Identification Of Target Genes Research Articles

Comprehensive Analysis of microRNA Methylation Profiles and Determination of Their Functional Significance in Colorectal Cancer: A Study Protocol

Colorectal cancer (CRC) is a leading cause of cancer-associated fatalities globally. Despite the notable progress in diagnostics and patient care, challenges persist in areas such as early detection, prognostic variable identification, metastatic disease treatment, and personalised treatment options. In CRC, microRNAs, a type of short non-coding RNA, are found to be deregulated and can significantly influence its onset and progression. However, previous microRNA research primarily focused on expression levels to ascertain their biological significance, leaving the microRNA methylation landscapes in CRC patients largely unexplored. This study aims to investigate the genome-wide methylome profiles of microRNA and clarify their roles in CRC. We will analyse the microRNA methylation profiles from our in-house data of more than 100 CRCs and correlate the differentially methylated microRNAs with clinicopathological features. To understand the biological significance of methylated microRNAs, we will perform pathway enrichment analysis and molecular dynamics simulations to examine the binding of argonaut protein to the differentially methylated microRNAs and the structural changes involved. Furthermore, we will conduct functional studies to determine the roles of selected microRNAs. CRC cell lines with hypermethylated microRNA of interest will be treated with a demethylating agent, followed by cell-based assays. Subsequent transcriptome-wide microRNA gene target identification and protein profiling will be performed to interrogate the molecular pathways affected by demethylation of the microRNA of interest. Methylation signifies a major transformation in cancer detection, as widespread epigenetic changes could potentially provide superior early-stage cancer detection and classification compared to somatic mutations. Effective CRC diagnosis ensures timely and appropriate treatment for patients, thereby improving their quality of life. The insights gained from this study could be applied to individualized health diagnostics, disease prognostication, and treatment monitoring.

Identification of potential target genes of cardiac glycosides from Vernonia amygdalina Delile in HER2+ breast cancer cells

Vernonia amygdalina Delile or bitter leaf, a traditional medicinal plant endemic to Africa, has shown anticancer properties by inhibiting the downstream signaling of human epidermal growth factor receptor 2 (HER2) in several cancer cells through the PI3K/AKT/mTOR pathways. This study explored the potential target of Vemonia cardiac glycosides for the treatment of HER2+ breast cancer (CTG) using bioinformatics and in vitro experiments. The similarity ensemble technique Swiss TargetPrediction was used to predict protein targets of cardiac glycosides. DisGeNET and UALCAN were used to collect the regulatory genes of HER2+ breast cancer cells. We obtained 75 CTG sequences from the predicted target and regulatory genes of HER2+ breast cancer. Subsequent analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that CTG was enriched for multiple pathways, such as PI3K-Akt signaling, breast cancer, EGFR tyrosine kinase inhibitor resistance, and ErbB signaling pathways. Further bioinformatic analysis identified five CTG: ERBB2, ESR1, EGFR, PIK3CA, and PTPN11. The ethanolic extract and its ethyl acetate fraction of V. amigdalina were referred to as REF and EA, respectively. Cytotoxicity tests showed that EA exerted strong cytotoxicity on MCF-7/HER2 cells by inducing S-phase cell cycle arrest and apoptosis, modulating the mRNA expression of CTG: ERBB2, ESR1, and proliferation and apoptosis markers, PCNA, CCND1, BAX, BCL2, and CASP7. Future studies should develop EA and cardiac glycosides as anticancer agents against HER2+breast cancer cells.

Plasma microRNA Profiling in Type 2 Diabetes Mellitus: A Pilot Study.

Type 2 diabetes mellitus (T2D) is a chronic metabolic disease characterized by insulin resistance and β-cell dysfunction and leading to many micro- and macrovascular complications. In this study we analyzed the circulating miRNA expression profiles in plasma samples from 44 patients with T2D and 22 healthy individuals using next generation sequencing and detected 229 differentially expressed miRNAs. An increased level of miR-5588-5p, miR-125b-2-3p, miR-1284, and a reduced level of miR-496 in T2D patients was verified. We also compared the expression landscapes in the same group of patients depending on body mass index and identified differential expression of miR-144-3p and miR-99a-5p in obese individuals. Identification and functional analysis of putative target genes was performed for miR-5588-5p, miR-125b-2-3p, miR-1284, and miR-496, showing chromatin modifying enzymes and apoptotic genes being among the significantly enriched pathways.

