MHC Genes Research Articles

A review of the genetics of type I diabetes

Type I diabetes susceptibility is caused by both environmental and genetic factors, the latter comprising approximately half of the total risk as evidenced by the fact that identical twins have approximately 50% concordance, suggesting 50% of the disease risk is environmental. The human leukocyte antigen (HLA) genes account for approximately half of the genetic risk, as demonstrated by the concordance between HLA identical siblings. Because environmental and genetic differences vary between racial groups, the incidence of type 1 diabetes (TID) differs across the world, being highest in Caucasians. Recent GWAS (genome-wide association studies) studies have suggested there may be up to 50 genomic regions contributing to the non-major histocompatibility complex (MHC) genetic risk contribution. This review presents and discusses the latest research on the MHC and non-MHC genes. Only the non-MHC regions, which have been confirmed in multiple studies and which are considered definite regions of genetic susceptibility, are included in the review.

Loss of heterozygosity impacts MHC expression on the immune microenvironment in CDK12-mutated prostate cancer

BackgroundIn prostate cancer (PCa), well-established biomarkers such as MSI status, TMB high, and PDL1 expression serve as reliable indicators for favorable responses to immunotherapy. Recent studies have suggested a potential association between CDK12 mutations and immunotherapy response; however, the precise mechanisms through which CDK12 mutation may influence immune response remain unclear. A plausible explanation for immune evasion in this subset of CDK12-mutated PCa may be reduced MHC expression.ResultsUsing genomic data of CDK12-mutated PCa from 48 primary and 10 metastatic public domain samples and a retrospective cohort of 53 low-intermediate risk primary PCa, we investigated how variation in the expression of the MHC genes affected associated downstream pathways. We classified the patients based on gene expression quartiles of MHC-related genes and categorized the tumors into “High” and “Low” expression levels. CDK12-mutated tumors with higher MHC-expressed pathways were associated with the immune system and elevated PD-L1, IDO1, and TIM3 expression. Consistent with an inflamed tumor microenvironment (TME) phenotype, digital cytometric analyses identified increased CD8 + T cells, B cells, γδ T cells, and M1 Macrophages in this group. In contrast, CDK12-mutated tumors with lower MHC expression exhibited features consistent with an immune cold TME phenotype and immunoediting. Significantly, low MHC expression was also associated with chromosome 6 loss of heterozygosity (LOH) affecting the entire HLA gene cluster. These LOH events were observed in both major clonal and minor subclonal populations of tumor cells. In our retrospective study of 53 primary PCa cases from this Institute, we found a 4% (2/53) prevalence of CDK12 mutations, with the confirmation of this defect in one tumor through Sanger sequencing. In keeping with our analysis of public domain data this tumor exhibited low MHC expression at the RNA level. More extensive studies will be required to determine whether reduced HLA expression is generally associated with primary tumors or is a specific feature of CDK12 mutated PCa.ConclusionsThese data show that analysis of CDK12 alteration, in the context of MHC expression levels, and LOH status may offer improved predictive value for outcomes in this potentially actionable genomic subgroup of PCa. In addition, these findings highlight the need to explore novel therapeutic strategies to enhance MHC expression in CDK12-defective PCa to improve immunotherapy responses.

Peripheral blood transcriptomic analysis identifies potential inflammation and immune signatures for central retinal artery occlusion

Central retinal artery occlusion (CRAO) is an acute retinal ischaemic disease, but early diagnosis is challenging due to a lack of biomarkers. Blood samples were collected from CRAO patients and cataract patients. Gene expression profiles were distinct between arterial/venous CRAO blood (A–V group) and venous CRAO/control blood (V–C group) samples. Differentially expressed genes (DEGs) were subjected to GO and KEGG enrichment analyses. Hub genes were identified by Cytoscape and used to predict gene interactions via GeneMANIA. Immune cell infiltration was analysed by CIBERSORT. More than 1400 DEGs were identified in the A–V group and 112 DEGs in the V–C group compared to controls. The DEGs in both groups were enriched in the ribosome pathway, and those in the V–C group were also enriched in antigen processing/MHC pathways. Network analysis identified ribosomal proteins (RPS2 and RPS5) as the core genes of the A–V group and MHC genes (HLA-F) as the core genes of the V–C group. Coexpression networks showed ribosomal involvement in both groups, with additional immune responses in the V–C group. Immune cell analysis indicated increased numbers of neutrophils and T cells. Ribosomal and MHC-related genes were identified as potential CRAO biomarkers, providing research directions for prevention, diagnosis, treatment and prognosis.

