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Rothwell DG, Chemi F, Pearce S, Clipson A, Hill S, Conway AM, Richardson S, Murat K, Caeser R, Egger J, Poirier JT, Kerr A, Blackhall F, Rudin CM, Dive C. Abstract 6238: Profiling of the circulating cell-free DNA methylome for detection and subtyping of small cell lung cancers. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Small-cell lung cancer (SCLC) is a high-grade neuroendocrine carcinoma characterised by high proliferation rate and early, rapid metastatic spread. Although SCLC is treated as a homogenous disease, recent studies revealed morphologic and transcriptomic heterogeneity with several molecular subtypes described based on predominant transcription factor expression (ASCL1, NEUROD1, ATOH1, POU2F3, YAP1) (Rudin et al., 2019; Simpson et al., 2020) which in preclinical studies exhibit differing vulnerabilities raising the potential of stratified therapy. DNA methylation is also thought be an important regulator of SCLC biology (Gazdar et al., 2017) and epigenetically distinct subtypes derived from SCLC primary tumour samples reported (Poirier et al., 2015). Here, we developed a robust workflow for genome-wide DNA methylation profiling to examine the potential use of cfDNA methylation profiling for detection and subtyping of SCLC.
Results: To evaluate SCLC genome-wide DNA methylation patterns we employed a bisulfite-free enrichment-based approach (T7-MBD-seq). We tested this approach on tissue samples from preclinical models and from normal lung (n=110) and on cfDNA samples from both patients with SCLC and from non-cancer controls (n=157). Methylation profiles from preclinical models (patient-derived xenografts (PDX) and CTC derived explant (CDX) models) were comparable to previously described methylation patterns from SCLC primary tumours and were recapitulated in patients’ cfDNA samples. A tumour/normal classifier, based on 4,061 genomic regions detected as being hypermethylated in SCLC preclinical models, correctly assigned 93% and 100% cfDNA samples from patients with limited and extensive stage SCLC respectively, with a statistically significant correlation of prediction scores with disease stage (P=0.0076). Finally, to determine whether cfDNA methylation profiling could subtype SCLC patients, we built a subtype classifier, based on methylation signatures derived from 59 established SCLC cell lines. We applied the classifier to cfDNA samples from 56 patients and 10/11 with known subtypes (identified from a donor matched CDX model) were correctly classified. Overall, 73% of cfDNA samples were classified as ASCL1, 13% were classified as NEUROD1 and 14% were classified as being double negative with the distribution of the subtypes correlating closely to previously published IHC data from SCLC tissue samples (Baine et al., 2020).
Conclusions: Our data reveal two potential clinical utilities of cfDNA methylation profiling; a universally applicable liquid biopsy approach for more sensitive detection and monitoring of SCLC and molecular subtyping to ease the path to future clinical trials of subtype stratified treatments for patients with SCLC.
Citation Format: Dominic G. Rothwell, Francesca Chemi, Simon Pearce, Alex Clipson, Steven Hill, Alicia Marie Conway, Sophie Richardson, Katarzyna Murat, Rebecca Caeser, Jacklynn Egger, John T. Poirier, Alastair Kerr, Fiona Blackhall, Charles M. Rudin, Caroline Dive. Profiling of the circulating cell-free DNA methylome for detection and subtyping of small cell lung cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6238.
