DNA methylation profiling of non-small cell lung cancer reveals a COPD-driven immune-related signature.
BACKGROUND
Non-small cell lung cancer (NSCLC) is a heterogeneous disorder consisting of distinct molecular subtypes each characterised by specific genetic and epigenetic profiles. Here, we aimed to identify novel NSCLC subtypes based on genome-wide methylation data, assess their relationship with smoking behaviour, age, COPD, emphysema and tumour histopathology, and identify the molecular pathways underlying each subtype.


METHODS
Methylation profiling was performed on 49 pairs of tumour and adjacent lung tissue using Illumina 450 K arrays. Transcriptome sequencing was performed using Illumina HiSeq2000 and validated using expression data from The Cancer Genome Atlas (TCGA). Tumour immune cell infiltration was investigated by immunohistochemistry.


RESULTS
Unsupervised hierarchical clustering of tumour methylation data revealed two subgroups characterised by a significant association between cluster membership and presence of COPD (p=0.024). Ontology analysis of genes containing differentially methylated CpGs (false discovery rate, FDR-adjusted p<0.05) revealed that immune genes were strongly enriched in COPD tumours, but not in non-COPD tumours. This COPD-specific immune signature was attributable to methylation changes in immune genes expressed either by tumour cells or tumour-infiltrating immune cells. No such differences were observed in adjacent tissue. Transcriptome profiling similarly revealed that genes involved in the immune response were differentially expressed in COPD tumours (FDR-adjusted p<0.05), an observation that was independently replicated using TCGA data. Immunohistochemistry validated these findings, revealing fewer CD4-positive T lymphocytes in tumours derived from patients with COPD.


CONCLUSIONS
Lung tumours of patients with COPD differ from those of patients without COPD, with differentially methylated and expressed genes being mainly involved in the immune response.
Vesalius Research Center (VRC), VIB, KU Leuven, Leuven, Belgium Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium Respiratory Division, University Hospital Gasthuisberg, KU Leuven, Leuven, Belgium.
Els
E
Wauters
Respiratory Division, University Hospital Gasthuisberg, KU Leuven, Leuven, Belgium.
Wim
W
Janssens
Respiratory Division, University Hospital Gasthuisberg, KU Leuven, Leuven, Belgium.
Johan
J
Vansteenkiste
Department of Thoracic surgery, University Hospital Gasthuisberg, KU Leuven, Leuven, Belgium.
Herbert
H
Decaluwé
Laboratory of Pneumology, KU Leuven, Leuven, Belgium.
Nele
N
Heulens
Vesalius Research Center (VRC), VIB, KU Leuven, Leuven, Belgium Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium.
Bernard
B
Thienpont
Vesalius Research Center (VRC), VIB, KU Leuven, Leuven, Belgium Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium.
Hui
H
Zhao
Vesalius Research Center (VRC), VIB, KU Leuven, Leuven, Belgium Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium.
Dominiek
D
Smeets
Centre for Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium.
Xavier
X
Sagaert
Department of Radiology, University Hospital Gasthuisberg, KU Leuven, Belgium.
Johan
J
Coolen
Respiratory Division, University Hospital Gasthuisberg, KU Leuven, Leuven, Belgium.
Marc
M
Decramer
Autoimmune Genetics Laboratory, VIB, KU Leuven, Leuven, Belgium.
Adrian
A
Liston
Department of Thoracic surgery, University Hospital Gasthuisberg, KU Leuven, Leuven, Belgium.
Paul
P
De Leyn
Vesalius Research Center (VRC), VIB, KU Leuven, Leuven, Belgium Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium.
Matthieu
M
Moisse
Vesalius Research Center (VRC), VIB, KU Leuven, Leuven, Belgium Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium.
Diether
D
Lambrechts
D002289:Carcinoma, Non-Small-Cell Lung / Q000453:epidemiology* / Q000276:immunology*; D015897:Comorbidity; D019175:DNA Methylation / Q000276:immunology*; D006801:Humans; D008175:Lung Neoplasms / Q000453:epidemiology* / Q000276:immunology*; D029424:Pulmonary Disease, Chronic Obstructive / Q000453:epidemiology* / Q000276:immunology*
COPD ÀÜ Mechanisms; Innate Immunity; Lung Cancer