Transcribed Ultraconserved Region Research Articles

A transcribed ultraconserved noncoding RNA, uc.285+, promotes colorectal cancer proliferation through dual targeting of CDC42 by directly binding mRNA and protein

The transcribed ultraconserved region (T-UCR) belongs to a new type of lncRNAs that are conserved in homologous regions of the rat, mouse and human genomes. A lot of research has reported that differential expression of T-UCRs can influence the development of various cancers, revealing the ability of T-UCRs as new therapeutic targets or potential cancer biomarkers. Most studies on the molecular mechanisms of T-UCRs in cancer have focused on ceRNA regulatory networks and interactions with target proteins, but the present study reveals an innovative dual-targeted regulatory approach in which T-UCRs bind directly to mRNAs and directly to proteins. We screened T-UCRs that may be related to colorectal cancer (CRC) by performing a whole-genome T-UCR gene microarray and further studied the functional mechanism of T-UCR uc.285+ in the development of CRC. Modulation of uc.285+ affected the proliferation of CRC cell lines and influenced the expression of the CDC42 gene. We also found that uc.285+ promoted the proliferation of CRC cells by directly binding to CDC42 mRNA and enhancing its stability while directly binding to CDC42 protein and affecting its stability. In short, our research on the characteristics of cell proliferation found that uc.285+ has a biological function in promoting CRC proliferation. uc.285+ may have considerable potential as a new diagnostic biomarker for CRC.

An In Silico Approach to Define Potential Biomarkers of miRNA-Associated ceRNAs for Breast Cancer

Breast cancer (BC) is the most common type of cancer with the highest incidence in women. Particularly in breast cancer, competing endogenous RNAs (ceRNAs) play crucial roles in a variety of metabolic pathways including proliferation, migration, and apoptosis. The aim of the present study is to identify combinatorial target genes (ceRNAs) by employing in silico research to identify miRNAs specific to BC. The other aim was to determine possible biomarkers for the diagnosis of BC by selecting those containing the Transcribed Ultra Conserved Region (T-UCR). Using the miRWalk database, 40 miRNAs that have been experimentally shown to be clinically linked with BC were found. T-UCR-containing genes with potential ceRNA activity were identified. Genes with statistically significant changes in expression between BC and normal breast tissue were identified using the GEPIA. The relationship of the CLK3 and NFAT5 genes was found using the Spearman correlation test. The Spearman correlation test was used to determine the association between the CLK3 and NFAT5 genes, and the genes were found to be significantly less expressed in BC. The NFAT5 and CLK3 gene pair have been found to be associated with BC (p<0.001; r=0.35), and may function as useful biomarkers for BC.

Lnc-uc.147 Is Associated with Disease Stage of Liver, Gastric, and Renal Cancer.

Lnc-uc.147, a long non-coding RNA derived from a transcribed ultraconserved region (T-UCR), was previously evidenced in breast cancer. However, the role of this region in other tumor types was not previously investigated. The present study aimed to investigate lnc-uc.147 in different types of cancer, as well as to suggest lnc-uc.147 functional and regulation aspects. From solid tumor datasets analysis of The Cancer Genome Atlas (TCGA), deregulated lnc-uc.147 expression was associated with the histologic grade of hepatocellular carcinoma, and with the tumor stage of clear cell renal and gastric adenocarcinoma. Considering the epidemiologic relevance of liver cancer, silencing lnc-uc.147 reduced the viability and clonogenic capacity of HepG2 cell lines. Additionally, we suggest a relation between the transcription factor TEAD4 and lnc-uc.147 in liver and breast cancer cells.

Role of transcribed ultraconserved regions in gastric cancer and therapeutic perspectives.

Gastric cancer (GC) is the fourth leading cause of cancer-related death. The occurrence and development of GC is a complex process involving multiple biological mechanisms. Although traditional regulation modulates molecular functions related to the occurrence and development of GC, the comprehensive mechanisms remain unclear. Ultraconserved region (UCR) refers to a genome sequence that is completely conserved in the homologous regions of the human, rat and mouse genomes, with 100% identity, without any insertions or deletions, and often located in fragile sites and tumour-related genes. The transcribed UCR (T-UCR) is transcribed from the UCR and is a new type of long noncoding RNA. Recent studies have found that the expression level of T-UCRs changes during the occurrence and development of GC, revealing a new mechanism underlying GC. Therefore, this article aims to review the relevant research on T-UCRs in GC, as well as the function of T-UCRs and their regulatory role in the occurrence and development of GC, to provide new strategies for GC diagnosis and treatment.

