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Bronchial Biopsy Specimen As a Surrogate for DNA Methylation Analysis in Inoperable Lung Cancer

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Bronchial Biopsy Specimen As a Surrogate for DNA Methylation Analysis in Inoperable Lung Cancer Um et al. Clinical Epigenetics (2017) 9:131 DOI 10.1186/s13148-017-0432-5 RESEARCH Open Access Bronchial biopsy specimen as a surrogate for DNA methylation analysis in inoperable lung cancer Sang-Won Um1†, Hong Kwan Kim2†, Yujin Kim3, Bo Bin Lee3, Dongho Kim3, Joungho Han4, Hojoong Kim1, Young Mog Shim2 and Duk-Hwan Kim3,5* Abstract Background: This study was aimed at understanding whether bronchial biopsy specimen can be used as a surrogate for DNA methylation analysis in surgically resected lung cancer. Methods: A genome-wide methylation was analyzed in 42 surgically resected tumor tissues, 136 bronchial washing, 12 sputum, and 8 bronchial biopsy specimens using the Infinium HumanMethylation450 BeadChip, and models for prediction of lung cancer were evaluated using TCGA lung cancer data. Results: Four thousand seven hundred and twenty-six CpGs (P < 1.0E-07) that were highly methylated in tumor tissues were identified from 42 lung cancer patients. Ten CpGs were selected for prediction of lung cancer. Genes including the 10 CpGs were classified into three categories: (i) transcription (HOXA9, SOX17, ZNF154, HOXD13); (ii) cell signaling (HBP1, SFRP1, VIPR2); and (iii) adhesion (PCDH17, ITGA5, CD34). Three logistic regression models based on the 10 CpGs classified 897 TCGA primary lung tissues with a sensitivity of 95.0~97.8% and a specificity of 97.4~98. 7%. However, the classification performance of the models was very poor in bronchial washing samples: the area under the curve (AUC) was equal to 0.72~0.78. The methylation levels of the 10 CpGs in bronchial biopsy were not significantly different from those in surgically resected tumor tissues (P > 0.05, Wilcoxon rank-sum test). However, their methylation levels were significantly different between paired bronchial biopsy and washing (P < 0.05, Wilcoxon signed-rank test). Conclusions: The present study suggests that bronchial biopsy specimen may be used as a surrogate for DNA methylation analysis in patient with inoperable lung cancer. Keywords: Hypermethylation, Lung cancer, Bronchial biopsy, Surrogate, Inoperable Background found in more than half of all patients with lung cancer at Lung cancer is the most common cause of cancer- the time of diagnosis, and from early recurrence after related deaths in the world. Despite significant advances curative surgical resection. Recently, precision medicines in the diagnosis and treatment of the disease, the prog- that target potential oncogenic driver mutations have been nosis remains extremely poor [1]. The poor prognosis approved to treat lung cancer [2]. However, some lung results largely from occult metastatic dissemination of cancer patients do not have targetable mutations, and cancer cells nearby lymph nodes or tissues, which are many patients develop resistance to targeted therapy. Tumor heterogeneity and mutational density are also a challenge in treating lung cancer, which underscores the * Correspondence: [email protected] †Equal contributors need for developing alternative therapeutic strategies for 3Department of Molecular Cell Biology, Samsung Biomedical Research treating lung cancer. Epigenetic changes involve DNA Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, methylation, histone modification, and microRNA alter- Korea 5Research Institute for Future Medicine, Samsung Medical Center, #50 ation. While oncogenic mutations in human cancer cells Ilwon-dong, Kangnam-gu, Professor Rm #5, Seoul 135-710, Korea are irreversible, alterations in epigenetic machinery are Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Um et al. Clinical Epigenetics (2017) 9:131 Page 2 of 10 potentially reversible, and this reversibility makes them tissues were obtained with written informed consent from promising therapeutic targets. all participants. Bronchoscopy in control group was per- Epigenetic changes have been increasingly studied in formed to rule out lung cancer. Paired bronchial washing lung cancer. These changes are observed frequently in and bronchial biopsy specimens were collected only lung cancer, and they correlate with tumor suppressor from eight (11%) of 76 lung cancer patients receiving gene silencing and oncogene activation. Among epigen- bronchoscopy. Flexible fiberoptic bronchoscopy and etic alterations, the de novo methylation of CpG islands sample preparation