Extracellular Matrix-receptor Interaction Research Articles

Analysis of the genetic characteristics and variations in disease-resistant grass carp based on whole-genome resequencing and transcriptome sequencing

Disease-resistant grass carp (DR-GGC) was obtained by backcrossing gynogenetic grass carp (GGC, 2n = 48, female) with common grass carp (Ctenopharyngodon idellus [GC], 2n = 48, male). The genetic constitution and the potential mutation associated with growth dominance in DR-GGC were analyzed by genomic in situ hybridization (GISH), whole-genome resequencing (WGRS) and RNA-sequencing (RNA-seq). The GISH results showed partial translocations and deletions in the chromosomes of DR-GGC compared with GC. The WGRS results demonstrated that there were numerous genetic variations between DR-GGC and its parents, among which DR-GGC had the highest genomic heterozygosity and GGC had the highest genomic purity. The RNA-seq results revealed that the differentially expressed genes (DEGs) were significantly enriched in cellular processes and immune pathways in DR-GGC and GGC compared with GC. Meanwhile, the combined analysis of WGRS and RNA-seq identified DEGs with overlapping mutation loci in DR-GGC and GGC compared with GC. These DEGs were significantly enriched in the pathways of growth, metabolism, and immunity, including cellular metabolism, biosynthesis, glycolysis/gluconeogenesis, and extra cellular matrix (ECM) receptor interactions. These results provide a genetic basis for exploring the better growth characteristics and disease resistance of DR-GGC than GC, valuable information on the genetic breeding for grass carp, and a further understanding of the genetic characteristics of gynogenetic individuals.

Transcriptomic Profiles of Pectoralis major Muscles Affected by Spaghetti Meat and Woody Breast in Broiler Chickens.

Spaghetti meat (SM) and woody breast (WB) are breast muscle myopathies of broiler chickens, characterized by separation of myofibers and by fibrosis, respectively. This study sought to investigate the transcriptomic profiles of breast muscles affected by SM and WB. Targeted sampling was conducted on a flock to obtain 10 WB, 10 SM, and 10 Normal Pectoralis major muscle samples from 37-day-old male chickens. Total RNA was extracted, cDNA was used for pair-end sequencing, and differentially expressed genes (DEGs) were determined by a false discovery rate of <0.1 and a >1.5-fold change. Principal component and heatmap cluster analyses showed that the SM and WB samples clustered together. No DEGs were observed between SM and WB fillets, while a total of 4018 and 2323 DEGs were found when comparing SM and WB, respectively, against Normal samples. In both the SM and WB samples, Gene Ontology terms associated with extracellular environment and immune response were enriched. The KEGG analysis showed enrichment of cytokine-cytokine receptor interaction and extracellular matrix-receptor interaction pathways in both myopathies. Although SM and WB are macroscopically different, the similar transcriptomic profiles suggest that these conditions may share a common pathogenesis. This is the first study to compare the transcriptomes of SM and WB, and it showed that, while both myopathies had profiles different from the normal breast muscle, SM and WB were similar, with comparable enriched metabolic pathways and processes despite presenting markedly different macroscopic features.

Bioinformatics Analysis Identifies Key Genes in the Effect of Resistance Training on Female Skeletal Muscle Aging.

Resistance training is used to combat skeletal muscle function decline in older adults. Few studies have been designed specific for females, resulting in very limited treatment options for skeletal muscle atrophy in aging women. Here, we analyzed the gene expression profiles of skeletal muscle samples from sedentary young women, sedentary older women, and resistance-trained older women, using microarray data from public database. A total of 45 genes that were differentially expressed during female muscle aging and reversed by resistance training were identified. Functional and pathway enrichment analysis, protein-protein interaction network analysis, and receiver operating characteristic analysis were performed to reveal the key genes and pathways involved in the effects of resistance training on female muscle aging. The collagen genes COL1A1, COL3A1, and COL4A1 were identified important regulators of female muscle aging and resistance training, by modulating multiple signaling pathways, such as PI3 kinase-Akt signaling, focal adhesions, extracellular matrix-receptor interactions, and relaxin signaling. Interestingly, the expression of CDKN1A and TP63 were increased during aging, and further upregulated by resistance training in older women, suggesting they may negatively affect resistance training outcomes. Our findings provide novel insights into the molecular mechanisms of resistance training on female muscle aging and identify potential biomarkers and targets for clinical intervention.

Identifying CEACAM1 as a potential prognostic biomarker for basal-like breast cancer by bioinformatics analysis and in vitro experiments.

