CRISPR/dCAS9-mediated DNA demethylation screen identifies functional epigenetic determinants of colorectal cancer
Abstract Background Promoter hypermethylation of tumour suppressor genes is frequently observed during the malignant transformation of colorectal cancer (CRC). However, whether this epigenetic mechanism is functional in cancer or is a mere consequence of the carcinogenic process remains to be elucid...
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | Clinical Epigenetics |
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| Online Access: | https://doi.org/10.1186/s13148-023-01546-1 |
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| author | Juan Ramón Tejedor Alfonso Peñarroya Javier Gancedo-Verdejo Pablo Santamarina-Ojeda Raúl F. Pérez Sara López-Tamargo Ana Díez-Borge Juan J. Alba-Linares Nerea González-del-Rey Rocío G. Urdinguio Cristina Mangas Annalisa Roberti Virginia López Teresa Morales-Ruiz Rafael R. Ariza Teresa Roldán-Arjona Mónica Meijón Luis Valledor María Jesús Cañal Daniel Fernández-Martínez María Fernández-Hevia Paula Jiménez-Fonseca Luis J. García-Flórez Agustín F. Fernández Mario F. Fraga |
| author_facet | Juan Ramón Tejedor Alfonso Peñarroya Javier Gancedo-Verdejo Pablo Santamarina-Ojeda Raúl F. Pérez Sara López-Tamargo Ana Díez-Borge Juan J. Alba-Linares Nerea González-del-Rey Rocío G. Urdinguio Cristina Mangas Annalisa Roberti Virginia López Teresa Morales-Ruiz Rafael R. Ariza Teresa Roldán-Arjona Mónica Meijón Luis Valledor María Jesús Cañal Daniel Fernández-Martínez María Fernández-Hevia Paula Jiménez-Fonseca Luis J. García-Flórez Agustín F. Fernández Mario F. Fraga |
| author_sort | Juan Ramón Tejedor |
| collection | DOAJ |
| description | Abstract Background Promoter hypermethylation of tumour suppressor genes is frequently observed during the malignant transformation of colorectal cancer (CRC). However, whether this epigenetic mechanism is functional in cancer or is a mere consequence of the carcinogenic process remains to be elucidated. Results In this work, we performed an integrative multi-omic approach to identify gene candidates with strong correlations between DNA methylation and gene expression in human CRC samples and a set of 8 colon cancer cell lines. As a proof of concept, we combined recent CRISPR-Cas9 epigenome editing tools (dCas9-TET1, dCas9-TET-IM) with a customized arrayed gRNA library to modulate the DNA methylation status of 56 promoters previously linked with strong epigenetic repression in CRC, and we monitored the potential functional consequences of this DNA methylation loss by means of a high-content cell proliferation screen. Overall, the epigenetic modulation of most of these DNA methylated regions had a mild impact on the reactivation of gene expression and on the viability of cancer cells. Interestingly, we found that epigenetic reactivation of RSPO2 in the tumour context was associated with a significant impairment in cell proliferation in p53−/− cancer cell lines, and further validation with human samples demonstrated that the epigenetic silencing of RSPO2 is a mid-late event in the adenoma to carcinoma sequence. Conclusions These results highlight the potential role of DNA methylation as a driver mechanism of CRC and paves the way for the identification of novel therapeutic windows based on the epigenetic reactivation of certain tumour suppressor genes. |
| first_indexed | 2024-03-10T17:37:43Z |
| format | Article |
| id | doaj.art-95cb022c2afa458ba4a52e0c37ea095b |
| institution | Directory Open Access Journal |
| issn | 1868-7083 |
| language | English |
| last_indexed | 2024-03-10T17:37:43Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Clinical Epigenetics |
| spelling | doaj.art-95cb022c2afa458ba4a52e0c37ea095b2023-11-20T09:48:20ZengBMCClinical Epigenetics1868-70832023-08-0115111710.1186/s13148-023-01546-1CRISPR/dCAS9-mediated DNA demethylation screen identifies functional epigenetic determinants of colorectal cancerJuan Ramón Tejedor0Alfonso Peñarroya1Javier Gancedo-Verdejo2Pablo Santamarina-Ojeda3Raúl F. Pérez4Sara López-Tamargo5Ana Díez-Borge6Juan J. Alba-Linares7Nerea González-del-Rey8Rocío G. Urdinguio9Cristina Mangas10Annalisa Roberti11Virginia López12Teresa Morales-Ruiz13Rafael R. Ariza14Teresa Roldán-Arjona15Mónica Meijón16Luis Valledor17María Jesús Cañal18Daniel Fernández-Martínez19María Fernández-Hevia20Paula Jiménez-Fonseca21Luis J. García-Flórez22Agustín F. Fernández23Mario F. Fraga24Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC)Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC)Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC)Health Research Institute of the Principality of Asturias (ISPA)Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC)Health Research Institute