Ras Protein Signal Transduction Research Articles

Exploring selective neuronal vulnerability in Alzheimer’s disease – key pathways are downregulated in vulnerable subpopulations of RORB and CDH9 excitatory neurons of the entorhinal cortex at Braak 0

AbstractBackgroundUnderstanding the molecular mechanisms underlying selective neuronal vulnerability is crucial for developing effective treatments for Alzheimer’s disease (AD). Our group has shown that RORB/CDH9‐positive excitatory neurons in the entorhinal cortex (EC) display selective vulnerability as early as Braak stage (BB) 2. However, not all RORB/CDH9‐positive neurons are vulnerable. By further leveraging single‐nucleus RNA sequencing (snRNA‐seq) data, we aimed to identify molecular signatures of selective neuronal vulnerability. This involved comparing resilient‐like subpopulations (BB0 cells with RNA expressions similar to BB6) and vulnerable‐like subpopulations (BB0 cells with different RNA expressions than BB6) within each RORB and CDH9 subpopulation.MethodBioinformatic analyses were conducted using the Seurat R library on a published snRNA‐seq dataset of isolated nuclei extracted from the EC of postmortem brain tissue from healthy controls and AD patients (BB0 [n = 3], BB2 [n = 4], and BB6 [n = 3]) (Fig. 1). The Wilcox statistical test (p‐adjusted <0.05) was applied throughout the FindMarkers function to identify differentially expressed genes (DEGs) on vulnerable‐ and resilient‐like cells.ResultFrom the original dataset, with EC excitatory neurons (11488 nuclei), we found one RORB‐ and two CDH9‐positive (CDH9.2 and CDH9.9) vulnerable‐like neuronal subpopulations (Fig. 1). In RORB neurons, downregulated genes are involved in insulin signaling, autophagy, and ErbB signaling pathways (Fig. 2A). In CDH9.2 neurons downregulated genes are involved in membrane trafficking, axon guidance, proteasome‐mediated ubiquitin‐dependent protein catabolic process, and protein polyubiquitination (Fig. 2B). Additionally, in CDH9.9 neurons downregulated genes are involved in membrane trafficking, Ras protein signal transduction, GTPase activator activity, and ubiquitin‐like protein ligase binding (Fig. 2C). These three susceptible subpopulations share eight downregulated genes, some of which are highly involved in the Heme Biosynthetic Process. Heme is a common element linking various metabolic disruptions in AD, including oxygenase, mitochondrial dysfunction, and inhibition of muscarinic acetylcholine receptor binding.ConclusionOur analyses suggest that changes in metabolic, ubiquitin‐proteasome, and cell growth/survival pathways occur in vulnerable‐like cells of the EC in BB0. Therefore, these pathways may be potential therapeutic targets in the earliest stages of AD. By looking into younger cohorts, we will further investigate if the molecular differences between these neuronal subpopulations are canonical (indicating a pathological predisposition) or an early pathological response.

Identification of potential key circular RNAs associated with Escherichia coli-infected bovine mastitis using RNA-sequencing: preliminary study results.

Escherichia coli (E. coli) is commonly found in dairy farms and can invade mammary gland tissue, often causing acute clinical mastitis. Mammary infections with E. coli have shown a wide range of clinical signs, causing abnormal appearance of the milk, udder inflammation and systemic signs of illness. Circular RNA is a class of endogenous non-coding RNA that plays an important role in the occurrence and development of various inflammatory diseases. However, there is little information on the circRNA associated with bovine mastitis. In this study investigated the involvement of circRNAs in bovine mastitis through the construction of an E. coli-infected bovine mastitis model by injecting of E. coli into the mammary gland of dairy cows, using healthy gland mammary tissue as a control (M_C). High-throughput RNA-seq was performed on the E. coli-infected mammary gland tissue (M_E) and differentially expressed circRNAs between theM_C and M_E groups, followed by an analysis of their potential functions using bioinformatics methods. A total of 164 differentially expressed circRNAs were identified, including 92 downregulated circRNAs and 72 upregulated circRNAs. As shown by Gene Ontology enrichment analysis these DE circRNAs were mostly enriched in ras protein signal transduction, cytoplasmic vesicle parts, and enzyme binding, and Kyoto Encyclopedia of Genes and genome singal pathway enrichment analysis indicated significant associations with phagosome signal pathway. Additionally, the expression of bovine mastitis-related circRNAs, including novel_circRNA_0000128, novel_circRNA_0011103, novel_circRNA_0012656, novel_circRNA_0015099, novel_circRNA_005648, novel_circRNA_000074, and novel_circRNA_0011796 were verified via quantitative reverse-transcription polymerase chain reaction (RT-qPCR). These results provide a new direction for further investigation of the molecular mechanisms underlying bovine mastitis.

