MS4A1 as a Potential Independent Prognostic Factor of Breast Cancer Related to Lipid Metabolism and Immune Microenvironment Based on TCGA Database Analysis.

BACKGROUND Lipid metabolism has been proved to be related to the prognosis of breast cancer patients in previous studies, and the tumor immune microenvironment (TIME) plays an important role in tumorigenesis and development, but the dynamic regulation of these is still a challenge. MATERIAL AND METHODS This study used lipid metabolism-related pathways to score the gene expression of 980 breast cancer patients in the TCGA database. We used 4 pathways in HALLMARK related to lipid metabolism to score the genes in the database. The differentially expressed genes (DEGs) were further analyzed through survival analysis and Cox regression analysis, and MS4A1, which is associated with better prognosis, was finally determined to be a predictor. In-depth analysis found that MS4A1 was negatively correlated with patient age, clinical stage, tumor size, and distant metastasis. In the MS4A1 high-expression group, most genes were enriched in immune-related pathways, and CIBERSORT analysis found that MS4A1 expression was positively correlated with the abundance of 10 kinds of immune cells, such as CD8+T cells, which are related to the active immune status. RESULTS Our results suggest that MS4A1 expression can indicate the situation of lipid metabolism in breast cancer patients and reflect the status of the immune microenvironment. CONCLUSIONS MS4A1 has the potential to be an independent indicator of prognosis. Since the expression of MS4A1 is also related to the immune checkpoint mutation burden, detecting its expression level can also provide guidance for choosing treatment options.

Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses.

Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Therefore, the fine control of immune effector functions to provide for a rapid, robust response to challenge is essential. Importantly, immune cells are heterogeneous due to various factors relating to cytokine exposure and cell-cell interaction. For instance, tissue-resident macrophages and T cells are phenotypically, transcriptionally, and functionally distinct from their circulating counterparts. Indeed, even the same cell types in the same environment show distinct transcription patterns at the single cell level due to cellular noise, despite being robust in concert. Additionally, immune cells must remain quiescent in a naive state to avoid autoimmunity or chronic inflammatory states but must respond robustly upon activation regardless of their microenvironment or cellular noise. In recent years, accruing evidence from next-generation sequencing, chromatin capture techniques, and high-resolution imaging has shown that local- and long-range genome architecture plays an important role in coordinating rapid and robust transcriptional responses. Here, we discuss the local- and long-range genome architecture of immune cells and the resultant changes upon pathogen or antigen exposure. Furthermore, we argue that genome structures contribute functionally to rapid and robust responses under noisy and distinct cellular environments and propose a model to explain this phenomenon.

Gouania willdenowi is a teleost fish without immunoglobulin genes.

Immunoglobulin (Ig) genes encode antibodies in jawed vertebrates. They are essential elements of the adaptive immune response. Ig exists in soluble form or as part of the B cell membrane antigen receptor (BCR). Studies of Ig genes in fish genomes reveal the absence of Ig genes in Gouania willdenowi by deletion of the entire Ig locus from the canonical chromosomal region. The genes coding for integral BCR proteins, CD79a and CD79b, are also absent. Genes exist for T α/ß lymphocyte receptors but not for the T γ/δ receptors. The results of the genomic analysis are independently corroborated with RNA-Seq transcriptomes from other Gobiesocidae species. From the transcriptome studies, Ig is also absent from these other Gobiesocidae species, Acyrtus sp. and Tomicodon sp. Present evidence suggests that Ig is missing from all species of the Gobiesocidae family.

Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments.

