Comprehensive analysis of differentially expressed lncRNAs as diagnostic and prognostic markers for colorectal cancer

The peel color is an important external quality of melon fruit. To explore the mechanisms of melon peel color formation, we performed an integrated analysis of transcriptome and metabolome with three different fruit peel samples (grey-green ‘W’, dark-green ‘B’, and yellow ‘H’). A total of 40 differentially expressed flavonoids were identified. Integrated transcriptomic and metabolomic analyses revealed that flavonoid biosynthesis was associated with the fruit peel coloration of melon. Twelve differentially expressed genes regulated flavonoids synthesis. Among them, nine (two 4CL, F3H, three F3′H, IFS, FNS, and FLS) up-regulated genes were involved in the accumulation of flavones, flavanones, flavonols, and isoflavones, and three (2 ANS and UFGT) down-regulated genes were involved in the accumulation of anthocyanins. This study laid a foundation to understand the molecular mechanisms of melon peel coloration by exploring valuable genes and metabolites.

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Comprehensive analysis of lncRNA-miRNA-mRNA regulatory networks for microbiota-mediated colorectal cancer associated with immune cell infiltration

Bioengineered ◽

10.1080/21655979.2021.1940614 ◽

2021 ◽

Vol 12 (1) ◽

pp. 3410-3425

Author(s):

Xiangzhou Tan ◽

Linfeng Mao ◽

Changhao Huang ◽

Weimin Yang ◽

Jianping Guo ◽

...

Keyword(s):

Colorectal Cancer ◽

Regulatory Networks ◽

Immune Cell ◽

Comprehensive Analysis ◽

Cell Infiltration ◽

Immune Cell Infiltration

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Soluble SIGLEC5: A New Prognosis Marker in Colorectal Cancer Patients

Cancers ◽

10.3390/cancers13153896 ◽

2021 ◽

Vol 13 (15) ◽

pp. 3896

Author(s):

Karla Montalbán-Hernández ◽

Ramón Cantero-Cid ◽

Roberto Lozano-Rodríguez ◽

Alejandro Pascual-Iglesias ◽

José Avendaño-Ortiz ◽

...

Keyword(s):

Colorectal Cancer ◽

Operating Characteristic ◽

Prognostic Markers ◽

Characteristic Curve ◽

Area Under The Curve ◽

Significant Heterogeneity ◽

Kaplan Meier ◽

Prognosis Marker ◽

Colorectal Cancer Patients ◽

Healthy Participants

Colorectal cancer (CRC) is the second most deadly and third most commonly diagnosed cancer worldwide. There is significant heterogeneity among patients with CRC, which hinders the search for a standard approach for the detection of this disease. Therefore, the identification of robust prognostic markers for patients with CRC represents an urgent clinical need. In search of such biomarkers, a total of 114 patients with colorectal cancer and 67 healthy participants were studied. Soluble SIGLEC5 (sSIGLEC5) levels were higher in plasma from patients with CRC compared with healthy volunteers. Additionally, sSIGLEC5 levels were higher in exitus than in survivors, and the receiver operating characteristic curve analysis revealed sSIGLEC5 to be an exitus predictor (area under the curve 0.853; cut-off > 412.6 ng/mL) in these patients. A Kaplan–Meier analysis showed that patients with high levels of sSIGLEC5 had significantly shorter overall survival (hazard ratio 15.68; 95% CI 4.571–53.81; p ≤ 0.0001) than those with lower sSIGLEC5 levels. Our study suggests that sSIGLEC5 is a soluble prognosis marker and exitus predictor in CRC.

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Identification of differentially expressed circular RNAs in chemoresistant colorectal cancer

Epigenomics ◽

10.2217/epi-2019-0042 ◽

2019 ◽

Vol 11 (8) ◽

pp. 875-884 ◽

Cited By ~ 13

Author(s):

Nadiah Abu ◽

Kha Wai Hon ◽

Shivapriya Jeyaraman ◽

Azyani Yahaya ◽

Nik MA Abdullah ◽

...

