Retinol Metabolism Pathway Research Articles

Laminarin ameliorates alcohol‐induced liver damage and its molecular mechanism in mice

Alcoholic liver disease (ALD) has become a health issue globally. Laminarin, a low molecular weight marine-derived β-glucan, has been identified with multiple biological activities. In this study, the ameliorative effect on ALD of laminarin isolated from brown algae was investigated. Phenotypic, pathological alterations and biochemical characteristics indicated that laminarin administration (100 mg/kg/day) significantly alleviated liver injury and improved liver function in the alcohol-induced mice. Gene chip results indicated that laminarin treatment caused 52 up-regulated and 13 down-regulated genes in the hepatic tissues of alcohol-induced damage mice, and most of these genes are associated with regulation of oxidative stress (such as CYP450/glutathione-dependent antioxidation), Wnt signaling pathway, retinol metabolism, and cAMP pathway based on GO and KEGG analysis. PPI network analysis indicated that the downstream target genes lied in the hub of the net. Our experiments also confirmed the changed expressions of some target genes. Taken together, these results suggest that laminarin can ameliorate alcohol-induced damage in mice and its molecular mechanism lies in modulating anti-oxidation pathway, WNT pathway, and cAMP pathway, which regulate the expressions of downstream target genes and alleviate alcohol-induced damage. Our study provides new clue to prevent alcohol-induced damage and will be benefit to develop functional foods. PRACTICAL APPLICATIONS: This study verified the positive effect on alcoholic liver disease (ALD) of laminarin, a water-soluble brown algae-derived β-glucan, linked by β-(1,3) glycosidic bonds with β-(1,6) branches. Laminarin significantly alleviated liver injury and improved liver function of ALD mice. Moreover, transcriptomics and bioinformatics analysis further revealed the gene expression patterns, hub targets, and signalings including CYP450/glutathione, Wnt, retinol metabolism, cAMP pathways regulated by laminarin. This research is the first evidence for hepatoprotective effect of laminarin against ALD and its molecular mechanism, which will be advantage to develop functional foods or adjuvant therapy of ALD.

MELTF Might Regulate Ferroptosis, Pyroptosis, and Autophagy in Platelet-Rich Plasma-Mediated Endometrial Epithelium Regeneration.

The endometrial basal layer is essential for endometrial regeneration, whose disruption leads to thin endometrium or intrauterine adhesion (IUA) with an unsatisfactory prognosis. Emerging data indicate that platelet-rich plasma (PRP) can promote endometrial proliferation, but the mechanism by which PRP regulates endometrial regeneration remains unclear. Herein, we investigated the therapeutic effects and possible mechanisms of PRP on endometrial regeneration. IUA animal model was generated by sham, mechanically damaging endometrium with or without PRP for 10days. The uterine section in the model group showed degenerative changes with a narrow endometrial lumen, atrophic columnar epithelium, decreased number of endometrial glands, decreased endometrial thickness, and increased collagen deposition. The above disruption could be ameliorated by the PRP. Transcriptome sequencing analysis displayed that the retinol metabolism pathway and extracellular matrix (ECM) receptor interaction pathway were up-regulated and enriched in differential expression genes (DEGs). Melanotransferrin (MELTF) was the key up-regulated gene in PRP-induced endometrial regeneration, which was verified in vivo and in vitro. Ferroptosis, autophagy, and pyroptosis were down-regulated in PRP-treated Ishikawa cells. Conclusively, PRP promotes endometrium regeneration by up-regulating the retinol metabolism and ECM receptor interaction pathway with MELTF. Meanwhile, PRP could also inhibit endometrial epithelial cell death by regulating ferroptosis, autophagy, and pyroptosis.

Limosilactobacillus reuteri FN041 prevents atopic dermatitis in pup mice by remodeling the ileal microbiota and regulating gene expression in Peyer's patches after vertical transmission.

ObjectivesLimosilactobacillus reuteri FN041 is a potential probiotic bacterium isolated from breast milk in traditional farming and pastoral areas of China. The purpose of this study was to investigate the optimal intervention mode and potential mechanism of FN041 to prevent atopic dermatitis (AD) in mice.MethodsIn intervention mode I, FN041 was supplemented to dams during the late trimester and lactation and pups after weaning; in intervention mode II, FN041 was supplemented after pups were weaned. AD was induced in pups with MC903 plus ovalbumin on the ear after weaning.ResultsThe effect of intervention mode I in preventing AD was significantly better than that of intervention mode II. Compared with the model group, the inflammatory response of the pup’s ears, the proportion of spleen regulatory T cells and the plasma IgE were significantly decreased in mice in intervention mode I. Furthermore, the intestinal mucosal barrier was enhanced, and the Shannon index of the ileal microbiota was significantly increased. The microbiota structure deviated from the AD controls and shifted toward the healthy controls according to the PCoA of unweighted UniFrac. The relative abundances of Limosilactobacillus, Faecalibacterium, Bifidobacterium, and Akkermansia in the ileum were significantly increased compared to the AD group. Based on RNA-seq analysis of pups’ Peyer’s patches (PPs), FN041 inhibits autoimmune pathways such as asthma and systemic lupus erythematosus and activates retinol metabolism and PPAR signaling pathways to reduce inflammatory responses. Intervention mode II also significantly reduced AD severity score, but the reduction was approximately 67% of that of intervention mode I. This may be related to its ineffective remodeling of the ileal microbiota.ConclusionPrenatal and postnatal administration of FN041 is an effective way to prevent AD in offspring, and its mechanism is related to remodeling of ileal microbiota and PPs immune response.

