active humoral immune defenses in Drosophila populations under high parasite pressure. PLoS Pathog 2024; 20:e1011729. [PMID: 38206983 PMCID: PMC10807768 DOI: 10.1371/journal.ppat.1011729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/24/2024] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
Both constitutive and inducible immune mechanisms are employed by hosts for defense against infection. Constitutive immunity allows for a faster response, but it comes with an associated cost that is always present. This trade-off between speed and fitness costs leads to the theoretical prediction that constitutive immunity will be favored where parasite exposure is frequent. We selected populations of Drosophila melanogaster under high parasite pressure from the parasitoid wasp Leptopilina boulardi. With RNA sequencing, we found the evolution of resistance in these populations was associated with them developing constitutively active humoral immunity, mediated by the larval fat body. Furthermore, these evolved populations were also able to induce gene expression in response to infection to a greater level, which indicates an overall more activated humoral immune response to parasitization. The anti-parasitoid immune response also relies on the JAK/STAT signaling pathway being activated in muscles following infection, and this induced response was only seen in populations that had evolved under high parasite pressure. We found that the cytokine Upd3, which induces this JAK/STAT response, is being expressed by immature lamellocytes. Furthermore, these immune cells became constitutively present when populations evolved resistance, potentially explaining why they gained the ability to activate JAK/STAT signaling. Thus, under intense parasitism, populations evolved resistance by increasing both constitutive and induced immune defenses, and there is likely an interplay between these two forms of immunity.
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Affiliation(s)
- Shuyu Olivia Zhou
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ramesh Arunkumar
- Section of population genetics, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Amina Irfan
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Alexandre B. Leitão
- Champalimaud Foundation, Champalimaud Centre of the Unknown, Lisbon, Portugal
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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6
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Gawra J, Valdivieso A, Roux F, Laporte M, de Lorgeril J, Gueguen Y, Saccas M, Escoubas JM, Montagnani C, Destoumieux-Garzόn D, Lagarde F, Leroy MA, Haffner P, Petton B, Cosseau C, Morga B, Dégremont L, Mitta G, Grunau C, Vidal-Dupiol J. Epigenetic variations are more substantial than genetic variations in rapid adaptation of oyster to Pacific oyster mortality syndrome. SCIENCE ADVANCES 2023; 9:eadh8990. [PMID: 37683000 PMCID: PMC10491289 DOI: 10.1126/sciadv.adh8990] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
Disease emergence is accelerating with global changes. Understanding by which mechanisms host populations can rapidly adapt will be crucial for management practices. Pacific oyster mortality syndrome (POMS) imposes a substantial and recurrent selective pressure on oyster populations, and rapid adaptation may arise through genetics and epigenetics. In this study, we used (epi)genome-wide association mapping to show that oysters differentially exposed to POMS displayed genetic and epigenetic signatures of selection. Consistent with higher resistance to POMS, the genes targeted included many genes in several pathways related to immunity. By combining correlation, DNA methylation quantitative trait loci, and variance partitioning, we revealed that a third of phenotypic variation was explained by interactions between the genetic and epigenetic information, ~14% by the genome, and up to 25% by the epigenome alone. Similar to genetically based adaptation, epigenetic mechanisms notably governing immune responses can contribute substantially to the rapid adaptation of hosts to emerging infectious diseases.