Background: Carcinoembryonic antigen related cell adhesion molecule-1 (CEACAM1) is a very important intercellular adhesion molecule, and its prognostic relevance to breast cancer (BC), especially basal-like breast cancer (BLBC), remains poorly understood. Methods: CEACAM1 mRNA expression data for BC were sourced from the Cancer Genome Atlas (TCGA) database. Kaplan-Meier survival analysis and Cox regression analysis were used to evaluate the prognostic relationship between CEACAM1 expression and BC. Signaling pathways associated with CEACAM1 were analysed using Gene Set Enrichment Analysis (GSEA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Moreover, cell counting kit-8 (CCK-8), flow cytometry, transwell and wound-healing assays were employed to identify the biological functions of CEACAM1 in BLBC. Results: CEACAM1 was correlated with overall survival (OS) of BLBC patients. Compared with the subgroup with better prognosis, the levels of CEACAM1 mRNA expression were significantly lower in the subgroup of BLBC with poorer prognosis. Both univariate and multivariate Cox regression analysis suggested that down-regulation of CEACAM1 expression may be an independent factor for poor prognosis in BLBC patients. GSEA and KEGG analysis revealed that CEACAM1 was negatively related with signaling pathways including extracellular matrix (ECM) receptor interaction, focal adhesion, and cell adhesion. The results of in vitro experiments indicated that CEACAM1 not only induced apoptosis of BLBC cells, but also inhibited the invasive and metastatic ability of cancer cells. Conclusions: CEACAM1 may contribute to improving the OS of BLBC patients due to its ability to inhibit the proliferation and metastasis of cancer cells. Therefore, CEACAM1 could be used as a potential prognostic biomarker and therapeutic target in BLBC.

CRABP2 regulates infiltration of cancer-associated fibroblasts and immune response in melanoma.

Finding biomarkers for immunotherapy is an urgent issue in cancer treatment. Cellular retinoic acid-binding protein 2 (CRABP2) is a controversial factor in the occurrence and development of human tumors. However, there is limited research on the relationship between CRABP2 and immunotherapy response. This study found that negative correlations of CRABP2 and immune checkpoint markers (PD-1, PD-L1, and CTLA-4) were observed in breast invasive carcinoma (BRCA), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD) and testicular germ cell tumors (TGCT). In particular, in SKCM patients who were treated with PD-1 inhibitors, high levels of CRABP2 predicted poor prognosis. Additionally, CRABP2 expression was elevated in cancer-associated fibroblasts (CAFs) at the single-cell level. The expression of CRABP2 was positively correlated with markers of CAFs, such as MFAP5, PDPN, ITGA11, PDGFRα/β and THY1 in SKCM. To validate the tumor-promoting effect of CRABP2 in vivo, SKCM xenograft mice models with CRABP2 overexpression have been constructed. These models showed an increase in tumor weight and volume. Enrichment analysis indicated that CRABP2 may be involved in immune-related pathways of SKCM, such as extracellular matrix (ECM) receptor interaction and epithelial-mesenchymal transition (EMT). The study suggests that CRABP2 may regulate immunotherapy in SKCM patients by influencing infiltration of CAFs. In conclusion, this study provides new insights into the role of CRABP2 in immunotherapy response. The findings suggest that CRABP2 may be a promising biomarker for PD-1 inhibitors in SKCM patients. Further research is needed to confirm these findings and to explore the clinical implications of CRABP2 in immunotherapy.

Lysyl oxidase-like 1 predicts the prognosis of patients with primary glioblastoma and promotes tumor invasion via EMT pathway.

Lysyl oxidase enzymes (LOXs), as extracellular matrix (ECM) protein regulators, play vital roles in tumor progression by remodeling the tumor microenvironment. However, their roles in glioblastoma (GBM) have not been fully elucidated. The genetic alterations and prognostic value of LOXs were investigated via cBioPortal. The correlations between LOXs and biological functions/molecular tumor subtypes were explored in The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). After Kaplan‒Meier and Cox survival analyses, a Loxl1-based nomogram and prognostic risk score model (PRSM) were constructed and evaluated by time-dependent receiver operating characteristic curves, calibration curves, and decision curve analyses. Tumor enrichment pathways and immune infiltrates were explored by single-cell RNA sequencing and TIMER. Loxl1-related changes in tumor viability/proliferation and invasion were further validated by CCK-8, western blot, wound healing, and Transwell invasion assays. GBM patients with altered LOXs had poor survival. Upregulated LOXs were found in IDH1-wildtype and mesenchymal (not Loxl1) GBM subtypes, promoting ECM receptor interactions in GBM. The Loxl1-based nomogram and the PRSM showed high accuracy, reliability, and net clinical benefits. Loxl1 expression was related to tumor invasion and immune infiltration (B cells, neutrophils, and dendritic cells). Loxl1 knockdown suppressed GBM cell proliferation and invasion by inhibiting the EMT pathway (through the downregulation of N-cadherin/Vimentin/Snai1 and the upregulation of E-cadherin). The Loxl1-based nomogram and PRSM were stable and individualized for assessing GBM patient prognosis, and the invasive role of Loxl1 could provide a promising therapeutic strategy.

