Differential expression of selected histone modifier genes in human solid cancers.
BACKGROUND
Post-translational modification of histones resulting in chromatin remodelling plays a key role in the regulation of gene expression. Here we report characteristic patterns of expression of 12 members of 3 classes of chromatin modifier genes in 6 different cancer types: histone acetyltransferases (HATs)- EP300, CREBBP, and PCAF; histone deacetylases (HDACs)- HDAC1, HDAC2, HDAC4, HDAC5, HDAC7A, and SIRT1; and histone methyltransferases (HMTs)- SUV39H1and SUV39H2. Expression of each gene in 225 samples (135 primary tumours, 47 cancer cell lines, and 43 normal tissues) was analysedby QRT-PCR, normalized with 8 housekeeping genes, and given as a ratio by comparison with a universal reference RNA.


RESULTS
This involved a total of 13,000 PCR assays allowing for rigorous analysis by fitting a linear regression model to the data. Mutation analysis of HDAC1, HDAC2, SUV39H1, and SUV39H2 revealed only two out of 181 cancer samples (both cell lines) with significant coding-sequence alterations. Supervised analysis and Independent Component Analysis showed that expression of many of these genes was able to discriminate tumour samples from their normal counterparts. Clustering based on the normalized expression ratios of the 12 genes also showed that most samples were grouped according to tissue type. Using a linear discriminant classifier and internal cross-validation revealed that with as few as 5 of the 12 genes, SIRT1, CREBBP, HDAC7A, HDAC5 and PCAF, most samples were correctly assigned.


CONCLUSIONS
The expression patterns of HATs, HDACs, and HMTs suggest these genes are important in neoplastic transformation and have characteristic patterns of expression depending on tissue of origin, with implications for potential clinical application.
Ozdağ
Hilal
H
Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 2XZ, UK. hilalozdag@gmail.com
Teschendorff
Andrew E
AE
Ahmed
Ahmed Ashour
AA
Hyland
Sarah J
SJ
Blenkiron
Cherie
C
Bobrow
Linda
L
Veerakumarasivam
Abhi
A
Burtt
Glynn
G
Subkhankulova
Tanya
T
Arends
Mark J
MJ
Collins
V Peter
VP
Bowtell
David
D
Kouzarides
Tony
T
Brenton
James D
JD
Caldas
Carlos
C
D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism; D002277:Carcinoma / Q000235:genetics / Q000378:metabolism; D002471:Cell Transformation, Neoplastic / Q000235:genetics; D016000:Cluster Analysis; D015179:Colorectal Neoplasms / Q000235:genetics / Q000378:metabolism; D018076:DNA, Complementary / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics; D005260:Female; D015971:Gene Expression Regulation, Enzymologic; D015972:Gene Expression Regulation, Neoplastic; D051548:Histone Acetyltransferases / Q000096:biosynthesis / Q000235:genetics*; D042421:Histone Code / Q000235:genetics*; D006655:Histone Deacetylases / Q000235:genetics*; D000076983:Histone Methyltransferases; D011495:Histone-Lysine N-Methyltransferase / Q000096:biosynthesis / Q000235:genetics*; D006657:Histones / Q000378:metabolism*; D006801:Humans; D016014:Linear Models; D008175:Lung Neoplasms / Q000235:genetics / Q000378:metabolism; D008297:Male; D009363:Neoplasm Proteins / Q000096:biosynthesis / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D010051:Ovarian Neoplasms / Q000235:genetics / Q000378:metabolism; D010190:Pancreatic Neoplasms / Q000235:genetics / Q000378:metabolism; D016133:Polymerase Chain Reaction; D018807:Polymorphism, Single-Stranded Conformational; D011496:Protein Methyltransferases; D011499:Protein Processing, Post-Translational / Q000235:genetics*
D018076:DNA, Complementary; D004273:DNA, Neoplasm; D006657:Histones; D009363:Neoplasm Proteins; D000076983:Histone Methyltransferases; D011496:Protein Methyltransferases; D011495:Histone-Lysine N-Methyltransferase; D051548:Histone Acetyltransferases; D006655:Histone Deacetylases