Keyword(s):

Colorectal Cancer ◽

Differentially Expressed ◽

Circular Rnas

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Gene expression and DNA methylation analyses suggest that two immune related genes are prognostic factors of colorectal cancer

BMC Medical Genomics ◽

10.1186/s12920-021-00966-3 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Xiao-Liang Xing ◽

Zhi-Yong Yao ◽

Chaoqun Xing ◽

Zhi Huang ◽

Jing Peng ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Risk Assessment ◽

Dna Methylation ◽

Differentially Expressed Genes ◽

Risk Score ◽

Immune Cells ◽

Assessment Model ◽

Differentially Expressed ◽

Risk Assessment Model

Abstract Background Colorectal cancer (CRC) is the second most prevalent cancer, as it accounts for approximately 10% of all annually diagnosed cancers. Studies have indicated that DNA methylation is involved in cancer genesis. The purpose of this study was to investigate the relationships among DNA methylation, gene expression and the tumor-immune microenvironment of CRC, and finally, to identify potential key genes related to immune cell infiltration in CRC. Methods In the present study, we used the ChAMP and DESeq2 packages, correlation analyses, and Cox regression analyses to identify immune-related differentially expressed genes (IR-DEGs) that were correlated with aberrant methylation and to construct a risk assessment model. Results Finally, we found that HSPA1A expression and CCRL2 expression were positively and negatively associated with the risk score of CRC, respectively. Patients in the high-risk group were more positively correlated with some types of tumor-infiltrating immune cells, whereas they were negatively correlated with other tumor-infiltrating immune cells. After the patients were regrouped according to the median risk score, we could more effectively distinguish them based on survival outcome, clinicopathological characteristics, specific tumor-immune infiltration status and highly expressed immune-related biomarkers. Conclusion This study suggested that the risk assessment model constructed by pairing immune-related differentially expressed genes correlated with aberrant DNA methylation could predict the outcome of CRC patients and might help to identify those patients who could benefit from antitumor immunotherapy.

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Differentially Expressed Mutant Genes Reveal Potential Prognostic Markers For Lung Adenocarcinoma

10.1109/bibm52615.2021.9669472 ◽

2021 ◽

Author(s):

Yue Liu ◽

Shizheng Qiu ◽

Yang Hu ◽

Yadong Wang

Keyword(s):

Lung Adenocarcinoma ◽

Prognostic Markers ◽

Differentially Expressed ◽

Mutant Genes

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Identification of a lncRNA prognostic signature-related to stem cell index and its significance in colorectal cancer

Future Oncology ◽

10.2217/fon-2020-1163 ◽

2021 ◽

Author(s):

Xiao-Cheng Wang ◽

Ya Liu ◽

Fei-Wu Long ◽

Liang-Ren Liu ◽

Chuan-Wen Fan

Keyword(s):

Colorectal Cancer ◽

Overall Survival ◽

Prognostic Markers ◽

The Cancer Genome Atlas ◽

Prognostic Signature ◽

Free Survival ◽

Cancer Genome Atlas ◽

Bioinformatic Approaches ◽

Cell Phenotypes ◽

The Relationship

Background: The relationship between long noncoding RNAs (lncRNAs) and the mRNA stemness index (mRNAsi) in colorectal cancer (CRC) is still unclear. Materials & methods: The mRNAsi, mRNAsi-related lncRNAs and their clinical significance were analyzed by bioinformatic approaches in The Cancer Genome Atlas (TCGA)-COREAD dataset. Results: mRNAsi was negatively related to pathological features but positively related to overall survival and recurrence-free survival in CRC. A five mRNAsi-related lncRNAs prognostic signature was further developed and showed independent prognostic factors related to overall survival in CRC patients, due to the five mRNAsi-related lncRNAs involved in several pathways of the cancer stem cells and malignant cancer cell phenotypes. Conclusion: The present study highlights the potential roles of mRNAsi-related lncRNAs as alternative prognostic markers.

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