of the Principality of Asturias (ISPA)Health Research Institute of the Principality of Asturias (ISPA)Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC)Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of OviedoHealth Research Institute of the Principality of Asturias (ISPA)Health Research Institute of the Principality of Asturias (ISPA)Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC)Health Research Institute of the Principality of Asturias (ISPA)Maimónides Biomedical Research Institute of Córdoba (IMIBIC)Maimónides Biomedical Research Institute of Córdoba (IMIBIC)Maimónides Biomedical Research Institute of Córdoba (IMIBIC)Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of OviedoDepartment of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of OviedoDepartment of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of OviedoHealth Research Institute of the Principality of Asturias (ISPA)Health Research Institute of the Principality of Asturias (ISPA)Health Research Institute of the Principality of Asturias (ISPA)Health Research Institute of the Principality of Asturias (ISPA)Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC)Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC)Abstract Background Promoter hypermethylation of tumour suppressor genes is frequently observed during the malignant transformation of colorectal cancer (CRC). However, whether this epigenetic mechanism is functional in cancer or is a mere consequence of the carcinogenic process remains to be elucidated. Results In this work, we performed an integrative multi-omic approach to identify gene candidates with strong correlations between DNA methylation and gene expression in human CRC samples and a set of 8 colon cancer cell lines. As a proof of concept, we combined recent CRISPR-Cas9 epigenome editing tools (dCas9-TET1, dCas9-TET-IM) with a customized arrayed gRNA library to modulate the DNA methylation status of 56 promoters previously linked with strong epigenetic repression in CRC, and we monitored the potential functional consequences of this DNA methylation loss by means of a high-content cell proliferation screen. Overall, the epigenetic modulation of most of these DNA methylated regions had a mild impact on the reactivation of gene expression and on the viability of cancer cells. Interestingly, we found that epigenetic reactivation of RSPO2 in the tumour context was associated with a significant impairment in cell proliferation in p53−/− cancer cell lines, and further validation with human samples demonstrated that the epigenetic silencing of RSPO2 is a mid-late event in the adenoma to carcinoma sequence. Conclusions These results highlight the potential role of DNA methylation as a driver mechanism of CRC and paves the way for the identification of novel therapeutic windows based on the epigenetic reactivation of certain tumour suppressor genes.https://doi.org/10.1186/s13148-023-01546-1DNA methylationGene expressionEpigeneticsTumour suppressor geneCRISPR screenColorectal cancer |
| spellingShingle | Juan Ramón Tejedor Alfonso Peñarroya Javier Gancedo-Verdejo Pablo Santamarina-Ojeda Raúl F. Pérez Sara López-Tamargo Ana Díez-Borge Juan J. Alba-Linares Nerea González-del-Rey Rocío G. Urdinguio Cristina Mangas Annalisa Roberti Virginia López Teresa Morales-Ruiz Rafael R. Ariza Teresa Roldán-Arjona Mónica Meijón Luis Valledor María Jesús Cañal Daniel Fernández-Martínez María Fernández-Hevia Paula Jiménez-Fonseca Luis J. García-Flórez Agustín F. Fernández Mario F. Fraga CRISPR/dCAS9-mediated DNA demethylation screen identifies functional epigenetic determinants of colorectal cancer Clinical Epigenetics DNA methylation Gene expression Epigenetics Tumour suppressor gene CRISPR screen Colorectal cancer |
| title | CRISPR/dCAS9-mediated DNA demethylation screen identifies functional epigenetic determinants of colorectal cancer |
| title_full | CRISPR/dCAS9-mediated DNA demethylation screen identifies functional epigenetic determinants of colorectal cancer |
| title_fullStr | CRISPR/dCAS9-mediated DNA demethylation screen identifies functional epigenetic determinants of colorectal cancer |
| title_full_unstemmed | CRISPR/dCAS9-mediated DNA demethylation screen identifies functional epigenetic determinants of colorectal cancer |
| title_short | CRISPR/dCAS9-mediated DNA demethylation screen identifies functional epigenetic determinants of colorectal cancer |
| title_sort | crispr dcas9 mediated dna demethylation screen identifies functional epigenetic determinants of colorectal cancer |
| topic | DNA methylation Gene expression Epigenetics Tumour suppressor gene CRISPR screen Colorectal cancer |
| url | https://doi.org/10.1186/s13148-023-01546-1 |
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