Copy number alterations in pancreatic cancer identify recurrent PAK4 amplification.
Pancreatic cancer is one of the most lethal of all cancers. The median survival is six months and less than 5% of those diagnosed survive five years. Recurrent genetic deletions and amplifications in 72 pancreatic adenocarcinomas, the largest sample set analyzed to date for pancreatic cancer, were defined using comparative genomic hybridization The recurrent genetic alterations identified target a number of previously well-characterized genes, as well as regions that contain possible new oncogenes and tumor suppressor genes. We have focused on chromosome 19q13, a region frequently found amplified in pancreatic cancer and demonstrate how boundaries of common regions of mutation can be mapped and how a gene, in this case PAK4 amplified on chromosome19q13, can be functionally validated. We show that although the PAK4 gene is not activated by mutation in cell lines with gene amplification, an oncogenic form of the KRAS2 gene is present in these cells and oncogenic KRAS2 can activate PAK4. In fact in the three samples we identified with PAK4 gene amplification, the KRAS2 gene was activated and genomically amplified. The kinase activity of the PAK4 protein is significantly higher in cells with genomic amplification as compared to cells without amplification. Our study demonstrates the utility of analyzing copy number data in a large set of neoplasms to identify genes involved in cancer. We have generated a useful dataset which will be particularly useful for the pancreatic cancer community as efforts are undertaken to sequence the pancreatic cancer genome.
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, New York, USA.
Shuaili
S
Chen
Theresa
T
Auletta
Ostap
O
Dovirak
Christina
C
Hutter
Karen
K
Kuntz
Samira
S
El-ftesi
Jude
J
Kendall
Haiyong
H
Han
Daniel D
DD
Von Hoff
Raheela
R
Ashfaq
Anirban
A
Maitra
Christine A
CA
Iacobuzio-Donahue
Ralph H
RH
Hruban
Robert
R
Lucito
D000818:Animals; D045744:Cell Line, Tumor; D002888:Chromosomes, Human, Pair 19 / Q000235:genetics; D005784:Gene Amplification; D018628:Gene Dosage; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D051379:Mice; D008957:Models, Genetic; D009154:Mutation; D009368:Neoplasm Transplantation; D010190:Pancreatic Neoplasms / Q000235:genetics / Q000378:metabolism*; D011518:Proto-Oncogene Proteins / Q000378:metabolism; D016283:Proto-Oncogene Proteins p21(ras); D054462:p21-Activated Kinases / Q000378:metabolism*; D018631:ras Proteins / Q000378:metabolism
C117307:KRAS protein, human; D011518:Proto-Oncogene Proteins; C116367:PAK4 protein, human; D054462:p21-Activated Kinases; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins