Expression Of Protein-coding Genes Research Articles

Investigation of Association Between Expression of DYX1C1, KIAA0319, and ROBO1 Genes and Specific Learning Disorder in Children and Adolescents.

Specific learning disorder (SLD) is prevalent worldwide and is a complex disorder with variable symptoms and significant differences among individuals. Epigenetic markers may alter susceptibility to neurodevelopmental disorders (NDDs). Aberrant expression of protein-coding (mRNA) genes in this pathology shows that the detection of epigenetic molecular biomarkers is of increasing importance in the diagnosis and treatment of individuals with SLD. We compared gene expression level of dyslexia susceptibility 1 candidate gene 1 (DYX1C1), dyslexia-associated protein KIAA0319 (KIAA0319), and roundabout guidance receptor 1 (ROBO1) between children with SLD and healthy children by performing quantitative polymerase chain reaction (qPCR). In addition, we evaluated these gene expressions of severe children with SLD compared to non-severe and male SLD children compared to females. The expression of the DYX1C1, KIAA0319, and ROBO1 genes was statistically significantly upregulated in children with SLD (P < 0.05*). DYX1C1 was also upregulated in severe SLD children (P = 0.03*). In addition, KIAA0319 and ROBO1 genes were differentially expressed in male SLD children compared to females (P < 0.05*). Furthermore, we found that DYX1C1 and ROBO1 genes significantly affect the likelihood of the SLD (respectively, P < 0.001** and P = 0.007*). We expect that the findings provided from this study may contribute to the determination expression level of the relevant genes in the diagnosis, prognosis, and treatment of SLD. In addition, our findings could be a guide for future epigenetics studies on the use of the DYX1C1, KIAA0319, and ROBO1 in therapeutic applications in the SLD.

Differential Protein-Coding Gene Expression Profile in Patients with Prostate Cancer

Background: Prostate cancer is the second most common neoplasm in men, with projections estimating over one million new cases by 2045. Differentially expressed genes can significantly enhance the diagnosis, treatment, monitoring, and prognosis of this disease. Purpose: to systematically review and analyze validated differentially expressed mRNAs in prostate cancer patients to propose a robust molecular profile for clinical diagnostics. Methods: A systematic review was conducted following PRISMA guidelines, searching literature databases for mRNAs with validated differential expression in adult prostate cancer patients. Identified mRNAs were analyzed using STRING, Cytoscape, and DrugBank to explore protein–protein interactions and potential drug targets. Results: A total of 5003 participants from Europe, Asia, America, and Oceania were included, and 144 mRNAs (p &lt; 0.05) were reported across 75 primary articles, predominantly validated using RT-qPCR with tissue samples. Among these, at least 36 mRNAs were identified as targets for cancer-related drugs. Enrichment analysis revealed the top pathways were associated with cancer, including specific prostate cancer terms. Key nodes emerged as hubs in the protein–protein interaction network. Conclusion: Based on our comprehensive in silico analysis of validated differentially expressed mRNAs, we propose a molecular profile of twenty-five mRNAs with significant potential for clinical diagnosis of prostate cancer. These findings offer a valuable foundation for developing precision oncology strategies to improve patient outcomes.

The 24-hour molecular landscape after exercise in humans reveals MYC is sufficient for muscle growth.

A detailed understanding of molecular responses to a hypertrophic stimulus in skeletal muscle leads to therapeutic advances aimed at promoting muscle mass. To decode the molecular factors regulating skeletal muscle mass, we utilized a 24-h time course of human muscle biopsies after a bout of resistance exercise. Our findings indicate: (1) the DNA methylome response at 30 min corresponds to upregulated genes at 3 h, (2) a burst of translation- and transcription-initiation factor-coding transcripts occurs between 3 and 8 h, (3) changes to global protein-coding gene expression peaks at 8 h, (4) ribosome-related genes dominate the mRNA landscape between 8 and 24 h, (5) methylation-regulated MYC is a highly influential transcription factor throughout recovery. To test whether MYC is sufficient for hypertrophy, we periodically pulse MYC in skeletal muscle over 4 weeks. Transient MYC increases muscle mass and fiber size in the soleus of adult mice. We present a temporally resolved resource for understanding molecular adaptations to resistance exercise in muscle ( http://data.myoanalytics.com ) and suggest that controlled MYC doses influencethe exercise-related hypertrophic transcriptional landscape.

