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1.
Genes (Basel) ; 15(6)2024 May 30.
Article in English | MEDLINE | ID: mdl-38927648

ABSTRACT

Infections with gastrointestinal nematodes (GINs) reduce the economic efficiency of sheep operations and compromise animal welfare. Understanding the host's response to GIN infection can help producers identify animals that are naturally resistant to infection. The objective of this study was to characterize the hepatic transcriptome of sheep that had been naturally exposed to GIN parasites. The hepatic transcriptome was studied using RNA-Sequencing technology in animals characterized as high (n = 5) or medium (n = 6) based on their innate immune acute-phase (AP) response phenotype compared with uninfected controls (n = 4), and with biased antibody-mediated (AbMR, n = 5) or cell-mediated (CMR, n = 5) adaptive immune responsiveness compared to uninfected controls (n = 3). Following the assessment of sheep selected for innate responses, 0, 136, and 167 genes were differentially expressed (DE) between high- and medium-responding animals, high-responding and uninfected control animals, and medium-responding and uninfected control animals, respectively (false discovery rate (FDR) < 0.05, and fold change |FC| > 2). When adaptive immune responses were assessed, 0, 53, and 57 genes were DE between antibody- and cell-biased animals, antibody-biased and uninfected control animals, and cell-biased and uninfected control animals, respectively (FDR < 0.05, |FC| > 2). Functional analyses identified enriched gene ontology (GO) terms and metabolic pathways related to the innate immune response and energy metabolism. Six functional candidate genes were identified for further functional and validation studies to better understand the underlying biological mechanisms of host responses to GINs. These, in turn, can potentially help improve decision making and management practices to increase the overall host immune response to GIN infection.


Subject(s)
Immunity, Innate , Liver , Nematode Infections , Sheep Diseases , Transcriptome , Animals , Sheep/parasitology , Liver/parasitology , Liver/metabolism , Liver/immunology , Nematode Infections/veterinary , Nematode Infections/genetics , Nematode Infections/immunology , Nematode Infections/parasitology , Sheep Diseases/parasitology , Sheep Diseases/genetics , Sheep Diseases/immunology , Immunity, Innate/genetics , Nematoda/pathogenicity , Adaptive Immunity/genetics , Gastrointestinal Diseases/genetics , Gastrointestinal Diseases/parasitology , Gastrointestinal Diseases/immunology , Gastrointestinal Diseases/veterinary
2.
BMC Gastroenterol ; 24(1): 197, 2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38877387

ABSTRACT

BACKGROUND: Innate/adaptive immunity is the key to anti-tumor therapy. However, its causal relationship to Gastrointestinal (GI) cancer remains unclear. METHODS: Immunity genes were extracted from the MSigDB database. The Genome-wide association studies (GWAS) summary data of GI cancer were integrated with expression quantitative trait loci (eQTL) and DNA methylation quantitative trait loci (mQTL) associated with genes. Summary-data-based Mendelian randomization (SMR) and co-localization analysis were used to reveal causal relationships between genes and GI cancer. Two-sample MR analysis was used for sensitivity analysis. Single cell analysis clarified the enrichment of genes. RESULTS: Three-step SMR analysis showed that a putative mechanism, cg17294865 CpG site regulating HLA-DRA expression was negatively associated with gastric cancer risk. HLA-DRA was significantly differentially expressed in monocyte/macrophage and myeloid cells in gastric cancer. CONCLUSION: This study provides evidence that upregulating the expression level of HLA-DRA can reduce the risk of gastric cancer.


Subject(s)
Adaptive Immunity , DNA Methylation , Gastrointestinal Neoplasms , Genome-Wide Association Study , Immunity, Innate , Mendelian Randomization Analysis , Quantitative Trait Loci , Humans , Immunity, Innate/genetics , Adaptive Immunity/genetics , Gastrointestinal Neoplasms/genetics , Gastrointestinal Neoplasms/immunology , Stomach Neoplasms/genetics , Stomach Neoplasms/immunology , HLA-DR alpha-Chains/genetics , CpG Islands/genetics , Multiomics
3.
J Mol Cell Cardiol ; 192: 48-64, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38734060

