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Combined array comparative genomic hybridization and tissue microarray analysis suggest PAK1 at 11q13.5-q14 as a
Peter Schraml1, Georg Schwerdtfeger, Felix Burkhalter
1Institute of Pathology, University Hospital, University of Basel, Schönbeinstrasse 40, 4031 Basel, Switzerland. peter.schraml@unibas.ch
Abstract:
Amplification of chromosomal regions leads to an increase of DNA copy numbers and expression of oncogenes in many human tumors. The identification of tumor-specific oncogene targets has potential diagnostic and therapeutic implications. To identify distinct spectra of oncogenic alterations in ovarian carcinoma, metaphase comparative genomic hybridization (mCGH), array CGH (aCGH), and ovarian tumor tissue microarrays were used in this study. Twenty-six primary ovarian carcinomas and three ovarian carcinoma cell lines were analyzed by mCGH. Frequent chromosomal overrepresentation was observed on 2q (31%), 3q (38%), 5p (38%), 8q (52%), 11q (21%), 12p (21%), 17q (21%), and 20q (52%). The role of oncogenes residing in gained chromosomal loci was determined by aCGH with 59 genetic loci commonly amplified in human tumors. DNA copy number gains were most frequently observed for PIK3CA on 3q (66%), PAK1 on 11q (59%), KRAS2 on 12p (55%), and STK15 on 20q (55%). The 11q13-q14 amplicon, represented by six oncogenes (CCND1, FGF4, FGF3, EMS1, GARP, and PAK1) revealed preferential gene copy number gains of PAK1, which is located at 11q13.5-q14. Amplification and protein expression status of both PAK1 and CCND1 were further examined by fluorescence in situ hybridization and immunohistochemistry using a tissue microarray consisting of 268 primary ovarian tumors. PAK1 copy number gains were observed in 30% of the ovarian carcinomas and PAK1 protein was expressed in 85% of the tumors. PAK1 gains were associated with high grade (P < 0.05). In contrast, CCND1 gene alterations and protein expression were less frequent (10.6% and 25%, respectively), suggesting that the critical oncogene target of amplicon 11q13-14 lies distal to CCND1. This study demonstrates that aCGH facilitates further characterization of oncogene candidates residing in amplicons defined by mCGH.
Insights
This study identified frequent chromosomal alterations in ovarian cancer, pinpointing PAK1 as a key oncogene target on chromosome 11q13-14. PAK1 amplification and expression correlate with high-grade tumors, suggesting its diagnostic and therapeutic potential.
Area of Science:
- Genomics and Cancer Biology
- Oncology
- Molecular Diagnostics
Background:
- Chromosomal amplifications increase oncogene copy numbers and expression in human tumors.
- Identifying tumor-specific oncogene targets is crucial for ovarian cancer diagnostics and therapeutics.
Purpose of the Study:
- To identify distinct spectra of oncogenic alterations in ovarian carcinoma.
- To characterize oncogene candidates within amplified chromosomal regions.
Main Methods:
- Metaphase comparative genomic hybridization (mCGH) and array CGH (aCGH) were employed.
- Ovarian tumor tissue microarrays were used for analyzing 268 primary ovarian tumors.
- Fluorescence in situ hybridization and immunohistochemistry assessed PAK1 and CCND1 amplification and protein expression.
Main Results:
- Frequent chromosomal overrepresentation was observed on 2q, 3q, 5p, 8q, 11q, 12p, 17q, and 20q in ovarian carcinomas.
- Array CGH identified frequent DNA copy number gains for PIK3CA (3q), PAK1 (11q), KRAS2 (12p), and STK15 (20q).
- PAK1 copy number gains (30%) and protein expression (85%) were frequent, associated with high-grade ovarian tumors, unlike CCND1.
Conclusions:
- Array CGH effectively characterizes oncogene candidates within amplicons identified by mCGH.
- PAK1 emerges as a critical oncogene target within the 11q13-14 amplicon in ovarian carcinoma.
- PAK1 amplification and expression correlate with high-grade tumors, indicating potential diagnostic and therapeutic value.