mRNA Expression Profiles Research Articles

MRNA expression profile and prognostic values of the CDHR family genes in lung adenocarcinoma

Lung adenocarcinoma (LUAD), the predominant subtype of lung cancer, has a high incidence and annual mortality worldwide. Members of the cadherin-related (CDHR) family are associated with many malignant tumor types. However, their role and clinical significance in LUAD have not been clarified. We analyzed the association of CDHRs mRNA expression profiles with prognostic significance, immune infiltration, and potential biological functional signatures in several public databases. We constructed a co-expressed mRNA network, and performed an intrinsic molecular structure and function enrichment analysis. Our results showed that CDHR2 mRNA expression was upregulated in LUAD, whereas CDHR1, CDHR3, CDHR4, and CDHR5 mRNAs were downregulated. Upregulation of CDHR2 mRNA is associated with a poor prognosis in patients with LUAD. Next, the correlation between CDHR family members and immune infiltration was observed. A receiver operating characteristic curve showed that the CDHR family is valuable for diagnosing LUAD. In this study, we found that CDHR2 mRNA expression was upregulated in LUAD. Upregulation of CDHR2 mRNA was associated with a poor prognosis in patients with LUAD.

The mRNA expression profile of simvastatin-treated SCAPs

The mRNA expression profile of simvastatin-treated SCAPs

Effects of moringa (Moringa oleifera) leaf powder supplementation on growth performance, haematobiochemical parameters and gene expression profile of stinging catfish, Heteropneustes fossilis

Moringa oleifera is a popular edible protein source due to its high concentration of micronutrients, macronutrients, and antioxidants. The present study investigated the effects of M. oleifera leaf at various levels on the growth performance, haematobiochemical response, and SOD2 and HSP70 gene expression of Heteropneustes fossilis for 90 days. The fish were randomly distributed into 12 glass aquaria (66×36×36 cm) at 50 fish/aquarium in triplicate treatments Four dietary groups were used to feed the H. fossilis, each group containing graded levels of M. oleifera leaf meal (0, 10 %, 20 %, and 40 %) with a basal diet. It was observed that H. fossilis fed a diet supplemented with 10 % MOLM produced the highest final weight, specific growth rate, condition factor, and survivability. Hemoglobin and red blood cell levels were significantly higher in the fish treatment fed with a 10 % M. oleifera diet compared to the other treatments. Significantly lower levels of ALT and AST were detected in the fish that were fed a diet containing 10 % MOLM. Frequencies of ECA and ENA were significantly higher at 40 % M. oleifera inclusion. The relative mRNA expression profile of SOD2 and HSP70 gene were significantly higher at 10 % MOLM supplementation diet in comparison to the control group. The results of the PCA showed that adding 10 % MOLM supplementation had a beneficial effect on the nutritional and haematobiochemical parameters. Overall, it can be stated that 10 % MOLM treated with basal diet as a supplement on stinging catfish have positive impact on growth performance, haematobiochemical response, and immune gene expression.

Comparison of the Effects of Inappropriate Meal Timing-Induced and Genetic Models of Circadian Clock Disruption on Uterine mRNA Expression Profiles

BackgroundAccumulating evidence reveals that inappropriate meal timing contributes to the development of lifestyle-related diseases. An underlying mechanism is thought to be the disruption of the intracellular circadian clock in various tissues based on observations in both systemic and tissue-specific clock gene-deficient mice. However, whether the effects of conditional clock gene knockout are comparable to those of inappropriate meal timing remains unclear. ObjectivesThis study aimed to compare the effects of a recently developed 28-h feeding cycle model with those of a core clock gene Bmal1 uterine conditional knockout (Bmal1 cKO) model on uterine mRNA expression profiles. MethodsThe models were generated by subjecting C57BL/6J mice to an 8-h/20-h feeding/fasting cycle for 2 wk and crossing Bmal1-floxed mice with PR-Cre mice. Microarray analyses were conducted using uterine samples obtained at the beginning of the dark and light periods. ResultsThe analyses identified 516 and 346, significantly 4-fold and 2-fold, up- or downregulated genes in the 28-h feeding cycle and Bmal1 cKO groups, respectively, compared with each control group. Among these genes, only 7 (1.4%) and 63 (18.2%) were significantly up- or downregulated in the other model. Moreover, most (n = 44, 62.9%) of these genes were oppositely regulated. These findings were confirmed by gene set enrichment analyses. ConclusionsThis study reveals that a 28-h feeding cycle and Bmal1 cKO differently affect gene expression profiles and highlights the need for considering this difference to assess the pathophysiology of diseases associated with inappropriate meal timing.

