1
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Barr KA, Rhodes KL, Gilad Y. The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees. Genome Biol 2023; 24:207. [PMID: 37697401 PMCID: PMC10496171 DOI: 10.1186/s13059-023-03019-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/21/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect transcriptomic data from over 70 cell types in three humans and three chimpanzees. RESULTS We find hundreds of genes whose regulation is conserved across cell types, as well as genes whose regulation likely evolves under directional selection in one or a handful of cell types. Using embryoid bodies from a human-chimpanzee fused cell line, we also infer the proportion of inter-species regulatory differences due to changes in cis and trans elements between the species. Using the cis/trans inference and an analysis of transcription factor binding sites, we identify dozens of transcription factors whose inter-species differences in expression are affecting expression differences between humans and chimpanzees in hundreds of target genes. CONCLUSIONS Here, we present the most comprehensive dataset of comparative gene expression from humans and chimpanzees to date, including a catalog of regulatory mechanisms associated with inter-species differences.
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Affiliation(s)
- Kenneth A Barr
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | | | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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2
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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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3
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Yao T, Wang R, Han P, Liu X, Wang X. Identification of olive flounder (Paralichthys olivaceus) toll-like receptor genes: Involvement in immune response to temperature stress and Edwardsiella tarda infection. FISH & SHELLFISH IMMUNOLOGY 2023; 138:108841. [PMID: 37209756 DOI: 10.1016/j.fsi.2023.108841] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 05/22/2023]
Abstract
Toll-like receptor (TLR) genes are best known for their roles in the innate immune defense. However, studies focusing on the reaction mechanisms of TLR genes in olive flounder (Paralichthys olivaceus) immune responses are still limited. In this study, 11 TLR family members (PoTLRs) were identified and classified from P. olivaceus genome. Phylogenetic analysis showed that PoTLRs were highly conserved in olive flounder. The analysis of motif prediction and gene structure indicated that TLRs had high sequence similarity. The expression patterns in developmental stages and different tissues showed that TLR members were spatially and temporally specific. RNA-Seq analysis of temperature stress and Edwardsiella tarda infection suggested that TLR members were involved in inflammatory responses, PoTLR5b and PoTLR22 showed significant differences in response to both temperature stress and E. tarda stress, indicating their potential immune functions. The results of this study suggested that TLR genes played important roles in the innate immune response of olive flounder, and would provide a solid basis for further study of their functions.
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Affiliation(s)
- Tingyan Yao
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, 315832, China; National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, 315832, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, 315832, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, 315832, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, 315832, China.
| | - Ruoxin Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, 315832, China.
| | - Ping Han
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, 315832, China.
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, 264005, China.
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, 315832, China; National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, 315832, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, 315832, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, 315832, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, 315832, China.
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4
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Ji X, Cai J, Liang L, Shi T, Liu J. Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages. BMC Bioinformatics 2023; 24:72. [PMID: 36858955 PMCID: PMC9976410 DOI: 10.1186/s12859-023-05198-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Two main subclasses of macrophages are found in almost all solid tissues: embryo-derived resident tissue macrophages and bone marrow-derived infiltrated macrophages. These macrophage subtypes show transcriptional and functional divergence, and the programs that have shaped the evolution of renal macrophages and related signaling pathways remain poorly understood. To clarify these processes, we performed data analysis based on single-cell transcriptional profiling of renal tissue-resident and infiltrated macrophages in human, mouse and rat. RESULTS In this study, we (i) characterized the transcriptional divergence among species and (ii) illustrated variability in expression among cells of each subtype and (iii) compared the gene regulation network and (iv) ligand-receptor pairs in human and mouse. Using single-cell transcriptomics, we mapped the promoter architecture during homeostasis. CONCLUSIONS Transcriptionally divergent genes, such as the differentially TF-encoding genes expressed in resident and infiltrated macrophages across the three species, vary among cells and include distinct promoter structures. The gene regulatory network in infiltrated macrophages shows comparatively better species-wide consistency than resident macrophages. The conserved transcriptional gene regulatory network in infiltrated macrophages among species is uniquely enriched in pathways related to kinases, and TFs associated with largely conserved regulons among species are uniquely enriched in kinase-related pathways.
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Affiliation(s)
- Xiangjun Ji
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515 China
| | - Junwei Cai
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515 China
| | - Lixin Liang
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515 China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China. .,Beijing Advanced Innovation Center, for Big Data-Based Precision Medicine, Beihang University and Capital Medical University, Beijing, 100083, China.
| | - Jinghua Liu
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
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5
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King SB, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol 2023; 19:e1010966. [PMID: 36952575 PMCID: PMC10035887 DOI: 10.1371/journal.pcbi.1010966] [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: 08/18/2022] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
Despite the vast phenotypic differences observed across primates, their protein products are largely similar to each other at the sequence level. We hypothesized that, since proteins accomplish all their functions via interactions with other molecules, alterations in the sites that participate in these interactions may be of critical importance. To uncover the extent to which these sites evolve across primates, we built a structurally-derived dataset of ~4,200 one-to-one orthologous sequence groups across 18 primate species, consisting of ~68,000 ligand-binding sites that interact with DNA, RNA, small molecules, ions, or peptides. Using this dataset, we identify functionally important patterns of conservation and variation within the amino acid residues that facilitate protein-ligand interactions across the primate phylogeny. We uncover that interaction sites are significantly more conserved than other sites, and that sites binding DNA and RNA further exhibit the lowest levels of variation. We also show that the subset of ligand-binding sites that do vary are enriched in components of gene regulatory pathways and uncover several instances of human-specific ligand-binding site changes within transcription factors. Altogether, our results suggest that ligand-binding sites have experienced selective pressure in primates and propose that variation in these sites may have an outsized effect on phenotypic variation in primates through pleiotropic effects on gene regulation.
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Affiliation(s)
- Sean B. King
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
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6
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Lea AJ, Peng J, Ayroles JF. Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels. Genome Res 2022; 32:1826-1839. [PMID: 36229124 PMCID: PMC9712631 DOI: 10.1101/gr.276430.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 09/07/2022] [Indexed: 01/18/2023]
Abstract
There is increasing appreciation that, in addition to being shaped by an individual's genotype and environment, most complex traits are also determined by poorly understood interactions between these two factors. So-called "genotype × environment" (G×E) interactions remain difficult to map at the organismal level but can be uncovered using molecular phenotypes. To do so at large scale, we used TM3'seq to profile transcriptomes across 12 cellular environments in 544 immortalized B cell lines from the 1000 Genomes Project. We mapped the genetic basis of gene expression levels across environments and revealed a context-dependent genetic architecture: The average heritability of gene expression levels increased in treatment relative to control conditions, and on average, each treatment revealed new expression quantitative trait loci (eQTLs) at 11% of genes. Across our experiments, 22% of all identified eQTLs were context-dependent, and this group was enriched for trait- and disease-associated loci. Further, evolutionary analyses suggested that positive selection has shaped G×E loci involved in responding to immune challenges and hormones but not to man-made chemicals. We hypothesize that this reflects a reduced opportunity for selection to act on responses to molecules recently introduced into human environments. Together, our work highlights the importance of considering an exposure's evolutionary history when studying and interpreting G×E interactions, and provides new insight into the evolutionary mechanisms that maintain G×E loci in human populations.
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Affiliation(s)
- Amanda J. Lea
- Department of Ecology and Evolution, Princeton University, Princeton, New Jersey 08544, USA;,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Julie Peng
- Department of Ecology and Evolution, Princeton University, Princeton, New Jersey 08544, USA;,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Julien F. Ayroles
- Department of Ecology and Evolution, Princeton University, Princeton, New Jersey 08544, USA;,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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7
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Hawash MBF, El-Deeb MA, Gaber R, Morsy KS. The buried gems of disease tolerance in animals: Evolutionary and interspecies comparative approaches: Interspecies comparative approaches are valuable tools for exploring potential new mechanisms of disease tolerance in animals: Interspecies comparative approaches are valuable tools for exploring potential new mechanisms of disease tolerance in animals. Bioessays 2022; 44:e2200080. [PMID: 36050881 DOI: 10.1002/bies.202200080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/31/2022] [Accepted: 08/08/2022] [Indexed: 11/07/2022]
Abstract
Host defense mechanisms are categorized into different strategies, namely, avoidance, resistance and tolerance. Resistance encompasses mechanisms that directly kill the pathogen while tolerance is mainly concerned with alleviating the harsh consequences of the infection regardless of the pathogen burden. Resistance is well-known strategy in immunology while tolerance is relatively new. Studies addressed tolerance mainly using mouse models revealing a wide range of interesting tolerance mechanisms. Herein, we aim to emphasize on the interspecies comparative approaches to explore potential new mechanisms of disease tolerance. We will discuss mechanisms of tolerance with focus on those that were revealed using comparative study designs of mammals followed by summarizing the reasons for adopting comparative approaches on disease tolerance studies. Disease tolerance is a relatively new concept in immunology, we believe combining comparative studies with model organism study designs will enhance our understanding to tolerance and unveil new mechanisms of tolerance.
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Affiliation(s)
- Mohamed B F Hawash
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt.,Biochemistry and Molecular Biomedicine Department, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - Mohamed A El-Deeb
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Rahma Gaber
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Kareem S Morsy
- Biology Department, College of Science, King Khalid University, Abha, Saudi Arabia
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8
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Ferrández-Peral L, Zhan X, Alvarez-Estape M, Chiva C, Esteller-Cucala P, García-Pérez R, Julià E, Lizano E, Fornas Ò, Sabidó E, Li Q, Marquès-Bonet T, Juan D, Zhang G. Transcriptome innovations in primates revealed by single-molecule long-read sequencing. Genome Res 2022; 32:1448-1462. [PMID: 35840341 PMCID: PMC9435740 DOI: 10.1101/gr.276395.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.
