A genome-wide screen indicates correlation between differentiation and expression of metabolism related genes

Identification of autophagy-related genes in intestinal ischemia-reperfusion injury and their role in immune infiltration

BACKGROUND

Intestinal ischemia-reperfusion (II/R) injury is a serious condition characterized by high morbidity and mortality rates. Research has shown that II/R injury is closely linked to autophagy and immune dysregulation. This study aims to investigate the potential correlations between autophagy-related genes and infiltrating immune cells in II/R injury.

METHODS

GSE96733, GSE37013, and autophagy-related genes were obtained from the Gene Expression Omnibus (GEO) and the Human Autophagy Database, respectively. Subsequently, the biological functions of the differentially expressed genes (DEGs) were explored through DEGs analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and Gene Ontology (GO) analysis. Using R software, human autophagy-related genes were converted to their mouse homologous autophagy-related genes (ARGs). The DEGs were then intersected with ARGs to obtain differentially expressed autophagy-related genes (DEARGs). To identify hub genes, protein-protein interaction (PPI) network analysis, Lasso regression, and random forest methods were employed. A nomogram model was constructed to assess its diagnostic value. Following this, immune infiltration analysis was performed to evaluate the potential correlation between Hub genes and immune cell infiltration. Additionally, a hub gene-related network was constructed, and potential drugs targeting hub genes for the treatment of II/R injury were predicted. Finally, the expression levels of hub genes in a mouse model of II/R injury were validated through dataset verification and quantitative real-time polymerase chain reaction (qRT-PCR).

RESULTS

Our analysis identified 11 DEARGs. Among these, 5 DEARGs (Myc, Hif1a, Zfyve1, Sqstm1, and Gabarapl1) were identified as hub genes. The nomogram model demonstrated excellent diagnostic value. Immune cell infiltration analysis indicated that these 5 hub genes are closely associated with dendritic cells and M2.Macrophage. Furthermore, the regulatory network illustrated a complex relationship between microRNAs (miRNAs) and the hub genes. Additionally, trigonelline and niacinamide were predicted as potential therapeutic agents for II/R injury. In both dataset validation and qRT-PCR validation, the four hub genes (Myc, Hif1a, Sqstm1, and Gabarapl1) showed consistency with the results of the bioinformatics analysis.

CONCLUSION

Myc, Hif1a, Sqstm1, and Gabarapl1 have been identified as ARGs closely associated with immune infiltration in II/R injury. These hub genes may represent potential therapeutic targets for II/R injury.

Transcriptomic analysis of ileal adaptations and growth responses in growing hens supplemented with alanyl-glutamine dipeptide

The growing phase of laying hens is crucial for growth and development due to its direct impact on their productivity during laying phase. During initial growth phase, intestinal tract undergoes rapid development which requires plenty of nutrients to help laying hens grow and mature. This study investigated the effect of Alanyl-Glutamine (Aln-Gln) levels on growth performance, ileal morphology and transcriptomic analysis of growing Hy-line brown hens. A total of 480 day old Hy-line brown chicks having similar body weight (BW) were randomly divided to be fed diets having 0%, 0.1%, 0.2% and 0.3% Aln-Gln for 6-wks (8 replicates/group, 15 birds/replicate). One bird from every pen was slaughtered and morphological parameters of ileum were evaluated. Results taken on day 42 revealed an improved average daily gain (ADG), final body weight (FBW) and feed-to-gain ratio (F/G) in the birds that consumed 0.2% and 0.3% Aln-Gln supplemented diet (P < 0.05). Ileal morphological assays showed that villus height, villus width and villus to crypts ratio (V/C) were significantly increased at 42 days of age in birds fed diets with 0.2% Aln-Gln (P<0.05). The RNA sequencing (RNA-Seq) was executed to identify differentially expressed genes (DEGs) among groups that found 2265 DEGs (1256 up-regulated; 1009 down-regulated) in ileum tissue. According to the Kyoto Encyclopedia of Genes (KEGG) and Genomic Pathway Enrichment Analysis, majority of DEGs indicated change in metabolic pathways. Genes related to growth factors, intestinal morphology and protein metabolism were up-regulated in test groups as compared to control group. In conclusion, addition of Aln-Gln to the diet improved growth performance and ileum development in growing hens; transcriptomic analysis revealed up-regulation of genes related to growth and intestinal morphology.

