The High Ratio of the Plasma miR-96/miR-99b Correlated With Poor Prognosis in Patients With Metastatic Colorectal Cancer

Object: This study aims to clarify the expression of plasma miRNA in CRC patients, and to clarify the potential use of these miRNAs in diagnosis and prognosis, and to establish a prognostic model to initially explore its clinical value.Methods: We detected the expression of 6 miRNAs in normal colon epithelial cell lines and colorectal cancer cell lines by qRT-PCR and they were validated in the tissues of three subtypes: 20 healthy subjects, 41 pCRC and 49 mCRC patients. COX regression and ROC analyses use to evaluate the diagnostic and prognostic efficacy of candidate miRNAs. Subsequently, we initially established a nomogram prognostic model. MiRNA is also used to construct miRNA-mRNA interaction network and PPI network modules.Results: Five miRNAs showed significant differential expression in pCRC, mCRC patients and normal groups. ROC analysis showed that CEA, miR-96, miR-99b and miR-96/miR-99b are distinguishable from pCRC and mCRC patients, with AUC ranging from 0.65 to 0.91; among them, the ratio of miR-96/miR-99b is stronger than any diagnostic indicators, such as CEA and CA125. Multivariate survival analysis identified miR-96, miR-99b, N stage, M stage and clinical stage as independent prognostic indicators of mCRC. The nomogram based on these 5 characteristics has satisfactory prognostic values.Conclusion: Our data indicate that plasma miR-96/miR-99b can be used as a promising biomarker for early detection of mCRC patients; our nomogram has a promising evaluation value.

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Predicting the Survival and Immune Landscape of Colorectal Cancer Patients Using an Immune-Related lncRNA Pair Model

Frontiers in Genetics ◽

10.3389/fgene.2021.690530 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chao Ma ◽

Xin Zhang ◽

Xudong Zhao ◽

Nan Zhang ◽

Sixin Zhou ◽

...

Keyword(s):

Colorectal Cancer ◽

Prognostic Model ◽

Risk Model ◽

Cox Regression ◽

Kinase Inhibitor ◽

Low Risk ◽

The Cancer Genome Atlas ◽

Prognostic Indicators ◽

Immune Checkpoints ◽

Cox Regression Analysis

BackgroundAccumulating evidence has demonstrated that immune-related long non-coding ribonucleic acids (irlncRNAs) can be used as prognostic indicators of overall survival (OS) in patients with colorectal cancer (CRC). Our aim in this research, therefore, was to construct a risk model using irlncRNA pairs with no requirement for a specific expression level, in hope of reliably predicting the prognosis and immune landscape of CRC patients.MethodsClinical and transcriptome profiling data of CRC patients downloaded from the Cancer Genome Atlas (TCGA) database were analyzed to identify differentially expressed (DE) irlncRNAs. The irlncRNA pairs significantly correlated with the prognosis of patients were screened out by univariable Cox regression analysis and a prognostic model was constructed by Lasso and multivariate Cox regression analyses. A receiver operating characteristic (ROC) curve was then plotted, with the area under the curve calculated to confirm the reliability of the model. Based on the optimal cutoff value, CRC patients in the high- or low-risk groups were distinguished, laying the ground for evaluating the risk model from the following perspectives: survival, clinicopathological traits, tumor-infiltrating immune cells (TIICs), antitumor drug efficacy, kinase inhibitor efficacy, and molecules related to immune checkpoints.ResultsA prognostic model consisting of 15 irlncRNA pairs was constructed, which was found to have a high correlation with patient prognosis in a cohort from the TCGA (p < 0.001, HR = 1.089, 95% CI [1.067–1.112]). According to both univariate and multivariate Cox analyses, this model could be used as an independent prognostic indicator in the TCGA cohort (p < 0.001). Effective differentiation between high- and low-risk patients was also accomplished, on the basis of aggressive clinicopathological characteristics, sensitivity to antitumor drugs, and kinase inhibitors, the tumor immune infiltration status, and the expression levels of specific molecules related to immune checkpoints.ConclusionThe prognostic model established with irlncRNA pairs is a promising indicator for prognosis prediction in CRC patients.