Transcriptomic study reveals alteration in the expression of long non-coding RNAs (lncRNAs) during reversal of HIV-1 latency in monocytic cell line.

The presence of latent HIV reservoirs continues to be the biggest obstacle to achieving an HIV cure. Thus, long non-coding RNAs (lncRNAs) may serve as the preferred targets for HIV latency reversal. The goal of the study was to identify prospective lncRNAs for subsequent in vitro molecular and functional characterization. RNA-sequencing was performed in latently HIV-infected monocytic cell line (U1) under stimulated and unstimulated condition using Illumina-HiSeqX platform, followed by its validation using qRT-PCR assay. Gene ontology (GO), KEGG pathway, and co-expression analyses were performed to identify the enriched biological processes and pathways in U1 cells post-stimulation with the latency reversal agent SAHA. A total of 3,576 and 1,467 significantly altered lncRNAs and protein-coding genes respectively, were identified in SAHA-stimulated U1 cells compared to unstimulated ones. The GO and KEGG pathway analyses of the differentially expressed protein-coding genes showed the enrichment of diverse biological processes and pathways respectively, in SAHA-stimulated U1 cells. Co-expression analysis between lncRNAs and protein-coding gene pairs, helped predict potential pathways with which these lncRNAs are associated. Further in vitro validation in HIV-infected monocytes showed that the expression of the top two candidate lncRNAs, LINC01231 and LINC00560, are specific to HIV infection. Transcriptome analysis revealed changes in the expression of numerous lncRNAs and protein-coding genes following stimulation with SAHA. Co-expression analysis identified candidate lncRNAs and their associated biological pathways. However, additional in vitro experimental exploration using gene knockdown strategies is needed to ascertain the specific role of LINC01231 and LINC00560 lncRNAs in latently infected monocytes.

Long Noncoding RNAs Expressed in Mouse Pituitary Development and Mature Hormone-Producing Cells.

Mammalian genomes contain thousands of genes for long noncoding RNA (lncRNAs), some of which have been shown to affect protein coding gene expression through diverse mechanisms. The lncRNA transcripts are longer than 200 nucleotides and are often capped, spliced, and polyadenylated, but not translated into protein. Nuclear lncRNAs can modify chromatin structure and transcription in trans or cis by interacting with the DNA, forming R-loops, and recruiting regulatory proteins. Not much is known about the role of lncRNA in pituitary gland differentiation and function. We mined transcriptome data from mouse pituitary glands collected at embryonic days 12.5 and 14.5 and identified over 200 different lncRNA transcripts. To develop a research resource for the study of lncRNA, we used pituitary cre transgenes to tag pituitary cell types in adult mice with fluorescent markers, and enriched for thyrotropes, gonadotropes, and somatotropes using fluorescence-activated cell sorting. We determined the transcriptome of each cell population using RNA sequencing and mined the data for lncRNA. We detected hundreds of lncRNAs in adult pituitary cells; a few were located immediately nearby genes that encode pituitary hormones or lineage-specific transcription factors. The location of these lncRNAs suggests the possibility of a cis-acting regulatory role in pituitary development or function, and we observe coordinated expression of 2 of them with their putative target genes in transgenic mice. This research resource sets the foundation for examining the actions of lncRNAs on their putative target genes and determining whether they have roles during development and in response to physiological demand.

Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters

The transcriptional interplay of human RNA polymerase I (RNA Pol I), RNA Pol II, and RNA Pol III remains largely uncharacterized due to limited integrative genomic analyses for all three enzymes. To address this gap, we applied a uniform framework to quantify global RNA Pol I, RNA Pol II, and RNA Pol III occupancies and identify both canonical and noncanonical patterns of gene localization. Most notably, our survey captures unexpected RNA Pol III recruitment at promoters of specific protein-coding genes. We show that such RNA Pol III-occupied promoters are enriched for small nascent RNAs terminating in a run of 4 Ts-a hallmark of RNA Pol III termination indicative of constrained RNA Pol III transcription. Taken further, RNA Pol III disruption generally reduces the expression of RNA Pol III-occupied protein-coding genes, suggesting RNA Pol III recruitment and transcription enhance RNA Pol II activity. These findings resemble analogous patterns of RNA Pol II activity at RNA Pol III-transcribed genes, altogether uncovering a reciprocal form of crosstalk between RNA Pol II and RNA Pol III.

