scholarly journals Identification of Candidate Biomarker ASXL2 and Its Predictive Value in Pancreatic Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Gaoming Wang ◽  
Ludi Yang ◽  
Jinli Gao ◽  
Huiling Mu ◽  
Yanxiang Song ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Epithelial Mesenchymal Transition ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Predictive Biomarker ◽  
R Package ◽  
Immune Checkpoint Blockade ◽  
Poor Overall Survival ◽  
Aberrant Expression ◽  
Mesenchymal Transition

Pancreatic adenocarcinoma is one of the most lethal diseases with a 5-year survival rate of about 8%. ASXL2 is an epigenetic regulator associated with various tumors including colorectal cancer, breast cancer, and myeloid leukemia. However, the role of ASXL2 in pancreatic cancer remains unclear. This is the first research focusing on the prognostic value of ASXL2 in pancreatic cancer. In this research, we aimed to explore the correlation between ASXL2 and the prognosis, as well as other features in PAAD. We obtained gene expression profiles of PAAD and normal tissues from TCGA, GEO, and Xena databases. TIMER and CIBERSORT algorithms were employed to investigate the effect of ASXL2 on tumor microenvironment. GSEA along with GO and KEGG enrichment analyses were conducted to uncover the biological functions of ASXL2. The response to various chemotherapeutic drugs was estimated by algorithms in R package “pRRophetic”, while the sensitivity to immunotherapy was quantified by TIDE score. We found that ASXL2 was upregulated in the PAAD samples and elevated expression of ASXL2 was linked to poor overall survival. ASXL2 DNA methylation contributed to ASXL2 expression. Functional annotation indicated that ASXL2 was mainly involved in inflammatory response and epithelial mesenchymal transition. Patients with high ASXL2 expression were more likely to benefit from immune checkpoint blockade, gemcitabine, and mitomycin-C. Finally, external datasets and biospecimens were used and the results further validated the aberrant expression of ASXL2 in PAAD samples. In summary, our results highlight that ASXL2 is a potential prognostic and predictive biomarker in pancreatic cancer.

scholarly journals AEBP1 Is One of the Epithelial-Mesenchymal Transition Regulatory Genes in Colon Adenocarcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Dandan Li ◽  
Zhi Liu ◽  
Xiaorong Ding ◽  
Zhensheng Qin
Keyword(s):  
Cancer Metastasis ◽  
Epithelial Mesenchymal Transition ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Colon Adenocarcinoma ◽  
The Cancer Genome Atlas ◽  
Mrna Levels ◽  
Mesenchymal Transition ◽  
Tumor Cell Migration ◽  
Promising Target

Epithelial-mesenchymal transition (EMT) is involved in various tumor processes, including tumorigenesis, tumor cell migration and metastasis, tumor stemness, and therapeutic resistance. Therefore, it is important to identify the genes most associated with EMT and develop them as therapeutic targets. In this work, we first analyzed EMT hallmark gene expression profiles among 10,535 pan-cancer samples from The Cancer Genome Atlas (TCGA) and divided them into EMT high and EMT low groups according to the metagene scores. Then, we identified 12 genes that were most associated with high EMT metagene score ( R > 0.9 ) in 329 colon adenocarcinoma (COAD) patients. Among them, only 4 genes (AEBP1, KCNE4, GFPT2, and FAM26E) had statistically significant differences in prognosis ( P < 0.05 ). Next, we selected AEBP1 as a candidate and showed that AEBP1 mRNA levels and EMT biomarkers strongly coexpressed in 329 COAD samples. In addition, AEBP1 was highly expressed and associated with poor clinical outcomes and prognosis in COAD patients. Finally, to explore whether AEBP1-mediated EMT was related to the tumor microenvironment (TME), we examined AEBP1 expression levels at the single-cell levels. Our results showed that AEBP1 levels were extremely high in tumor-associated fibroblasts, which may induce EMT. AEBP1 expression was also positively correlated with the expression of fibroblast biomarkers and also with EMT metascores, suggesting that AEBP1-mediated EMT may be associated with the stimulation of fibroblast activation. Therefore, AEBP1 may be a promising target for EMT inhibition, which reduces cancer metastasis and drug resistance in COAD patients.

scholarly journals A COMPARATIVE ANALAYSIS OF INTER-SITE GENE EXPRESSION HETEROGENICITY OF NORMAL HUMAN BUCCAL MUCOSA WITH NORMAL GINGIVAL MUCOSA

2021 ◽  
Author(s):  
Rooban Thavarajah ◽  
Kannan Ranganathan
Keyword(s):  
Gene Expression ◽  
Buccal Mucosa ◽  
Epithelial Mesenchymal Transition ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Gene Expression Omnibus ◽  
Genotypic Difference ◽  
Mesenchymal Transition ◽  
Normal Human ◽  
The Difference

BACKGROUND: Description of heterogeneity of gene expression of various human intraoral sites are not adequate. The aim of this study was to explore the difference of gene expression profiles of whole tissue obtained from apparently normal human gingiva and buccal mucosa (HGM, HBM). MATERIALS AND METHODS: Gene sets fulfilling inclusion and exclusion criteria of HGM and HBM in gene Expression Omnibus(GEO) database were identified, segregated, filtered and analysed using the ExAtlas online web tool using pre-determined cut-off. The differentially expressed genes were studied for epithelial keratinization related, housekeeping(HKG), extracellular matrix related(ECMRG) and epithelial-mesenchymal transition related genes(EMTRGs). RESULTS: In all 40 HBM and 64 HGM formed the study group. In all there were 18012 significantly expressed genes. Of this, 1814 were over-expressed and 1862 under-expressed HBM genes as compared to HGM. One in five of all studied genes significantly differed between HBM and HGM. For the keratinization genes, 1 in 6 differed. One of every 5 HKG-proteomics genes differed between HBM and HGM, while this ratio was 1-in 4 for all ECMRGs and EMTRGs. DISCUSSION: This difference in the gene expression between the HBM and HGM could possibly influence a multitude of biological pathways. This result could explain partly the difference in clinicopathological features of oral lesions occurring in HBM and HGM. The innate genotypic difference between the two intra-oral niches could serve as confounding factor in genotypic studies. Hence studies that compare the HBM and HGM should factor-in these findings while evaluating their results.

scholarly journals Gene expression profiling of fast- and slow-growing non-functioning gonadotroph pituitary adenomas

2018 ◽  
Vol 178 (3) ◽  
pp. 295-307 ◽  
Author(s):  
Camilla Maria Falch ◽  
Arvind Y M Sundaram ◽  
Kristin Astrid Øystese ◽  
Kjersti Ringvoll Normann ◽  
Tove Lekva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Tumor Growth ◽  
Epithelial Mesenchymal Transition ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Growth Potential ◽  
Mesenchymal Transition ◽  
Volume Doubling Time ◽  
Slow Growing

ObjectiveReliable biomarkers associated with aggressiveness of non-functioning gonadotroph adenomas (GAs) are lacking. As the growth of tumor remnants is highly variable, molecular markers for growth potential prediction are necessary. We hypothesized that fast- and slow-growing GAs present different gene expression profiles and reliable biomarkers for tumor growth potential could be identified, focusing on the specific role of epithelial-mesenchymal transition (EMT).Design and methodsEight GAs selected for RNA sequencing were equally divided into fast- and slow-growing group by the tumor volume doubling time (TVDT) median (27.75 months). Data were analyzed by tophat2, cufflinks and cummeRbund pipeline. 40 genes were selected for RT-qPCR validation in 20 GAs based on significance, fold-change and pathway analyses. The effect of silencingMTDH(metadherin) andEMCN(endomucin) onin vitromigration of human adenoma cells was evaluated.Results350 genes were significantly differentially expressed (282 genes upregulated and 68 downregulated in the fast group,P-adjusted <0.05). Among 40 selected genes, 11 showed associations with TVDT (−0.669<R<−0.46,P < 0.05). These werePCDH18, UNC5D, EMCN, MYO1B, GPM6Aand six EMT-related genes (SPAG9, SKIL, MTDH, HOOK1, CNOT6LandPRKACB).MTDH, but notEMCN, demonstrated involvement in cell migration and association with EMT markers.ConclusionsFast- and slow-growing GAs present different gene expression profiles, and genes related to EMT have higher expression in fast-growing tumors. In addition toMTDH, identified as an important contributor to aggressiveness, the other genes might represent markers for tumor growth potential and possible targets for drug therapy.

scholarly journals Identification of Upregulated HNRNPs Associated with Poor Prognosis in Pancreatic Cancer

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Lu Qiao ◽  
Ning Xie ◽  
Yuru Bai ◽  
Yan Li ◽  
Yongquan Shi ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Target Genes ◽  
Rna Binding ◽  
Epithelial Mesenchymal Transition ◽  
Expression Patterns ◽  
Poor Overall Survival ◽  
Mesenchymal Transition ◽  
Heterogeneous Nuclear Ribonucleoproteins ◽  
And Function

Heterogeneous nuclear ribonucleoproteins (HNRNPs) are reported to play a crucial role in the pathogenic process of multiple malignancies. However, the expression patterns and prognostic values of HNRNPs in pancreatic cancer (PC) are lacking. In this study, several public databases were explored to identify the commonly upregulated HNRNPs in PC. The clinical significance of HNRNPL (heterogeneous nuclear ribonucleoproteins L) in PC was analyzed. We further performed a series of experiments to elucidate the biological functions of HNRNPL. Bioinformatics analysis including pathway enrichment and interactors with HNRNPL was used to explain the potential mechanisms of HNRNPL in PC pathogenesis. Herein, we reported that HNRNPL was commonly overexpressed in public databases and that high expression of HNRNPL in PC was positively associated with aggressive disease and poor overall survival. Downregulation of HNRNPL suppressed the abilities of migration and epithelial mesenchymal transition of PC cells in vitro, while depletion of HNRNPL did not affect the proliferation rate of PC cells. We further showed that HNRNPL might combine with RNA-binding protein, PTBP1, and function as a part of the spliceosome to regulate alternative splicing of target genes in the occurrence and development of PC. HNRNPL could be employed as an innovative prognostic biomarker and therapeutic target for PC.

scholarly journals STC2 Is a Potential Prognostic Biomarker for Pancreatic Cancer and Promotes Migration and Invasion by Inducing Epithelial–Mesenchymal Transition

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Chen Lin ◽  
Lina Sun ◽  
Shenglei Huang ◽  
Xiangqun Weng ◽  
Zhixian Wu
Keyword(s):  
Pancreatic Cancer ◽  
Survival Rate ◽  
Epithelial Mesenchymal Transition ◽  
Prognostic Biomarker ◽  
Tumor Promoter ◽  
Migration And Invasion ◽  
Aberrant Expression ◽  
Mesenchymal Transition ◽  
Pancreatic Cancer Cells ◽  
Stanniocalcin 2

Aberrant expression of stanniocalcin 2 (STC2) is implicated in cancer development. STC2 acts as a tumor promoter to drive some cancers. However, its contribution to the development of pancreatic cancer remains unclear. This study showed that the expression of STC2 was significantly upregulated in pancreatic cancer tissues. Moreover, its expression was positively correlated with tumor size and lymph node metastasis and negatively correlated with 5-year survival rate of pancreatic cancer patients. Additionally, the expression levels of STC2 were a novel biomarker for predicting overall survival rate after surgery. Furthermore, overexpression of STC2 could promote the proliferation, migration, and invasion of pancreatic cancer cell lines, while knocking down of STC2 led to antiproliferation and antimetastasis activities. Further mechanistic investigations revealed that the expression of STC2 could significantly promote the epithelial–mesenchymal transition (EMT) in pancreatic cancer cells. These data indicated that the overexpression of STC2 in pancreatic cancer contributes to the metastasis through the promotion of EMT, suggesting that STC2 is a potential prognostic biomarker and therapeutic target for pancreatic cancer.

scholarly journals Master Regulators of Epithelial-Mesenchymal Transition and WNT Signaling Pathways in Juvenile Nasopharyngeal Angiofibromas

Biomedicines ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 1258
Author(s):  
Naiade Calanca ◽  
Sara Martoreli Silveira Binato ◽  
Sabrina Daniela da Silva ◽  
Helena Paula Brentani ◽  
Luiz Ubirajara Sennes ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Signaling Pathways ◽  
Epithelial Mesenchymal Transition ◽  
Expression Profiles ◽  
Protein Profile ◽  
Gene Expression Profiles ◽  
Microarray Platform ◽  
Inflammatory Cells ◽  
Nasopharyngeal Angiofibroma ◽  
Mesenchymal Transition