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Affiliation(s)
- Janan Gawra
- IHPE, Université de Perpignan Via Domitia, CNRS, Ifremer, Université de Montpellier, Perpignan, France
| | - Alejandro Valdivieso
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Fabrice Roux
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Martin Laporte
- Division de l'expertise sur la faune Aquatique, Ministère des Forêts, de la Faune et des Parcs (MFFP), 880 chemin Sainte-Foy, G1S 4X4 Québec, Québec, Canada
| | - Julien de Lorgeril
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, ENTROPIE, Nouméa, Nouvelle-Calédonie, France
| | - Yannick Gueguen
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Mathilde Saccas
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Jean-Michel Escoubas
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Caroline Montagnani
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | | | - Franck Lagarde
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Marc A. Leroy
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Philippe Haffner
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Bruno Petton
- Université de Brest, Ifremer, CNRS, IRD, LEMAR, F-29280 Plouzané, France
| | - Céline Cosseau
- IHPE, Université de Perpignan Via Domitia, CNRS, Ifremer, Université de Montpellier, Perpignan, France
| | - Benjamin Morga
- Ifremer, ASIM, Adaptation Santé des Invertébrés Marins, La Tremblade, France
| | - Lionel Dégremont
- Ifremer, ASIM, Adaptation Santé des Invertébrés Marins, La Tremblade, France
| | - Guillaume Mitta
- IHPE, Université de Perpignan Via Domitia, CNRS, Ifremer, Université de Montpellier, Perpignan, France
- Université de la Polynésie Française, ILM, IRD, Ifremer, F-98719 Tahiti, French Polynesia, France
| | - Christoph Grunau
- IHPE, Université de Perpignan Via Domitia, CNRS, Ifremer, Université de Montpellier, Perpignan, France
| | - Jeremie Vidal-Dupiol
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
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7
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Rutkowski NAJ, McNamara KB, Jones TM, Foo YZ. Trans-generational immune priming is not mediated by the sex of the parent primed: a meta-analysis of invertebrate data. Biol Rev Camb Philos Soc 2023; 98:1100-1117. [PMID: 36879482 DOI: 10.1111/brv.12946] [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: 07/28/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Traditionally, only vertebrates were thought capable of acquired immune responses, such as the ability to transfer immunological experience vertically to their offspring (known as trans-generational immune priming, TGIP). Increasing evidence challenges this belief and it is now clear that invertebrates also have the ability to exhibit functionally equivalent TGIP. This has led to a surge in papers exploring invertebrate TGIP, with most focusing on the costs, benefits or factors that affect the evolution of this trait. Whilst many studies have found support for the phenomenon, not all studies do, and there is considerable variation in the strength of positive results. To address this, we conducted a meta-analysis to answer the question: what is the overall effect of TGIP in invertebrates? Then, to understand the specific factors that affect its presence and intensity, we conducted a moderator analysis. Our results corroborate that TGIP occurs in invertebrates (demonstrated by a large, positive effect size). The strength of the positive effect was related to if and how offspring were immune challenged (i.e. whether they were challenged with the same or different insult as their parents or not challenged at all). Interestingly, there was no effect of the ecology or life history of the species or the sex of the parent or the offspring primed, and responses were comparable across different immune elicitors. Our publication bias testing suggests that the literature may suffer from some level of positive-result bias. However, even after accounting for potential bias, our effect size remains positive. Publication bias testing can be influenced by diversity in the data set, which was considerable in our data, even after moderator analysis. It is therefore conceivable that differences among studies could be caused by other moderators that were unable to be included in our meta-analysis. Nonetheless, our results suggest that TGIP does occur in invertebrates, whilst providing some potential avenues to examine the factors that account for variation in effect sizes.
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Affiliation(s)
- Nicola-Anne J Rutkowski
- School of BioSciences, University of Melbourne, Biosciences 4, Royal Parade, Parkville, VIC, 3052, Australia
| | - Kathryn B McNamara
- School of BioSciences, University of Melbourne, Biosciences 4, Royal Parade, Parkville, VIC, 3052, Australia
| | - Therésa M Jones
- School of BioSciences, University of Melbourne, Biosciences 4, Royal Parade, Parkville, VIC, 3052, Australia
| | - Yong Zhi Foo
- Centre for Evolutionary Biology & School of Biological Sciences, University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
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8
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Carneiro CFD, Drude N, Hülsemann M, Collazo A, Toelch U. Mapping strategies towards improved external validity in preclinical translational research. Expert Opin Drug Discov 2023; 18:1273-1285. [PMID: 37691294 DOI: 10.1080/17460441.2023.2251886] [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: 02/24/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023]
Abstract
INTRODUCTION Translation is about successfully bringing findings from preclinical contexts into the clinic. This transfer is challenging as clinical trials frequently fail despite positive preclinical results. Limited robustness of preclinical research has been marked as one of the drivers of such failures. One suggested solution is to improve the external validity of in vitro and in vivo experiments via a suite of complementary strategies. AREAS COVERED In this review, the authors summarize the literature available on different strategies to improve external validity in in vivo, in vitro, or ex vivo experiments; systematic heterogenization; generalizability tests; and multi-batch and multicenter experiments. Articles that tested or discussed sources of variability in systematically heterogenized experiments were identified, and the most prevalent sources of variability are reviewed further. Special considerations in sample size planning, analysis options, and practical feasibility associated with each strategy are also reviewed. EXPERT OPINION The strategies reviewed differentially influence variation in experiments. Different research projects, with their unique goals, can leverage the strengths and limitations of each strategy. Applying a combination of these approaches in confirmatory stages of preclinical research putatively increases the chances of success in clinical studies.