Systematic screening of protein-coding gene expression identified VWF as a potential key regulator in anthracycline-based chemotherapy-exacerbated metastasis of breast cancer

BackgroundBreast cancer is the most commonly diagnosed cancer worldwide. Although major treatments represented by chemotherapy have shown effectiveness at the initial period, recurrence and metastasis still occur later after treatments. The alternation of the tumor microenvironment by chemotherapy is confirmed as a trigger of the elevated proliferation and migration of the remaining tumor cells.MethodsUsing bioinformatic methods, differential gene expression analysis was used to determine DEGs between post-chemotherapy and pre-chemotherapy samples of breast cancer patients, followed by survival analysis and ELISA analysis of the potential key genes. An in vitro model of 2 breast cancer cells lines was used to demonstrate the role of VWF in the evasion and migration of breast cancer cells, using cell migration, evasion and wound healing assays, PCR and molecular docking analysis.Results19 hub genes were further identified using GO and KEGG pathway analyses and WGCNA. The 5 secreted protein-coding genes with reported carcinogenesis effects (VWF, SVEP1, DPT, ADIPOQ, and LPL) were further analyzed in breast cancer patients and VWF was identified as a potential key regulator in the anthracycline-based chemotherapy-exacerbated metastasis. It was further confirmed that anthracycline-based chemotherapeutics doxorubicin exacerbated VWF upregulation and the evasion and migration of breast cancer cells. Based on molecular docking analysis and previous study, berberine was used as an inhibitor of VWF, and showed an effective inhibition of the doxorubicin-exacerbated VWF upregulation, migration and evasion in breast cancer.ConclusionsDoxorubicin-exacerbated evasion and migration through VWF upregulation. Berberine as an inhibitor of VWF was able to reversed the doxorubicin-exacerbated VWF upregulation and evasion and migration in breast cancer cells.

Long Non-coding RNA and Progression of Breast Cancer

Breast cancer is a major problem in the health sector worldwide. The prevalence of breast cancer incidence is on the rise in many countries despite efforts to eradicate it. The substantial efforts for the treatment of breast cancer are quite successful but the main hindrance is early detection which in turn is dependent on various factors i.e. genetic history, environmental exposures, hormonal causes, and sedentary lifestyle. In previous studies, lncRNAs were known to modulate the progression of many cancers like gastric, lung, ovarian, and colorectal cancers. This study was designed to find these lncRNAs role in breast cancer development. Bioinformatics tools were used for in silco analysis of these lncRNAs LINC01356, LINC01357, ARF4-AS1, and FAM83B. These lncRNAs were evaluated in GEPIA2 for subtype analysis and survival probability, Phylo CSF UCSC genome browser for conserved sequences and protein-coding potential, BcGenExMiner for correlation analysis and UALCAN for protein-coding gene expression. These above-mentioned lncRNAs showed high expression in the basal subtype of TNBC as compared with other subtypes and they showed poor survival rates in the basal subtype. LINC01356 and LINC01357 showed positive correlation with TAFA3 and SLC16A1. ARF4-AS1 positively correlated with ASB14 and FAM83B positively correlated with HCRTR2. These lncRNAs showing positive correlation with different genes have a role in breast cancer development and progression.

Expression of Long Noncoding RNAs and Protein-Coding Genes Involved in Oxidative Stress and Cell Senescence in Patients with Chronic Obstructive Pulmonary Disease

Expression of Long Noncoding RNAs and Protein-Coding Genes Involved in Oxidative Stress and Cell Senescence in Patients with Chronic Obstructive Pulmonary Disease

Abstract C092: Transcriptome analysis of human endogenous retroviral elements in tumor microenvironment of prostate cancer patients of different ancestry

