New research using comprehensive bioinformatics techniques have identified long non-coding RNAs (lncRNA) as biomarkers for cancer diagnosis and treatment.
The study, published in Genomics, utilised the cancer data set in The Cancer Genome Atlas (TCGA) and constructed a global map of long non-coding RNA regulated by abnormal DNA methylation across 10 cancers.
Using the map, researchers from Capital Medical University in Beijing identified biomarkers that could predict the survival of cancer and offer diagnosing and treatment targets.
Long non-coding RNA
Long non-coding RNAs (lncRNAs) are non-coding RNAs with more than 200 nucleotides and complex structures. Compared with other non-coding RNAs, lncRNA has stronger tissue specificity and vitality. Its main functions include mediating chromatin modification, transcription and post-transcriptional regulation.
LncRNAs are related to the occurrence and development of many diseases including cancer. Changes in the expression of lncRNA may help cancer cells acquire a proliferation advantage, replicate and activate metastasis.
“Although the function and expression of lncRNA are closely related to cancer, the understanding of how the molecular mechanisms affect cancer progression is still limited, especially the potential pathogenic mechanism of lncRNA affected by abnormal DNA methylation,” the authors noted.
DNA methylation is an important epigenetic mechanism. It plays a role in stabilising the cell genome and in cell growth. Previous studies have shown that the development of cancer is accompanied by abnormal DNA methylation.
How lncRNA regulated by abnormal DNA methylation (ADM-lncRNA) participates in cancer progression has remained unclear until this study.
lncRNAs as cancer biomarkers
The Cancer Genome Atlas (TCGA) project has preserved multi-omics data for up to 33 cancers.
The researchers revealed different DNA methylation regulation patterns between cancers and obtained 2,371 lncRNAs whose expressions were regulated by abnormal DNA methylation. 6 of these had pan-cancer characteristics.
Next, they constructed a co-expression network in 10 cancers to explore the molecular mechanism of ADM-lncRNA in pan-cancer. They found that the distribution characteristics of pan-cancer ADM-lncRNA-mRNA co-expression pairs were highly correlated with cancer heterogeneity.
This indicates that these pan-cancerous co-expression pairs may be related to cancer cell proliferation and resistance to programmed cell death.
This study utilised bioinformatics analysis and further studies are required using effective biological experimental verification. Nevertheless, the researchers identified co-expression pairs that have the potential to predict the survival of cancer patients, providing valuable resources for the development of cancer biomarkers.
“Due to the reversibility of DNA methylation, ADM-lncRNA may be used as a new type of cell regulator and has the potential to become a precise target for cancer diagnosis and treatment,” the authors proposed.
Written by Poppy Jayne Morgan, Front Line Genomics
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