Expression profile analysis of two antisense lncRNAs to improve prognosis prediction of colorectal adenocarcinoma

Shademan, Milad; Salanghuch, Azam Naseri; Zare, Khadijeh; Zahedi, Morteza; Foroughi, Mohammad Ali; Rezayat, Kambiz Akhavan; Mozaffari, Hooman Mosannen; Ghaffarzadegan, Kamran; Goshayeshi, Ladan; Dehghani, Hesam

doi:10.1186/s12935-019-1000-1

Cited by 21 publications

(11 citation statements)

References 26 publications

(31 reference statements)

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“…The loss or gain of interaction of long noncoding RNAs with DNA methyltransferases could be very important for LINE-1 expression. For instance, studies have shown that CCAT1 long noncoding RNA which is involved in the regulation of proliferation and anchorage-independent growth of cancer cells and affects other regulatory lncR-NAs may function as a scaffold for epigenetic regulators of gene function and determine CpG island methylator phenotype [46][47][48][49]. One of our observations was that the normal (at risk) mucosa adjacent to advanced and adenocarcinoma had a significantly higher copy number of LINE-1 transcripts than the normal mucosa adjacent to non-advanced adenomas (Fig.…”

Section: Discussionmentioning

confidence: 99%

Promoter methylation, transcription, and retrotransposition of LINE-1 in colorectal adenomas and adenocarcinomas

et al. 2020

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Background: The methylation of the CpG islands of the LINE-1 promoter is a tight control mechanism on the function of mobile elements. However, simultaneous quantification of promoter methylation and transcription of LINE-1 has not been performed in progressive stages of colorectal cancer. In addition, the insertion of mobile elements in the genome of advanced adenoma stage, a precancerous stage before colorectal carcinoma has not been emphasized. In this study, we quantify promoter methylation and transcripts of LINE-1 in three stages of colorectal non-advanced adenoma, advanced adenoma, and adenocarcinoma. In addition, we analyze the insertion of LINE-1, Alu, and SVA elements in the genome of patient tumors with colorectal advanced adenomas. Methods: LINE-1 hypomethylation status was evaluated by absolute quantitative analysis of methylated alleles (AQAMA) assay. To quantify the level of transcripts for LINE-1, quantitative RT-PCR was performed. To find mobile element insertions, the advanced adenoma tissue samples were subjected to whole genome sequencing and MELT analysis. Results: We found that the LINE-1 promoter methylation in advanced adenoma and adenocarcinoma was significantly lower than that in non-advanced adenomas. Accordingly, the copy number of LINE-1 transcripts in advanced adenoma was significantly higher than that in non-advanced adenomas, and in adenocarcinomas was significantly higher than that in the advanced adenomas. Whole-genome sequencing analysis of colorectal advanced adenomas revealed that at this stage polymorphic insertions of LINE-1, Alu, and SVA comprise approximately 16%, 51%, and 74% of total insertions, respectively. Conclusions: Our correlative analysis showing a decreased methylation of LINE-1 promoter accompanied by the higher level of LINE-1 transcription, and polymorphic genomic insertions in advanced adenoma, suggests that the early and advanced polyp stages may host very important pathogenic processes concluding to cancer.

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Section: Discussionmentioning

confidence: 99%

Promoter methylation, transcription, and retrotransposition of LINE-1 in colorectal adenomas and adenocarcinomas

et al. 2020

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“…PRKCQ-AS1 may be a potential biomarker for predicting survival in colorectal cancer (Shademan et al, 2019). LINC01096 involves in cell migration and invasion, and it can predict clinical outcomes in breast cancer (Wang et al, 2019).…”

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confidence: 99%

Immune‐related long noncoding RNA signature for predicting survival and immune checkpoint blockade in hepatocellular carcinoma