Analysis of the circRNA and T-UCR populations identifies convergent pathways in mouse and human models of Rett syndrome

Noncoding RNAs play regulatory roles in physiopathology, but their involvement in neurodevelopmental diseases is poorly understood. Rett syndrome is a severe, progressive neurodevelopmental disorder linked to loss-of-function mutations of the MeCP2 gene for which no cure is yet available. Analysis of the noncoding RNA profile corresponding to the brain-abundant circular RNA (circRNA) and transcribed-ultraconserved region (T-UCR) populations in a mouse model of the disease reveals widespread dysregulation and enrichment in glutamatergic excitatory signaling and microtubule cytoskeleton pathways of the corresponding host genes. Proteomic analysis of hippocampal samples from affected individuals confirms abnormal levels of several cytoskeleton-related proteins together with key alterations in neurotransmission. Importantly, the glutamate receptor GRIA3 gene displays altered biogenesis in affected individuals and in vitro human cells and is influenced by expression of two ultraconserved RNAs. We also describe post-transcriptional regulation of SIRT2 by circRNAs, which modulates acetylation and total protein levels of GluR-1. As a consequence, both regulatory mechanisms converge on the biogenesis of AMPA receptors, with an effect on neuronal differentiation. In both cases, the noncoding RNAs antagonize MeCP2-directed regulation. Our findings indicate that noncoding transcripts may contribute to key alterations in Rett syndrome and are not only useful tools for revealing dysregulated processes but also molecules of biomarker value.

The transcribed ultraconserved region uc.160+ enhances processing and A-to-I editing of the miR-376 cluster: hypermethylation improves glioma prognosis.

Transcribed ultraconserved regions (T‐UCRs) are noncoding RNAs derived from DNA sequences that are entirely conserved across species. Their expression is altered in many tumor types, and, although a role for T‐UCRs as regulators of gene expression has been proposed, their functions remain largely unknown. Herein, we describe the epigenetic silencing of the uc.160+ T‐UCR in gliomas and mechanistically define a novel RNA–RNA regulatory network in which uc.160+ modulates the biogenesis of several members of the miR‐376 cluster. This includes the positive regulation of primary microRNA (pri‐miRNA) cleavage and an enhanced A‐to‐I editing on its mature sequence. As a consequence, the expression of uc.160+ affects the downstream, miR‐376‐regulated genes, including the transcriptional coregulators RING1 and YY1‐binding protein (RYBP) and forkhead box P2 (FOXP2). Finally, we elucidate the clinical impact of our findings, showing that hypermethylation of the uc.160+ CpG island is an independent prognostic factor associated with better overall survival in lower‐grade gliomas, highlighting the importance of T‐UCRs in cancer pathophysiology.

Comprehensive analyses of T-UCR expression profiles and exploration of the efficacy of uc.63- and uc.280+ as biomarkers for lung cancer in Xuanwei, China

