Reduced Representation Bisulfite Sequencing Determination of Distinctive DNA Hypermethylated Genes in the Progression to Colon Cancer in African Americans.
Background and Aims. Many studies have focused on the determination of methylated targets in colorectal cancer. However, few analyzed the progressive methylation in the sequence from normal to adenoma and ultimately to malignant tumors. This is of utmost importance especially in populations such as African Americans who generally display aggressive tumors at diagnosis and for whom markers of early neoplasia are needed. We aimed to determine methylated targets in the path to colon cancer in African American patients using Reduced Representation Bisulfite Sequencing (RRBS). Methods. Genomic DNA was isolated from fresh frozen tissues of patients with different colon lesions: normal, a tubular adenoma, a tubulovillous adenoma, and five cancers. RRBS was performed on these DNA samples to identify hypermethylation. Alignment, mapping, and confirmed CpG methylation analyses were performed. Preferential hypermethylated pathways were determined using Ingenuity Pathway Analysis (IPA). Results. We identified hypermethylated CpG sites in the following genes: L3MBTL1, NKX6-2, PREX1, TRAF7, PRDM14, and NEFM with the number of CpG sites being 14, 17, 10, 16, 6, and 6, respectively, after pairwise analysis of normal versus adenoma, adenoma versus cancer, and normal versus cancer. IPA mapped the above-mentioned hypermethylated genes to the Wnt/β-catenin, PI3k/AKT, VEGF, and JAK/STAT3 signaling pathways. Conclusion. This work provides insight into novel differential CpGs hypermethylation sites in colorectal carcinogenesis. Functional analysis of the novel gene targets is needed to confirm their roles in their associated carcinogenic pathways.
Department of Medicine and Cancer Center, Howard University, Washington, DC, USA.
Hassan
0000-0002-4048-4666
H
Ashktorab
Department of Genetics, Howard University, Washington, DC, USA; Umm AL-Qura University, Makkah, Saudi Arabia.
Afnan
A
Shakoori
Department of Genetics, Howard University, Washington, DC, USA.
Shatha
S
Zarnogi
DNA Sequencing and Genotyping Core, Cincinnati, OH 45229, USA.
Xueguang
X
Sun
Hithru Analytics, Laurel, MD, USA.
Sudhir
S
Varma
Department of Pathology, Howard University, Washington, DC, USA.
Edward
E
Lee
Department of Pathology, Howard University, Washington, DC, USA.
Babak
0000-0003-2201-6188
B
Shokrani
Department of Medicine and Cancer Center, Howard University, Washington, DC, USA.
Adeyinka O
AO
Laiyemo
Department of Genetics, Howard University, Washington, DC, USA.
Kareem
K
Washington
Department of Pathology, Howard University, Washington, DC, USA.
Hassan
0000-0001-7055-2298
H
Brim
Cancer Res. 2007 Oct 15;67(20):9649-57
17942894
BMC Mol Biol. 2014 Jul 16;15:14
25029911
Epigenetics. 2014 Apr;9(4):503-12
24441198
N Engl J Med. 2012 Jan 5;366(1):44-53
22216841
PLoS Genet. 2007 Sep;3(9):1709-23
17892325
Carcinogenesis. 2012 Aug;33(8):1487-93
22610075
J Cancer Res Clin Oncol. 2014 Dec;140(12):2119-27
24996990
PLoS One. 2009 Sep 11;4(9):e7012
19750230
Clin Cancer Res. 2008 May 1;14 (9):2560-9
18451217
Cancer Res. 1996 Dec 1;56(23):5470-4
8968103
Cancer Res. 2001 Apr 15;61(8):3225-9
11309270
J Gastroenterol Hepatol. 2012 Sep;27(9):1423-31
22694276
BMC Med Genet. 2013 Jul 23;14:76
23879380
N Engl J Med. 2009 Dec 17;361(25):2449-60
20018966
Nat Genet. 2006 Jul;38(7):787-93
16804544
J Clin Oncol. 2010 Feb 1;28(4):605-13
20038729
Epigenetics. 2013 Mar;8(3):317-32
23417056
Cancer Res. 2004 Nov 15;64(22):8156-9
15548679
Carcinogenesis. 2013 Aug;34(8):1756-63
23598468
Clin Epigenetics. 2013 Sep 13;5(1):16
24034811
Int J Mol Sci. 2013 Aug 07;14(8):16365-85
23965959
Breast Cancer Res Treat. 2012 May;133(1):127-35
21837478
Epigenetics. 2013 Aug;8(8):807-15
23975090
Gastroenterol Hepatol Bed Bench. 2013 Summer;6(3):120-8
24834258
Cancer Epidemiol Biomarkers Prev. 2011 Jul;20(7):1483-91
21586619
Clin Cancer Res. 2009 Feb 15;15(4):1155-61
19190129
BMC Syst Biol. 2013 Dec 26;7:141
24369052
Carcinogenesis. 2012 Oct;33(10 ):1889-96
22739025
Oncol Rep. 2013 Jan;29(1):283-7
23128672