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Affiliation(s)
- Clarissa F D Carneiro
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité, Berlin, Germany
| | - Natascha Drude
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité, Berlin, Germany
| | - Maren Hülsemann
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité, Berlin, Germany
| | - Anja Collazo
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité, Berlin, Germany
| | - Ulf Toelch
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité, Berlin, Germany
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9
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Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-Meijers HE, Wu P, Wen X, Slatcher RB, Zhou X, Luca F, Pique-Regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution. Genome Res 2023; 33:839-856. [PMID: 37442575 PMCID: PMC10519413 DOI: 10.1101/gr.276765.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/08/2023] [Indexed: 07/15/2023]
Abstract
Synthetic glucocorticoids, such as dexamethasone, have been used as a treatment for many immune conditions, such as asthma and, more recently, severe COVID-19. Single-cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single-cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated peripheral blood mononuclear cells from 96 African American children. We used novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we showed that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and showed widespread genetic regulation of the transcriptional dynamics of the gene expression response.
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Affiliation(s)
- Justyna A Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Samuele Zilioli
- Department of Psychology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, Michigan 48201, USA
| | - Edward Sendler
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Henriette E Mair-Meijers
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Peijun Wu
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Richard B Slatcher
- Department of Psychology, University of Georgia, Athens, Georgia 30602, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Biology, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
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10
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Downs CJ, Schoenle LA, Goolsby EW, Oakey SJ, Ball R, Jiang RHY, Martin LB. Large Mammals Have More Powerful Antibacterial Defenses Than Expected from Their Metabolic Rates. Am Nat 2023; 201:287-301. [PMID: 36724463 DOI: 10.1086/722504] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractTerrestrial mammals span seven orders of magnitude in body size, ranging from the <2-g Etruscan pygmy shrew (Suncus etruscus) to the >3,900-kg African elephant (Loxodonta africana). Although body size profoundly affects the behavior, physiology, ecology, and evolution of species, how investment in functional immune defenses changes with body size across species is unknown. Here, we (1) developed a novel 12-point dilution curve approach to describe and compare antibacterial capacity against three bacterial species among >160 terrestrial species of mammals and (2) tested published predictions about the scaling of immune defenses. Our study focused on the safety factor hypothesis, which predicts that broad, early-acting immune defenses should scale hypermetrically with body mass. However, our three statistical approaches demonstrated that antibacterial activity in sera across mammals exhibits isometry; killing capacity did not change with body size across species. Intriguingly, this result indicates that the serum of a large mammal is less hospitable to bacteria than would be predicted by its metabolic rates. In other words, if metabolic rates underlie the rates of physiological reactions as postulated by the metabolic theory of ecology, large species should have disproportionately lower antibacterial capacity than small species, but they do not. These results have direct implications for effectively modeling the evolution of immune defenses and identifying potential reservoir hosts of pathogens.