PSIII-20 Transcriptional and Functional Analyses of Intramuscular, Subcutaneous, and Visceral Adipose Tissue in Finished Beef Cattle

Abstract Intramuscular adipose tissue (IMAT; marbling) deposition is a highly desired trait in beef cattle. Unlike excessive subcutaneous (SCAT) and visceral (VIAT) adipose tissue, which have relatively low value, increased marbling is associated with meat sensory traits and is a primary factor influencing beef quality grading in the U.S. However, this trait is difficult to achieve. Our objective was to assess depot-specific characteristics and gene profile of IMAT, SCAT, and VIAT in beef cattle. IMAT and SCAT samples from the longissimus muscle (9-11th ribs), and VIAT from the greater omentum were collected from four beef animals at harvest. Adipose tissue (AT) samples were flash frozen in liquid nitrogen, followed by RNA extraction (Trizol reagent) and RNA sequencing analysis on an Illumina Novaseq 6000 platform to generate 150 bp paired-end reads. DESeq2 R package was used for differential gene expression analysis (DEG) and DEG (P ≤ 0.05, log2FC ≥ 1) were evaluated for KEGG enrichment pathways. Remainder tissue samples were assessed for viscoelasticity (rheometer), collagen fibrillogenesis (kinetics), and adipocyte size (K2 Cellometer). Transcriptome analysis revealed over 4,000 DEG between IMAT and SCAT, over 3,000 DEG between VIAT and IMAT, and 1,018 DEG between VIAT and SCAT, thus indicating substantial transcriptional diversity among AT depots (Figure 1). Top upregulated genes in SCAT vs. IMAT were associated with increased lipid accumulation and regulation such as LIPE, LEP, ADIPOQ, PPARG, and extracellular matrix (ECM) remodeling, including collagens, MMP14, and TIMP4. Accordingly, enrichment analysis revealed an activation of PPARG signaling pathways and fatty acid metabolism in SCAT vs. IMAT, which are key for lipogenesis and adipogenesis (Figure 2). IMAT showed activation of pathways for thermogenesis and oxidative phosphorylation compared with both SCAT and VIAT, indicating that IMAT utilization may be more directed towards muscle function and development (Figure 2 and 3). Top VIAT DEG were primarily associated with immune cell adhesion, and immune response (CDHR1, TENM2, and TNFRSF9), suggesting a pro-inflammatory profile of visceral adiposity. Notably, enrichment analysis showed an activation of the immune function in VIAT compared with IMAT and SCAT (Figures 3 and 4). In agreement with transcriptome analysis, adipocyte size was increased in SCAT vs. IMAT and VIAT, implying higher lipid accumulation (Figure 5). SCAT was also stiffer and had increased collagen fibrillogenesis compared with IMAT, suggesting a key role for ECM in mechanisms of AT adipogenesis and lipogenesis (Figure 5). In summary, these results indicate that AT anatomical location impacts AT transcriptome, which may translate into functional differences in adipogenesis and ECM remodeling. Understanding transcriptional and functional differences among IMAT, SCAT and VIAT can help on the identification of target genes to modulate AT deposition in distinct areas of the body, therefore, improving quality of beef carcasses and industry profitability.

PYGO2-MDR1 Axis in Multiple Myeloma Patients with 1q21 Amplification As Promising Target to Overcome Carfilzomib Resistance

