Epigenetic inactivation of the candidate tumor suppressor USP44 is a frequent and early event in colorectal neoplasia.
In mouse models, loss of the candidate tumor suppressor gene Ubiquitin Specific Protease 44 (USP44) is associated with aneuploidy and cancer. USP44 is also transcriptionally silenced in human cancers. Here we investigated the molecular mechanism of USP44 silencing and whether this correlated with aneuploidy in colorectal adenomas. DNA methylation at the USP44 CpG island (CGI) promoter was measured using combined bisulfite restriction analysis (COBRA) in colorectal cancer (CRC) cell lines (n = 18), and with COBRA and bisulfite sequencing in colorectal adenomas (n = 89) and matched normal colonic mucosa (n = 51). The USP44 CGI was hypermethylated in all CRC cell lines, in most colorectal adenomas (79 of 89, 89%) but rarely in normal mucosa samples (3 of 51, 6%). USP44 expression was also compared between normal mucosa and paired hypermethylated adenomas in six patients using qRT-PCR. Hypermethylation of the USP44 CGI in adenomas was associated with a 1.8 to 5.5-fold reduction in expression compared with paired normal mucosa. Treatment of CRC cell lines with the DNA hypomethylating agent decitabine resulted in a 14 to 270-fold increase in USP44 expression. Whole genome SNP array data showed that gain or loss of individual chromosomes occurred in adenomas, but hypermethylation did not correlate with more aneuploidy. In summary, our data shows that USP44 is epigenetically inactivated in colorectal adenomas, but this alone is not sufficient to cause aneuploidy in colorectal neoplasia.
Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia.
Mathew A
MA
Sloane
Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia.
Jason W H
JW
Wong
Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia.
Dilmi
D
Perera
Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia.
Andrea C
AC
Nunez
Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia.
John E
JE
Pimanda
School of Medical Sciences; University of New South Wales; Sydney, NSW Australia.
Nicholas J
NJ
Hawkins
Colorectal Cancer Genetics Laboratory; Systems Biology and Personalised Medicine Division; Walter and Eliza Hall Institute of Medial Research; Parkville, VIC Australia; Faculty of Medicine, Dentistry and Health Sciences; Department of Medical Biology; University of Melbourne; Parkville, VIC Australia.
Oliver M
OM
Sieber
Department of Gastroenterology and Hepatology; Westmead Hospital; Sydney, NSW Australia.
Michael J
MJ
Bourke
Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia.
Luke B
LB
Hesson
Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia.
Robyn L
RL
Ward
D000236:Adenoma / Q000235:genetics* / Q000378:metabolism; D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000782:Aneuploidy; D000964:Antimetabolites, Antineoplastic / Q000494:pharmacology; D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D045744:Cell Line, Tumor; D003106:Colon / Q000378:metabolism; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000378:metabolism; D018899:CpG Islands; D000077209:Decitabine; D044127:Epigenesis, Genetic; D015870:Gene Expression; D016147:Genes, Tumor Suppressor; D006801:Humans; D007413:Intestinal Mucosa / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D012007:Rectum / Q000378:metabolism; D043222:Ubiquitin Thiolesterase; D064570:Ubiquitin-Specific Proteases / Q000235:genetics*; D055815:Young Adult
D000964:Antimetabolites, Antineoplastic; D000077209:Decitabine; C579216:USP44 protein, human; D043222:Ubiquitin Thiolesterase; D064570:Ubiquitin-Specific Proteases; D001374:Azacitidine
CpG island; DNA methylation; adenoma; aneuploidy; colorectal cancer; deubiquitinase; epigenetic