Chromosome-centric human proteome project: Deciphering proteins associated with glioma and neurodegenerative disorders on chromosome 12

Manoj Kumar Gupta, Savita Jayaram, Anil K. Madugundu, Sandip Chavan, Jayshree Advani, Akhilesh Pandey, Visith Thongboonkerd, Ravi Sirdeshmukh

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

In line with the aims of the Chromosome-centric Human Proteome Project (C-HPP) to completely annotate proteins of each chromosome and biology/disease driven HPP (B/D-HPP) to decipher their relation to diseases, we have generated a nonredundant catalogue of protein-coding genes for Chromosome 12 (Chr. 12) and further annotated proteins associated with major neurological disorders. Integrating high level proteomic evidence from four major databases (neXtProt, Global Proteome Machine (GPMdb), PeptideAtlas, and Human Protein Atlas (HPA)) along with Ensembl data resource resulted in the identification of 1066 protein coding genes, of which 171 were defined as "missing proteins" based on the weak or complete absence of experimental evidence. With functional annotations using DAVID and GAD, about 40% of the proteins could be grouped as brain related with implications in cancer or neurological disorders. We used published and unpublished high confidence mass spectrometry data from our group and other literature consisting of more than 5000 proteins derived from clinical specimens from patients with human gliomas, Alzheimers disease, and Parkinsons disease and mapped it onto Chr. 12. We observed a total of 202 proteins mapping to human Chr. 12, 136 of which were differentially expressed in these disease conditions as compared to the normal. Functional grouping indicated their association with cell cycle, cell-to-cell signaling, and other important processes and networks, whereas their disease association analysis confirmed neurological diseases and cancer as the major group along with psycological disorders, with several overexpressed genes/proteins mapping to 12q13-15 amplicon region. Using multiple strategies and bioinformatics tools, we identified 103 differentially expressed proteins to have secretory potential, 17 of which have already been reported in direct analysis of the plasma or cerebrospinal fluid (CSF) from the patients and 21 of them mapped to cancer associated protein (CAPs) database that are amenable to selective reaction monitoring (SRM) assays for targeted proteomic analysis. Our analysis also reveals, for the first time, mass spectrometric evidence for two "missing proteins" from Chr. 12, namely, synaptic vesicle 2-related protein (SVOP) and IQ motif containing D (IQCD). The analysis provides a snapshot of Chr. 12 encoded proteins associated with gliomas and major neurological conditions and their secretability which can be used to drive efforts for clinical applications.

Original languageEnglish (US)
Pages (from-to)3178-3190
Number of pages13
JournalJournal of Proteome Research
Volume13
Issue number7
DOIs
StatePublished - Jul 3 2014
Externally publishedYes

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Chromosomes, Human, Pair 12
Human Chromosomes
Proteome
Chromosomes
Glioma
Neurodegenerative Diseases
Proteins
Nervous System Diseases
Proteomics
Genes
Association reactions
Cell signaling
Neoplasms
Cerebrospinal fluid
Protein Databases
Synaptic Vesicles
Atlases
Chromosome Mapping
Computational Biology
Bioinformatics

Keywords

  • "missing proteins"
  • Alzheimers disease
  • B/D-HPP
  • CHPP
  • chromosome 12
  • glioma
  • Parkinsons disease
  • secretory proteins

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Chromosome-centric human proteome project : Deciphering proteins associated with glioma and neurodegenerative disorders on chromosome 12. / Gupta, Manoj Kumar; Jayaram, Savita; Madugundu, Anil K.; Chavan, Sandip; Advani, Jayshree; Pandey, Akhilesh; Thongboonkerd, Visith; Sirdeshmukh, Ravi.

In: Journal of Proteome Research, Vol. 13, No. 7, 03.07.2014, p. 3178-3190.

Research output: Contribution to journalArticle

Gupta, Manoj Kumar ; Jayaram, Savita ; Madugundu, Anil K. ; Chavan, Sandip ; Advani, Jayshree ; Pandey, Akhilesh ; Thongboonkerd, Visith ; Sirdeshmukh, Ravi. / Chromosome-centric human proteome project : Deciphering proteins associated with glioma and neurodegenerative disorders on chromosome 12. In: Journal of Proteome Research. 2014 ; Vol. 13, No. 7. pp. 3178-3190.
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