Inducible deletion of microRNA activity in kidney mesenchymal cells exacerbates renal fibrosis

MicroRNAs (miRNAs) are sequence-specific inhibitors of post-transcriptional gene expression. However, the physiological functions of these non-coding RNAs in renal interstitial mesenchymal cells remain unclear. To conclusively evaluate the role of miRNAs, we generated conditional knockout (cKO) mice with platelet-derived growth factor receptor-β (PDGFR-β)-specific inactivation of the key miRNA pathway gene Dicer. The cKO mice were subjected to unilateral ureteral ligation, and renal interstitial fibrosis was quantitatively evaluated using real-time polymerase chain reaction and immunofluorescence staining. Compared with control mice, cKO mice had exacerbated interstitial fibrosis exhibited by immunofluorescence staining and mRNA expression of PDGFR-β. A microarray analysis showed decreased expressions of miR-9-5p, miR-344g-3p, and miR-7074-3p in cKO mice compared with those in control mice, suggesting an association with the increased expression of PDGFR-β. An analysis of the signaling pathways showed that the major transcriptional changes in cKO mice were related to smooth muscle cell differentiation, regulation of DNA metabolic processes and the actin cytoskeleton, positive regulation of fibroblast proliferation and Ras protein signal transduction, and focal adhesion-PI3K/Akt/mTOR signaling pathways. Depletion of Dicer in mesenchymal cells may downregulate the signaling pathway related to miR-9-5p, miR-344g-3p, and miR-7074-3p, which can lead to the progression of chronic kidney disease. These findings highlight the possibility for future diagnostic or therapeutic developments for renal fibrosis using miR-9-5p, miR-344g-3p, and miR-7074-3p.

DNA methylation profiling in Trisomy 21 females with and without breast cancer.

Down Syndrome (DS) is the most common chromosome anomaly in humans and occurs due to an extra copy of chromosome 21. The malignancy profile in DS is unique, since DS patients have a low risk of developing solid tumors such as breast cancer however they are at higher risk of developing acute myeloid leukemia and acute lymphoblastic leukemia. In this study, we investigated DNA methylation signatures and epigenetic aging in DS individuals with and without breast cancer. We analyzed DNA methylation patterns in Trisomy 21 (T21) individuals without breast cancer (T21-BCF) and DS individuals with breast cancer (T21-BC), using the Infinium Methylation EPIC BeadChip array. Our results revealed several differentially methylated sites and regions in the T21-BC patients that were associated with changes in gene expression. The differentially methylated CpG sites were enriched for processes related to serine-type peptidase activity, epithelial cell development, GTPase activity, bicellular tight junction, Ras protein signal transduction, etc. On the other hand, the epigenetic age acceleration analysis showed no difference between T21-BC and T21-BCF patients. This is the first study to investigate DNA methylation changes in Down syndrome women with and without breast cancer and it could help shed light on factors that protect against breast cancer in DS.

High Throughput Sequencing Analysis of Exosomal miRNA Expressions in Early-Onset Preeclampsia Patients.

The goal of this study was to screen for differentially expressed exosomal miRNAs in peripheral blood samples of early-onset preeclampsia and normal pregnant patients using high-throughput sequencing methods and explore their effects on the pathogenesis of preeclampsia. Peripheral blood samples from 5 patients with early-onset preeclampsia and 5 normal pregnant women (control group) were enrolled. Then, exosomes were extracted from each sample, and the procedure was replicated three times. An Illumina HiSeq4000 sequencing platform was used to analyze exosomal miRNAs in all samples before comparison. The target genes and signaling pathway predictions and the biological function enrichments of significant and differentially expressed miRNAs were assessed using Miranda and Starbase software, as well as GO and KEGG databases. Compared with the control, patients in the early-onset preeclampsia group had 65 significantly and differentially expressed exosomal miRNAs in their peripheral blood samples. The results have shown that of the 65 differentially expressed miRNAs, 17, including has-miR-6855, has-miR-7151, and has-miR-6777, were up-regulated, and 48, including has-miR-1247, has-miR-29B2, and has-miR-941, were down-regulated (p < 0.05). The Miranda and TargetScanS algorithms predicted a total of 2,231 target genes from the differentially expressed miRNAs. The Go and KEGG analyses showed that the principal biological function of these target genes was the regulation of Ras protein signal transduction, histone modification, GTPase-mediated signal transduction, and transforming growth factor (TGF)-β. Additionally, the results also showed that the major pathways involved in the regulation of these functions were the PI3K Akt, MAPK, tumor necrosis factor, and EGFR tyrosine kinase inhibition signaling pathways. There are significant differences in the expression profiles of exosomal miRNAs between early-onset preeclampsia patients and normal pregnant women. These differentially expressed miRNAs may not only play an important regulatory role in the occurrence of early-onset preeclampsia but also participate in its pathophysiological process through genetic regulation of a variety of biological functions and signal pathways.

