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Table 2 Genes showing concomitant evidence for differential DNA methylation and gene expression in blood from SSc patients

From: Integrative analysis of DNA methylation in discordant twins unveils distinct architectures of systemic sclerosis subsets

  

DNA methylation

Reported gene expression

Gene

Location

This study

Other reports

Expression

Refs

CpG

Gene location

CpG island location

All

lcSSc

dcSSc

SLE

SSc

Naïve T cells [17, 23]

T cells [15]

B cells [15]

Mono- cytes [15]

Neutro- phils [45, 8]

WBC [47]

skin fibrob [34]

  

RPS6KA1

1p36.11

cg24585377

Body

S_Shore

  

down-

 

down-

     

up-

[53]

IFI44L

1p31.1

cg03607951

TSS1500

-

down-

 

down-

down-

down-

down-

down-

down-

down-

 

up-

[49, 50, 52, 29, 27]

RSAD2

2p25.2

cg15346781

TSS1500

-

down-

  

down-

down-

down-

down-

 

up-

 

up-

[49, 52, 27]

LPIN1

2p25.1

cg02069619

TSS1500

N_Shore

  

down-

       

down-

[49]

LPP

3q27.3

cg05685023

TSS1500

N_Shore

  

down-

       

down-

[53]

RPL37

5p13.1

cg08754067

Body

N_Shelf

up-

         

down-

[49]

HMGCR

5q13.3

cg26399773

5'UTR

Island

 

up-

        

up-

[50]

TNXB

6p21.33

cg06580770

Body

N_Shore

up-

        

down-

down-

[53]

cg02673305

5'UTR

S_Shore

 

down-

       

down-

down-

[53]

KCNQ1

11p15.5

cg07824422

Body

Island

  

down-

       

up-

[53]

CD248

11q13.2

cg00350296

TSS1500

S_Shore

down-

         

up-

[48]

CACNA2D4

12p13.33

cg19069360

Body

-

  

down-

       

up-

[50]

TNFRSF1A

12p13.31

cg26254667

TSS1500

-

  

up-

 

up-

     

up-

[50, 53, 24]

WDFY2

13q14.3

cg08029014

Body

-

up-

         

up-

[50]

ITPK1

14q32.12

cg25095171

Body

N_Shelf

 

down-

        

up-

[53]

CRIP2

14q32.33

cg15532667

TSS1500

N_Shore

 

down-

        

down-

[49]

CYFIP1

15q11.2

cg22432269*

1stExon

Island

 

down-

        

up-

[50]

SQRDL

15q21.1

cg01626885

5'UTR

-

  

down-

       

up-

[50]

TLE3

15q23

cg01666796

Body

-

up-

         

up-

[48]

cg12349571

Body

-

up-

         

up-

[48]

ALOX15

17p13.2

cg06222638

Body

Island

down-

         

down-

[53]

STAT3

17q21.2

cg24312520

Body

-

  

up-

 

up-

up-

    

up-

[48, 50, 26]

CBX4

17q25.3

cg00483030

Body

N_Shore

  

down-

       

up-

[52]

PTPRS

19p13.3

cg08857677

TSS1500

S_Shore

 

down-

        

up-

[53]

TYROBP

19q13.12

cg17925829

TSS200

-

  

down-

       

up-

[52, 53, 27]

RASGRP4

19q13.2

cg24376214

TSS1500

-

  

up-

       

up-

[50]

RIN2

20p11.23

cg12049875

Body

Island

  

down-

       

up-

[50]

PRIC285

20q13.33

cg01458054

Body

N_Shore

up-

  

up-

up- or down-

up- or down-

down-

 

up-

 

up-

[49]

CERK

22q13.31

cg05602642

3'UTR

N_Shore

 

down-

        

down-

[49]

  1. Up- and down- refer to hypo- or hypermethylation, or over- or underexpression, respectively. Italics denotes methylation of different CpG sites in the gene. TSS1500 (TSS200), within 1500 bps (200 bps) from transcription start site; 5′UTR (3'UTR), 5′ (3') untranslated region. WBC: white blood cells. Skin fibrob: skin fibroblasts. Refs: references. *Age-associated CpG [42].
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Clinical Epigenetics

ISSN: 1868-7083

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