Ubiquitin D Research Articles

Transcriptome profiling of the cancer and adjacent nontumor tissues from cervical squamous cell carcinoma patients by RNA sequencing.

Cervical cancer is the third most common cancer and the fourth leading cause of cancer deaths among women in the world. The discovery of vital diagnostic and therapeutic markers against cervical squamous cell carcinoma (CSCC) would broaden our understanding on the molecular basis of CSCC. In this study, we thoroughly analyzed the transcriptome of CSCC and matched adjacent nontumor (ATN) tissue. RNA sequencing was performed to screen the differentially expressed genes (DEGs) of three pairs of CSCC and ATN tissues. Functional enrichment analysis was used to uncover the biological functions of DEGs. Protein interaction network was carried out to reveal interaction of DEGs. Quantitative real-time PCR was conducted to validate the expression of DEGs. Immunohistochemistry was used to detect the relationship between clinicopathological parameters of CSCC and DEGs. There were a total of 347 significantly common DEGs in the three paired examples, including 104 consistent upregulated and 148 consistent downregulated DEGs. The 347 DEGs were categorized into 73 functional categories by Gene Ontology (GO) analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis suggested six significantly signal pathways. The protein interaction network uncovered three important DEGs, including retinol dehydrogenase 12 (RDH12), ubiquitin D (UBD), and serum amyloid A1 (SAA1). We found that RDH12 expression was decreased in 74.5 % of CSCC tissues. RDH12 expression was negatively associated with tumor size and depth of cervical invasion. The UBD was overexpressed in 61.7 % of CSCC tissues and was positively related with tumor size and lymphatic metastasis. The SAA1 protein was overexpressed in 57.4 % of CSCC tissues and was positively related with clinicopathological parameters of tumor size, lymphatic metastasis, and depth of cervical invasion. The RDH12, UBD, and SAA1 genes might participate in the progression of CSCC.

MicroRNA-146a alleviates chronic skin inflammation in atopic dermatitis through suppression of innate immune responses in keratinocytes

Chronic skin inflammation in atopic dermatitis (AD) is associated with elevated expression of proinflammatory genes and activation of innate immune responses in keratinocytes. microRNAs (miRNAs) are short, single-stranded RNA molecules that silence genes via the degradation of target mRNAs or inhibition of translation. The aim of this study was to investigate the role of miR-146a in skin inflammation in AD. RNA and protein expression was analyzed using miRNA and mRNA arrays, RT-quantitative PCR, Western blotting, and immunonohistochemistry. Transfection of miR-146a precursors and inhibitors into human primary keratinocytes, luciferase assays, and MC903-dependent mouse model of AD were used to study miR-146a function. We show that miR-146a expression is increased in keratinocytes and chronic lesional skin of patients with AD. miR-146a inhibited the expression of numerous proinflammatory factors, including IFN-γ-inducible and AD-associated genes CCL5, CCL8, and ubiquitin D (UBD) in human primary keratinocytes stimulated with IFN-γ, TNF-α, or IL-1β. In a mouse model of AD, miR-146a-deficient mice developed stronger inflammation characterized by increased accumulation of infiltrating cells in the dermis, elevated expression of IFN-γ, CCL5, CCL8, and UBD in the skin, and IFN-γ, IL-1β, and UBD in draining lymph nodes. Both tissue culture and invivo experiments in mice demonstrated that miR-146a-mediated suppression in allergic skin inflammation partially occurs through direct targeting of upstream nuclear factor kappa Bsignal transducers caspase recruitment domain-containing protein 10 and IL-1 receptor-associated kinase 1. In addition, human CCL5 was determined as a novel, direct target of miR-146a. Our data demonstrate that miR-146a controls nuclear factor kappa B-dependent inflammatory responses in keratinocytes and chronic skin inflammation in AD.

The positive ubiquitin D expression predicts poor survival in postoperative stage II colon cancer patients treated with postoperative adjuvant chemotherapy