Prediction of mRNA Targets of miR-101-3p in Diabetic Kidney Disease by Bioinformatics Tools

Introduction: Diabetic kidney disease (DKD) remains the leading cause of chronic kidney disease (CKD) worldwide. Current biomarkers and treatment still fall short at preventing its progression. In search for a better diagnostic or therapeutic target, much interest in microRNAs, which act as post-translational regulators of gene expression has emerged. An upregulation of miR-101-3p was identified in the sera of type 2 diabetic patients with macroalbuminuria in a selected Malaysian population by profiler RT-PCR array. Using bioinformatics tools, this study aimed to predict the mRNA targets of miR-101-3p. Given the scarcity of bioinformatics studies in DKD, this study also attempted to fill the gap. Methods: The mRNA targets were identified from two experimentally validated databases, namely Tarbase and MirTarBase. The commonly identified mRNA targets were submitted to Metascape and Enrichr bioinformatic tools. Results: A total of 2630 and 342 mRNA targets of miR-101-3p were identified by Tarbase and miRTarbase, respectively. One-hundred ninety-seven (197) mRNA targets were submitted for functional enrichment analysis. Our bioinformatics and bibliographical analyses suggested that ras-related C3 botulinum toxin substrate 1 (RAC1) and Ras-associated protein-1 b (RAP1b) were the most promising putative mRNA targets of miR-101-3p. The most enriched Gene Ontology term and pathway associated with these putative mRNA targets included Ras protein signal transduction and focal adhesion, respectively. Based on these analyses, their molecular mechanisms were proposed. Conclusion: Given the structural heterogeneity of the kidneys and cell type-dependent miRNA modulation, an in-silico target prediction of miR-101-3p increases the probability of a successful future in-vitro experimental verification.

Somatic Mutations in T Cells in Patients with Hematological Diseases

Somatic mutations accumulate in cells during aging, and the mutation rate and spectrum vary between tissues. Mutation accumulation can be associated with inflammation: for example, myeloid driver gene mutations in hematopoietic stem cells (clonal hematopoiesis, CH), has been linked with atherosclerosis. Somatic mutations can also accumulate in T cells, where they are connected with immune dysregulation in large granular lymphocytic leukemia, characterized by autoimmunity and STAT3 mutations in T cells. However, the mutation spectrum in T cells in other hematological disorders is not yet fully discovered. We hypothesized that T cell lineage specific somatic mutations are associated with T cell clonality in various diseases involving the hematopoietic system. We systematically characterized the spectrum of somatic mutations in CD4+ and CD8+ T cells in altogether 207 samples from 95 patients with chronic graft-versus-host disease (cGVHD, number of patients: 40), myelodysplastic syndrome (MDS, n = 15), immune thrombocytopenia (n = 2), aplastic anemia (AA, n = 21, previously published), and immunodeficiency (n = 17, previously published). Age at sampling was similar between disease cohorts. DNA was extracted from bead separated CD4+ and CD8+ cells from peripheral blood or bone marrow samples. We applied a custom-made targeted NGS panel, consisting of 2533 immune-related genes. Variant calling was performed using Mutect2. In variant filtering, we used 42 healthy T cell and skin samples as panel of normals. To explore the association between somatic mutations and clonal T cell expansions, we performed TCRb deep sequencing from 148 matched patient samples. With mean sequencing depth of 382x, we identified 888 non-synonymous somatic variants in total. 784 (86%) of the variants were only found in either CD4+ or CD8+ fraction. 52 variants were shared between individual patient's CD4+ and CD8+ T cells, suggesting that they were acquired prior to T cell lineage differentiation. On the average, we observed 3.8 fraction-specific variants per sample. Mean variant allele frequency (VAF) was 4.5% and 12.7% for fraction-specific and shared variants, respectively. Variant types included missense (91%), nonsense (5.1%), splice-site (1.7%), frameshift (1.3%), and non-stop (0.2%) mutations. The most common mutational signatures were age-associated Signature 1 and defective DNA mismatch repair associated Signature 15. Immunodeficiency patients had lower number of fraction-specific variants compared to AA, MDS and cGVHD patients (p = 0.027). In all cohorts, CD8+ T cells had acquired more variants than CD4+ T cells (p = 0.00012; mean [median] for CD8: 4.4 [4] and CD4: 3.2 [2]). The highest fraction-specific VAF in each sample was associated with the largest T cell clone size in CD8+ but not in CD4+ samples (R = 0.59, p = 3.1e-09 and p = ns, respectively). In CD8+ T cells, age was associated with number of fraction-specific variants (R = 0.38, p = 1.1e-4) but not with the highest CD8-specific VAF (p = ns). Among the variants shared between individual patients' CD4+ and CD8+ T cells, we found mutations in DNMT3A (n = 3) and TET2 (n = 2) and ASXL1 (n = 1), the most recurrently mutated CH genes. In addition to shared mutations, in 12% of patients had fraction-specific myeloid driver gene mutations (e.g. DNMT3A, TET2, KRAS, NRAS) in CD4+ or CD8+ T cells. To identify pathways enriched for putative driver mutations, we performed analyses of fraction-specific T cell variants with OncodriveFM. The most significantly mutated gene ontology pathways included T cell co-stimulation, leukocyte migration, Ras protein signal transduction, and positive regulation of MAP kinase activity. In conclusion, T cell fraction-specific somatic mutations are common in patients with various hematological diseases, and they are enriched in pathways important for T cell function. CD8+ T cells accumulate more mutations than CD4+ T cells. In CD8+ T cells, the number of somatic mutations was associated with age, reflecting stochastic accumulation of mutations. Based on mutational signatures, somatic mutations in T cells are mainly result of endogenous mutational processes. In addition, mutational clone size CD8+ T cells was significantly associated with the largest TCR clone, suggesting that mutations have accumulated in expanded CD8+ T cell clones. Further studies are warranted to determine the functional effects of somatic mutations in T cells.

