Aldosterone-regulated Sodium Reabsorption Research Articles

Microbial and Metabolic Profiling of Obese and Lean Luchuan Pigs: Implications for Phenotypic Divergence.

Luchuan (LC) pigs are a Chinese breed renowned for their distinctive black and white coloring, superior meat quality and rapid reproduction, but their growth rate is slow. Over the course of approximately two decades of controlled breeding, the LC pigs maintained at the Shanghai Academy of Agricultural Sciences (Shanghai, China) have diverged into two phenotypes: one characterized by obesity (FLC) and the other by leanness (LLC). Recent studies indicate a correlation between microorganisms and the differentiation of host phenotypes. In this study, we examined the fecal microbiota profiles and serum metabolites of FLC and LLC pigs. The body weight, chest circumference, and alanine aminotransferase and aspartate aminotransferase enzyme activities were increased in the FLC pigs compared to the LLC pigs. Conversely, the levels of the Fusobacterium and Streptococcus genera were lower in the FLC pigs, while the number of Firmicutes, Lactobacillus, Phascolartobacterium, and Rikenellaceae_RC9_gut_group members were higher. A total of 52 metabolites were altered between the two groups, with many playing crucial roles in prolactin signaling, oocyte meiosis, and aldosterone-regulated sodium reabsorption pathways. The correlation analyses demonstrated a significant association between the modified microbiota and metabolites and the phenotypic variations observed in the LC pigs. Specifically, Jeotgalicoccus was positively correlated with the body weight and chest circumference, but was negatively correlated with metabolites such as 2-mercaptobenzothiazole and N1-pyrazin-2-yl-4-chlorobenzamide, which were positively associated with Bacteroides. These results provide compelling evidence for a novel relationship between the gut microbiome and metabolome in the phenotypic differentiation of LC pigs.

CCNA2 and KIF23 are molecular targets for the prognosis of adenoid cystic carcinoma.

Adenoid cystic carcinoma (ACC) is a tumor type derived from glands. However, relationship between CCNA2 and KIF23, and adenoid cystic carcinoma remains unclear. GSE36820 and GSE88804 profiles for ACC were obtained from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were identified, and Weighted Gene Co-expression Network Analysis (WGCNA) was conducted. Subsequently, the construction and analysis of protein-protein interaction (PPI) network, functional enrichment analysis, and Gene Set Enrichment Analysis (GSEA) were performed. A gene expression heat map was generated to visually depict the expression difference of core genes between adenoid cystic carcinoma and normal samples. TargetScan was employed to identify miRNAs that regulated central DEGs. Western blotting (WB) was conducted for cell verification. A total of 885 DEGs were identified. GO and KEGG analyses revealed their main enrichment in responses to chemical stimuli, cell proliferation, tissue development, and regulation of cell proliferation. The GO and KEGG results indicated significant enrichment in aldosterone-regulated sodium reabsorption, the cell cycle, and the PPAR signaling pathway. Notably, core genes (CCNA2 and KIF23) were found to be highly expressed in Adenoid Cystic Carcinoma samples and expressed at low levels in normal samples. WB validated the overexpression of CCNA2 and KIF23 in the Adenoid Cystic Carcinoma group, confirming the protein-level changes associated with cell cycle, metastasis, apoptosis, and inflammatory factors in Adenoid Cystic Carcinoma groups with gene overexpression and knockout. CCNA2 and KIF23 exhibit high expression levels in ACC, suggesting their potential role as molecular targets for this malignancy.

Deciphering molecular basis of pesticide-induced recurrent pregnancy loss: insights from transcriptomics analysis

Recent studies have revealed a notable connection between pesticide exposure and Recurrent Pregnancy Loss (RPL), yet the precise molecular underpinning of this toxicity remains elusive. Through the alignment of Differentially Expressed Genes (DEGs) of healthy and RPL patients with the target genes of 9 pesticide components, we identified a set of 12 genes responsible for RPL etiology. Interestingly, biological process showed that besides RPL, those 12 genes also associated with preeclampsia and cardiovascular disease. Enrichment analysis showed the engagement of these genes associated with essential roles in the molecular transport of small molecules, as well as the aldosterone-regulated sodium reabsorption, endocrine and other factor-regulated calcium reabsorption, mineral absorption, ion homeostasis, and ion transport by P-type ATPases. Notably, the crosstalk targets between pesticide components played crucial roles in influencing RPL results, suggesting a role in attenuating pesticide agents that contribute to RPL. It is important to note that non-significant concentration of the pesticide components observed in both control and RPL samples should not prematurely undermine the potential for pesticides to induce RPL in humans. This study emphasizes the complexity of pesticide induced RPL and highlights avenues for further research and precautionary measures.