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Prediction of Prognostic Biomarkers and Construction of an Autophagy Prognostic Model for Colorectal Cancer Using Bioinformatics

Technology in Cancer Research & Treatment ◽

10.1177/1533033820984177 ◽

2020 ◽

Vol 19 ◽

pp. 153303382098417

Author(s):

Ting-ting Liu ◽

Shu-min Liu

Keyword(s):

Colorectal Cancer ◽

Regression Analysis ◽

Prognostic Model ◽

Cox Regression ◽

Small Gtpase ◽

Functional Enrichment ◽

Clinical Correlation ◽

Cox Regression Analysis ◽

Prognostic Analysis ◽

Key Genes

Objective: The incidence of colorectal cancer is increasing every year, and autophagy may be related closely to the pathogenesis of colorectal cancer. Autophagy is a natural catabolic mechanism that allows the degradation of cellular components in eukaryotic cells. However, autophagy plays a dual role in tumorigenesis. It not only promotes normal cell survival and tumor growth but also induces cell death and suppresses tumors survival. In addition, the pathogenesis of various conditions, including inflammation, neurodegenerative diseases, or tumors, is associated with abnormal autophagy. The present work aimed to examine the significance of autophagy-related genes (ARGs) in prognosis prediction, to construct an autophagy prognostic model, and to identify independent prognostic factors for colorectal cancer (CRC). Methods: This study discovered a total of 36 ARGs in CRC cases using The Cancer Genome Atlas (TCGA) and Human Autophagy-dedicated (HADd) databases along with functional enrichment analysis. Then, an autophagy prognostic model was constructed using univariate Cox regression analysis, and the key prognostic genes were screened. Finally, independent prognostic markers were determined through independent prognostic analysis and clinical correlation analysis of key genes. Results: Of the 36 differentially expressed ARGs, 13 were related to prognosis, as determined by univariate Cox regression analysis. A total of 6 key genes were obtained by a multivariate Cox regression analysis. Independent prognostic values were shown by 3 genes, namely, microtubule-associated protein 1 light chain 3 (MAP1LC3C), small GTPase superfamily and Rab family (RAB7A), and WD-repeat domain phosphoinositide-interacting protein 2 (WIPI2) by independent prognostic analysis and clinical correlation. Conclusions: In this study, molecular bioinformatics technology was employed to determine and construct a prognostic model of autophagy for colon cancer patients, which revealed 3 autophagy-related features, namely, MAP1LC3C, WIPI2, and RAB7A.

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Prediction and Validation of Hub Genes Associated with Colorectal Cancer by Integrating PPI Network and Gene Expression Data

BioMed Research International ◽

10.1155/2017/2421459 ◽

2017 ◽

Vol 2017 ◽

pp. 1-12 ◽

Cited By ~ 4

Author(s):

Yongfu Xiong ◽

Wenxian You ◽

Rong Wang ◽

Linglong Peng ◽

Zhongxue Fu

Keyword(s):

Colorectal Cancer ◽

Mrna Expression ◽

Interaction Network ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Advanced Tumor Stage ◽

Ppi Network ◽

Hub Genes ◽

Clinical Value ◽

Advanced Tumor

Although hundreds of colorectal cancer- (CRC-) related genes have been screened, the significant hub genes still need to be further identified. The aim of this study was to identify the hub genes based on protein-protein interaction network and uncover their clinical value. Firstly, 645 CRC patients’ data from the Tumor Cancer Genome Atlas were downloaded and analyzed to screen the differential expression genes (DEGs). And then, the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed, and PPI network of the DEGs was constructed by Cytoscape software. Finally, four hub genes (CXCL3, ELF5, TIMP1, and PHLPP2) were obtained from four subnets and further validated in our clinical setting and TCGA dataset. The results showed that mRNA expression of CXCL3, ELF5, and TIMP1 was increased in CRC tissues, whereas PHLPP2 mRNA expression was decreased. More importantly, high expression of CXCL3, ELF5, and TIMP1 was significantly associated with lymphatic invasion, distance metastasis, and advanced tumor stage. In addition, a shorter overall survival was observed in patients with increased CXCL3, TIMP1, and ELF5 expression and decreased PHLPP2 expression. In conclusion, the four hub genes screened by our strategy could serve as novel biomarkers for prognosis prediction of CRC patients.