Comparison of transcriptome profiles of mesenchymal stem cells derived from umbilical cord and bone marrow of giant panda (Ailuropoda melanoleuca)

Mesenchymal stem cells (MSCs) have pluripotent differentiation ability and play an important role in human clinical cell therapy. While, the research on MSCs in endangered wild animals is extremely rare. In our previous studies, the bone marrow mesenchymal stem cells (bmMSCs) and umbilical cord mesenchymal stem cells (ucMSCs) of giant panda (Ailuropoda melanoleuca) were successfully isolated. We aimed to characterize the differences in gene expression profiles between these two types of MSCs using RNA sequencing (RNA-Seq) and to determine which potential pathways are involved in functional regulation. In total, 1079 significantly differentially expressed genes (DEGs) were identified, of which 478 genes were upregulated and 601 genes were downregulated. The significantly enriched Gene Ontology (GO) terms mainly contained cell adhesion, biological adhesion, intracellular signal transduction, molecular function regulator, Ras protein signal transduction, small GTPase mediated signal transduction, and regulation of Rho protein signal transduction. The most enrichment pathways of DEGs enriched in Kyoto Encyclopedia of Genes Genomes (KEGG) were PI3K-AKT signaling pathway, Rap1 signaling pathway, MAPK signaling pathway, Hippo signaling pathway, Wnt signaling pathway, cGMP-PKG signaling pathway and Signaling pathways regulating pluripotency of stem cells. In addition, quantitative real time polymerase chain reaction (qRT-PCR) showed that the AKT3, CDK2, MAPK3, mTOR, PI3K and PTK2 genes associated with PI3K-AKT pathway were highly expressed (P < 0.01), and Caspase-3 was low expressed (P < 0.05) in ucMSCs group when compared with bmMSCs. After treatment with the PI3K inhibitor LY294002, genes AKT3, CDK2, MAPK3, mTOR, and PTK2 were significantly decreased in ucMSCs (P < 0.01), and Caspase-3 was significantly up regulated (P < 0.001). In conclusion, we for the first time compared and analyzed the transcriptome profiles of giant panda ucMSCs and bmMSCs, and found the PI3K-AKT pathway was highly activated and might be a key signaling pathway in the ucMSCs regulation. This study will be beneficial for the research on MSCs proliferation regulation and differentiation of giant pandas in the future, and lay the foundation for MSCs application and clinical therapy for endangered wild animals.

One-Week Dynamic Changes in Cardiac Proteomes After Cardiac Radioablation in Experimental Rat Model.

BackgroundRecently, stereotactic ablative radiotherapy (SABR) has been adopted to non-invasively treat catheter ablation-refractory ventricular tachycardia (VT). VT episodes have been dramatically reduced after SABR, within weeks; however the underlying mechanisms of these clinical effects and potential mediators of early anti-arrhythmic effect remain unclear.MethodsIn this study, cardiac tissue was harvested from non-irradiated control (0 Gy), conventional irradiated control (2 Gy), and radioablative test (25 Gy) rat groups after 3 and 7 days of irradiation. The samples were proteomically analyzed to identify the differentially expressed proteins (DEP) between different groups. Validation experiments were performed similar to validation in profiling where Data independent acquisition and parallel reaction monitoring methods were used. Data are available via ProteomeXchange with identifier PXD030878.ResultsFunctional enrichment analysis of 25 Gy sample showed that among the downregulated proteins, “intracellular signal transduction” and “cell to cell adhesion” proteins were significantly affected at day 3 while “Ras protein signal transduction,” “GTPase regulation,” and “actin filament-based process” proteins were majorly affected at day 7. GO analysis demonstrated that most of the upregulated proteins belonged to the classes “cellular stress response,” “endomembranal organization,” or “endoplasmic reticulum stress response” at day 3. At day 7, 42 proteins, mainly associated with response to drug, organic substance, or radiation, were specifically upregulated in 25 Gy. DEP analysis of cardiac conduction showed Ryr2 and Cav1 upregulation and Cacna2d2, Gja3, Scnb2, and Kcnn3 downregulation in the 25 Gy group compared to 0 Gy. In validation experiments, four proteins (Gsta1, Myot, Ephx1, and Capg) were repeatedly detected with 25 Gy-specific patterns at day 7.Conclusions25 Gy single fractional irradiation induces considerable cardiac proteome changes within the first 7 days, distinct from 2 Gy. Several candidate proteins displayed 25 Gy-specific changes and were related to oxidative stress-induced innate response or cardiac remodeling processes. Future studies should explore the specific role of these proteins upon cardiac radioablation.