Abstract 6575: Selective targeting of integrins αVβ8 and αVβ1 within the dynamic ecosystem of pancreatic cancer to improve the overall anti-tumor response

Abstract Pancreatic ductal adenocarcinoma (PDA) has a 5-year survival of less than 10% and remains the 3rd leading cause of cancer-related death in Western societies. New treatment options are urgently needed. TGF-β promotes stromal cell reprogramming, immunosuppression, and fibrinogenesis in cancers, including PDA. Integrins αVβ8 and αVβ1 are important activators of TGF-β signalling. Selective integrin blockade has recently emerged as a promising therapeutic approach to address TGF-β-mediated immunotherapy resistance and improve anti-tumour response across cancer models. The purpose of this study was to assess the in vivo efficacy of small molecule inhibitor PLN-104, a selective inhibitor of αVβ1, and PLN-101095, a dual inhibitor of αVβ8 and αVβ1, in well-annotated models of advanced PDA. We determined the preclinical efficacy and detailed anti-stromal effect of PLN-101095 inhibitor in genetically defined and patient-derived PDA models, including clinically relevant combinations with standard of care (SoC) chemotherapy and anti-programmed death receptor-1 antibody (anti-mPD-1). Mechanistic assessment of alterations in tumour cell-stromal cell crosstalk was performed using comprehensive transcriptomics and immunofluorescence approaches. Dual targeting of αVβ8 and αVβ1 with PLN-101095 in the syngeneic LSL-KrasG12D/+;LSL-Trp53R172H/+;Pdx1-Cre (KPC) model effectively reduced tumour growth by 45% in comparison to the vehicle, and significantly delayed disease progression in vivo. Single-cell analysis of PLN-101095-treated KPC pancreatic tumours revealed a positive reprogramming of malignant cells from a mesenchymal to a more epithelial-like state. This effect was further associated with an upregulation of MHC type I/II markers and corresponding downregulation of pro-metastatic factors across diverse cancer sub-populations. Additionally, combining PLN-101095 with anti-mPD-1 antibody further improved survival in this aggressive model of metastatic PDA. In a second syngeneic model, Pan02, PLN-101095 in combination with anti-mPD-1 antibody significantly reduced tumour growth, while increasing CD8+ lymphocyte infiltration. The combination of PLN-101095 with Anti-PD1 increased MHC and IFN gene expression. Finally, utilizing patient-derived models of metastatic PDA revealed that both PLN-104 and PLN-101095 significantly blocked tumour growth, improved the response to SoC chemotherapy Gemcitabine/Abraxane, and reduced metastatic spread to distant sites. In conclusion, these data provide scientific rationale for the design of future PLN-101095 and SoC chemotherapy as well as immunotherapy combinations in pancreatic cancer, with Phase I first-in-human oncology studies with PLN-101095 plus ICB already underway. Citation Format: Dannielle Upton, Diego Chacon Fajardo, Sofia Omari, Sean Porazinski, Benjamin McLean, Diana Schuhmacher, Aji Istadi, Australian Pancreatic Cancer Genome Initiative, Vishal Kothari, Darren Finkelstein, Tim Machajewski, Fernando Rock, Scott Turner, Marina Pajic. Selective targeting of integrins αVβ8 and αVβ1 within the dynamic ecosystem of pancreatic cancer to improve the overall anti-tumor response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6575.

Abstract 180: LINC00261 is functionally linked to tumor DNA mutational burden and tumor immune microenvironment composition in lung adenocarcinoma

Abstract Immunotherapy has emerged as a breakthrough in the improvement of survival outcomes for lung adenocarcinoma (LUAD), however effective response requires the combination of blocking inhibitory signals on the tumor surface and antigen presentation to the tumor surface for proper immune recognition. Several commercially available and robust methods exist for identification of tumors displaying immune-inhibitory surface receptors, such as PD-L1, however it is currently difficult to predict effectiveness of antigen presentation on the cell surface. To address this, we utilized clinical and next-generation sequencing data from The Cancer Genome Atlas (TCGA) to identify gene signatures that are correlated to tumor mutational burden (TMB) within cancers of epithelial origins as a surrogate for neoantigen signatures. We identified LINC00261 as a top gene correlated to TMB, whose expression activates DNA damage response pathways in vitro along with resistance to cisplatin. LINC00261 expression was also significantly correlated to MHC class I and II genes involved in endogenous neoantigen presentation expression within the TCGA-LUAD cohort. This relationship was confirmed in vitro through ectopic reintroduction of LINC00261 for key MHC class II presentation genes. Interferon gamma-induced MHC gene activation in vitro was also able to induce endogenous expression of LINC00261. Staining of primary human lung cancer sections suggested that loss of LINC00261 is associated with an immunosuppressive tumor microenvironment. Taken together, our results suggest there is a mechanistic relationship in the silencing of LINC00261 in LUAD and compromised DNA repair, accumulation of mutations, and reduced antitumor immune response. Citation Format: Jonathan Castillo, Tianchun Xue, Mayela Norwood, Samantha Joseph, Alan L. Epstein, William D. Wallace, Anthony W. Kim, Crystal N. Marconett. LINC00261 is functionally linked to tumor DNA mutational burden and tumor immune microenvironment composition in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 180.