Phenotypic reaction norms are often shaped and constrained by selection and are important for allowing organisms to respond to environmental change. However, selection cannot constrain reaction norms for environmental conditions that populations have not experienced. Consequently, cryptic neutral genetic variation for the reaction norm can accumulate such that a release of phenotypic variation occurs upon exposure to novel14 conditions. Most genomic diversity behaves as if functionally neutral. Therefore, genome-wide diversity metrics may correlate with levels of cryptic genetic variation and, as a result, exhibit a positive relationship with a release of phenotypic variation in novel environments. To test this hypothesis, we conducted translocations of juvenile brook trout (Salvelinus fontinalis) from 12 populations to novel uninhabited ponds that represented a gradient of environmental conditions. We assessed reaction norms for morphological traits (body size and four morphometric relative warps) across pond environmental gradients and evaluated the effect of genome-wide heterozygosity on phenotypic variability. All traits displayed plastic reaction norms. Overall, we found some evidence that a release of phenotypic variation consistent with cryptic genetic variation can occur in novel environmental conditions. However, the extent to which this release correlated with average genome-wide diversity was limited to only one of five traits examined. Our results suggest a limited link between genomic diversity26 and the accumulation of cryptic genetic variation in reaction norms. Similarly, reaction norms were constrained for many of the morphological traits examined. Past conditions may have constrained reaction norms in the putatively novel environments despite significant deviations from contemporary source population habitat. Additionally, as a generalist colonizing species brook trout may exhibit plastic phenotypes across a wide range of environmental conditions.

Antigen presentation genes in gadoid species (haddock: Melanogrammus aeglefinus and Atlantic cod: Gadus morhua) raise questions about cross-presentation pathways and glycosylated beta-2-microglobulin.

The Atlantic cod immune system deviates from antigen presentation processes seen in other vertebrates in that it lacks the necessary genes for exogenous antigen presentation (i.e., MHC-II and li) and a key MHC-II interacting molecule necessary for T-helper cell function (i.e., CD4), while possessing an expanded repertoire of MHC-I genes that facilitate endogenous antigen presentation. These observations, combined with the identification of putative endosomal sorting signals in MHC-I cytoplasmic tails, have led to speculation that cod rely on cross-presentation of exogenous antigens to elicit cytotoxic T-lymphocyte responses against extracellular threats. In light of this suggestion, we investigated MHC-I transcriptional profiles and endosomal sorting signals in a closely related gadoid species, the haddock. Analysis of transcripts from one individual identified 13 unique MHC-I molecules, including two non-classical molecules as determined by the level of conservation at their peptide anchoring sites. This suggests that like the cod, the haddock has an expanded MHC-I repertoire. Analysis of haddock MHC-I cytoplasmic tail sequences revealed that the dileucine- and tyrosine-based endosomal signaling motifs, that are suggested to facilitate cross-presentation in cod, were absent. Closer examination of the cod signaling motifs, including their relative position in the cytoplasmic tail region, indicates that these motifs might be non-functional, further supporting the need for functional studies to assess cross-presentation. Finally, in silico analysis and in vitro N-type de-glycosylation experiments demonstrate that haddock and cod beta-2-microglobulin (ß2M) are glycosylated at the same NQT sequon. Interestingly, whole genome tBLASTn searches also revealed that putative ß2 M glycosylation sites appear frequently within the Gadiformes lineage, as the predictive NQT and other N-X-S/T sequons were located in ß2M orthologues from 19 of the 25 additional gadoid genomes analyzed. Though the exact significance of ß2M glycosylation has yet to be elucidated, phylogenetic comparisons predict that the same NQT glycosylation sequence occurs in 13 additional species comprising four different orders of Actinopterygii (Gymnotiformes, Esociformes, Beryciformes and Perciformes). This suggests either that this feature has arisen independently in multiple lineages or that it comes from a common ancestor and has been lost or modified in many species. Together, the analysis of gadoid MHC-I genes and ß2M molecules highlights the challenges in generalizing immune system paradigms across the most diverse vertebrate lineage (i.e., fish) and between fish and more well-studied mammals.

Evolution of the T-Cell Receptor (TR) Loci in the Adaptive Immune Response: The Tale of the TRG Locus in Mammals.