ObjectivesLung cancer in Xuanwei (LCXW), China, is known worldwide for occurring frequently with high morbidity and mortality, which necessitates research to determine its pathogenesis. This study attempted to screen potential transcribed ultraconserved region (T-UCR) biomarkers related to LCXW. MethodsWe performed T-UCR microarrays on 26 paired lung adenocarcinoma and adjacent tissues to explore the T-UCR expression profile of LCXW. Then, bioinformatics analysis was carried out to identify potential T-UCRs, which were further validated by real-time quantitative PCR (RT-qPCR). Then, clinical relevance analysis and Kaplan–Meier tests were performed on 50 paired tissues. ResultsT-UCRs and RNA transcripts whose transcription units overlap UCRs (RTOUs) were significantly dysregulated in LCXW tissues compared with the corresponding noncancerous lung (NCL) tissues and presented an increasing trend from stage I to III. The expression between T-UCRs and host genes or flanking genes presented a positive or negative correlation. RT-qPCR analysis showed that uc.63- and uc.280+ were significantly up-regulated in LCXW tissues (P < 0.05). Uc.63- up-regulation was associated with tumor stage and poor prognosis of patients (P < 0.05), and uc.280+ up-regulation was associated with patient age (P < 0.05). Bioinformatics analysis of RTOUs showed that the transcripts of XPO1, uc002sbh and uc002sbg, were potentially regulated targets of uc.63−. Gene Ontology and pathway analyses showed XPO1 was involved in many important biological functions. ConclusionThis study depicted T-UCR and RTOU expression profiling of LCXW and revealed some potential T-UCR biomarkers that may be involved in the carcinogenesis of LCXW.

Transcribed ultraconserved region Uc.63+ promotes resistance to cisplatin through regulation of androgen receptor signaling in bladder cancer

Cisplatin (CDDP)‑based combination chemotherapy is the standard for muscle‑invasive bladder cancer (MIBC). However, nearly all patients undergoing CDDP chemotherapy become refractory due to the development of CDDP resistance. Therefore, clarification of the mechanisms of CDDP resistance is urgently needed. The transcribed ultraconserved regions (T‑UCRs) are a novel class of non‑coding RNAs that are highly conserved across species and are associated with carcinogenesis and cancer progression. In addition, emerging evidence has shown the involvement of androgen receptor (AR) signals in urothelial carcinoma (UC) progression. The aim of the present study was to investigate the expression of transcribed ultraconserved region Uc.63+, and to analyze the effects of Uc.63+ on AR expression and CDDP resistance in UC. Quantitative reverse transcription‑polymerase chain reaction (qRT‑PCR) revealed that the expression of Uc.63+ was higher in UC tissues than that in non‑neoplastic bladder tissues and 15types of normal tissue. An MTT assay revealed that Uc.63+ was involved in cell proliferation. Western blotting demonstrated that the expression of AR was disrupted by the overexpression or knockdown of Uc.63+ in AR‑positive UMUC3cells. Furthermore, knockdown of Uc.63+ increased sensitivity to CDDP in UMUC3cells. Conversely, overexpression of Uc.63+ had no effect on CDDP sensitivity in AR‑negative RT112cells. Additionally, we observed that the expression of Uc.63+ was increased in CDDP‑resistant UMUC3cells (UMUC3‑CR) in comparison with that in parental UMUC3cells. Knockdown of Uc.63+ re‑sensitized the UMUC3‑CR cells to CDDP. These results indicated that Uc.63+ may be a promising therapeutic target to overcome CDDP resistance in UC.

Transcribed ultraconserved region (T-UCR) uc.261 expression is closely correlated with disease activity and intestinal permeability in Crohn's disease.

Objectives:Transcribed ultraconserved region (T-UCR) uc.261 is reported to participate in intestinal mucosa barrier damage in Crohn’s disease (CD). The aim of this study was to determine the association with disease activity and intestinal permeability.Methods:Uc.261 level in colon mucosa and Harvey-Bradshaw Index (HBI) were evaluated in 20 active CD patients. Uc.261 expression and transepithelial electrical resistance (TEER) were determined in Caco2 and T84 cells treated with tumor necrosis factor alpha (TNF-α), respectively. Body weight, disease activity index (DAI), colon length, histological index (HI), intestinal permeability to FITC-dextran, uc.261, and tight junction proteins (TJPs) levels were evaluated in BALB/C mice treated with saline enema, trinitrobenzene sulfonic acid (TNBS)/ethanol enema, and anti-TNF-α monoclonal antibody injection, respectively.Results:Uc.261 expression was overexpressed in CD patients, TNF-α treated cells, and colitis mice. Uc.261 expression was positively correlated with HBI (r = 0.582, p = 0.007) in CD patients, and positively correlated with TNF-α concentration and negatively correlated TEER in Caco2 and T84 cells (all p < 0.05). Furthermore, uc.261 was positively correlated with DAI (r = 0.824, p = 0.008), HI (r = 0.672, p = 0.021), and intestinal permeability (r = 0.636, p = 0.012), while negatively correlated with body weight (r = –0.574, p = 0.035), colon length (r = –0.866, p = 0.017), and TJP expression (all p < 0.05) in colitis mice.Conclusions:Uc.261 expression was closely correlated with disease activity and intestinal permeability in CD. Anti-TNF-α treatment may play its role through suppressing uc.261 expression in colitis mice.