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Affiliation(s)
| | | | | | - Cristina Chiva
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | | | | | - Eva Julià
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Òscar Fornas
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Eduard Sabidó
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen 2200, Denmark
- Evolutionary and Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou 310058, China
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9
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Genetic variations in evolutionary accelerated regions disrupt cognition in schizophrenia. Psychiatry Res 2022; 314:114586. [PMID: 35623238 PMCID: PMC10150587 DOI: 10.1016/j.psychres.2022.114586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/03/2022] [Accepted: 04/30/2022] [Indexed: 02/03/2023]
Abstract
Cognition is believed to be a product of human evolution, while schizophrenia is ascribed as the by-product with cognitive impairment as it's genetically mediated endophenotype. Genomic loci associated with these traits are enriched with recent evolutionary markers such as Human accelerated regions (HARs). HARs are markedly different in humans since their divergence with chimpanzees and mostly regulate gene expression by binding to transcription factors and/or modulating chromatin interactions. We hypothesize that variants within HARs may alter such functions and thus contribute to disease pathogenesis. 49 systematically prioritized variants from 2737 genome-wide HARs were genotyped in a north-Indian schizophrenia cohort (331 cases, 235 controls). Six variants were significantly associated with cognitive impairment in schizophrenia, thirteen with general cognition in healthy individuals. These variants were mapped to 122 genes; predicted to alter 79 transcription factors binding sites and overlapped with promoters, enhancers and/or repressors. These genes and TFs are implicated in neurocognitive phenotypes, autism, schizophrenia and bipolar disorders; a few are targets of common or repurposable antipsychotics suggesting their draggability; and enriched for immune response and brain developmental pathways. Immune response has been more strongly targeted by natural selection during human evolution and has a prominent role in neurodevelopment. Thus, its disruption may have deleterious consequences for neuronal and cognitive functions. Importantly, among the 15 associated SNPs, 12 showed association in several independent GWASs of different neurocognitive functions. Further analysis of HARs may be valuable to understand their role in cognition biology and identify improved therapeutics for schizophrenia.
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10
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Han F, Zhang Y, Xu A, Wang X, He Y, Song N, Gao T. Genome-wide identification and characterization of Toll-like receptor genes in black rockfish (Sebastes schlegelii) and their response mechanisms following poly (I:C) injection. Comp Biochem Physiol C Toxicol Pharmacol 2022; 254:109277. [PMID: 35085815 DOI: 10.1016/j.cbpc.2022.109277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/10/2022] [Accepted: 01/19/2022] [Indexed: 12/13/2022]
Abstract
Toll-like receptors (TLRs) are canonical transmembrane receptors that play an important role in defending against invading pathogens. In this study, we identified a total of 12 TLR genes in black rockfish (Sebastes schlegelii) with an analysis of their sequence characterizations. The phylogenetic analysis suggested that 12 distinct TLRs were grouped into five subfamilies (i.e., TLR1, TLR3, TLR5, TLR7, and TLR11 subfamilies), and each SsTLR gene respectively corresponded to the orthologs genes of other species. The protein domain analysis indicated that TLRs are type I transmembrane proteins, including an extracellular leucine-rich repeat (LRR), a transmembrane region (TM) domain and an intracellular Toll/IL-1 receptor (TIR) domain. The evolutionary ratios indicted that 12 SsTLRs were under purifying selection. qRT-PCR assays exhibited diverse TLRs molecular expression patterns in the heart, brain, head kidney, kidney, liver, intestine, and spleen of 3 black rockfish, and the expression levels were high in some immune tissues (e.g., head kidney, kidney, and spleen). Subsequently, 30 fish were equally divided into 2 groups i.e., poly (I:C)-treated and PBS-Control groups. After poly (I:C) injection, eight SsTLRs, i.e., SsTLR2, SsTLR2-1, SsTLR2-2, SsTLR3, SsTLR5S, SsTLR7, SsTLR8 and SsTLR22, were dramatically increased. Altogether these results contribute to understanding how SsTLRs respond to immune defense after poly (I:C) injection and provide researchers with comprehensive TLR gene family data of black rockfish.
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Affiliation(s)
- Fei Han
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China
| | - Yuan Zhang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China
| | - Anle Xu
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Xiaoyan Wang
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Yan He
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong 266003, China
| | - Na Song
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
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11
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Bjornson-Hooper ZB, Fragiadakis GK, Spitzer MH, Chen H, Madhireddy D, Hu K, Lundsten K, McIlwain DR, Nolan GP. A Comprehensive Atlas of Immunological Differences Between Humans, Mice, and Non-Human Primates. Front Immunol 2022; 13:867015. [PMID: 35359965 PMCID: PMC8962947 DOI: 10.3389/fimmu.2022.867015] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 01/01/2023] Open
Abstract
Animal models are an integral part of the drug development and evaluation process. However, they are unsurprisingly imperfect reflections of humans, and the extent and nature of many immunological differences are unknown. With the rise of targeted and biological therapeutics, it is increasingly important that we understand the molecular differences in the immunological behavior of humans and model organisms. However, very few antibodies are raised against non-human primate antigens, and databases of cross-reactivity between species are incomplete. Thus, we screened 332 antibodies in five immune cell populations in blood from humans and four non-human primate species generating a comprehensive cross-reactivity catalog that includes cell type-specificity. We used this catalog to create large mass cytometry universal cross-species phenotyping and signaling panels for humans, along with three of the model organisms most similar to humans: rhesus and cynomolgus macaques and African green monkeys; and one of the mammalian models most widely used in drug development: C57BL/6 mice. As a proof-of-principle, we measured immune cell signaling responses across all five species to an array of 15 stimuli using mass cytometry. We found numerous instances of different cellular phenotypes and immune signaling events occurring within and between species, and detailed three examples (double-positive T cell frequency and signaling; granulocyte response to Bacillus anthracis antigen; and B cell subsets). We also explore the correlation of herpes simian B virus serostatus on the immune profile. Antibody panels and the full dataset generated are available online as a resource to enable future studies comparing immune responses across species during the evaluation of therapeutics.
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Affiliation(s)
| | - Gabriela K. Fragiadakis
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
- Department of Medicine, Division of Rheumatology, University of California San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- University of California, San Francisco (UCSF) Data Science CoLab and University of California, San Francisco (UCSF) Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Matthew H. Spitzer
- Immunology Program, Stanford University, Stanford, CA, United States
- Departments of Otolaryngology – Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Han Chen
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Deepthi Madhireddy
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Kevin Hu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Kelly Lundsten
- BioLegend Inc, Advanced Cytometry, San Diego, CA, United States
| | - David R. McIlwain
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Garry P. Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
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12
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Hyland EM, Webb AE, Kennedy KF, Gerek Ince ZN, Loscher CE, O'Connell MJ. Adaptive Evolution in TRIF Leads to Discordance between Human and Mouse Innate Immune Signaling. Genome Biol Evol 2021; 13:6454097. [PMID: 34893845 PMCID: PMC8691055 DOI: 10.1093/gbe/evab268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 02/06/2023] Open
Abstract
The TIR domain-containing adapter inducing IFN-β (TRIF) protein is an innate immune system protein that mediates the MyD88-independent toll-like receptor response pathway in mice and humans. Previously, we identified positive selection at seven distinct residues in mouse TRIF (mTRIF), as compared with human and other mammalian orthologs, thus predicting protein functional shift in mTRIF. We reconstructed TRIF for the most recent common ancestor of mouse and human, and mutated this at the seven sites to their extant mouse/human states. We overexpressed these TRIF mutants in immortalized human and mouse cell lines and monitored TRIF-dependent cytokine production and gene expression induction. We show that optimal TRIF function in human and mouse is dependent on the identity of the positively selected sites. These data provide us with molecular data relating observed differences in response between mouse and human MyD88-independent signaling in the innate immune system with protein functional change.
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Affiliation(s)
- Edel M Hyland
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Kathy F Kennedy
- Immunomodulation Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Z Nevin Gerek Ince
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Christine E Loscher
- Immunomodulation Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
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13
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14
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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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15
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Packialakshmi B, Stewart IJ, Burmeister DM, Chung KK, Zhou X. Large animal models for translational research in acute kidney injury. Ren Fail 2021; 42:1042-1058. [PMID: 33043785 PMCID: PMC7586719 DOI: 10.1080/0886022x.2020.1830108] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
While extensive research using animal models has improved the understanding of acute kidney injury (AKI), this knowledge has not been translated into effective treatments. Many promising interventions for AKI identified in mice and rats have not been validated in subsequent clinical trials. As a result, the mortality rate of AKI patients remains high. Inflammation plays a fundamental role in the pathogenesis of AKI, and one reason for the failure to translate promising therapeutics may lie in the profound difference between the immune systems of rodents and humans. The immune systems of large animals such as swine, nonhuman primates, sheep, dogs and cats, more closely resemble the human immune system. Therefore, in the absence of a basic understanding of the pathophysiology of human AKI, large animals are attractive models to test novel interventions. However, there is a lack of reviews on large animal models for AKI in the literature. In this review, we will first highlight differences in innate and adaptive immunities among rodents, large animals, and humans in relation to AKI. After illustrating the potential merits of large animals in testing therapies for AKI, we will summarize the current state of the evidence in terms of what therapeutics have been tested in large animal models. The aim of this review is not to suggest that murine models are not valid to study AKI. Instead, our objective is to demonstrate that large animal models can serve as valuable and complementary tools in translating potential therapeutics into clinical practice.
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Affiliation(s)
| | - Ian J Stewart
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - David M Burmeister
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Kevin K Chung
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Xiaoming Zhou
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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16
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Spruit CM, Nemanichvili N, Okamatsu M, Takematsu H, Boons GJ, de Vries RP. N-Glycolylneuraminic Acid in Animal Models for Human Influenza A Virus. Viruses 2021; 13:815. [PMID: 34062844 PMCID: PMC8147317 DOI: 10.3390/v13050815] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/14/2022] Open
Abstract
The first step in influenza virus infection is the binding of hemagglutinin to sialic acid-containing glycans present on the cell surface. Over 50 different sialic acid modifications are known, of which N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) are the two main species. Animal models with α2,6 linked Neu5Ac in the upper respiratory tract, similar to humans, are preferred to enable and mimic infection with unadapted human influenza A viruses. Animal models that are currently most often used to study human influenza are mice and ferrets. Additionally, guinea pigs, cotton rats, Syrian hamsters, tree shrews, domestic swine, and non-human primates (macaques and marmosets) are discussed. The presence of NeuGc and the distribution of sialic acid linkages in the most commonly used models is summarized and experimentally determined. We also evaluated the role of Neu5Gc in infection using Neu5Gc binding viruses and cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH)-/- knockout mice, which lack Neu5Gc and concluded that Neu5Gc is unlikely to be a decoy receptor. This article provides a base for choosing an appropriate animal model. Although mice are one of the most favored models, they are hardly naturally susceptible to infection with human influenza viruses, possibly because they express mainly α2,3 linked sialic acids with both Neu5Ac and Neu5Gc modifications. We suggest using ferrets, which resemble humans closely in the sialic acid content, both in the linkages and the lack of Neu5Gc, lung organization, susceptibility, and disease pathogenesis.