T lymphocytes are the principal actors of vertebrates' cell-mediated immunity. Like B cells, they can recognize an unlimited number of foreign molecules through their antigen-specific heterodimer receptors (TRs), which consist of αß or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, ß, γ, and δ chains. For each chain, multi-gene families are arranged in a TR locus, and their expression is guaranteed by the somatic recombination process. A great plasticity of the gene organization within the TR loci exists among species. Marked structural differences affect the TR γ (TRG) locus. The recent sequencing of multiple whole genome provides an opportunity to examine the TR gene repertoire in a systematic and consistent fashion. In this review, we report the most recent findings on the genomic organization of TRG loci in mammalian species in order to show differences and similarities. The comparison revealed remarkable diversification of both the genomic organization and gene repertoire across species, but also unexpected evolutionary conservation, which highlights the important role of the T cells in the immune response.

Genome-wide identification, expression signature and immune functional analysis of two cathepsin S (CTSS) genes in turbot (Scophthalmus maximus L.).

Cathepsins, a superfamily of hydrolytic enzymes produced and enclosed within lysosomes, play multiple roles at physiological and pathological states. Cathepsin S is a lysosomal cysteine endopeptidase of the papain family, and exerts critical roles in the regulation of MHC class II immune responses. In the present study, we captured two Cathepsin S genes in turbot (SmCTSS1 and SmCTSS2.1), characterized their expression patterns following V. anguillarum and S. iniae infections, and explored their binding ability and agglutination capability. Firstly, the SmCTSS1 contained a 990 bp ORF encoding 329 amino acids, while SmCTSS2.1 contained a 1,014 bp ORF encoding 337 amino acids. The phylogenetic analysis revealed that both genes showed the closest relationship to their counterparts of Japanese flounder (Paralichthys olivaceus). In addition, both genes were ubiquitously expressed in all examined healthy tissues, with the highest expression level observed in spleen and intestine, respectively, while the lowest expression level both observed in liver. Both SmCTSS1 and SmCTSS2.1 were significantly differentially expressed, and exhibited general down-regulations at most time points in skin and intestine after two bacterial infections. Finally, both rSmCTSS1 and rSmCTSS2.1 showed significant binding ability to three examined microbial ligands (LPS, PGN and LTA), and strong agglutination effect to different bacteria (E. tarda, S. agalactiae, S. aureus and V. anguillarum). Collectively, this study provided valuable data for understanding the roles of CTSS in the host defense against bacterial infections in turbot, and indicated the potential vital roles of CTSS in innate immune responses of teleost species.

Chromosome-level assembly of wild Bactrian camel genome reveals organization of immune gene loci.

Camelids are characterized by their unique adaptive immune system that exhibits the generation of homodimeric heavy-chain immunoglobulins, somatic hypermutation of T-cell receptors, and low genetic diversity of major histocompatibility complex (MHC) genes. However, short-read assemblies are typically highly fragmented in these gene loci owing to their repetitive and polymorphic nature. Here, we constructed a chromosome-level assembly of wild Bactrian camel genome based on high-coverage long-read sequencing and chromatin interaction mapping. The assembly with a contig N50 of 5.37 Mb and a scaffold N50 of 76.03 Mb, represents the most contiguous camelid genome to date. The genomic organization of immunoglobulin heavy-chain locus was similar between the wild Bactrian camel and alpaca, and genes encoding for conventional and heavy-chain antibodies were intermixed. The organizations of two immunoglobulin light-chain loci and four T cell receptor loci were also fully deciphered using the new assembly. Additionally, the complete classical MHC region was resolved into a single contig. The high-quality assembly presented here provides an essential reference for future investigations examining the camelid immune system.

Genome-wide identification, evolution, and mRNA expression of complement genes in common carp (Cyprinus carpio).

Complement is a complex component of innate immune system, playing an important role in defense against pathogens and host homeostasis. The complement system has been comprehensively studied in mammals, however less is known about complement in teleost, especially in tetraploid common carp (Cyprinus carpio). In this study, a total of 110 complement genes were identified and characterized in common carp, which include almost all the homologs of mammalian complement genes. These genes were classified into three pathways (alternative pathways, lectin pathways and classical pathways), similar to those in mammals. Phylogenetic and selection pressure analysis showed that the complement genes were evolving-constrained and the function was conserved. Most of the complement genes were highly expressed in spleen, liver, brain and skin among the tested 12 health tissues of common carp. After Aeromonas hydrophila infection in the common carp, many members of complement genes were activated to bring about an immune response and expressed to against any pathogenic encroachment. Gene expression divergences which were found between two homoeologous genes suggested the functional divergences of the homoeologous genes after the 4R WGD event, revealing the evolutionary fate of the tetraploid common carp after the recent WGD.

