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

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.

对人类细胞的分子活性全景开展系统性研究，可整合两种截然不同却互为补充的研究视角：转录组学（transcriptomics）与蛋白质组学（proteomics）。后基因组时代，蛋白质组学已成为强大的研究工具，可同时鉴定并表征细胞内活跃的数千种不同蛋白质的全集。因此，染色体中心人类蛋白质组计划（C-HPP）正推动人类蛋白质组的全面解析工作，将高通量蛋白质组学与蛋白质编码基因的全基因组表达谱数据相结合。本研究针对人类淋巴瘤B细胞系（Ramos）开展了全面的蛋白质组学表征，采用纳流超高效液相色谱-线性离子阱轨道阱Velos（nanoUPLC-LTQ-Orbitrap Velos）蛋白质组学平台，并同步对同一细胞类型进行了深度转录组学表征。相关数据可通过蛋白质组交换数据库（ProteomeXchange）获取，标识符为PXD001933。整合蛋白质组学与转录组学数据集后发现，两种组学方法鉴定得到的蛋白质重合度达94%。此外，对蛋白质组学表征结果进行功能富集分析后发现，多个与B细胞的生物学及形态学特征直接相关的功能模块得到显著富集。进一步分析显示，人类全基因组中约30%的蛋白质编码基因被鉴定为在Ramos细胞中表达（所有染色体上的基因平均表达占比稳定维持在30%左右），这一结果揭示了单一种类人类细胞所拥有的蛋白质表达谱规模。本研究还在数据集中鉴定到了缺失蛋白质（missing proteins），凸显了本研究方法的有效性。此外，本研究还针对neXtProt数据库与通用蛋白质知识库（UniProt）开展了检索比对分析。综上，本研究的转录组学与蛋白质组学实验表征实现了对人类淋巴瘤B细胞系表达蛋白质组的高覆盖度分析，并清晰揭示了该类细胞的核心生物学过程。本研究证实了整合多种组学技术对特定生物系统开展系统性解析的实用价值。