Identification of potential key genes for colorectal cancer based on bioinformatics analysis.

This study aimed to explore key genes as potential biomarkers for colorectal cancer (CRC) diagnosis and prognosis in order to improve their clinical utility. To identify and screen candidate genes involved in CRC carcinogenesis and disease progression, we downloaded the microarray datasets GSE143939, GSE196006, and GSE200427 from the GEO database and applied the GEO2R tool to obtain differentially expressed genes (DEGs) between colorectal cancer tissue samples and normal tissue samples. Differentially expressed genes were analyzed using the DAVID online database for gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses. Protein-protein interaction network was constructed and related module analysis was performed using STRING and Cytoscape. In total, 241 DEGs were identified, including 127 downregulated and 114 upregulated genes. DEGs enriched functions and pathways included cellular response to chemical stimulus, extracellular region, carbonate dehydratase activity, cell division, spindle, and cell division. The abundant functions and pathways of DEGs included cellular response to chemical stimulus, extracellular region, carbonate dehydratase activity, cell division, spindle, cell adhesion molecule binding, Aldosterone-regulated sodium reabsorption, and Cell cycle-related processes. Fifteen key genes were identified, and bioprocess analyses showed that these genes were mainly enriched in cell cycle, cell division, mitotic spindle, and tubulin binding processes. It was found that CDK1, CEP55, MKI67, and TOP2A may be involved in CRC cancer invasion and recurrence. The pivotal genes identified in this study contribute to our understanding of the molecular and pathogenic mechanisms of CRC carcinogenesis and progression, and provide possible biomarkers for the diagnosis and treatment of CRC.

Genomic Fabrics of the Excretory System's Functional Pathways Remodeled in Clear Cell Renal Cell Carcinoma.

Clear cell renal cell carcinoma (ccRCC) is the most frequent form of kidney cancer. Metastatic stages of ccRCC reduce the five-year survival rate to 15%. In this report, we analyze the ccRCC-induced remodeling of the five KEGG-constructed excretory functional pathways in a surgically removed right kidney and its metastasis in the chest wall from the perspective of the Genomic Fabric Paradigm (GFP). The GFP characterizes every single gene in each region by these independent variables: the average expression level (AVE), relative expression variability (REV), and expression correlation (COR) with each other gene. While the traditional approach is limited to only AVE analysis, the novel REV analysis identifies the genes whose correct expression level is critical for cell survival and proliferation. The COR analysis determines the real gene networks responsible for functional pathways. The analyses covered the pathways for aldosterone-regulated sodium reabsorption, collecting duct acid secretion, endocrine and other factor-regulated sodium reabsorption, proximal tubule bicarbonate reclamation, and vasopressin-regulated water reabsorption. The present study confirms the conclusion of our previously published articles on prostate and kidney cancers that even equally graded cancer nodules from the same tumor have different transcriptomic topologies. Therefore, the personalization of anti-cancer therapy should go beyond the individual, to his/her major cancer nodules.

Novel insights into perfluorinated compound-induced hepatotoxicity: Chronic dietary restriction exacerbates the effects of PFBS on hepatic lipid metabolism in mice

