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Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project

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Author

  • Paula Diez
  • Conrad Droste
  • Rosa M. Degano
  • Maria Gonzalez-Munoz
  • Nieves Ibarrola
  • Martin Perez-Andres
  • Alba Garin-Muga
  • Victor Segura
  • György Marko-Varga
  • Joshua LaBaer
  • Alberto Orfao
  • Fernando J. Corrales
  • Javier De Las Rivas
  • Manuel Fuentes
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Summary, in English

A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of different proteins active in a cell. Thus, the Chromosome-centric Human Proteome Project (C-HPP) is promoting a full characterization of the human proteome combining high-throughput proteomics with the data derived from genome-wide expression profiling of protein-coding genes. Here we present a full proteomic profiling of a human lymphoma B-cell line (Ramos) performed using a nanoUPLC-LTQ-Orbitrap Velos proteomic platform, combined to an in-depth transcriptomic profiling of the same cell type. Data are available via ProteomeXchange with identifier PXD001933. Integration of the proteomic and transcriptomic data sets revealed a 94% overlap in the proteins identified by both -omics approaches. Moreover, functional enrichment analysis of the proteomic profiles showed an enrichment of several functions directly related to the biological and morphological characteristics of B-cells. In turn, about 30% of all protein-coding genes present in the whole human genome were identified as being expressed by the Ramos cells (stable average of 30% genes along all the chromosomes), revealing the size of the protein expression-set present in one specific human cell type. Additionally, the identification of missing proteins in our data sets has been reported, highlighting the power of the approach. Also, a comparison between neXtProt and UniProt database searches has been performed. In summary, our transcriptomic and proteomic experimental profiling provided a high coverage report of the expressed proteome from a human lymphoma B-cell type with a clear insight into the biological processes that characterized these cells. In this way, we demonstrated the usefulness of combining -omics for a comprehensive characterization of specific biological systems.

Publishing year

2015

Language

English

Pages

3530-3540

Publication/Series

Journal of Proteome Research

Volume

14

Issue

9

Document type

Journal article

Publisher

The American Chemical Society (ACS)

Topic

  • Medical Biotechnology
  • Cell and Molecular Biology

Keywords

  • C-HPP
  • lymphoma B-cell line
  • protein expression profile
  • transcriptomics
  • subcellular fractionation

Status

Published

ISBN/ISSN/Other

  • ISSN: 1535-3893