Integrative RNA-Seq and H3 Trimethylation ChIP-Seq Analysis of Human Lung Cancer Cells Isolated by Laser-Microdissection
Our previous integrative study in gastric cancer discovered cryptic promoter activation events that drive the expression of important developmental genes. However, it was unclear if such cancer-associated epigenetic changes occurred in cancer cells or other cell types in bulk tissue samples. An inte...
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MDPI AG
2021-04-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/13/7/1719 |
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| author | Quang Ong Shingo Sakashita Emi Hanawa Naomi Kaneko Masayuki Noguchi Masafumi Muratani |
| author_facet | Quang Ong Shingo Sakashita Emi Hanawa Naomi Kaneko Masayuki Noguchi Masafumi Muratani |
| author_sort | Quang Ong |
| collection | DOAJ |
| description | Our previous integrative study in gastric cancer discovered cryptic promoter activation events that drive the expression of important developmental genes. However, it was unclear if such cancer-associated epigenetic changes occurred in cancer cells or other cell types in bulk tissue samples. An integrative analysis consisting of RNA-Seq and H3K4me3 ChIP-Seq was used. This workflow was applied to a set of matched normal lung tissues and non-small cell lung cancer (NSCLC) tissues, for which the stroma and tumor cell parts could be isolated by laser-microdissection microscopy (LMD). RNA-Seq analysis showed subtype-specific differential expressed genes and enriched pathways in NSCLC. ChIP-Seq analysis results suggested that the proximal altered H3K4me3 regions were located at differentially expressed genes involved in cancer-related pathways, while altered distal H3K4me3 regions were annotated with enhancer activity of cancer regulatory genes. Interestingly, integration with ENCODE data revealed that proximal tumor-gained promoters were associated with EZH2 and SUZ12 occupancies, which are the core components of polycomb repressive complex 2 (PRC2). This study used LMD on clinical samples for an integrative analysis to overcome the tissue heterogeneity problem in cancer research. The results also contribute to the overall understanding of genetic and epigenetic dysregulation of lung malignancy. |
| first_indexed | 2024-03-10T12:35:51Z |
| format | Article |
| id | doaj.art-817bb3cf216449cc9996e47478079bd6 |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-10T12:35:51Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-817bb3cf216449cc9996e47478079bd62023-11-21T14:16:01ZengMDPI AGCancers2072-66942021-04-01137171910.3390/cancers13071719Integrative RNA-Seq and H3 Trimethylation ChIP-Seq Analysis of Human Lung Cancer Cells Isolated by Laser-MicrodissectionQuang Ong0Shingo Sakashita1Emi Hanawa2Naomi Kaneko3Masayuki Noguchi4Masafumi Muratani5Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, JapanDepartment of Diagnostic Pathology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, JapanDepartment of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, JapanDepartment of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, JapanDepartment of Diagnostic Pathology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, JapanDepartment of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, JapanOur previous integrative study in gastric cancer discovered cryptic promoter activation events that drive the expression of important developmental genes. However, it was unclear if such cancer-associated epigenetic changes occurred in cancer cells or other cell types in bulk tissue samples. An integrative analysis consisting of RNA-Seq and H3K4me3 ChIP-Seq was used. This workflow was applied to a set of matched normal lung tissues and non-small cell lung cancer (NSCLC) tissues, for which the stroma and tumor cell parts could be isolated by laser-microdissection microscopy (LMD). RNA-Seq analysis showed subtype-specific differential expressed genes and enriched pathways in NSCLC. ChIP-Seq analysis results suggested that the proximal altered H3K4me3 regions were located at differentially expressed genes involved in cancer-related pathways, while altered distal H3K4me3 regions were annotated with enhancer activity of cancer regulatory genes. Interestingly, integration with ENCODE data revealed that proximal tumor-gained promoters were associated with EZH2 and SUZ12 occupancies, which are the core components of polycomb repressive complex 2 (PRC2). This study used LMD on clinical samples for an integrative analysis to overcome the tissue heterogeneity problem in cancer research. The results also contribute to the overall understanding of genetic and epigenetic dysregulation of lung malignancy.https://www.mdpi.com/2072-6694/13/7/1719RNA-SeqChIP-SeqNSCLCH3K4me3laser-microdissectionlung cancer |
| spellingShingle | Quang Ong Shingo Sakashita Emi Hanawa Naomi Kaneko Masayuki Noguchi Masafumi Muratani Integrative RNA-Seq and H3 Trimethylation ChIP-Seq Analysis of Human Lung Cancer Cells Isolated by Laser-Microdissection Cancers RNA-Seq ChIP-Seq NSCLC H3K4me3 laser-microdissection lung cancer |
| title | Integrative RNA-Seq and H3 Trimethylation ChIP-Seq Analysis of Human Lung Cancer Cells Isolated by Laser-Microdissection |
| title_full | Integrative RNA-Seq and H3 Trimethylation ChIP-Seq Analysis of Human Lung Cancer Cells Isolated by Laser-Microdissection |
| title_fullStr | Integrative RNA-Seq and H3 Trimethylation ChIP-Seq Analysis of Human Lung Cancer Cells Isolated by Laser-Microdissection |
| title_full_unstemmed | Integrative RNA-Seq and H3 Trimethylation ChIP-Seq Analysis of Human Lung Cancer Cells Isolated by Laser-Microdissection |
| title_short | Integrative RNA-Seq and H3 Trimethylation ChIP-Seq Analysis of Human Lung Cancer Cells Isolated by Laser-Microdissection |
| title_sort | integrative rna seq and h3 trimethylation chip seq analysis of human lung cancer cells isolated by laser microdissection |
| topic | RNA-Seq ChIP-Seq NSCLC H3K4me3 laser-microdissection lung cancer |
| url | https://www.mdpi.com/2072-6694/13/7/1719 |
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