Objective To investigate the expression of human ubiquitin D (UBD) and its role in tumor relapse and non-relapse group patients who received 5-fluoruracil-based adjuvant chemotherapy after surgery.Methods In this study 106 stage Ⅱ patients treated with postoperative 5-fluoruracil (5-fu)-based adjuvant chemotherapy were enrolled,and divided into two groups:recurrence group (35 cases) and nonrecurrence group (71 cases).The expression of UBD mRNA was detected by real-time quantitative polymerase chain reaction (real-time PCR) in respective 20 matched cancer and normal colonic membrane tissues of stage Ⅱ colon cancer patients in the two groups.Immunohistochemistry was used to study UBD expression in 35 patients with recurrence and 71 non-relapse patient's cancer and normal tissues.Chi-square test or Fisher's exact test were used and evaluated the hazard ratio (HR) of disease-free survival(DFS) and overall survival(OS) by using Cox proportional hazard model.Results The average expression level of UBD mRNA in 20 relapse and non-relapse group patients were 7.64 and 2.07 (x2 =10.7,P ＜ 0.01),respectively ; UBD positive staining in relapse and non-relapse group patients were 86％ (30/35),and 59％ (42/71) (x2 =7.59,P ＜ 0.01).The 5-years DFS (P ＜ 0.05) and OS (P ＜ 0.05) decreased significantly in UBD positive cases.Conclusions UBD is an independent prognostic factor for DFS and OS in postoperative Stage Ⅱ colonic cancer patients treated by post oprative chemotherapy. Key words: Ubiquitins; Colon neoplasms; Antineoplastic combined chemotherapy protocols

Screening for differentially expressed genes between left- and right-sided colon carcinoma by microarray analysis

Left-sided colon carcinoma (LSCC) and right-sided colon carcinoma (RSCC) differ in their genetic susceptibilities to neoplastic transformation. The present study identified 11 genes that were differentially expressed in LSCC and RSCC by expression profiling with microarray analysis. Compared with RSCC, the human genes for L-lactate dehydrogenase B chain (LDHB), cyclin-dependent kinase 4 inhibitor D (CDKN2D), phosphatidylinositol-4-phosphate-3-kinase C2 domain-containing subunit α (PI3KC2α), protocadherin fat 1 (FAT; a human protein that closely resembles the Drosophila tumor suppressor, fat) and dual specificity protein phosphatase 2 (DUSP2) were upregulated in LSCC. By contrast, genes for ubiquitin D (UBD), casein kinase-1 binding protein (CK1BP), synaptotagmin-13 (SYT1), zinc finger protein 560 (ZNF560), pleckstrin homology domain-containing family B member 2 (PLEKHB2) and IgGFc-binding protein (FCGBP) were downregulated in LSCC compared with RSCC. A quantitative polymerase chain reaction (qPCR) analysis revealed that the mRNA levels of UBD and CK1BP in LSCC were significantly lower compared with those in RSCC (P=0.033 and P= 0.005, respectively), whereas the mRNA levels of LDHB and CDKN2D in LSCC were significantly higher compared with those in RSCC (P=0.008 and P=0.017, respectively). Western blot and immunohistochemical analyses demonstrated that the expression of CDKN2D in LSCC was significantly higher compared with that in RSCC, while the expression of UBD in LSCC was significantly lower compared with that in RSCC. The present study provides important insights into the understanding of the molecular genetic basis for the different biological behaviors observed between LSCC and RSCC. These insights may therefore serve as a basis for the identification of novel colon cancer markers and therapeutic targets.

UBD (ubiquitin D)

Review on UBD (ubiquitin D), with data on DNA, on the protein encoded, and where the gene is implicated.

Ubiquitin D is correlated with colon cancer progression and predicts recurrence for stage II-III disease after curative surgery

Background:Our recent study observed that the expression of ubiquitin D (UBD), a member of ubiquitin-like modifier family, was upregulated in colon cancer parenchymal cells. The present study further investigated the clinical signicance of UBD in colon cancer.Methods:Using quantitative PCR, tissue microarray (TMA), western blot analysis and immunohistochemical stain, we evaluated UBD mRNA and protein levels in tumour tissues from patients with colon cancer at different stages and in paired adjacent normal epithelium.Results:Immunohistochemical detection of UBD on a TMA containing 203 paired specimens showed that increased cytoplasmic UBD was signicantly associated with depth of cancer invasion, lymph node metastasis, distant metastasis, tumour histologic grade, advanced clinical stage and Ki-67 proliferative index. Patients with UBD-positive tumours had a significantly higher disease recurrence rate and poorer survival than patients with UBD-negative tumours after the radical surgery. Stratification analysis according to tumour stage revealed UBD as an independent predictor for tumour recurrence in patients with stage II and III tumours.Conclusion:UBD may contribute to the progression of colon carcinogenesis and function as a novel prognostic indicator of forecasting recurrence of stage II and III patients after curative operations.

