Table 2.

Genes altered during progression

Gene name	Normal to ADH/DCIS	DCIS to IDC	Reversible?	Source
MGMT		Increase DNA methylation	yes	Verschuur-Maes [27]
CACNA1A		Increase DNA methylation	yes	Verschuur-Maes [27]
APC	Increase DNA methylation		yes	Park [28], Hoque [32]
DLEC1	Increase DNA methylation		yes	Park [28]
HOXA1	Increase DNA methylation		yes	Park [28]
SFRP1		Increase DNA methylation	yes	Park [28]
HOXA10		Increase DNA methylation	yes	Park [28]
RASSF1A	Increase DNA methylation		yes	Park [28], van Hoesel [29], Lehhman [30], Fackler [31]
RARβ	Increase DNA methylation		yes	van Hoesel [29], Fackler [31]
CCND2	Increase DNA methylation		yes	Lehhman [30], Fackler [31]
TWIST	Increase DNA methylation		yes	Fackler [31]
HIN-1	Increase DNA methylation		yes	Fackler [31]
CDH1		Increase DNA methylation	yes	Hoque [32]
Homeobox family genes	Differentially methylated	Differentially methylated	yes	Tommasi [37], Johnson [38]
Polycomb repressive complex target genes	Differentially methylated	Differentially methylated	yes	Tommasi [37], Johnson [38], Cai [39]
HOTAIR	Increase DNA methylation, Increase expression		yes	Johnson [38]
CPA1	Increase DNA methylation	Increase DNA methylation	yes	Fleischer [34]
CUL7	Increase DNA methylation	Increase DNA methylation	yes	Fleischer [34]
LRRTM2	Increase DNA methylation	Increase DNA methylation	yes	Fleischer [34]
POU2AF1	Increase DNA methylation	Increase DNA methylation	yes	Fleischer [34]
EZH2	Increased Expression	Increased Expression		Cai [39], Kleer [47], Ding [48]
HDAC1,2,6	Decreased expression			Suzuki [63]
H4K16ac	Decreased		yes	Suzuki [63]
H4K12ac	Decreased		yes	Suzuki [63]
HDAC9	Increased Expression			Lapierre [69]
RACK7		Decreased expression		Shen [87]
PRNCR1		Increased Expression		Gooding [121]
linc-ROR	Increased Expression	Increased Expression		Eades [119]
BORG	Increased Expression			Gooding [121]
NKILA		Decreased expression		Liu [120]
BC200	Increased Expression	Increased Expression		Iacoangeli [116]
miR-21	Increased Expression			Farazi [107], Volinia [108], Hannafon
miR-98	Decreased expression			Farazi [107], Volinia [108], Hannafon [105]
let-7	Decreased expression	Increased Expression		Farazi [107], Volinia [108]
miR-181a		Increased Expression		Volinia [108]
miR-210		Increased Expression		Volinia [108]
miR-221		Increased Expression		Volinia [108]
miR-10b	Decreased expression	Decreased expression		Hannafon [105], Volinia [108]
miR-143	Decreased expression	Decreased expression		Farazi [107], Volinia [108]
miR-126		Decreased expression		Volinia [108]
miR-218		Decreased expression		Volinia [108]
miR-335-5p		Decreased expression		Volinia [108]
miR-200c	Increased Expression			Hannafon [105], Volinia [108]

Many of the genes identified in this review were only identified by one study, underscoring the challenges to understanding the DCIS to IDC transition