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Affiliation(s)
- Cindy M. Spruit
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (C.M.S.); (G.-J.B.)
| | - Nikoloz Nemanichvili
- Division of Pathology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands;
| | - Masatoshi Okamatsu
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan;
| | - Hiromu Takematsu
- Department of Molecular Cell Biology, Faculty of Medical Technology, Graduate School of Health Sciences, Fujita Health University, 1-98 Dengakugakubo, Kutsukake, Toyoake 470-1192, Aichi, Japan;
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (C.M.S.); (G.-J.B.)
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Robert P. de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (C.M.S.); (G.-J.B.)
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17
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Shew CJ, Carmona-Mora P, Soto DC, Mastoras M, Roberts E, Rosas J, Jagannathan D, Kaya G, O'Geen H, Dennis MY. Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes. Mol Biol Evol 2021; 38:3060-3077. [PMID: 34009325 PMCID: PMC8321529 DOI: 10.1093/molbev/msab131] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/08/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022] Open
Abstract
Emerging evidence links genes within human-specific segmental duplications (HSDs) to traits and diseases unique to our species. Strikingly, despite being nearly identical by sequence (>98.5%), paralogous HSD genes are differentially expressed across human cell and tissue types, though the underlying mechanisms have not been examined. We compared cross-tissue mRNA levels of 75 HSD genes from 30 families between humans and chimpanzees and found expression patterns consistent with relaxed selection on or neofunctionalization of derived paralogs. In general, ancestral paralogs exhibited greatest expression conservation with chimpanzee orthologs, though exceptions suggest certain derived paralogs may retain or supplant ancestral functions. Concordantly, analysis of long-read isoform sequencing data sets from diverse human tissues and cell lines found that about half of derived paralogs exhibited globally lower expression. To understand mechanisms underlying these differences, we leveraged data from human lymphoblastoid cell lines (LCLs) and found no relationship between paralogous expression divergence and post-transcriptional regulation, sequence divergence, or copy-number variation. Considering cis-regulation, we reanalyzed ENCODE data and recovered hundreds of previously unidentified candidate CREs in HSDs. We also generated large-insert ChIP-sequencing data for active chromatin features in an LCL to better distinguish paralogous regions. Some duplicated CREs were sufficient to drive differential reporter activity, suggesting they may contribute to divergent cis-regulation of paralogous genes. This work provides evidence that cis-regulatory divergence contributes to novel expression patterns of recent gene duplicates in humans.
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Affiliation(s)
- Colin J Shew
- Genome Center, University of California Davis, CA, USA.,Integrative Genetics and Genomics Graduate Group, University of California Davis, CA, USA
| | - Paulina Carmona-Mora
- Genome Center, University of California Davis, CA, USA.,MIND Institute, University of California, Davis, CA, USA.,Autism Research Training Program, University of California, Davis, CA, USA
| | - Daniela C Soto
- Genome Center, University of California Davis, CA, USA.,Integrative Genetics and Genomics Graduate Group, University of California Davis, CA, USA
| | - Mira Mastoras
- Genome Center, University of California Davis, CA, USA
| | | | - Joseph Rosas
- Genome Center, University of California Davis, CA, USA.,Postbaccalaureate Research Education Program, University of California, Davis, CA, USA
| | | | - Gulhan Kaya
- Genome Center, University of California Davis, CA, USA
| | | | - Megan Y Dennis
- Genome Center, University of California Davis, CA, USA.,Integrative Genetics and Genomics Graduate Group, University of California Davis, CA, USA.,MIND Institute, University of California, Davis, CA, USA.,Autism Research Training Program, University of California, Davis, CA, USA.,Postbaccalaureate Research Education Program, University of California, Davis, CA, USA.,Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
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18
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Primate innate immune responses to bacterial and viral pathogens reveals an evolutionary trade-off between strength and specificity. Proc Natl Acad Sci U S A 2021; 118:2015855118. [PMID: 33771921 PMCID: PMC8020666 DOI: 10.1073/pnas.2015855118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Humans and our close evolutionary relatives respond differently to a large number of infections. Such differences are thought to result, at least in part, from interspecies differences in immune function. Here, we report on the whole-genome expression of blood leukocytes from four primate species responding to bacterial and viral stimulation. We show that apes mount a markedly stronger early transcriptional response to both viral and bacterial stimulation when compared to African and Asian monkeys. In addition, our findings suggest that apes activate a broader array of defense molecules that may be beneficial for early pathogen killing at the potential cost of increased energy expenditure and tissue damage. Our results provide insight into the evolution of immune responses in primates. Despite their close genetic relatedness, apes and African and Asian monkeys (AAMs) differ in their susceptibility to severe bacterial and viral infections that are important causes of human disease. Such differences between humans and other primates are thought to be a result, at least in part, of interspecies differences in immune response to infection. However, because of the lack of comparative functional data across species, it remains unclear in what ways the immune systems of humans and other primates differ. Here, we report the whole-genome transcriptomic responses of ape species (human and chimpanzee) and AAMs (rhesus macaque and baboon) to bacterial and viral stimulation. We find stark differences in the responsiveness of these groups, with apes mounting a markedly stronger early transcriptional response to both viral and bacterial stimulation, altering the transcription of ∼40% more genes than AAMs. Additionally, we find that genes involved in the regulation of inflammatory and interferon responses show the most divergent early transcriptional responses across primates and that this divergence is attenuated over time. Finally, we find that relative to AAMs, apes engage a much less specific immune response to different classes of pathogens during the early hours of infection, up-regulating genes typical of anti-viral and anti-bacterial responses regardless of the nature of the stimulus. Overall, these findings suggest apes exhibit increased sensitivity to bacterial and viral immune stimulation, activating a broader array of defense molecules that may be beneficial for early pathogen killing at the potential cost of increased energy expenditure and tissue damage.
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19
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Brinkworth JF, Valizadegan N. Sepsis and the evolution of human increased sensitivity to lipopolysaccharide. Evol Anthropol 2021; 30:141-157. [PMID: 33689211 DOI: 10.1002/evan.21887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/29/2020] [Accepted: 01/30/2021] [Indexed: 01/03/2023]
Abstract
Among mammals, humans are exquisitely sensitive to lipopolysaccharide (LPS), an environmentally pervasive bacterial cell membrane component. Very small doses of LPS trigger powerful immune responses in humans and can even initiate symptoms of sepsis. Close evolutionary relatives such as African and Asian monkeys require doses that are an order of magnitude higher to do the same. Why humans have evolved such an energetically expensive antimicrobial strategy is a question that biological anthropologists are positioned to help address. Here we compare LPS sensitivity in primate/mammalian models and propose that human high sensitivity to LPS is adaptive, linked to multiple immune tactics against pathogens, and part of multi-faceted anti-microbial strategy that strongly overlaps with that of other mammals. We support a notion that LPS sensitivity in humans has been driven by microorganisms that constitutively live on us, and has been informed by human behavioral changes over our species' evolution (e.g., meat eating, agricultural practices, and smoking).
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Affiliation(s)
- Jessica F Brinkworth
- Evolutionary Immunology and Genomics Laboratory, Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA.,Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Animal Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Negin Valizadegan
- Evolutionary Immunology and Genomics Laboratory, Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA.,Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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20
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Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly. Viruses 2020; 12:v12101089. [PMID: 32993145 PMCID: PMC7650545 DOI: 10.3390/v12101089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
The human genome has been under selective pressure to evolve in response to emerging pathogens and other environmental challenges. Genome evolution includes the acquisition of new genes or new isoforms of genes and changes to gene expression patterns. One source of genome innovation is from transposable elements (TEs), which carry their own promoters, enhancers and open reading frames and can act as ‘controlling elements’ for our own genes. TEs include LINE-1 elements, which can retrotranspose intracellularly and endogenous retroviruses (ERVs) that represent remnants of past retroviral germline infections. Although once pathogens, ERVs also represent an enticing source of incoming genetic material that the host can then repurpose. ERVs and other TEs have coevolved with host genes for millions of years, which has allowed them to become embedded within essential gene expression programmes. Intriguingly, these host genes are often subject to the same epigenetic control mechanisms that evolved to combat the TEs that now regulate them. Here, we illustrate the breadth of host gene regulation through TEs by focusing on examples of young (The New), ancient (The Old), and disease-causing (The Ugly) TE integrants.
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21
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Cavaillon J, Singer M, Skirecki T. Sepsis therapies: learning from 30 years of failure of translational research to propose new leads. EMBO Mol Med 2020; 12:e10128. [PMID: 32176432 PMCID: PMC7136965 DOI: 10.15252/emmm.201810128] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/12/2020] [Accepted: 02/17/2020] [Indexed: 12/13/2022] Open
Abstract
Sepsis has been identified by the World Health Organization (WHO) as a global health priority. There has been a tremendous effort to decipher underlying mechanisms responsible for organ failure and death, and to develop new treatments. Despite saving thousands of animals over the last three decades in multiple preclinical studies, no new effective drug has emerged that has clearly improved patient outcomes. In the present review, we analyze the reasons for this failure, focusing on the inclusion of inappropriate patients and the use of irrelevant animal models. We advocate against repeating the same mistakes and propose changes to the research paradigm. We discuss the long-term consequences of surviving sepsis and, finally, list some putative approaches-both old and new-that could help save lives and improve survivorship.