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Micrometastasis volume in stage II colorectal cancer: A prospective study by Clinical Study Group of Osaka University (CSGO).

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.4_suppl.597 ◽

2017 ◽

Vol 35 (4_suppl) ◽

pp. 597-597

Author(s):

Kohei Murata ◽

Hirofumi Yamamoto ◽

Mutsumi Fukunaga ◽

Tadashi Ohnishi ◽

Shingo Noura ◽

...

Keyword(s):

Colorectal Cancer ◽

Prognostic Factor ◽

Cox Regression ◽

Stage Ii ◽

Significant Prognostic Factor ◽

Rt Pcr ◽

Clinical Value ◽

Poor Prognostic Factor ◽

Stage Ii Colorectal Cancer ◽

Cea Mrna

597 Background: We reported in a retrospective study that the presence of micrometastasis in lymph nodes (LNs), when assessed by CEA-specific RT-PCR, is a significant prognostic factor in stage II colorectal cancer (CRC). The aim of this study was to clarify the clinical value of micrometastasis in a prospective multicenter trial. Methods: From November 2001 to December 2005, a total of 419 CRC cases were preoperatively registered at a central data center. Of them, 315 node-negative stage II CRC were enrolled. After RNA quality check, 304 CRC cases were analyzed for CEA mRNA in LNs by both conventional RT-PCR (a band method) and quantitative RT-PCR. Long-term prognosis of the patients was determined by each method. Results: A positive band for CEA mRNA was detected in 73 (24.0%) of 304 patients. Post-operative adjuvant chemotherapy was applied in 31 CEA band-positive cases with an oral 5-FU derivative HCFU (1-hexylcarbamoyl-5-fluorouracil) for one year, while chemotherapy was not administered to CEA band-negative group. Multivariate Cox regression analyses revealed that a high micrometastasis volume (High-MMV, n = 95) was an independent poor prognostic factor for 5-year DFS ( P= 0.001) and 5-year OS ( P= 0.016). Conclusions: This prospective clinical trial demonstrates that micrometastasis volume is a useful marker in identifying patients who are at high or low risk for recurrence of stage II CRC.

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Upregulation of GNPNAT1 Predicts Poor Prognosis and Correlates With Immune Infiltration in Lung Adenocarcinoma

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.605754 ◽

2021 ◽

Vol 8 ◽

Author(s):

Wenting Liu ◽

Kaiting Jiang ◽

Jingya Wang ◽

Ting Mei ◽

Min Zhao ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Signaling Pathways ◽

Poor Prognosis ◽

Cox Regression ◽

Clinical Stage ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Clinical Value ◽