Perfluorobutane sulfonates (PFBS) have garnered extensive utilization because of their distinctive physicochemical properties. The liver acts as a key target organ for toxicity within the body and is vital for regulating metabolic processes, particularly lipid metabolism. However, there is currently a significant research gap regarding the influences of PFBS on hepatic lipid metabolism, especially in individuals with different dietary statuses. Here, the objective of this research was to examine the effects of PFBS on hepatic function under different dietary conditions. The results suggested that the levels of liver injury biomarkers were significantly upregulated, e.g., transaminase (GPT, GOT), while liver lipid levels were downregulated after exposure to PFBS at concentration of 50 μg/L for 42 days. Moreover, restricted diet further intensified the adverse effects of PFBS on the liver. Metabolomics analysis identified significant alterations in lipid-related metabolites in PFBS-induced hepatotoxicity, PFBS exposure induced a decrease in lysophosphatidylethanolamine and lysophosphatidylcholine. PFBS exposure caused an increase in aldosterone and prostaglandin f2alpha under restricted diet. In PFBS treatment group, histidine metabolism, beta-alanine metabolism, and arginine biosynthesis were the main pathway for PFBS toxicity. Aldosterone-regulated sodium reabsorption as a vital factor in inducing PFBS toxicity in the RD-PFBS treatment group. The analysis of 16S rRNA sequencing revealed that exposure to PFBS resulted in imbalance of gut microbial communities. PFBS exposure induced a decrease in Akkermansia and Lactobacillus, but an increase in Enterococcus. PFBS exposure caused the abundance of Lachnospiraceae_NK4A136_group was significantly elevated under restricted diet. Additionally, disruptions in the expression of genes involved in lipid production and consumption may significantly contribute to lipid imbalance in the liver. This study underscores the importance of recognizing the harmful impact of PFBS on liver function, along with the biotoxicity of contaminant influenced by dietary habits.

To Explore Genes Related to the Prognosis of Colorectal Cancer

To explore the genes correlated with the prognosis in colorectal cancer is the main objective of the study. Identification of differential genes through series of GSE20970, GSE37182, GSE44861 and GSE64392 from gene expression Omnibus database and then the differential genes were analyzed by gene ontology and Kyoto encyclopedia of genes and genomes enrichment. Through protein-protein interaction networks, screening of key genes was done and then we analyzed the prognosis of colorectal cancer from the cancer genome Atlas database. We obtained the differential genes through limma screening in series data GSE20970, GSE37182, GSE44861 and GSE64392 from gene expression Omnibus database. Venn diagram was used to screen 206 intersecting differentially expressed genes. Gene ontology enrichment analysis terms used were cytosol, transcription, deoxyribonucleic acid-templated, nucleic acid-templated transcription, ribonucleic acid biosynthetic process, nucleobase-containing compound biosynthetic process, heterocycle biosynthetic process, aromatic compound biosynthetic process, regulation of nucleobase-containing compound metabolic process, regulation of ribonucleic acid metabolic process, organic cyclic compound biosynthetic process. Kyoto encyclopedia of genes and genomes pathway terms were interleukin-17 signaling pathway, bladder cancer, phospholipase D signaling pathway, human cytomegalovirus infection, aldosterone-regulated sodium reabsorption, Kaposi’s sarcoma-associated herpesvirus infection, forkhead box O signaling pathway, nuclear factor kappa B signaling pathway, hepatitis B. Protein-protein interaction network has shown 206 key genes. According to the top 50 of betweenness value, we analyzed the prognosis of colorectal cancer from the cancer genome Atlas database. We found Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, C-X-C motif chemokine ligand 8, partner and localizer of breast cancer gene 2, peroxiredoxin 4 and translocase of outer mitochondrial membrane 20 are the key genes which impact prognosis in colorectal cancer. We predict that these genes can promote the survival time of colorectal cancer in future.

Nanoplastics induce molecular toxicity in earthworm: Integrated multi-omics, morphological, and intestinal microorganism analyses.

The toxicity of nanoplastics (NPs) at relatively low concentrations to soil fauna at different organismal levels is poorly understood. We investigated the responses of earthworm (Eisenia fetida) to polystyrene NPs (90-110nm) contaminated soil at a relatively low concentration (0.02% w:w) based on multi-omics, morphological, and intestinal microorganism analyses. Results showed that NPs accumulated in earthworms' intestinal tissues. The NPs damaged earthworms' digestive and immune systems based on injuries of the intestinal epithelium and chloragogenous tissues (tissue level) and increased the number of changed genes in the digestive and immune systems (transcriptome level). The NPs reduced gut microorganisms' diversity (Shannon index) and species richness (Chao 1 index). Proteomic, transcriptome, and histopathological analyses showed that earthworms suffered from oxidative and inflammatory stresses. Moreover, NPs influenced the osmoregulatory metabolism of earthworms as NPs damaged intestinal epithelium (tissue level), increased aldosterone-regulated sodium reabsorption (transcriptome level), inositol phosphate metabolism (proteomic level) and 2-hexyl-5-ethyl-furan-3-sulfonic acid, and decreased betaine and myo-inositol concentrations (metabolic level). Transcriptional-metabolic and transcriptional-proteomic analyses revealed that NPs disrupted earthworm carbohydrate and arachidonic acid metabolisms. Our multi-level investigation indicates that NPs at a relatively low concentration induced toxicity to earthworms and suggests that NPs pollution has significant environmental toxicity risks for soil fauna.

