Application of mRNA-Seq and Metagenomic Sequencing to Study Salmonella pullorum Infections in ChickensChao, Fan, Wu
et alInt J Mol Sci (2025) 26 (4)
Abstract: The disease caused by Salmonella pullorum has been demonstrated to exert a deleterious effect on the performance of poultry, giving rise to elevated mortality and considerable economic losses within the breeding industry. However, there is a paucity of research investigating the relationship between cecal gene expression and different isomer and Salmonella pullorum infection, and research on the relationship between intestinal microbiota and Salmonella pullorum infection is also limited. In this study, mRNA-Seq and metagenomic sequencing were performed on the cecal tissues and fresh feces of individuals who tested positive (n = 4) and negative (n = 4) for Salmonella pullorum, with the aim of exploring the chickens infected with Salmonella pullorum from two perspectives: the gene transcription level and the microbial level. The mRNA sequencing results revealed 1560 differentially expressed genes (DEGs), of which 380 genes were found to be up-regulated and 1180 genes were down-regulated. A number of genes were reported to be associated with immunity, including AQP8, SLC26A3, CBS, IFI6, DDX60, IL8L1 and IL8L2. Furthermore, a total of 1047 differentially expressed alternative splicings (DEASs) were identified through alternative splicing analysis, including CBS, SLC6A9, ILDR2, OCRL, etc. The joint analysis of DEGs and DEASs revealed 70 genes that exhibited both differentially expressed alternative splicings and differential expression, including CTNND1, TPM1, SPPL2A, etc. The results of metagenomic sequencing demonstrated that the abundances of Bacteroides, Firmicutes, and Verrucobacteria underwent a significant alteration subsequent to the infection of Salmonella pullorum. In summary, the present study conducted a preliminary exploration of the genetic basis of chickens infected with Salmonella pullorum. TPM1 and SPPL2A were found to be differentially expressed by mRNA-Seq, and differences in alternative splicing events. Furthermore, metagenomic sequencing revealed significant changes in the microbial communities of Bacteroidetes, Firmicutes, and Verrucobacteria during infection with Salmonella pullorum.
The role of the tricellular junction protein ILDR2 in glomerulopathies: Expression patterns and functional insightsSiegerist, Kliewe, Hammer
et aliScience (2024) 27 (12), 111329
Abstract: The tricellular tight junctions are crucial for the regulation of paracellular flux at tricellular junctions, where tricellulin (MARVELD2) and angulins (ILDR1, ILDR2, or LSR) are localized. The role of ILDR2 in podocytes, specialized epithelial cells in the kidney, is still unknown. We investigated the role of ILDR2 in glomeruli and its influence on blood filtration. Western blots, single-cell RNA sequencing (scRNA-seq), and superresolution microscopy showed a strong expression of ILDR2 in podocytes that colocalized with the podocyte-specific claudin CLDN5. Co-immunoprecipitation revealed that ILDR2 interacts with CLDN5. In glomerulopathies, induced by nephrotoxic serum and by desoxycorticosterone acetate (DOCA)-salt heminephrectomy, ILDR2 was strongly up-regulated. Furthermore, Ildr2 knockout mice exhibited glomerular hypertrophy and decreased podocyte density. However, they did not develop effacement of podocyte foot processes or proteinuria. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic analysis of isolated glomeruli showed an increase in matrix proteins, such as fibronectin and collagens. This suggests a protective role of ILDR2 in glomerulopathies.© 2024 The Authors.
Sublingual macrophage-associated ILDR2 contributes to immune tolerance via Treg inductionSultana, Widyagarini, Kawano
et alBiochem Biophys Res Commun (2025) 742, 151009
Abstract: The sublingual mucosa (SLM) has been used for sublingual immunotherapy (SLIT) which has the potential to induce antigen-specific immune tolerance. We previously demonstrated the CD206+ macrophages that were increased in the SLM after repeated antigen exposure. These macrophages showed high expression of the gene encoding ILDR2 (Ig-like domain-containing receptor 2), an immune checkpoint molecule. Here, we found a subpopulation of SLM CD206hi macrophages expressed cell surface ILDR2, using a newly developed monoclonal antibody that was specific to mouse ILDR2. ILDR2 expression in the CD206+ macrophages was restricted to the SLM, and the percentage of CD206hiILDR2+ macrophages increased after the repeated antigen painting. RNA-seq analysis revealed that this CD206hiILDR2+ fraction displayed downregulated expression of pro-inflammatory genes and preferentially expressed M2 macrophage related genes. This CD206hiILDR2+ fraction preferentially increased Foxp3+ regulatory T cells (Tregs) from naive CD4+ T cell coculture in vitro, and the induction of Tregs was blocked by a neutralizing anti-TGF-β antibody. Our results demonstrated that ILDR2-expressed in the SLM CD206+ macrophages contribute to immune tolerance by generating Tregs in a TGF-β dependent manner.Copyright © 2024 Elsevier Inc. All rights reserved.
Weighted single step GWAS reveals genomic regions associated with economic traits in Murrah buffaloesGeorge, Alex, Gowane
et alAnim Biotechnol (2024) 35 (1), 2319622
Abstract: The objective of the present study was to identify genomic regions influencing economic traits in Murrah buffaloes using weighted single step Genome Wide Association Analysis (WssGWAS). Data on 2000 animals, out of which 120 were genotyped using a double digest Restriction site Associated DNA (ddRAD) sequencing approach. The phenotypic data were collected from NDRI, India, on growth traits, viz., body weight at 6M (month), 12M, 18M and 24M, production traits like 305D (day) milk yield, lactation length (LL) and dry period (DP) and reproduction traits like age at first calving (AFC), calving interval (CI) and first service period (FSP). The biallelic genotypic data consisted of 49353 markers post-quality check. The heritability estimates were moderate to high, low to moderate, low for growth, production, reproduction traits, respectively. Important genomic regions explaining more than 0.5% of the total additive genetic variance explained by 30 adjacent SNPs were selected for further analysis of candidate genes. In this study, 105 genomic regions were associated with growth, 35 genomic regions with production and 42 window regions with reproduction traits. Different candidate genes were identified in these genomic regions, of which important are OSBPL8, NAP1L1 for growth, CNTNAP2 for production and ILDR2, TADA1 and POGK for reproduction traits.
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