Tributyltin exposure disrupted the locomotor activity rhythms in adult zebrafish (Danio rerio) and the mechanism involved

The fish circadian rhythm system might be an emerging target of tributyltin (TBT), however, the mechanism by which TBT interferes with the circadian rhythm is poorly understood. Therefore, in the present study, zebrafish were used to assess the effects of TBT at environmental concentrations (1 and 10 ng/L) on locomotor activity rhythm. Furthermore, we focused on the visual system to explore the potential mechanism involved. After 90 d of exposure, TBT disturbed the locomotor activity rhythms in zebrafish, which manifested as: (1) low activities and lethargy during the arousing period; (2) inability to fall asleep quickly and peacefully during the period of latency to sleep; and (3) no regular “waves” of locomotor activities during the active period. After TBT exposure, the histological structure of the eyes significantly changed, the boundary between layers became blurred, and the melanin concentrations significantly decreased. Using KEGG and GSEA pathway analyses, the differentially expressed genes in the eyes screened by transcriptomics were significantly enriched in the tyrosine metabolism pathway and retinol metabolism pathway. Furthermore, a decrease in melanin and disruption of retinoic acid were found after TBT exposure, which would affect the reception of phototransduction, and then interfere with the circadian rhythm in fish. The disruption of the circadian rhythm of fish by aquatic pollutants would decrease their ecological adaptability, which should be considered in future research.

Identification of a chromatin regulator signature and potential prognostic ability for adrenocortical carcinoma.

Objective: Adrenocortical carcinoma (ACC) is a rare malignant tumor. Chromatin regulators (CRs) can drive epigenetic changes, which have been considered as one of the most vital hallmarks of tumors. This study aimed to explore the CR signature for ACC in order to clarify the molecular basis of ACC’s pathogenic mechanism and provide novel methods to diagnose and treat ACC clinically. Methods: This study obtained transcriptome sequencing datasets of ACC patients and sequencing data on normal adrenal tissues in TCGA and GTEx databases, respectively. Meanwhile, prognostic genes were selected through Lasso and Cox regression analyses. Using the transcriptome sequencing datasets of ACC patients downloaded from the GEO database to finish validation, we performed Kaplan–Meier (KM) analysis for evaluating the differential survival between low- and high-risk groups. Then, this work constructed the risk model for predicting ACC prognosis. TIMER 2.0 was employed to assess the differences in immune infiltration between the two groups. Furthermore, this work adopted the R package “pRRophetic” for exploring and estimating the sensitivity of patients to different chemotherapeutic agents. Results: A 5-CR model was established to predict ACC survival, and the CR signature was confirmed as a factor in order to independently predict ACC patient prognosis. In addition, a nomogram composed of the risk score and clinical T stage performed well in the prediction of patients’ prognosis. Differentially expressed CRs (DECRs) were mostly associated with the cell cycle, base excision repair, colon cancer, gene duplication, homologous recombination, and other signaling pathways for the high-risk group. As for the low-risk group, DECRs were mainly enriched in allograft rejection, drug metabolism of cytochrome P450, metabolism of xenogeneic organisms by cytochrome P450, retinol metabolism, and other signaling pathways. According to TIMER analysis, the immune infiltration degrees of endothelial cells, M2 macrophages, myeloid dendritic cells, CD4+ Th1 cells, NKT cells, and M0 macrophages showed significant statistical differences between the high- and low-risk groups, and high infiltration levels of M0 and M2 macrophages were more pronounced in higher T stage (T3 and T4), N stage (N1), and clinical stages (III and IV). In addition, high-risk cases exhibited higher sensitivity to etoposide and doxorubicin. Additionally, low-risk patients had significantly decreased expression of RRM1 compared with high-risk cases, suggesting the better effect of mitotane treatment. Conclusion: This study identified the DECRs, which might be related to ACC genesis and progression. The pathways enriched by these DECRs were screened, and these DECRs were verified with excellent significance for estimating ACC survival. Drug sensitivity analysis also supported the current clinical treatment plan. Moreover, this study will provide reliable ideas and evidence for diagnosing and treating ACC in the clinic.