CELSR3 is a prognostic marker in HNSCC and correlates with immune cell infiltration in the tumor microenvironment

PurposeTo look at the diagnostic value of the CELSR receptor 3 (CELSR3) gene in head and neck squamous cell carcinoma (HNSCC) and its effect on tumor immune invasion, which is important for enhancing HNSCC treatment.MethodsSeveral bioinformatics tools were employed to investigate CELSR3’s putative oncogenic pathway in HNSCC, and datasets from The Tumor Genome Atlas (TCGA), Tumor Immune Estimation Resource (TIMER), Gene Expression Profile Interaction Analysis (GEPIA) and LinkedOmics were extracted and evaluated. CELSR3 has been linked to tumor immune cell infiltration, immunological checkpoints, and immune-related genes. CELSR3’s putative roles were investigated using Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and pathway enrichment analysis. The expression level of CELSR3 in HNSCC tissues and cells was detected by RT-qPCR. The effects of CELSR3 on proliferation of HNSCC cells were detected by CCK-8 assay.ResultsCELSR3 was shown to be expressed differently in different types of cancer and normal tissues. CELSR3 gene expression was linked to pN-stage and pM-stage. Patients with high CELSR3 expression also have a well prognosis. CELSR3 expression was found to be an independent predictive factor for HNSCC in both univariate and multivariate Cox regression analyses. We discovered the functional network of CELSR3 in HNSCC using GO and KEGG analysis. CELSR3 expression levels were found to be favorably associated with immune cell infiltration levels. Furthermore, CELSR3 expression levels were significantly correlated with the expression levels of many immune molecules, such as MHC genes, immune activation genes, chemokine receptors, and chemokines. CELSR3 is highly expressed in HNSCC tissues and cells. CELSR3 overexpression significantly inhibited the proliferation of HNSCC cells. CELSR3 expression may affect the immune microenvironment and, as a result, the prognosis of HNSCC.ConclusionCELSR3 expression is elevated in HNSCC tumor tissues, and high CELSR3 expression is associated with well prognosis, which inhibited the proliferation of NHSCC cells. CELSR3 has the potential to influence tumor formation by controlling tumor-infiltrating cells in the tumor microenvironment (TME). As a result, CELSR3 may have diagnostic significance in HNSCC.

Phenome-wide Mendelian randomization analysis reveals multiple health comorbidities of coeliac disease

Coeliac disease (CeD) has been associated with a broad range of diseases in observational data; however, whether these associations are causal remains undetermined. We conducted a phenome-wide Mendelian randomization analysis (MR-PheWAS) to investigate the comorbidities of CeD. Single nucleotide polymorphisms (SNPs) associated with CeD at the genome-wide significance threshold and without linkage disequilibrium (R2 <0.001) were selected from a genome-wide association study including 12,041 CeD cases as the instrumental variables. We first constructed a polygenic risk score for CeD and estimated its associations with 1060 unique clinical outcomes in the UK Biobank study (N=385,917). We then used two-sample MR analysis to replicate the identified associations using data from the FinnGen study (N=377,277). We performed a secondary analysis using a genetic instrument without extended MHC gene SNPs. Genetic liability to CeD was associated with 68 clinical outcomes in the UK Biobank, and 38 of the associations were replicated in the FinnGen study. Genetic liability to CeD was associated with a higher risk of several autoimmune diseases (type 1 diabetes and its complications, Graves' disease, Sjögren syndrome, chronic hepatitis, systemic and cutaneous lupus erythematosus, and sarcoidosis), non-Hodgkin's lymphoma, and osteoporosis and a lower risk of prostate diseases. The associations for type 1 diabetes and non-Hodgkin's lymphoma attenuated when excluding SNPs in the MHC region, indicating shared genetic aetiology. This study uncovers multiple clinical outcomes associated with genetic liability to CeD, which suggests the necessity of comorbidity monitoring among this population. This project was funded by Karolinska Institutet and the Swedish Research Council.

