ArticleCancer research2009
Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer.
Article in Cancer research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it, 74 citations in OpenAlex.
- Glucose metabolic phenotype of pancreatic cancer.World journal of gastroenterology · 2016Pooled it
- A Proteogenomic Approach for the Identification of Virulence Factors in Leishmania Parasites.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Splice variants as novel targets in pancreatic ductal adenocarcinoma.Scientific reports · 2017Article
- Tutorial on Protein Ontology Resources.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Review
- Strategies for Genomic and Proteomic Profiling of Cancers.Statistics in biosciences · 2016Article
- Decreased Serum Thrombospondin-1 Levels in Pancreatic Cancer Patients Up to 24 Months Prior to Clinical Diagnosis: Association with Diabetes Mellitus.Clinical cancer research : an official journal of the American Association for Cancer Research · 2016Article
- Proteomics analysis of bodily fluids in pancreatic cancer.Proteomics · 2015Review
- Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.PLoS computational biology · 2015Article
- Overexpression of Rad51C splice variants in colorectal tumors.Oncotarget · 2015Article
- Identification of sialylated glycoproteins from metabolically oligosaccharide engineered pancreatic cells.Clinical proteomics · 2015Article
- Mapping Splicing Quantitative Trait Loci in RNA-Seq.Cancer informatics · 2015Article
- Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence.Proteomics · 2014Article
- Proteogenomics: concepts, applications and computational strategies.Nature methods · 2014Review
- Onco-proteogenomics: cancer proteomics joins forces with genomics.Nature methods · 2014Article
- The emerging era of genomic data integration for analyzing splice isoform function.Trends in genetics : TIG · 2014Review
- A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines.Journal of proteomics · 2014Review
- Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics.Journal of proteome research · 2014Review
- Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins.Biochimica et biophysica acta · 2014Article
- Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani.Journal of proteomics · 2014Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 1 country.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.