Effects and potential mechanism of Ca2+/calmodulin‑dependent protein kinase II pathway inhibitor KN93 on the development of ovarian follicle

Adequate regulation of the speed of follicular development has been reported to prolong the reproductive life of the ovary. The aim of the present study was to assess the potential effects and mechanism of the Ca2+/calmodulin-dependent protein kinase II (CaMKII) pathway on the development of ovarian follicle. In the present study, the expression of CaMKII was measured in the ovary of mice at different developmental stages by immunofluorescence, confirming that CaMKII has a role in follicular development. Subsequently, the 17.5 days post-coitus (dpc) embryonic ovaries were collected and cultured with KN93 for 4 days in vitro. It was revealed that KN93 inhibited the development of follicles, where it reduced the expression levels of oocyte and granulosa cell markers DEAD-box helicase 4 (DDX4) and forkhead box L2 (FOXL2). These results suggested that KN93 could delay follicular development. Proteomics technology was then used to find that 262 proteins of KN93 treated 17.5 dpc embryonic ovaries were significantly altered after in vitro culture. Bioinformatics analysis was used to analyze these altered proteins. In total, four important Kyoto Encyclopedia of Genes and Genome pathways, namely steroid biosynthesis, p53 signaling pathway and retinol metabolism and metabolic pathways, were particularly enriched. Further analysis revealed that the upregulated proteins NADP-dependent steroid dehydrogenase-like (Nsdhl), lanosterol synthase (Lss), farnesyl-diphosphate farnesyltransferase 1 (Fdft1), cytochrome P450 family 51 family A member 1 (Cyp51a1), hydroxymethylglutaryl-CoA synthase 1 (Hmgcs1), fatty acid synthase (Fasn) and dimethylallyltranstransferase (Fdps) were directly interacting with each other in the four enriched pathways. In summary, the potential mechanism of KN93 in slowing down follicular development most likely lies in its inhibitory effects on CaMKII, which upregulated the expression of Nsdhl, Lss, Fdft1, Cyp51a1, Hmgcs1, Fasn and Fdps. This downregulated the expression of oocyte and granulosa cell markers DDX4 and FOXL2 in the follicles, thereby delaying follicular development. Overall, these results provide novel insight into the potential mechanism by which KN93 and CaMKII can delay follicular development.

Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analysis Provide Insights Into the Ovarian Maturation of Exopalaemon carinicauda

The ridgetail white shrimp Exopalaemon carinicauda has the potential to be used as a useful experimental organism in the field of crustacean research due to its transparent body, large egg, and short reproductive cycle. However, little is known about the regulatory mechanisms of ovarian maturation in E. carinicauda. In this study, we applied PacBio single-molecule long-read sequencing technology to unveil the whole transcriptome landscape of Exopalaemon carinicauda to better understand the molecular mechanisms of ovarian development. A total of 49.05 G polymerase read bases were generated, finally, 15, 151 unigenes were successfully identified with a mean length of 4, 257 bp and an N50 of 4, 884 bp from ovary tissues (five different ovarian developmental stages). A total of 14, 007 unigenes were successfully annotated in at least one public database. In addition, 8, 861 coding sequences, 4, 594 lncRNAs and 895 transcription factors were identified. Furthermore, we performed RNA-Seq analysis combined with Iso-Seq results to investigate ovarian maturation regulation mechanism and validated the results by quantitative real-time PCR. We annotated five vitellogenin isoforms in the full-length transcriptome, meanwhile these five genes and vitellogenin receptor suggested an important role during previtellogenesis of E. carinicauda. Genes were involved in PI3K-Akt signaling pathway, retinol metabolism, cell cycle and hedgehog signaling pathway, which showed obvious associations with ovarian maturation of E. carinicauda. We identified 40 DEGs, such as forkhead box protein L2, which may be related to ovarian development in the comparisons. The expression profiles of genes such as ecdysone receptor, ecdysone-induced protein 74EF, ecdysone inducible gene E75 and post-molt protein suggest that they were significantly associated with reproductive molting in the ovarian mature stage. In conclusion, the present study identified important genes and pathways involved in ovarian maturation, which might be useful for studying the reproductive regulation and mechanisms of ovarian maturation in E. carinicauda.

Socializing Models During Lactation Alter Colonic Mucosal Gene Expression and Fecal Microbiota of Growing Piglets.