Cox Regression Analysis ◽

Normal Tissues

BackgroundGlucosamine 6-phosphate N-acetyltransferase (GNPNAT1) is a key enzyme in the hexosamine biosynthetic pathway (HBP), which functions as promoting proliferation in some tumors, yet its potential biological function and mechanism in lung adenocarcinoma (LUAD) have not been explored.MethodsThe mRNA differential expression of GNPNAT1 in LUAD and normal tissues was analyzed using the Cancer Genome Atlas (TCGA) database and validated by real-time PCR. The clinical value of GNPNAT1 in LUAD was investigated based on the data from the TCGA database. Then, immunohistochemistry (IHC) of GNPNAT1 was applied to verify the expression and clinical significance in LUAD from the protein level. The relationship between GNPNAT1 and epigenetics was explored using the cBioPortal database, and the miRNAs regulating GNPNAT1 were found using the miRNA database. The association between GNPNAT1 expression and tumor-infiltrating immune cells in LUAD was observed through the Tumor IMmune Estimation Resource (TIMER). Finally, Gene set enrichment analysis (GSEA) was used to explore the biological signaling pathways involved in GNPNAT1 in LUAD.ResultsGNPNAT1 was upregulated in LUAD compared with normal tissues, which was verified through qRT-PCR in different cell lines (P < 0.05), and associated with patients’ clinical stage, tumor size, and lymphatic metastasis status (all P < 0.01). Kaplan–Meier (KM) analysis suggested that patients with upregulated GNPNAT1 had a relatively poor prognosis (P < 0.0001). Furthermore, multivariate Cox regression analysis indicated that GNPNAT1 was an independent prognostic factor for LUAD (OS, TCGA dataset: HR = 1.028, 95% CI: 1.013–1.044, P < 0.001; OS, validation set: HR = 1.313, 95% CI: 1.130–1.526, P < 0.001). GNPNAT1 overexpression was correlated with DNA copy amplification (P < 0.0001), low DNA methylation (R = −0.52, P < 0.0001), and downregulation of hsa-miR-30d-3p (R = −0.17, P < 0.001). GNPNAT1 expression was linked to B cells (R = −0.304, P < 0.0001), CD4+T cells (R = −0.218, P < 0.0001), and dendritic cells (R = −0.137, P = 0.002). Eventually, GSEA showed that the signaling pathways of the cell cycle, ubiquitin-mediated proteolysis, mismatch repair and p53 were enriched in the GNPNAT1 overexpression group.ConclusionGNPNAT1 may be a potential prognostic biomarker and novel target for intervention in LUAD.

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NDRG2 combined with EGFR improved its prognostic value for lung adenocarcinoma

10.21203/rs.2.14181/v1 ◽

2019 ◽

Author(s):

Bo Yang ◽

Xiao-Ping Li ◽

Hong-Gang Zhou ◽

Tao Jiang ◽

Ting Xiao ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Cox Regression ◽

Growth Factor Receptor ◽

Prognostic Indicators ◽

Clinicopathological Parameters ◽

Clinical Value ◽

Cox Regression Analysis ◽

Egfr Expression ◽

Serum Carcinoembryonic Antigen ◽

Prediction Of Prognosis

Abstract Background N-Myc downstream-regulated gene2 (NDRG2) plays an important role in lung adenocarcinoma (LUAD). Epidermal growth factor receptor (EGFR) mutation has significantly improved prognosis in patients with adenocarcinoma. We aimed to elucidate the clinical value of NDRG2/EGFR as a prediction of prognosis in patients with lung adenocarcinoma.Materials and Methods Immunohistochemistry and western blot analysis were conducted to detect the expression of NDRG2 protein. Association between NDRG2/EGFR expression and clinicopathological parameters of the patients were examined. Serum Carcinoembryonic antigen (CEA) level was examined prior to treatment in patients with LUAD. Patients’ survival rate was assessed by Kaplan–Meier. Candidates for independent prognostic biomarkers were analyzed using a COX proportional hazard model.Results NDRG2 levels were significantly decreased in patients with lung adenocarcinoma. NDRG2 levels were positively correlated with CEA and EGFR. Advanced stages were significantly associated with low expression of NDRG2. Patients with NDRG2-high combined with EGFR-positive expression had the best prognosis during the 5-year follow-up period. Meanwhile, COX regression analysis showed that the conjoined expressions of NDRG2-low/EGFR-positive, NDRG2-high/EGFR-positive and vascular invasion were independent prognostic indicators for lung adenocarcinoma.Conclusion NDRG2 is of more prognosis value as the biomarker for lung adenocarcinoma when analyzed combined with the EGFR expression.