ABSTRACT

INTRODUCTION: Chronic immunopathology contributes to the development of heart failure after a myocardial infarction. Both T and B cells of the adaptive immune system are present in the myocardium and have been suggested to be involved in post-MI immunopathology. METHODS: We analyzed the B and T cell populations isolated from previously published single cell RNA-sequencing data sets (PMID: 32130914, PMID: 35948637, PMID: 32971526 and PMID: 35926050), of the mouse and human heart, using differential expression analysis, functional enrichment analysis, gene regulatory inferences, and integration with autoimmune and cardiovascular GWAS. RESULTS: Already at baseline, mature effector B and T cells are present in the human and mouse heart, having increased activity in transcription factors maintaining tolerance (e.g. DEAF1, JDP2, SPI-B). Following MI, T cells upregulate pro-inflammatory transcript levels (e.g. Cd11, Gzmk, Prf1), while B cells upregulate activation markers (e.g. Il6, Il1rn, Ccl6) and collagen (e.g. Col5a2, Col4a1, Col1a2). Importantly, pro-inflammatory and fibrotic transcription factors (e.g. NFKB1, CREM, REL) remain active in T cells, while B cells maintain elevated activity in transcription factors related to immunoglobulin production (e.g. ERG, REL) in both mouse and human post-MI hearts. Notably, genes differentially expressed in post-MI T and B cells are associated with cardiovascular and autoimmune disease. CONCLUSION: These findings highlight the varied and time-dependent dynamic roles of post-MI T and B cells. They appear ready-to-go and are activated immediately after MI, thus participate in the acute wound healing response. However, they subsequently remain in a state of pro-inflammatory activation contributing to persistent immunopathology.


Subject(s)
B-Lymphocytes , Myocardial Infarction , Myocardium , Sequence Analysis, RNA , Single-Cell Analysis , Myocardial Infarction/genetics , Myocardial Infarction/immunology , Myocardial Infarction/metabolism , Myocardial Infarction/pathology , Humans , Animals , Mice , Myocardium/metabolism , Myocardium/pathology , B-Lymphocytes/metabolism , B-Lymphocytes/immunology , T-Lymphocytes/metabolism , T-Lymphocytes/immunology , Adaptive Immunity/genetics , Gene Expression Regulation , Gene Expression Profiling , Transcriptome/genetics , Transcription, Genetic , Genome-Wide Association Study
4.
Brief Bioinform ; 25(3)2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38752856

ABSTRACT

Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency, reproducibility, and collaboration in AIRR-seq data analysis, serving as a model for handling and documenting bioinformatics pipelines in other research domains.


Subject(s)
Computational Biology , Software , Humans , Computational Biology/methods , Reproducibility of Results , Receptors, Immunologic/genetics , High-Throughput Nucleotide Sequencing/methods , Adaptive Immunity/genetics , Guidelines as Topic
5.
Curr Opin Immunol ; 87: 102429, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38805851

ABSTRACT

Recognition of antigens by T cell receptors (TCRs) and B cell receptors (BCRs) is a key step in lymphocyte activation. T and B cells mediate adaptive immune responses, which protect us against infections and provide immunological memory, and also, in some instances, drive pathogenic responses in autoimmune diseases. TCRs and BCRs are encoded within loci that are known to be genetically diverse. However, the extent and functional impact of this variation, both in humans and model animals used in immunological research, remain largely unknown. Experimental and genetic evidence has demonstrated that the complementarity determining regions 1 and 2 (HCDR1 and HCDR2), encoded by the variable (V) region of TCRs and BCRs, also often make critical contacts with the targeted antigen. Thus, knowledge about allelic variation in the genes encoding TCRs and BCRs is critically important for understanding adaptive immune responses in outbred populations and to define responder and non-responder phenotypes.


