Proteogenomic characterization and comprehensive integrative genomic analysis of human colorectal cancer liver metastasis

Ma, Yu‐Shui; Huang, Tao; Zhong, Xiaoming; Zhang, Hongwei; Cong, Xianling; Xu, Hong; Lu, Gai‐Xia; Yu, Fei; Xue, Sheng; Lv, Zhongwei; Fu, Da

doi:10.1186/s12943-018-0890-1

Cited by 63 publications

(55 citation statements)

References 26 publications

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“…Sequences of PCR primers are shown in the Additional file 1 : Table S1. U6 and GAPDH were used as the endogenous controls, and the 2 -ΔΔCT method was used to analyze expression levels [ 22 ].…”

Section: Methodsmentioning

confidence: 99%

MicroRNA-302a/d inhibits the self-renewal capability and cell cycle entry of liver cancer stem cells by targeting the E2F7/AKT axis

et al. 2018

J Exp Clin Cancer Res

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BackgroundThere is increasing evidence that liver cancer stem cells (LCSCs) contribute to hepatocellular carcinoma (HCC) initiation and progression. MicroRNA (miRNA) plays a significant functional role by directly regulating respective targets in LCSCs-triggered HCC, however, little is known about the function of the miRNA-302 family in LCSCs.MethodsMiRNAs microarray was used to detect the miRNAs involved in LCSCs maintenance and differentiation. Biological roles and the molecular mechanism of miRNA-302a/d and its target gene E2F7 were detected in HCC in vitro. The expression and correlation of miRNA-302a/d and E2F7 in HCC patients was evaluated by quantitative PCR and Kaplan–Meier survival analysis.ResultsWe found that the miRNA-302 family was downregulated during the spheroid formation of HCC cells and patients with lower miRNA-302a/d expression had shorter overall survival (OS) and progression-free survival (PFS). Moreover, E2F7 was confirmed to be directly targeted and inhibited by miRNA-302a/d. Furthermore, concomitant low expression of miRNA-302a/d and high expression of E2F7 correlated with a shorter median OS and PFS in HCC patients. Cellular functional analysis demonstrated that miRNA-302a/d negatively regulates self-renewal capability and cell cycle entry of liver cancer stem cells via suppression of its target gene E2F7 and its downstream AKT/β-catenin/CCND1 signaling pathway.ConclusionsOur data provide the first evidence that E2F7 is a direct target of miRNA-302a/d and miRNA-302a/d inhibits the stemness of LCSCs and proliferation of HCC cells by targeting the E2F7/AKT/β-catenin/CCND1 signaling pathway.Electronic supplementary materialThe online version of this article (10.1186/s13046-018-0927-8) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

MicroRNA-302a/d inhibits the self-renewal capability and cell cycle entry of liver cancer stem cells by targeting the E2F7/AKT axis

et al. 2018

J Exp Clin Cancer Res

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“…For example, NEUROD1/2 functions as growth-promoting gene in HPNE cells, but as suppressor of proliferation in HMEC cells (Sack et al, 2018). DMRT like family B with proline rich C-terminal 1 (DMRTB1) mutation might relate to human colorectal cancer liver metastasis (Ma et al, 2018). Ahmadreza Niavarani et al found that strong expression of apolipoprotein B mRNA editing enzyme catalytic subunit 1 (APOBEC1) was associated with short survival time in pan-cancer, which was in line with our result (Niavarani et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Immune cell landscape analysis reveals prognostic immune cells and its potential mechanism in squamous cell lung carcinoma

Wang

Guo

2020

PeerJ

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Background Squamous cell lung carcinoma (LUSC) was closely associated with smoking which was known to have a distant immunosuppression effect. In this study, we aimed to explore the relationship between immune cells and clinical outcomes of LUSC patients with smoking history. Methods The immune cell infiltration and RNA expression profiles of LUSC patients were collected from The Cancer Genome Atlas (TCGA). Then, the correlation between immune cell infiltration and clinical characteristics was explored. According to the level of immune cell infiltration, LUSC patients with smoking history were divided into high or low group to screen the differentially expressed lncRNAs and mRNAs. The prediction of target genes was performed by miRanda. Finally, the prognostic value of a certain signature was confirmed in an independent dataset. Results Higher abundance of tumor-infiltrating T follicular helper (Tfh) cells together with a lower abundance of resting memory CD4 T cells had been found in LUSC current reformed smokers for ≤15 years and current smoking patients. Moreover, Tfh cell infiltration was not only associated with better overall survival (OS) but also varied from different degrees of TNM stage. Low expression of lncRNA PWRN1 and its potential regulating genes DMRTB1, PIRT, APOBEC1, and ZPBP2 were associated with better OS. Combining PWRN1 and four regulating genes as a signature, patients with higher-level expression of the signature had shorter survival time in not only the TCGA but also in the GEO dataset. Conclusions It was found that Tfh cells presented higher infiltration in LUSC current reformed smokers for ≤15 years and current smokers, while resting memory CD4 T cells had lower infiltration. The signature consisting of PWRN1 as well as its predicted targeted mRNAs was dysregulated in different levels of Tfh cell infiltration and might indicate patients’ OS.

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“…It has been shown that CCT6A protein expression levels are elevated in tumor tissues of patients with hepatocellular carcinoma and that the overall survival of these patients is relatively shorter [5] . Previous studies have also con rmed that the number of mutant peptides has potential prognostic value, with somatic variants showing increased expression of CCT6A, which has clinical signi cance [6] . CCT6A is expression-inducible and ampli cation-inducible in glioblastoma, and shows a signi cant negative correlation with survival [7] .…”

Section: Introductionmentioning

confidence: 92%

CCT6A, a novel prognostic biomarker for Ewing's sarcoma

Jiang

et al. 2020

Preprint

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Background Ewing's sarcoma (ES) is the second most prevalent malignancy among bone tissue tumors, and there is no adequate prognosis biomarker. The protein encoded by CCT6A is a molecular chaperone. Early studies have suggested that CCT6A is involved in the development of many cancers, however, there is no clear evidence of a role for CCT6A in ES. Methods In this study, we performed a bioinformatics analysis of 32 Ewing sarcoma specimens from the GSE17618 dataset for differences in gene expression and overall survival, event-free survival, and gene expression in different subgroups. Results After three screenings, we identified CCT6A as highly correlated with Ewing's sarcoma prognosis. Survival analysis showed low overall survival (OS) for CCT6A high expression (P = 0.024). On the other hand, Cox regression analysis showed that CCT6A expression, event-free survival (EFS), and age were strongly associated with the prognosis of Ewing sarcoma, identified as independent poor prognostic biomarkers. (CCT6A: P = 0.015; Age: P-value = 0.026; EFS: P-value = 0.001). Conclusion The expression level of CCT6A is strongly associated with the prognosis of Ewing's sarcoma. High expression of the CCT6A gene may serve as a biomarker for poor prognosis in patients with Ewing's sarcoma.

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Proteogenomic characterization and comprehensive integrative genomic analysis of human colorectal cancer liver metastasis

Cited by 63 publications

References 26 publications

MicroRNA-302a/d inhibits the self-renewal capability and cell cycle entry of liver cancer stem cells by targeting the E2F7/AKT axis

MicroRNA-302a/d inhibits the self-renewal capability and cell cycle entry of liver cancer stem cells by targeting the E2F7/AKT axis

Immune cell landscape analysis reveals prognostic immune cells and its potential mechanism in squamous cell lung carcinoma

CCT6A, a novel prognostic biomarker for Ewing's sarcoma

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