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Affiliation(s)
| | - Mervyn Singer
- Bloomsbury Institute of Intensive Care MedicineUniversity College LondonLondonUK
| | - Tomasz Skirecki
- Laboratory of Flow Cytometry and Department of Anesthesiology and Intensive Care MedicineCentre of Postgraduate Medical EducationWarsawPoland
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22
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A Differential Diagnosis of Osteolytic Lesions in the Curated Skeletal Remains of a Tantalus Monkey (Chlorocebus tantalus). INT J PRIMATOL 2020. [DOI: 10.1007/s10764-020-00150-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractIn the veterinary and anthropological literature, the pathology of nonhuman primates is heavily focused on soft-tissue involvement and there is scant reference to nonhuman primates in zoopalaeopathology, the study of ancient and historical diseases in animals. We present the curated skeletal remains of a nonhuman primate present with osteolytic lesions consistent with a pathological process. We evaluated the observed pathological changes via an extensive macroscopic analysis of the skeleton, coupled with radiographic images of the affected bones, and provide a differential diagnosis of the skeletal remains using relevant clinical and zoopalaeopathological data. Multiple osteolytic lesions of varying sizes, as well as periosteal new bone, were present on several elements. The lesions affected the skeleton bilaterally, asymmetrically and with no clear focus or pattern. The skeletal lesions were differentially diagnosed as the result of either a metastatic neoplastic disease or a chronic infection. This case provides a zoopalaeopathological example for the study of skeletal lesions in nonhuman primates in anthropological and archaeological collections, where contextual data may not be available.
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23
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Mostajo-Radji MA, Schmitz MT, Montoya ST, Pollen AA. Reverse engineering human brain evolution using organoid models. Brain Res 2020; 1729:146582. [PMID: 31809699 PMCID: PMC7058376 DOI: 10.1016/j.brainres.2019.146582] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 02/06/2023]
Abstract
Primate brains vary dramatically in size and organization, but the genetic and developmental basis for these differences has been difficult to study due to lack of experimental models. Pluripotent stem cells and brain organoids provide a potential opportunity for comparative and functional studies of evolutionary differences, particularly during the early stages of neurogenesis. However, many challenges remain, including isolating stem cell lines from additional great ape individuals and species to capture the breadth of ape genetic diversity, improving the reproducibility of organoid models to study evolved differences in cell composition and combining multiple brain regions to capture connectivity relationships. Here, we describe strategies for identifying evolved developmental differences between humans and non-human primates and for isolating the underlying cellular and genetic mechanisms using comparative analyses, chimeric organoid culture, and genome engineering. In particular, we focus on how organoid models could ultimately be applied beyond studies of progenitor cell evolution to decode the origin of recent changes in cellular organization, connectivity patterns, myelination, synaptic development, and physiology that have been implicated in human cognition.
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Affiliation(s)
- Mohammed A Mostajo-Radji
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew T Schmitz
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA
| | - Sebastian Torres Montoya
- Health Co-creation Laboratory, Medellin General Hospital, Medellin, Antioquia, Colombia; Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alex A Pollen
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA.
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24
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O’Connell AK, Douam F. Humanized Mice for Live-Attenuated Vaccine Research: From Unmet Potential to New Promises. Vaccines (Basel) 2020; 8:E36. [PMID: 31973073 PMCID: PMC7157703 DOI: 10.3390/vaccines8010036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/11/2020] [Accepted: 01/13/2020] [Indexed: 01/24/2023] Open
Abstract
Live-attenuated vaccines (LAV) represent one of the most important medical innovations in human history. In the past three centuries, LAV have saved hundreds of millions of lives, and will continue to do so for many decades to come. Interestingly, the most successful LAVs, such as the smallpox vaccine, the measles vaccine, and the yellow fever vaccine, have been isolated and/or developed in a purely empirical manner without any understanding of the immunological mechanisms they trigger. Today, the mechanisms governing potent LAV immunogenicity and long-term induced protective immunity continue to be elusive, and therefore hamper the rational design of innovative vaccine strategies. A serious roadblock to understanding LAV-induced immunity has been the lack of suitable and cost-effective animal models that can accurately mimic human immune responses. In the last two decades, human-immune system mice (HIS mice), i.e., mice engrafted with components of the human immune system, have been instrumental in investigating the life-cycle and immune responses to multiple human-tropic pathogens. However, their use in LAV research has remained limited. Here, we discuss the strong potential of LAVs as tools to enhance our understanding of human immunity and review the past, current and future contributions of HIS mice to this endeavor.
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Affiliation(s)
| | - Florian Douam
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA;
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25
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Weed L, Ammar MJ, Zhou S, Wei Z, Serrano LW, Sun J, Lee V, Maguire AM, Bennett J, Aleman TS. Safety of Same-Eye Subretinal Sequential Readministration of AAV2-hRPE65v2 in Non-human Primates. Mol Ther Methods Clin Dev 2019; 15:133-148. [PMID: 31660416 PMCID: PMC6807311 DOI: 10.1016/j.omtm.2019.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 08/26/2019] [Indexed: 01/28/2023]
Abstract
We have demonstrated safe and effective subretinal readministration of recombinant adeno-associated virus serotype (rAAV) to the contralateral eye in large animals and humans even in the setting of preexisting neutralizing antibodies (NAbs). Readministration of AAV to the same retina may be desirable in order to treat additional areas of the retina not targeted initially or to boost transgene expression levels at a later time point. To better understand the immune and structural consequences of subretinal rAAV readministration to the same eye, we administered bilateral subretinal injections of rAAV2-hRPE65v2 to three unaffected non-human primates (NHPs) and repeated the injections in those same eyes 2 months later. Ophthalmic exams and retinal imaging were performed after the first and second injections. Peripheral blood monocytes, serum, and intraocular fluids were collected at baseline and post-injection time points to characterize the cellular and humoral immune responses. Histopathologic and immunohistochemical studies were carried out on the treated retinas. Ipsilateral readministration of AAV2-hRPE65v2 in NHPs did not threaten the ocular or systemic health through the time span of the study. The repeat injections were immunologically and structurally well tolerated, even in the setting of preexisting serum NAbs. Localized structural abnormalities confined to the outer retina and retinal pigmented epithelium (RPE) after readministration of the treatment do not differ from those observed after single or contralateral administration of an AAV carrying a non-therapeutic transgene in NHPs and were not observed in a patient treated with the nearly identical, FDA-approved, AAV2-hRPE65v2 vector (voretigene neparvovec-rzyl), suggesting NHP-specific abnormalities.
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Affiliation(s)
- Lindsey Weed
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael J. Ammar
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shangzhen Zhou
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Zhangyong Wei
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Leona W. Serrano
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Junwei Sun
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Vivian Lee
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Albert M. Maguire
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jean Bennett
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- The Children’s Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
| | - Tomas S. Aleman
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- The Children’s Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
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26
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Ishino T, Kurita H, Kirisawa R, Shimamoto Y, Numano R, Kitamura H. Introduction of a plasmid and a protein into bovine and swine cells by water-in-oil droplet electroporation. J Vet Med Sci 2019; 82:14-22. [PMID: 31776296 PMCID: PMC6983666 DOI: 10.1292/jvms.19-0475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Instrument cost is a major problem for the transduction of DNA fragments and proteins into cells. Water-in-oil droplet electroporation (droplet-EP) was recently invented as a low-cost and
effective method for the transfection of plasmids into cultured human cells. We here applied droplet-EP to livestock animal cells. Although it is difficult to transfect plasmids into bovine
fibroblasts using conventional lipofection methods, droplet-EP enabled us to introduce an enhanced green fluorescent protein (EGFP)-expressing plasmid into bovine earlobe fibroblasts. The
optimal transfection condition was 3.0 kV, which allowed 19.1% of the cells to be transfected. For swine earlobe fibroblasts, the maximum transfection efficacy was 14.0% at 4.0 kV. After
transfection with droplet-EP, 69.1% of bovine and 76.5% of swine cells were viable. Furthermore, droplet-EP successfully transduced Escherichia coli recombinant EGFP into
frozen-thawed bovine sperm at 1.5 kV. Flow cytometry analysis revealed that 71.5% of spermatozoa exhibited green fluorescence after transfection. Overall, droplet-EP is suitable for the
transfection of plasmids and proteins into cultured livestock animal cells.
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Affiliation(s)
- Takeshi Ishino
- Laboratory of Veterinary Physiology, Departments of Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan
| | - Hirofumi Kurita
- Department of Applied Chemistry and Life Sciences, Graduate School of Engineering, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Rikio Kirisawa
- Laboratory of Veterinary Virology, Departments of Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan
| | - Yoshinori Shimamoto
- Laboratory of Animal Therapeutics, Department of Veterinary Science, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan
| | - Rika Numano
- Department of Applied Chemistry and Life Sciences, Graduate School of Engineering, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Hiroshi Kitamura
- Laboratory of Veterinary Physiology, Departments of Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan
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27
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Gaska JM, Parsons L, Balev M, Cirincione A, Wang W, Schwartz RE, Ploss A. Conservation of cell-intrinsic immune responses in diverse nonhuman primate species. Life Sci Alliance 2019; 2:2/5/e201900495. [PMID: 31649152 PMCID: PMC6814850 DOI: 10.26508/lsa.201900495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 02/03/2023] Open
Abstract
The transcriptomic response of diverse nonhuman primate (NHP) species to poly(I:C) is highly conserved, and this novel RNA sequencing dataset will help improve NHP genome annotations. Differences in immune responses across species can contribute to the varying permissivity of species to the same viral pathogen. Understanding how our closest evolutionary relatives, nonhuman primates (NHPs), confront pathogens and how these responses have evolved over time could shed light on host range barriers, especially for zoonotic infections. Here, we analyzed cell-intrinsic immunity of primary cells from the broadest panel of NHP species interrogated to date, including humans, great apes, and Old and New World monkeys. Our analysis of their transcriptomes after poly(I:C) transfection revealed conservation in the functional consequences of their response. In mapping reads to either the human or the species-specific genomes, we observed that with the current state of NHP annotations, the percent of reads assigned to a genetic feature was largely similar regardless of the method. Together, these data provide a baseline for the cell-intrinsic responses elicited by a potent immune stimulus across multiple NHP donors, including endangered species, and serve as a resource for refining and furthering the existing annotations of NHP genomes.