Single cell RNA-sequencing and RNA-tomography of the avian embryo extending body axis

Introduction: Vertebrate body axis formation initiates during gastrulation and continues within the tail bud at the posterior end of the embryo. Major structures in the trunk are paired somites, which generate the musculoskeletal system, the spinal cord-forming part of the central nervous system, and the notochord, with important patterning functions. The specification of these different cell lineages by key signalling pathways and transcription factors is essential, however, a global map of cell types and expressed genes in the avian trunk is missing. Methods: Here we use high-throughput sequencing approaches to generate a molecular map of the emerging trunk and tailbud in the chick embryo. Results and Discussion: Single cell RNA-sequencing (scRNA-seq) identifies discrete cell lineages including somites, neural tube, neural crest, lateral plate mesoderm, ectoderm, endothelial and blood progenitors. In addition, RNA-seq of sequential tissue sections (RNA-tomography) provides a spatially resolved, genome-wide expression dataset for the avian tailbud and emerging body, comparable to other model systems. Combining the single cell and RNA-tomography datasets, we identify spatially restricted genes, focusing on somites and early myoblasts. Thus, this high-resolution transcriptome map incorporating cell types in the embryonic trunk can expose molecular pathways involved in body axis development.

CNKSR2, a downstream mediator of retinoic acid signaling, modulates the Ras/Raf/MEK pathway to regulate patterning and invagination of the chick forebrain roof plate

During embryonic development, the forebrain roof plate undergoes invagination, leading to separation of the cerebral hemispheres. Any defects in this process, in humans, lead to middle interhemispheric holoprosencephaly (MIH-HPE). In this study, we have identified a previously unreported downstream mediator of retinoic acid (RA) signaling, CNKSR2, which is expressed in the forebrain roof plate in the chick embryo. Knockdown of CNKSR2 affects invagination, cell proliferation and patterning of the roof plate, similar to the phenotypes observed upon inhibition of RA signaling. We further demonstrate that CNKSR2 functions by modulating the Ras/Raf/MEK signaling. This appears to be crucial for patterning of the forebrain roof plate and its subsequent invagination, leading to the formation of the cerebral hemispheres. Thus, a set of novel molecular players have been identified that regulate the morphogenesis of the avian forebrain.

The Role of Maternal Thyroid Hormones in Avian Embryonic Development

During avian embryonic development, thyroid hormones (THs) coordinate the expression of a multitude of genes thereby ensuring that the correct sequence of cell proliferation, differentiation and maturation is followed in each tissue and organ. Although THs are needed from the start of development, the embryonic thyroid gland only matures around mid-incubation in precocial birds and around hatching in altricial species. Therefore, maternal THs deposited in the egg yolk play an essential role in embryonic development. They are taken up by the embryo throughout its development, from the first day till hatching, and expression of TH regulators such as distributor proteins, transporters, and deiodinases in the yolk sac membrane provide the tools for selective metabolism and transport starting from this level. TH receptors and regulators of local TH availability are expressed in avian embryos in a dynamic and tissue/cell-specific pattern from the first stages studied, as shown in detail in chicken. Maternal hyperthyroidism via TH supplementation as well as injection of THs into the egg yolk increase TH content in embryonic tissues while induction of maternal hypothyroidism by goitrogen treatment results in a decrease. Both increase and decrease of maternal TH availability were shown to alter gene expression in early chicken embryos. Knockdown of the specific TH transporter monocarboxylate transporter 8 at early stages in chicken cerebellum, optic tectum, or retina allowed to reduce local TH availability, interfering with gene expression and confirming that development of the central nervous system (CNS) is highly dependent on maternal THs. While some of the effects on cell proliferation, migration and differentiation seem to be transient, others result in persistent defects in CNS structure. In addition, a number of studies in both precocial and altricial birds showed that injection of THs into the yolk at the start of incubation influences a number of parameters in posthatch performance and fitness. In conclusion, the data presently available clearly indicate that maternal THs play an important role in avian embryonic development, but how exactly their influence on cellular and molecular processes in the embryo is linked to posthatch fitness needs to be further explored.

