Universal lung epithelium DNA methylation markers for detection of lung damage in liquid biopsies

Abstract

BackgroundCirculating biomarkers for lung damage are lacking. Lung epithelium-specific DNA methylation patterns can potentially report the presence of lung-derived cell-free DNA (cfDNA) in blood, as an indication of lung cell death.MethodsWe sorted human lung alveolar and bronchial epithelial cells from surgical specimens, and obtained their methylomes using whole-genome bisulfite sequencing. We developed a PCR-sequencing assay determining the methylation status of 17 loci with lung-specific methylation patterns, and used it to assess lung-derived cfDNA in the plasma of healthy volunteers and patients with lung disease.ResultsLoci that are uniquely unmethylated in alveolar or bronchial epithelial cells are enriched for enhancers controlling lung-specific genes. Methylation markers extracted from these methylomes revealed that normal lung cell turnover likely releases cfDNA into the air spaces, rather than to blood. People with advanced lung cancer show a massive elevation of lung cfDNA concentration in blood. Among individuals undergoing bronchoscopy, lung-derived cfDNA is observed in the plasma of those later diagnosed with lung cancer, and to a lesser extent in those diagnosed with other lung diseases. Lung cfDNA is also elevated in patients with acute exacerbation of chronic obstructive pulmonary disease (COPD) compared with patients with stable disease, and is associated with future exacerbation and mortality in these patients.ConclusionsUniversal cfDNA methylation markers of normal lung epithelium allow for mutation-independent, sensitive and specific detection of lung-derived cfDNA, reporting on ongoing lung injury. Such markers can find broad utility in the study of normal and pathologic human lung dynamics.

Detection of the DNA methylation of seven genes contribute to the early diagnosis of lung cancer

“…Ajona et al (Ajona et al 2021 ) developed a diagnostic model based on the quantification in plasma of complement-derived fragment C4c, CYFRA 21–1 and C-reactive protein (CRP) with an AUC of 0.86 and a specificity of 92%. Among the multiple biomarkers, DNA methylation shows good performance (P. Li et al 2022a ; Magenheim et al 2022 ; Liang et al 2021 ). SOX17 , TAC1 , CDO1 , HOXA9 and ZFP4 2 were the 5 genes that were identified in the Cancer Genome Atlas (TCGA) with highly prevalent DNA methylation in lung squamous and adenocarcinoma, but not in normal lung tissue (Cancer Genome Atlas Research, 2012 ; Wrangle et al 2014 ; Diaz-Lagares et al 2016 ).…”

Phase II trial of delta-tocotrienol in neoadjuvant breast cancer with evaluation of treatment response using ctDNA

“…In general, ctDNA detection in patients with a low tumor burden is challenging due to low concentrations of ctDNA 17 . The assay sensitivity has been reported to increase with an increasing number of independent ctDNA targets 18 and when bisulfite converted DNA is targeted in both the sense and the antisense direction 19 . We developed a multiplex ctDNA ddPCR assay including two breast tissue specific ( LMX1B and ZNF296 ) and one cancer specific target ( HOXA9 ).…”

Methylomics and cancer: the current state of methylation profiling and marker development for clinical care

“…Similarly in mice, WGBS was used to establish hydroxymethylation profiles for progressive stages of cervical cancer to screen for potential epigenomic biomarkers [ 61 ]. More recently, Magenheim et al [ 62 ] utilized WGBS to obtain methylome profiling in human alveolar and bronchial epithelial tissue. Despite its distinct advantages, such as broad coverage of methylation sites and reduced interference by repetitive regions, SNPs, and other factors [ 63 ], WGBS also has drawbacks, most notably its poor accuracy in sequence alignment and low alignment rates.…”