Methamphetamine-induced impairment of memory and fleeting neuroinflammation: Profiling mRNA changes in mouse hippocampus following short-term and long-term exposure

Methamphetamine (METH) has been implicated in inducing memory impairment, but the precise mechanisms underlying this effect remain unclear. Current research often limits itself to singular models or focuses on individual gene or protein functions, which hampers a comprehensive understanding of the underlying mechanisms. In this study, we established three METH mouse exposure models, extracted hippocampal nuclei, and utilized RNA sequencing to analyze changes in mRNA expression profiles. Our results indicate that METH significantly impairs the learning and memory capabilities of mice. Additionally, we observed that METH-induced inflammatory responses occur in the early phase and do not further exacerbate with repeated injections. However, RNA sequencing revealed the persistent enrichment of inflammatory pathway molecules, which correlated with worsened behaviors. This suggests that although METH-induced neuroinflammation plays a critical role in learning and memory impairment, the continued enrichment of inflammatory pathway molecules is associated with behavioral outcomes. These findings provide crucial evidence for the potential application of immune intervention in METH-related disorders.

Host miRNA and mRNA profiles during in DEF and duck after DHAV-1 infection

DHAV-1 is a highly infectious pathogen that can cause acute hepatitis in ducklings. MicroRNA (miRNA) plays an essential regulatory role in virus response. We characterized and compared miRNA and mRNA expression profiles in duck embryonic fibroblasts (DEF) and the liver of ducklings infected with DHAV-1. DHAV-1 infected DEF was divided into infection group (D group) and blank group (M group), and DHAV-1 infected duckling group was divided into infection group (H group) and blank group (N group). D vs. M have 130 differentially expressed (DE) miRNA (DEM) and 2204 differentially expressed (DE) mRNA (DEG), H vs. N have 72 DEM and 1976 DEG. By the intersection of D vs. M and H vs. N comparisons, 15 upregulated DEM, 5 downregulated DEM, 340 upregulated DEG and 50 downregulated DEG were found with both in vivo and in vitro DHAV-1 infection. In particular, we identified the same DE miRNA target genes and functional annotations of DE mRNA. We enriched with multiple gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which may have important roles in viral virulence, host immunity, and metabolism. We selected miR-155, which is co-upregulated, and found that miR-155 targets SOCS1 to inhibit DHVA-1 replication.

DbGTi protein attenuates chromium (VI)-induced oxidative stress via activation of the Nrf2/HO-1 signalling pathway in zebrafish (Danio rerio) larval model

Hexavalent chromium (Cr (VI)) contamination poses a significant threat to environmental and human health due to its ability to induce oxidative stress. Conventional strategies to counter Cr (VI)-induced oxidative stress, like antioxidants and chelating agents, face efficacy limitations and adverse effects. The present study is intended to counteract the limitations of conventional strategies by introducing a trypsin inhibitor isolated from Dioscorea bulbifera L. tubers, known as DbGTi protein, against Cr (VI)-induced developmental toxicity and oxidative stress. Through a comprehensive array of biochemical assays, behavioural tests, and gene expression analyses, this study interprets the underlying mechanisms of the DbGTi protein. Results demonstrated that the DbGTi protein effectively restored antioxidant defense systems, including superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), glutathione S-transferase (GST), and glutathione peroxidase (GTPx), thereby mitigating cellular damage, reducing cell death, and enhancing neuro-biomarkers. qRT-PCR analysis of mRNA expression profiling revealed the upregulation of genes associated with antioxidant defense (sod, cat, gpx) and defense pathway (nrf2, hmox-1a), further highlighting the protective effects of DbGTi protein against Cr (VI)-induced oxidative stress.