Multi-omics and pathway analyses of genome-wide associations implicate regulation and immunity in verbal declarative memory performance

BackgroundUncovering the functional relevance underlying verbal declarative memory (VDM) genome-wide association study (GWAS) results may facilitate the development of interventions to reduce age-related memory decline and dementia.MethodsWe performed multi-omics and pathway enrichment analyses of paragraph (PAR-dr) and word list (WL-dr) delayed recall GWAS from 29,076 older non-demented individuals of European descent. We assessed the relationship between single-variant associations and expression quantitative trait loci (eQTLs) in 44 tissues and methylation quantitative trait loci (meQTLs) in the hippocampus. We determined the relationship between gene associations and transcript levels in 53 tissues, annotation as immune genes, and regulation by transcription factors (TFs) and microRNAs. To identify significant pathways, gene set enrichment was tested in each cohort and meta-analyzed across cohorts. Analyses of differential expression in brain tissues were conducted for pathway component genes.ResultsThe single-variant associations of VDM showed significant linkage disequilibrium (LD) with eQTLs across all tissues and meQTLs within the hippocampus. Stronger WL-dr gene associations correlated with reduced expression in four brain tissues, including the hippocampus. More robust PAR-dr and/or WL-dr gene associations were intricately linked with immunity and were influenced by 31 TFs and 2 microRNAs. Six pathways, including type I diabetes, exhibited significant associations with both PAR-dr and WL-dr. These pathways included fifteen MHC genes intricately linked to VDM performance, showing diverse expression patterns based on cognitive status in brain tissues.ConclusionsVDM genetic associations influence expression regulation via eQTLs and meQTLs. The involvement of TFs, microRNAs, MHC genes, and immune-related pathways contributes to VDM performance in older individuals.

Abstract A016: LINC00261 is functionally linked to tumor DNA mutational burden and tumor immune microenvironment composition in lung adenocarcinoma

Abstract Immunotherapy has emerged as a breakthrough in the improvement of survival outcomes for lung adenocarcinoma (LUAD), however effective response requires the combination of blocking inhibitory signals on the tumor surface and antigen presentation to the tumor surface for proper immune recognition. Several commercially available and robust methods exist for identification of tumors displaying immune-inhibitory surface receptors, such as PD-L1, however it is currently difficult to predict effectiveness of antigen presentation on the cell surface. To address this, we utilized clinical and next-generation sequencing data from The Cancer Genome Atlas (TCGA) to identify gene signatures that are correlated to tumor mutational burden (TMB) within cancers of epithelial origins as a surrogate for neoantigen signatures. We identified LINC00261 as a top gene correlated to TMB, whose expression activates DNA damage response pathways in vitro along with resistance to cisplatin. LINC00261 expression was also significantly correlated to MHC class I and II genes involved in endogenous neoantigen presentation expression within the TCGA-LUAD cohort. This relationship was confirmed in vitro through ectopic reintroduction of LINC00261 for key MHC class II presentation genes. Interferon gamma-induced MHC gene activation in vitro was also able to induce endogenous expression of LINC00261. The staining of primary human lung cancer sections suggested that loss of LINC00261 is associated with an immunosuppressive tumor microenvironment. Taken together, our results suggest there is a mechanistic relationship in the silencing of LINC00261 in LUAD and compromised DNA repair, accumulation of mutations, and reduced antitumor immune response. Citation Format: Jonathan Castillo, Tianchun Xue, Mayela Norwood, Samantha Joseph, Alan L. Epstein, W. Dean Wallace, Anthony W. Kim, Crystal N. Marconett. LINC00261 is functionally linked to tumor DNA mutational burden and tumor immune microenvironment composition in lung adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr A016.

The Potential Impact of HNRNPA2B1 on Human Cancers Prognosis and Immune Microenvironment.