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A Novel Autophagy-Related Prognostic Risk Model and a Nomogram for Survival Prediction of Oral Cancer Patients

BioMed Research International ◽

10.1155/2022/2067540 ◽

2022 ◽

Vol 2022 ◽

pp. 1-13

Author(s):

Hongjun Fei ◽

Xiongming Chen

Keyword(s):

Survival Data ◽

Prognostic Model ◽

Risk Model ◽

Cox Regression ◽

Characteristic Curve ◽

Interaction Network ◽

Receiver Operator Characteristic Curve ◽

Functional Enrichment ◽

Survival Prediction ◽

Sequencing Data

Background. This study is aimed at constructing a risk signature to predict survival outcomes of ORCA patients. Methods. We identified differentially expressed autophagy-related genes (DEARGs) based on the RNA sequencing data in the TCGA database; then, four independent survival-related ARGs were identified to construct an autophagy-associated signature for survival prediction of ORCA patients. The validity and robustness of the prognostic model were validated by clinicopathological data and survival data. Subsequently, four independent prognostic DEARGs that composed the model were evaluated individually. Results. The expressions of 232 autophagy-related genes (ARGs) in 127 ORCA and 13 control tissues were compared, and 36 DEARGs were filtered out. We performed functional enrichment analysis and constructed protein–protein interaction network for 36 DEARGs. Univariate and multivariate Cox regression analyses were adopted for searching prognostic ARGs, and an autophagy-associated signature for ORCA patients was constructed. Eventually, 4 desirable independent survival-related ARGs (WDR45, MAPK9, VEGFA, and ATIC) were confirmed and comprised the prognostic model. We made use of multiple ways to verify the accuracy of the novel autophagy-related signature for survival evaluation, such as receiver-operator characteristic curve, Kaplan–Meier plotter, and clinicopathological correlational analyses. Four independent prognostic DEARGs that formed the model were also associated with the prognosis of ORCA patients. Conclusions. The autophagy-related risk model can evaluate OS for ORCA patients independently since it is accurate and stable. Four prognostic ARGs that composed the model can be studied deeply for target treatment.

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Development and validation of nomograms for prediction of overall survival and cancer-specific survival of patients of colorectal cancer

Japanese Journal of Clinical Oncology ◽

10.1093/jjco/hyz182 ◽

2019 ◽

Vol 50 (3) ◽

pp. 261-269

Author(s):

Jieyun Zhang ◽

Yue Yang ◽

Xiaojian Fu ◽

Weijian Guo

Keyword(s):

Colorectal Cancer ◽

Overall Survival ◽

Prognostic Factors ◽

Prognostic Model ◽

Cox Regression ◽

External Validation ◽

Cancer Prognosis ◽

Cancer Specific Survival ◽

Internal Validation ◽

Development And Validation

Abstract Purpose Nomograms are intuitive tools for individualized cancer prognosis. We sought to develop a clinical nomogram for prediction of overall survival and cancer-specific survival for patients with colorectal cancer. Methods Patients with colorectal cancer diagnosed between 1988 and 2006 and those who underwent surgery were retrieved from the Surveillance, Epidemiology, and End Results database and randomly divided into the training (n = 119 797) and validation (n = 119 797) cohorts. Log-rank and multivariate Cox regression analyses were used in our analysis. To find out death from other cancer causes and non-cancer causes, a competing-risks model was used, based on which we integrated these significant prognostic factors into nomograms and subjected the nomograms to bootstrap internal validation and to external validation. Results The 1-, 3-, 5- and 10-year probabilities of overall survival in patients of colorectal cancer after surgery intervention were 83.04, 65.54, 54.79 and 38.62%, respectively. The 1-, 3-, 5- and 10-year cancer-specific survival was 87.36, 73.44, 66.22 and 59.11%, respectively. Nine independent prognostic factors for overall survival and nine independent prognostic factors for cancer specific survival were included to build the nomograms. Internal and external validation CI indexes of overall survival were 0.722 and 0.721, and those of cancer-specific survival were 0.765 and 0.766, which was satisfactory. Conclusions Nomograms for prediction of overall survival and cancer-specific survival of patients with colorectal cancer. Performance of the model was excellent. This practical prognostic model may help clinicians in decision-making and design of clinical studies.