Potential antihypertensive mechanism of egg white-derived peptide QIGLF revealed by proteomic analysis

Previous work has shown that egg white-derived peptide QIGLF has significant in vivo antihypertensive activity. This study aimed to clarify the antihypertensive mechanisms of QIGLF on spontaneously hypertensive rats (SHRs) by a serum proteomic approach. Here, the tandem mass tag (TMT) quantitative proteomic was performed to discover serum protein changes in SHRs with QIGLF. As a result, SHRs with 4 weeks of QIGLF treatment have distinct serum protein expression profiles by principal component and Pearson's correlation coefficient analysis. Based on Gene Ontology (GO) annotation, oxygen transport and organelle fusion were found to be a regulated major biological process. Besides, aldosterone regulated sodium reabsorption, mitophagy, gap junction, and tight junction were significantly regulated based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. QIGLF might exert antihypertensive effects in the SHRs by inhibiting Na+ reabsorption and oxidative stress, restoring gap junction and tight junction.

Identification of the pivotal role of SPP1 in kidney stone disease based on multiple bioinformatics analysis

BackgroundKidney stone disease (KSD) is a multifactorial disease involving both environmental and genetic factors, whose pathogenesis remains unclear. This study aims to explore the hub genes related to stone formation that could serve as potential therapeutic targets.MethodsBased on the GSE73680 dataset with 62 samples, differentially expressed genes (DEGs) between Randall’s plaque (RP) tissues and normal tissues were screened and weighted gene co-expression network analysis (WGCNA) was applied to identify key modules associated with KSD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed to explore the biological functions. The protein–protein interaction (PPI) network was constructed to identify hub genes. Meanwhile, CIBERSORT and ssGSEA analysis were used to estimate the infiltration level of the immune cells. The correlations between hub genes and immune infiltration levels were also investigated. Finally, the top hub gene was selected for further GSEA analysis.ResultsA total of 116 DEGs, including 73 up-regulated and 43 down-regulated genes, were screened in the dataset. The red module was identified as the key module correlated with KSD. 53 genes were obtained for functional enrichment analysis by taking the intersection of DEGs and genes in the red module. GO analysis showed that these genes were mainly involved in extracellular matrix organization (ECM) and extracellular structure organization, and others. KEGG analysis revealed that the pathways of aldosterone-regulated sodium reabsorption, cell adhesion molecules, arachidonic acid (AA) metabolism, and ECM-receptor interaction were enriched. Through PPI network construction, 30 hub genes were identified. CIBERSORT analysis revealed a significantly increased proportion of M0 macrophages, while ssGSEA revealed no significant differences. Among these hub genes, SPP1, LCN2, MMP7, MUC1, SCNN1A, CLU, SLP1, LAMC2, and CYSLTR2 were positively correlated with macrophages infiltration. GSEA analysis found that positive regulation of JNK activity was enriched in RP tissues with high SPP1 expression, while negative regulation of IL-1β production was enriched in the low-SPP1 subgroup.ConclusionsThere are 30 hub genes associated with KSD, among which SPP1 is the top hub gene with the most extensive links with other hub genes. SPP1 might play a pivotal role in the pathogenesis of KSD, which is expected to become a potential therapeutic target, while its interaction with macrophages in KSD needs further investigation.

Identification of competing endogenous RNA network in laryngeal squamous cell carcinoma.