Multiple myeloma (MM) is a hematological malignancy characterized by an accumulation of clonal plasma cells (PCs) in the bone marrow (BM). Gain and/or amplification of 1q21 (1q21+) is one of the most frequent secondary cytogenetic abnormalities present in MM patients and in smoldering MM (SMM). The incidence and copy number alteration (CNA) of the 1q21 region increase during the progression and relapse of the disease; in fact, additional copies of 1q21 can be detected in around 40% of newly diagnosed MM (NDMM) and 70% of relapse-refractory MM (RRMM). Recently, 1q21+ has been identified as an adverse prognostic factor in MM patients and its presence has been correlated with a shorter duration of the response in MM patients treated with carfilzomib (CFZ)-based regimens. Thus, the identification of possible target genes in 1q21 region is an emerging unmet medical need in MM patients. PYGOPUS2 (PYGO2) is a gene located in the 1q21 chromosomal region and it is a downstream target of β-catenin, and it has been shown to promote the transcription of gene target of the Wnt-signaling, forming a nuclear complex with β-catenin/BCL9. Different studies have reported that upregulation of PYGO2 is involved in tumorigenesis in breast and lung cancers, showing that overexpression of PYGO2 leads to drug resistance by promoting the activation of the multidrug resistance 1 polypeptide ( MDR1). The expression profile of PYGO2 in1q21+ MM patients and its possible role in CFZ resistance is still unknown and have been investigated in this study. Firstly, we purified CD138 + PCs from BM samples from 18 NDMM and from 11 SMM patients. Fluorescent in situ hybridization (FISH) analysis was performed on purified CD138 + PCs for all patients to access CNA in the region 1q21. A score indicating the number of 1q21 copies was calculated based on the FISH hybridization pattern of each patient. 14/29 (48%) patients presented CNA in the 1q21 region. The expression profile of all 29 samples was generated using GeneChip ClariomD Arrays (Affymetrix Inc., Santa Clara, CA, USA) . The sam package was used to identify differentially expressed genes between 1q21+ and control samples. Our analysis identified PYGO2 to be significantly upregulated in patients with 1q21+ when compared with controls (p= 0.0008). Additionally, we found a positive correlation between gene expression and the 1q21 copy number (p= <0.0001, r= 0.6738). Secondly, we evaluated PYGO2 mRNA expression levels in several human myeloma cell lines (HMCLs) with 1q21 CNA. Our results showed that PYGO2 is overexpressed in HMCLs with 1q21 CNA. Previous studies in solid tumor have shown that PYGO2 is upregulated in drug resistant cancer cells, and this upregulation results in overexpression of MDR1; indeed, we evaluated the mRNA expression of PYGO2 in CFZ-resistant HMCLs. Interestingly our results showed that both PYGO2 and MDR1 expression are upregulated in CFZ-R cells. We next examined the relationship between PYGO2 and MDR1. We generated a PYGO2-knockdown in JJN3 MM cell line using short hairpin RNA (shRNA) lentivectors. Knockdown of PYGO2 resulted in a significant decrease in expression PYGO2, a decrease in cell viability, and a reduction in MDR1 expression. In conclusion, our results show that PYGO2 expression is significantly upregulated in MM patients carrying 1q21+ and that its expression is correlated with 1q21 copy number. Moreover, we found that the PYGO2-MDR1 axis is involved in the CFZ resistance in HMCLs MM cells suggesting that PYGO2 could be a possible future druggable target in 1q21+ MM patients.

Loss of function of ribosomal protein L13a blocks blastocyst formation and reveals a potential nuclear role in gene expression.

Ribosomal proteins play diverse roles in development and disease. Most ribosomal proteins have canonical roles in protein synthesis, while some exhibit extra-ribosomal functions. Previous studies in our laboratory revealed that ribosomal protein L13a (RPL13a) is involved in the translational silencing of a cohort of inflammatory proteins in myeloid cells. This prompted us to investigate the role of RPL13a in embryonic development. Here we report that RPL13a is required for early development in mice. Crosses between Rpl13a+/- mice resulted in no Rpl13a-/- offspring. Closer examination revealed that Rpl13a-/- embryos were arrested at the morula stage during preimplantation development. RNA sequencing analysis of Rpl13a-/- morulae revealed widespread alterations in gene expression, including but not limited to several genes encoding proteins involved in the inflammatory response, embryogenesis, oocyte maturation, stemness, and pluripotency. Exvivo analysis revealed that RPL13a was localized to the cytoplasm and nucleus between the two-cell and morula stages. RNAi-mediated depletion of RPL13a phenocopied Rpl13a-/- embryos and knockdown embryos exhibited increased expression of IL-7 and IL-17 and decreased expression of the lineage specifier genes Sox2, Pou5f1, and Cdx2. Lastly, a protein-protein interaction assay revealed that RPL13a is associated with chromatin, suggesting an extra ribosomal function in transcription. In summary, our data demonstrate that RPL13a is essential for the completion of preimplantation embryo development. The mechanistic basis of the absence of RPL13a-mediated embryonic lethality will be addressed in the future through follow-up studies on ribosome biogenesis, global protein synthesis, and identification of RPL13a target genes using chromatin immunoprecipitation and RNA-immunoprecipitation-based sequencing.