A glycolysis-based ten-gene signature correlates with the clinical outcome, molecular subtype and IDH1 mutation in glioblastoma

Reprogrammed metabolism is a hallmark of cancer. Glioblastoma (GBM) tumor cells predominantly utilize aerobic glycolysis for the biogenesis of energy and intermediate nutrients. However, in GBM, the clinical significance of glycolysis and its underlying relations with the molecular features such as IDH1 mutation and subtype have not been elucidated yet. Herein, based on glioma datasets including TCGA (The Cancer Genome Atlas), REMBRANDT (Repository for Molecular Brain Neoplasia Data) and GSE16011, we established a glycolytic gene expression signature score (GGESS) by incorporating ten glycolytic genes. Then we performed survival analyses and investigated the correlations between GGESS and IDH1 mutation as well as the molecular subtypes in GBMs. The results showed that GGESS independently predicted unfavorable prognosis and poor response to chemotherapy of GBM patients. Notably, GGESS was high in GBMs of mesenchymal subtype but low in IDH1-mutant GBMs. Furthermore, we found that the promoter regions of tumor-promoting glycolytic genes were hypermethylated in IDH1-mutant GBMs. Finally, we found that high GGESS also predicted poor prognosis and poor response to chemotherapy when investigating IDH1-wildtype GBM patients only. Collectively, glycolysis represented by GGESS predicts unfavorable clinical outcome of GBM patients and is closely associated with mesenchymal subtype and IDH1 mutation in GBMs.

Precise spatial restriction of BMP signaling is essential for articular cartilage differentiation

The articular cartilage, which lines the joints of the limb skeleton, is distinct from the adjoining transient cartilage, and yet, it differentiates as a unique population within a contiguous cartilage element. Current literature suggests that articular cartilage and transient cartilage originate from different cell populations. Using a combination of lineage tracing and pulse-chase of actively proliferating chondrocytes, we here demonstrate that, similar to transient cartilage, embryonic articular cartilage cells also originate from the proliferating chondrocytes situated near the distal ends of skeletal anlagen. We show that nascent cartilage cells are capable of differentiating as articular or transient cartilage, depending on exposure to Wnt or BMP signaling, respectively. The spatial organization of the articular cartilage results from a band of Nog-expressing cells, which insulates these proliferating chondrocytes from BMP signaling and allows them to differentiate as articular cartilage under the influence of Wnt signaling emanating from the interzone. Through experiments conducted in both chick and mouse embryos we have developed a model explaining simultaneous growth and differentiation of transient and articular cartilage in juxtaposed domains.

Spatio-temporally restricted expression of cell adhesion molecules during chicken embryonic development

Differential cell adhesive properties are known to regulate important developmental events like cell sorting and cell migration. Cadherins and protocadherins are known to mediate these cellular properties. Though a large number of such molecules have been predicted, their characterization in terms of interactive properties and cellular roles is far from being comprehensive. To narrow down the tissue context and collect correlative evidence for tissue specific roles of these molecules, we have carried out whole-mount in situ hybridization based RNA expression study for seven cadherins and four protocadherins. In developing chicken embryos (HH stages 18, 22, 26 and 28) cadherins and protocadherins are expressed in tissue restricted manner. This expression study elucidates precise expression domains of cell adhesion molecules in the context of developing embryos. These expression domains provide spatio-temporal context in which the function of these genes can be further explored.