Global DNA methylation reflects spatial heterogeneity and molecular evolution of lung adenocarcinomas
Steffen Dietz
Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
German Cancer Consortium (DKTK), Heidelberg, Germany
Medical Faculty Heidelberg, University of Heidelberg, Heidelberg, Germany
Search for more papers by this authorAviezer Lifshitz
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
Search for more papers by this authorDaniel Kazdal
Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
German Cancer Consortium (DKTK), Heidelberg, Germany
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
Search for more papers by this authorAlexander Harms
Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
German Cancer Consortium (DKTK), Heidelberg, Germany
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
Search for more papers by this authorVolker Endris
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
Search for more papers by this authorHauke Winter
Department of Thoracic Surgery, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
Search for more papers by this authorAlbrecht Stenzinger
German Cancer Consortium (DKTK), Heidelberg, Germany
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
Search for more papers by this authorArne Warth
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
Institute of Pathology, Cytopathology, and Molecular Pathology, ÜGP Gießen, Wetzlar, Limburg, Germany
Search for more papers by this authorMartin Sill
Division of Pediatric Neurooncology, Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ) and German Cancer Research Center (DKFZ), Heidelberg, Germany
Search for more papers by this authorAmos Tanay
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
Search for more papers by this authorCorresponding Author
Holger Sültmann
Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
German Cancer Consortium (DKTK), Heidelberg, Germany
Correspondence to: Prof. Dr. rer. nat. Holger Sültmann Division of Cancer Genome Research Im Neuenheimer Feld 460 D-69120 Heidelberg, Germany, E-mail: [email protected]; Tel.: +49 6221 56-5934; Fax: +49 6221 56-5382Search for more papers by this authorSteffen Dietz
Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
German Cancer Consortium (DKTK), Heidelberg, Germany
Medical Faculty Heidelberg, University of Heidelberg, Heidelberg, Germany
Search for more papers by this authorAviezer Lifshitz
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
Search for more papers by this authorDaniel Kazdal
Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
German Cancer Consortium (DKTK), Heidelberg, Germany
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
Search for more papers by this authorAlexander Harms
Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
German Cancer Consortium (DKTK), Heidelberg, Germany
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
Search for more papers by this authorVolker Endris
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
Search for more papers by this authorHauke Winter
Department of Thoracic Surgery, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
Search for more papers by this authorAlbrecht Stenzinger
German Cancer Consortium (DKTK), Heidelberg, Germany
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
Search for more papers by this authorArne Warth
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
Institute of Pathology, Cytopathology, and Molecular Pathology, ÜGP Gießen, Wetzlar, Limburg, Germany
Search for more papers by this authorMartin Sill
Division of Pediatric Neurooncology, Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ) and German Cancer Research Center (DKFZ), Heidelberg, Germany
Search for more papers by this authorAmos Tanay
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
Search for more papers by this authorCorresponding Author
Holger Sültmann
Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
German Cancer Consortium (DKTK), Heidelberg, Germany
Correspondence to: Prof. Dr. rer. nat. Holger Sültmann Division of Cancer Genome Research Im Neuenheimer Feld 460 D-69120 Heidelberg, Germany, E-mail: [email protected]; Tel.: +49 6221 56-5934; Fax: +49 6221 56-5382Search for more papers by this authorAbstract
Lung adenocarcinoma (ADC) is the most prevalent subtype of lung cancer and characterized by considerable morphological and mutational heterogeneity. However, little is known about the epigenomic intratumor variability between spatially separated histological growth patterns of ADC. In order to reconstruct the clonal evolution of histomorphological patterns, we performed global DNA methylation profiling of 27 primary tumor regions, seven matched normal tissues and six lymph node metastases from seven ADC cases. Additionally, we investigated the methylation data from 369 samples of the TCGA ADC cohort. All regions showed varying degrees of methylation changes between segments of different, but also of the same growth patterns. Similarly, copy number variations were seen between spatially distinct segments of each patient. Hierarchical clustering of promoter methylation revealed extensive heterogeneity within and between the cases. Intratumor DNA methylation heterogeneity demonstrated a branched clonal evolution of ADC regions driven by genomic instability with subclonal copy number changes. Notably, methylation profiles within tumors were not more similar to each other than to those from other individuals. In two cases, different tumor regions of the same individuals were represented in distant clusters of the TCGA cohort, illustrating the extensive epigenomic intratumor heterogeneity of ADCs. We found no evidence for the lymph node metastases to be derived from a common growth pattern. Instead, they had evolved early and separately from a particular pattern in each primary tumor. Our results suggest that extensive variation of epigenomic features contributes to the molecular and phenotypic heterogeneity of primary ADCs and lymph node metastases.