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Affiliation(s)
- Jenna M Gaska
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Lance Parsons
- Carl Icahn Laboratory, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Metodi Balev
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ann Cirincione
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wei Wang
- Carl Icahn Laboratory, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Robert E Schwartz
- Weill Cornell Medical College, Belfer Research Building, New York, NY, USA
| | - Alexander Ploss
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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28
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Lavender KJ, Williamson BN, Saturday G, Martellaro C, Griffin A, Hasenkrug KJ, Feldmann H, Prescott J. Pathogenicity of Ebola and Marburg Viruses Is Associated With Differential Activation of the Myeloid Compartment in Humanized Triple Knockout-Bone Marrow, Liver, and Thymus Mice. J Infect Dis 2019; 218:S409-S417. [PMID: 30085162 DOI: 10.1093/infdis/jiy269] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ebola virus (EBOV) and Marburg virus (MARV) outbreaks are highly lethal, and infection results in a hemorrhagic fever with complex etiology. These zoonotic viruses dysregulate the immune system to cause disease, in part by replicating within myeloid cells that would normally innately control viral infection and shape the adaptive immune response. We used triple knockout (TKO)-bone marrow, liver, thymus (BLT) humanized mice to recapitulate the early in vivo human immune response to filovirus infection. Disease severity in TKO-BLT mice was dissimilar between EBOV and MARV with greater severity observed during EBOV infection. Disease severity was related to increased Kupffer cell infection in the liver, higher levels of myeloid dysfunction, and skewing of macrophage subtypes in EBOV compared with MARV-infected mice. Overall, the TKO-BLT model provided a practical in vivo platform to study the human immune response to filovirus infection and generated a better understanding of how these viruses modulate specific components of the immune system.
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Affiliation(s)
- Kerry J Lavender
- Laboratory of Persistent Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Brandi N Williamson
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Greg Saturday
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Cynthia Martellaro
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Amanda Griffin
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Kim J Hasenkrug
- Laboratory of Persistent Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Heinz Feldmann
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Joseph Prescott
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
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29
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Li S, Kvon EZ, Visel A, Pennacchio LA, Ovcharenko I. Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation. Genome Biol 2019; 20:140. [PMID: 31307522 PMCID: PMC6631995 DOI: 10.1186/s13059-019-1750-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/28/2019] [Indexed: 12/13/2022] Open
Abstract
Background Despite continual progress in the identification and characterization of trait- and disease-associated variants that disrupt transcription factor (TF)-DNA binding, little is known about the distribution of TF binding deactivating mutations (deMs) in enhancer sequences. Here, we focus on elucidating the mechanism underlying the different densities of deMs in human enhancers. Results We identify two classes of enhancers based on the density of nucleotides prone to deMs. Firstly, fragile enhancers with abundant deM nucleotides are associated with the immune system and regular cellular maintenance. Secondly, stable enhancers with only a few deM nucleotides are associated with the development and regulation of TFs and are evolutionarily conserved. These two classes of enhancers feature different regulatory programs: the binding sites of pioneer TFs of FOX family are specifically enriched in stable enhancers, while tissue-specific TFs are enriched in fragile enhancers. Moreover, stable enhancers are more tolerant of deMs due to their dominant employment of homotypic TF binding site (TFBS) clusters, as opposed to the larger-extent usage of heterotypic TFBS clusters in fragile enhancers. Notably, the sequence environment and chromatin context of the cognate motif, other than the motif itself, contribute more to the susceptibility to deMs of TF binding. Conclusions This dichotomy of enhancer activity is conserved across different tissues, has a specific footprint in epigenetic profiles, and argues for a bimodal evolution of gene regulatory programs in vertebrates. Specifically encoded stable enhancers are evolutionarily conserved and associated with development, while differently encoded fragile enhancers are associated with the adaptation of species. Electronic supplementary material The online version of this article (10.1186/s13059-019-1750-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shan Li
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Evgeny Z Kvon
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,United States Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA.,School of Natural Sciences, University of California, Merced, CA, 95343, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,United States Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
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30
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Pollen A, Pavlovic BJ. Getting to the heart of cardiovascular evolution in humans. eLife 2019; 8:47807. [PMID: 31135336 PMCID: PMC6538371 DOI: 10.7554/elife.47807] [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] [Received: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 12/23/2022] Open
Abstract
Differences in the response of cardiomyocytes to oxygen deprivation in humans and chimpanzees may explain why humans are more prone to certain heart diseases.
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Affiliation(s)
- Alex Pollen
- Department of Neurology, University of California, San Francisco, San Francisco, United States.,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, United States
| | - Bryan J Pavlovic
- Department of Neurology, University of California, San Francisco, San Francisco, United States.,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, United States
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31
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James WPT, Johnson RJ, Speakman JR, Wallace DC, Frühbeck G, Iversen PO, Stover PJ. Nutrition and its role in human evolution. J Intern Med 2019; 285:533-549. [PMID: 30772945 DOI: 10.1111/joim.12878] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Our understanding of human evolution has improved rapidly over recent decades, facilitated by large-scale cataloguing of genomic variability amongst both modern and archaic humans. It seems clear that the evolution of the ancestors of chimpanzees and hominins separated 7-9 million years ago with some migration out of Africa by the earlier hominins; Homo sapiens slowly emerged as climate change resulted in drier, less forested African conditions. The African populations expanded and evolved in many different conditions with slow mutation and selection rates in the human genome, but with much more rapid mutation occurring in mitochondrial DNA. We now have evidence stretching back 300 000 years of humans in their current form, but there are clearly four very different large African language groups that correlate with population DNA differences. Then, about 50 000-100 000 years ago a small subset of modern humans also migrated out of Africa resulting in a persistent signature of more limited genetic diversity amongst non-African populations. Hybridization with archaic hominins occurred around this time such that all non-African modern humans possess some Neanderthal ancestry and Melanesian populations additionally possess some Denisovan ancestry. Human populations both within and outside Africa also adapted to diverse aspects of their local environment including altitude, climate, UV exposure, diet and pathogens, in some cases leaving clear signatures of patterns of genetic variation. Notable examples include haemoglobin changes conferring resistance to malaria, other immune changes and the skin adaptations favouring the synthesis of vitamin D. As humans migrated across Eurasia, further major mitochondrial changes occurred with some interbreeding with ancient hominins and the development of alcohol intolerance. More recently, an ability to retain lactase persistence into adulthood has evolved rapidly under the environmental stimulus of pastoralism with the ability to husband lactating ruminants. Increased amylase copy numbers seem to relate to the availability of starchy foods, whereas the capacity to desaturase and elongate monounsaturated fatty acids in different societies seems to be influenced by whether there is a lack of supply of readily available dietary sources of long-chain polyunsaturated fatty acids. The process of human evolution includes genetic drift and adaptation to local environments, in part through changes in mitochondrial and nuclear DNA. These genetic changes may underlie susceptibilities to some modern human pathologies including folate-responsive neural tube defects, diabetes, other age-related pathologies and mental health disorders.
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Affiliation(s)
- W P T James
- London School of Hygiene and Tropical Medicine, London, UK
| | - R J Johnson
- Division of Renal Diseases and Hypertension, University of Colorado, Denver, CO, USA
| | - J R Speakman
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - D C Wallace
- Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - G Frühbeck
- Endocrinology and Nutrition, Clinica Universidad de Navarra, Pamplona, Spain
| | - P O Iversen
- Department of Nutrition, University of Oslo, Oslo, Norway
| | - P J Stover
- Vice Chancellor and Dean for Agriculture and Life Sciences, Texas A&M AgriLife, College Station, TX, USA
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32
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Ward MC, Gilad Y. A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees. eLife 2019; 8:42374. [PMID: 30958265 PMCID: PMC6538380 DOI: 10.7554/elife.42374] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/07/2019] [Indexed: 12/23/2022] Open
Abstract
Despite anatomical similarities, there are differences in susceptibility to cardiovascular disease (CVD) between primates; humans are prone to myocardial ischemia, while chimpanzees are prone to myocardial fibrosis. Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) allow for direct inter-species comparisons of the gene regulatory response to CVD-relevant perturbations such as oxygen deprivation, a consequence of ischemia. To gain insight into the evolution of disease susceptibility, we characterized gene expression levels in iPSC-CMs in humans and chimpanzees, before and after hypoxia and re-oxygenation. The transcriptional response to hypoxia is generally conserved across species, yet we were able to identify hundreds of species-specific regulatory responses including in genes previously associated with CVD. The 1,920 genes that respond to hypoxia in both species are enriched for loss-of-function intolerant genes; but are depleted for expression quantitative trait loci and cardiovascular-related genes. Our results indicate that response to hypoxic stress is highly conserved in humans and chimpanzees.
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Affiliation(s)
- Michelle C Ward
- Department of Medicine, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
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33
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Colli ML, Paula FM, Marselli L, Marchetti P, Roivainen M, Eizirik DL, Op de Beeck A. Coxsackievirus B Tailors the Unfolded Protein Response to Favour Viral Amplification in Pancreatic β Cells. J Innate Immun 2019; 11:375-390. [PMID: 30799417 DOI: 10.1159/000496034] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/03/2018] [Indexed: 12/15/2022] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease characterized by islet inflammation and progressive pancreatic β cell destruction. The disease is triggered by a combination of genetic and environmental factors, but the mechanisms leading to the triggering of early innate and late adaptive immunity and consequent progressive pancreatic β cell death remain unclear. The insulin-producing β cells are active secretory cells and are thus particularly sensitive to endoplasmic reticulum (ER) stress. ER stress plays an important role in the pathologic pathway leading to autoimmunity, islet inflammation, and β cell death. We show here that group B coxsackievirus (CVB) infection, a putative causative factor for T1D, induces a partial ER stress in rat and human β cells. The activation of the PERK/ATF4/CHOP branch is blunted while the IRE1α branch leads to increased spliced XBP1 expression and c-Jun N-terminal kinase (JNK) activation. Interestingly, JNK1 activation is essential for CVB amplification in both human and rat β cells. Furthermore, a chemically induced ER stress preceding viral infection increases viral replication, in a process dependent on IRE1α activation. Our findings show that CVB tailors the unfolded protein response in β cells to support their replication, preferentially triggering the pro-viral IRE1α/XBP1s/JNK1 pathway while blocking the pro-apoptotic PERK/ATF4/CHOP pathway.