Chromosome-level genome assembly of Bactrocera correcta provides insights into its adaptation and invasion mechanisms

Bactrocera correcta is an invasive polyphagous pest with significant ecological and economic implications. Understanding its genetic characteristics and the molecular mechanisms that drive its rapid adaptation to new environments requires genomic information. In this study, we successfully assembled the chromosome-level genome of B. correcta using PacBio long-read sequencing, Illumina sequencing, and chromatin conformation capture (Hi-C) methods. The final genome assembly spans a total length of 702.65 Mb. We managed to anchor approximately 86.88% of the assembled contigs into 6 linkage groups, ranging from 17.97 Mb to 166.49 Mb. Additionally, our analysis predicted a total of 21,015 genes, with repetitive sequences accounting for 58.22% of the genome. We further identified retroelements and DNA transposons as the major contributors to the larger size of the B. correcta genome, constituting 36.06% and 30.92% of the repetitive sequences, respectively. Our divergence time estimation placed B. correcta's split from other Bactrocera species at around 5.99–16.71 million years ago. Through gene family analyses, we discovered significant expansions in chemosensory-related gene families (IR, GR), heat shock proteins (HSP60), and resistance-related gene families (ABC) in B. correcta compared to its closest relatives. Transcriptomic analysis revealed substantial upregulation of HSP genes, especially those from the HSP20 subfamily, in response to high temperatures. The availability of this reference genome serves as a foundation for the identification of precise target genes in B. correcta, facilitating molecular prevention and control strategies.

PRMT5 regulates the polysaccharide content by controlling the splicing of thaumatin-like protein in Ganoderma lucidum.

In the current study, the silencing of protein arginine methyltransferase 5 (PRMT5) decreased the polysaccharide content of Ganoderma lucidum compared to that of the wild-type (WT) strain. Furthermore, RNA-seq screening showed that the glycan degradation process-related gene thaumatin-like protein (TLP) was alternatively spliced in WT strains via retained introns, leading to the production of a longer TLP1 isoform and a shorter TLP2 isoform; however, only the TLP2 isoform was observed in PRMT5i strains. Experiments examining the polysaccharide content of the TLP silencing, TLP1 overexpression (OE-TLP1), and TLP2 overexpression (OE-TLP2) transformants revealed that TLP2 plays a more important role than TLP1 in polysaccharide degradation. Through a combination of yeast two-hybrid, bimolecular fluorescence complementation and surface plasmon resonance assays, we found that TLP2 directly physically interacted with phosphoglucose isomerase (PGI), a key enzyme in polysaccharide synthesis, and thereby increased PGI activity. However, TLP1 failed to interact with PGI, and PGI activity was not affected. Further inspection showed that the polysaccharide content was decreased in the OE-TLP2 strains but not significantly changed in the OE-TLP1 strains compared with that in the WT strains. In addition, the polysaccharide content of the PRMT5-TLP-cosilenced strains was not significantly different from that of the WT strains. These results demonstrate that PRMT5 modulates TLP processing of pre-mRNA transcripts and thereby decreases the polysaccharide content.IMPORTANCEPRMT5 contributes to secondary metabolite biosynthesis in Ganoderma lucidum. However, the mechanism through which PRMT5 regulates the biosynthesis of secondary metabolites remains unclear. In the current study, PRMT5 silencing led to a significant decrease in the biosynthesis of polysaccharides from G. lucidum through the action of the alternative splicing of TLP. A shorter TLP2 isoform can directly bind to PGI and regulated polysaccharide biosynthesis. These results suggest that PRMT5 enhances PGI activity by regulating TLP binding to PGI. The results of the current study reveal a novel target gene for PRMT5-mediated alternative splicing and provide a reference for the identification of PRMT5 regulatory target genes.

MicroRNA-582-3p knockdown alleviates non-alcoholic steatohepatitis by altering the gut microbiota composition and moderating TMBIM1.

