Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation
Abstract Background Wnt signaling is an evolutionarily conserved developmental pathway that is frequently hyperactivated in cancer. While multiple protein-coding genes regulated by Wnt signaling are known, the functional lncRNAs regulated by Wnt signaling have not been systematically characterized....
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doaj-b3c6a64a96b844899270d2ed76e7be322020-11-25T03:43:27ZengBMCGenome Medicine1756-994X2020-10-0112112210.1186/s13073-020-00788-5Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validationShiyang Liu0Nathan Harmston1Trudy Lee Glaser2Yunka Wong3Zheng Zhong4Babita Madan5David M. Virshup6Enrico Petretto7Program in Cancer and Stem Cell Biology, Duke-NUS Medical SchoolScience Division, Yale-NUS CollegeProgram in Cancer and Stem Cell Biology, Duke-NUS Medical SchoolProgram in Cancer and Stem Cell Biology, Duke-NUS Medical SchoolProgram in Cancer and Stem Cell Biology, Duke-NUS Medical SchoolProgram in Cancer and Stem Cell Biology, Duke-NUS Medical SchoolProgram in Cancer and Stem Cell Biology, Duke-NUS Medical SchoolProgram in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolAbstract Background Wnt signaling is an evolutionarily conserved developmental pathway that is frequently hyperactivated in cancer. While multiple protein-coding genes regulated by Wnt signaling are known, the functional lncRNAs regulated by Wnt signaling have not been systematically characterized. Methods We comprehensively mapped Wnt-regulated lncRNAs from an orthotopic Wnt-addicted pancreatic cancer model and examined the response of lncRNAs to Wnt inhibition between in vivo and in vitro cancer models. We further annotated and characterized these Wnt-regulated lncRNAs using existing genomic classifications (using data from FANTOM5) in the context of Wnt signaling and inferred their role in cancer pathogenesis (using GWAS and expression data from the TCGA). To functionally validate Wnt-regulated lncRNAs, we performed CRISPRi screens to assess their role in cancer cell proliferation both in vivo and in vitro. Results We identified 3633 lncRNAs, of which 1503 were regulated by Wnt signaling in an orthotopic Wnt-addicted pancreatic cancer model. These lncRNAs were much more sensitive to changes in Wnt signaling in xenografts than in cultured cells. Our analysis suggested that Wnt signaling inhibition could influence the co-expression relationship of Wnt-regulated lncRNAs and their eQTL-linked protein-coding genes. Wnt-regulated lncRNAs were also implicated in specific gene networks involved in distinct biological processes that contribute to the pathogenesis of cancers. Consistent with previous genome-wide lncRNA CRISPRi screens, around 1% (13/1503) of the Wnt-regulated lncRNAs were found to modify cancer cell growth in vitro. This included CCAT1 and LINC00263, previously reported to regulate cancer growth. Using an in vivo CRISPRi screen, we doubled the discovery rate, identifying twice as many Wnt-regulated lncRNAs (25/1503) that had a functional effect on cancer cell growth. Conclusions Our study demonstrates the value of studying lncRNA functions in vivo, provides a valuable resource of lncRNAs regulated by Wnt signaling, and establishes a framework for systematic discovery of functional lncRNAs.http://link.springer.com/article/10.1186/s13073-020-00788-5Functional lncRNAsWnt signalingCancerCRISPRi screen |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Shiyang Liu Nathan Harmston Trudy Lee Glaser Yunka Wong Zheng Zhong Babita Madan David M. Virshup Enrico Petretto |
spellingShingle |
Shiyang Liu Nathan Harmston Trudy Lee Glaser Yunka Wong Zheng Zhong Babita Madan David M. Virshup Enrico Petretto Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation Genome Medicine Functional lncRNAs Wnt signaling Cancer CRISPRi screen |
author_facet |
Shiyang Liu Nathan Harmston Trudy Lee Glaser Yunka Wong Zheng Zhong Babita Madan David M. Virshup Enrico Petretto |
author_sort |
Shiyang Liu |
title |
Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation |
title_short |
Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation |
title_full |
Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation |
title_fullStr |
Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation |
title_full_unstemmed |
Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation |
title_sort |
wnt-regulated lncrna discovery enhanced by in vivo identification and crispri functional validation |
publisher |
BMC |
series |
Genome Medicine |
issn |
1756-994X |
publishDate |
2020-10-01 |
description |
Abstract Background Wnt signaling is an evolutionarily conserved developmental pathway that is frequently hyperactivated in cancer. While multiple protein-coding genes regulated by Wnt signaling are known, the functional lncRNAs regulated by Wnt signaling have not been systematically characterized. Methods We comprehensively mapped Wnt-regulated lncRNAs from an orthotopic Wnt-addicted pancreatic cancer model and examined the response of lncRNAs to Wnt inhibition between in vivo and in vitro cancer models. We further annotated and characterized these Wnt-regulated lncRNAs using existing genomic classifications (using data from FANTOM5) in the context of Wnt signaling and inferred their role in cancer pathogenesis (using GWAS and expression data from the TCGA). To functionally validate Wnt-regulated lncRNAs, we performed CRISPRi screens to assess their role in cancer cell proliferation both in vivo and in vitro. Results We identified 3633 lncRNAs, of which 1503 were regulated by Wnt signaling in an orthotopic Wnt-addicted pancreatic cancer model. These lncRNAs were much more sensitive to changes in Wnt signaling in xenografts than in cultured cells. Our analysis suggested that Wnt signaling inhibition could influence the co-expression relationship of Wnt-regulated lncRNAs and their eQTL-linked protein-coding genes. Wnt-regulated lncRNAs were also implicated in specific gene networks involved in distinct biological processes that contribute to the pathogenesis of cancers. Consistent with previous genome-wide lncRNA CRISPRi screens, around 1% (13/1503) of the Wnt-regulated lncRNAs were found to modify cancer cell growth in vitro. This included CCAT1 and LINC00263, previously reported to regulate cancer growth. Using an in vivo CRISPRi screen, we doubled the discovery rate, identifying twice as many Wnt-regulated lncRNAs (25/1503) that had a functional effect on cancer cell growth. Conclusions Our study demonstrates the value of studying lncRNA functions in vivo, provides a valuable resource of lncRNAs regulated by Wnt signaling, and establishes a framework for systematic discovery of functional lncRNAs. |
topic |
Functional lncRNAs Wnt signaling Cancer CRISPRi screen |
url |
http://link.springer.com/article/10.1186/s13073-020-00788-5 |
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