A regulatory single nucleotide polymorphism in the ubiquitin D gene associated with celiac disease

An aberrant immune response triggered by dietary gluten is the main driving force underlying celiac disease (CD), but other biologic pathways that are dysregulated also participate in disease development. Genetic variation within these pathways might influence expression, contributing to susceptibility to CD. We have investigated the implication of ubiquitin D ( UBD), a member of the ubiquitin–proteasome system that is strongly upregulated in the intestinal mucosa of active CD. Reverse transcriptase-polymerase chain reaction analysis of intestinal biopsy sample pairs (at diagnosis vs treated) from 30 CD patients confirmed overexpression of UBD in active disease tissue (fold change = 8.3; p = 0.0022). In silico prediction tools identified rs11724 as a putative regulatory single nucleotide polymorphism and association analysis of 468 CD patients and 459 controls revealed that the minor rs11724*C allele was more frequent among patients (minor allele frequency = 0.44 vs 0.39; odds ratio [OR] = 1.23; p = 0.028) and suggested a dominant allele effect (OR = 1.49; p = 0.0045). Correlation of the rs11724 genotype and UBD mRNA levels (OR = 0.76; p = 0.0021) further supports its implication in disease development.

Insights into adaptor binding to the AAA protein p97

The AAA (ATPase associated with various cellular activities) p97 [also known as VCP (valosin-containing protein)] participates in numerous biological activities and is an essential component of the ubiquitin signalling pathway. A plethora of adaptors have been reported for p97, and increasing evidence is suggesting that it is through adaptor binding that p97 is diverted into different cellular pathways. Studying the interaction between p97 and its adaptors is therefore crucial to our understanding of the physiological roles of the protein. The interactions between p97 and the PUB [PNGase (peptide N-glycosidase)/ubiquitin-associated] domain of PNGase, the UBX (ubiquitin regulatory X) domain of p47, and the UBD (ubiquitin D) domain of Npl4 have been structurally characterized. UBX and UBD are structural homologues that share similar p97-binding modes; it is plausible that other proteins that contain a UBX/UBX-like domain also interact with p97 via similar mechanisms. In addition, several short p97-interacting motifs, such as VBM (VCP-binding motif), VIM (VCP-interacting motif) and SHP, have been identified recently and are also shared between p97 adaptors, hinting that proteins possessing the same p97-binding motif might also share common p97-binding mechanisms. In this review, we aim to summarize our current knowledge on adaptor binding to p97.

SNP mapping and candidate gene sequencing in the class I region of the HLA complex: searching for multiple sclerosis susceptibility genes in Tasmanians

This study is an extension to previously published work that has linked variation in the human leukocyte antigen (HLA) class I region with susceptibility to multiple sclerosis (MS) in Australians from the Island State of Tasmania. Single nucleotide polymorphism (SNP) mapping was performed on an 865-kb candidate region (D6S1683-D6S265) in 166 Tasmanian MS families, and seven candidate genes [ubiquitin D (UBD), olfactory receptor 2H3 (OR2H3), gamma-aminobutyric acid B receptor 1 (GABBR1), myelin oligodendrocyte glycoprotein (MOG), HLA-F, HLA complex group 4 (HCG4) and HLA-G] were resequenced. SNPs tagging the extended MS susceptibility haplotype were genotyped in an independent sample of 356 Australian MS trios and SNPs in the MOG gene were significantly over-transmitted to MS cases. We identified significant effects on MS susceptibility of HLA-A*2 (OR: 0.51; P = 0.05) and A*3 (OR: 2.85; P = 0.005), and two coding polymorphisms in the MOG gene (V145I: P = 0.01, OR: 2.2; V142L: P = 0.04, OR: 0.45) after full conditioning on HLA-DRB1. We have therefore identified plausible candidates for the causal MS susceptibility allele, and although not conclusive at this stage, our data provide suggestive evidence for multiple class I MS susceptibility genes.

Distinct Gene Expression Profiles Characterize Cellular Phenotypes of Follicle-Associated Epithelium and M Cells

Follicle-associated epithelium (FAE) covering Peyer's patches contains specialized epithelial M cells that take up ingested macromolecules and microorganisms from the lumen of the gut by transcytosis. Using high-density oligonucleotide microarrays, we analyzed the gene expression profiles of FAE and M cells in order to characterize their cellular phenotypes. The microarray data revealed that, among approximately 14,000 genes, 409 were expressed in FAE at twofold or higher levels compared to the intestinal epithelial cells (IECs) of the villi. These included genes involved in membrane traffic, host defense and transcriptional regulation, as well as uncharacterized genes. Real-time PCR and in situ hybridization analyses identified three molecules, ubiquitin D (Ub-D), tumor necrosis factor receptor superfamily 12a (TNFRsf12a), and transmembrane 4 superfamily 4 (Tm4sf4), which were predominantly distributed throughout FAE, but were expressed little, if at all, in IECs. By contrast, transcripts of secretory granule neuroendocrine protein 1 (Sgne-1) were scattered in FAE, and were co-localized with Ulex europaeus agglutinin-1 (UEA-1)-positive cells. This clearly suggests that expression of Sgne-1 in the gut is specific to M cells. Such a unique pattern of gene expression distinguishes FAE and M cells from IECs, and may reflect their cellular phenotype(s) associated with specific functional features.