Abstract Background: Prostate cancer (PCa) poses unique challenges for Non-Hispanic Black Americans (BA), who often face poorer outcomes than Non-Hispanic White Americans (WA). Even after adjusting for socioeconomic factors, BAs are diagnosed younger and experience more severe clinical effects, potentially due to the tumor microenvironment. Within PCa, Endogenous Retroviruses (ERVs) have been shown to regulate immune response genes and have prognostic value in PCa. Despite constituting 8% of the human, ERVs' role in the tumor microenvironment remains incompletely understood. These findings highlight the need to target microenvironment dysregulation in solid tumor therapies, especially for ERV expression in prostate cancer. Methods: Using RNA-sequencing, we investigated the expression of ERVs in BA (n=18) and WA (n=14) tumor adjacent stroma (TAS) samples. We analyzed reads by mapping them to the human genome (hg38). We then used bedtools and data from the Human Endogenous Retrovirus database (HERVd) to calculate the number of reads at each ERV locus (n=519,060). Differentially expressed ERV elements were then identified in an Audic Claverie Test (fold- change cutoff of 2 and padj &amp;lt; 0.05). The expression of protein-coding genes in the same BA (n=18) and WA (n=14) TAS samples was investigated using RNA-sequencing. Regulation of significant ERV elements were compared to the regulation of nearby immune response genes between the two races. We developed primary stroma (carcinoma associated fibroblast, CAFs) culture of different races with PCa using fresh prostatectomy tissues. To investigate the biological functions of ERVs in CAFs, we developed FANA oligonucleotides (synthetic single- stranded nucleic acid analogs that can modulate gene expression by enzymatic degradation of a target RNA) and corresponding primers to knock down specific ERV sequences near key immune response genes in prostate cancer. Results: We examined 32 prostatectomy specimens of BA (n=18) and WA (n=14) PCa. Of the 5,786 statistically significant differentially expressed ERV elements between BA and WA TAS that were identified, 3,274 elements had an increase in ERV expression for BA TAS, and 2,512 elements had a decrease in ERV expression for BA TAS. 61 MER41 elements were found to be differentially expressed between the two races. The MER family sequences contain binding sites for transcription factors that are crucial in cancer, such as STAT1. This transcription factor can regulate genes involved in cell proliferation, apoptosis, and DNA repair. MER41 is in close proximity (within 5000 base pairs) to IFNA6, an immune response gene. We found both MER41 and IFNA6 to be downregulated in BA TAS, as compared to their WA counterparts. We developed FANA oligonucleotides to knockdown MER41E, MER61-Int, HERVL-Int, MLT1A, and LTR61E1 to investigate their effect on nearby gene expression. Conclusion: The CAF models from PCa patients of different races can be used to explore the biological function of ERV inactivation on anti-tumor immune response genes within the tumor microenvironment. Citation Format: Tara S. K. Jennings, Vinay Kumar, Anton N. Nguyen, Michael M. Ittmann, Patricia Castro, Farah Rahmatpanah. Transcriptome analysis of human endogenous retroviral elements in tumor microenvironment of prostate cancer patients of different ancestry [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C092.

Evaluation of circulating plasma proteins in prostate cancer using mendelian randomization

BackgroundThe proteome is an important resource for exploring potential diagnostic and therapeutic targets for cancer. This study aimed to investigate the causal associations between plasma proteins and prostate cancer (PCa), and to explore the downstream phenotypes that plasma proteins may influence and potential upstream intervening factors.MethodsProteome-wide Mendelian randomization was used to investigate the causal effects of plasma proteins on PCa. Colocalization analysis examined the common causal variants between plasma proteins and PCa. Summary-statistics-based Mendelian Randomization (SMR) analyses identified associations between the expression of protein-coding genes and PCa. Phenome-wide association study was performed to explore the effect of target proteins on downstream phenotypes. Finally, a systematic Mendelian randomization analysis between lifestyle factors and plasma proteins was performed to assess upstream intervening factors for plasma proteins.ResultsThe findings revealed a positive genetic association between the predicted plasma levels of nine proteins and an elevated risk of PCa, while four proteins exhibited an inverse association with PCa risk. SMR analyses revealed ZG16B, PEX14 in blood and ZG16B, NAPG in prostate tissue were potential drug targets for PCa. The genetic association of PEX14 with PCa was further supported by colocalization analysis. Further Phenome-wide association study showed possible side effects of ZG16B, PEX14 and NAPG as drug targets. 10 plasma proteins (RBP7, TPST1, NFASC, LAYN, HDGF, SERPIMA5, DLL4, EFNA3, LIMA1, and CCL27) could be modulated by lifestyle-related factors.ConclusionThis study explores the genetic associations between plasma proteins and PCa, provides evidence that plasma proteins serve as potential drug targets and enhances the understanding of the molecular etiology, prevention and treatment of PCa.