Identification and Validation of Aging-Related Genes in Alzheimer's Disease.

Aging is recognized as the key risk factor for Alzheimer’s disease (AD). This study aimed to identify and verify potential aging-related genes associated with AD using bioinformatics analysis. Aging-related differential expression genes (ARDEGs) were determined by the intersection of limma test, weighted correlation network analysis (WGCNA), and 1153 aging and senescence-associated genes. Potential biological functions and pathways of ARDEGs were determined by GO, KEGG, GSEA, and GSVA. Then, LASSO algorithm was used to identify the hub genes and the diagnostic ability of the five ARDEGs in discriminating AD from the healthy control samples. Further, the correlation between hub ARDEGs and clinical characteristics was explored. Finally, the expression level of the five ARDEGs was validated using other four GEO datasets and blood samples of patients with AD and healthy individuals. Five ARDEGs (GFAP, PDGFRB, PLOD1, MAP4K4, and NFKBIA) were obtained. For biological function analysis, aging, cellular senescence, and Ras protein signal transduction regulation were enriched. Diagnostic ability of the five ARDEGs in discriminating AD from the control samples demonstrated a favorable diagnostic value. Eventually, quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) validation test revealed that compared with healthy controls, the mRNA expression level of PDGFRB, PLOD1, MAP4K4, and NFKBIA were elevated in AD patients. In conclusion, this study identified four ARDEGs (PDGFRB, PLOD1, MAP4K4, and NFKBIA) associated with AD. They provide an insight into potential novel biomarkers for diagnosing AD and monitoring progression.

Pan-Cancer Analysis of Clinical Relevance via Telomere Maintenance Mechanism.

Understanding the telomere maintenance mechanism (TMM) in immortal cancer cells is vital for TMM-targeted therapies in clinical settings. In this study, we classified four telomere maintenance mechanisms into telomerase, ALT, telomerase + ALT, and non-defined telomere maintenance mechanism (NDTMM) across 31 cancer types using 10,704 transcriptomic datasets from The Cancer Genome Atlas. Our results demonstrated that approximately 50% of the total cohort displayed ALT activity with high telomerase activity in most cancer types. We confirmed significant patient prognoses according to distinct TMMs in six cancer types: adrenocortical carcinoma (ACC), PAAD, HNSC, SARC, GBM, and metastatic cancer. Patients with metastasis had a poor prognosis in the ALT group (p < 0.006) subjected to RAS protein signal transduction. Glioblastoma patients had poor prognosis in NDTMM (p < 0.0043) and showed high levels of myeloid leukocyte activation. Pancreatic adenocarcinoma (p < 0.04) and head and neck squamous cell carcinoma (p < 0.046) patients had a good prognosis in the ALT group with high immune cell activation. Furthermore, we showed that master transcriptional regulators might affect the selection of the TMM pathway and explained why different telomere maintenance mechanisms exist. Furthermore, they can be used to segregate patients and predict responders to different TMM-targeted therapeutics.

Gastrodin Exerts Cardioprotective Action via Inhibition of Insulin-Like Growth Factor Type 2/Insulin-Like Growth Factor Type 2 Receptor Expression in Cardiac Hypertrophy.

Pathological cardiac hypertrophy is commonly associated with an upregulation of fetal genes, fibrosis, cardiac dysfunction, and heart failure. Previous studies have demonstrated that gastrodin (GAS) exerts cardioprotective action in the treatment of cardiac hypertrophy. However, the mechanism by which GAS protects against cardiac hypertrophy is yet to be elucidated. A mouse model of myocardial hypertrophy was established using an angiotensin II (Ang II) induction. GAS (5 or 50 mg/kg/d) was orally administered every day starting 7 days prior to the Ang II infusion combined with sham-operated controls. Heart samples from each group were collected for RNA sequencing. Using bioinformatics analysis, the key differentially expressed genes (DEGs) that are involved in reversing cardiac function were identified. Through bioinformatics analysis, the key DEGs that are involved in GAS’s inhibition of Ang II-induced abnormal gene expression within the heart were identified. This was further validated using quantitative real-time PCR and Western blotting in neonatal rat cardiomyocytes (NRCMs). Oral administration of GAS significantly suppressed the Ang II-induced increase in heart size and heart weight to body weight. Furthermore, pretreatment of the NRCMs with GAS led to a dose-dependent inhibition of Ang II-induced increases in Nppb mRNA expression. We identified 620 upregulated and 87 downregulated Ang II-induced DEGs II, among which the expression patterns of 58 and 146 genes were inverted by low-dose and high-dose GAS, respectively. These inverted DEGs were found to be mainly enriched in the biological processes of regulation of Ras protein signal transduction, heart contraction, covalent chromatin modification, glucose metabolism, and positive regulation of cell cycle. Among them, the insulin-like growth factor type 2 (Igf2) gene, which was found to be highly reversed and downregulated by GAS, served as a core gene linking energy metabolism, immune regulation, and systemic development. Subsequent functional verification demonstrated that IGF2, and its receptor IGF2R, is one of the targets of GAS that helps protect against cardiac hypertrophy. Taken together, we have identified, for the first time, IGF2/IGF2R as a potential target influenced by GAS in the prevention of cardiac hypertrophy.

