Noncoding RNA Drug Target for Colon Cancer Discovered

     Long noncoding RNAs (lncRNAs) are, as the name suggests, long transcripts of RNA that do not code for proteins, but have been found to regulate a wide range of cell functions. Scientists at Case Western Reserve School of Medicine have now discovered that one lncRNA, designated lincDUSP, may play a role in initiating colon cancer and promoting disease progression, and so represent a novel target for drug development.

The team found that lincDUSP was overexpressed in nearly every human colon cancer sample examined. Laboratory tests then showed that the characteristic unrestricted growth of human tumor-derived colon cancer lines stopped when lincDUSP was deleted, and the cells began to replicate at normal rates.

“Our work demonstrates that not only protein-coding genes but also noncoding genes contribute to colon cancer progression,” comments Ahmad Khalil, Ph.D., assistant professor of genetic and genome sciences at Case Western Reserve University School of Medicine. “lincRNAs could be exploited as direct drug targets in this and other human diseases.” Dr. Khalil, who is also a member of the Case Comprehensive Cancer Center, is senior author of the researchers’ published work in Scientific Reports, which is entitled “Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis.”

lncRNAs are RNA transcripts of more than 200 nucleotides in length that have no protein coding function. Research indicates that they do, however, regulate cellular processes, including development and differentiation, cell cycle progression, and apoptosis, the researchers note. “Thus far, lncRNAs have been shown to regulate gene expression at both the transcriptional and post-transcriptional levels by a variety of mechanisms.”

Interestingly, studies by the Case Western team and others have shown that lncRNAs are dysregulated in cancer, and so could “potentially affect tumor initiation and progression.” In a study designed to identify putative oncogenic lncRNAs in colon cancer, the researchers first examined RNA sequencing data for 22 colon tumors and adjacent normal colon tumors, held in The Cancer Genome Atlas (TCGA) database. Initial data analyses showed that about 200 lncRNAs were differentially expressed in normal colon tissue and colon tumors. Of the 20 lncRNAs with the greatest differential expression levels, one in particular, lincDUSP, was overexpressed in 20 out of the 22 of TCGA database samples, with some of the tumors expressing more than 15 times the normal amount of lincDUSP. Analysis of an independent cohort of normal colon tissues and patient-derived colon tumor cell lines confirmed the initial findings, and demonstrated that lincDUSP was overexpressed in 12/21 of the analyzed patient-derived tumor cell lines.

To test whether lincDUSP might have have oncogenic activity, the team genetically depleted lincDUSP in two patient-derived colon tumor cell lines that otherwise expressed the lncRNA at high levels. “Strikingly,” the authors comment, lincDUSP knockdown led to a significant decrease in cell proliferation within just 24 hours, and also sensitized the cells to doxorubicin-induced apoptosis. Lack of lincDUSP effectively increased the cell’s susceptibility to cellular checkpoints that regulate cellular growth, and the cells underwent apoptosis when subjected to DNA damage. A comparison of gene expression in lincDUSP-expressing colon cancer cells and lincDUSP knockdown cells found that deleting the RNA affected the expression of more than 800 genes, with these genetic studies further indicating that lincDUSP may be involved in regulating DNA damage response and/or cell cycle progression.

Interestingly, the results from chromatin-binding experiments suggested that lincDUSP might mediate long-range chromatin looping. “Notably, lincDUSP ChIRP-seq showed chromatin occupancy near EXO1, PCNA, and RFC3, which are known to be involved in replication-associated DNA repair,” the authors point out. “Analysis of gene expression changes and lincDUSP chromatin occupancy suggest that lincDUSP directly regulates expression of key genes involved in cell cycle progression and DNA replication-associated repair.”

Further examination of the effects of lincDUSP knockdown on cell cycle and DNA damage response provided further evidence pointing to a role for the RNA in “dysregulation of the replication-associated DNA repair response in colon cancer.”

The authors suggest that their findings add to the growing body of evidence demonstrating what they call “a clear involvement” of lncRNAs in tumorigenesis and metastasis. “These lncRNAs could be exploited as biomarkers and/or therapeutic targets in various cancers, and may result in fewer side effects due to their cell-type specific expression,” they write “Taken together, these results demonstrate a key role of lincDUSP in the regulation of important pathways in colon cancer.…The identification of lncRNAs, such as lincDUSP, with oncogenic functions in human cancers is a key first step toward exploring the feasibility of targeting these RNAs using small molecules.”

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