Subject(s)
Genetic Variation , Receptors, Antigen, B-Cell , Humans , Animals , Receptors, Antigen, B-Cell/genetics , Receptors, Antigen, B-Cell/immunology , Adaptive Immunity/genetics , Receptors, Antigen, T-Cell/genetics , Receptors, Antigen, T-Cell/immunology , B-Lymphocytes/immunology , Complementarity Determining Regions/genetics , Complementarity Determining Regions/immunology
6.
Genome Res ; 34(4): 515-529, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38702197

ABSTRACT

RNA modifications, also termed epitranscriptomic marks, encompass chemical alterations to individual nucleotides, including processes such as methylation and editing. These marks contribute to a wide range of biological processes, many of which are related to host immune system defense. The functions of immune-related RNA modifications can be categorized into three main groups: regulation of immunogenic RNAs, control of genes involved in innate immune response, and facilitation of adaptive immunity. Here, we provide an overview of recent research findings that elucidate the contributions of RNA modifications to each of these processes. We also discuss relevant methods for genome-wide identification of RNA modifications and their immunogenic substrates. Finally, we highlight recent advances in cancer immunotherapies that aim to reduce cancer cell viability by targeting the enzymes responsible for RNA modifications. Our presentation of these dynamic research avenues sets the stage for future investigations in this field.


Subject(s)
Epigenesis, Genetic , Immunity, Innate , Neoplasms , Transcriptome , Humans , Neoplasms/genetics , Neoplasms/immunology , Immunity, Innate/genetics , RNA Processing, Post-Transcriptional , Animals , Adaptive Immunity/genetics , RNA/genetics , RNA/metabolism
7.
Immun Inflamm Dis ; 12(5): e1272, 2024 May.
Article in English | MEDLINE | ID: mdl-38780047

ABSTRACT

BACKGROUND: Peri-implantitis and periodontitis have similar immunological bioprocesses and inflammatory phenotypes. In the inflammatory process, the adaptive immune cells can drive the development of disease. This research investigated the differences and diagnostic significance of peri-implantitis and periodontitis in adaptive immune responses. METHODS: We acquired four GEO datasets of gene expressions in surrounding tissues in healthy person, healthy implant, periodontitis, and peri-implantitis patients. The structural characteristics and enrichment analyses of differential expression genes were examined. The adaptive immune landscapes in peri-implantitis and periodontitis were then evaluated using single sample gene set enrichment analysis. The STRING database and Cytoscape were used to identify adaptive hub genes, and the ROC curve was used to verify them. Finally, qRT-PCR method was used to verify the expression level of Hub gene in activated T cells on the titanium-containing or titanium-free culture plates. RESULTS: At the transcriptome level, the data of healthy implant, peri-implantitis and periodontitis were highly dissimilar. The peri-implantitis and periodontitis both exhibited adaptive immune response. Except for the activated CD4+T cells, there was no significant difference in other adaptive immune cells between peri-implantitis and periodontitis. In addition, correlation analysis showed that CD53, CYBB, and PLEK were significantly positively linked with activated CD4+T cells in the immune microenvironment of peri-implantitis, making them effective biomarkers to differentiate it from periodontitis. CONCLUSIONS: Peri-implantitis has a uniquely immunogenomic landscape that differs from periodontitis. This study provides new insights and ideas into the activated CD4+T cells and hub genes that underpin the immunological bioprocess of peri-implantitis.


Subject(s)
Adaptive Immunity , Computational Biology , Peri-Implantitis , Periodontitis , Humans , Peri-Implantitis/genetics , Peri-Implantitis/immunology , Peri-Implantitis/diagnosis , Periodontitis/genetics , Periodontitis/immunology , Periodontitis/diagnosis , Adaptive Immunity/genetics , Computational Biology/methods , Transcriptome , Gene Expression Profiling
8.
Front Immunol ; 15: 1380971, 2024.
Article in English | MEDLINE | ID: mdl-38799462

ABSTRACT

Mycobacterium tuberculosis (Mtb) remains a major threat worldwide, although only a fraction of infected individuals develops tuberculosis (TB). TB susceptibility is shaped by multiple genetic factors, and we performed comparative immunological analysis of two mouse strains to uncover relevant mechanisms underlying susceptibility and resistance. C57BL/6 mice are relatively TB-resistant, whereas I/St mice are prone to develop severe TB, partly due to the MHC-II allelic variant that shapes suboptimal CD4+ T cell receptor repertoire. We investigated the repertoires of lung-infiltrating helper T cells and B cells at the progressed stage in both strains. We found that lung CD4+ T cell repertoires of infected C57BL/6 but not I/St mice contained convergent TCR clusters with functionally confirmed Mtb specificity. Transcriptomic analysis revealed a more prominent Th1 signature in C57BL/6, and expression of pro-inflammatory IL-16 in I/St lung-infiltrating helper T cells. The two strains also showed distinct Th2 signatures. Furthermore, the humoral response of I/St mice was delayed, less focused, and dominated by IgG/IgM isotypes, whereas C57BL/6 mice generated more Mtb antigen-focused IgA response. We conclude that the inability of I/St mice to produce a timely and efficient anti-Mtb adaptive immune responses arises from a suboptimal helper T cell landscape that also impacts the humoral response, leading to diffuse inflammation and severe disease.