Aberrant expression of HDL-bound microRNA induced by a high-fat diet in a pig model: implications in the pathogenesis of dyslipidaemia

BackgroundA high-fat diet can affect lipid metabolism and trigger cardiovascular diseases. A growing body of studies has revealed the HDL-bound miRNA profiles in familial hypercholesterolaemia; in sharp contrast, relevant studies on high-fat diet-induced dyslipidaemia are lacking. In the current study, HDL-bound miRNAs altered by a high-fat diet were explored to offer some clues for elucidating their effects on the pathogenesis of dyslipidaemia.MethodsSix pigs were randomly divided into two groups of three pigs each, namely, the high-fat diet and the balanced diet groups, which were fed a high-fat diet and balanced diet separately for six months. HDL was separated from plasma, which was followed by dissociation of the miRNA bound to HDL. miRNA sequencing of the isolated miRNA was performed to identify the differential expression profiles between the two groups, which was validated by real-time PCR. TargetScan, miRDB, and miRWalk were used for the prediction of genes targeted by the differential miRNAs.ResultsCompared with the balanced diet group, the high-fat diet group had significantly higher levels of TG, TC, LDL-C and HDL-C at six months. miRNA sequencing revealed 6 upregulated and 14 downregulated HDL-bound miRNAs in the high-fat diet group compared to the balanced diet group, which was validated by real-time PCR. GO enrichment analysis showed that dysregulated miRNAs in the high-fat diet group were associated with the positive regulation of lipid metabolic processes, positive regulation of lipid biosynthetic processes, and positive regulation of Ras protein signal transduction. Insulin resistance and the Ras signalling pathway were enriched in the KEGG pathway enrichment analysis.ConclusionsTwenty HDL-bound miRNAs are significantly dysregulated in high-fat diet-induced dyslipidaemia. This study presents an analysis of a new set of HDL-bound miRNAs that are altered by a high-fat diet and offers some valuable clues for novel mechanistic insights into high-fat diet-induced dyslipidaemia. Further functional verification study using a larger sample size will be required.

Integrating Clinical and Genomic Analyses of Hippocampal-Prefrontal Circuit Disorder in Depression.

Major depressive disorder (MDD) is a prevalent, devastating and recurrent mental disease. Hippocampus (HIP)-prefrontal cortex (PFC) neural circuit abnormalities have been confirmed to exist in MDD; however, the gene-related molecular features of this circuit in the context of depression remain unclear. To clarify this issue, we performed gene set enrichment analysis (GSEA) to comprehensively analyze the genetic characteristics of the two brain regions and used weighted gene correlation network analysis (WGCNA) to determine the main depression-related gene modules in the HIP-PFC network. To clarify the regional differences and consistency for MDD, we also compared the expression patterns and molecular functions of the key modules from the two brain regions. The results showed that candidate modules related to clinical MDD of HIP and PFC, which contained with 363 genes and 225 genes, respectively. Ninety-five differentially expressed genes (DEGs) were identified in the HIP candidate module, and 51 DEGs were identified in the PFC candidate module, with only 11 overlapping DEGs in these two regional modules. Combined with the enrichment results, although there is heterogeneity in the molecular functions in the HIP-PFC network of depression, the regulation of the MAPK cascade, Ras protein signal transduction and Ephrin signaling were significantly enriched in both brain regions, indicating that these biological pathways play important roles in MDD pathogenesis. Additionally, the high coefficient protein–protein interaction (PPI) network was constructed via STRING, and the top-10 coefficient genes were identified as hub genes via the cytoHubba algorithm. In summary, the present study reveals the gene expression characteristics of MDD and identifies common and unique molecular features and patterns in the HIP-PFC network. Our results may provide novel clues from the gene function perspective to explain the pathogenic mechanism of depression and to aid drug development. Further research is needed to confirm these findings and to investigate the genetic regulation mechanisms of different neural networks in depression.