The cytotoxic activities of the major diterpene extracted from Salvia multicaulis (Bardakosh) are mediated by the regulation of heat-shock response and fatty acid metabolism pathways in human leukemia cells

BackgroundLeukemia is one of the most lethal cancers worldwide and represents the sixth-leading cause of cancer deaths. The results of leukemia treatment have not been as positive as desired, and recurrence is common. PurposeThus, there is an urgent requirement for the development of new therapeutic drugs. Salvia multicaulis (Bardakosh) is a widespread species that contains multiple phytochemical components with anti-cancer activities. MethodsWe isolated and characterized the major diterpene candesalvone B methyl ester from S. multicaulis and investigated its action as a cytotoxic agent towards sensitive and drug-resistant leukemia cells by the resazurin reduction assay. Additionally, the targeted genes and the affected molecular mechanisms attributed to the potent cytotoxic activities were discovered by transcriptome-wide mRNA expression profiling. The targets predicted to be regulated by candesalvone B methyl ester in each cell line were confirmed by qRT-PCR, molecular docking, microscale thermophoresis, and western blotting. Moreover, cell cycle distribution and apoptosis were analyzed by flow cytometry. ResultsCandesalvone B methyl ester was cytotoxic with IC50 values of 20.95 ± 0.15 µM against CCRF-CEM cells and 4.13 ± 0.10 µM against multidrug-resistant CEM/ADR5000 leukemia cells. The pathway enrichment analysis disclosed that candesalvone B methyl ester could regulate the heat-shock response signaling pathway via targeting heat shock factor 1 (HSF1) in CCRF-CEM cells and ELOVL fatty acid elongase 5 (ELOVL5) controls the fatty acid metabolism pathway in CEM/ADR5000 cells. Microscale thermophoresis showed the binding of candesalvone B methyl ester with HSF1 and ELOVL5, confirming the results of molecular docking analysis. Down-regulation of both HSF1 and ELOVL5 by candesalvone B methyl ester as detected by both western blotting and RT-qPCR was related to the reversal of drug resistance in the leukemia cells. Furthermore, candesalvone B methyl ester increased the arrest in the sub-G1 phase of the cell cycle in a dose-dependent manner from 1.3 % to 32.3 % with concomitant induction of apoptosis up to 29.0 % in CCRF-CEM leukemic cells upon inhibition of HSF1. ConclusionCandesalvone B methyl ester isolated from S. multicaulis exerted cytotoxicity by affecting apoptosis, cell division, and modulation of expression levels of genes contributing to the heat stress signaling and fatty acid metabolism pathways that could relieve drug resistance of leukemia cells.

Unique Gene Expression Profiles within South Africa Are Associated with Varied Chemotherapeutic Responses in Conventional Osteosarcoma.