Juvenile nasopharyngeal angiofibroma (JNA) is a rare fibrovascular benign tumor showing an invasive growth pattern and affecting mainly male adolescents. We investigated the role of epithelial–mesenchymal transition (EMT) and WNT signaling pathways in JNA. Gene expression profiles using nine JNA paired with four inferior nasal turbinate samples were interrogated using a customized 2.3K microarray platform containing genes mainly involved in EMT and WNT/PI3K pathways. The expression of selected genes (BCL2, CAV1, CD74, COL4A2, FZD7, ING1, LAMB1, and RAC2) and proteins (BCL2, CAV1, CD74, FZD7, RAF1, WNT5A, and WNT5B) was investigated by RT-qPCR (28 cases) and immunohistochemistry (40 cases), respectively. Among 104 differentially expressed genes, we found a significantly increased expression of COL4A2 and LAMB1 and a decreased expression of BCL2 and RAC2 by RT-qPCR. The immunohistochemistry analysis revealed a low expression of BCL2 and a negative to moderate expression of FZD7 in most samples, while increased CAV1 and RAF1 expression were detected. Moderate to strong CD74 protein expression was observed in endothelial and inflammatory cells. A significant number of JNAs (78%) presented reduced WNT5A and increased WNT5B expression. Overall, the transcript and protein profile indicated the involvement of EMT and WNT pathways in JNA. These candidates are promising druggable targets for treating JNA.

scholarly journals Modular signature of long non-coding RNA association networks as a prognostic biomarker in lung cancer

2021 ◽  
Vol 14 (S3) ◽  
Author(s):  
Albert Li ◽  
Wen-Hsuan Yu ◽  
Chia-Lang Hsu ◽  
Hsuan-Cheng Huang ◽  
Hsueh-Fen Juan
Keyword(s):  
Lung Cancer ◽  
Epithelial Mesenchymal Transition ◽  
Prognostic Biomarker ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
The Cancer Genome Atlas ◽  
Operating Characteristics ◽  
Mesenchymal Transition ◽  
Cancer Hallmarks ◽  
Non Coding Rna

Abstract Background Increasing amount of long non-coding RNAs (lncRNAs) have been found involving in many biological processes and played salient roles in cancers. However, up until recently, functions of most lncRNAs in lung cancer have not been fully discovered, particularly in the co-regulated lncRNAs. Thus, this study aims to investigate roles of lncRNA modules and uncover a module-based biomarker in lung adenocarcinoma (LUAD). Results We used gene expression profiles from The Cancer Genome Atlas (TCGA) to construct the lncRNA association networks, from which the highly-associated lncRNAs are connected as modules. It was found that the expression of some modules is significantly associated with patient’s survival, including module N1 (HR = 0.62, 95% CI = 0.46–0.84, p = 0.00189); N2 (HR = 0.68, CI = 0.50–0.93, p = 0.00159); N4 (HR = 0.70, CI = 0.52–0.95, p = 0.0205) and P3 (HR = 0.68, CI = 0.50–0.92, p = 0.0123). The lncRNA signature consisting of these four prognosis-related modules, a 4-modular lncRNA signature, is associated with favourable prognosis in TCGA-LUAD (HR = 0.51, CI = 0.37–0.69, p value = 2.00e−05). Afterwards, to assess the performance of the generic modular signature as a prognostic biomarker, we computed the time-dependent area under the receiver operating characteristics (AUC) of this 4-modular lncRNA signature, which showed AUC equals 68.44% on 336th day. In terms of biological functions, these modules are correlated with several cancer hallmarks and pathways, including Myc targets, E2F targets, cell cycle, inflammation/immunity-related pathways, androgen/oestrogen response, KRAS signalling, DNA repair and epithelial-mesenchymal transition (EMT). Conclusion Taken together, we identified four novel LUAD prognosis-related lncRNA modules, and assessed the performance of the 4-modular lncRNA signature being a prognostic biomarker. Functionally speaking, these modules involve in oncogenic hallmarks as well as pathways. The results unveiled the co-regulated lncRNAs in LUAD and may provide a framework for further lncRNA studies in lung cancer.

