title: Proteogenomic Study beyond Chromosome 9: New Insight into Expressed Variant Proteome and Transcriptome in Human Lung Adenocarcinoma Tissues.
abstract: This is a report of a human proteome project (HPP) related to chromosome 9 (Chr 9). To reveal missing proteins and undiscovered features in proteogenomes, both LC-MS/MS analysis and next-generation RNA sequencing (RNA-seq)-based identification and characterization were conducted on five pairs of lung adenocarcinoma tumors and adjacent nontumor tissues. Before our previous Chromosome-Centric Human Proteome Project (C-HPP) special issue, there were 170 remaining missing proteins on Chr 9 (neXtProt 2013.09.26 rel.); 133 remain at present (neXtProt 2015.04.28 rel.). In the proteomics study, we found two missing protein candidates that require follow-up work and one unrevealed protein across all chromosomes. RNA-seq analysis detected RNA expression for four nonsynonymous (NS) single nucleotide polymorphisms (SNPs) (in CDH17, HIST1H1T, SAPCD2, and ZNF695) and three synonymous SNPs (in CDH17, CST1, and HNF1A) in all five tumor tissues but not in any of the adjacent normal tissues. By constructing a cancer patient sample-specific protein database based on individual RNA-seq data and by searching the proteomics data from the same sample, we identified four missense mutations in four genes (LTF, HDLBP, TF, and HBD). Two of these mutations were found in tumor samples but not in paired normal tissues. In summary, our proteogenomic study of human primary lung tumor tissues detected additional and revealed novel missense mutations and synonymous SNP signatures, some of which are specific to lung cancers. Data from mass spectrometry have been deposited in the ProteomeXchange with the identifier PXD002523.
authors.affiliation: Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, South Korea.
authors.forename: Yong-In
authors.initials: YI
authors.lastname: Kim
authors.affiliation: Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul 06351, South Korea.
authors.forename: Jongan
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, South Korea.|ProtAnBio , Seoul 08826, South Korea.
authors.forename: Young-Jin
authors.initials: YJ
authors.lastname: Choi
authors.affiliation: Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, South Korea.
authors.forename: Jawon
authors.initials: J
authors.lastname: Seo
authors.affiliation: Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul 06351, South Korea.
authors.forename: Jisook
authors.initials: J
authors.lastname: Park
authors.affiliation: Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul 06351, South Korea.|Department of Clinical Pharmacology & Therapeutics, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul 06351, South Korea.
authors.forename: Soo-Youn
authors.initials: SY
authors.lastname: Lee
authors.affiliation: Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, South Korea.
authors.forename: Je-Yoel
authors.initials: JY
authors.lastname: Cho
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000378:metabolism*; D000077192:Adenocarcinoma of Lung; D000328:Adult; D000368:Aged; D015820:Cadherins / Q000235:genetics / Q000378:metabolism; D002899:Chromosomes, Human, Pair 9; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000378:metabolism*; D008297:Male; D008875:Middle Aged; D020125:Mutation, Missense; D010455:Peptides / Q000032:analysis / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D020543:Proteome / Q000235:genetics; D011544:Pseudogenes; D062085:RNA, Long Noncoding; D017423:Sequence Analysis, RNA; D053719:Tandem Mass Spectrometry
chemical_list: C490584:CDH17 protein, human; D015820:Cadherins; D010455:Peptides; D020543:Proteome; D062085:RNA, Long Noncoding
keywords: C-HPP; lung cancer; missense mutation; missing protein; proteogenomics; variant protein