147 The ‘horse-side’ of host-microbe interactions and gastrointestinal homeostasis in the equine hindgut

Abstract Homeostasis is a complex physiological process that enables biological systems to maintain balanced internal environments in response to internal and external stimuli. In the equine gastrointestinal (GI) tract, homeostasis involves a network of factors that regulate gene expression, maintain the integrity of the mucosal barrier, and modulate immune responses to pathogenic microorganisms while supporting commensal bacteria that provide benefits to the host (Figure 1). These factors work together and respond to changes in diet, environment, external stress, and challenges by infectious agents or toxins. Proper gastrointestinal function is dependent on maintaining homeostasis in the system, and the dynamic interactions between the microbial population (the microbiota) and the equine host are central to this equilibrium. The regulation and interplay between the equine host and GI microbiota are evident in the distribution of distinct microbial communities within the various compartments of the equine hindgut. The contributions of each compartment to digestive physiology and the overlap with various stages of microbial fermentation in the equine hindgut are well-researched. What remains to be documented is gene expression in tissues of the equine GI and the underlying role this might play in the processes of digestion, physiology, and homeostasis in the GI. To better understand the roles that host gene expression plays in the interactions with the microbiota, it is critical that we investigate gene expression in the different tissues along the intestinal tract. Protein-coding genes are crucial in maintaining the health of the gastrointestinal tract. They direct the synthesis of various structural elements, molecular transporters, and digestive enzymes, which support digestion, nutrient absorption, and gut integrity. Non-coding genes also play an important role in regulating protein-coding gene expression, modulating immune responses, and maintaining gut barrier function. Moreover, there is evidence that non-coding transcripts regulate the composition of microbial communities in the GI tract. The presentation will focus on the current research and future directions for investigating protein-coding and non-coding gene expression to understand the mechanisms involved in the host-microbe interaction in the equine hindgut and their potential role in maintaining GI homeostasis.

Long intergenic non-coding RNAs modulate proximal protein-coding gene expression and tolerance to Candidatus Liberibacter spp. in potatoes

Long intergenic non-coding RNAs (lincRNAs) are emerging as regulators of protein-coding genes (PCGs) in many plant and animal developmental processes and stress responses. In this study, we characterize the genome-wide lincRNAs in potatoes responsive to a vascular bacterial disease presumably caused by Candidatus Liberibacter solanacearum (CLso). Approximately 4397 lincRNAs were detected in healthy and infected potato plants at various stages of zebra chip (ZC) disease progression. Of them, ~65% (2844) were novel lincRNAs, and less than 1% (9) were orthologs of Arabidopsis and rice based on reciprocal BLAST analysis, suggesting species-specific expansion. Among the proximal lincRNAs within 50 kbp from a PCG, ~49% were transcribed from the same strand, while ~39% and ~15% followed convergent (head-to-head) and divergent (tail-to-tail) orientations, respectively. Approximately 30% (1308) were differentially expressed following CLso infection, with substantial changes occurring 21 days after infection (DAI). Weighted Gene Co-expression Network Analysis (WGCNA) of lincRNAs and PCGs identified 46 highly correlated lincRNA–PCG pairs exhibiting co-up or co-downregulation. Furthermore, overexpression of selected lincRNAs in transgenic potato hairy roots resulted in perturbation of neighboring PCG expression and conferred tolerance to CLso infection. Our results provide novel insights into potato lincRNAs’ identity, expression dynamics, and functional relevance to CLso infection.

Abstract 75: CTCF and Rad21 Mediated Regulation of Gene Expression in Human-Induced Pluripotent Stem Cells-derived Endothelial Cells