In silico analysis of biomarker potentials of miRNA-mediated ceRNAs in prostate cancer

Objective:&#x0D; The objective of this study is to define novel biomarkers for Prostate Cancer&#x0D; (PCa) via in silico analysis that takes PCa-specific miRNAs, finds their&#x0D; combinatorial target genes (potential ceRNAs), selects ones containing&#x0D; Transcribed Ultra Conserved Region (T-UCR) among them and potentiates their&#x0D; relevance with PCa.&#x0D; &#x0D; Methods:&#x0D; Thirty-four miRNAs of which clinical relevances with PCa were proved&#x0D; experimentally were exported via miRWalk database.Using the ComiR database, 859&#x0D; genes targeted by these 34 miRNAs simultaneously were identified. Genes with&#x0D; ComiR score above 0.911 were taken into account. Genes containing T-UCR and&#x0D; showing potential ceRNA activity were extracted. Among PCa-associated ceRNAs&#x0D; including T-UCR, we identified genes with significant expression differences between&#x0D; PCa and normal prostate tissue using the GEPIA database. The statistical&#x0D; evaluation of the association of NFAT5 and PTBP2 genes with PCa was performed&#x0D; by Spearman correlation test in GEPIA database.&#x0D; &#x0D; Results:&#x0D; PCa-associated ceRNAs cross-matching with genes including T-UCR in their exonic&#x0D; regions were NFAT5, CLK3, PTBP2, CPEB4, MIPOL1 and TCF4. We identified genes&#x0D; with significant expression differences between PCa and normal prostate tissues&#x0D; among PCa-associated ceRNAs including T-UCR. According to this analysis, NFAT5&#x0D; and PTBP2 genes were significantly less expressed in PCa than in normal&#x0D; prostate tissue while the others didn’t show any significant differential&#x0D; expression pattern. NFAT5 and PTBP2 genes were found to be significantly&#x0D; associated with PCa (p=0.000012; R=0.72).&#x0D; &#x0D; Conclusion:&#x0D; All in all, this is the study associating NFAT5 and PTBP2 genes with PCa and&#x0D; giving them tumor suppressive potential for PCa. Still, larger and more&#x0D; comprehensive studies are needed on this issue.

Noncoding transcribed ultraconserved region (T-UCR) UC.48+ is a novel regulator of high-fat diet induced myocardial ischemia/reperfusion injury.

Increasing evidence has suggested high-fat diet (HFD) is an independent risk factor for myocardial ischemia/reperfusion (MI/R) injury. Long noncoding RNAs (lncRNAs) recently attracted much attraction in the study of MI/R injury. However, the functional questions of specific lncRNAs in HFD-induced MI/R injury have not been well elucidated. Uc.48+ is a lncRNA from a transcribed ultraconserved region (T-UCR) of human, mouse, and rat genomes. Here, we explored the aggravating role of uc.48+and identified purinergic P2X7 receptor (P2X7R) as a downstream regulator of uc.48+ in HFD-induced MI/R vulnerability. We demonstrated uc.48+ expression was upregulated, accompanied by the corresponding upregulation of P2X7R in HFD I/R myocardium and HFD-induced MI/R vulnerability. Overexpression of uc.48+enhanced, whereas silencing of uc.48 + decreased the expression of P2X7R, cardiomyocyte apoptosis, and MI/R injury. The functional relevance of uc.48+ regulated P2X7R expression and the subsequent NF-κB signaling to promote cardiomyocyte apoptosis was supported by inhibition of P2X7R with its specific antagonist (A438079) as well as the inhibitor of NF-κB signaling (pyrrolidine dithiocarbamate, PDTC) in H9c2 hypoxia/reoxygenation (H/R) cells transfected with pcDNA3.0-uc.48 + plasmid, and RNA immunoprecipitation (RIP) suggested uc.48+ could interact with transcription factor Sp1. Importantly, Sp1 inhibitor (mithramycin, MIT) was found to suppress uc.48+ -induced P2X7R expression and the NF-κB signaling and cardiomyocyte apoptosis. Our findings provide a potential novel mechanism through which uc.48+ boosts cardiomyocyte apoptosis and MI/R vulnerability to HFD. Thus, uc.48+ is a novel regulator of HFD-induced MI/R injury; targeting uc.48+ may be a novel therapeutic approach of MI/R vulnerability to HFD.

