New prognostic markers revealed by RNA-Seq transcriptome analysis after <i>MYC</i> silencing in a metastatic gastric cancer cell line

Lopes, Luana de Oliveira; Maués, Jersey Heitor da Silva; Ferreira-Fernandes, Hygor; Yoshioka, France Keiko N.; Júnior, Severino Cavalcante de Sousa; Santos, Alcemir Rodrigues; Ribeiro, Helem Ferreira; Rey, Juan A.; Soares, Paulo Cardoso; Burbano, Rommel Rodríguez; Pinto, Giovanny R.

doi:10.18632/oncotarget.27208

Cited by 7 publications

(8 citation statements)

References 49 publications

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“…In our previous study, the serum CIAPIN1 levels was an independent unfavorable prognostic factor for patients with CCA [7]. Already, Lopes et al reported that the expression analysis of CIAPIN1 may predict metastasis and poor prognosis of patients with gastric cancer [26]. Furthermore, the decrease in CIAPIN1 expression is significantly associated with a longer survival time of diffuse large B cell lymphoma [27], colorectal cancer [28], pancreatic cancer [29], and non-small-cell lung carcinoma [30].…”

Section: Discussionmentioning

confidence: 73%

Prediction of CIAPIN1 (Cytokine-Induced Apoptosis Inhibitor 1) Signaling Pathway and Its Role in Cholangiocarcinoma Metastasis

Truong

Wongwattanakul

Proungvitaya

et al. 2022

JCM

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Cholangiocarcinoma (CCA), a malignancy of the biliary epithelium, can arise at any point in the biliary system. We previously reported that CIAPIN1 is detectable in the sera and that its overexpression was associated with poor prognosis and metastasis of CCA patients. In this study, we investigated further its expression in CCA tissues, biological functions, and related signaling pathways in CCA cells. First, we examined CIAPIN1 expression in CCA tissues of 39 CCA patients using immunohistochemistry (IHC). Then, CIAPIN1-related proteins expressed in CCA cells were identified using RNA interference (siRNA) and liquid chromatography–mass spectrometry (LC–MS/MS). To predict the functions and signaling pathways of CIAPIN1 in CCA cells, the identified proteins were analyzed using bioinformatics tools. Then, to validate the biological functions of CIAPIN1 in the CCA cell line, transwell migration/invasion assays were used. CIAPIN1 was overexpressed in CCA tissues compared with adjacent noncancerous tissues. Its overexpression was correlated with lymph node metastasis. Bioinformatic analyses predicted that CIAPIN1 is connected to the TGF-β/SMADs signaling pathway via nitric oxide synthase 1 (NOS1) and is involved in the metastasis of CCA cells. In fact, cell migration and invasion activities of the KKU-100 CCA cell line were significantly suppressed by CIAPIN1 gene silencing. Our results unravel its novel function and potential signaling pathway in metastasis of CCA cells. CIAPIN1 can be a poor prognostic factor and can be a promising target molecule for CCA chemotherapy.

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Section: Discussionmentioning

confidence: 73%

Prediction of CIAPIN1 (Cytokine-Induced Apoptosis Inhibitor 1) Signaling Pathway and Its Role in Cholangiocarcinoma Metastasis

Truong

Wongwattanakul

Proungvitaya

et al. 2022

JCM

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“…As illustrated here for one case of prostate cancer, and in previous papers on cases of papillary thyroid cancer [ 46 , 92 ] and clear cell renal cell carcinoma [ 35 , 93 ], GFP offers a comprehensive personalized alternative to the biomarkers approach to determine the cancer transcriptional identity (e.g., [ 112 ]) and explore gene therapy.…”

Section: Discussionmentioning

confidence: 97%

“…REV analysis pointed also to some interesting genes for oncogenomics. Thus, MRPS12 , the most stably expressed gene in “N”, is a potential prognostic candidate for ovarian cancer [ 92 ], while UXT the most unstably expressed gene in “N” is associated with advanced stages of gastric cancer [ 93 ]. ENTPD2 , the most stably expressed gene in “A” is a biomarker for lung [ 94 ] and hepatocellular [ 72 ] carcinomas, while USP31 , the most variably expressed gene in “A”, could be a potential target for sarcomas [ 95 ].…”