We determined the predictive gene expression profiles associated with chemo-response in conventional osteosarcomas (COS) within South Africa. In 28 patients, we performed an RNA extraction, cDNA synthesis, and quantitative analysis using the RT-PCR 2-∆∆CT method to determine the fold change in gene expression alongside GAPDH (housekeeping gene). We observed a significant downregulation in the mRNA expression profiles of ABCB1-p-glycoprotein (p = 0.0007), ABCC3 (p = 0.002), ERCC1 (p = 0.007), p-53 (p = 0.007), and RFC1 (p = 0.003) in the COS patients compared to the healthy donors. Furthermore, ABCB1-p-glycoprotein (p = 0.008) and ABCC3 (p = 0.020) exhibited a significant downregulation in the COS tumour tissues when compared to the healthy donors. In our univariate logistic regression, the predictors of chemotherapeutic response comprised ERCC1 [restricted cubic spline (RCS) knot: OR -0.27; CI -0.504 to -0.032; p = 0.036]; osteoblastic subtype [OR -0.36; CI -0.652 to -0.092; p = 0.026); fibroblastic subtype [OR 0.91; CI 0.569 to 1.248; p < 0.001]; and mixed subtype [OR 0.53; CI 0.232 to 0.032; p = 0.032]. In our multivariable logistic regression, the significant predictors of chemotherapeutic response comprised age [RCS knot: OR -2.5; CI -3.616 to -1.378; p = 0.022]; ABCC3 [RCS knot: OR 0.67; CI 0.407 to 0.936, p = 0.016]; ERCC1 [RCS knot: OR 0.57; CI 0.235 to 0.901; p = 0.044]; RFC1 [RCS knot: OR -1.04; CI -1.592 to -0.487; p = 0.035]; chondroblastic subtype [OR -0.83; CI -1.106 to -0.520; p = 0.012]; and osteoblastic subtype [OR -1.28; CI -1.664 to -0.901; p = 0.007]. In this South African cohort, we observed the unique gene expression profiles of osteosarcoma tumourigenesis and chemotherapeutic responses. These may serve as prognostication and therapeutic targets. Larger-scale research is needed on the African continent.

The Transcriptome Characterization of the Hypothalamus and the Identification of Key Genes during Sexual Maturation in Goats.

Sexual maturation in goats is a dynamic process regulated precisely by the hypothalamic-pituitary-gonadal axis and is essential for reproduction. The hypothalamus plays a crucial role in this process and is the control center of the reproductive activity. It is significant to study the molecular mechanisms in the hypothalamus regulating sexual maturation in goats. We analyzed the serum hormone profiles and hypothalamic mRNA expression profiles of female goats during sexual development (1 day old (neonatal, D1, n = 5), 2 months old (prepuberty, M2, n = 5), 4 months old (sexual maturity, M4, n = 5), and 6 months old (breeding period, M6, n = 5)). The results indicated that from D1 to M6, serum hormone levels, including FSH, LH, progesterone, estradiol, IGF1, and leptin, exhibited an initial increase followed by a decline, peaking at M4. Furthermore, we identified a total of 508 differentially expressed genes in the hypothalamus, with a total of four distinct expression patterns. Nuclear receptor subfamily 1, group D, member 1 (NR1D1), glucagon-like peptide 1 receptor (GLP1R), and gonadotropin-releasing hormone 1 (GnRH-1) may contribute to hormone secretion, energy metabolism, and signal transduction during goat sexual maturation via circadian rhythm regulation, ECM receptor interactions, neuroactive ligand-receptor interactions, and Wnt signaling pathways. This investigation offers novel insights into the molecular mechanisms governing the hypothalamic regulation of goat sexual maturation.

Identification and Validation of Oxidative Stress-Related Biomarkers for Bronchopulmonary Dysplasia.