LncRNA Uc.173 is a key molecule for the regulation of lead-induced renal tubular epithelial cell apoptosis

Transcribed ultra-conserved region (T-UCR) transcripts are a novel class of long non-coding RNAs (lncRNAs) transcribed from ultra-conserved region which is highly conserved in human, rat, and mouse genome. LncRNA UC.173 has been found significantly down-regulated in lead-exposed population and lead-exposed animal mode, and had an inhibitory effect on lead-induced nerve cell apoptosis. We supposed that lncRNA UC.173 had an inhibitory effect on lead-induced renal tubular epithelial cell apoptosis. Thus, the aim of our study was to explore the function of lncRNA UC.173 in lead-exposed renal tubular epithelial cells. In our results, lead exposure inhibited renal tubular epithelial cells viability and promoted cell apoptosis and apoptosis-associated genes expression, but no effect on cell-cycle distribution. Lead exposure inhibited the expression of lncRNA UC.173 in renal tubular epithelial cells, and the inhibition effect was time-dependent and concentration-dependent. Up-regulation of lncRNA UC.173 had no effect on renal tubular epithelial cell viability, cell cycle and apoptosis, but significantly rescued lead-induced inhibition of renal tubular epithelial cell viability and suppressed lead-induced cell apoptosis. In summary, our experiments suggest that lncRNA UC.173 is certainly involved in the regulation of lead-induced renal tubular epithelial cell apoptosis, which may supply a new strategy to minimize lead-induced nephrotoxicity.

Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs

The transcribed ultraconserved regions (T-UCRs) encode long non-coding RNAs implicated in human carcinogenesis. Their mechanisms of action and the factors regulating their expression in cancers are poorly understood. Here we show that high expression of uc.339 correlates with lower survival in 210 non-small cell lung cancer (NSCLC) patients. We provide evidence from cell lines and primary samples that TP53 directly regulates uc.339. We find that transcribed uc.339 is upregulated in archival NSCLC samples, functioning as a decoy RNA for miR-339-3p, -663b-3p, and -95-5p. As a result, Cyclin E2, a direct target of all these microRNAs is upregulated, promoting cancer growth and migration. Finally, we find that modulation of uc.339 affects microRNA expression. However, overexpression or downregulation of these microRNAs causes no significant variations in uc.339 levels, suggesting a type of interaction for uc.339 that we call “entrapping”. Our results support a key role for uc.339 in lung cancer.

Transcribed ultraconserved region Uc.63+ promotes resistance to docetaxel through regulation of androgen receptor signaling in prostate cancer.

Docetaxel is the standard chemotherapy for metastatic castration-resistant prostate cancer (CRPC). However, nearly all patients ultimately become refractory due to the development of docetaxel resistance. The transcribed ultraconserved regions (T-UCRs) are a novel class of non-coding RNAs that are absolutely conserved across species and are involved in carcinogenesis including prostate cancer (PC). In this study, we investigated the transcriptional levels of 26 representative T-UCRs and determined the regions that were differentially expressed in PC. Quantitative real-time polymerase chain reaction analysis revealed that the expression of T-UCR Uc.63+ was increased in PC tissues. MTT assay and wound healing assay revealed that Uc.63+ was involved in cell growth and cell migration. miR-130b was predicted to have binding sites within the Uc.63+ sequence. The expression of miR-130b was significantly disturbed by the overexpression or knockdown of Uc.63+. We also showed that Uc.63+ regulated the expression of MMP2 via miR-130b regulation. Furthermore, overexpression of Uc.63+ increased the expression of AR and its downstream molecule PSA and promoted resistance to docetaxel through AR regulation. In patients treated with docetaxel, the expression of serum Uc.63+ in the docetaxel-resistant patients was higher than that in the docetaxel-sensitive patients (P = 0.011). Moreover, Kaplan-Meier analysis showed that the high expression of serum Uc.63+ correlated with a worse prognosis (P = 0.020). These results substantially support the important role that Uc.63+ plays in PC progression by interacting with miR-130b and indicate that Uc.63+ could potentially be a promising serum marker for deciding the best treatment for patients with CRPC.