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Affiliation(s)
- Maikel L Colli
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Flavia M Paula
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Merja Roivainen
- Viral Infections Unit, Department of Infectious Disease, National Institute for Health and Welfare, Helsinki, Finland
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Anne Op de Beeck
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium,
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de Souza PRK, Ferreira SS, Nunes FPB, Casagrande FB, Tessaro FHG, Silva MCF, Cruz JWMC, Mamizuka EM, Martins JO. Cytokine and Adhesion Molecule Expression Induced by Different Strains of Staphylococcus aureus in Type 1 Diabetic Rats: Role of Insulin. Front Immunol 2019; 9:3165. [PMID: 30705678 PMCID: PMC6344427 DOI: 10.3389/fimmu.2018.03165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/21/2018] [Indexed: 12/24/2022] Open
Abstract
Introduction: Staphylococcus aureus may provoke peritonitis and death, especially in immunocompromized individuals such as diabetic patients. We evaluated the role of insulin in S. aureus-induced peritoneal infection in diabetic and non-diabetic rats. Materials/Methods: Alloxan-diabetic male Wistar rats and their respective controls received intraperitoneal injections of different strains of S. aureus or sterile phosphate-buffered saline. After 3 days of infection, the first set of diabetic and non-diabetic rats received 4 and 1 IU, respectively, of neutral protamine Hagedorn insulin and were analyzed 8 h later. The second set of diabetic and non-diabetic rats received 4 and 1 IU, respectively, of insulin 2 h before intraperitoneal infection and a half dose of insulin at 5 p.m. for the next 2 days and were analyzed 16 h later. The following measurements were performed: (a) number of cells in the peritoneal lavage fluid (PeLF), white blood cell count, and blood glucose; (b) serum insulin and corticosterone; (c) cytokine levels in the PeLF; (d) expression of adhesion molecules in the vascular endothelium; and (e) microbicidal activity. Results: Diabetic rats showed an increased number of polymorphonuclear leukocytes (PMNs) and increased concentrations of CINC-1, IL-4, and IFN-γ in the PeLF after infection with the ATCC 25923 or N315 αHL+ strain. The mesenteric expression of PECAM-1 was increased after infection with the N315 HLA+ strain. ICAM-1 expression was increased with ATCC infection. Treatment of diabetic rats with a single dose of insulin restored CINC-1 levels in the PeLF for both strains; however, PMN migration, IL-4, and IFN-γ were restored in rats infected with the ATCC strain, whereas the PeLF concentrations of CINC-2, IL-1β, and IL-4 were increased in N315-infected animals. Insulin restored PMN migration and CINC-2 levels in the PeLF in ATCC-infected rats. After multiple treatments with insulin, the levels of IL-1β, IL-6, and IFN-γ were increased in the PeLF of diabetic rats after infection with either strain, and CINC-2 levels were restored in N315-infected animals. Conclusion: These results suggest that insulin distinctively modulates cytokine production or release, PMN leukocyte migration, and adhesion molecule expression during the course of peritonitis induced by different strains of S. aureus.
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Affiliation(s)
- Paula R Knox de Souza
- Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences (FCF), University of São Paulo (USP), São Paulo, Brazil.,Universidade Paulista, São Paulo, Brazil
| | - Sabrina S Ferreira
- Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences (FCF), University of São Paulo (USP), São Paulo, Brazil
| | - Fernanda P B Nunes
- Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences (FCF), University of São Paulo (USP), São Paulo, Brazil
| | - Felipe B Casagrande
- Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences (FCF), University of São Paulo (USP), São Paulo, Brazil
| | - Fernando H G Tessaro
- Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences (FCF), University of São Paulo (USP), São Paulo, Brazil
| | - Mariana C F Silva
- Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences (FCF), University of São Paulo (USP), São Paulo, Brazil
| | | | - Elsa M Mamizuka
- Laboratory of Microbiology, Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences (FCF), University of São Paulo (USP), São Paulo, Brazil
| | - Joilson O Martins
- Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences (FCF), University of São Paulo (USP), São Paulo, Brazil
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35
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Tan T, Xia L, Tu K, Tang J, Yin S, Dai L, Lei P, Dong B, Hu H, Fan Y, Yu Y, Xie D. Improved Macaca fascicularis gene annotation reveals evolution of gene expression profiles in multiple tissues. BMC Genomics 2018; 19:787. [PMID: 30382841 PMCID: PMC6211470 DOI: 10.1186/s12864-018-5183-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 10/17/2018] [Indexed: 02/05/2023] Open
Abstract
Backgrounds Macaca fascicularis (M. fascicularis) is a primate model organism that played important role in studying human health. It is vital to better understand the similarity and differences of gene regulation between M. fascicularis and human. Current comparative study of gene regulation between the two species are limited by low quality of gene annotation and lack of regulatory element data on M. fascicularis genome. Results In this study, we improved the M. fascicularis gene annotation with 57 gene expression data from multiple tissues and, more importantly, a manual curation procedure. The new annotation enabled us to map gene expression and identify gene location more accurately. Conclusions Comparing with human gene expression data from the same cell types, we characterized the evolution of expression patterns of homologous genes. Electronic supplementary material The online version of this article (10.1186/s12864-018-5183-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tao Tan
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Lin Xia
- State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Kailing Tu
- State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Tang
- State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Senlin Yin
- State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lunzhi Dai
- State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Lab of PTM and Department of General Practice, West China Hospital, Sichuan University, Chengdu, China
| | - Peng Lei
- State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Biao Dong
- State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Hongbo Hu
- State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yong Fan
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yang Yu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
| | - Dan Xie
- State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China. .,Center of Precision medicine, West China Hospital, Sichuan University, Chengdu, China.
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36
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Gene expression variability across cells and species shapes innate immunity. Nature 2018; 563:197-202. [PMID: 30356220 PMCID: PMC6347972 DOI: 10.1038/s41586-018-0657-2] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 08/17/2018] [Indexed: 11/09/2022]
Abstract
As the first line of defence against pathogens, cells mount an innate immune response, which varies widely from cell to cell. The response must be potent but carefully controlled to avoid self-damage. How these constraints have shaped the evolution of innate immunity remains poorly understood. Here we characterize the innate immune response's transcriptional divergence between species and variability in expression among cells. Using bulk and single-cell transcriptomics in fibroblasts and mononuclear phagocytes from different species, challenged with immune stimuli, we map the architecture of the innate immune response. Transcriptionally diverging genes, including those that encode cytokines and chemokines, vary across cells and have distinct promoter structures. Conversely, genes that are involved in the regulation of this response, such as those that encode transcription factors and kinases, are conserved between species and display low cell-to-cell variability in expression. We suggest that this expression pattern, which is observed across species and conditions, has evolved as a mechanism for fine-tuned regulation to achieve an effective but balanced response.
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37
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Blake LE, Thomas SM, Blischak JD, Hsiao CJ, Chavarria C, Myrthil M, Gilad Y, Pavlovic BJ. A comparative study of endoderm differentiation in humans and chimpanzees. Genome Biol 2018; 19:162. [PMID: 30322406 PMCID: PMC6191992 DOI: 10.1186/s13059-018-1490-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 07/20/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND There is substantial interest in the evolutionary forces that shaped the regulatory framework in early human development. Progress in this area has been slow because it is difficult to obtain relevant biological samples. Induced pluripotent stem cells (iPSCs) may provide the ability to establish in vitro models of early human and non-human primate developmental stages. RESULTS Using matched iPSC panels from humans and chimpanzees, we comparatively characterize gene regulatory changes through a four-day time course differentiation of iPSCs into primary streak, endoderm progenitors, and definitive endoderm. As might be expected, we find that differentiation stage is the major driver of variation in gene expression levels, followed by species. We identify thousands of differentially expressed genes between humans and chimpanzees in each differentiation stage. Yet, when we consider gene-specific dynamic regulatory trajectories throughout the time course, we find that at least 75% of genes, including nearly all known endoderm developmental markers, have similar trajectories in the two species. Interestingly, we observe a marked reduction of both intra- and inter-species variation in gene expression levels in primitive streak samples compared to the iPSCs, with a recovery of regulatory variation in endoderm progenitors. CONCLUSIONS The reduction of variation in gene expression levels at a specific developmental stage, paired with overall high degree of conservation of temporal gene regulation, is consistent with the dynamics of a conserved developmental process.
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Affiliation(s)
- Lauren E. Blake
- Department of Human Genetics, University of Chicago, Chicago, IL USA
| | | | - John D. Blischak
- Department of Human Genetics, University of Chicago, Chicago, IL USA
| | | | - Claudia Chavarria
- Department of Human Genetics, University of Chicago, Chicago, IL USA
| | - Marsha Myrthil
- Department of Human Genetics, University of Chicago, Chicago, IL USA
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, IL USA
- Department of Medicine, University of Chicago, Chicago, IL USA
- Cummings Life Sciences Center, 920 E. 58th Street, CLSC 317, Chicago, IL 60637 USA
| | - Bryan J. Pavlovic
- Department of Human Genetics, University of Chicago, Chicago, IL USA
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Abstract
Like many other pathological infectious processes, sepsis is mainly studied in vivo using mice models. Over the past 30 years, such studies have led to significant achievements in understanding of the sepsis pathophysiology. However, unfortunately, none of them led to any «discoveries» in the treatment of patients. In this review, we question the relevance of the experimental models applied, list some aspects rarely taken into account and discuss ways to resolve the deadlock.The text is a translation of the article: Cavail-lon J. M. New methods of treating sepsis: failure of animal models, Bull. Assoc. Anc. El. Inst. Pastor, 2017, 59,230, 58—60. Translation from French by «Akademperevod», Moscow, Russia.