The enrichment of the social environment during lactation alleviates the stress of weaned piglets. It is significant to understand how the enriched social environment improves the weaning stress of piglets. RNA sequencing (RNA-seq) of colonic mucosa, 16S rRNA sequencing of feces, and short-chain fatty acids (SCFAs) of colonic content were used to determine the effects of social contact during lactation. In this study, thirty litter lactating piglets were divided into intermittent social contact (ISC) group that contacted with neighbors intermittently, continuous social contact (CSC) group that contacted with neighbors starting at day (D) 14 after birth, and control (CON) group in which piglets were kept in their original litter. The piglets were weaned at D35 and regrouped at D36. The colonic mucosal RNA-seq, fecal microbes, and SCFAs of colonic contents of 63-day-old piglets were analyzed. The results of RNA-seq showed that compared with the CON group, the pathways of digestion and absorption of minerals, protein, and vitamins of piglets were changed in the ISC group, whereas the pathways of retinol metabolism and nitrogen metabolism in the colonic mucosal were affected and stimulated the immune response in the CSC group. Compared with the CON group, the abundances of pernicious microorganisms (Desulfovibrio, Pseudomonas, Brevundimonas, etc.) in the CSC group and pernicious microorganisms (Desulfovibrio, Neisseria, Sutterella, etc.) and beneficial bacteria (Bifidobacterium, Megamonas, and Prevotella_9) in the ISC group were significantly higher (p < 0.05). The abundances of proinflammatory bacteria (Coriobacteriaceae_unclassified, Coprococcus_3, and Ruminococcus_2) in the CSC group were significantly increased (p < 0.05), but the abundances of SCFAs producing bacteria (Lachnospiraceae_UCG-010, Parabacteroides, Anaerotruncus, etc.) and those of anti-inflammatory bacteria (Eubacterium, Parabacteroides, Ruminiclostridium_9, and Alloprevotella) were significantly reduced (p < 0.05) in the CSC group. Compared with the CON group, the concentrations of microbial metabolites, acetate, and propionate in the colonic contents were reduced (p < 0.05) in the ISC group, whereas the concentration of acetate was reduced (p < 0.05) in the CSC group. Therefore, both ISC and CSC during lactation affected the composition of fecal microbes and changed the expression of intestinal mucosal genes related to nutrient metabolism and absorption of piglets.

Anti-liver fibrosis effects of the total flavonoids of litchi semen on CCl4-induced liver fibrosis in rats associated with the upregulation of retinol metabolism

Context The litchi semen are traditional medications for treating liver fibrosis (LF) in China. The mechanism remains unclear. Objective This study investigates the anti-liver fibrotic mechanism of the total flavonoids of litchi semen (TFL). Materials and methods Sprague-Dawley rats with carbon tetrachloride-induced LF were treated with TFL (50 and 100 mg/kg) for 4 weeks. The anti-liver fibrotic effects of TFL were evaluated and the underlying mechanisms were investigated via histopathological analysis, proteomic analysis and molecular biology technology. Results Significant anti-LF effects were observed in the high-TFL-dose group (TFL-H, p < 0.05). Five hundred and eighty-five and 95 differentially expressed proteins (DEPs) were identified in the LF rat model (M group) and TFL-H group, respectively. The DEPs were significantly enriched in the retinol metabolism pathway (p < 0.0001). The content of 9-cis-retinoic acid (0.93 ± 0.13 vs. 0.66 ± 0.10, p < 0.05, vs. the M group) increased significantly in the TFL-H group. The upregulation of RXRα (0.50 ± 0.05 vs. 0.27 ± 0.13 protein, p < 0.05), ALDH2 (1.24 ± 0.09 vs. 1.04 ± 0.08 protein, p < 0.05), MMP3 (0.89 ± 0.02 vs. 0.61 ± 0.12 protein, p < 0.05), Aldh1a7 (0.20 ± 0.03 vs. 0.03 ± 0.00 mRNA, p < 0.05) and Aox3 (0.72 ± 0.14 vs. 0.05 ± 0.01 mRNA, p < 0.05) after TFL treatment was verified. Conclusions TFL exhibited good anti-liver fibrotic effects, which may be related to the upregulation of the retinol metabolism pathway. TFL may be promising anti-LF agents with potential clinical application prospects.

Abstract 5414: RNA sequencing reveals that CYP3A5 siRNA treatment induces cell cycle blockade and senescence in MDAPCa2b human prostate cancer cells