The gut dysbiosis correlates with non-alcoholic steatohepatitis (NASH), involving the moderation of miRNAs. This study was aimed to investigate the correlation between gut microbiota and miR-582-3p in patients with non-alcoholic steatohepatitis (NASH) and to explore the possible regulation of miR-582-3p in the function of the activated hepatic stellate cells (HSCs). GSE69670 and GSE14435 datasets were analyzed by GEO2R. Plasma and fecal samples were obtained from the subjects, non-steatosis (n = 35), simple steatosis (n = 35), and NASH (n = 35). The variations in intestinal microbiota in the non-steatosis and NASH groups were analyzed using 16S rRNA sequencing. The expression of miR-582-3p among the groups was detected using RT-qPCR. Correlations between top-changed intestinal microbiota and miR-582-3p expression were analyzed using the Pearson correlation coefficient. Target gene identification was performed by prediction and dual-luciferase reporter assay. The effect of miR-582-3p on the cell function of TGF-β1-induced HSCs was assessed in vitro. miR-582-3p was the common differentially expressed miRNA between GSE69670 and GSE14435. miR-582-3p was upregulated in NASH patients' plasma, as well as in TGF-β1-induced LX-2 cells. The non-steatosis and NASH groups showed significantly different intestinal microbiota distribution. miR-582-3p was positively correlated with specific microbiota populations. TMBIM1 was a target gene for miR-582-3p. Knockdown of miR-582-3p suppressed HSC proliferation and myofibroblast markers' expression but induced cell apoptosis, via TMBIM1. This present study suggests that miR-582-3p promotes the progression of NASH. Knockdown of miR-582-3p may alleviate NASH by altering the gut microbiota composition and moderating TMBIM1.

Potential value of mitochondrial regulatory pathways in the clinical application of clear cell renal cell carcinoma: a machine learning-based study

BackgroundRenal clear cell carcinoma (RCC) is a common cancer in urinary system with increasing incidence. At present, targeted therapy and immunotherapy are the main therapeutic programs in clinical therapy. To develop novel drugs and provide new ideas for clinical therapy, the identification of potential ccRCC subtypes and potential target genes or pathways has become a current research focus.AimThe aim of this study was to explore the underlying mechanisms of mitochondrial function in ccRCC. This regulatory pathway is closely related to tumor development and metastasis in ccRCC patients, and their abnormal changes may affect the prognosis of cancer patients. Therefore, we decided to construct a prognostic model of ccRCC patients based on mitochondrial regulatory genes, aiming to provide new methods and ideas for clinical therapy.ResultThe 5-year survival prediction model based on iterative LASSO reached 0.746, and the cox model based on coxph reached C-index = 0.77, integrated c/D AUC = 0.61, and integrated brier score = 0.14. The rsf model based on randomForestSRC was built with C-index = 0.82, integrated c/D AUC = 0.69, and integrated brier score = 0.11. The results show that mitochondrial regulatory pathway is a potential target pathway for clinical therapy of ccRCC, which can provide guidelines for clinical targeted therapy, immunotherapy and other first-line therapy.

Altered Smooth Muscle Cell Histone Acetylome by the SPHK2/S1P Axis Promotes Pulmonary Hypertension.

Epigenetic regulation of vascular remodeling in pulmonary hypertension (PH) is poorly understood. Transcription regulating, histone acetylation code alters chromatin accessibility to promote transcriptional activation. Our goal was to identify upstream mechanisms that disrupt epigenetic equilibrium in PH. Human pulmonary artery smooth muscle cells (PASMCs), human idiopathic pulmonary arterial hypertension (iPAH):human PASMCs, iPAH lung tissue, failed donor lung tissue, human pulmonary microvascular endothelial cells, iPAH:PASMC and non-iPAH:PASMC RNA-seq databases, NanoString nCounter, and cleavage under targets and release using nuclease were utilized to investigate histone acetylation, hyperacetylation targets, protein and gene expression, sphingolipid activation, cell proliferation, and gene target identification. SPHK2 (sphingosine kinase 2) knockout was compared with control C57BL/6NJ mice after 3 weeks of hypoxia and assessed for indices of PH. We identified that Human PASMCs are vulnerable to the transcription-promoting epigenetic mediator histone acetylation resulting in alterations in transcription machinery and confirmed its pathological existence in PH:PASMC cells. We report that SPHK2 is elevated as much as 20-fold in iPAH lung tissue and is elevated in iPAH:PASMC cells. During PH pathogenesis, nuclear SPHK2 activates nuclear bioactive lipid S1P (sphingosine 1-phosphate) catalyzing enzyme and mediates transcription regulating histone H3K9 acetylation (acetyl histone H3 lysine 9 [Ac-H3K9]) through EMAP (endothelial monocyte activating polypeptide) II. In iPAH lungs, we identified a 4-fold elevation of the reversible epigenetic transcription modulator Ac-H3K9:H3 ratio. Loss of SPHK2 inhibited hypoxic-induced PH and Ac-H3K9 in mice. We discovered that pulmonary vascular endothelial cells are a priming factor of the EMAP II/SPHK2/S1P axis that alters the acetylome with a specificity for PASMC, through hyperacetylation of histone H3K9. Using cleavage under targets and release using nuclease, we further show that EMAP II-mediated SPHK2 has the potential to modify the local transcription machinery of pluripotency factor KLF4 (Krüppel-like factor 4) by hyperacetylating KLF4 Cis-regulatory elements while deletion and targeted inhibition of SPHK2 rescues transcription altering Ac-H3K9. SPHK2 expression and its activation of the reversible histone H3K9 acetylation in human pulmonary artery smooth muscle cell represent new therapeutic targets that could mitigate PH vascular remodeling.