Section: Discussionmentioning

confidence: 99%

A Personalized Genomics Approach of the Prostate Cancer

Iacobaş

2021

Cells

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Decades of research identified genomic similarities among prostate cancer patients and proposed general solutions for diagnostic and treatments. However, each human is a dynamic unique with never repeatable transcriptomic topology and no gene therapy is good for everybody. Therefore, we propose the Genomic Fabric Paradigm (GFP) as a personalized alternative to the biomarkers approach. Here, GFP is applied to three (one primary—“A”, and two secondary—“B” & “C”) cancer nodules and the surrounding normal tissue (“N”) from a surgically removed prostate tumor. GFP proved for the first time that, in addition to the expression levels, cancer alters also the cellular control of the gene expression fluctuations and remodels their networking. Substantial differences among the profiled regions were found in the pathways of P53-signaling, apoptosis, prostate cancer, block of differentiation, evading apoptosis, immortality, insensitivity to anti-growth signals, proliferation, resistance to chemotherapy, and sustained angiogenesis. ENTPD2, AP5M1 BAIAP2L1, and TOR1A were identified as the master regulators of the “A”, “B”, “C”, and “N” regions, and potential consequences of ENTPD2 manipulation were analyzed. The study shows that GFP can fully characterize the transcriptomic complexity of a heterogeneous prostate tumor and identify the most influential genes in each cancer nodule.

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“…Unfortunately, GC is difficult to diagnose at an early stage. Therefore, people are very interested in finding prognostic markers for these potentially curable patients [9][10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Identification of novel biomarkers, MUC5AC, MUC1, KRT7, GAPDH, CD44 for gastric cancer

Yang¹

2020

Med Oncol

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Gastric cancer (GC) is one of the most common malignant tumors in the world, and it is also the third largest cause of cancerrelated death in the world. As far as we know, no biomarker has been widely accepted for early diagnosis and prognosis prediction of gastric cancer. The purpose of this study is to find potential biomarkers to predict the prognosis of GC. The gene expression profiles of GSE2685 were downloaded from GEO database. Morpheus was used to calculate the differentially expressed genes (DEGs) between primary advanced gastric cancer tissues and noncancerous gastric tissues. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed, and protein-protein interaction (PPI) network of DEGs was constructed. Kaplan-Meier Plotter was used to determine the overall survival (OS) outcomes of UC5AC, MUC1, KRT7, GAPDH, CD44, and GEPIA was used to determine the Pearson correlation analysis. In total, 710 DEGs were identified in GC, including 396 upregulated genes and 314 downregulated genes. GO enrichment revealed that they were mainly enriched in binding, catalytic activity, cellular process and cell. KEGG pathway revealed that they were mainly enriched in metabolic pathways, pathways in cancer and PI3K-Akt signaling pathway. MUC5AC, MUC1, KRT7, GAPDH, CD44 were identified from the PPI network. MUC5AC, MUC1, KRT7, GAPDH, CD44 were demonstrated to have prognostic value for patients with GC. MUC5AC, MUC1 exhibited low expression levels in GC tissues, KRT7, GAPDH, CD44 presented high expression levels in GC tissues. In particular, KRT7 is hardly expressed in normal gastric tissues. MUC5AC and MUC1 were negatively correlated with GAPDH, CD44, respectively; and GAPDH was positively correlated with CD44 and KRT7, respectively. Moreover. MUC5AC, MUC1, KRT7, GAPDH, and CD44 are not only related to GC but also to apoptosis pathway. Results from the present study suggested that MUC5AC, MUC1, KRT7, GAPDH, CD44 may represent novel prognostic biomarkers for GC.

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New prognostic markers revealed by RNA-Seq transcriptome analysis after MYC silencing in a metastatic gastric cancer cell line

Cited by 7 publications

References 49 publications

Prediction of CIAPIN1 (Cytokine-Induced Apoptosis Inhibitor 1) Signaling Pathway and Its Role in Cholangiocarcinoma Metastasis

Prediction of CIAPIN1 (Cytokine-Induced Apoptosis Inhibitor 1) Signaling Pathway and Its Role in Cholangiocarcinoma Metastasis

A Personalized Genomics Approach of the Prostate Cancer

Identification of novel biomarkers, MUC5AC, MUC1, KRT7, GAPDH, CD44 for gastric cancer

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