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11
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Jaric I, Voelkl B, Clerc M, Schmid MW, Novak J, Rosso M, Rufener R, von Kortzfleisch VT, Richter SH, Buettner M, Bleich A, Amrein I, Wolfer DP, Touma C, Sunagawa S, Würbel H. The rearing environment persistently modulates mouse phenotypes from the molecular to the behavioural level. PLoS Biol 2022; 20:e3001837. [PMID: 36269766 PMCID: PMC9629646 DOI: 10.1371/journal.pbio.3001837] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/02/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
The phenotype of an organism results from its genotype and the influence of the environment throughout development. Even when using animals of the same genotype, independent studies may test animals of different phenotypes, resulting in poor replicability due to genotype-by-environment interactions. Thus, genetically defined strains of mice may respond differently to experimental treatments depending on their rearing environment. However, the extent of such phenotypic plasticity and its implications for the replicability of research findings have remained unknown. Here, we examined the extent to which common environmental differences between animal facilities modulate the phenotype of genetically homogeneous (inbred) mice. We conducted a comprehensive multicentre study, whereby inbred C57BL/6J mice from a single breeding cohort were allocated to and reared in 5 different animal facilities throughout early life and adolescence, before being transported to a single test laboratory. We found persistent effects of the rearing facility on the composition and heterogeneity of the gut microbial community. These effects were paralleled by persistent differences in body weight and in the behavioural phenotype of the mice. Furthermore, we show that environmental variation among animal facilities is strong enough to influence epigenetic patterns in neurons at the level of chromatin organisation. We detected changes in chromatin organisation in the regulatory regions of genes involved in nucleosome assembly, neuronal differentiation, synaptic plasticity, and regulation of behaviour. Our findings demonstrate that common environmental differences between animal facilities may produce facility-specific phenotypes, from the molecular to the behavioural level. Furthermore, they highlight an important limitation of inferences from single-laboratory studies and thus argue that study designs should take environmental background into account to increase the robustness and replicability of findings. The phenotype of an organism results not only from its genotype but also the influence of its environment throughout development. This study shows that common environmental differences between animal facilities can induce substantial variation in the phenotype of mice, thereby highlighting an important limitation of inferences from single-laboratory studies in animal research.
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Affiliation(s)
- Ivana Jaric
- Animal Welfare Division, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- * E-mail: (IJ); (HW)
| | - Bernhard Voelkl
- Animal Welfare Division, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Melanie Clerc
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | | | - Janja Novak
- Animal Welfare Division, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Marianna Rosso
- Animal Welfare Division, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto Rufener
- Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | | | - S. Helene Richter
- Department of Behavioural Biology, University of Münster, Münster, Germany
| | - Manuela Buettner
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | - André Bleich
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | - Irmgard Amrein
- Institute of Anatomy, Division of Functional Neuroanatomy, University of Zürich, Zürich, Switzerland; Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - David P. Wolfer
- Institute of Anatomy, Division of Functional Neuroanatomy, University of Zürich, Zürich, Switzerland; Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Chadi Touma
- Department of Behavioural Biology, Osnabrück University, Osnabrück, Germany
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Hanno Würbel
- Animal Welfare Division, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- * E-mail: (IJ); (HW)
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12
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Corbally MK, Regan JC. Fly immunity comes of age: The utility of Drosophila as a model for studying variation in immunosenescence. FRONTIERS IN AGING 2022; 3:1016962. [PMID: 36268532 PMCID: PMC9576847 DOI: 10.3389/fragi.2022.1016962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 11/05/2022]
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13
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Martin LB, Ruhs EC, Oakey S, Downs CJ. Leukocyte allometries in birds are not affected by captivity. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2022; 337:576-582. [PMID: 35286769 DOI: 10.1002/jez.2591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/17/2022] [Accepted: 02/11/2022] [Indexed: 12/15/2022]
Abstract
Body size affects many traits, but often in allometric, or disproportionate ways. For example, large avian and mammalian species circulate far more of some immune cells than expected for their size based on simple geometric principles. To date, such hypermetric immune scaling has mostly been described in zoo-dwelling individuals, so it remains obscure whether immune hyper-allometries have any natural relevance. Here, we asked whether granulocyte and lymphocyte allometries in wild birds differ from those described in captive species. Our previous allometric studies of avian immune cell concentrations were performed on animals kept for their lifetimes in captivity where conditions are benign and fairly consistent. In natural conditions, infection, stress, nutrition, climate, and myriad other forces could alter immune traits and hence mask any interspecific scaling relationships between immune cells and body size. Counter to this expectation, we found no evidence that immune cell allometries differed between captive and wild species, although we had to rely on cell proportion data, as insufficient concentration data were available for wild species. Our results indicate that even in variable and challenging natural contexts, immune allometries endure and might affect disease ecology and evolution.