Exploration of the Mechanism of Shengxian Decoction Against Chronic Obstructive Pulmonary Disease Based on Network Pharmacology and Experimental Verification.

Shengxian decoction (SXT) is clinically used in chronic obstructive pulmonary disease (COPD) treatment. This study aimed to explore the mechanism and target genes of SXT acting on COPD. Differentially expressed genes (DEGs) between COPD and controls were identified and then performed enrichment analysis. The effective active compounds and corresponding target genes were obtained from the traditional Chinese medicine systems pharmacology database. We also compiled COPD related genes from the GeneCards database. Through the protein-protein interaction (PPI) network and least absolute shrinkage and selection operator (LASSO) regression was performed to identify key genes. Molecular docking was used for docking of key genes and compounds. The expression of key genes was detected by quantitative real-time PCR in COPD patients and bronchial epithelial cells stimulated with cigarette stroke extract (CSE). We identified 1,458 intersected DEGs from GSE47460 and GSE57148 datasets. Compared with intersected DEGs, we obtained 33 SXT target COPD-related genes. PI3K-Akt signaling pathway, MAPK signaling pathway, and focal adhesion were enriched by these 33 genes, as well as intersected DEGs. According to LASSO regression, there were 12 genes considered as signature genes. Then we constructed active compounds and corresponding six target genes. Finally, HIF1A and IL1B were selected as key genes by combining PPI network. HIF1A and IL1B were all upregulated expression in COPD and CSE stimulated cells and recovered in SXT treated CSE stimulated cells. This study provides a scientific basis for the identification of active compounds and target genes of SXT in the treatment of COPD.

MiRNA-4769-5p/MBP and miRNA-1827/AR as key components in intervertebral disc degeneration: A network-based analysis approach

Intervertebral disc degeneration (IDD) is a common cause of low back pain and disability. Standard treatment of IDD is conservative therapies and surgical treatment, that have some limitations including low success rate. Therefore, there is a high demand for novel and more effective treatments which target the molecular mechanisms of the disease. The aim of present study was the identification of key miRNAs and target genes involved in intervertebral disc degeneration using a network-based analysis approach. Two datasets of miRNA and mRNA microarray profiling was obtained from gene expression omnibus (GEO) and analyzed using ExAtlas and GEO2R to find differentially expressed miRNAs and genes, respectively. Functional annotation was performed in DAVID database and miEAA tool. Protein-protein interaction network (PPIN) was created in STRING and analyzed using Cytoscape. MicroRNA target prediction was done using miRWalk database. Overlapping genes was identified using Venn diagram. Overall, 320 differentially expressed genes (DEGs) and 14 differentially expressed miRNAs with 1323 predicted targets was selected. Some gene ontology and pathway enriched terms were glycosaminoglycan binding, neutrophil degranulation, extracellular matrix organization, immune system, cell cycle, GTPase activity and MAPK signaling. Twenty-eight and 90 hub genes were identified after analyzing DEGs network and predicted miRNAs targets network, respectively. DEGs and targets networks had 5 and 4 clusters/functional module, respectively. Two hub genes of AR and MBP were common between networks, which were the targets of hsa-miR-1827 and hsa-miR-4769-5p, respectively. These miRNAs/targets potentially are good candidates for diagnostic (biomarker) and therapeutic applications. However, this was only a in silico study and many in vitro, in vivo and clinical evidences are needed for validation.