Quantitative proteomic analysis reveals regulatory networks of extracellular matrix receptor interaction pathways in endothelial cells after myocardial infarction

Cardiac fibrosis, a significant pathological alteration following myocardial infarction (MI), remains enigmatic with respect to the role of cardiac endothelial cells (ECs). To elucidate the proteomic shifts in cardiac ECs accompanying MI-induced cardiac fibrosis, a standard MI mice model was established through ligation of the left anterior descending branch. Following 14 days of effective modeling, we isolated primary ECs from the hearts of both sham and MI models utilizing the CD31 microbeads sorting technique. Quantitative proteomics and bioinformatics methodologies, including tandem mass spectrometry, were employed to discern proteomic alterations in the primary endothelial cells of the experimental groups. Comprehensive analyses, including Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, functional enrichment analysis, and functional enrichment cluster analysis, revealed an up-regulation of proteins associated with extracellular matrix-receptor interaction pathway in cardiac fibrosis post-MI. Subsequent Western blot analysis confirmed the up-regulation of specific proteins involved in this pathway, namely collagen type VI alpha 2 (Col6&amp;alpha;2), vitronectin (Vtn), and integrin beta (Itg&amp;beta;). We conclude that the expression levels of Col6&amp;alpha;2, Vtn, and Itg&amp;beta; in primary ECs during the early stage of cardiac fibrosis, 14 days post-MI, were significantly elevated compared to the sham group (P &lt; 0.05). This observation suggests that ECM-receptor interaction could potentially influence the progression of cardiac fibrosis following MI.

Syringic acid promotes cartilage extracellular matrix generation and attenuates osteoarthritic cartilage degradation by activating TGF-β/Smad and inhibiting NF-κB signaling pathway.

Osteoarthritis (OA) is a common chronic degenerative disease which is characterized by the disruption of articular cartilage. Syringic acid (SA) is a phenolic compound with anti-inflammatory, antioxidant, and other effects including promoting osteogenesis. However, the effect of SA on OA has not yet been reported. Therefore, the purpose of our study was to investigate the effect and mechanism of SA on OA in a mouse model of medial meniscal destabilization. The expressions of genes were evaluated by qPCR or western blot or immunofluorescence. RNA-seq analysis was performed to examine gene transcription alterations in chondrocytes treated with SA. The effect of SA on OA was evaluated using destabilization of the medial meniscus model of mice. We found that SA had no obvious toxic effect on chondrocytes, while promoting the expressions of chondrogenesis-related marker genes. The results of RNA-seq analysis showed that extracellular matrix-receptor interaction and transforming growth factor-β (TGF-β) signaling pathways were enriched among the up-regulated genes by SA. Mechanistically, we demonstrated that SA transcriptionally activated Smad3. In addition, we found that SA inhibited the overproduction of lipopolysaccharide-induced inflammation-related cytokines including tumor necrosis factor-α and interleukin-1β, as well as matrix metalloproteinase 3 and matrix metalloproteinase 13. The cell apoptosis and nuclear factor-kappa B (NF-κB) signaling were also inhibited by SA treatment. Most importantly, SA attenuated cartilage degradation in a mouse OA model. Taken together, our study demonstrated that SA could alleviate cartilage degradation in OA by activating the TGF-β/Smad and inhibiting NF-κB signaling pathway.

A Noninvasive Circulating Signature of Combined Right Ventricular Pressure and Volume Overload in Tetralogy of Fallot/Pulmonary Atresia/Major Aortopulmonary Collateral Arteries.

Background: Despite surgical advances, children with tetralogy of Fallot/pulmonary atresia/major aortopulmonary collaterals (TOF/PA/MAPCAs) are subject to chronic right ventricular (RV) pressure and volume overload. Current diagnostic tools do not identify adverse myocardial remodeling and cannot predict progression to RV failure. We sought to identify a noninvasive, circulating signature of the systemic response to right heart stress to follow disease progression. Methods: Longitudinal data were collected from patients with TOF/PA/MAPCAs (N = 5) at the time of (1) early RV pressure overload and (2) late RV pressure and volume overload. Plasma protein and microRNA expression were evaluated using high-throughput data-independent mass spectroscopy and Agilent miR Microarray, respectively. Results: At the time of early RV pressure overload, median patient age was 0.34 years (0.02-9.37), with systemic RV pressures, moderate-severe hypertrophy, and preserved systolic function. Late RV pressure and volume overload occurred at a median age of 4.08 years (1.51-10.83), with moderate RV hypertrophy and dilation, and low normal RV function; 277 proteins were significantly dysregulated (log2FC ≥0.6/≤-0.6, FDR≤0.05), predicting downregulation in lipid transport (apolipoproteins), fibrinolytic system, and extracellular matrix structural proteins (talin 1, profilin 1); and upregulation in the respiratory burst. Increasing RV size and decreasing RV function correlated with decreasing structural protein expression. Similarly, miR expression predicted downregulation of extracellular matrix-receptor interactions and upregulation in collagen synthesis. Conclusion: To our knowledge, we show for the first time a noninvasive protein and miR signature reflecting the systemic response to adverse RV myocardial remodeling in TOF/PA/MAPCAs which could be used to follow disease progression.