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Affiliation(s)
- Lynn B Martin
- Global Health and Infectious Disease Research, University of South Florida, Tampa, Florida, USA
| | - Emily Cornelius Ruhs
- Global Health and Infectious Disease Research, University of South Florida, Tampa, Florida, USA
| | - Samantha Oakey
- Global Health and Infectious Disease Research, University of South Florida, Tampa, Florida, USA
| | - Cynthia J Downs
- Department of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, New York, USA
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14
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Gilbertson SE, Weinmann AS. Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis. Trends Immunol 2021; 42:1077-1087. [PMID: 34740529 DOI: 10.1016/j.it.2021.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023]
Abstract
Model organisms such as mice are important for basic research and serve as valuable tools in preclinical translational studies. A challenge with translating findings from mice to humans is identifying and separating evolutionarily conserved mechanisms in the immune system from those diverging between species. A significant emphasis has been placed on defining conserved gene regulation principles, with divergent mechanisms often overlooked. We put forward the perspective that both conserved and divergent mechanisms that regulate gene expression programs are of equal importance. With recent advances and availability of datasets, immunologists should take a closer look at the role for genetic diversity in altering gene expression programs between mouse and human immune cells.
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Affiliation(s)
- Sarah E Gilbertson
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Amy S Weinmann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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15
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Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-meijers HE, Wu P, Slatcher RB, Zhou X, Luca F, Pique-regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution.. [PMID: 35313584 PMCID: PMC8936121 DOI: 10.1101/2021.09.30.462672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Synthetic glucocorticoids, such as dexamethasone, have been used as treatment for many immune conditions, such as asthma and more recently severe COVID-19. Single cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated Peripheral Blood Mononuclear Cells from 96 African American children. We employed novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we demonstrated that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and demonstrated widespread genetic regulation of the transcriptional dynamics of the gene expression response.
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16
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Tobias ZJC, Fowler AE, Blakeslee AMH, Darling JA, Torchin ME, Miller AW, Ruiz GM, Tepolt CK. Invasion history shapes host transcriptomic response to a body-snatching parasite. Mol Ecol 2021; 30:4321-4337. [PMID: 34162013 PMCID: PMC10128110 DOI: 10.1111/mec.16038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/27/2021] [Accepted: 06/11/2021] [Indexed: 01/04/2023]
Abstract
By shuffling biogeographical distributions, biological invasions can both disrupt long-standing associations between hosts and parasites and establish new ones. This creates natural experiments with which to study the ecology and evolution of host-parasite interactions. In estuaries of the Gulf of Mexico, the white-fingered mud crab (Rhithropanopeus harrisii) is infected by a native parasitic barnacle, Loxothylacus panopaei (Rhizocephala), which manipulates host physiology and behaviour. In the 1960s, L. panopaei was introduced to the Chesapeake Bay and has since expanded along the southeastern Atlantic coast, while host populations in the northeast have so far been spared. We use this system to test the host's transcriptomic response to parasitic infection and investigate how this response varies with the parasite's invasion history, comparing populations representing (i) long-term sympatry between host and parasite, (ii) new associations where the parasite has invaded during the last 60 years and (iii) naïve hosts without prior exposure. A comparison of parasitized and control crabs revealed a core response, with widespread downregulation of transcripts involved in immunity and moulting. The transcriptional response differed between hosts from the parasite's native range and where it is absent, consistent with previous observations of increased susceptibility in populations lacking exposure to the parasite. Crabs from the parasite's introduced range, where prevalence is highest, displayed the most dissimilar response, possibly reflecting immune priming. These results provide molecular evidence for parasitic manipulation of host phenotype and the role of gene regulation in mediating host-parasite interactions.