Genome-wide identification and characterization of toll-like receptor genes in spotted sea bass (Lateolabrax maculatus) and their involvement in the host immune response to Vibrio harveyi infection.

Toll-like receptor (TLR) genes are the earliest reported pathogen recognition receptors (PRRs) and have been extensively studied. These genes play pivotal roles in the innate immune defense against pathogen invasion. In this study, a total of 16 tlr genes were identified and characterized in spotted sea bass (Lateolabrax maculatus). The tlr genes of spotted sea bass were classified into five subfamilies (tlr1-subfamily, tlr3-subfamily, tlr5-subfamily, tlr7-subfamily, and tlr11-subfamily) according to the phylogenetic analysis, and their annotations were confirmed by a syntenic analysis. The protein domain analysis indicated that most tlr genes had the following three major TLR protein domains: a leucine-rich repeat (LRR) domain, a transmembrane region (TM) and a Toll/interleukin-1 receptor (TIR) domain. The tlr genes in spotted sea bass were distributed in 11 of 24 chromosomes. The mRNA expression levels of 16 tlr genes in response to Vibrio harveyi infection were quantified in the head kidney. Most genes were downregulated following V. harveyi infection, while only 5 tlr genes, including tlr1-1, tlr1-2, tlr2-2, tlr5, and tlr7, were significantly upregulated. Collectively, these results help elucidate the crucial roles of tlr genes in the immune response of spotted sea bass and may supply valuable genomic resources for future studies investigating fish disease management.

Genome and transcriptome analyses providing insight into the immune response of pearl oysters after allograft and xenograft transplantations.

The immune response after allograft or xenograft transplantation in the pearl oyster is a major factor that cause its nucleus rejection and death. To determine the mechanism underlying the immune response after allograft and xenograft transplantations in the pearl oyster Pinctada fucata martensii, we constructed two sets of transcriptomes of hemocytes at different times (6 and 12 h; 1, 3, 6, 12, and 30 d) after allograft and xenograft transplantations, in which the xenografted mantle tissue was from Pinctada maxima. The transcriptomic analysis reveals many genes are involved in the immune response to transplantation, such as transient receptor potential cation channel (TRP), calmodulin (CaM), DNA replication-related genes, and sugar and lipid metabolism-related genes. The expression of these identified genes was higher in the host pearl oyster transplanted with xenograft than that by allograft. The histological analysis of the pearl sac also confirmed that many hemocytes were still gathered around the transplanted nucleus, and no pearl sac was formed in the host pearl oysters at 30 d after xenograft transplantation. The genomic analysis indicated that pearl oysters evolved many copies of genes, such as TRP, CaM, and GST, to sense and cope with the immune response after transplantation. "Ribosome" and "Cytosolic DNA-sensing pathway" were specifically induced in the xenograft group, whereas "Notch signaling pathway" specifically responded to the allograft transplantation. These results can improve our understanding of the mechanism underlying the immune response of pearl oysters after allograft and xenograft transplantations.

Genomics and immunity of the Mediterranean mussel Mytilus galloprovincialis in a changing environment.

The Mediterranean mussel (Mytilus galloprovincialis) is a marine invasive species cultured all over the world. Mussels are an appreciated resource in local aquaculture enterprises because of their robust production and resilience that translates into a reliable economic value. So far, no massive mortalities have been reported in natural or cultured populations of this species. In the last years, the knowledge about its immune system has greatly improved but there are still many questions to be answered. One of them is why mussels, with their high filtering activity, are able to be exposed to a high number of potential pathogens without getting infected and without developing an elevated inflammatory response. The sequencing of the mussel genome has revealed a very complex organization with high heterozygosity, abundance of repetitive sequences and extreme intraspecific sequence diversity among individuals, mainly in immune related genes. Among those genes, antimicrobial peptides are the most expressed gene families in mussels, highly polymorphic and with antimicrobial effect against molluscs pathogens, but also against pathogens of lower vertebrates and humans. The combination of a complex genome with the adaptation of mussel immune system to a changing environment could explain this high variability, not only in immune-related genes, but also in the functional response among individuals sampled in the same location and date.