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Regulation of the maturation of human monocytes into immunosuppressive macrophages. Blood Adv 2017; 1:2510-2519. [PMID: 29296902 DOI: 10.1182/bloodadvances.2017011221] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/27/2017] [Indexed: 12/22/2022] Open
Abstract
Human monocytes differentiate into either proinflammatory or immunosuppressive macrophages in response to distinct stimuli. Results show that the Toll-like receptor 2/1 agonist PAM3 replicates the ability of macrophage colony-stimulating factor (M-CSF) to induce the preferential generation of immunosuppressive macrophages in vitro, an activity confirmed by in vivo studies of rhesus macaques. By comparing the gene expression pattern of monocytes treated with M-CSF vs PAM3, the pathways regulating macrophage maturation were identified. NF-κB and Akt were found to play a central role in the overall process of monocyte into macrophage differentiation. Pathways regulated by p38 MAPK and PTGS2 biased this process toward the generation of immunosuppressive rather than proinflammatory macrophages. ERK and JNK contribute to PAM3- but not M-CSF-driven monocyte maturation. These findings clarify the mechanisms underlying the generation of immunosuppressive macrophages and support the use of PAM3 in the treatment of autoimmune and inflammatory diseases.
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Schönrich G, Raftery MJ. Exploring the Immunopathogenesis of Viral Hemorrhagic Fever in Mice with a Humanized Immune System. Front Immunol 2017; 8:1202. [PMID: 29018450 PMCID: PMC5622932 DOI: 10.3389/fimmu.2017.01202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/11/2017] [Indexed: 01/23/2023] Open
Abstract
Viral hemorrhagic fever (VHF) as a disease entity was first codified in the 1930s by soviet scientists investigating patients suffering from hantavirus infection. The group of hemorrhagic fever viruses (HFVs) has since expanded to include members from at least four different virus families: Arenaviridae, Bunyaviridae, Filoviridae, and Flaviviridae, all enveloped single-stranded RNA viruses. After infection, the natural hosts of HFVs do not develop symptoms, whereas humans can be severely affected. This observation and other evidence from experimental data suggest that the human immune system plays a crucial role in VHF pathogenesis. For this reason mice with a human immune system, referred to here as humanized mice (humice), are valuable tools that provide insight into disease mechanisms and allow for preclinical testing of novel vaccinations approaches as well as antiviral agents. In this article, we review the impact of humice in VHF research.
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Affiliation(s)
- Günther Schönrich
- Institute of Medical Virology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Martin J Raftery
- Institute of Medical Virology, Charité - Universitätsmedizin Berlin, Berlin, Germany
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41
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Mahmoudi Saber M, Saitou N. Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development. Genome Biol Evol 2017; 9:2037-2048. [PMID: 28633494 PMCID: PMC5591954 DOI: 10.1093/gbe/evx105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2017] [Indexed: 12/12/2022] Open
Abstract
Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes. We discovered 679 such HCNSs from human, chimpanzee, gorilla, orangutan and gibbon genomes. These HCNSs were demonstrated to be under purifying selection but with lineage-restricted characteristics different from old CNSs. A significant proportion of their ancestral sequences had accelerated rates of nucleotide substitutions, insertions and deletions during the evolution of common ancestor of Hominoidea, suggesting the intervention of positive Darwinian selection for creating those HCNSs. In contrary to enhancer elements and similar to silencer sequences, these Hominoidea-restricted HCNSs are located in close proximity of transcription start sites. Their target genes are enriched in the nervous system, development and transcription, and they tend to be remotely located from the nearest coding gene. Chip-seq signals and gene expression patterns suggest that Hominoidea-restricted HCNSs are likely to be functional regulatory elements by imposing silencing effects on their target genes in a tissue-restricted manner during fetal brain development. These HCNSs, emerged through adaptive evolution and conserved through purifying selection, represent a set of promising targets for future functional studies of the evolution of Hominoidea-restricted phenotypes.
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Affiliation(s)
- Morteza Mahmoudi Saber
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
| | - Naruya Saitou
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
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42
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Okerblom J, Varki A. Biochemical, Cellular, Physiological, and Pathological Consequences of Human Loss of N-Glycolylneuraminic Acid. Chembiochem 2017; 18:1155-1171. [PMID: 28423240 DOI: 10.1002/cbic.201700077] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Indexed: 12/15/2022]
Abstract
About 2-3 million years ago, Alu-mediated deletion of a critical exon in the CMAH gene became fixed in the hominin lineage ancestral to humans, possibly through a stepwise process of selection by pathogen targeting of the CMAH product (the sialic acid Neu5Gc), followed by reproductive isolation through female anti-Neu5Gc antibodies. Loss of CMAH has occurred independently in some other lineages, but is functionally intact in Old World primates, including our closest relatives, the chimpanzee. Although the biophysical and biochemical ramifications of losing tens of millions of Neu5Gc hydroxy groups at most cell surfaces remains poorly understood, we do know that there are multiscale effects functionally relevant to both sides of the host-pathogen interface. Hominin CMAH loss might also contribute to understanding human evolution, at the time when our ancestors were starting to use stone tools, increasing their consumption of meat, and possibly hunting. Comparisons with chimpanzees within ethical and practical limitations have revealed some consequences of human CMAH loss, but more has been learned by using a mouse model with a human-like Cmah inactivation. For example, such mice can develop antibodies against Neu5Gc that could affect inflammatory processes like cancer progression in the face of Neu5Gc metabolic incorporation from red meats, display a hyper-reactive immune system, a human-like tendency for delayed wound healing, late-onset hearing loss, insulin resistance, susceptibility to muscular dystrophy pathologies, and increased sensitivity to multiple human-adapted pathogens involving sialic acids. Further studies in such mice could provide a model for other human-specific processes and pathologies involving sialic acid biology that have yet to be explored.
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Affiliation(s)
- Jonathan Okerblom
- Biomedical Sciences Graduate Program, University of California in San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0687, USA
| | - Ajit Varki
- Glycobiology Research and Training Center, GRTC) and, Center for Academic Research and Training in Anthropogeny, CARTA), Departments of Medicine and Cellular and Molecular Medicine, University of California in San Diego, La Jolla, CA, 92093-0687, USA
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Okerblom JJ, Schwarz F, Olson J, Fletes W, Ali SR, Martin PT, Glass CK, Nizet V, Varki A. Loss of CMAH during Human Evolution Primed the Monocyte-Macrophage Lineage toward a More Inflammatory and Phagocytic State. THE JOURNAL OF IMMUNOLOGY 2017; 198:2366-2373. [PMID: 28148732 DOI: 10.4049/jimmunol.1601471] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/04/2017] [Indexed: 12/21/2022]
Abstract
Humans and chimpanzees are more sensitive to endotoxin than are mice or monkeys, but any underlying differences in inflammatory physiology have not been fully described or understood. We studied innate immune responses in Cmah-/- mice, emulating human loss of the gene encoding production of Neu5Gc, a major cell surface sialic acid. CMP-N-acetylneuraminic acid hydroxylase (CMAH) loss occurred ∼2-3 million years ago, after the common ancestor of humans and chimpanzees, perhaps contributing to speciation of the genus HomoCmah-/- mice manifested a decreased survival in endotoxemia following bacterial LPS injection. Macrophages from Cmah-/- mice secreted more inflammatory cytokines with LPS stimulation and showed more phagocytic activity. Macrophages and whole blood from Cmah-/- mice also killed bacteria more effectively. Metabolic reintroduction of Neu5Gc into Cmah-/- macrophages suppressed these differences. Cmah-/- mice also showed enhanced bacterial clearance during sublethal lung infection. Although monocytes and monocyte-derived macrophages from humans and chimpanzees exhibited marginal differences in LPS responses, human monocyte-derived macrophages killed Escherichia coli and ingested E. coli BioParticles better. Metabolic reintroduction of Neu5Gc into human macrophages suppressed these differences. Although multiple mechanisms are likely involved, one cause is altered expression of C/EBPβ, a transcription factor affecting macrophage function. Loss of Neu5Gc in Homo likely had complex effects on immunity, providing greater capabilities to clear sublethal bacterial challenges, possibly at the cost of endotoxic shock risk. This trade-off may have provided a selective advantage when Homo transitioned to butchery using stone tools. The findings may also explain why the Cmah-/- state alters severity in mouse models of human disease.
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Affiliation(s)
- Jonathan J Okerblom
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093.,Department of Medicine, University of California, San Diego, La Jolla, CA 92093.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Flavio Schwarz
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093.,Department of Medicine, University of California, San Diego, La Jolla, CA 92093.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Josh Olson
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - William Fletes
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093.,Initiative for Maximizing Student Development Program, University of California, San Diego, La Jolla, CA 92093
| | - Syed Raza Ali
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093.,Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Paul T Martin
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 42305.,Department of Physiology and Cell Biology, The Ohio State University College of Medicine, Columbus, OH 43210; and.,Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205
| | - Christopher K Glass
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093.,Department of Medicine, University of California, San Diego, La Jolla, CA 92093.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Victor Nizet
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093.,Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Ajit Varki
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093; .,Department of Medicine, University of California, San Diego, La Jolla, CA 92093.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
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44
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Haile LA, Puig M, Polumuri SK, Ascher J, Verthelyi D. In Vivo Effect of Innate Immune Response Modulating Impurities on the Skin Milieu Using a Macaque Model: Impact on Product Immunogenicity. J Pharm Sci 2016; 106:751-760. [PMID: 27923493 DOI: 10.1016/j.xphs.2016.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/13/2016] [Accepted: 11/01/2016] [Indexed: 01/04/2023]
Abstract
Unwanted immune responses to therapeutic proteins can severely impact their safety and efficacy. Studies show that the presence of trace amounts of host cells and process-related impurities that stimulate pattern recognition receptors (PRR) can cause local inflammation and enhance product immunogenicity. Here we used purified PRR agonists as model impurities to assess the minimal level of individual innate immune response modulating impurities (IIRMIs) that could activate a local immune response. We show that levels of endotoxin as low as 10 pg (0.01 EU), 1 ng for polyinosinic:polycytidylic acid (PolyI:C), 100 ng for synthetic diacylated liopprotein, thiazoloquinolone compound, or muramyl dipeptide, 1 μg for flagellin or β-glucan, or 5 μg for CpG-oligodeoxynucleotide increased expression of genes linked to innate immune activation and inflammatory processes in the skin of rhesus macaques. Furthermore, spiking studies using rasburicase as a model therapeutic showed that the levels of PRR agonists that induced detectable gene upregulation in the skin were associated with increased immunogenicity for rasburicase. This study underscores the need for testing multiple IIRMIs in biologics, strengthening the connection between the local mRNA induction in skin, innate immune activation, and antibody development in primates, and provides an indication of the levels of IIRMI in therapeutic products that could impact product immunogenicity.