Differential Expression and Bioinformatics Analysis of circRNA in Non-small Cell Lung Cancer.

Circular RNA (CircRNA) plays an important role in tumorigenesis and progression of non-small cell lung cancer (NSCLC), but the pathogenesis of NSCLC caused by circRNA has not been fully elucidated. This study aimed to investigate differentially expressed circRNAs and identify the underlying pathogenesis hub genes of NSCLC by comprehensive bioinformatics analysis. Data of gene expression microarrays (GSE101586, GSE101684, and GSE112214) were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed circRNAs (DECs) were obtained by the “limma” package of R programs and the overlapping operation was implemented of DECs. CircBase database and Cancer-Specific CircRNA database (CSCD) were used to find miRNAs binding to DECs. Target genes of the found miRNAs were identified utilizing Perl programs based on miRDB, miRTarBase, and TargetScan databases. Functional and enrichment analyses of selected target genes were performing using the “cluster profiler” package. Protein-protein interaction (PPI) network was constructed by the Search Tool for the STRING database and module analysis of selected hub genes was performed by Cytoscape 3.7.1. Survival analysis of hub genes were performed by Gene Expression Profiling Interactive Analysis (GEPIA). Respectively, 1 DEC, 249 DECs, and 101 DECs were identified in GSE101586, GSE101684, and GSE112214. A total of eight overlapped circRNAs, 43 miRNAs and 427 target genes were identified. Gene Ontology (GO) enrichment analysis showed these target genes were enriched in biological processes of regulation of histone methylation, Ras protein signal transduction and covalent chromatin modification etc. Pathway enrichment analysis showed these target genes are mainly involved in AMPK signaling pathway, signaling pathways regulating pluripotency of stem cells and insulin signaling pathway etc. A PPI network was constructed based on 427 target genes of the 43 miRNAs. Ten hub genes were found, of which the expression of MYLIP, GAN, and CDC27 were significantly related to NSCLC patient prognosis. Our study provide a deeper understanding the circRNAs-miRNAs-target genes by bioinformatics analysis, which may provide novel insights for unraveling pathogenesis of NSCLC. MYLIP, GAN, and CDC27 genes might serve as novel biomarker for precise treatment and prognosis of NSCLC in the future.

Polyphyllin VII suppresses cell proliferation, the cell cycle and cell migration in colorectal cancer.

Colorectal cancer (CRC) is one of the most common types of human cancer. However, there is still an urgent need to identify novel treatment strategies for CRC. The present study aimed to validate the potential antitumor effects of polyphyllin VII in CRC. The present study revealed that polyphyllin VII could significantly inhibit CRC proliferation and induce cell cycle arrest and apoptosis. Moreover, the anti-metastatic effect of polyphyllin VII in CRC cells was implicated. Microarray analysis identified that polyphyllin VII could affect multiple protein coding genes and non-coding RNAs. Bioinformatics analysis revealed that polyphyllin VII regulated multiple pathways in CRC, including ‘ER to Golgi vesicle-mediated transport’, ‘response to cAMP’, ‘Ras protein signal transduction’, ‘metabolic pathways’, ‘MAPK signaling pathway’ and ‘cell cycle’. Protein-Protein Interaction network analysis identified a series of key polyphyllin VII-regulating genes in CRC, including ribonucleoside-diphosphate reductase subunit M2, structural maintenance of chromosomes protein 4 and DNA replication licensing factor MCM4. Finally, the present results demonstrated that these key polyphyllin VII-regulating genes were dysregulated in CRC. Taken together, these results indicated that polyphyllin VII could be a novel antitumor drug for the treatment of CRC.

Hsa_circ_0012152 and Hsa_circ_0001857 Accurately Discriminate Acute Lymphoblastic Leukemia From Acute Myeloid Leukemia

Acute leukemia (AL) is a group of highly heterogeneous hematological malignancies. Circular RNAs (circRNAs) are covalently closed circRNA molecules implicated in the development of many diseases. However, the role of circRNAs in AL remains largely unknown. Therefore, this study aimed to identify new classification diagnostic biomarkers for subgroups of AL. The circRNA expression signatures discriminating acute lymphoblastic leukemia (ALL) from acute myeloid leukemia (AML) were identified by microarray, followed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) validation. Receiver operating characteristic curve analysis was used to evaluate the diagnostic efficiencies of hsa_circ_0001857 and hsa_circ_0012152, and hsa_circ_0012152 was selected for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. The results showed that the circRNA expression profiles, hsa_circ_0001857, and hsa_circ_0012152 could clearly discriminate ALL from AML. The target genes of hsa_circ_0012152 might be involved in biological processes, such as myeloid cell differentiation, covalent chromatin modification, histone modification, and rat sarcoma (Ras) protein signal transduction, and participate in pathways such as mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3′-kinase (PI3K)-Akt signaling pathway. Hsa_circ_0012152 might be involved in the initiation and development of AML through miR-491-5p/epidermal growth factor receptor (EGFR)/MAPK1 or miR-512-3p/EGFR/MAPK1 axis. Our results showed that circRNA expression profiles and specifically expressed circRNAs were promising classification biomarkers to designate AL into ALL or AML.