The objective of this study was to identify and characterize oxidative stress (OS)-related biomarkers in bronchopulmonary dysplasia (BPD) through a combination of bioinformatics analyses and wet experiments. The study utilized the Gene Expression Omnibus database to obtain the mRNA expression profile dataset GSE32472. Differential expression analysis and functional enrichment analysis were employed to investigate the role of OS-related genes in BPD. Gene Ontology Function Enrichment Analysis and Gene Set Enrichment Analysis were conducted to understand the mechanisms behind the signature. Protein-protein interaction analysis to identify hub genes in BPD, and predictions were made for microRNAs (miRNAs), transcription factors (TFs), and potential medications targeting these genes. CIBERSORT was utilized to investigate the correlation between hub genes and the infiltration of immune cells. Hub genes were ultimately determined and confirmed using expression analysis, correlation analysis, receiver operating characteristic (ROC) analysis, and quantitative real-time PCR (qRT-PCR). A novel OS-related gene signature (ARG1, CSF3R, IL1R1, IL1R2, MMP9, RETN, S100A12, and SOCS3) was constructed for the prediction of BPD. We identified 18 miRNAs, 14 TFs, and 30 potential medications targeting these genes. ROC analysis further validated that these genes could diagnose BPD with high specificity and sensitivity. The qRT-PCR revealed that IL1R1 and ARG1 were highly expressed in the lung tissue of the model group, while the expressions of RETN, SOCS3, IL1R2, and MMP9 were decreased. This study demonstrated that ARG1, CSF3R, IL1R1, IL1R2, MMP9, RETN, S100A12, and SOCS3 may serve as potential diagnostic biomarkers in BPD. Furthermore, a significant association between IL1R1 and the pathogenesis of BPD is observed.

Participation of the insulin-like growth factor system in the early maturity in juvenile male European sea bass

It is known that the insulin-like growth factor (Igf) system is involved in gonadal development and, in turn, reproduction in vertebrates. In this study, the circulating levels of Igf-1 and follicle-stimulating hormone (Fsh) were assessed as physiological signals related to gonadal maturation stage in juvenile male European sea bass at 1 year of age. The seasonal profiles of Igf-1 and Fsh were analyzed in non-precocious (NP) and precocious (PR) fish during the early onset of puberty. Subsequently, gonadal expression patterns of the three igf genes and their two receptors, igf-1r and igf-2r, were studied during their first year of life. The analysis was continued to evaluate the mRNA expression profiles of three genes (sox17, scf, nf2) mediating spermatogenesis progression. Collectively, these results demonstrated that PR males have higher circulating levels of Igf-1 as compared to NP fish before and during the putative gonadal development period (PGD). Plasma Fsh levels were significantly higher in PR males as compared to NP fish before the start of the PGD period, although this was followed by a decrease in Fsh levels and a subsequent recovery, coinciding with the reproductive season (February). Results showed that the total variance associated with the appearance of precocity may be explained by the contribution of factors such as body size and plasma levels of Igf-1, Fsh and sex steroids in male sea bass. Expression of igfs was high during stage I, and this was significantly correlated with the expression of genes related to cell cycle progression, including sox17, scf and nf2. Finally, the decreased expression of all these gonadal factors in precocious animals suggests their potential involvement in regulating the proliferative growth of spermatogonia and supporting cells during the early stages of spermatogenesis, thus evoking the onset of puberty in male sea bass.

Characteristic changes in the mRNA expression profile of plasma exosomes from patients with MPO-ANCA-associated vasculitis and its possible correlations with pathogenesis

To explore the expression patterns and potential roles of mRNAs in exosomes from patients with myeloperoxidase-specific anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (MPO-AAV). Plasma exosomes were isolated from MPO-AAV patients and healthy controls (HCs) to screen for differential mRNA expression via exosomal mRNA sequencing. The differentially expressed mRNAs in exosomes from the 2 groups were comparatively explored by bioinformatics analysis. The six most differentially expressed mRNAs were selected and validated in larger groups of MPO-AAV patients and HCs by real-time quantitative polymerase chain reaction (RT‒qPCR). The relationships between these selected mRNAs and patient characteristics were statistically analyzed. Compared with HCs, a total of 1077 mRNAs in exosomes from MPO-AAV patients were found to be significantly upregulated, including DEPDC1B and TPST1, while NSUN4 and AK4 were significantly downregulated. Statistical analysis did not reveal any correlation between the six selected mRNAs and clinical indicators, including disease activity. GO enrichment analysis revealed that these differentially expressed genes participate in various enzyme activities, protein synthesis, etc. KEGG pathway analysis revealed that metabolic pathways, cell adhesion molecules, epithelial signaling, and mitogen-activated protein kinase (MAPK) signaling pathways were significantly enriched in the exosomal mRNAs. There were significant differences in the expression of exosomal mRNAs between MPO-AAV patients and HCs, which may be related to the occurrence and development of MPO-AAV. These findings provide clues for further investigations of MPO-AAV pathogenesis and the identification of new potential therapeutic targets.