Identification of candidate target genes of oral squamous cell carcinoma using high-throughput RNA-Seq data and in silico studies of their interaction with naturally occurring bioactive compounds

Oral Squamous Cell Carcinoma (OSCC) accounts for more than 90% of all kinds of oral neoplasms that develop in the oral cavity. It is a type of malignancy that shows high morbidity and recurrence rate, but data on the disease’s target genes and biomarkers is still insufficient. In this study, in silico studies have been performed to find out the novel target genes and their potential therapeutic inhibitors for the effective and efficient treatment of OSCC. The DESeq2 package of RStudio was used in the current investigation to screen and identify differentially expressed genes for OSCC. As a result of gene expression analysis, the top 10 novel genes were identified using the Cytohubba plugin of Cytoscape, and among them, the ubiquitin-conjugating enzyme (UBE2D1) was found to be upregulated and playing a significant role in the progression of human oral cancers. Following this, naturally occurring compounds were virtually evaluated and simulated against the discovered novel target as prospective drugs utilizing the Maestro, Schrodinger, and Gromacs software. In a simulated screening of naturally occurring potential inhibitors against the novel target UBE2D1, Epigallocatechin 3-gallate, Quercetin, Luteoline, Curcumin, and Baicalein were identified as potent inhibitors. Novel identified gene UBE2D1 has a significant role in the proliferation of human cancers through suppression of ‘guardian of genome’ p53 via ubiquitination dependent pathway. Therefore, the treatment of OSCC may benefit significantly from targeting this gene and its discovered naturally occurring inhibitors. Communicated by Ramaswamy H. Sarma

The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones

BackgroundPod size is an important yield target trait for peanut breeding. However, the molecular mechanism underlying the determination of peanut pod size still remains unclear.ResultsIn this study, two peanut varieties with contrasting pod sizes were used for comparison of differences on the transcriptomic and endogenous hormonal levels. Developing peanut pods were sampled at 10, 15, 20, 25 and 30 days after pegging (DAP). Our results showed that the process of peanut pod-expansion could be divided into three stages: the gradual-growth stage, the rapid-growth stage and the slow-growth stage. Cytological analysis confirmed that the faster increase of cell-number during the rapid-growth stage was the main reason for the formation of larger pod size in Lps. Transcriptomic analyses showed that the expression of key genes related to the auxin, the cytokinin (CK) and the gibberellin (GA) were mostly up-regulated during the rapid-growth stage. Meanwhile, the cell division-related differentially expressed genes (DEGs) were mostly up-regulated at 10DAP which was consistent with the cytological-observation. Additionally, the absolute quantification of phytohormones were carried out by liquid-chromatography coupled with the tandem-mass-spectrometry (LC–MS/MS), and results supported the findings from comparative transcriptomic studies.ConclusionsIt was speculated that the differential expression levels of TAA1 and ARF (auxin-related), IPT and B-ARR (CK-related), KAO, GA20ox and GA3ox (GA-related), and certain cell division-related genes (gene-LOC112747313 and gene-LOC112754661) were important participating factors of the determination-mechanism of peanut pod sizes. These results were informative for the elucidation of the underlying regulatory network in peanut pod-growth and would facilitate further identification of valuable target genes.

Retracted: Identification of Candidate Therapeutic Target Genes and Profiling of Tumor-Infiltrating Immune Cells in Pancreatic Cancer via Integrated Transcriptomic Analysis.

[This retracts the article DOI: 10.1155/2022/3839480.].

Analysis of the role of glucose metabolism-related genes in dilated cardiomyopathy based on bioinformatics.

Dilated cardiomyopathy (DCM) is a prevalent condition with diverse etiologies, including viral infection, autoimmune response, and genetic factors. Despite the crucial role of energy metabolism in cardiac function, therapeutic targets for key genes in DCM's energy metabolism remain scarce. Our study employed the GSE79962 and GSE42955 datasets from the Gene Expression Omnibus (GEO) database for myocardial tissue sample collection and target gene identification via differential gene expression screening. Using various R packages, GSEA software, and the STRING database, we conducted data analysis, gene set enrichment, and protein-protein interaction predictions. The least absolute shrinkage and selection operator (LASSO) and Support Vector Machine (SVM) algorithms aided in feature gene selection, while the predictive model's efficiency was evaluated via the receiver operating characteristic (ROC) curve analysis. We used the non-negative matrix factorization (NMF) method for molecular typing and the cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm for predicting immune cell infiltration. The DLAT and LDHA genes may regulate the immune microenvironment of DCM by influencing activated dendritic cells, activated mast cells, and M0 macrophages, respectively. The BPGM, DLAT, PGM2, ADH1A, ADH1C, LDHA, and PFKM genes may regulate m6A methylation in DCM by affecting the ZC3H13, ALKBH5, RBMX, HNRNPC, METTL3, and YTHDC1 genes. Further regulatory mechanism analysis suggested that PFKM, DLAT, PKLR, PGM2, LDHA, BPGM, ADH1A, and ADH1C could be involved in the development of cardiomyopathy by regulating the Toll-like receptor signaling pathway. PFKM, DLAT, PKLR, PGM2, LDHA, BPGM, ADH1A, and ADH1C may serve as potential targets for guiding the diagnosis, treatment, and follow-up of DCM.