scholarly journals Overexpressed P75CUX1 promotes EMT in glioma infiltration by activating β-catenin

2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Anqi Xu ◽  
Xizhao Wang ◽  
Jie Luo ◽  
Mingfeng Zhou ◽  
Renhui Yi ◽  
...  
Keyword(s):  
Epithelial Mesenchymal Transition ◽  
Tumor Grade ◽  
Prognostic Indicator ◽  
Migration And Invasion ◽  
Poor Overall Survival ◽  
Mesenchymal Transition ◽  
Kaplan Meier ◽  
Homeobox Protein

AbstractThe homeobox protein cut-like 1 (CUX1) comprises three isoforms and has been shown to be involved in the development of various types of malignancies. However, the expression and role of the CUX1 isoforms in glioma remain unclear. Herein, we first identified that P75CUX1 isoform exhibited consistent expression among three isoforms in glioma with specifically designed antibodies to identify all CUX1 isoforms. Moreover, a significantly higher expression of P75CUX1 was found in glioma compared with non-tumor brain (NB) tissues, analyzed with western blot and immunohistochemistry, and the expression level of P75CUX1 was positively associated with tumor grade. In addition, Kaplan–Meier survival analysis indicated that P75CUX1 could serve as an independent prognostic indicator to identify glioma patients with poor overall survival. Furthermore, CUX1 knockdown suppressed migration and invasion of glioma cells both in vitro and in vivo. Mechanistically, this study found that P75CUX1 regulated epithelial–mesenchymal transition (EMT) process mediated via β-catenin, and CUX1/β-catenin/EMT is a novel signaling cascade mediating the infiltration of glioma. Besides, CUX1 was verified to promote the progression of glioma via multiple other signaling pathways, such as Hippo and PI3K/AKT. In conclusion, we suggested that P75CUX1 could serve as a potential prognostic indicator as well as a novel treatment target in malignant glioma.

scholarly journals A novel homeostatic loop of sorcin drives paclitaxel-resistance and malignant progression via Smad4/ZEB1/miR-142-5p in human ovarian cancer

Oncogene ◽  
2021 ◽  
Author(s):  
Jinguo Zhang ◽  
Wencai Guan ◽  
Xiaolin Xu ◽  
Fanchen Wang ◽  
Xin Li ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Calcium Binding ◽  
Molecular Mechanisms ◽  
Epithelial Mesenchymal Transition ◽  
Malignant Progression ◽  
Bioinformatics Analyses ◽  
Aberrant Expression ◽  
Mesenchymal Transition ◽  
E Box

AbstractThe primary chemotherapy of ovarian cancer (OC) often acquires chemoresistance. Sorcin (SRI), a soluble resistance-related calcium-binding protein, has been reported to be an oncogenic protein in cancer. However, the molecular mechanisms of SRI regulation and the role and aberrant expression of SRI in chemoresistant OC remain unclear. Here, we identified SRI as a key driver of paclitaxel (PTX)-resistance and explored its regulatory mechanism. Using transcriptome profiles, qRT-PCR, proteomics, Western blot, immunohistochemistry, and bioinformatics analyses, we found that SRI was overexpressed in PTX-resistant OC cells and the overexpression of SRI was related to the poor prognosis of patients. SRI was a key molecule required for growth, migration, and PTX-resistance in vitro and in vivo and was involved in epithelial–mesenchymal transition (EMT) and stemness. Mechanistic studies showed that miR-142-5p directly bound to the 3ʹ-UTR of SRI to suppress its expression, whereas a transcription factor zinc-finger E-box binding homeobox 1 (ZEB1) inhibited the transcription of miR-142-5p by directly binding to the E-box fragment in the miR-142 promoter region. Furthermore, ZEB1 was negatively regulated by SRI which physically interacted with Smad4 to block its translocation from the cytosol to the nucleus. Taken together, our findings unveil a novel homeostatic loop of SRI that drives the PTX-resistance and malignant progression via Smad4/ZEB1/miR-142-5p in human OC. Targeting this SRI/Smad4/ZEB1/miR-142-5p loop may reverse the PTX-resistance.

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