Subject(s)
Adaptive Immunity , Genetic Predisposition to Disease , Mice, Inbred C57BL , Mycobacterium tuberculosis , Tuberculosis , Animals , Mice , Mycobacterium tuberculosis/immunology , Adaptive Immunity/genetics , Tuberculosis/immunology , Tuberculosis/genetics , Lung/immunology , Lung/pathology , B-Lymphocytes/immunology , Disease Models, Animal , Receptors, Antigen, T-Cell/genetics , Receptors, Antigen, T-Cell/immunology
9.
Cell Commun Signal ; 22(1): 243, 2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38671495

ABSTRACT

BACKGROUND: Coronary artery disease (CAD) is a leading cause of death in women. Epicardial adipose tissue (EAT) secretes cytokines to modulate coronary artery function, and the release of fatty acids from EAT serves as a readily available energy source for cardiomyocytes. However, despite having beneficial functions, excessive amounts of EAT can cause the secretion of proinflammatory molecules that increase the instability of atherosclerotic plaques and contribute to CAD progression. Although exercise mitigates CAD, the mechanisms by which exercise impacts EAT are unknown. The Yucatan pig is an excellent translational model for the effects of exercise on cardiac function. Therefore, we sought to determine if chronic aerobic exercise promotes an anti-inflammatory microenvironment in EAT from female Yucatan pigs. METHODS: Sexually mature, female Yucatan pigs (n = 7 total) were assigned to sedentary (Sed, n = 3) or exercise (Ex, n = 4) treatments, and coronary arteries were occluded (O) with an ameroid to mimic CAD or remained non-occluded (N). EAT was collected for bulk (n = 7 total) and single nucleus transcriptomic sequencing (n = 2 total, 1 per exercise treatment). RESULTS: Based on the bulk transcriptomic analysis, exercise upregulated S100 family, G-protein coupled receptor, and CREB signaling in neurons canonical pathways in EAT. The top networks in EAT affected by exercise as measured by bulk RNA sequencing were SRC kinase family, fibroblast growth factor receptor, Jak-Stat, and vascular endothelial growth factor. Single nucleus transcriptomic analysis revealed that exercise increased the interaction between immune, endothelial, and mesenchymal cells in the insulin-like growth factor pathway and between endothelial and other cell types in the platelet endothelial cell adhesion molecule 1 pathway. Sub-clustering revealed nine cell types in EAT, with fibroblast and macrophage populations predominant in O-Ex EAT and T cell populations predominant in N-Ex EAT. Unlike the findings for exercise alone as a treatment, there were not increased interactions between endothelial and mesenchymal cells in O-Ex EAT. Coronary artery occlusion impacted the most genes in T cells and endothelial cells. Genes related to fatty acid metabolism were the most highly upregulated in non-immune cells from O-Ex EAT. Sub-clustering of endothelial cells revealed that N-Ex EAT separated from other treatments. CONCLUSIONS: According to bulk transcriptomics, exercise upregulated pathways and networks related to growth factors and immune cell communication. Based on single nucleus transcriptomics, aerobic exercise increased cell-to-cell interaction amongst immune, mesenchymal, and endothelial cells in female EAT. Yet, exercise was minimally effective at reversing alterations in gene expression in endothelial and mesenchymal cells in EAT surrounding occluded arteries. These findings lay the foundation for future work focused on the impact of exercise on cell types in EAT.


Subject(s)
Adipose Tissue , Pericardium , Physical Conditioning, Animal , Transcriptome , Animals , Female , Swine , Pericardium/metabolism , Adipose Tissue/metabolism , Transcriptome/genetics , Adaptive Immunity/genetics , Immunity, Innate , Cell Nucleus/metabolism , Coronary Artery Disease/metabolism , Coronary Artery Disease/genetics , Epicardial Adipose Tissue
10.
Invest Ophthalmol Vis Sci ; 65(4): 44, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38687493

ABSTRACT

Purpose: Fungal endophthalmitis is characterized by chronic inflammation leading to the partial or complete vision loss. Herein, we analyzed the transcriptomic landscape of Aspergillus flavus (A. flavus) endophthalmitis in C57BL/6 mice to understand the host-pathogen interactions. Methods: Endophthalmitis was induced by intravitreal injection of A. flavus spores in C57BL/6 mice and monitored for disease progression up to 72 hours. The enucleated eyeballs were subjected to histopathological analysis and mRNA sequencing using the Illumina Nextseq 2000. Pathway enrichment analysis was performed to further annotate the functions of differentially expressed genes (DEGs) and validation of cytokines was performed in vitreous of patients with fungal endophthalmitis using multiplex ELISA. Results: Transcriptomic landscape of A. flavus endophthalmitis revealed upregulated T-cell receptor signaling, PI3K-AKT, MAPK, NF-κB, JAK-STAT, and NOD like receptor signaling pathways. We observed significant increase in the T-cells during infection especially at 72 hours infection along with elevated expression levels of IL-6, IL-10, IL-12, IL-18, IL-19, IL-23, CCR3, and CCR7. Furthermore, host-immune response associated genes, such as T-cell interacting activating receptor, TNF receptor-associated factor 1, TLR1, TLR9, and bradykinin receptor beta 1, were enriched. Histopathological assessment validated the significant increase in inflammatory cells, especially T-cells at 72 hours post-infection along with increased disruption in the retinal architecture. Additionally, IL-6, IL-8, IL-17, TNF-α, and IL-1ß were also significantly elevated, whereas IL-10 was downregulated in vitreous of patients with Aspergillus endophthalmitis. Conclusions: Regulating T-cell influx could be a potential strategy to modulate the excessive inflammation in the retina and potentially aid in better vision recovery in fungal endophthalmitis.


Subject(s)
Adaptive Immunity , Aspergillosis , Aspergillus flavus , Cytokines , Disease Models, Animal , Endophthalmitis , Eye Infections, Fungal , Gene Expression Profiling , Immunity, Innate , Mice, Inbred C57BL , Animals , Aspergillus flavus/genetics , Mice , Eye Infections, Fungal/microbiology , Eye Infections, Fungal/genetics , Eye Infections, Fungal/immunology , Endophthalmitis/microbiology , Endophthalmitis/immunology , Endophthalmitis/genetics , Aspergillosis/microbiology , Aspergillosis/genetics , Aspergillosis/immunology , Adaptive Immunity/genetics , Immunity, Innate/genetics , Cytokines/metabolism , Cytokines/genetics , Transcriptome , Enzyme-Linked Immunosorbent Assay , Vitreous Body/microbiology
11.
Dev Comp Immunol ; 156: 105165, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38499166

ABSTRACT

Renibacterium salmoninarum causes Bacterial Kidney Disease (BKD) in several fish species. Atlantic lumpfish, a cleaner fish, is susceptible to R. salmoninarum. To profile the transcriptome response of lumpfish to R. salmoninarum at early and chronic infection stages, fish were intraperitoneally injected with either a high dose of R. salmoninarum (1 × 109 cells dose-1) or PBS (control). Head kidney tissue samples were collected at 28- and 98-days post-infection (dpi) for RNA sequencing. Transcriptomic profiling identified 1971 and 139 differentially expressed genes (DEGs) in infected compared with control samples at 28 and 98 dpi, respectively. At 28 dpi, R. salmoninarum-induced genes (n = 434) mainly involved in innate and adaptive immune response-related pathways, whereas R. salmoninarum-suppressed genes (n = 1537) were largely connected to amino acid metabolism and cellular processes. Cell-mediated immunity-related genes showed dysregulation at 98 dpi. Several immune-signalling pathways were dysregulated in response to R. salmoninarum, including apoptosis, alternative complement, JAK-STAT signalling, and MHC-I dependent pathways. In summary, R. salmoninarum causes immune suppression at early infection, whereas lumpfish induce a cell-mediated immune response at chronic infection. This study provides a complete depiction of diverse immune mechanisms dysregulated by R. salmoninarum in lumpfish and opens new avenues to develop immune prophylactic tools to prevent BKD.


Subject(s)
Fish Diseases , Gene Expression Profiling , Head Kidney , Immunity, Innate , Renibacterium , Transcriptome , Animals , Head Kidney/immunology , Fish Diseases/immunology , Fish Diseases/microbiology , Renibacterium/immunology , Renibacterium/genetics , Immunity, Innate/genetics , Fish Proteins/genetics , Fish Proteins/metabolism , Adaptive Immunity/genetics , Fishes/immunology , Fishes/microbiology , Chronic Disease , Perciformes/immunology , Perciformes/microbiology , Gram-Negative Bacterial Infections/immunology , Kidney Diseases/immunology , Kidney Diseases/microbiology , Kidney Diseases/genetics , Kidney Diseases/veterinary , Micrococcaceae/genetics , Micrococcaceae/immunology
12.
Nat Rev Immunol ; 24(7): 487-502, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38383754

ABSTRACT

There are notable sex-based differences in immune responses to pathogens and self-antigens, with female individuals exhibiting increased susceptibility to various autoimmune diseases, and male individuals displaying preferential susceptibility to some viral, bacterial, parasitic and fungal infections. Although sex hormones clearly contribute to sex differences in immune cell composition and function, the presence of two X chromosomes in female individuals suggests that differential gene expression of numerous X chromosome-linked immune-related genes may also influence sex-biased innate and adaptive immune cell function in health and disease. Here, we review the sex differences in immune system composition and function, examining how hormones and genetics influence the immune system. We focus on the genetic and epigenetic contributions responsible for altered X chromosome-linked gene expression, and how this impacts sex-biased immune responses in the context of pathogen infection and systemic autoimmunity.


Subject(s)
Sex Characteristics , Humans , Female , Male , Animals , Gonadal Steroid Hormones/immunology , Gonadal Steroid Hormones/metabolism , Autoimmune Diseases/immunology , Autoimmune Diseases/genetics , Epigenesis, Genetic/immunology , Chromosomes, Human, X/genetics , Genes, X-Linked , Autoimmunity/immunology , Autoimmunity/genetics , Immunity, Innate/immunology , Sex Factors , Adaptive Immunity/genetics , Adaptive Immunity/immunology
13.
Trends Immunol ; 45(2): 113-126, 2024 02.
Article in English | MEDLINE | ID: mdl-38302340

ABSTRACT

New discoveries in the field of human monogenic immune diseases highlight critical genes and pathways governing immune responses. Here, I describe how the ~500 currently defined human inborn errors of immunity help shape what I propose is an 'adaptive arsenal model of rapid defenses', emphasizing the set of immunological defenses poised for rapid responses in the natural environment. This arsenal blurs the lines between innate and adaptive immunity and is established through molecular relays between cell types, often traversing from sensors (pathogen detection) to intermediates to executioners (pathogen clearance) via soluble factors. Predictions and missing information based on the adaptive arsenal model are discussed, as are emergent and outstanding questions fundamental to advances in the field.


Subject(s)
Adaptive Immunity , Immunity, Innate , Humans , Adaptive Immunity/genetics , Human Genetics
14.
Nature ; 626(8000): 827-835, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38355791

ABSTRACT

Individuals differ widely in their immune responses, with age, sex and genetic factors having major roles in this inherent variability1-6. However, the variables that drive such differences in cytokine secretion-a crucial component of the host response to immune challenges-remain poorly defined. Here we investigated 136 variables and identified smoking, cytomegalovirus latent infection and body mass index as major contributors to variability in cytokine response, with effects of comparable magnitudes with age, sex and genetics. We find that smoking influences both innate and adaptive immune responses. Notably, its effect on innate responses is quickly lost after smoking cessation and is specifically associated with plasma levels of CEACAM6, whereas its effect on adaptive responses persists long after individuals quit smoking and is associated with epigenetic memory. This is supported by the association of the past smoking effect on cytokine responses with DNA methylation at specific signal trans-activators and regulators of metabolism. Our findings identify three novel variables associated with cytokine secretion variability and reveal roles for smoking in the short- and long-term regulation of immune responses. These results have potential clinical implications for the risk of developing infections, cancers or autoimmune diseases.


Subject(s)
Adaptive Immunity , Smoking , Female , Humans , Male , Adaptive Immunity/drug effects , Adaptive Immunity/genetics , Autoimmune Diseases/etiology , Autoimmune Diseases/immunology , Body Mass Index , Cytokines/blood , Cytokines/immunology , Cytomegalovirus/immunology , Cytomegalovirus/pathogenicity , Cytomegalovirus/physiology , DNA Methylation/drug effects , Epigenesis, Genetic/drug effects , Immunity, Innate/drug effects , Immunity, Innate/genetics , Infections/etiology , Infections/immunology , Neoplasms/etiology , Neoplasms/immunology , Signal Transduction/drug effects , Signal Transduction/immunology , Smoking/adverse effects , Smoking/blood , Smoking/genetics , Smoking/immunology
15.
Sci Adv ; 10(4): eadj5640, 2024 Jan 26.
Article in English | MEDLINE | ID: mdl-38266093

ABSTRACT

The extent to which AIRRs differ among and within individuals remains elusive. Via ultra-deep repertoire sequencing of 22 and 25 tissues in three cynomolgus macaques, respectively, we identified 84 and 114 novel IGHV and TRBV alleles, confirming 72 (85.71%) and 100 (87.72%) of them. The heterogeneous V gene usage patterns were influenced, in turn, by genetics, isotype (for BCRs only), tissue group, and tissue. A higher proportion of intragroup shared clones in the intestinal tissues than those in other tissues suggests a close intra-intestinal adaptive immunity network. Significantly higher mutation burdens in the public clones and the inter-tissue shared IgM and IgD clones indicate that they might target the shared antigens. This study reveals the extensive heterogeneity of the AIRRs at various levels and has broad fundamental and clinical implications. The data generated here will serve as an invaluable resource for future studies on adaptive immunity in health and diseases.


Subject(s)
Adaptive Immunity , Immunoglobulin Isotypes , Animals , Adaptive Immunity/genetics , Alleles , Macaca fascicularis/genetics , Receptors, Immunologic
16.
J Adv Res ; 55: 73-87, 2024 Jan.
Article in English | MEDLINE | ID: mdl-36871615

ABSTRACT

INTRODUCTION: Both innate and adaptive immune system undergo evolution from low to high vertebrates. Due to the limitation of conventional approaches in identifying broader spectrum of immune cells and molecules from various vertebrates, it remains unclear how immune molecules evolve among vertebrates. OBJECTIVES: Here, we utilized carry out comparative transcriptome analysis in various immune cells across seven vertebrate species. METHODS: Single-cell RNA sequencing (scRNA-seq). RESULTS: We uncovered both conserved and species-specific profiling of gene expression in innate and adaptive immunity. Macrophages exhibited highly-diversified genes and developed sophisticated molecular signaling networks along with evolution, indicating effective and versatile functions in higher species. In contrast, B cells conservatively evolved with less differentially-expressed genes in analyzed species. Interestingly, T cells represented a dominant immune cell populations in all species and unique T cell populations were identified in zebrafish and pig. We also revealed compensatory TCR cascade components utilized by different species. Inter-species comparison of core gene programs demonstrated mouse species has the highest similarity in immune transcriptomes to human. CONCLUSIONS: Therefore, our comparative study reveals gene transcription characteristics across multiple vertebrate species during the evolution of immune system, providing insights for species-specific immunity as well as the translation of animal studies to human physiology and disease.


Subject(s)
Adaptive Immunity , Immunity, Innate , Transcriptome , Animals , Humans , Mice , Adaptive Immunity/genetics , Macrophages , Swine , Zebrafish/genetics , Immunity, Innate/genetics
17.
Genes Immun ; 24(6): 295-302, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37925533

ABSTRACT

Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a proteolytic enzyme involved in adaptive immunity. The ERAP2 gene is highly polymorphic and encodes haplotypes that confer resistance against lethal infectious diseases, but also increase the risk for autoimmune disorders. Identifying how ERAP2 influences susceptibility to these traits requires an understanding of the selective pressures that shaped and maintained allelic variation throughout human evolution. Our review discusses the genetic regulation of haplotypes and diversity in naturally occurring ERAP2 allotypes in the global population. We outline how these ERAP2 haplotypes evolved during human history and highlight the presence of Neanderthal DNA sequences in ERAP2 of modern humans. Recent evidence suggests that human adaptation during the last ~10,000 years and historic pandemics left a significant mark on the ERAP2 gene that determines susceptibility to infectious and inflammatory diseases today.