Identification of ecdysone receptor target genes in the worker honey bee brains during foraging behavior

Ecdysone signaling plays central roles in morphogenesis and female ovarian development in holometabolous insects. In the European honey bee (Apis mellifera L.), however, ecdysone receptor (EcR) is expressed in the brains of adult workers, which have already undergone metamorphosis and are sterile with shrunken ovaries, during foraging behavior. Aiming at unveiling the significance of EcR signaling in the worker brain, we performed chromatin-immunoprecipitation sequencing of EcR to search for its target genes using the brains of nurse bees and foragers. The majority of the EcR targets were common between the nurse bee and forager brains and some of them were known ecdysone signaling-related genes. RNA-sequencing analysis revealed that some EcR target genes were upregulated in forager brains during foraging behavior and some were implicated in the repression of metabolic processes. Single-cell RNA-sequencing analysis revealed that EcR and its target genes were expressed mostly in neurons and partly in glial cells in the optic lobes of the forager brain. These findings suggest that in addition to its role during development, EcR transcriptionally represses metabolic processes during foraging behavior in the adult worker honey bee brain.

Identification of Glucocorticoid Receptor Target Genes That Potentially Inhibit Collagen Synthesis in Human Dermal Fibroblasts.

Over several decades, excess glucocorticoids (GCs) of endogenous or exogenous origin have been recognized to significantly inhibit collagen synthesis and accelerate skin aging. However, little is known regarding their molecular mechanisms. We hypothesized that the action of GCs on collagen production is at least partially through the glucocorticoid receptor (GR) and its target genes, and therefore aimed to identify GR target genes that potentially inhibit collagen synthesis in Hs68 human dermal fibroblasts. We first confirmed that dexamethasone, a synthetic GC, induced canonical GR signaling in dermal fibroblasts. We then collected 108 candidates for GR target genes reported in previous studies on GR target genes and verified that 17 genes were transcriptionally upregulated in dexamethasone-treated dermal fibroblasts. Subsequently, by individual knockdown of the 17 genes, we identified that six genes, AT-rich interaction domain 5B, FK506 binding protein 5, lysyl oxidase, methylenetetrahydrofolate dehydrogenase (NADP + dependent) 2, zinc finger protein 36, and zinc fingers and homeoboxes 3, are potentially involved in GC-mediated inhibition of collagen synthesis. The present study sheds light on the molecular mechanisms of GC-mediated skin aging and provides a basis for further research on the biological characteristics of individual GR target genes.

ADAMTSL3 - a potential direct target of miR-144-3p in chondrocyte cell

The miR-144-3p was discovered to upregulate in osteoarthritis. However, the function of this molecule is still poorly understood. Identification of microRNA target genes could shed a light on miRNA functions. In this project, we aim to identify a direct target of miR-144-3p. Potential targets of miR-144-3p were predicted by bioinformatic algorithms. Expression of ADAMTSL3 in miRNA-144-3p gain-and- loss- of function experiment was quantified by Realtime-PCR. Next, the 3’UTR of ADAMTSL3 containing miR-144-3p-binding sites was subcloned in the 3’;UTR of the Firefly luciferase gene on the pmiRGlo. To test the complementary binding of miR-144-3p to ADAMTSL3 mRNA, we employed the luciferase assay using pmiRGlo-ADAMTSL3 vector or pmiRGlo-ADAMTSL3 mutant in which miR-144-3p binding sites in the 3’UTR was mutated. Results showed that miRNA-144-3p directly inhibits the expression of ADAMTSL3 through its ability to pair at “seed” sites. This study provides evidence for the interaction of miRNA-144-3p and its target, ADAMTSL3 mRNA, in chondrocytes.