Identification of long non‑coding RNAs expressed during the�osteogenic differentiation of human bone marrow‑derived mesenchymal stem cells obtained from patients with ONFH

Long non-coding RNAs (lncRNAs) are crucial for the occurrence and development of numerous diseases. Although lncRNAs are involved in the biological activities of stem cells and play crucial roles in stem cell differentiation, the expression of specific lncRNAs during human bone marrow-derived mesenchymal stem cell (hBMSC) osteogenic differentiation in osteonecrosis of the femoral head (ONFH) and their regulatory roles have not yet been fully elucidated. To the best of our knowledge, the present study is the first to characterize lncRNA expression profiles during hBMSC osteogenic differentiation in ONFH using microarray analysis and RT-qPCR to confirm the microarray data. A total of 24 downregulated and 24 upregulated lncRNAs were identified and the results of RT-qPCR were found to be consistent with those of microarray analysis. Bioinformatics analyses, using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, were conducted to explore the possible mechanisms and identify the signaling pathways that the lncRNAs are involved in. GO analysis revealed significant changes in the intracellular organelle, Ras protein signal transduction and transferase activity. KEGG pathway analysis revealed that the lncRNAs were closely associated with fatty acid metabolism, apoptosis and the TGF-β signaling pathway. The overexpression of MAPT antisense RNA 1 (MAPT-AS1) was found to promote osteogenesis and inhibit the adipogenesis of hBMSCs at the cellular and mRNA levels. On the whole, the findings of the present study identified the lncRNAs and their roles in hBMSCs undergoing osteogenic differentiation in ONFH and provide a new perspective for the pathogenesis of ONFH.

Extracellular Vesicles of Human Periodontal Ligament Stem Cells Contain MicroRNAs Associated to Proto-Oncogenes: Implications in Cytokinesis.

The human Periodontal Ligament Stem Cells (hPDLSCs) exhibit self-renewal capacity and clonogenicity potential. The Extracellular Vesicles (EVs) secreted by hPDLSCs are particles containing lipids, proteins, mRNAs, and non-coding RNAs, among which microRNAs, that are important in intercellular communication. The purpose of this study was the analysis of the non-coding RNAs contained in the EVs derived from hPDLSCs using Next Generation Sequencing. Moreover, our data were enriched using bioinformatic tools. The analysis highlighted the presence of non-coding RNAs and five microRNAs: MIR24-2, MIR142, MIR335, MIR490, and MIR296. Our results show that these miRNAs target the genes classified in two terms of the Gene Ontology: “Ras protein signal transduction” and “Actin/microtubule cytoskeleton organization.” Noteworthy, the in-deep analysis of our EVs highlights that the miRNAs could be implicated in the silencing of proto-oncogenes involved in 12 different types of tumors.

FAM83H overexpression predicts worse prognosis and correlates with less CD8+ T cells infiltration and Ras-PI3K-Akt-mTOR signaling pathway in pancreatic cancer.

Family with sequence similarity 83 members H (FAM83H) is one member of Family with sequence similarity 83 (FAM83) family, which possess oncogenic properties in several types of cancer. However, the potential function of FAM83H in pancreatic cancer (PC) still remain unknown. This study aims to explore the role of FAM83H during pancreatic carcinogenesis and the regulation of immune infiltration in PC. In the current study, the clinical significance and potential biological of FAM83H were evaluated by bioinformatics analysis. Possible associations between FAM83H expression and tumor immunity were analyzed using ESTIMATE algorithm and single-sample gene set enrichment analysis (ssGSEA). FAM83H expression was significantly upregulated in tumor tissues, and positively associated with higher histologic grade, tumor recurrence, and worse prognosis. FAM83H overexpression is notably associated with KRAS activation. And functional enrichment analysis demonstrated that FAM83H may be involved in positive regulation of cell proliferation and migration, Ras protein signal transduction, regulation of cell-matrix adhesion, epithelial to mesenchymal transition (EMT), TGF-β receptor signaling in EMT, and activated NOTCH transmits signal to the nucleus. ESTIMATE algorithm and ssGSEA demonstrated that FAM83H overexpression suppressed the infiltration and antitumor activity of tumor-infiltrating lymphocytes (TILs), especially for CD8+ T cells. Besides, FAM83H overexpression significantly correlated with low expression of TIL-related gene markers (e.g. CD8A, CD8B, CD2, CD3D, and CD3E). The study suggests that FAM83H overexpression predicts poor prognosis and correlates with less CD8+ T cells infiltration and Ras-PI3K-Akt-mTOR signaling pathway in PC.