Abstract Background: Previously we have demonstrated that CYP3A5 inhibition blocks prostate cancer (PC) cell growth partly by attenuating androgen receptor (AR) activation and downstream signaling. We further investigated whether CYP3A5 inhibition blocks PC cell growth independently of AR signaling. Initially, most PCs respond to androgen deprivation therapy (ADT), but eventually PC becomes castration resistant and does not respond to ADT. With very limited options available for patients with castration resistant prostate cancer (CRPC), there is an urgent need for the development of novel targeted therapies for this subtype of PC. Additionally, understanding the role of CYP3A5 as promoter of PC growth in African Americans (AA) is very relevant as AAs preferentially carry wild type CYP3A5 gene, often present with aggressive disease, and have higher mortality rate versus Caucasian (CA) patients, who typically express the mutant CYP3A5. Method: We used MDAPCa2b PC cell line of AA origin carrying one copy of wild type CYP3A5 for our study. After inhibiting the CYP3A5 using siRNA pool of 3 siRNAs, we performed Illumina RNA sequencing. Differentially expressed genes (DEGs) between non-target and CYP3A5 siRNA triplicate samples were identified using DESeq2, at a false discovery rate of adjusted p &amp;lt; 0.05. Furthermore, KEGG pathway analysis was performed to identify the roles of the differentially expressed genes in regulating prostate cancer growth. Results: We identified 1814 DEGs after inhibiting CYP3A5 using siRNA pool in MDAPCa2b cells, 825 of which increased or decreased expression greater than two-fold. The differentially down-regulated genes associate with several growth regulatory pathways: cell cycle progression (39), cellular senescence (16) DNA replication (18) and base excision repair (9). Additionally, we identified that CYP3A5 siRNA downregulates several genes which are dysregulated (including oncogenes and tumor suppressors) in different cancer type including RAS, c-Met, ERBB2, FGFR2, cyclin E, p53, Myc, PTEN, RARβ and CDK2. The upregulated genes correspond to two pathways, retinol metabolism pathway (arrests proliferation) and steroid hormone biosynthesis. We also identified several unique genes which are down regulated with CYP3A5 siRNA treatment like Glo1, FoxM1 (often upregulated in several cancers) and Tk1 (marker for chemotherapy sensitivity). Conclusion: CYP3A5 siRNA inhibits several genes involved in cell growth and proliferation. Targeting CYP3A5 represents a potential novel therapeutic approach, especially for AAs expressing wild type CYP3A5. Citation Format: Richard L. Tillett, Shirley Shen, Edwin C. Oh, Oscar B. Goodman Jr., Ranjana Mitra. RNA sequencing reveals that CYP3A5 siRNA treatment induces cell cycle blockade and senescence in MDAPCa2b human prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5414.

Human Plasma Metabolomics Identify 9-cis-retinoic Acid and Dehydrophytosphingosine Levels as Novel biomarkers for Early Ventricular Fibrillation after ST-elevated Myocardial Infarction

ABSTRACT The relevant metabolite biomarkers for risk prediction of early onset of ventricular fibrillation (VF) after ST-segment elevation myocardial infarction (STEMI) remain unstudied. Here, we aimed to identify these imetabolites and the important metabolic pathways involved, and explore whether these metabolites could be used as predictors for the phenotype. Plasma samples were obtained retrospectively from a propensity-score matched cohort including 42 STEMI patients (21 consecutive VF and 21 non-VF). Ultra-performance liquid chromatography and mass spectrometry in combination with a comprehensive analysis of metabolomic data using Metaboanalyst 5.0 version were performed. As a result, the retinal metabolism pathway proved to be the most discriminative for the VF phenotype. Furthermore, 9-cis-Retinoic acid (9cRA) and dehydrophytosphingosine proved to be the most discriminative biomarkers. Biomarker analysis through receiver operating characteristic (ROC) curve showed the 2-metabolite biomarker panel yielding an area under the curve (AUC) of 0.836. The model based on Monte Carlo cross-validation found that 9cRA had the greatest probability of appearing in the predictive panel of biomarkers in the model. Validation of model efficiency based on an ROC curve showed that the combination model constructed by 9cRA and dehydrophytosphingosine had a good predictive value for early-onset VF after STEMI, and the AUC was 0.884 (95% CI 0.714–1). Conclusively, the retinol metabolism pathway was the most powerful pathway for differentiating the post-STEMI VF phenotype. 9cRA was the most important predictive biomarker of VF, and a plasma biomarker panel made up of two metabolites, may help to build a potent predictive model for VF.

Serum Metabolomic Profiling Reveals Biomarkers for Early Detection and Prognosis of Esophageal Squamous Cell Carcinoma.

Esophageal squamous cell carcinoma (ESCC) is one of the most common aggressive malignancies worldwide, particularly in northern China. The absence of specific early symptoms and biomarkers leads to late-stage diagnosis, while early diagnosis and risk stratification are crucial for improving overall prognosis. We performed UPLC-MS/MS on 450 ESCC patients and 588 controls consisting of a discovery group and two validation groups to identify biomarkers for early detection and prognosis. Bioinformatics and clinical statistical methods were used for profiling metabolites and evaluating potential biomarkers. A total of 105 differential metabolites were identified as reliable biomarker candidates for ESCC with the same tendency in three cohorts, mainly including amino acids and fatty acyls. A predictive model of 15 metabolites [all-trans-13,14-dihydroretinol, (±)-myristylcarnitine, (2S,3S)-3-methylphenylalanine, 3-(pyrazol-1-yl)-L-alanine, carnitine C10:1, carnitine C10:1 isomer1, carnitine C14-OH, carnitine C16:2-OH, carnitine C9:1, formononetin, hyodeoxycholic acid, indole-3-carboxylic acid, PysoPE 20:3, PysoPE 20:3(2n isomer1), and resolvin E1] was developed by logistic regression after LASSO and random forest analysis. This model held high predictive accuracies on distinguishing ESCC from controls in the discovery and validation groups (accuracies > 89%). In addition, the levels of four downregulated metabolites [hyodeoxycholic acid, (2S,3S)-3-methylphenylalanine, carnitine C9:1, and indole-3-carboxylic acid] were significantly higher in early cancer than advanced cancer. Furthermore, three independent prognostic markers were identified by multivariate Cox regression analyses with and without clinical indicators: a high level of MG(20:4)isomer and low levels of 9,12-octadecadienoic acid and L-isoleucine correlated with an unfavorable prognosis; the risk score based on these three metabolites was able to stratify patients into low or high risk. Moreover, pathway analysis indicated that retinol metabolism and linoleic acid metabolism were prominent perturbed pathways in ESCC. In conclusion, metabolic profiling revealed that perturbed amino acids and lipid metabolism were crucial metabolic signatures of ESCC. Both panels of diagnostic and prognostic markers showed excellent predictive performances. Targeting retinol and linoleic acid metabolism pathways may be new promising mechanism-based therapeutic approaches. Thus, this study would provide novel insights for the early detection and risk stratification for the clinical management of ESCC and potentially improve the outcomes of ESCC.