Genome-Wide CRISPR Screening Identifies JAK1 Deficiency as a Mechanism of T-Cell Resistance.

Somatic gene mutations play a critical role in immune evasion by tumors. However, there is limited information on genes that confer immunotherapy resistance in melanoma. To answer this question, we established a whole-genome knockout B16/ovalbumin cell line by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease technology, and determined by in vivo adoptive OT-I T-cell transfer and an in vitro OT-I T-cell-killing assay that Janus kinase (JAK)1 deficiency mediates T-cell resistance via a two-step mechanism. Loss of JAK1 reduced JAK-Signal transducer and activator of transcription signaling in tumor cells-resulting in tumor resistance to the T-cell effector molecule interferon-and suppressed T-cell activation by impairing antigen presentation. These findings provide a novel method for exploring immunotherapy resistance in cancer and identify JAK1 as potential therapeutic target for melanoma treatment.

Innate immunity in the simplest animals - placozoans.

BACKGROUND: Innate immunity provides the core recognition system in animals for preventing infection, but also plays an important role in managing the relationship between an animal host and its symbiont. Most of our knowledge about innate immunity stems from a few animal model systems, but substantial variation between metazoan phyla has been revealed by comparative genomic studies. The exploration of more taxa is still needed to better understand the evolution of immunity related mechanisms. Placozoans are morphologically the simplest organized metazoans and the association between these enigmatic animals and their rickettsial endosymbionts has recently been elucidated. Our analyses of the novel placozoan nuclear genome of Trichoplax sp. H2 and its associated rickettsial endosymbiont genome clearly pointed to a mutualistic and co-evolutionary relationship. This discovery raises the question of how the placozoan holobiont manages symbiosis and, conversely, how it defends against harmful microorganisms. In this study, we examined the annotated genome of Trichoplax sp. H2 for the presence of genes involved in innate immune recognition and downstream signaling. RESULTS: A rich repertoire of genes belonging to the Toll-like and NOD-like receptor pathways, to scavenger receptors and to secreted fibrinogen-related domain genes was identified in the genome of Trichoplax sp. H2. Nevertheless, the innate immunity related pathways in placozoans deviate in several instances from well investigated vertebrates and invertebrates. While true Toll- and NOD-like receptors are absent, the presence of many genes of the downstream signaling cascade suggests at least primordial Toll-like receptor signaling in Placozoa. An abundance of scavenger receptors, fibrinogen-related domain genes and Apaf-1 genes clearly constitutes an expansion of the immunity related gene repertoire specific to Placozoa. CONCLUSIONS: The found wealth of immunity related genes present in Placozoa is surprising and quite striking in light of the extremely simple placozoan body plan and their sparse cell type makeup. Research is warranted to reveal how Placozoa utilize this immune repertoire to manage and maintain their associated microbiota as well as to fend-off pathogens.

Identification of a Transcriptionally Forward α Gene and Two υ Genes within the Pigeon (Columba livia) IgH Gene Locus.

Compared with mammals, the bird Ig genetic system relies on gene conversion to create an Ab repertoire, with inversion of the IgA-encoding gene and very few cases of Ig subclass diversification. Although gene conversion has been studied intensively, class-switch recombination, a mechanism by which the IgH C region is exchanged, has rarely been investigated in birds. In this study, based on the published genome of pigeon (Columba livia) and high-throughput transcriptome sequencing of immune-related tissues, we identified a transcriptionally forward α gene and found that the pigeon IgH gene locus is arranged as µ-α-υ1-υ2. In this article, we show that both DNA deletion and inversion may result from IgA and IgY class switching, and similar junction patterns were observed for both types of class-switch recombination. We also identified two subclasses of υ genes in pigeon, which share low sequence identity. Phylogenetic analysis suggests that divergence of the two pigeon υ genes occurred during the early stage of bird evolution. The data obtained in this study provide new insight into class-switch recombination and Ig gene evolution in birds.