This study was conducted to investigate key long noncoding RNAs (lncRNAs) involved in competitive endogenous RNA (ceRNA) network associated with laryngeal squamous cell carcinoma (LSCC). Three mRNA datasets, two miRNA datasets, and one lncRNA dataset of LSCC were downloaded from GEO database. Following the identification of differentially expressed mRNAs (DEmRNAs), (microRNAs) miRNAs (DEmiRNAs), and lncRNAs (DElncRNAs) in LSCC compared with adjacent tissues, functional enrichment of DEmRNAs was performed. Then, construction of the ceRNA (DElncRNA-DEmiRNA-DEmRNA) regulatory network and functional analyses of all DEmRNAs in ceRNA regulatory network were conducted. Quantitative real-time polymerase chain reactions (qRT-PCR) were used to detect the expression levels of selected DEmRNAs, DEmiRNAs, and DElncRNAs. A total of 3449 DEmRNAs, 40 DEmiRNAs, and 100 DElncRNAs were identified in LSCC. The ceRNA networks, which contained 132 DElncRNA-DEmiRNA pairs and 287 DEmiRNA-DEmRNA pairs, involving 44lncRNAs, 3miRNAs, and 271mRNAs, were obtained. DEmRNAs in ceRNA regulatory networks were significantly enriched in pathways in cancer, prostate cancer, and aldosterone-regulated sodium reabsorption. Except for HCG22 and hsa-miR-1246, expressions of the others in the qRT-PCR results played the same pattern with that in our integrated analysis, generally. We concluded that HCG22/EGOT-hsa-miR-1275-FAM107A and HCG22/EGOT-hsa-miR-1246-Glycerol-3-phosphate dehydrogenase 1like interaction pairs may play a central role in LSCC.

Study on potential molecular mechanism of Mongolian medicine Bawei Sanxiang San in treatment of chronic heart failure based on network pharmacology and molecular docking

To explore the potential molecular mechanism of Mongolian medicine Bawei Sanxiang San in the treatment of chronic heart failure(CHF) through network pharmacology and molecular docking technology. The active ingredients and potential targets of Bawei Sanxiang San were collected by applying TCMSP, BATMAN databases and literature mining. CHF-related genes were collected through TTD, GeneCards and CTD databases. After the potential common targets between Bawei Sanxiang San and CHF were disco-vered, the interaction network diagram of "compound-target-pathway" was constructed using Cytoscape. The intersecting targets were imported into the DAVID database for GO function and KEGG pathway enrichment analysis. Finally, the Autodock_vina software was used to molecularly dock the selected proteins with the active ingredients of Bawei Sanxiang San. The results showed that there were 60 active ingredients in Bawei Sanxiang San that might be used to treat CHF, involving 311 target genes and 7 signaling pathways that directly related to CHF, such as HIF-1 signaling pathway, TNF signaling pathway, adrenergic signaling in cardiomyocytes, aldosterone-regulated sodium reabsorption, calcium signaling pathway, cGMP-PKG signaling pathway, renin secretion. Additionally, molecular docking showed that the bioactive compounds had good binding activity with the protein receptors of key target genes. Bawei Sanxiang San might exert therapeutic effects on CHF by regulating cardiomyocytes, angiogenic and inflammation related targets and pathways in a multi-component, multi-target and multi-pathway manner.

Identification of key genes in type 2 diabetes-induced erectile dysfunction rats with stem cell therapy through high-throughput sequencing and bioinformatic analysis.

Diabetes mellitus erectile dysfunction (DMED) is a frequent complication of diabetes. Mesenchymal stem cell (MSC) therapy was demonstrated to improve erectile function in DMED. However, the pathogenesis of DMED and the mechanism by which MSCs function are still unclear. We established a rat model of DMED and gave MSC therapy through intracavernous injection. After transcriptome sequencing of rats' penile tissue, we identified a total of 1,097 overlapped differentially expressed genes (DEGs) of the normal control group, DMED group, and MSC-treated group, containing 189 upregulated genes and 908 downregulated genes. The enriched functions of upregulated DEGs included extracellular matrix organisation (GO:0030198), extracellular structure organisation (GO:0043062), and wound healing (GO:0042060), PPAR signalling pathway (rno03320), arachidonic acid metabolism (rno00590) and retinol metabolism (rno00830). The enriched functions of downregulated DEGs included peptidase activity (GO:0052547), hair follicle development (GO:0001942), intermediate filament-based process (GO:0045103), nitrogen metabolism (rno00910), aldosterone-regulated sodium reabsorption (rno04960) and retinol metabolism (rno00830). We constructed a PPI network with 547 nodes and 2,365 edges and identified 15 hub genes with high connectivity degree. In summary, 15 hub genes with potential roles in the development of ED were identified. Further functional research would be required to elucidate the molecular mechanism underlying misregulated genes.

Construction of circRNA-miRNA-mRNA Network for Exploring Underlying Mechanisms of Lubrication Disorder.