Characterization of the microRNA Expression Profiles in the Goat Kid Liver.

The liver is the largest digestive gland in goats with an important role in early metabolic function development. MicroRNAs (miRNA) are crucial for regulating the development and metabolism in the goat liver. In the study, we sequenced the miRNAs in the liver tissues of the goat kid to further research their regulation roles in early liver development. The liver tissues were procured at 5-time points from the Laiwu black goats of 1 day (D1), 2 weeks (W2), 4 weeks (W4), 8 weeks (W8), and 12 weeks (W12) after birth, respectively with five goats per time point, for a total of 25 goats. Our study identified 214 differential expression miRNAs, and the expression patterns of 15 randomly selected miRNAs were examined among all five age groups. The Gene ontology annotation results showed that differential expression miRNA (DE miRNA) target genes were significantly enriched in the fatty acid synthase activity, toxin metabolic process, cell surface, and antibiotic metabolic process. The KEGG analysis result was significantly enriched in steroid hormone synthesis and retinol metabolism pathways. Further miRNA-mRNA regulation network analysis reveals 9 differently expressed miRNA with important regulation roles. Overall, the DE miRNAs were mainly involved in liver development, lipid metabolism, toxin related metabolism-related biological process, and pathways. Our results provide new information about the molecular mechanisms and pathways in the goat kid liver development.

Discovery of Sex-Determining Genes in Portunus trituberculatus: A Comparison of Male and Female Transcriptomes During Early Developmental Stages

Portunus trituberculatus is one of the main mariculture crabs of high economic value. To identify genes involved in sex determination, we first performed sex-specific transcriptome sequencing at six larval development stages using a DNA/RNA co-extraction method. A total of 907,952,938 and 828,774,880 reads were obtained from female and male crabs, respectively. 2,379 differentially expressed genes (DEGs) were found between females and males, and were mainly enriched in DNA replication, folate biosynthesis, and retinol metabolism pathways. Furthermore, transcription patterns of genes in the sex-determining region (SD) were analyzed based on the transcriptome data, and one Dmrt gene (PtDMY) was found to be exclusively expressed in males during early developmental stages. Notably, some known sex-related genes, including IAG, Dmrt11E, DmrtB1, and DmrtC2 were significantly down-regulated after knocking down PtDMY. Our results suggested that PtDMY is involved in sex determination and may be one of the key upstream regulators of the sex determination pathway. In addition, the massive volume of transcriptome data obtained in this study provided an important basis for the systematic study of sex determination mechanisms in P. trituberculatus.

Role of CD5L and SRD5A2 as Prognostic Biomarkers for Hepatocellular Carcinoma.

PurposeDue to the limitations of currently available biomarkers, new biomarkers are needed to accurately predict the prognosis of patients with hepatocellular carcinoma (HCC) patients.MethodsIn this study, we screened for differentially expressed genes (DEGs) in the tumor and the adjacent tissues using the four gene expression array (GSE14520, GSE45267, GSE121248, GSE62232) of the Gene Express Omnibus (GEO) database.ResultsSubsequently, 47 overlapping DEGs were identified in four GEO datasets, which were mostly located on chromosomes 5q and 6q, distributed in the liver and CD105-positive endothelial cells, and closely related to HCC. Function enrichment revealed 47 DEGs were related to HCC, and involved in steroid /lipid /retinol metabolism, bile secretion and p53 signalling pathway. The Kaplan–Meier plotter analysis (http://www.kmplot.com/) identified 26 and 40 genes associated with the 5-year overall survival (OS) and relapse-free survival (RFS). We found that CD5L and SRD5A2 were independent prognostic factors for 5-year OS (P=0.036) and RFS (P=0.044) in HCC patients from GSE14520, respectively. Clinicopathological features including BCLC stage, cirrhosis, and risk signature for predicted metastasis were used to construct and validate a nomogram for 5-year OS with C-index of 0.732 and 0.717 in the training and validation cohort, respectively. SRD5A2, BCLC stage and gender was independent prognostic factors for RFS which were used to build a nomogram with the C-index of 0.666 and 0.682 in the training and validation cohort, respectively.ConclusionCD5L can facilitate individualized, targeted therapy for HCC patients.