Development of myofibers and muscle transcriptomic analysis in growing Yili geese

In poultries, muscle growth is a quantitative trait controlled by multiple genes. The regulatory mechanisms governing muscle tissue growth and development in poultry, particularly during the early stages of growth, are intricate. Through the examination of leg muscle transcripts from Yili geese during various stages of development, this study offers valuable insights into the molecular mechanisms underlying the growth and development of Yili geese. This study aimed to perform a comparative analysis of the histological characteristics of leg muscles and the mRNA expression profiles of leg muscles in Yili geese at different ages (2, 4, 6, 8, and 10 wk). The objective was to identify differentially expressed genes related to muscle development in Yili geese and utilize bioinformatics to predict the potential biological functions of these genes. Through histological studies on leg muscle tissues, it was discerned that male geese at 4 wk exhibit a significantly reduced muscle fiber density in comparison to females (P < 0.01). In contrast, by the time they reach 6, 8, and 10 wk, their muscle fiber diameter and cross-sectional dimensions significantly outpace the females (P < 0.01). With the advancement in age, muscle fiber density tends to decrease. It is worth noting that 4- and 6-wk-old male geese have a substantially elevated muscle fiber density when matched against females (P < 0.01). Conversely, at the age of 10 wk, their muscle fiber density is notably inferior to the females (P < 0.01). Furthermore, male geese exhibit the most rapid increase in muscle fiber diameter and cross-sectional area between 4 and 6 wk of age. The density of muscle fibers in these geese significantly decreases from 4 to 8 wk. In contrast, female geese show the most pronounced growth in muscle fiber diameter and cross-sectional area between 2 and 6 wk, with a swift decline in density following the 6-wk mark, accompanied by a gradual reduction in the rate of muscle fiber growth. A comprehensive analysis of the leg muscle mRNA expression profiles from 12 Yili geese generated a cumulative total of 502,065,268 valid sequence reads, corresponding to a data volume of 75.30 Gb. In a comparative analysis between 4-wk-old and 2-wk-old groups (T4 vs. T2), 8-wk-old and 2-wk-old groups (T8 vs. T2), and 8-wk-old and 4-wk-old groups (T8 vs. T4), we identified 1,700, 1,583, and 221 differentially expressed genes (DEGs), respectively. Differentially expressed genes were significantly enriched in Gene Ontology (GO) terms such as organelle organization, cytoskeletal protein binding, cation transport, myosin complex, and actin cytoskeleton. Among the significantly enriched signaling pathways, 5 pathways were found to be significantly related to growth and development: adhesion patch, extracellular matrix receptor interaction, tight junction, TGF-β signaling pathway, and MAPK signaling pathway, with a total of 38 differentially differentiated genes contained in these 5 pathways, and it was hypothesized that the above pathways as well as the DEGs in the pathways played an important role in the regulation of early growth and development of the Yili goose. This investigation serves as a foundational reference for elucidating the molecular regulatory mechanisms involved in the development of goose muscle. Furthermore, it contributes to the expansion of the theoretical framework concerning the genetic regulation of muscle growth in geese.

Genomic and transcriptomic analysis of cutaneous squamous cell carcinoma arising in immunocompetent and immunosuppressed patients

BackgroundCutaneous squamous cell carcinoma (cSCC) is the most common skin malignancy arising in immunocompromised patients such as solid organ transplant recipients. In addition to an abundance in number, the morbidity and mortality of these tumors in this patient population exceeds that of immune competent individuals. Here, we used whole exome and bulk RNA sequencing to analyze mutation profiles between tumors arising in immunocompetent and immunosuppressed patients. MethodsDNA and RNA extracted from twenty formalin-fixed, paraffin embedded tumors and adjacent skin was sequenced. Bioinformatic analysis revealed tumor mutational burden, mutational signatures, microsatellite instability, and aberrant signaling pathways. ResultsSimilar median tumor mutational burden was found in both the tumors from the immunocompetent and the immunosuppressed cohorts. Mutation signature analysis revealed UVR signatures and evidence of azathioprine exposure. 50% of tumors from the immunosuppressed patients have mutations consistent with microsatellite instability, yet mismatch repair protein expression was preserved in the samples analyzed. Additionally, frequently mutated genes in this cohort belong to the extracellular matrix receptor interaction and calcium signaling pathways, suggesting these may be targets for future treatments of this disease. ConclusionsThis study utilizes whole exome and bulk RNA sequencing to identify difference between cSCC arising in immunosuppressed and immunocompetent patients using the patient’s photo exposed, but histologically normal appearing skin as the “germline” comparison. We demonstrate an enrichment in microsatellite instability in the tumors from immunosuppressed patients and differences in oxidative phosphorylation and epithelial-mesenchymal transition which may be targets for therapeutic intervention based on identification of mutations.