Lubrication disorder is a common health issue that manifests as insufficient sexual arousal at the beginning of sex. It often causes physical and psychological distress. However, there are few studies on lubrication disorder, and the complexity of circular RNA (circRNA) and the related competing endogenous RNA (ceRNA) network in lubrication disorder is still poorly known. Therefore, this study aims to build a regulatory circRNA-micro (mi)RNA-mRNA network and explore potential molecular markers of lubrication disorder. In the study, 12 subjects were recruited, including 6 in the lubrication disorder group and 6 in the normal control group. RNA sequencing was exploited to identify the expression profiles of circRNA, miRNA and mRNA between two groups, and then to construct the circRNA-miRNA-mRNA networks. The enrichment analyses of the differentially expressed (DE)-mRNAs were examined via Gene Set Enrichment Analysis (GSEA). Furthermore, the expression level and interactions among circRNA, miRNA, and mRNA were validated using real-time quantitative polymerase chain reaction (RT-qPCR) and dual-luciferase reporter assays. In the results, 73 circRNAs, 287 miRNAs, and 354 target mRNAs were differentially expressed between two groups when taking | Log2 (fold change)| > 1 and P-value < 0.05 as criteria, and then the results of GSEA revealed that DE-mRNAs were linked with “vascular smooth muscle contraction,” “aldosterone regulated sodium reabsorption,” “calcium signaling pathway,” etc. 19 target relationships among 5 circRNAs, 4 miRNAs, and 7 mRNAs were found and constructed the ceRNA network. Among them, hsa-miR-212-5p and hsa-miR-874-3p were demonstrated to be related to the occurrence of lubrication disorder. Eventually, consistent with sequencing, RT-qPCR showed that hsa_circ_0026782 and ASB2 were upregulated while hsa-miR-874-3p was downregulated, and dual-luciferase reporter assays confirmed the interactions among them. In summary, the findings indicate that the circRNA-miRNA-mRNA regulatory network is presented in lubrication disorder, and ulteriorly provide a deeper understanding of the specific regulatory mechanism of lubrication disorder from the perspective of the circRNA-miRNA-mRNA network.

Identification of significant genes with prognostic influence in clear cell renal cell carcinoma via bioinformatics analysis.

BackgroundClear cell renal cell carcinoma (ccRCC) is the most common malignant tumor of kidney with high mortality. The pathogenesis of ccRCC is complicated and effective prognostic predictors for clinical practice are still limited. This study aimed to identify significant genes with prognostic influence in ccRCC via bioinformatics analysis.MethodsFour gene expression profiles were acquired from the Gene Expression Omnibus (GEO) database, including 168 ccRCC tissues and 143 normal tissues. Common differentially expressed genes (DEGs) between ccRCC tissues and normal kidney tissues were screened out. Then gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were investigated. Protein-protein interaction (PPI) network of the common DEGs was diagrammed and analyzed. Kaplan–Meier analysis was conducted to identify genes with prognostic influence in ccRCC. Gene Expression Profiling Interactive Analysis (GEPIA) was finally applied to validating differential expression of genes.ResultsNinety-nine common DEGs between ccRCC tissues and normal kidney tissues were eventually screened out (P<0.05, |log FC| >2). GO functional analysis showed that the down-regulated genes were enriched in excretion, negative regulation of cell proliferation, heparin binding and cellular response to BMP stimulus, etc. KEGG pathway analysis indicated that the common DEGs were particularly enriched in HIF-1 signaling pathway and aldosterone-regulated sodium reabsorption. Seven core DEGs were distinguished through PPI network analysis, of which 6 core genes ANGPTL4, CA9, CXCR4, LOX, EGF and HRG showed significantly prognostic difference in patients with ccRCC by Kaplan–Meier analysis (P<0.05). And GEPIA confirmed these genes were expressed differentially between tumor and normal tissues (P<0.05). High expression of HRG was correlated with good OS in ccRCC patients. Specifically, HRG was commonly down-regulated in ccRCC tissues compared with normal tissues according to GEPIA.ConclusionsOur study shows that high expression of HRG denotes a better prognosis in ccRCC patients. HRG is down-regulated in ccRCC tissues compared with normal kidney tissues. The selective expression pattern suggests that HRG could be a novel prognostic predictor and potential therapeutic target for ccRCC patients.