Zhang

et al. 2020

Journal Cellular Physiology

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Long noncoding RNAs (lncRNAs) show multiple functions, including immune response. Recently, the immune‐related lncRNAs have been reported in some cancers. We first investigated the immune‐related lncRNA signature as a potential target in hepatocellular carcinoma (HCC) survival. The training set (n = 368) and the independent external validation cohort (n = 115) were used. Immune genes and lncRNAs coexpression were constructed to identify immune‐related lncRNAs. Cox regression analyses were perfumed to establish the immune‐related lncRNA signature. Regulatory roles of this signature on cancer pathways and the immunologic features were investigated. The correlation between immune checkpoint inhibitors and this signature was examined. In this study, the immune‐related lncRNA signature was identified in HCC, which could stratify patients into high‐ and low‐risk groups. This immune‐related lncRNA signature was correlated with disease progression and worse survival and was an independent prognostic biomarker. Our immune‐related lncRNA signature was still a powerful tool in predicting survival in each stratum of age, gender, and tumor stage. This signature mediated cell cycle, glycolysis, DNA repair, mammalian target of rapamycin signaling, and immunologic characteristics (i.e., natural killer cells vs. Th1 cells down, etc). This signature was associated with immune cell infiltration (i.e., macrophages M0, Tregs, CD4 memory T cells, and macrophages M1, etc.,) and immune checkpoint blockade (ICB) immunotherapy‐related molecules (i.e., PD‐L1, PD‐L2, and IDO1). Our findings suggested that the immune‐related lncRNA signature had an important value for survival prediction and may have the potential to measure the response to ICB immunotherapy. This signature may guide the selection of the immunotherapy for HCC.

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“…Among these five enlisted lncRNAs, PRKCQ-AS1 acts as a protective player, and its high expression is relevant to longer survival. Interestingly, it has been reported that PRKCQ-AS1 was upregulated in colorectal cancer and associated with reduced survival in colorectal cancer ( Shademan et al, 2019 ), suggesting the complexity and heterogeneity of tumor biology. In contrast, AC046143.1 , AC021054.1 , AC080112.1 , and MIR222HG were associated with poor prognosis.…”

Section: Discussionmentioning

confidence: 99%

A Five Immune-Related lncRNA Signature as a Prognostic Target for Glioblastoma

Sun

Wang

et al. 2021

Front. Mol. Biosci.

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Background: A variety of regulatory approaches including immune modulation have been explored as approaches to either eradicate antitumor response or induce suppressive mechanism in the glioblastoma microenvironment. Thus, the study of immune-related long noncoding RNA (lncRNA) signature is of great value in the diagnosis, treatment, and prognosis of glioblastoma.Methods: Glioblastoma samples with lncRNA sequencing and corresponding clinical data were acquired from the Cancer Genome Atlas (TCGA) database. Immune-lncRNAs co-expression networks were built to identify immune-related lncRNAs via Pearson correlation. Based on the median risk score acquired in the training set, we divided the samples into high- and low-risk groups and demonstrate the survival prediction ability of the immune-related lncRNA signature. Both principal component analysis (PCA) and gene set enrichment analysis (GSEA) were used for immune state analysis.Results: A cohort of 151 glioblastoma samples and 730 immune-related genes were acquired in this study. A five immune-related lncRNA signature (AC046143.1, AC021054.1, AC080112.1, MIR222HG, and PRKCQ-AS1) was identified. Compared with patients in the high-risk group, patients in the low-risk group showed a longer overall survival (OS) in the training, validation, and entire TCGA set (p = 1.931e-05, p = 1.706e-02, and p = 3.397e-06, respectively). Additionally, the survival prediction ability of this lncRNA signature was independent of known clinical factors and molecular features. The area under the ROC curve (AUC) and stratified analyses were further performed to verify its optimal survival predictive potency. Of note, the high-and low-risk groups exhibited significantly distinct immune state according to the PCA and GSEA analyses.Conclusions: Our study proposes that a five immune-related lncRNA signature can be utilized as a latent indicator of prognosis and potential therapeutic approach for glioblastoma.

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Expression profile analysis of two antisense lncRNAs to improve prognosis prediction of colorectal adenocarcinoma

Cited by 21 publications

References 26 publications

Promoter methylation, transcription, and retrotransposition of LINE-1 in colorectal adenomas and adenocarcinomas

Promoter methylation, transcription, and retrotransposition of LINE-1 in colorectal adenomas and adenocarcinomas

Immune‐related long noncoding RNA signature for predicting survival and immune checkpoint blockade in hepatocellular carcinoma

A Five Immune-Related lncRNA Signature as a Prognostic Target for Glioblastoma

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