Crosstalk between Heart Failure and Cognitive Impairment via hsa-miR-933/RELB/CCL21 Pathway.

Background The association between heart failure (HF) and cognitive impairment has received increasing attention from scholars and researchers in recent years. However, no systematic studies have been carried out yet focused on the crosstalk between heart failure and cognitive impairment via miRNAs. Methods GSE104150, GSE53473, GSE120584, and GSE116250 with RNA-seq data and clinical data were downloaded from the GSE database. All data were statistically analysed using R software to detect DE-miRNAs and DE-mRNAs associated with both HF and cognitive impairment. Protein-protein interaction (PPI) networks were mapped, and a logistic regression model for cognitive impairment prediction was developed. Furthermore, the TTRUST database and miRWalk were used to map miRNA-transcription factor (TF) and messenger RNA (mRNA) regulatory pathways. Finally, core TFs were enriched for analysis. Results Differentially enriched DE-miRNAs and DE-mRNAs both present in HF and cognitive impairment were determined. A logistic regression model established based on DE-miRNAs was validated to have a strong performance in cognitive impairment prediction. The core miRNA-TF-mRNA pathway was formed by mapping the PPI networks associated with the two diseases. Further GSEA was performed with V-rel reticuloendotheliosis viral oncogene homolog B (RELB) as the core TF, and the retinol metabolism and gap junction pathways were analysed. Conclusions This study was the first attempt to predict the crosstalk and examine underlying mechanisms between HF and cognitive impairment applying bioinformatics. The findings suggested a potential hsa-miR-933/RELB/CCL21 regulatory axis correlated with HF and neurological disorders (or cognitive impairment), according to PPI networks.

Mechanism of Sanhuang Decoction in alleviating dextran sulfate sodium induced ulcerative colitis in mice with Candida albicans colonization:based on high-throughput transcriptome sequencing

This study explored the mechanism of Sanhuang Decoction(SHD) in treating dextran sulfate sodium(DSS)-induced ulcerative colitis(UC) in mice with Candida albicans(Ca) colonization via high-throughput transcriptome sequencing. Specifically, the animal model was established by oral administration of 3.0% DSS for 7 days followed by intragastrical administration of Ca suspension at 1.0 × 10~8 cells for 4 days and then the mice were treated with SHD enema for 7 days. Afterwards, the general signs were observed and the disease activity index(DAI) was recorded every day. After mice were sacrificed, colon length and colon mucosa damage index(CMDI) were determined and the histomorphology was observed with the HE staining method. The fungal loads of feces were detected with the plate method. Anti-saccharomyces cerevisiae antibody(ASCA) and β-1,3-glucan in serum, and TNF-α, IL-1β, and IL-6 in serum and colon were detected by ELISA. High-throughput RNA sequencing method was adopted to identify transcriptome of colon tissues from the control, model and SHD(15.0 g·kg~(-1)) groups. Differentially expressed genes(DEGs) among groups were screened and the GO and KEGG pathway enrichment analysis of the DEGs was performed. The expression levels of NLRP3, ASC, caspase-1, and IL-1β genes related to the NOD-like receptor signaling pathway which involved 9 DEGs, were examined by qRT-PCR and Western blot. The results demonstrated that SHD improved the general signs, decreased DAI and Ca loads of feaces, alleviated colon edema, erosion, and shortening, and lowered the content of β-1,3-glucan in serum and TNF-α, IL-1β, and IL-6 in serum and colon tissues of mice. Transcriptome sequencing revealed 383 DEGs between SHD and model groups, which were mainly involved in the biological processes of immune system, response to bacterium, and innate immune response. They were mainly enriched in the NOD-like signaling pathway, cytokine-cytokine interaction pathway, and retinol metabolism pathway. Moreover, SHD down-regulated the mRNA and protein levels of NLRP3, caspase-1, and IL-1β. In a word, SHD ameliorates DSS-induced UC in mice colonized with Ca, which probably relates to its regulation of NOD-like receptor signaling pathway.

Multi-omics integration reveals the hepatoprotective mechanisms of ursolic acid intake against chronic alcohol consumption.