290 Ewe Undernutrition Alters Cotyledon Development and Function

Abstract Undernutrition is common for animals maintained in a range setting, particularly during periods of drought, and during gestation can be detrimental to offspring development. The placenta is a known mediator for maternal-fetal nutrient exchange, and developmental impacts to the placenta during times of nutritional stress contribute to poor offspring outcomes. The objective of this study was to determine the impacts of maternal nutrient restriction on the development and function of placental cotyledons. Targhee ewes were allocated into two dietary treatment groups for the entirety of gestation. The control group (CON; n = 10) was fed to meet 100% of NRC requirements and the nutrient restricted group (NR; n = 11) was fed to meet 60% of NRC requirements, to mimic the nutritional stress experienced by range ewes during drought. At the time of lambing total placental weight, total cotyledon number, and lamb birth weight were recorded. Cotyledons (n = 3 / placenta) were removed from multiple locations, weighed, and processed for RNA-sequencing. Total placental weight, total cotyledon number, and lamb birth weight were not affected by maternal diet restriction (P &amp;gt; 0.05). Average cotyledon weight was greater in the CON group compared with the NR group (P &amp;lt; 0.05). Gene ontology (GO) and Kyoto encyclopedia of genes and genomes pathways (KEGG) analyses were performed to identify biological pathways involved in placental function and nutrient transfer. Cotyledons from NR singletons vs CON singletons expressed 470 differentially expressed genes (DEGs; P &amp;lt; 0.05; 187 up-regulated, 283 down-regulated). Gene ontology terms represented by DEGs include hormone activity (P = 0.0003) and antigen processing and presentation (P = 0.0004). KEGG pathways of interest include pyruvate metabolism, estrogen signaling, extracellular matrix receptor interaction, and antigen processing and presentation. There were also 426 DEGs (P &amp;lt; 0.05; 195 up-regulated, 231 down-regulated) in cotyledons of NR twins vs CON twins. Represented GO categories include heme binding (P = 0.003) and oxidoreductase activity (P = 0.03). These data show that prolonged nutrient restriction alters cotyledon development and gene expression indicating modifications in placental function. These changes in placental function likely mediate poor offspring developmental outcomes observed following gestational under nutrition.

Transcriptome analysis of divergent residual feed intake phenotypes in the M. longissimus thoracis et lumborum of Wannan Yellow rabbits

Introduction: Feed efficiency is an important economic trait in rabbit meat production. The identification of molecular mechanisms and candidate genes for feed efficiency may improve the economic and environmental benefits of the rabbit meat industry. As an alternative to the conventional feed conversion ratio, residual feed intake (RFI) can be used as an accurate indicator of feed efficiency.Methods: RNA sequencing was used to identify the differentially expressed genes (DEGs) in the M. longissimus thoracis et lumborum of eight Wannan Yellow rabbits with excessively high or low RFIs (HRFI or LRFI, respectively). Thereafter, Gene Ontology (GO) analysis, enrichment using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, gene set enrichment analysis (GSEA), and protein–protein interaction (PPI) network analysis was conducted.Results: In total, 445 DEGs were identified in the M. longissimus thoracis et lumborum of rabbits with high and low RFIs. The significantly enriched GO terms identified in these two groups were primarily involved in energy and mitochondrial metabolism and oxidation–reduction processes. KEGG analysis identified 11 significantly enriched pathways, including oxidative phosphorylation, PI3K-Akt signaling, and extracellular matrix-receptor interaction pathways. According to GSEA, the expressions of genes and pathways related to mitochondrial function were upregulated in HRFI rabbits, whereas genes with upregulated expressions in LRFI rabbits were related to immune response and energy metabolism. Additionally, PPI network analysis revealed five potential candidate genetic markers.Conclusion: Comparative analysis of the M. longissimus thoracis et lumborum transcriptomes in HRFI and LRFI rabbits revealed FOS, MYC, PRKACB, ITGA2, and FN1 as potential candidate genes that affect feed efficiency in rabbits. In addition, key signaling pathways involved in oxidative phosphorylation and PI3K-Akt and ECM-receptor interaction signaling impact rabbit feed efficiency. These findings will aid in breeding programs to improve feed efficiency and optimize RFI selection of rabbits for meat production.

