title: Identification and selective degradation of neopeptide-containing truncated mutant proteins in the tumors with high microsatellite instability.
abstract: OBJECTIVE
  Frameshift mutations in coding mononucleotide repeats (cMNR) are common in tumors with high microsatellite instability (MSI-H). These mutations generate mRNAs containing abnormal coding sequences and premature termination codons (PTC). Normally, mRNAs containing PTCs are degraded by nonsense-mediated mRNA decay (NMD). However, mRNAs containing PTCs located in the last exon are not subject to degradation by NMD (NMD-irrelevant). This study aimed to discover whether genes with frameshift mutations in the last exon generate truncated mutant proteins.
  
  
  METHODS
  We identified 66 genes containing cMNRs in the last exon by bioinformatic analysis. We found frequent insertion/deletion mutations in the cMNRs of 29 genes in 10 MSI-H cancer cell lines and in the cMNRs of 3 genes in 19 MSI-H cancer tissues. We selected 7 genes (TTK, TCF7L2, MARCKS, ASTE1, INO80E, CYHR1, and EBPL) for mutant mRNA expression analysis and 3 genes (TTK, TCF7L2, and MARCKS) for mutant protein expression analysis.
  
  
  RESULTS
  The PTC-containing NMD-irrelevant mRNAs from mutated genes were not degraded. However, only faint amounts of endogenous mutant TTK and TCF7L2 were detected, and we failed to detect endogenous mutant MARCKS. By polysome analysis, we showed that mRNAs from genomic mutant MARCKS constructs are normally translated. After inhibiting 3 protein degradation pathways, we found that only inhibition of the proteasomal pathway facilitated the rescue of endogenous mutant TTK, TCF7L2, and MARCKS.
  
  
  CONCLUSIONS
  Our findings indicate that cancer cells scavenge potentially harmful neopeptide-containing mutant proteins derived from NMD-irrelevant abnormal mRNAs via the ubiquitin-proteasome system, and these mutant proteins may be important substrates for tumor-specific antigens.
authors.affiliation: Department of Pathology and Brain Korea 21 Projects for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea.
authors.forename: Won Kyu
authors.initials: WK
authors.lastname: Kim
authors.forename: Misun
authors.initials: M
authors.lastname: Park
authors.forename: Minhee
authors.initials: M
authors.lastname: Park
authors.forename: Yun Ji
authors.initials: YJ
authors.lastname: Kim
authors.forename: Nara
authors.initials: N
authors.lastname: Shin
authors.forename: Hyun Ki
authors.initials: HK
authors.lastname: Kim
authors.forename: Kwon Tae
authors.initials: KT
authors.lastname: You
authors.forename: Hoguen
authors.initials: H
authors.lastname: Kim
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D045744:Cell Line, Tumor; D018385:Centrosome / Q000378:metabolism; D018389:Codon, Nonsense; D015179:Colorectal Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D005091:Exons; D005260:Female; D016368:Frameshift Mutation; D015870:Gene Expression; D020869:Gene Expression Profiling; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics / Q000378:metabolism; D008297:Male; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D053842:Microsatellite Instability; D008875:Middle Aged; D050505:Mutant Proteins / Q000235:genetics* / Q000378:metabolism*; D000076250:Myristoylated Alanine-Rich C Kinase Substrate; D060787:Neoplasm Grading; D009367:Neoplasm Staging; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism*; D011132:Polyribosomes / Q000378:metabolism; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism; D017346:Protein Serine-Threonine Kinases / Q000235:genetics / Q000378:metabolism; D021381:Protein Transport; D011505:Protein-Tyrosine Kinases / Q000235:genetics / Q000378:metabolism; D059748:Proteolysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D058118:Transcription Factor 7-Like 2 Protein / Q000235:genetics / Q000378:metabolism; D054875:Ubiquitination
chemical_list: D018797:Cell Cycle Proteins; D018389:Codon, Nonsense; D047908:Intracellular Signaling Peptides and Proteins; C000619710:MARCKS protein, human; D008565:Membrane Proteins; D050505:Mutant Proteins; D012333:RNA, Messenger; D058118:Transcription Factor 7-Like 2 Protein; D000076250:Myristoylated Alanine-Rich C Kinase Substrate; D011505:Protein-Tyrosine Kinases; D017346:Protein Serine-Threonine Kinases; C075840:TTK protein, human; D046988:Proteasome Endopeptidase Complex