Subject(s)
Adaptive Immunity , Aminopeptidases , Endoplasmic Reticulum , Evolution, Molecular , Humans , Aminopeptidases/genetics , Aminopeptidases/immunology , Autoimmune Diseases/genetics , Autoimmune Diseases/immunology , Endoplasmic Reticulum/enzymology , Haplotypes , Minor Histocompatibility Antigens/genetics , Adaptive Immunity/genetics
18.
Mol Biol Evol ; 40(11)2023 Nov 03.
Article in English | MEDLINE | ID: mdl-37850912

ABSTRACT

A series of "molecular domestication" events are thought to have converted an invertebrate RAG-like (RAGL) transposase into the RAG1-RAG2 (RAG) recombinase, a critical enzyme for adaptive immunity in jawed vertebrates. The timing and order of these events are not well understood, in part because of a dearth of information regarding the invertebrate RAGL-A transposon family. In contrast to the abundant and divergent RAGL-B transposon family, RAGL-A most closely resembles RAG and is represented by a single orphan RAG1-like (RAG1L) gene in the genome of the hemichordate Ptychodera flava (PflRAG1L-A). Here, we provide evidence for the existence of complete RAGL-A transposons in the genomes of P. flava and several echinoderms. The predicted RAG1L-A and RAG2L-A proteins encoded by these transposons intermingle sequence features of jawed vertebrate RAG and RAGL-B transposases, leading to a prediction of DNA binding, catalytic, and transposition activities that are a hybrid of RAG and RAGL-B. Similarly, the terminal inverted repeats (TIRs) of the RAGL-A transposons combine features of both RAGL-B transposon TIRs and RAG recombination signal sequences. Unlike all previously described RAG2L proteins, RAG2L-A proteins contain an acidic hinge region, which we demonstrate is capable of efficiently inhibiting RAG-mediated transposition. Our findings provide evidence for a critical intermediate in RAG evolution and argue that certain adaptations thought to be specific to jawed vertebrates (e.g. the RAG2 acidic hinge) actually arose in invertebrates, thereby focusing attention on other adaptations as the pivotal steps in the completion of RAG domestication in jawed vertebrates.


Subject(s)
DNA Transposable Elements , Homeodomain Proteins , Animals , Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism , Vertebrates/genetics , Vertebrates/metabolism , Adaptive Immunity/genetics
19.
J Evol Biol ; 36(6): 847-873, 2023 06.
Article in English | MEDLINE | ID: mdl-37255207

ABSTRACT

Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.


Subject(s)
Adaptive Immunity , Biological Evolution , Animals , Adaptive Immunity/genetics , Vertebrates/genetics , Evolution, Molecular , Immunity, Innate/genetics
20.
Cancer Lett ; 564: 216219, 2023 06 28.
Article in English | MEDLINE | ID: mdl-37146937

ABSTRACT

Tumor immunotherapy is a new therapeutic approach that has been evolving in the last decade and has dramatically changed the treatment options for cancer. Circular RNAs (circRNAs) are non-coding RNAs (ncRNAs) with high stability, tissue-specific and cell-specific expression. There is growing evidence that circRNAs are involved in the regulation of both adaptive and innate immunity. They play important roles in tumor immunotherapy by affecting macrophage, NK and T cell function. The high stability and tissue specificity make them ideal candidate biomarkers for therapeutic effects. CircRNAs also represent one of promising targets or adjuvant for immunotherapy. Investigations in this field progress rapidly and provide essential support for the diagnosis, prognosis and treatment guidance of cancers in the future. In this review, we summarize the role of circRNAs on tumor immunity from the viewpoint of innate and adaptive immunity, and explore the role of circRNAs in tumor immunotherapy.


Subject(s)
Neoplasms , RNA, Circular , Humans , RNA, Circular/genetics , Biomarkers , Neoplasms/genetics , Neoplasms/therapy , Adaptive Immunity/genetics , Immunotherapy
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