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

Paula Díez, Conrad Droste, Rosa M. Dégano, María González-Muñoz, Nieves Ibarrola, Martín Pérez-Andrés, Alba Garin-Muga, Víctor Segura, Gyorgy Marko-Varga, Joshua LaBaer, Alberto Orfao, Fernando J. Corrales, Javier De Las Rivas, Manuel Fuentes

Research output: Contribution to journalArticle

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Abstract

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.

Original languageEnglish (US)
Pages (from-to)3530-3540
Number of pages11
JournalJournal of Proteome Research
Volume14
Issue number9
DOIs
StatePublished - Sep 4 2015

Fingerprint

Human Chromosomes
Proteome
Chromosomes
Proteomics
Lymphoma
Cells
Cell Line
Genes
Proteins
Genome
Biological Phenomena
Depth profiling
Datasets
B-Cell Lymphoma
Human Genome
Biological systems
B-Lymphocytes
Throughput
Databases

Keywords

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

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

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. / Díez, Paula; Droste, Conrad; Dégano, Rosa M.; González-Muñoz, María; Ibarrola, Nieves; Pérez-Andrés, Martín; Garin-Muga, Alba; Segura, Víctor; Marko-Varga, Gyorgy; LaBaer, Joshua; Orfao, Alberto; Corrales, Fernando J.; De Las Rivas, Javier; Fuentes, Manuel.

In: Journal of Proteome Research, Vol. 14, No. 9, 04.09.2015, p. 3530-3540.

Research output: Contribution to journalArticle

Díez, P, Droste, C, Dégano, RM, González-Muñoz, M, Ibarrola, N, Pérez-Andrés, M, Garin-Muga, A, Segura, V, Marko-Varga, G, LaBaer, J, Orfao, A, Corrales, FJ, De Las Rivas, J & Fuentes, M 2015, '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', Journal of Proteome Research, vol. 14, no. 9, pp. 3530-3540. https://doi.org/10.1021/acs.jproteome.5b00474
Díez, Paula ; Droste, Conrad ; Dégano, Rosa M. ; González-Muñoz, María ; Ibarrola, Nieves ; Pérez-Andrés, Martín ; Garin-Muga, Alba ; Segura, Víctor ; Marko-Varga, Gyorgy ; LaBaer, Joshua ; Orfao, Alberto ; Corrales, Fernando J. ; De Las Rivas, Javier ; Fuentes, Manuel. / 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. In: Journal of Proteome Research. 2015 ; Vol. 14, No. 9. pp. 3530-3540.
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