Abstract 3478: Expression of the transcribed ultraconserved region Uc.63+ in prostate cancer

Abstract Prostate cancer (PCa) is the most prevalent cancer among men and the second leading cause of cancer related death in western world. Currently, there is a lack of effective treatment options for advanced PCa. Understanding the molecular mechanisms in prostate cancer development and progression would allow the identification of novel prognostic markers or therapeutic targets. The transcribed-ultraconserved regions (T-UCRs) are novel class of noncoding RNAs that are absolutely conserved (100%) between orthologous regions of the human, rat and mouse genomes. Some studies showed that T-UCRs exhibit distinct profiles in various human cancers. We examined the expression profile of representative 26 T-UCRs using qRT-PCR in 12 PCa tissues and 10 non-neoplastic prostate tissues, and found that the expression of Uc.63+ was higher in PCa tissues than that in non-neoplastic tissues. Further analysis revealed that the expression of Uc.63+ significantly correlated with higher PSA levels (p = 0.007) and higher Gleason score (p &amp;lt; 0.001). In order to verify biological function of Uc.63+ in PCa, we firstly transfected Uc.63+ expression vector into LNCaP cells expressing low level of Uc.63+. MTT assay and wound healing assay revealed that overexpression of Uc.63+ significantly increased the cell growth and migration. We also confirmed that downregulation of Uc.63+ using siRNA in DU145 and PC3 expressing high level of Uc.63+. Knockdown of Uc.63+ decreased the cell growth and migration. A recent report indicates that T-UCRs may act as endogenous competing RNA. miR-130b was found to have binding sites within the Uc.63+ using online software. We examined the expression of miR-130b by qRT-PCR in PCa tissues and non-neoplastic prostate tissues. We found a significant downregulation of miR-130b in PCa tissues compared with non-neoplastic prostate tissues, which figured out that there was a significant inverse correlation between Uc.63+ and miR-130b in PCa (p = 0.002). The expression of miR-130b in LNCaP was higher than that in DU145 and PC3. It has been shown that MMP2 is a direct target of miR-130b. Western blot analysis and qRT-PCR revealed that MMP2 expression was higher in LNCaP cells transfected with Uc.63+ expression than that in LNCaP cells transfected with empty vector. These results suggest that Uc.63+ may contribute to the progression of PC through miR-130b interaction. Citation Format: Yohei Sekino, Keisuke Goto, Ririno Honma, Yoshinori Shigematsu, Naoya Sakamoto, Kazuhiro Sentani, Naohide Oue, Jun Teishima, Akio Matsubara, Wataru Yasui. Expression of the transcribed ultraconserved region Uc.63+ in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3478. doi:10.1158/1538-7445.AM2017-3478

Expression and function of Uc.160+, a transcribed ultraconserved region, in gastric cancer.