Occlusal disharmony promotes anxiety-like behaviours by suppressing Sirt1.

Previous studies have indicated that occlusal disharmony (OD) can promote anxiety-like behaviours. However, the specific molecules involved in the development of anxiety-like behaviours and their underlying mechanisms remain unknown. OD was produced by anterior crossbite of female mice. We measured the anxiety levels of mice in each group and screened the hippocampal mRNA expression profiles of mice in the control group and OD group. The role of target mRNA in OD-induced anxiety-like behaviours was evaluated and we preliminarily explored the possible downstream pathways. The results suggested that OD can induce and promote anxiety-like behaviours with/without chronic unpredictable mild stress. We found that Sirt1 was significantly downregulated within the hippocampus in OD mice. In addition, the downregulation of Sirt1 within the hippocampus in OD and control mice promoted anxiety-like behaviours, increased acetylated histone H3 expression and decreased Dnah12 transcription levels. In contrast, in OD mice subjected to an injection of resveratrol, there was a remission of anxiety-like behaviours and an upregulation of Sirt1 in the hippocampus, the effects of which were accompanied by decreased acetylated histone H3 expression and increased Dnah12 transcription levels. OD leads to increased sensitivity to chronic stress in mice, resulting in anxiety-like behaviours. During this process, Sirt1 acts as an effective factor in the regulation of OD-induced anxiety-like behaviours. OD, as a stressor, could induce anxiety-like behaviours. It investigates the impact of OD (a stressor) on the molecular genetic of the pathophysiology of major neuropsychiatric disorders.

Transcriptome profiles of the skin associated with the color of the black and white coat of Angora goats

The coat color of mammals, determined by the distribution of melanin, particularly eumelanin and pheomelanin, reflects intricate genetic and molecular processes. However, our understanding of the relationship between coat color, gene expression, and polymorphisms in goats remains nascent. This study investigates transcriptomic differences between black and white Angora goats across three distinct hair growth phases. Skin tissue samples from both colored and white Angora goats were analyzed using mRNA expression profiling. Three skin samples were taken from each goat as biological duplicates at every stage of hair follicle growth (September, January, and March). In total, 36 samples were analyzed in this study, including samples from two Angora goat varieties, three developmental stages (three biological replicates), and two technical replicates for RNA sequencing. Significant differences in gene expression were observed between black and white goats at each growth phase, particularly in genes associated with the melanogenesis pathway. Specifically, several pigmentation genes were identified solely in black goats, indicating phase-specific and breed-specific regulation. Noteworthy genes, such as SLC2A1, STAR, and SLC7A5, exhibited differential expression patterns across growth phases in black goats, further highlighting the complexity of melanogenesis regulation. This is the first study to use mRNA expression profiling of skin tissues to analyze coat color differences between black and white coated Angora goats at the anagen, catagen, and telogen stages. The identification of phase-specific and black goat-specific pigmentation genes provides valuable insights into the complex mechanisms governing coat color formation.

Transcriptomic Analysis and Finding of Potential Key mRNA Expression Profile in Human Cumulus Cells During in Vitro Culture and Different Passages Based on Integrated Bioinformatics Analysis.