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Downregulation of miR-1826 Indicates a Poor Prognosis for Osteosarcoma Patients and Regulates Tumor Cell Proliferation, Migration, and Invasion

International Journal of Genomics ◽

10.1155/2020/7968407 ◽

2020 ◽

Vol 2020 ◽

pp. 1-6

Author(s):

Peng Li ◽

Lei Wei ◽

Wenshuai Zhu

Keyword(s):

Cell Proliferation ◽

Cell Lines ◽

Poor Prognosis ◽

Cox Regression ◽

Clinical Stage ◽

Prognostic Significance ◽

Prognostic Indicator ◽

Migration And Invasion ◽

Kaplan Meier ◽

Low Levels

Background. Osteosarcoma (OS) is the most frequent bone tumor with high metastasis. This study is aimed at assessing the expression and prognostic significance of microRNA-1826 (miR-1826) in OS patients, as well as its biological function in tumor progression. Methods. Quantitative Real-Time PCR was employed to measure the expression of miR-1826 in OS tissues and cell lines. Kaplan-Meier survival analysis and Cox regression model were used to evaluate the prognostic value of miR-1826. CCK-8 and Transwell assay were conducted to investigate the effect of miR-1826 on OS cell proliferation, migration, and invasion. Results. miR-1826 expression was downregulated in OS tissues and cell lines and associated with OS patients’ clinical stage and distant metastasis. Low levels of miR-1826 were related with shorter survival time and determined as an independent prognostic indicator for the overall survival of OS patients. The overexpression of miR-1826 in OS cells led to inhibited cell proliferation, migration, and invasion. Conclusion. The decreased expression of miR-1826 predicts a poor prognosis in OS patients, and its overexpression inhibits OS cell proliferation, migration, and invasion. This newly identified miR-1826 provides a novel sight into the pathogenesis of OS and offers a candidate prognostic biomarker and therapeutic target for OS treatment.

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N1, N12-Diacetylspermine Is Elevated in Colorectal Cancer and Promotes Proliferation through the miR-559/CBS Axis in Cancer Cell Lines

Journal of Oncology ◽

10.1155/2021/6665704 ◽

2021 ◽

Vol 2021 ◽

pp. 1-15

Author(s):

Teng Mu ◽

Tingguang Chu ◽

Wenxin Li ◽

Qianze Dong ◽

Yong Liu

Keyword(s):

Colorectal Cancer ◽

Cell Lines ◽

Cell Cycle Progression ◽

Polyclonal Antibodies ◽

Biological Effects ◽

Clinical Stage ◽

Luciferase Reporter ◽

E Proteins ◽

Atp Production ◽

Underlying Mechanisms

N1, N12-Diacetylspermine (DiAcSpm) has been reported to be upregulated in the urine of cancer patients. Mass spectrometry has shown elevated DiAcSpm expressions in colorectal cancer (CRC) tissues. However, the diagnostic application of DiAcSpm is not available due to a lack of diagnostic grade antibodies. Also, its biological roles in CRC cells remain unexplored. In the present study, we developed an antibody that directly detected DiAcSpm expression in paraffin-embedded tissues. We also characterized its biological characteristics and underlying mechanisms. Polyclonal antibodies were generated by immunizing animals with a synthetic product of DiAcSpm. Antibody DAS AB016 showed strong sensitivity against DiAcSpm in CRC tissues. Immunohistochemistry results showed that DiAcSpm expression was significantly elevated in CRC tissues. High levels of DiAcSpm correlated with the clinical stage and Ki67 index. DiAcSpm treatment increased levels of proliferation, cell cycle progression, and cyclin D1 and cyclin E proteins in CRC cell lines, SW480 and Caco-2. DiAcSpm also upregulated ATP production in these two cell lines. RNA-sequencing showed that DiAcSpm downregulated miR-559, which was confirmed using RT-qPCR. The luciferase reporter assay, western blotting, and RT-qPCR showed that cystathionine β-synthase (CBS) was the target of miR-559. miR-559 inhibited, while CBS accelerated, CRC proliferation. In addition, CBS siRNA knockdown blocked the biological effects of DiAcSpm on CRC cells. In conclusion, DiAcSpm was found to be increased in CRC tissues using a newly developed antibody. DiAcSpm accelerated CRC proliferation by regulating the miR-559/CBS axis.

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