HNRNPA2B1 is a member of the HNRNP family, which is associated with telomere function, mRNA translation, and splicing, and plays an important role in tumor development. To date, there have been no pan-cancer studies of HNRNPA2B1, particularly within the TME. Therefore, we conducted a pan-cancer analysis of HNRNPA2B1 using TCGA data. Based on datasets from TCGA, TARGET, Genotype-Tissue Expression, and Human Protein Atlas, we employed a range of bioinformatics approaches to explore the potential oncogenic role of HNRNPA2B1. This included analyzing the association of HNRNPA2B1 expression with prognosis, tumor mutation burden (TMB), microsatellite instability (MSI), immune response, and immune cell infiltration of individual tumors. We further validated the bioinformatic findings using immunohistochemistry techniques. HNRNPA2B1 was found to be differentially expressed across most tumor types in TCGA's pan-cancer database and was predictive of poorer clinical staging and survival status. HNRNPA2B1 expression was also closely linked to TMB, MSI, tumor stemness, and chemotherapy response. HNRNPA2B1 plays a significant role in the TME and is involved in the regulation of novel immunotherapies. Its expression is significantly associated with the infiltration of macrophages, dendritic cells, NK cells, and T cells. Furthermore, HNRNPA2B1 is closely associated with immune checkpoints, immune-stimulatory genes, immune-inhibitory genes, MHC genes, chemokines, and chemokine receptors. We performed a comprehensive evaluation of HNRNPA2B1, revealing its potential role as a prognostic indicator for patients and its immunomodulatory functions.

AmpliSAS and AmpliHLA: Web Server and Local Tools for MHC Typing of Non-model Species and Human Using NGS Data.

AmpliSAS and AmpliHLA are tools for automatic genotyping of MHC genes from high-throughput sequencing data. AmpliSAS is designed specifically to analyze amplicon sequencing data from non-model species and it is able to perform de novo genotyping without any previous knowledge of the reference alleles. AmpliHLA is a human specific version; it performs HLA typing by comparing sequenced variants against human reference alleles from the IMGT/HLA database. Both tools are available in AmpliSAT web-server as well as scripts for local/server installation. Here we describe the installation and deployment of AmpliSAS and AmpliHLA Perl scripts and dependencies on a local or a server computer. We will show how to run them in the command line using as examples four genotyping protocols: the first two use amplicon sequencing data to genotype the MHC genes of a passerine bird and human respectively; the third and fourth present the HLA typing of a human cell line starting from RNA and exome sequencing data respectively.

Characterization of the polymorphisms of dog MHC genes and intra- and interbreed DLA haplotype diversity

Characterization of the polymorphisms of dog MHC genes and intra- and interbreed DLA haplotype diversity

HLA-DQ8 Supports Development of Insulitis Mediated by Insulin-Reactive Human TCR-Transgenic T Cells in Nonobese Diabetic Mice.

In an effort to improve HLA-"humanized" mouse models for type 1 diabetes (T1D) therapy development, we previously generated directly in the NOD strain CRISPR/Cas9-mediated deletions of various combinations of murine MHC genes. These new models improved upon previously available platforms by retaining β2-microglobulin functionality in FcRn and nonclassical MHC class I formation. As proof of concept, we generated H2-Db/H2-Kd double knockout NOD mice expressing human HLA-A*0201 or HLA-B*3906 class I variants that both supported autoreactive diabetogenic CD8+ T cell responses. In this follow-up work, we now describe the creation of 10 new NOD-based mouse models expressing various combinations of HLA genes with and without chimeric transgenic human TCRs reactive to proinsulin/insulin. The new TCR-transgenic models develop differing levels of insulitis mediated by HLA-DQ8-restricted insulin-reactive T cells. Additionally, these transgenic T cells can transfer insulitis to newly developed NSG mice lacking classical murine MHC molecules, but expressing HLA-DQ8. These new models can be used to test potential therapeutics for a possible capacity to reduce islet infiltration or change the phenotype of T cells expressing type 1 diabetes patient-derived β cell autoantigen-specific TCRs.

Chromatin accessibility dynamics in colorectal cancer liver metastasis: Uncovering the liver tropism at single cell resolution

Tumor metastasis causes over 90% of cancer related death and no currently available therapies target it. However, there is limited understanding regarding the epigenetic regulation of genes during this complex process. Here by integrating single-cell ATAC-seq (scATAC-seq), single-cell RNA-seq (scRNA-seq), microarray, bulk RNA-seq, immunohistochemistry (IHC) staining, as well as proteomics datasets from paired primary and liver metastatic colorectal cancer (CRC) patient-derived xenograft (PDX) model and patients, we discovered that liver metastatic CRC cells lose their colon-specific chromatin accessible sites yet gain liver-specific ones. Importantly, we observed elevated accessibility of HNF4A, a liver-specific transcription factor, in liver metastatic CRC cells. Subsequently, we performed clustering analysis of liver metastatic CRC cells together with cells involved in liver development, revealing significant heterogeneity among the liver metastatic CRC cells. Over 50% of the liver metastatic CRC cells exhibited characteristics similar to those of erythroid progenitors and hepatocytes, showing increased expression of genes involved in oxidative phosphorylation and glycolysis. Moreover, our discovery further revealed that the MHC and IFN response genes in these cells exhibit moderate epigenetic activity, which is significantly associated with the low objective response rates in checkpoint blockade immunotherapy. Our findings uncovered the critical roles of HNF4A and the cell populations within liver metastatic CRC cells might serve as crucial therapeutic targets for addressing liver metastasis and improving the immunotherapy response in patients with CRC.