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution.

The cancer immunoediting hypothesis postulates a dual role of the immune system: protecting the host by eliminating tumor cells, and shaping the tumor by editing its genome. Here, we elucidate the impact of evolutionary and immune-related forces on editing the tumor in a mouse model for hypermutated and microsatellite-instable colorectal cancer. Analyses of wild-type and immunodeficient RAG1 knockout mice transplanted with MC38 cells reveal that upregulation of checkpoint molecules and infiltration by Tregs are the major tumor escape mechanisms. Our results show that the effects of immunoediting are weak and that neutral accumulation of mutations dominates. Targeting the PD-1/PD-L1 pathway using immune checkpoint blocker effectively potentiates immunoediting. The immunoediting effects are less pronounced in the CT26 cell line, a non-hypermutated/microsatellite-instable model. Our study demonstrates that neutral evolution is another force that contributes to sculpting the tumor and that checkpoint blockade effectively enforces T-cell-dependent immunoselective pressure.

Germline Genome Protection on an Evolutionary Treadmill.

Preservation of genome integrity is a conserved, essential function, yet genome defense machinery evolves rapidly. In this issue of Developmental Cell, Parhad et al. (2017) harness an evolution-guided approach to define the genetic determinants of genome defense and to reveal the molecular and cellular mechanisms shaped by adaptive evolution.

Instructed subsets or agile swarms: how T-helper cells may adaptively counter uncertainty with variability and plasticity.

Over recent years, extensive phenotypic variability and plasticity have been revealed among the T-helper cells of the mammalian adaptive immune system, even within clonal lineages of identical antigen specificity. This challenges the conventional view that T-helper cells assort into functionally distinct subsets following differential instruction by the innate immune system. We argue that the adaptive value of coping with uncertainty can reconcile the 'instructed subset' framework with T-helper variability and plasticity. However, we also suggest that T-helper cells might better be understood as agile swarms engaged in collective decision-making to promote host fitness. With rigorous testing, the 'agile swarms' framework may illuminate how variable and plastic individual T-helper cells interact to create coherent immunity.

Genome-wide characterization of Toll-like receptor gene family in common carp (Cyprinus carpio) and their involvement in host immune response to Aeromonas hydrophila infection.

The Toll-like receptor (TLR) gene family is a class of conserved pattern recognition receptors, which play an essential role in innate immunity providing efficient defense against invading microbial pathogens. Although TLRs have been extensively characterized in both invertebrates and vertebrates, a comprehensive analysis of TLRs in common carp is lacking. In the present study, we have conducted the first genome-wide systematic analysis of common carp (Cyprinus carpio) TLR genes. A set of 27 common carp TLR genes were identified and characterized. Sequence similarity analysis, functional domain prediction and phylogenetic analysis supported their annotation and orthologies. By examining the gene copy number of TLR genes across several vertebrates, gene duplications and losses were observed. The expression patterns of TLR genes were examined during early developmental stages and in various healthy tissues, and the results showed that TLR genes were ubiquitously expressed, indicating a likely role in maintaining homeostasis. Moreover, the differential expression of TLRs was examined after Aeromons hydrophila infection, and showed that most TLR genes were induced, with diverse patterns. TLR1, TLR4-2, TLR4-3, TLR22-2, TLR22-3 were significantly up-regulated at minimum one timepoint, whereas TLR2-1, TLR4-1, TLR7-1 and TLR7-2 were significantly down-regulated. Our results suggested that TLR genes play critical roles in the common carp immune response. Collectively, our findings provide fundamental genomic resources for future studies on fish disease management and disease-resistance selective breeding strategy development.