Transcribed ultraconserved regions (T-UCRs) are a novel class of noncoding RNAs that are highly conserved among the orthologous regions in most vertebrates. It has been reported that T-UCRs have distinct signatures in human cancers. We previously discovered the downregulation of T-UCR expression in gastric cancer (GC), indicating that T-UCRs could play an important role in GC biology. Uc.160+, a T-UCR reported to be downregulated in human cancer, has not been examined in GC. We analyzed the expression pattern of Uc.160+ in nonneoplastic and tumor tissues of the stomach by using uantitative reverse transcription polymerase chain reaction (qRT-PCR) and in situ hybridization (ISH), specifically focusing on the mechanism of transcriptional regulation and target genes that are regulated by T-UCRs. We also attempted to determine the effect of Uc.160+ expression on biological features of GC cell lines by Western blotting. On the basis of the qRT-PCR and ISH results, Uc.160+ expression in adenoma and GC tissues was clearly downregulated compared with that in nonneoplastic mucosa tissues of the stomach. Cancer-specific DNA methylation in the promoter region of Uc.160 was observed by bisulfite genomic DNA sequencing analysis. The effect of DNA methylation on Uc.160+ expression was further confirmed by reporter gene assay. We also revealed that Uc.160+ inhibited the phosphorylation of Akt by regulating phosphatase and tensin homolog (PTEN) expression. These results indicate that Uc.160+ could possibly have a tumor suppressive role in GC.

Noncoding Transcribed Ultraconserved Region (T-UCR) uc.261 Participates in Intestinal Mucosa Barrier Damage in Crohn's Disease.

To date, 481 ultraconserved regions (UCRs) have been discovered in human genome. We aimed to investigate the transcribed UCR (T-UCR) characteristics in Crohn's disease (CD ) and determine whether T-UCR uc.261 participated in intestinal mucosa barrier damage. T-UCRs were screened in active CD mucosa using the Arraystar Human T-UCR Microarray and validated with quantitative real-time reverse transcription PCR, together with tight junction proteins (TJPs) including junctional adhesion molecule-A, occludin, claudin-1, and zonula occluden-1. T-UCR uc.261 in active CD mucosa was validated by RNA fluorescence in situ hybridization. Caco2 and T84 cells were employed to determine transepithelial electrical resistance. Cdc42, protein kinase C ζ, PAR3, and PAR6 were assessed with quantitative real-time reverse transcription PCR and Western blotting. The assembly of TJPs was detected using cell immunofluorescence assay. Four T-UCRs were significantly upregulated (uc.290-, uc.144-, uc.261-, and uc.477+) and 4 T-UCRs were downregulated (uc.166-, uc.141-, uc.478+, and uc.479+). Uc.261 was inversely correlated with transepithelial electrical resistance during tight junction formation. The levels of TJPs were diminished in active CD mucosa. Most uc.261s were located in the cytoplasm of colonic epithelial cells. Overexpression of uc.261 reduced transepithelial electrical resistance, inhibited the expression and assembly of TJPs, activated Cdc42, and suppressed protein kinase C ζ. Silencing of uc.261 in TNF-α-treated cells reversed the tight junction damage. Overexpression of uc.261 participates in intestinal mucosa barrier damage. Suppression of uc.261 reverses the damage to tight junction in inflammation. Attenuation of uc.261 overexpression might be a rational strategy to manage patients with CD.

Integrated analyses of a major histocompatibility complex, methylation and transcribed ultra-conserved regions in systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease which affects different organs and systems that, has a complex genetic inheritance, and is affected by both epigenetic and environmental risk factors. Previous studies on SLE have lacked the statistical power and genetic resolution to fully determine the influence of major histocompatibility complex (MHC) on SLE. In this study, in order to determine this influence, a total of 15 patients with SLE and 15 healthy controls were enrolled. MHC region capture technology, hMeDIP-chip, transcribed ultra-conserved region (T-UCR) microarray and bioinformatics analysis were utilized for both groups. The results revealed methylated CpG enrichment at 6 loci in the MHC segment of SLE. We found 4 single-nucleotide polymorphisms (SNPs) in the CpG promoter of human leukocyte antigen-B (HLA-B) and 2 SNPs in chr6:29521110‑29521833. No significant GO term or KEGG pathway enrichment was noted for an immune-correlated process in the SLE patients for the corresponding CpG-methylated genes. In this study, T-UCR was not discovered in the MHC segment. The analysis of SNPs (rs1050683, rs12697943, rs17881210, rs1065378, rs17184255 and rs16895070) and gene expression in peripheral blood lymphocytes indicated that these SNPs were associated with the occurrence of SLE. Further studies are warranted to examine the roles of these SNPs in the pathogenesis of SLE. Integrative analysis technology provided a view of the molecular signaling pathways in SLE.