Abstract
What's new?
Non-small cell lung cancer is a tumor with extensive histological heterogeneity caused by spatial and temporal genomic changes, posing major challenges for the treatment and prognosis of patients with lung adenocarcinoma. To date, however, little is known about epigenomic intratumor variability. In our study, the authors investigate the spatial variations of somatic DNA methylation and copy number aberrations in comparison with histological growth patterns of seven resected lung adenocarcinomas and six corresponding lymph node metastases. The results suggest that epigenomic variation contributes considerably to the molecular and phenotypic heterogeneity and evolution of lung adenocarcinomas and lymph node metastases.
Supporting Information
| Filename | Description |
|---|---|
| ijc31939-sup-0001-FigS1.tifTIFF image, 507.5 KB | Figure S1: Predominant histological growth patterns of all segments of the seven cases included for methylation profiling. Segments selected for methylation analysis are indicated by red frames. Histologies are color coded. L1 = N1 lymph node metastasis, L2 = N2 lymph node metastasis, N = non-neoplastic tissue. |
| ijc31939-sup-0002-FigS2.tifTIFF image, 489.8 KB | Figure S2: Global somatic methylation depends on genomic CG content. Global alterations of DNA methylation levels in each tumor segment normalized to the average methylation of non-neoplastic tissues are compared to the GC content. Histologies are color coded. |
| ijc31939-sup-0003-FigS3.tifTIFF image, 687 KB | Figure S3: Scatter plots comparing average methylation levels of non-neoplastic tissues against the methylation levels of the tumor segments. Color indicates density from blue (low) to red (high). |
| ijc31939-sup-0004-FigS4.tifTIFF image, 979.9 KB | Figure S4: Unsupervised hierarchical clustering of methylation patterns of regulatory regions (A) in putative enhancer sites (n = 4,977, rows) of all malignant segments and the average methylation of non-neoplastic tissues (columns), and (B) in promoter-associated sites (n = 1,502, rows) of all malignant segments and the average methylation of the corresponding non-neoplastic tissues (columns). |
| ijc31939-sup-0005-FigS5.tifTIFF image, 2.7 MB | Figure S5: Hierarchical clustering of methylation patterns of enhancer-associated sites (n = 3,301) of all segments from the seven cases and 369 cases (366 tumor samples, 38 normal samples) of the TCGA lung ADC cohort. Columns show tumor regions and rows display the DNA methylation status. Blue indicates low, and yellow represents high methylation level (from 0% to 100%). Cases and histologies are color coded as in Figure 2. |
| ijc31939-sup-0006-FigS6.tifTIFF image, 789.3 KB | Figure S6: Differential methylation analysis. (A) Volcano plot showing the mean beta value difference (median tumor—median non-neoplastic tissues; x-axis;) versus the log10 transformed p values for each CpG (y-axis). Significantly hypomethylated CpGs are marked in blue, significantly hypermethylated CpGs are highlighted in red. (B) Comparison of methylation levels of tumor and non-neoplastic segments at differentially methylated (Benjamini-Hochberg corrected p < 0.05; mean β value >0.15) CpGs in promoter regions of selected genes. (C) Differential methylation levels of tumor and non-neoplastic samples of promoter- and transcription start site-associated CpGs (corrections as in (C)). (D) Methylation levels of all CpGs related to miR-21, and miR-124-2, respectively. |
| ijc31939-sup-0007-TableS1.xlsxExcel 2007 spreadsheet , 3.9 MB | Table S1: 10,000 probes with the greatest intratumoral methylation variance. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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