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Affiliation(s)
- Dominic G. Rothwell
- 1CRUK Lung Cancer Centre of Excellence, Cancer Biomarker Centre, CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Francesca Chemi
- 1CRUK Lung Cancer Centre of Excellence, Cancer Biomarker Centre, CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Simon Pearce
- 1CRUK Lung Cancer Centre of Excellence, Cancer Biomarker Centre, CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Alex Clipson
- 1CRUK Lung Cancer Centre of Excellence, Cancer Biomarker Centre, CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Steven Hill
- 1CRUK Lung Cancer Centre of Excellence, Cancer Biomarker Centre, CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Alicia Marie Conway
- 1CRUK Lung Cancer Centre of Excellence, Cancer Biomarker Centre, CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Sophie Richardson
- 1CRUK Lung Cancer Centre of Excellence, Cancer Biomarker Centre, CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Katarzyna Murat
- 1CRUK Lung Cancer Centre of Excellence, Cancer Biomarker Centre, CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Rebecca Caeser
- 2Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacklynn Egger
- 2Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - John T. Poirier
- 2Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alastair Kerr
- 1CRUK Lung Cancer Centre of Excellence, Cancer Biomarker Centre, CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Fiona Blackhall
- 3Division of Cancer Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Charles M. Rudin
- 2Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Caroline Dive
- 1CRUK Lung Cancer Centre of Excellence, Cancer Biomarker Centre, CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
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Murat K, Grüning B, Poterlowicz PW, Westgate G, Tobin DJ, Poterlowicz K. Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy. Gigascience 2020; 9:5836679. [PMID: 32401319 PMCID: PMC7219210 DOI: 10.1093/gigascience/giaa049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 02/24/2020] [Accepted: 04/21/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Infinium Human Methylation BeadChip is an array platform for complex evaluation of DNA methylation at an individual CpG locus in the human genome based on Illumina's bead technology and is one of the most common techniques used in epigenome-wide association studies. Finding associations between epigenetic variation and phenotype is a significant challenge in biomedical research. The newest version, HumanMethylationEPIC, quantifies the DNA methylation level of 850,000 CpG sites, while the previous versions, HumanMethylation450 and HumanMethylation27, measured >450,000 and 27,000 loci, respectively. Although a number of bioinformatics tools have been developed to analyse this assay, they require some programming skills and experience in order to be usable. RESULTS We have developed a pipeline for the Galaxy platform for those without experience aimed at DNA methylation analysis using the Infinium Human Methylation BeadChip. Our tool is integrated into Galaxy (http://galaxyproject.org), a web-based platform. This allows users to analyse data from the Infinium Human Methylation BeadChip in the easiest possible way. CONCLUSIONS The pipeline provides a group of integrated analytical methods wrapped into an easy-to-use interface. Our tool is available from the Galaxy ToolShed, GitHub repository, and also as a Docker image. The aim of this project is to make Infinium Human Methylation BeadChip analysis more flexible and accessible to everyone.
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Affiliation(s)
- Katarzyna Murat
- Center for Skin Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, UK
| | - Björn Grüning
- Freiburg Galaxy Team, University of Freiburg, Fahnenbergplatz, 79085 Freiburg im Breisgau, Germany
| | | | - Gillian Westgate
- Center for Skin Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, UK
| | - Desmond J Tobin
- The Charles Institute for Dermatology, Belfield, School of Medicine, University College Dublin, Ireland
| | - Krzysztof Poterlowicz
- Center for Skin Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, UK
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Sibel O, Beyza A, Murat K, Fatma E, Göksel K, Sevin B. Respiratory symptoms and pulmonary function of workers employed in textile dyeing factory in Turkey. Med J Malaysia 2012; 67:375-378. [PMID: 23082444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Dyes are known to be a causative agent of occupational asthma exposed to them. We evaluate respiratory symptoms among textile. The study population comprised 106 exposed workers and control (unexposed) group. Data were collected by a questionnaire. Pulmonary Function Tests (PFTs) were performed. Among the exposed workers 36.8% defined phlegm. Respiratory symptoms were not significantly different between two groups. The employment duration of the exposed workers with phlegm was longer than those without phlegm (p = 0.027). The mean % predicted of forced expiratory flow (FEF) 25-75 of the exposed workers was found to be significantly lower than the control (unexposed) group (p = 0.01). Our study suggests that textile dyeing might cause respiratory symptoms at workers.
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Affiliation(s)
- O Sibel
- Pamukkale University Medical Faculty, Pulmonary Medicine Department, Denizli, Turkey.
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Serik O, Ainur I, Murat K, Tetsno M, Masaki I. Silicon carbide fiber-mediated DNA delivery into cells of wheat (Triticum acstivum L.) mature embryos. Plant Cell Rep 1996; 16:133-136. [PMID: 24177538 DOI: 10.1007/bf01890853] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/1996] [Revised: 05/27/1996] [Indexed: 06/02/2023]
Abstract
We have demonstrated that foreign DNA can be delivered into cells of mature embryos of wheat (Triticum aestivum L.) using silicon carbide fibers (SCF). The highest transient expression of thegusA (GUS) gene was detected when dry embryos were vortexed for 10-30 min in a SCF-DNA solution containing 90-120 g/l of sucrose. Up to 100 (on average 20-40) blue expression units per embryo were observed. Scutellum side and epiblast of the intact wheat embryos are preferentially transformed. When embryos with the coleoptilar tip removed were treated and allowed to germinate, GUS staining was observed in emerging leaf tissues. The potential of this new approach for stable transformation of wheat is under investigation. It has been found that callus tissues induced from the SCF treated embryos contain GUS-expressing sectors one month after treatment.
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Affiliation(s)
- O Serik
- Department of Botany, Faculty of Science, Kyoto University, 606-01, Sakyo-Ku, Kyoto, Japan
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