Alcoholic liver disease (ALD) is a major health issue globally. In addition to pharmacotherapy, dietary support is also regarded as reliable strategy for ALD management. As a widely distributed natural constituent within edible plants, the present study aims to investigate the hepatoprotective effects of ursolic acid (UA) against ALD and also to deepen insights into the underlying targets and mechanisms comprehensively. The hepatoprotective activity of UA against chronic alcohol-induced liver injury was investigated on Lieber-DeCarli liquid diet-based mouse model. In-depth RNA-seq transcriptomics and TMT-based proteomics analyses were conducted in parallel. Data integration as well as bioinformatics analysis were also performed to unravel the targets and mechanisms associated with the hepatoprotective activity of UA intake against alcoholic liver injury comprehensively. The serum biomarkers and pathological characteristics indicated the hepatoprotective effects of UA intake on alcoholic liver injury. 567 target genes and 377 target proteins related to the hepatoprotective activity of UA were identified in transcriptomics and proteomics analysis respectively, most of which were associated with function of cellular process, cell part and binding. After data integration, 56 co-regulated targets, including ADH4, CYP450 enzymes, NQO1, apolipoproteins, glutathione-S-transferase, etc. which were consistently modulated on both mRNA and protein levels were identified. These co-regulated targets were found to be correlated with 70 KEGG pathways led by carcinogenesis, retinol metabolism and CYP450 metabolism pathways. UA intake ameliorated chronic alcohol-induced liver injury. Given the role of the co-regulated targets in ALD and the bioinformatics analysis results, CYP450-, glutathione and redox homeostasis-dependent antioxidation, promotion of lipid transport, and restoration of ethanol metabolic capacity are the potentially underlying mechanisms. This information will further deepen our insights into the hepatoprotective effects of UA-rich edible plants, and provide us valuable instruction for ALD management.

Vitamin A and retinoic acid accelerate the attenuation of intestinal adaptability upon feeding induced by high-fat diet in mice

With its unique cellular plasticity, the small intestinal mucosa exhibits efficient adaptability upon feeding. However, little is known about the effect of high-fat diet (HFD) feeding on this adaption and its underlying mechanism. Herein, we demonstrated that the cell proliferation ability, mitochondrial morphology, and global transcriptomic profile of the small intestine exhibited a prominent discrepancy between the fasted and refed state in mice, which were markedly attenuated by long-term HFD feeding. The retinol (Vitamin A, VA) metabolism pathway was dramatically affected by HFD feeding in the small intestine. Both VA and its active metabolite retinoic acid (RA), with the administration of lipid micelles, promoted the expression of genes involved in lipid absorption and suppressed the expression of genes involved in the cell proliferation of intestinal organoids. Via chip-qPCR and RT-qPCR, genes involved in lipid metabolism and cell proliferation were target genes of RARα/RXRα in small intestinal organoids treated with RA and lipid micelles. The role of VA in the in vivo attenuation of intestinal adaptability, in response to HFD, was evaluated. Mice were fed a normal chow diet, HFD, or HFD diet supplemented with additional 1.5-fold VA for 12 weeks. VA supplementation in HFD accelerated the attenuation of intestinal adaptability upon feeding induced by HFD, promoted lipid absorption gene expression, and increased body weight and serum cholesterol levels. In conclusion, the discrepancy of the small intestine between the fasted and refed state was dramatically attenuated by HFD feeding, in which VA and RA might play important roles.

Protective effect and mechanisms of action of Mongolian medicine Sulongga-4 on pyloric ligation-induced gastroduodenal ulcer in rats.

BACKGROUNDSulongga-4 (SL-4) is a herbal formula used in traditional Mongolian medical clinics for the treatment of peptic ulcers and gastroenteritis, even though its pharmacological mechanism has not been well characterized.AIMTo evaluate the protective effect and identify the mechanisms of action of SL-4 on gastroduodenal ulcer induced by pyloric ligation (PL) in rats.METHODSPL was performed to induce gastric and duodenal ulcers in rats, which were then treated with oral SL-4 (1.3, 2.6, or 3.9 g/kg per day) for 15 d. PL-induced gastroduodenal ulceration. Therapeutic effects were characterized by pathological and histological evaluations and inflammatory indicators were analyzed by enzyme-linked immunosorbent assay. Microarray analyses were conducted to identify gene expression profiles of gastroduodenal tissue in PL rats with or without SL-4 treatment. The candidate target genes were selected and verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR).RESULTSSL-4 decreased histopathological features in the PL-induced ulcerated rats. SL-4 significantly (P < 0.05) decreased expression of tumor necrosis factor-α, interleukin (IL)-1β, IL-6, endotoxin, platelet-activating factor, and increased prostaglandin E2 and epidermal growth factor in ulcer tissue. Microarray analysis was used to identify a panel of candidate target genes for SL-4 acting on PL-induced ulceration. Genes included some complement and coagulation cascade and retinol metabolism pathways that are closely associated with inflammatory responses and gastric mucosal protective mechanisms. qRT-PCR showed that altered expression of the selected genes, such as CYP2b2, UGT2b1, A2m, and MASP1 was consistent with the microarray results.CONCLUSIONSL-4 exerts protective effects against PL-induced gastroduodenal ulcers via reducing inflammatory cytokines and elevating expression of gastric acid inhibitory factors. Downregulation of CYP2b2 and UGT2b1 genes in retinol metabolism and upregulation of A2m and MASP1 genes in the complement and coagulation cascades pathways are possibly involved in SL-4-mediated protection against gastroduodenal ulcer.