were performed as described pre- in the promoter regions of tumor suppressor genes is viously [13]. Bronchial washing was performed by in- usually associated with transcriptional silencing of such stilling 10 mL of sterile warm saline before obtaining genes and is one of the acquired epigenetic changes that biopsy samples to avoid contamination by the sloughing- occur during the pathogenesis of lung cancer. Epigenetic off of bronchial cells during bronchial biopsy. The pres- therapies may circumvent the problems of tumor cell ence of malignant cells in the bronchial washing fluid was heterogeneity and drug resistance by inducing the ex- confirmed by cytologic examination. Individuals who were pression of silenced tumor suppressor genes and may be clinically free of any cancer at the time of bronchoscopy more effective for lung cancer relapses that follow con- and did not have malignancy on their chest X-rays or CTs ventional treatment [3, 4]. In addition, there is growing were included in the control group. The control group emphasis on using epigenetic therapies to reprogram had tuberculosis, actinomycosis, bronchiolitis, pneumonia, neoplastic cells prior to other anti-cancer therapies. To or anthracofibrosis. Benign lung tumors such as hamar- date, DNA methyltransferase (DNMT) inhibitors or his- toma and localized organizing pneumonia were excluded tone deacetylase (HDAC) inhibitors in combination with in this study because their methylation profiling is not cytotoxic agents and targeted therapies have been clinic- known and can lead to misclassification. This study was ally tested in lung cancer [5–12]. Recent studies have re- approved by our Institutional Review Board (IRB #: ported that epigenetic priming agents may render tumor 2010-07-204) at the center. The pathologic stage was cells more susceptible to cytotoxic chemotherapy and determined according to the guidelines of the tumor- molecular targeted therapy including immunotherapy. node-metastasis (TNM) classification of the American Pretreatment with epigenetic drugs prior to immune Joint Committee on Cancer Staging Manual [14]. checkpoint modulators such as CTLA-4, PD-1, and PD- L1 inhibitors has shown observable responses in lung Genome-wide methylation analysis cancer patient [5, 12]; cytotoxic chemotherapy after epi- Genomic DNA was isolated from bronchial washing using genetic therapy has also shown remarkable responses in a QIAamp DNA Blood Mini Kit (Qiagen, Valencia, CA), lung cancer [6]. from sputum using the Sputum DNA Isolation Kit (Cat# For precision medicine using epigenetic priming prior 46200; Norgen Biotek, Thorold, ON, Canada) and from to conventional standard therapy or targeted cancer fresh-frozen tissue using the DNeasy Blood & Tissue kit therapy in lung cancer, analyzing clinically relevant pre- (Qiagen) according to the manufacturers’ instructions. Bi- dictive response biomarkers in lung tumor tissue is sulfite conversion was performed using the Zymo EZ needed. However, it is difficult to obtain tumor tissues in DNA Methylation Kit (Zymo Research, Orange, CA), and inoperable patients with advanced lung cancer. In situa- methylation levels were measured using the Infinium tions where obtaining tumor tissue is difficult, an alter- HumanMethylation450 BeadChip (450K) (Illumina, San native approach is to use surrogate specimens for Diego, CA) according to the manufacturer’sprotocol. analyzing DNA methylation in tumor tissues and to Scanned images were processed using the GenomeStudio apply the results to epigenetic therapy. In this study, we Methylation Module (version 2011.2). Preprocessing of analyzed if bronchial washing and bronchial biopsy spec- 450K data was conducted using wateRmelon package in R imens can be used as a surrogate for analyzing DNA (version 3.1.1) with Bioconductor 3.1 [15]. Methylation methylation in surgically resected tumor tissues. levels (β-values) were estimated as the ratio of signal in- tensity of methylated alleles to the sum of methylated and Methods unmethylated signal intensity of the alleles. The β-values Study population vary from 0 (no methylation) to 1 (100% methylation). A total of 118 lung cancer patients and 60 healthy individ- uals who were admitted for curative surgical resection of lung cancer or for bronchoscopy at the Samsung Medical Pyrosequencing Center in Seoul, Korea between March 2010 and August To validate the methylation levels from the 450K array, 2016 participated in this study. One hundred and thirty-six pyrosequencing for cg27364741 at the promoter region of (76 lung cancer patients
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