Identification of PTPRR and JAG1 as key genes in castration-resistant prostate cancer by integrated bioinformatics methods.

To identify novel genes in castration-resistant prostate cancer (CRPC), we downloaded three microarray datasets containing CRPC and primary prostate cancer in Gene Expression Omnibus (GEO). R packages affy and limma were performed to identify differentially expressed genes (DEGs) between primary prostate cancer and CRPC. After that, we performed functional enrichment analysis including gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway. In addition, protein-protein interaction (PPI) analysis was used to search for hub genes. Finally, to validate the significance of these genes, we performed survival analysis. As a result, we identified 53 upregulated genes and 58 downregulated genes that changed in at least two datasets. Functional enrichment analysis showed significant changes in the positive regulation of osteoblast differentiation pathway and aldosterone-regulated sodium reabsorption pathway. PPI network identified hub genes like cortactin-binding protein 2 (CTTNBP2), Rho family guanosine triphosphatase (GTPase) 3 (RND3), protein tyrosine phosphatase receptor-type R (PTPRR), Jagged1 (JAG1), and lumican (LUM). Based on PPI network analysis and functional enrichment analysis, we identified two genes (PTPRR and JAG1) as key genes. Further survival analysis indicated a relationship between high expression of the two genes and poor prognosis of prostate cancer. In conclusion, PTPRR and JAG1 are key genes in the CRPC, which may serve as promising biomarkers of diagnosis and prognosis of CRPC.

Temporal changes in the spinal cord transcriptome after peripheral nerve injury.

Peripheral nerve injury may trigger changes in mRNA levels in the spinal cord. Finding key mRNAs is important for improving repair after nerve injury. This study aimed to investigate changes in mRNAs in the spinal cord following sciatic nerve injury by transcriptomic analysis. The left sciatic nerve denervation model was established in C57BL/6 mice. The left L4-6 spinal cord segment was obtained at 0, 1, 2, 4 and 8 weeks after severing the sciatic nerve. mRNA expression profiles were generated by RNA sequencing. The sequencing results of spinal cord mRNA at 1, 2, 4, and 8 weeks after severing the sciatic nerve were compared with those at 0 weeks by bioinformatic analysis. We identified 1915 differentially expressed mRNAs in the spinal cord, of which 4, 1909, and 2 were differentially expressed at 1, 4, and 8 weeks after sciatic nerve injury, respectively. Sequencing results indicated that the number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury. These mRNAs were associated with the cellular response to lipid, ATP metabolism, energy coupled proton transmembrane transport, nuclear transcription factor complex, vacuolar proton-transporting V-type ATPase complex, inner mitochondrial membrane protein complex, tau protein binding, NADH dehydrogenase activity and hydrogen ion transmembrane transporter activity. Of these mRNAs, Sgk1, Neurturin and Gpnmb took part in cell growth and development. Pathway analysis showed that these mRNAs were mainly involved in aldosterone-regulated sodium reabsorption, oxidative phosphorylation and collecting duct acid secretion. Functional assessment indicated that these mRNAs were associated with inflammation and cell morphology development. Our findings show that the number and type of spinal cord mRNAs involved in changes at different time points after peripheral nerve injury were different. The number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury. These results provide reference data for finding new targets for the treatment of peripheral nerve injury, and for further gene therapy studies of peripheral nerve injury and repair. The study procedures were approved by the Ethics Committee of the Peking University People's Hospital (approval No. 2017PHC004) on March 5, 2017.

Dietary prebiotic inulin benefits on growth performance, antioxidant capacity, immune response and intestinal microbiota in Pacific white shrimp (Litopenaeus vannamei) at low salinity