This study leveraged microarray datasets to investigate differentially expressed genes (DEGs) in cumulus cells and their relevance in predicting the successful implantation of embryos in human in-vitro fertilization procedures. The microarray data were obtained from the GEO database, encompassing samples of cumulus cells during in vitro culture and different passages. To ensure data consistency, inter-batch normalization was performed, and Principal Component Analysis (PCA) was applied to assess the impact of normalization on sample group clustering. The integrated dataset included samples from cumulus cells during in vitro culture, comprising 17,662 genes. Utilizing the "limma" software package, 1906 DEGs were identified, with 437 genes downregulated and 589 genes upregulated in the cumulus cells of infertility cases, while 748 genes were upregulated, and 1317 genes were downregulated in cumulus cells of successful implantation cases. Functional enrichment analysis utilized Gene Ontology, Metascape, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment tools. Biological processes and molecular functions were enriched, including protein targeting, mRNA processing, and molecular binding among the identified DEGs. Furthermore, target prediction and functional enrichment analysis of microRNAs (miRNAs) revealed 25 key genes and 13 relevant miRNAs were identified. Notably, hsa-miR-149, hsa-miR23b, hsa-miR-877, hsa-miR593, hsa-miR-18a, hsa-miR25, hsa-miR185, mmu-miR-207, hsa-miR425, hsa-miR214, hsa-miR-129, hsa-miR-629, and hsa-miR-194 emerged as the most prominent miRNAs with potential regulatory roles in successful embryo implantation. This comprehensive analysis provides valuable insights into the molecular mechanisms underlying embryo implantation, offering potential targets for further research and therapeutic interventions in assisted reproductive technologies.

Identifying hub genes for chemo-radiotherapy sensitivity in cervical cancer: a bi-dataset in silico analysis

PurposeTo identify the hub genes that associated with chemo-radiotherapy sensitivity for cervical cancer and to explore the relationship between hub genes and various cellular processes and potential mechanism of cervical cancer.MethodsThe gene expression data of 21 patients with CESC and the mRNA expression profiles of 296 patients with CESC were obtained from the Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) databases, respectively. The potential functions and regulatory mechanisms of differentially expressed genes (DEGs) were identified using GO and KEGG enrichment analyses. Hub genes were identified using random survival forest analysis. The relationship between hub genes and various cellular processes was comprehensively analyzed. The expression of hub genes was assessed using clinical data extracted from the Human Protein Atlas (HPA) database.ResultsA total of 139 and 13 DEGs were found to be upregulated and downregulated, respectively, in CESC. The six hub genes, namely, SELP, PIM2, CCL19, SDS, NRP1, and SF3A2, were significantly correlated with immune cell infiltration, chemotherapy sensitivity, disease-related genes, and enriched signaling pathways (all p-value < 0.05). A nomogram and calibration curve were generated using the six hub genes to predict prognosis with high accuracy. A regulatory network comprising TFs (ZBTB3) and mRNAs (NRP1/PIM2/SELP) and several competitive endogenous RNA (ceRNA) networks comprising mRNAs, miRNAs, and lncRNAs were constructed. Data from HPA indicated that the protein expression of the six hub genes differed significantly between patients with CESC and healthy individuals.ConclusionUpregulation of SELP, PIM2, CCL19, SDS, NRP1, and SF3A2 is associated with radiotherapy sensitivity and is involved in various cellular processes in CESC. These six genes may serve as biomarkers for predicting the radiotherapy response and prognosis in patients with CESC.

Multiscale mapping of transcriptomic signatures for cardiotoxic drugs

Drug-induced gene expression profiles can identify potential mechanisms of toxicity. We focus on obtaining signatures for cardiotoxicity of FDA-approved tyrosine kinase inhibitors (TKIs) in human induced-pluripotent-stem-cell-derived cardiomyocytes, using bulk transcriptomic profiles. We use singular value decomposition to identify drug-selective patterns across cell lines obtained from multiple healthy human subjects. Cellular pathways affected by cardiotoxic TKIs include energy metabolism, contractile, and extracellular matrix dynamics. Projecting these pathways to published single cell expression profiles indicates that TKI responses can be evoked in both cardiomyocytes and fibroblasts. Integration of transcriptomic outlier analysis with whole genomic sequencing of our six cell lines enables us to correctly reidentify a genomic variant causally linked to anthracycline-induced cardiotoxicity and predict genomic variants potentially associated with TKI-induced cardiotoxicity. We conclude that mRNA expression profiles when integrated with publicly available genomic, pathway, and single cell transcriptomic datasets, provide multiscale signatures for cardiotoxicity that could be used for drug development and patient stratification.