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Affiliation(s)
- Lydia A Haile
- Laboratory of Immunology, Division of Biotechnology Review and Research III, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993
| | - Montserrat Puig
- Laboratory of Immunology, Division of Biotechnology Review and Research III, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993
| | - Swamy K Polumuri
- Laboratory of Immunology, Division of Biotechnology Review and Research III, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993
| | - Jill Ascher
- Laboratory of Immunology, Division of Biotechnology Review and Research III, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993
| | - Daniela Verthelyi
- Laboratory of Immunology, Division of Biotechnology Review and Research III, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993.
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45
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Spengler JR, Lavender KJ, Martellaro C, Carmody A, Kurth A, Keck JG, Saturday G, Scott DP, Nichol ST, Hasenkrug KJ, Spiropoulou CF, Feldmann H, Prescott J. Ebola Virus Replication and Disease Without Immunopathology in Mice Expressing Transgenes to Support Human Myeloid and Lymphoid Cell Engraftment. J Infect Dis 2016; 214:S308-S318. [PMID: 27601621 DOI: 10.1093/infdis/jiw248] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The study of Ebola virus (EBOV) pathogenesis in vivo has been limited to nonhuman primate models or use of an adapted virus to cause disease in rodent models. Herein we describe wild-type EBOV (Makona variant) infection of mice engrafted with human hematopoietic CD34+ stem cells (Hu-NSG™-SGM3 mice; hereafter referred to as SGM3 HuMice). SGM3 HuMice support increased development of myeloid immune cells, which are primary EBOV targets. In SGM3 HuMice, EBOV replicated to high levels, and disease was observed following either intraperitoneal or intramuscular inoculation. Despite the high levels of viral antigen and inflammatory cell infiltration in the liver, the characteristic histopathology of Ebola virus disease was not observed, and this absence of severe immunopathology may have contributed to the recovery and survival of some of the animals. Future investigations into the underlying mechanisms of the atypical disease presentation in SGM3 HuMice will provide additional insights into the immunopathogenesis of severe EBOV disease.
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Affiliation(s)
- Jessica R Spengler
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | | | - Andreas Kurth
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - James G Keck
- In Vivo Services, The Jackson Laboratory, Sacramento, California
| | - Greg Saturday
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Dana P Scott
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Stuart T Nichol
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
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46
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Bailey J. Monkey-based research on human disease: the implications of genetic differences. Altern Lab Anim 2016; 42:287-317. [PMID: 25413291 DOI: 10.1177/026119291404200504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Assertions that the use of monkeys to investigate human diseases is valid scientifically are frequently based on a reported 90-93% genetic similarity between the species. Critical analyses of the relevance of monkey studies to human biology, however, indicate that this genetic similarity does not result in sufficient physiological similarity for monkeys to constitute good models for research, and that monkey data do not translate well to progress in clinical practice for humans. Salient examples include the failure of new drugs in clinical trials, the highly different infectivity and pathology of SIV/HIV, and poor extrapolation of research on Alzheimer's disease, Parkinson's disease and stroke. The major molecular differences underlying these inter-species phenotypic disparities have been revealed by comparative genomics and molecular biology - there are key differences in all aspects of gene expression and protein function, from chromosome and chromatin structure to post-translational modification. The collective effects of these differences are striking, extensive and widespread, and they show that the superficial similarity between human and monkey genetic sequences is of little benefit for biomedical research. The extrapolation of biomedical data from monkeys to humans is therefore highly unreliable, and the use of monkeys must be considered of questionable value, particularly given the breadth and potential of alternative methods of enquiry that are currently available to scientists.
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Affiliation(s)
- Jarrod Bailey
- New England Anti-Vivisection Society (NEAVS), Boston, MA, USA
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47
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van Meer L, Moerland M, Gallagher J, van Doorn MBA, Prens EP, Cohen AF, Rissmann R, Burggraaf J. Injection site reactions after subcutaneous oligonucleotide therapy. Br J Clin Pharmacol 2016; 82:340-51. [PMID: 27061947 DOI: 10.1111/bcp.12961] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 12/22/2022] Open
Abstract
Oligonucleotides (ONs) are short fragments of nucleic acids, currently being investigated as therapeutic agents. When administered subcutaneously (sc), ONs cause a specific local reaction originating around the injection site, such as erythema, itching, discomfort and pain, including more severe manifestations such as ulceration or necrosis. These injection site reactions (ISRs) are common, but rather poorly described in the literature. With this review, we aim to provide an overview on the extent of the problem of ISRs, based on reported incidence. A structured literature search was performed to identify reported incidence and clinical features of ISRs which yielded 70 manuscripts that contained information regarding ISRs. The data from literature was combined with data on file available at our institution. All sc administered ONs described in the literature lead to the occurrence of ISRs. The percentage of trial subjects that developed ISRs ranged from 22 to 100% depending on ON. The majority of ONs caused ISRs in more than 70% of the trial subjects. The severity of the observed reactions varied between different ONs. Occurrence rate as well as severity of ISRs increases with higher doses. For chemistry and target of the compounds, no clear association regarding ISR incidence or severity was identified. All ONs developed to date are associated with ISRs. Overcoming the problem of ISRs might add greatly to the potential success of sc-administered ONs. Knowledge of these skin reactions and their specific immunostimulatory properties should be increased in order to obtain ONs that are more suitable for long-term use and clinically applicable in a broader patient population.
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Affiliation(s)
| | | | | | | | - Errol P Prens
- Department of Dermatology Erasmus MC, University Medical Center Rotterdam
| | - Adam F Cohen
- Centre for Human Drug Research, Leiden, the Netherlands
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48
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Varki NM, Varki A. On the apparent rarity of epithelial cancers in captive chimpanzees. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0225. [PMID: 26056369 DOI: 10.1098/rstb.2014.0225] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Malignant neoplasms arising from epithelial cells are called carcinomas. Such cancers are diagnosed in about one in three humans in 'developed' countries, with the most common sites affected being lung, breast, prostate, colon, ovary and pancreas. By contrast, carcinomas are said to be rare in captive chimpanzees, which share more than 99% protein sequence homology with humans (and possibly in other related 'great apes'-bonobos, gorillas and orangutans). Simple ascertainment bias is an unlikely explanation, as these nonhuman hominids are recipients of excellent veterinary care in research facilities and zoos, and are typically subjected to necropsies when they die. In keeping with this notion, benign tumours and cancers that are less common in humans are well documented in this population. In this brief overview, we discuss other possible explanations for the reported rarity of carcinomas in our closest evolutionary cousins, including inadequacy of numbers surveyed, differences in life expectancy, diet, genetic susceptibility, immune responses or their microbiomes, and other potential environmental factors. We conclude that while relative carcinoma risk is a likely difference between humans and chimpanzees (and possibly other 'great apes'), a more systematic survey of available data is required for validation of this claim.
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Affiliation(s)
- Nissi M Varki
- Department of Pathology, Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, CA 92093, USA
| | - Ajit Varki
- Department of Pathology, Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, CA 92093, USA Department of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, CA 92093, USA Department of Cellular and Molecular Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, CA 92093, USA
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49
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Chuong EB, Elde NC, Feschotte C. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 2016; 351:1083-7. [PMID: 26941318 DOI: 10.1126/science.aad5497] [Citation(s) in RCA: 557] [Impact Index Per Article: 69.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Endogenous retroviruses (ERVs) are abundant in mammalian genomes and contain sequences modulating transcription. The impact of ERV propagation on the evolution of gene regulation remains poorly understood. We found that ERVs have shaped the evolution of a transcriptional network underlying the interferon (IFN) response, a major branch of innate immunity, and that lineage-specific ERVs have dispersed numerous IFN-inducible enhancers independently in diverse mammalian genomes. CRISPR-Cas9 deletion of a subset of these ERV elements in the human genome impaired expression of adjacent IFN-induced genes and revealed their involvement in the regulation of essential immune functions, including activation of the AIM2 inflammasome. Although these regulatory sequences likely arose in ancient viruses, they now constitute a dynamic reservoir of IFN-inducible enhancers fueling genetic innovation in mammalian immune defenses.
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Affiliation(s)
- Edward B Chuong
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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50
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Rasid O, Cavaillon JM. Recent developments in severe sepsis research: from bench to bedside and back. Future Microbiol 2016; 11:293-314. [PMID: 26849633 DOI: 10.2217/fmb.15.133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Severe sepsis remains a worldwide threat, not only in industrialized countries, due to their aging population, but also in developing countries where there still are numerous cases of neonatal and puerperal sepsis. Tools for early diagnosis, a prerequisite for rapid and appropriate antibiotic therapy, are still required. In this review, we highlight some recent developments in our understanding of the associated systemic inflammatory response that help deciphering pathophysiology (e.g., epigenetic, miRNA, regulatory loops, compartmentalization, apoptosis and synergy) and discuss some of the consequences of sepsis (e.g., immune status, neurological and muscular alterations). We also emphasize the challenge to better define animal models and discuss past failures in clinical investigations in order to define new efficient therapies.
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Affiliation(s)
- Orhan Rasid
- Unit Cytokines & Inflammation, Institut Pasteur, 28 rue Dr. Roux, Paris, France
| | - Jean-Marc Cavaillon
- Unit Cytokines & Inflammation, Institut Pasteur, 28 rue Dr. Roux, Paris, France
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