Assessing micro-macroparasite selective pressures and anthropogenic disturbance as drivers of immune gene diversity in a Neotropical wild cat

Anthropogenic environmental change is reducing available habitat for wild species, providing novel selection pressures such as infectious diseases and causing species to interact in new ways. The potential for emerging infectious diseases and zoonoses at the interface between humans, domestic animals, and wild species is a key global concern. In vertebrates, diversity at the major histocompatibility complex MHC is critical to disease resilience, and its study in wild populations provides insights into eco-evolutionary dynamics that human activities alter. In natural populations, variation at MHC loci is partly maintained by balancing selection, driven by pathogenic selective pressures. We hypothesize that MHC genetic diversity differs between guigna populations inhabiting human-dominated landscapes (higher pathogen pressures) versus more natural habitats (lower pathogen pressures). We predict that MHC diversity in guignas would be highest in human-dominated landscapes compared with continuous forest habitats. We also expected to find higher MHC diversity in guignas infected with micro and macro parasites (higher parasite load) versus non infected guignas. We characterized for the first time the genetic diversity at three MHC class I and II exons in 128 wild guignas (Leopardus guigna) across their distribution range in Chile (32–46° S) and Argentina, representing landscapes with varying levels of human disturbance. We integrated MHC sequence diversity with multiple measures of anthropogenic disturbance and both micro and macro parasite infection data. We also assessed signatures of positive selection acting on MHC genes. We found significantly higher MHC class I diversity in guignas inhabiting landscapes where houses were present, and with lower percentage of vegetation cover, and also in animals with more severe cardiorespiratory helminth infection (richness and intensity) and micro-macroparasite co-infection. This comprehensive, landscape-level assessment further enhances our knowledge on the evolutionary dynamics and adaptive potential of vertebrates in the face of emerging infectious disease threats and increasing anthropogenic impacts.

Transcriptome analysis reveals modulation of differentially expressed genes in LPS-treated mouse macrophages (RAW264.7cells) by grouper (Epinephelus coioides) Epinecidin-1.

The marine antimicrobial peptide Epinecidin (Epi)-1 has been shown to exert direct antimicrobial and immunomodulatory actions in teleost, mammalian and avian organisms. For instance, Epi-1 can suppress bacterial endotoxin lipolysachcharide (LPS)-induced proinflammatory cytokines in RAW264.7 murine macrophages. However, it remains unknown how Epi-1 might broadly affect non-activated and LPS-activated macrophages. To address this question, we performed a comparative transcriptomic analysis of non-treated and LPS-treated RAW264.7cells in the presence and absence of Epi-1. Gene enrichment analysis was conducted on filtered reads, followed by GO and KEGG analyses. The results showed that Epi-1 treatment modulated pathways and genes associated with nucleoside binding, intramolecular oxidoreductase activity, GTPase activity, peptide antigen binding, GTP binding, ribonucleoside/nucleotide binding, phosphatidylinositol binding and phosphatidylinositol-4-phosphate binding. Based on the GO analysis results, we performed real-time PCR at different treatment times to compare expression levels of selected proinflammatory cytokines, anti-inflammatory cytokines, MHC, proliferation and differentiation genes. Epi-1 decreased expression of the proinflammatory cytokines, TNF-α, IL-6 and IL-1β, and it increased the anti-inflammatory cytokine TGFβ and Sytx1. MHC-associated genes, GM7030, Arfip1, Gpb11 and Gem, were induced by Epi-1, which is expected to enhance the immune response against LPS. Immunoglobulin-associated Nuggc was also upregulated by Epi-1. Finally, we found that Epi-1 downregulated the expression of host defense peptides CRAMP, Leap2 and BD3. Taken together, these findings suggest that Epi-1 treatment induces orchestrated changes in the transcriptome of LPS-stimulated RAW264.7cells.

Alternative relay regulates the adenosine triphosphatase activity of Locusta migratoria striated muscle myosin.

Locust (Locusta migratoria) has a single striated muscle myosin heavy chain (Mhc) gene, which contains 5 clusters of alternative exclusive exons and 1 differently included penultimate exon. The alternative exons of Mhc gene encode 4 distinct regions in the myosin motor domain, that is, the N-terminal SH3-like domain, one lip of the nucleotide-binding pocket, the relay, and the converter. Here, we investigated the role of the alternative regions on the motor function of locust muscle myosin. Using Sf9-baculovirus protein expression system, we expressed and purified 5 isoforms of the locust muscle myosin heavy meromyosin (HMM), including the major isoform in the thorax dorsal longitudinal flight muscle (FL1) and 4 isoforms expressed in the abdominal intersegmental muscle (AB1 to AB4). Among these 5 HMMs, FL1-HMM displayed the highest level of actin-activated adenosine triphosphatase (ATPase) activity (hereafter referred as ATPase activity). To identify the alternative region(s) responsible for the elevated ATPase activity of FL1-HMM, we produced a number of chimeras of FL1-HMM and AB4-HMM. Substitution with the relay of AB4-HMM (encoded by exon-14c) substantially decreased the ATPase activity of FL1-HMM, and conversely, the relay of FL1-HMM (encoded by exon-14a) enhanced the ATPase activity of AB4-HMM. Mutagenesis showed that the exon-14a-encoded residues Gly474 and Asn509 are responsible for the elevated ATPase activity of FL1-HMM. Those results indicate that the alternative relay encoded by exon-14a/c play a key role in regulating the ATPase activity of FL1-HMM and AB4-HMM.

Chlamydia trachomatis and the HLA involvement in the development of infection and disease: a narrative review.

CT (Chlamydia trachomatis) is among the most common pathogens leading to sexually transmitted diseases. Considering the uncertain mechanism by which HLA polymorphisms influence the CT infection, reinfection, comorbidities or evolution and because there is no consensus regarding the alleles involved in the pathogenesis of the infection, we considered necessary to perform a review to summarize the current knowledge of HLA related to CT. Pubmed was researched using key terms. Out of the 198 results found, we analyzed articles of all types which describe how the MHC, through HLA alleles, participates in the different stages of CT penetration in the body, including studies about cells or other molecules involved in the process. Almost 40% of the variation in the clinical course of CT infection depends on host genetic factors. There are haplotypes that influence the infection susceptibility/resistance, haplotypes that are involved in the recurrence of the infection, haplotypes that are related to tubal infertility, pelvic inflammatory disease development or trachoma. Antibody to Chsp60 (influenced by MHC genes) has been observed to correlate with late tissue-damaging sequelae. Toll-like receptors were found to increase the susceptibility to CT. The association of HLA-B27 creates susceptibility of reactive arthritis in the organisms infected by CT, but does not influence the carriage of CT. We identified HLA haplotypes belonging both to MHC class l and ll, which influence different stages of CT infection. Genetic risk factors still need research, especially on Caucasians. Studies are moving towards designing a safe and effective vaccine.

Curcumin loaded liposome formulation: Enhanced efficacy on performance, flesh quality, immune response with defense against Streptococcus agalactiae in Nile tilapia (Orechromis niloticus).

Application of novel trend comprising antioxidant phytogenics is aiming to minimize the stress related factors and associated diseases in intensive fish culturing. Today, the concept of exploiting and protecting natural antioxidants represents a paradigm shift for the aqua feed industry. Therefore, our principal goal targeting liposome as a novel nanocarrier for curcumin is directed to attain superior performance, fillet antioxidant stability and bacterial resistance in Nile tilapia. A total of 500 Nile tilapia fingerlings (average body weight, 10.27±0.10g) assigned into five experimental groups in 25 glass aquaria of 120L capacity at the density 20 fish/aquaria. The experimental groups were supplemented with varying doses of liposomal curcumin-NPs, LipoCur-NPs (0, 5, 15, 25 and 35mg/kg diet) were reared for 12 weeks and later Streptococcus agalactiae (S. agalactiae) challenged model was performed. Inclusion of LipoCur-NPs (25 and 35mg/kg diet) had the most prominent impact on Nile tilapia growth rate and feed conversion ratio. The immune boosting outcomes post supplementing 35mg/kg diet of LipoCur-NPs were evidenced by higher myeloperoxidase, lysozyme and total immunoglobulin levels. Even after 4 weeks frozen storage, LipoCur-NPs at the dose of 35mg/kg diet prominently increased (P < 0.05) the fillet scavenging capability for free radicals (1,1-diphenyl-2-picrylhydrazyl and 2,2'-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) with an inverse reduction in lipid peroxidation biomarker (malondialdehyde). Notably, upregulation of GSH-Px, CAT, and SOD genes in fillet of 35mg/kg LipoCur-NPs fed fish coordinated with higher T-AOC and lower oxidative markers (ROS and H2O2). Post S. agalactiae challenge, higher supplementation levels of LipoCur-NPs (35mg/kg diet) greatly attenuated the expression of its vital virulence genes (cfb, fbsA and cpsA) with higher expression of Igm, CXC-chemokine and MHC genes. Concordantly, downregulation of inflammatory markers (IL-1β, TNF-α and IL-8) and upregulation of anti-inflammatory ones (IL-10 and TGF-β) were remarkably documented. Based on these findings, the innovative curcumin loaded liposome was considered a novel multitargeting alternative not only playing an imperative role in Nile tilapia growth promotion and fillet stability upon storage, but also protecting efficiently against S. agalactiae.

The initial report of phase I trial of VG2025, a non-attenuated HSV-1 oncolytic virus expressing IL-12 and IL-15/RA payloads, in patients with advanced solid tumors.

2580 Background: VG2025 is a non-attenuated HSV-1 Oncolytic virus (OV). The wildtype neurovirulence is controlled by the Transcription and Translation Dual Regulation (TTDR) of ICP27 and ICP34.5 proteins. IL-12, IL-15, IL-15Ra payloads are controlled by tumor promoter CxCR4. The native promoter of ICP27 was replaced with a promoter for Carcinoembryonic Antigen (CEA). Here we report a first-in-human, open label, study to evaluate the safety, pharmacokinetics (PK), and biologic effects of VG2025 in patients (pts) with advanced solid tumors progressed after standard of care from China and United States. The study is actively recruiting. NCT05266612. Methods: Dose escalation follows a 3+3 design at 4 dose levels as intratumoral, and image guided injections into deep lesions on days 1 and 15 of each 28 days treatment cycle. PK and viral shedding (DNA), samples from biopsies, blood, urine, and swabs from injection site and other anatomical locations were analyzed by PCR. Changes of cytokines and lymphocyte subsets in blood were also observed as pharmacodynamic parameters. Results: As of 10 Jan 2023, 10 pts received doses of 1.0x10^8 and 2.0x10^8 PFU. 5 males and 5 females with the median age of 58 years were enrolled. 20% were PD(L)1 refractory, 20% had 2 Prior lines of therapy and 60% ≥3. The Median CEA level was 7.4. Tumor types were: 2 Duodenal Adeno Ca., 1 Pancreatic, 1 Ovarian, 1 Leiomyosarcoma, 1 Salivary Duct Ca., 1 Hepatocellular Ca (HCC), 1 Intrahepatic Cholangiocarcinoma (ICC), 1 Colorectal Ca (CRC) and 1 Colon Ca. No Dose Limiting Toxicities were observed. Any grade treatment-related AEs (TRAEs) was 70%, the most common TRAEs was fever 60%. Grade ≥3 TRAEs were 50% [3 pts had grade 4 Lymphocyte decreased (all recovered)], 1 had grade 3 COVID-19 and 1 had grade 3 nausea and vomiting. 4 pt had SAEs (2 cases of COVID-19, 1 Ascites and 1 Nausea and Vomiting). No TRAEs leading to dose reduction and treatment discontinuation. No pts had positive viral shedding. 4 pts were efficacy evaluable; ORR 25% (1 pt with ICC had confirmed PR with -45%) and DCR 100% based on RECIST v1.1. The PR pt had meaningful reductions in CEA levels. Tumor shrinkage was also observed in non-injected lesions demonstrating an abscopal effect. Nanostring analysis of paired biopsies from the PR pt demonstrate upregulation of genes for integrin signaling pathway, activation of CD8+ T cells and T cell-based immunity, upregulation of antigen-presenting MHC (HLA-DQA1 and HLA-DRB1) and chemokine receptor (CMKLR1) genes. Cellular immunity was activated by upregulation of Th1 cells, macrophage-associated genes and downregulation of Treg-associated genes. The results are consistent with the mechanism of action of VG2025. Analysis is ongoing with other subjects. Conclusions: Monotherapy activity was observed with an acceptable safety profile in heavily pretreated pts with advanced solid tumors. Clinical trial information: NCT05266612 .