Transcriptome sequencing analysis reveals the molecular regulatory mechanism of myocardial hypertrophy induced by angiotensin II

The pathogenesis of myocardial hypertrophy remains incompletely understood, highlighting the critical need for in-depth investigation into its pathogenesis and pathophysiology to develop innovative strategies for preventing and treating heart diseases. In this study, a model of angiotensin II (Ang II)-induced myocardial hypertrophy was established using subcutaneous administration with a micropump. Echocardiography, wheat germ agglutinin staining, and western blot analysis were used to evaluate the myocardial hypertrophy model after 5, 10, and 15 days of Ang II treatment. RNA-seq was employed to analyze the differential expression profile of mRNA, followed by bioinformatics analysis. Subsequently, the anti-inflammatory drug meloxicam was utilized to explore its impact on cardiac hypertrophy in mice. The findings demonstrated that mice developed myocardial hypertrophy following subcutaneous administration of Ang II. Transcriptomic analysis revealed significant changes in gene expression in the myocardium induced by Ang II, with the most pronounced differences observed at day 10. Functional analysis and verification of differentially expressed genes indicated that Ang II triggered an inflammatory response in the myocardium, leading to up-regulation of genes associated with fibrosis and apoptosis while decreasing energy metabolism; alterations were also observed in genes related to oxidative stress and calcium ion binding. Treatment with meloxicam improved Ang II-induced myocardial hypertrophy. This study not only elucidated the molecular regulatory mechanism underlying mouse myocardial hypertrophy at a transcriptional level but also provided new insights into clinical prevention and treatment strategies for cardiac diseases such as dilated cardiomyopathy and heart failure.

Proteogenomic Identification and Analysis of KIF5B as a Prognostic Signature for Hepatocellular Carcinoma.

Metabolic disorders are significant risk factors for liver cancer, particularly Hepatocellular Carcinoma (HCC). However, the molecular genetic basis of metabolic reprogramming in the liver remains largely uncertain. This study aimed to investigate some novel prognostic biomarkers in HCC by using proteogenomic and transcriptomic analysis and explore the potential role of specific prognostic genes in HCC. Here, we have presented a proteogenomic analysis of 10 pairs of HCC. Protein co-expression and pathway analysis were performed to investigate the biological characteristics of HCC. Protein and mRNA expression profiles of multi-cohorts were integrated to detect novel prognostic protein markers of HCC. The carcinogenic roles of candidate prognostic markers were further evaluated by MTS assay, colony formation, monolayer wound healing assay, and xenograft models. A total of 2086 proteins with significantly different expressions were detected in HCC. Pathways related to oncogenic signaling and insulin-related metabolism have been found to be dysregulated and differentially regulated in HCC. We have identified the novel prognostic biomarkers, KIF5B, involved in liver metabolic reprogramming. The biomarkers were identified using multivariable COX regression analysis from two independent proteomic datasets (Fudan Cohort and our recruited cohort) and the TCGA mRNA database. Both the protein and mRNA up-regulation of KIF5B have been found to be associated with a poor clinical outcome in HCC. Insulin activated the protein expression of KIF5B in HCC. Knocking out KIF5B expression by sgRNA decreased the protein expression of FASN and SCD1 and the intracellular triglyceride concentration. Silencing KIF5B suppressed HCC cell proliferation and colony formation in vitro, as well as HCC growth in xenograft models. Our findings have suggested KIF5B protein to function as a novel prognostic biomarker in HCC. KIF5B expression has been found to activate the AKT/mTOR pathway and reprogram triglyceride metabolism, leading to HCC development. Targeting KIF5B may be an effective strategy in the clinical treatment of HCC.