Transcriptomic Analysis on Pectoral Muscle of European Meat Pigeons and Shiqi Pigeons during Embryonic Development.

In avian muscle development, embryonic muscle development determines the number of myofibers after birth. Therefore, in this study, we investigated the phenotypic differences and the molecular mechanism of pectoral muscle development of the European meat pigeon Mimas strain (later called European meat pigeon) and Shiqi pigeon on embryonic day 6 (E6), day 10 (E10), day 14 (E14) and day 1 after birth (P1). The results showed that the myofiber density of the Shiqi pigeon was significantly higher than that of the European meat pigeon on E6, and myofibers with a diameter in the range of 50~100 μm of the Shiqi pigeon on P1 were significantly higher than those of European meat pigeon. A total of 204 differential expressed genes (DEGs) were obtained from RNA-seq analysis in comparison between pigeon breeds at the same stage. DEGs related to muscle development were found to significantly enrich the cellular amino acid catabolism, carboxylic acid catabolism, extracellular matrix receptor interaction, REDOX enzyme activity, calcium signaling pathway, ECM receptor interaction, PPAR signaling pathway and other pathways. Using Cytoscape software to create mutual mapping, we identified 33 candidate genes. RT-qPCR was performed to verify the 8 DEGs selected-DES, MYOD, MYF6, PTGS1, MYF5, MYH1, MSTN and PPARG-and the results were consistent with RNA-seq. This study provides basic data for revealing the distinct embryonic development mechanism of pectoral muscle between European meat pigeons and Shiqi pigeons.

Multi-omic analysis revealed the therapeutic mechanisms of Alpinia oxyphylla fructus water extract against bladder overactivity in spontaneously hypertensive rats

ObjectiveAlpinia oxyphylla fructus without impurities and shells is called “Yi-Zhi-Ren” (YZR) in Chinese, and traditionally used to alleviate enuresis. The aim of this study was to investigate the effects and underlying mechanisms of YZR in the treatment of overactive bladder (OAB) in spontaneously hypertensive rats (SHR), a vascular disorder-related OAB model. MethodsA 3-week administration of YZR water extract (p.o.) was done, followed by urodynamics to measure bladder parameters. Changes in bladder structure were observed through H&E staining and Masson's staining. An integrated approach involving network pharmacology, transcriptomics and metabolomics was employed to elucidate the potential mechanisms of YZR, and the key proteins involved in the mechanisms were validated by Western blotting. Additionally, network pharmacology was used to predict the relationship between YZR's active components and validated proteins. ResultsYZR treatment significantly improved the bladder storage parameters, tightened the detrusor layer, reduced inflammatory infiltration, and decreased collagen proportion in the SHR bladder. These results indicated that YZR water extract can alleviate OAB symptoms and improve bladder structure. Integrated analysis suggested that YZR may affect extracellular matrix-receptor interaction and calcium signaling pathway. Western blotting results further confirmed that the reduction in key proteins, such as TGFβ1, p-SMAD3, collagen III, Gq and PLCβ1, involved in collagen synthesis and calcium signaling pathways after YZR treatment. Network pharmacology predicted that sitosterol, chrysin, and nootkatone were potential components responsible for YZR's therapeutic effect on OAB. ConclusionYZR's mechanisms of action in treating OAB involved the TGFβ1-SMAD3 signaling pathway-related collagen synthesis and Gq-PLCβ1 calcium signaling pathway, which are associated with detrusor contraction frequency and strength, respectively.

Mechanism of transforming growth factor-β1 inducing renal fibrosis based on transcriptome sequencing analysis.