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Affiliation(s)
- Zachary J C Tobias
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amy E Fowler
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | | | - John A Darling
- National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Mark E Torchin
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | | | - Gregory M Ruiz
- Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - Carolyn K Tepolt
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,Smithsonian Environmental Research Center, Edgewater, MD, USA
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17
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Madelaire CB, Zena LA, Dillon D, Silva DP, Hunt KE, Loren Buck C, Bícego KC, Gomes FR. Who rules over immunology? Sseasonal variation in body temperature,, steroid hormones, and immune variables in a tegu lizard. Integr Comp Biol 2021; 61:1867-1880. [PMID: 34022037 DOI: 10.1093/icb/icab093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multiple factors can influence the immune response of ectothermic vertebrates, including body temperature, gonadal steroids, and seasonality, in ways that are thought to reflect trade-offs between energetic investment in immunity vs. reproduction. Hibernating tegu lizards (Salvator merianae) are a unique model to investigate how immunocompetence might be influenced by different factors during their annual cycle. We assessed immunological measures (plasma bacterial killing ability, total and differential leukocyte count), plasma hormone levels (testosterone in males, estradiol and progesterone in females, and corticosterone in both sexes), body temperature, and body condition from adult tegus during each stage of their annual cycle: reproduction, post-reproduction/preparation for hibernation, and hibernation. Our hypothesis that immune traits present higher values during the reproductive phase, and a sharp decrease during hibernation, was partially supported. Immune variables did not change between life history stages, except for total number of leukocytes, which was higher at the beginning of the reproductive season (September) in both males and females. Average body temperature of the week prior to sampling was positively correlated with number of eosinophils, basophils, monocytes and azurophils, corroborating other studies showing that when animals maintain a high Tb, there is an increase in immune activity. Surprisingly, no clear relationship between immune traits and gonadal steroids or corticosterone levels was observed, even when including life history stage in the model. When gonadal hormones peaked in males and females, heterophil:lymphocyte ratio (which often elevates during physiological stress) also increased. Additionally, we did not observe any trade-off between reproduction and immunity traits, sex differences in immune traits or a correlation between body condition and immune response. Our results suggest that variation in patterns of immune response and correlations with body condition and hormone secretion across the year can depend upon the specific hormone and immune trait, and that experienced Tb is an important variable determining immune response in ectotherms.
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Affiliation(s)
- Carla B Madelaire
- Department of Biological Sciences, Northern Arizona University, 1899 S San Francisco St, Flagstaff, AZ, 86001, USA.,Department of Physiology, Institute of Biosciences, University of São Paulo, Trav. 14 da Rua do Matão, 321, São Paulo, SP, 05508-090, Brazil
| | - Lucas A Zena
- Department of Biological Sciences, Northern Arizona University, 1899 S San Francisco St, Flagstaff, AZ, 86001, USA.,Department of Physiology, Institute of Biosciences, University of São Paulo, Trav. 14 da Rua do Matão, 321, São Paulo, SP, 05508-090, Brazil.,Department of Animal Morphology and Physiology, College of Agricultural and Veterinary Sciences, São Paulo State University, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Danielle Dillon
- Department of Biological Sciences, Northern Arizona University, 1899 S San Francisco St, Flagstaff, AZ, 86001, USA
| | - Diego P Silva
- Smithsonian-Mason School of Conservation & George Mason University, 1500 Remount Rd, Front Royal, VA, 22630, USA
| | - Kathleen E Hunt
- Department of Biological Sciences, Northern Arizona University, 1899 S San Francisco St, Flagstaff, AZ, 86001, USA
| | - C Loren Buck
- Department of Biological Sciences, Northern Arizona University, 1899 S San Francisco St, Flagstaff, AZ, 86001, USA
| | - Kênia C Bícego
- Department of Animal Morphology and Physiology, College of Agricultural and Veterinary Sciences, São Paulo State University, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Fernando R Gomes
- Department of Physiology, Institute of Biosciences, University of São Paulo, Trav. 14 da Rua do Matão, 321, São Paulo, SP, 05508-090, Brazil
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