Dietary manipulation is a useful approach to improve production and health of farmed shrimp. However, no study has investigated the effect of prebiotic inulin on intestinal microbiota response and physiological status of shrimp at low salinity of 3 psu (practical salinity unit). The effects of dietary inulin additive at 0%, 0.1%, 0.2%, and 0.4% on growth performance, antioxidant capacity, immune response and intestinal microbiota of Pacific white shrimp (Litopenaeus vannamei) at a low salinity of 3 psu were evaluated after an 8-week feeding trial. Shrimp fed the 0.2% and 0.4% inulin diet significantly increased final weight, weight gain, specific growth rate compared to those fed the control diet. Body ash content tended to increases with the increasing level of inulin. Intestinal amylase and hepatopancreas superoxide dismutase (SOD) activity in 0.4% inulin group were higher than in control group. The acid phosphatase (ACP) and phenol oxidase (PO) activities of hepatopancreas were significantly increased in 0.2% and 0.4% inulin group, respectively, compared to control group. Shrimp fed the 0.2% and 0.4% inulin diet reduced hepatopancreas oxidative stress by increasing the catalase (CAT) activity and decreasing the malondialdehyde (MDA) content compared to those fed the control diet. Shrimp fed 0.4% inulin changed intestinal microbiota by increasing the relative abundance of Firmicutes phylum and Bacillus genus. PICRUSt analysis show that the KEGG pathway involved in aldosterone-regulated sodium reabsorption was significantly increased in shrimp fed 0.4% inulin. The shrimp fed 0.4% inulin exhibited more negative interspecies interactions than those fed the control diet. This study suggests that inulin can serve as a potential feed additive that helps shrimp to cope with low salinity stress.

Identification of key pathways and genes in colorectal cancer to predict the prognosis based on mRNA interaction network.

The aim of the present study was to identify key genes in colorectal cancer (CRC) that could be used to reliably diagnose this disease and to explore the potential underlying mechanisms in silico. The gene expression profiles of primary human cancer datasets GSE21510 and GSE32323 were downloaded from the Gene Expression Omnibus database. The limma R software package was used to identify differentially expressed (DE) genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on DE genes using the Database for Annotation, Visualization and Integrated Discovery. The Search Tool for the Retrieval of Interacting Genes/Proteins database was used to construct a protein-protein interaction (PPI) network of the DE genes. Survival rate was analyzed and visualized using The Cancer Genome Atlas (TCGA). A total of 1,126 genes were significantly DE in the present study. All DE genes were enriched in KEGG pathways including ‘cell cycle’, ‘mineral absorption’, ‘pancreatic secretion’, ‘pathways in cancer’, ‘metabolic pathways’, ‘aldosterone-regulated sodium reabsorption’ and ‘Wnt signaling pathway’. A total of 5 hub genes enriched in cell cycle and tumor-associated pathways, including E2F2, SKP2, MYC, CDKN1A and CDKN2B, were significantly DE and validated between tumor and normal tissues. CDKN1A and CDKN2B were identified within the PPI network using the Molecular Complex Detection algorithm. Survival and content distribution analyses of 362 clinical samples from TCGA revealed that CDKN1A effectively predicted the prognosis of patients. The present study identified key genes and potential signaling pathways involved in CRC. These findings may provide new insights for survival assessment during the clinical diagnosis of CRC.

Identification of key genes involved in the metastasis of clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) is the most common and lethal renal malignant tumor in adults. The aim of the present study was to identify the key genes involved in ccRCC metastasis. Expression profiling data for ccRCC patients with metastasis and without metastasis were obtained from The Cancer Genome Atlas database. The datasets were used to identify differentially expressed genes (DEGs) between the metastasis group and the non-metastasis group using the DESeq2 package. Function enrichment analyses of DEGs were performed. The protein-protein interaction (PPI) network was constructed and analyzed using the Search Tool for the Retrieval of Interacting Genes and Cytoscape for further analysis of the identified hub genes. A total of 472 DEGs were identified, including 247 that were upregulated and 225 that were downregulated in the metastasis group. Gene Ontology enrichment analysis revealed that DEGs were mainly enriched in cell transmembrane movement and mitotic cell cycle process. Kyoto Encyclopedia of Genes Genomes pathway analysis revealed that the DEGs were mainly involved in the ‘cell cycle’ (hsa04110), ‘collecting duct acid secretion’ (hsa04966), ‘complement and coagulation cascades’ (hsa04610) and ‘aldosterone-regulated sodium reabsorption’ (hsa04960) pathways. Using the PPI network, 35 hub genes were identified, and the majority of them were upregulated in ccRCC tissue compared with normal kidney tissue. The expression levels of certain hub genes (CDKN3, TPX2, BUB1B, CDCA8, UBE2C, NDC80, RRM2, NCAPG, NCAPH, PTTG1, FAM64A, ANLN, KIF4A, CEP55, CENPF, KIF20A, ASPM and HJURP) were significantly associated with overall survival and recurrence-free survival in ccRCC. The present study has identified key genes associated with the metastasis of ccRCC.