Integrated genomic and transcriptional profiling identifies chromosomal loci with altered gene expression in cervical cancer.
For a better understanding of the consequences of recurrent chromosomal alterations in cervical carcinomas, we integrated genome-wide chromosomal and transcriptional profiles of 10 squamous cell carcinomas (SCCs), 5 adenocarcinomas (AdCAs) and 6 normal controls. Previous genomic profiling showed that gains at chromosome arms 1q, 3q, and 20q as well as losses at 8q, 10q, 11q, and 13q were common in cervical carcinomas. Altered regions spanned multiple megabases, and the extent to which expression of genes located there is affected remains unclear. Expression analysis of these previously chromosomally profiled carcinomas yielded 83 genes with significantly differential expression between carcinomas and normal epithelium. Application of differential gene locus mapping (DIGMAP) analysis and the array CGH expression integration tool (ACE-it) identified hotspots within large chromosomal alterations in which gene expression was altered as well. Chromosomal gains of the long arms of chromosome 1, 3, and 20 resulted in increased expression of genes located at 1q32.1-32.2, 3q13.32-23, 3q26.32-27.3, and 20q11.21-13.33, whereas a chromosomal loss of 11q22.3-25 was related to decreased expression of genes located in this region. Overexpression of DTX3L, PIK3R4, ATP2C1, and SLC25A36, all located at 3q21.1-23 and identified by DIGMAP, ACE-it or both, was confirmed in an independent validation sample set consisting of 12 SCCs and 13 normal ectocervical samples. In conclusion, integrated chromosomal and transcriptional profiling identified chromosomal hotspots at 1q, 3q, 11q, and 20q with altered gene expression within large commonly altered chromosomal regions in cervical cancer.
Wilting
Saskia M
SM
Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
de Wilde
Jillian
J
Meijer
Chris J L M
CJ
Berkhof
Johannes
J
Yi
Yajun
Y
van Wieringen
Wessel N
WN
Braakhuis
Boudewijn J M
BJ
Meijer
Gerrit A
GA
Ylstra
Bauke
B
Snijders
Peter J F
PJ
Steenbergen
Renske D M
RD
D000230:Adenocarcinoma / Q000235:genetics* / Q000473:pathology / Q000821:virology; D000293:Adolescent; D000328:Adult; D000368:Aged; D000252:Calcium-Transporting ATPases / Q000235:genetics; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000473:pathology / Q000821:virology; D002584:Cervix Uteri / Q000378:metabolism; D002869:Chromosome Aberrations; D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D015894:Genome, Human; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D007621:Karyotyping; D008875:Middle Aged; D009363:Neoplasm Proteins / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D027383:Papillomaviridae / Q000235:genetics; D030361:Papillomavirus Infections / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D012334:RNA, Neoplasm / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic; D044767:Ubiquitin-Protein Ligases / Q000235:genetics; D002583:Uterine Cervical Neoplasms / Q000235:genetics* / Q000473:pathology / Q000821:virology
D009363:Neoplasm Proteins; D012333:RNA, Messenger; D012334:RNA, Neoplasm; C475669:DTX3L protein, human; D044767:Ubiquitin-Protein Ligases; C403624:ATP2C1 protein, human; D000252:Calcium-Transporting ATPases