Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer.
To assess the potential of tumor-associated, alternatively spliced gene products as a source of biomarkers in biological fluids, we have analyzed a large data set of mass spectra derived from the plasma proteome of a mouse model of human pancreatic ductal adenocarcinoma. MS/MS spectra were interrogated for novel splice isoforms using a nonredundant database containing an exhaustive three-frame translation of Ensembl transcripts and gene models from ECgene. This integrated analysis identified 420 distinct splice isoforms, of which 92 did not match any previously annotated mouse protein sequence. We chose seven of those novel variants for validation by reverse transcription-PCR. The results were concordant with the proteomic analysis. All seven novel peptides were successfully amplified in pancreas specimens from both wild-type and mutant mice. Isotopic labeling of cysteine-containing peptides from tumor-bearing mice and wild-type controls enabled relative quantification of the proteins. Differential expression between tumor-bearing and control mice was notable for peptides from novel variants of muscle pyruvate kinase, malate dehydrogenase 1, glyceraldehyde-3-phosphate dehydrogenase, proteoglycan 4, minichromosome maintenance, complex component 9, high mobility group box 2, and hepatocyte growth factor activator. Our results show that, in a mouse model for human pancreatic cancer, novel and differentially expressed alternative splice isoforms are detectable in plasma and may be a source of candidate biomarkers.
Menon
Rajasree
R
Center for Computational Medicine and Biology and Pediatric Endocrinology, University of Michigan, 100 Washtenaw Avenue, Palmer Commons, Ann Arbor, MI 48109, USA.
Zhang
Qing
Q
Zhang
Yan
Y
Fermin
Damian
D
Bardeesy
Nabeel
N
DePinho
Ronald A
RA
Lu
Chunxia
C
Hanash
Samir M
SM
Omenn
Gilbert S
GS
States
David J
DJ
D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D001798:Blood Proteins / Q000235:genetics; D004195:Disease Models, Animal; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins / Q000097:blood* / Q000235:genetics*; D010190:Pancreatic Neoplasms / Q000097:blood* / Q000235:genetics*; D020033:Protein Isoforms; D020133:Reverse Transcriptase Polymerase Chain Reaction
D001798:Blood Proteins; D009363:Neoplasm Proteins; D020033:Protein Isoforms