Blood pressure (BP)-relevant non-coding SNPs identified by GWAS may influence the expression of distal protein-coding genes. Our previous study detected 195 SNPs (out of 26585) in CTCF-binding sites. CTCF and Cohesin are known to modulate cell-type-specific gene expression from a distance by forming chromatin loops. We hypothesized that both may regulate gene expression in BP-relevant cell types. To test this, we depleted CTCF and Rad21 (Cohesin subunit) in human induced pluripotent stem cells-derived endothelial cells (iEC) and performed genome-wide transcriptomic analysis. We detected 366 and 4184 differentially expressed genes (DEGs) in CTCF and Rad21 depleted iEC (CTCF-/Rad21-KD-iEC) compared to iEC control, respectively. Among them, 111 DEGs are common between the CTCF-KD and Rad21-KD-iEC, though majority showed opposite regulatory effects (Figure 1A). We found 5619 DEGs in the CTCF-KD vs Rad21-KD-iEC (Figure 1B). Pathway analysis detected elevated cell cycle (G2M checkpoint), DNA replication (E2F targets), and repair pathways in Rad21-KD compared to the CTCF-KD-iEC. Rad21 plays an important role in chromosome partitioning and repair, so its depletion may cause dysregulation of these pathways. While the CTCF-KD-iEC showed enrichment of the Epithelial-to-mesenchymal transition (EMT), inflammatory (IFN-gamma, IFN-alpha), and hypoxia pathways (Figure 1C). As CTCF maintains the chromosome boundaries, CTCF-KD may affect chromatin compactness and trigger abnormal gene expression related to these pathways. In conclusion, our study detected different effects of depletion of CTCF and Rad21 on gene expression in a BP-relevant cell type. The findings provide a basis to explore the role of chromatin looping in BP-relevant gene regulation.

TRAP1 modulates mitochondrial biogenesis via PGC-1α/TFAM signalling pathway in colorectal cancer cells

Metabolic rewiring promotes cancer cell adaptation to a hostile microenvironment, representing a hallmark of cancer. This process involves mitochondrial function and is mechanistically linked to the balance between mitochondrial biogenesis (MB) and mitophagy. The molecular chaperone TRAP1 is overexpressed in 60–70% of human colorectal cancers (CRC) and its over-expression correlates with poor clinical outcome, being associated with many cancer cell functions (i.e. adaptation to stress, protection from apoptosis and drug resistance, protein synthesis quality control, metabolic rewiring from glycolysis to mitochondrial respiration and vice versa). Here, the potential new role of TRAP1 in regulating mitochondrial dynamics was investigated in CRC cell lines and human CRCs. Our results revealed an inverse correlation between TRAP1 and mitochondrial-encoded respiratory chain proteins both at transcriptional and translational levels. Furthermore, TRAP1 silencing is associated with increased mitochondrial mass and mitochondrial DNA copy number (mtDNA-CN) as well as enhanced MB through PGC-1α/TFAM signalling pathway, promoting the formation of new functioning mitochondria and, likely, underlying the metabolic shift towards oxidative phosphorylation. These results suggest an involvement of TRAP1 in regulating MB process in human CRC cells.Key messagesTRAP1 inversely correlates with protein-coding mitochondrial gene expression in CRC cells and tumours.TRAP1 silencing correlates with increased mitochondrial mass and mtDNA copy number in CRC cells.TRAP1 silencing favours mitochondrial biogenesis in CRC cells.

Potential Roles of Long Non-coding RNAs in the Pathogenesis of Periodontitis: Inflammation Response, Immune Infiltration, Collagen Fibers Synthesis, and Bone Remodeling.

It is evident that long non-coding RNAs (lncRNAs) are implicated in the pathogenesis of periodontitis. However, the detailed functional mechanisms remain unknown. This study aimed to elucidate the pathogenic mechanisms of lncRNAs in periodontitis by investigating their regulation of protein-coding gene expression. Human Gingival Fibroblasts-1 (HGF-1) were stimulated with 5 μg/mL of Lipopolysaccharide (LPS) for 24 hours to construct the periodontitis cell model. qRTPCR and western blot analyses were carried out to determine mRNA and protein levels of genes induced by LPS or involved in the inflammatory response. Cytokine levels and inflammatory proteins were assayed using ELISA. Transcriptome sequencing and analysis were conducted to reveal the expression signatures of lncRNAs. DESeq2 (v1.4.5) was used to analyze differentially expressed genes. Gene function enrichment was carried out using Phyper. AnimalTFDB v3.0 was used to analyze transcription factors involved in the pathogenesis of periodontitis. Prot\ein domains and families of the target proteins were identified based on the Pfam protein family database. In LPS-treated HGF-1 cells, we detected the secretion of TNF-α and IL-1β, along with the production of MDA and ROS, indicating that LPS significantly triggered inflammatory responses and oxidative stress in HGF-1 cells. A total of 15,295 lncRNAs were detected in both the control (ConT) and LPS-treated groups. We selected 10 significantly differentially co-expressed lncRNA-coding genes (MIR222HG, SNHG15, SNHG12, URS00005F6AA3, URS00009C153E, URS0000D57D7F, URS00019A4688, URS00019AF240, URS00019C6526, and URS0001A00B79) as potential biomarkers for diagnosing the progression of periodontitis. An interaction network consisting of 2 lncRNA- encoding genes (MIR222HG and SNHG15) and protein-encoding genes (CBX5, NUPR1, CHAC1, and MAB21L3) may be involved in the pathogenesis of periodontitis. The ceRNA network analysis revealed the differentially expressed lncRNAs to be involved in inflammatory response, immune infiltration, collagen fiber synthesis, and bone remodeling in LPS-induced periodontitis. This study has identified pivotal molecules implicated in the pathogenesis of periodontitis, including those involved in inflammation regulation, collagen fiber synthesis, and bone remodeling. Our findings may contribute to explaining how lncRNAs participate in the pathological process of periodontitis.

Molecular signatures of longissimus dorsi differ between dairy cattle based on prepartum muscle reserves and branched-chain volatile fatty acid supplementation.

Dairy cattle with high (HM) versus low muscle (LM) reserves exhibit distinct temporal changes in longissimus dorsi muscle depth (LDD) in late gestation. Branched-chain volatile fatty acids (BCVFA) supplementation increased blood glucose levels. We hypothesized that differences in HM and LM reflect distinct muscle metabolism and BCVFA supplementation altered metabolic pathways. At 42 d before expected calving (BEC) Holstein dairy cows were enrolled in a 2 x 2 factorial study of diet and muscle reserves, by assigning to control (CON) or BCVFA supplemented diets and LDD of HM (>4.6 cm) or LM (≤4.6 cm) groups: HM-CON (n=13), HM-BCVFA (n=10), LM-CON (n=9), and LM-BCVFA (n=9). Longisumus dorsi was biopsied at 21 d BEC, total RNA isolated and protein coding gene expression measured with RNA-seq. Between HM and LM 713 genes were differentially expressed and 481 between BCVFA and CON (P<0.05). Transcriptional signatures indicated differential distribution of Type II fibers between groups, with MYH1 greater in LM and MYH2 greater in HM cattle (P<0.05). Signatures of LM cattle relative to HM indicated greater activation of autophagy, ubiquitin-proteasome, and Ca2+-calpain pathways. HM cattle displayed greater expression of genes that encode extracellular matrix proteins and factors that regulate their proteolysis and turnover. BCVFA modified transcriptomes by increasing expression of genes that regulate fatty acid degradation and flux of carbons into the TCA cycle as acetyl CoA. Molecular signatures support distinct metabolic strategies between LM and HM cattle, and that BCVFA supplementation increased substrates for energy generation.

Methylation of a group of microRNA genes as a marker for the diagnosis and prognosis of non-small cell lung cancer

Objectives. Lung cancer, representing a difficult-to-diagnose heterogeneous malignant neoplasm, is characterized by an asymptomatic course up to late stages, a high incidence of adverse outcomes, and a high probability of metastasis. Its most common form is non-small cell lung cancer (NSCLC). Recent studies have demonstrated a significant role of non-coding RNAs—in particular, microRNAs—in the development of NSCLC. MicroRNAs, which function as post-transcriptional regulators of the expression of protein-coding genes, including those associated with oncogenesis, are involved in the processes of cell proliferation, differentiation, and apoptosis. One of the approaches for regulating the expression of microRNAs themselves is to change the methylation of the CpG island adjacent to the microRNA gene or overlapping it. It has been shown that microRNA genes are several times more likely to undergo methylation than protein-coding genes. The aim of the present work is to study changes in the level of methylation of a number of microRNA genes and compile a potential panel of markers for the diagnosis and prognosis of NSCLC.Methods. Samples of NSCLC tumors were collected and clinically characterized at the Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia. High-molecular-weight DNA was isolated from tissues using a standard method. The level of methylation was analyzed using bisulfite conversion of DNA and quantitative methyl-specific polymerase chain reaction with real-time detection. The significance of differences between the studied groups was assessed by the nonparametric Mann–Whitney U test for independent samples. Differences were considered significant at p &lt; 0.05.Results. The analysis of methylation levels of microRNA genes revealed a significant (p &lt; 0.05) increase in the methylation level of eight microRNA genes: MIR124-1/2/3, MIR125В-1, MIR129-2, MIR137, MIR375, MIR1258, and MIR339 (p &lt; 0.01, false discovery rate ≤ 0.25). On the basis of receiver operating characteristic analysis, a panel of markers is proposed for the diagnosis of NSCLC according to the nature of methylation of the studied microRNA genes in the tumor and in the normal tissue.Conclusions. Our results, which contribute to the understanding of molecular mechanisms involved in NSCLC development, can be used in the development of new diagnostic and prognostic approaches in clinical oncology.

