eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways
Curation statements for this article:-
Curated by eLife
Evaluation Summary:
In this manuscript, the authors identify enhancer-associated (e)RNAs that are specifically associated with esophageal adenocarcinoma. Based on combining the data with analyses of patient gene expression data and epigenetic data from cell lines, they conclude that eRNAs are markers of enhancers relevant to the transition from Barrett's esophagus to cancer. This work provides new insights into the epigenetic alterations that occur in cancer progression, and it will be of interest to the cancer and epigenetics fields.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (eLife)
- Cancer Biology (eLife)
Abstract
Cancer is driven by both genetic and epigenetic changes that impact on gene expression profiles and the resulting tumourigenic phenotype. Enhancers are transcriptional regulatory elements that are key to our understanding of how this rewiring of gene expression is achieved in cancer cells. Here, we have harnessed the power of RNA-seq data from hundreds of patients with oesophageal adenocarcinoma (OAC) or its precursor state Barrett’s oesophagus coupled with open chromatin maps to identify potential enhancer RNAs and their associated enhancer regions in this cancer. We identify ~1000 OAC-specific enhancers and use these data to uncover new cellular pathways that are operational in OAC. Among these are enhancers for JUP , MYBL2 , and CCNE1 , and we show that their activity is required for cancer cell viability. We also demonstrate the clinical utility of our dataset for identifying disease stage and patient prognosis. Our data therefore identify an important set of regulatory elements that enhance our molecular understanding of OAC and point to potential new therapeutic directions.
Article activity feed
-
-
Evaluation Summary:
In this manuscript, the authors identify enhancer-associated (e)RNAs that are specifically associated with esophageal adenocarcinoma. Based on combining the data with analyses of patient gene expression data and epigenetic data from cell lines, they conclude that eRNAs are markers of enhancers relevant to the transition from Barrett's esophagus to cancer. This work provides new insights into the epigenetic alterations that occur in cancer progression, and it will be of interest to the cancer and epigenetics fields.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)
-
Reviewer #1 (Public Review):
Ahmed et al. examine the changes in the enhancer landscape that may contribute to the transition from Barrett's oesophagus (BO) to oesophageal adenocarcinoma (OAC), building upon their past works looking at the chromatin changes within this transition. They identified a repertoire of eRNA regions that display differential expression between OAC and BO, validating their association to enhancers using H3K27ac levels, CUT&TAG, and KAS-seq. The authors look further into the target genes and regulatory TFs that may define eRNA levels, finding several TFs - AP1, KLF5, CTCF, and HNF1 - that have previously been implicated in OAC and confirming that sets of eRNA target genes were downregulated upon depletion of these TFs. Ahmed et al. also showed that eRNA target genes were relevant to OAC phenotypes, akin to that …
Reviewer #1 (Public Review):
Ahmed et al. examine the changes in the enhancer landscape that may contribute to the transition from Barrett's oesophagus (BO) to oesophageal adenocarcinoma (OAC), building upon their past works looking at the chromatin changes within this transition. They identified a repertoire of eRNA regions that display differential expression between OAC and BO, validating their association to enhancers using H3K27ac levels, CUT&TAG, and KAS-seq. The authors look further into the target genes and regulatory TFs that may define eRNA levels, finding several TFs - AP1, KLF5, CTCF, and HNF1 - that have previously been implicated in OAC and confirming that sets of eRNA target genes were downregulated upon depletion of these TFs. Ahmed et al. also showed that eRNA target genes were relevant to OAC phenotypes, akin to that of DEGs in whole RNA-seq datasets. The authors lastly validate the activity of certain eRNAs targeting JUP, MYBL2, and CCNE1 using functional methods to confirm enhancer activity and effects on cell viability, as well as clinical features such as the age of diagnosis and survival time.
The landscape of eRNA activity seems to be well validated. However, deeper analyses to support the relevance of the function of key eRNAs, their specificity in regulating target genes, and the interaction with other OAC features would further support these findings.
-
Reviewer #2 (Public Review):
Enhancer RNAs (eRNAs) are small non-coding RNAs transcribed from distal gene regulatory regions and are associated with the gene activation function of these regions. The authors set out to determine if a comparison of the level of eRNAs in large existing data sets from oesophageal adenocarcinoma and the precursor state, Barrett's oesophagus could differentiate these different states, and can point the way to new regulatory functions. The authors successfully used eRNAs to differentiate oesophageal adenocarcinoma from Barrett's oesophagus. Further, they utilized rigorous bioinformatic analyses to demonstrate that regions with eRNAs are active enhancer elements. They clearly demonstrate that eRNA mapping can identify both transcription factor binding sites and target genes that are known to function …
Reviewer #2 (Public Review):
Enhancer RNAs (eRNAs) are small non-coding RNAs transcribed from distal gene regulatory regions and are associated with the gene activation function of these regions. The authors set out to determine if a comparison of the level of eRNAs in large existing data sets from oesophageal adenocarcinoma and the precursor state, Barrett's oesophagus could differentiate these different states, and can point the way to new regulatory functions. The authors successfully used eRNAs to differentiate oesophageal adenocarcinoma from Barrett's oesophagus. Further, they utilized rigorous bioinformatic analyses to demonstrate that regions with eRNAs are active enhancer elements. They clearly demonstrate that eRNA mapping can identify both transcription factor binding sites and target genes that are known to function specifically in oesophageal adenocarcinoma. Several genes associated with eRNA regions were shown to be important for oesophageal adenocarcinoma cell growth. While this approach was successful, the benefit of eRNA identification compared to the simpler comparison of steady-state mRNA levels remains unclear. It is not clear if there is relevance to a cancer-specific eRNA that is associated with a gene for which the mRNA expression is not cancer-specific. The approach used in the manuscript could be very useful for identifying new transcription factor binding motifs that point to important new mechanisms, but in this case, none of the motifs identified were novel. However, this work could point the way for this type of analysis in other cancer types where motif identification lags.
-
Reviewer #3 (Public Review):
This study uses RNA-seq data sets from pre-cancerous Barrett's Oesophagus (BO) and Oesophageal adenocarcinoma (OAC) patients to identify enhancer-associated (e)RNAs that are specifically associated with the transformed OAC state. Integrative genomics and functional analyses using patient data and data from an OAC-derived cell line provide evidence that eRNA-producing regions are bone fide enhancers driving the expression of genes relevant for AOC tumour biology. These analyses defined a 6-gene signature that shows a strong association with the overall survival of AOC patients but did not compare the clinical value of this signature with signatures based on genes differentially expressed in BO and OAC.
The strength of this study lies in using patient RNA-seq data to identify eRNAs and enhancers unbiased …
Reviewer #3 (Public Review):
This study uses RNA-seq data sets from pre-cancerous Barrett's Oesophagus (BO) and Oesophageal adenocarcinoma (OAC) patients to identify enhancer-associated (e)RNAs that are specifically associated with the transformed OAC state. Integrative genomics and functional analyses using patient data and data from an OAC-derived cell line provide evidence that eRNA-producing regions are bone fide enhancers driving the expression of genes relevant for AOC tumour biology. These analyses defined a 6-gene signature that shows a strong association with the overall survival of AOC patients but did not compare the clinical value of this signature with signatures based on genes differentially expressed in BO and OAC.
The strength of this study lies in using patient RNA-seq data to identify eRNAs and enhancers unbiased pertinent to AOC tumour biology. General application of this approach to other tumours should be possible but may be limited by the availability of high-quality RNA-seq data sets and tumour purity. Nevertheless, this novel approach provided novel insights into AOC biology.
-
