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Table 8 Associations of smoking and cancer with differential methylation of AHRR and CYP1B1

From: A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers

 

CpG

Chr

Position in bp (hg19a)

Association with SPY (EWAS samples)

Association with smoking status (EWAS samples)

Association with OSCC

Δβ/10 SPY

p nom

q

Δβ

p nom

q

Δβ

p nom

p adj

CYP1B1

cg01584760b

2

38,296,474

− 0.046

3.8 × 10−10

3.1 × 10−4

− 0.045

1.0 × 10−4

0.853

Not analysed

cg02162897

2

38,300,537

− 0.11

1.2 × 10−7

0.014

− 0.183

5.5 × 10−8

0.022

0.197

4.7 × 10−6

6.1 × 10−4

cg20408276

2

38,300,586

− 0.108

1.1 × 10−7

0.014

− 0.176

3.6 × 10−7

0.04

Not analysed

cg00565882

2

38,300,707

− 0.041

1.7 × 10−6

0.042

− 0.044

0.005

1

0.16

8.6 × 10−7

1.1 × 10−4

cg01410359

2

38,302,230

− 0.037

3.4 × 10−6

0.047

− 0.032

0.023

1

0.177

8.8 × 10−7

1.1 × 10−4

AHRR

cg04551776

5

393,366

− 0.007

4.3 × 10−1

0.97

− 0.011

0.43

1

0.149

2.7 × 10−5

3.5 × 10−3

cg06036945

5

394,869

− 0.067

1.0 × 10−4

0.18

− 0.125

3.7 × 10−7

0.04

Not analysed

cg04066994c

5

394,891

− 0.041

8.2 × 10−6

0.067

− 0.083

5.9 × 10−10

4.7 × 10−4

Not analysed

cg25648203

5

395,444

− 0.007

0.42

0.99

− 0.012

0.37

1

− 0.081

9.7 × 10−3

1

  1. Shown are the results for all CpGs within CYP1B1 and AHRR that were significantly associated with SPY levels or smoking status in our EWAS. We compared AHRR and CYP1B1 methylation levels in 16 oral squamous cell carcinoma (OSCC) samples from TCGA to our healthy never smoker samples. Differential methylation analysis was performed using an ANCOVA adjusting for sex and unknown variation. The CpGs cg01584760, cg20408276, cg06036945 and cg04066994 were not covered by the 450k analysis of the OSCC samples. For AHRR, we added the results for cg04551776 and cg25648203, which flanked our EWAS-CpGs with a distance of 1503 bp and 553 bp, respectively, albeit these CpGs were not associated in our EWAS
  2. aNCBI build GRCh37
  3. bTop significant CpG in the differential methylation analysis with SPY
  4. cTop significant CpG in the differential methylation analysis with smoking status. Chr chromosome, bp basepairs, SPY smoke pack years, Padj Bonferroni-adjusted for 130 tests