To explore the mechanism of transforming growth factor-β1 (TGF-β1) inducing renal fibrosis. Renal fibroblast NRK-49F cells treated with and without TGF-β1 were subjected to RNA-seq analysis. DESeq2 was used to analyze the sequencing results. Differentially expressed genes were screened with the criteria of false discovery rate<0.05 and l o g 2 F C >1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed for differentially expressed genes. Genes encoding transcription factors were further screened in differentially expressed genes. Then, the expression of these genes during renal fibrosis were verified using unilateral ureteral obstruction (UUO)-induced mouse renal fibrosis model and data set GSE104954 in high-throughput gene expression database. After TGF-β1 treatment for 6, 12, and 24 h, 552, 1209 and 1028 differentially expressed genes were identified, respectively. GO analysis indicated that these genes of differential expression were significantly enriched in development, cell death, and cell migration. KEGG pathway analysis showed that in the early stage of TGF-β1 induction (TGF-β1 treatment for 6 h), the changes of Hippo, TGF-β and Wnt signaling pathways were mainly manifested, while in the late stage of TGF-β1 induction (TGF-β1 treatment for 24 h), the changes of extracellular matrix-receptor interaction, focal adhesion and adherens junction were mainly enriched. Among 291 up-regulated differentially expressed genes treated with TGF-β1 for 6 h, 13 genes (Snai1, Irf8, Bhlhe40, Junb, Arid5a, Vdr, Lef1, Ahr, Foxo1, Myc, Tcf7, Foxc2, Glis1) encoded transcription factors. Validation in cell model showed that TGF-β1 induced 9 transcription factors expressions (encoded by Snai1, Irf8, Bhlhe40, Junb, Arid5a, Vdr, Lef1, Myc, Tcf7), while the expression levels of the other 4 genes did not change significantly after TGF-β1 treatment. Validation results in UUO-induced mouse renal fibrosis model showed that Snai1, Irf8, Bhlhe40, Junb, Arid5a, Myc and Tcf7 were up-regulated after UUO, Vdr was down-regulated and there was no significant change in Lef1. Validation in the GSE104954 dataset showed that IRF8 was significantly overexpressed in the renal tubulointerstitium of patients with diabetic nephropathy or IgA nephropathy, MYC was highly expressed in diabetic nephropathy, and the expressions of the other 7 genes were not significantly different compared with the control group. TGF-β1 induces genes differentially expressed in renal fibroblasts, and Irf8 and Myc were identified as potential targets of chronic kidney disease and renal fibrosis.

Subacute Cutaneous Toxicity with Single-Fraction Electron FLASH RT in Yorkshire Swine

Information regarding acute/subacute skin toxicity of electron FLASH radiation therapy (RT) is limited. We evaluated short-term safety of electron FLASH for human trials by investigating subacute toxicity compared to conventional dose-rate RT (CONV) in the Yorkshire pig, an animal model known to closely approximate human skin and routinely used for toxicity studies. Two healthy 50 kg pigs underwent CT imaging for RT treatment planning with field visualization via BBs and tattoos on each dorsolateral flank. Each target received a single fraction of 20, 25 or 30 Gy with FLASH and CONV on opposing sides delivered using a dedicated mobile linear accelerator. FLASH dose rates ranged from 164-245 Gy/sec (12 pulses delivered over 0.122 sec) while the CONV dose rate was set at 0.18 Gy/sec. Doses were verified using thermo- and optically stimulated luminescent dosimeters, and Gafchromic films. We obtained baseline and weekly images up to 98 days post-RT (D98) for blinded toxicity grading by 3 expert radiation oncologists using the modified RTOG radiation dermatitis (RD) scale. We measured erythema and pigmentation indices on those timepoints using a handheld spectrophotometer. We also obtained punch biopsies of targets and non-irradiated controls on D10 and D30 for RNA sequencing and two 6-marker multiplex immunofluorescence analyses of inflammation, immune response, and fibrosis. FLASH and CONV data were compared using repeated measures ANOVA and transcriptomic analyses using DESeq2. All RT targets developed peak median grade 4 (ulceration, hemorrhage, or necrosis) RD by D84 regardless of FLASH or CONV delivery. However, FLASH targets developed peak RD later than CONV targets after 20 Gy (D84 vs D63), 25 Gy (D84 vs D49) and 30 Gy (D63 vs D42). FLASH induced qualitatively lower mean pigmentation and erythema indices than CONV for all 3 doses. Similarly, peak mean pigmentation indices occurred later with FLASH vs CONV for 20 Gy (D84 vs D63), 25 Gy (D84 vs D49) and 30 Gy (D77 vs D63). However, peak mean erythema indices occurred on the same day for FLASH and CONV (D63 for 20 Gy and D42 for 25 and 30 Gy). Transcriptomic analyses revealed significantly upregulated signals for wound healing (including TGF-beta, cell adhesion and extracellular matrix receptor interaction) and leukocyte infiltration with 20 Gy CONV mostly by D10, while FLASH upregulated those pathways only after 25 or 30 Gy, or by D30, or never at all. Preliminary immunofluorescence data showed FLASH may induce less T cell infiltrate and TGF-beta-expressing macrophages than CONV. Single-fraction electron FLASH resulted in delayed onsets of both subacute cutaneous toxicity and wound healing with leukocytic infiltration signaling than dose-matched CONV based on both subjective and objective metrics of skin injury. Our findings suggest further investigations of optimal dose of electron FLASH for safe clinical translation is warranted, and we have a dose-finding study currently underway.

Integrin β5 is an independent prognostic marker for intrahepatic cholangiocarcinoma in a Chinese population.

Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver tumor and a major cause of cancer mortality worldwide. Integrin β5 (ITGB5) is considered to be involved in the intercellular signal transduction and regulation of tumorigenesis and development. The present study investigated the association between ITGB5 expression levels and the prognosis of ICC, as well as the effects of ITGB5 on the proliferation and invasion of ICC cells. RNA-sequencing transcriptomic profiling data of ICC samples were retrieved from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Tissue specimens from patients with ICC treated at Taizhou People's Hospital were collected and the ITGB5 expression levels were evaluated using immunohistochemical staining. The biological function of ITGB5 in ICC was investigated using Gene Ontology (GO), Gene Set Enrichment Analysis (GSEA) and in vitro experiments using HuCCT1 cells. After knocking down ITGB5 expression, cell proliferation was detected using Cell Counting Kit-8 assay, while cell invasion was assessed using Transwell assays. According to TCGA dataset, ITGB5 was highly expressed in ICC; however, there was no significant difference in prognosis between patients with high and low ITGB5 expression levels. High expression of ITGB5 was present in the tissues of patients with ICC from the GEO database, which was associated with poor prognosis. Survival analyses of the clinical data obtained in the present study revealed that high expression levels of ITGB5 in patients with ICC were associated with a reduced overall survival. GO and GSEA indicated that genes associated with ITGB5 were enriched in the extracellular matrix-receptor interaction and focal adhesion signaling pathways. Silencing ITGB5 inhibited the proliferation and invasion of ICC cells. In conclusion, ITGB5 may act as an essential regulator of ICC development and progression by influencing the proliferation and invasion of ICC cells. However, future studies with larger sample sizes are required to validate the role of ITGB5 in the prognosis of patients with ICC.

Alterations of gut microbiota in a mouse model with partial small intestinal obstruction.

Changes in the gut microbiota of patients with partial small intestinal obstruction (PSIO) have not been widely clarified. We aimed to explore bacterial diversity in a PSIO mouse model. A PSIO mouse model was established using male C57BL/6 mice, and feces samples from the distal ileum and ileum epithelium tissues were collected. MiSeq sequencing of the 16S rRNA gene was conducted to characterize microbiota diversity and composition. RNA sequencing for differences in transcriptomic programming of the ileum tissue was performed between the PSIO and (Control) Ctrl groups. Bacterial diversity in the PSIO group was significantly lower than that in the controls. Pseudomonadota was predominant in the feces of the PSIO group. Unclassified_Muribaculaceae (p = 0.008) and Akkermansia (p = 0.007) were more abundant in the Ctrl group than those in the PSIO group. Furthermore, Escherichia_Shigella (p = 0.008) was more predominant in the feces of the PSIO group. The Kyoto Encyclopedia of Genes and Genomes pathways related to metabolism were depleted in the PSIO group. Pathways associated with intestinal fibrosis, including extracellular matrix-receptor interaction, focal adhesion, phosphoinositide 3-kinase (PI3K)-Akt signaling pathway and transforming growth factor (TGF)-beta signaling pathway, which were enriched in ileum epithelial tissue in the PSIO group. PSIO can lead to changes in the predominant intestinal bacterial groups. Depleted functional profiles of the gut microbiota were identified in the PSIO group. Functional pathways associated with intestinal fibrosis were activated by PSIO. The potential regulation by the microbiota needs to be explored in the future.

The potential role of miRNAs and regulation of their expression in the development of mare endometrial fibrosis

Mare endometrial fibrosis (endometrosis), is one of the main causes of equine infertility. Despite the high prevalence, both ethology, pathogenesis and the nature of its progression remain poorly understood. Recent studies have shown that microRNAs (miRNAs) are important regulators in multiple cellular processes and functions under physiological and pathological circumstances. In this article, we reported changes in miRNA expression at different stages of endometrosis and the effect of transforming growth factor (TGF)-β1 on the expression of the most dysregulated miRNAs. We identified 1, 26, and 5 differentially expressed miRNAs (DEmiRs), in categories IIA (mild fibrosis), IIB (moderate fibrosis), and III (severe fibrosis) groups compared to category I (no fibrosis) endometria group, respectively (Padjusted < 0.05, log2FC ≥ 1.0/log2FC ≤ − 1.0). This study indicated the potential involvement of miRNAs in the regulation of the process associated to the development and progression of endometrosis. The functional enrichment analysis revealed, that DEmiRs target genes involved in the mitogen-activated protein kinases, Hippo, and phosphoinositide-3-kinase (PI3K)-Akt signalling pathways, focal adhesion, and extracellular matrix-receptor interaction. Moreover, we demonstrated that the most potent profibrotic cytokine—TGF-β1—downregulated novel-eca-miR-42 (P < 0.05) expression in fibroblasts derived from endometria at early-stage endometrosis (category IIA).