Efficient activation of hundreds of LTR12C elements reveals cis-regulatory function determined by distinct epigenetic mechanisms.

Long terminal repeats (LTRs), which often contain promoter and enhancer sequences of intact endogenous retroviruses (ERVs), are known to be co-opted as cis-regulatory elements for fine-tuning host-coding gene expression. Since LTRs are mainly silenced by the deposition of repressive epigenetic marks, substantial activation of LTRs has been found in human cells after treatment with epigenetic inhibitors. Although the LTR12C family makes up the majority of ERVs activated by epigenetic inhibitors, how these epigenetically and transcriptionally activated LTR12C elements can regulate the host-coding gene expression remains unclear due to genome-wide alteration of transcriptional changes after epigenetic inhibitor treatments. Here, we specifically transactivated >600 LTR12C elements by using single guide RNA-based dCas9-SunTag-VP64, a site-specific targeting CRISPR activation (CRISPRa)system, with minimal off-target events. Interestingly, most of the transactivated LTR12C elements acquired the H3K27ac-marked enhancer feature, while only 20% were co-marked with promoter-associated H3K4me3 modifications. The enrichment of the H3K4me3 signal was intricately associated with downstream regions of LTR12C, such as internal regions of intact ERV9 or other types of retrotransposons. Here, we leverage an optimized CRISPRa system to identify two distinct epigenetic signatures that define LTR12C transcriptional activation, which modulate the expression of proximal protein-coding genes.

CBFA2T3 Is PPARA Sensitive and Attenuates Fasting-Induced Lipid Accumulation in Mouse Liver.

Peroxisome proliferator-activated receptor alpha (PPARA) is a ligand-activated transcription factor that is a key mediator of lipid metabolism and metabolic stress in the liver. Accumulating evidence shows that PPARA regulates the expression of various protein coding and non-coding genes that modulate metabolic stress in the liver. CBFA2/RUNX1 partner transcriptional co-repressor 3 (CBFA2T3) is a DNA-binding transcription factor that belongs to the myeloid translocation gene family. Many studies have shown that CBFA2T3 is associated with acute myeloid leukemia. Especially, CBFA2T3-GLIS2 fusion is a chimeric oncogene associated with a poor survival rate in pediatric acute megakaryocytic leukemia. A previous study identified that PPARA activation promoted Cbfa2t3 induction in liver and that Cbfa2t3 may have a modulatory role in metabolic stress. However, the effect of CBFA2T3 gene expression on metabolic stress is not understood. In this study, the PPARA ligand WY14643 activated Cbfa2t3 expression in mouse liver. Glucose tolerance test and insulin tolerance test data showed that insulin resistance is increased in Cbfa2t3-/- mice compared to Cbfa2t3+/+ mice. Hepatic CBFA2T3 modulates heat shock protein family A member 1b and carbonic anhydrase 5a expression. Histology analysis revealed lipid droplet and lipid accumulation in the liver of fasting Cbfa2t3-/- mice but not Cbfa2t3+/+ mice. The expression of lipid accumulation-related genes, such as Cd36, Cidea, and Fabp1, was increased in the liver of fasting Cbfa2t3-/- mice. Especially, basal expression levels of Cidea mRNA were elevated in the liver of Cbfa2t3-/- mice compared to Cbfa2t3+/+ mice. Much higher induction of Cidea mRNA was seen in the liver of Cbfa2t3-/- mice after WY14643 administration. These results indicate that hepatic CBFA2T3 is a PPARA-sensitive gene that may modulate metabolic stress in mouse liver.