PXD021014-1

PXD021014 is an original dataset announced via ProteomeXchange.

Title	Compartmentalized proteomic profiling outlines the crucial role of the Classical secretory pathway during recombinant protein production in Chinese hamster ovary cells
Description	Chinese hamster ovary (CHO) cells have been widely employed for production of recombinant proteins (RP) for research and therapeutic purposes. Indeed, this expression system was used for production of most of approved antibodies (84%) in 2015-2018 period. The success of this cell line for RP production relies on several advantages that comprise but are not limited to a safety viral profile, human compatible glycosylation, development of specific culture mediums and supplements, availability of sub-lines with different capabilities and the improvement in design of DNA vectors and selection strategies that allows to obtain higher producer clones in an easier way. Given the high importance of this cell line, a deeper knowledge of their biology through genomic, transcriptomic, proteomic and metabolomic studies has been gained in the last years. These studies have aid in the exploration of molecular and cellular mechanisms that could explain cell behavior and to propose new targets to improve production and quality of RP. Some of these transcriptomic and proteomic profiles have been acquired under low temperature, butyrate addition, hyperosomotic pressure, protein degradation phenotypes, cellular engineering, production stability and productive phenotypes. In case of productive phenotypes, several whole cell proteomic studies have been previously reported, where cell populations secreting fusion proteins, monoclonal antibodies (mAb) and antibody fragments, at different specific productivity (Qp), have been compared. However, because of this information has been obtained from whole cell homogenates, highlighted categories represent abundant proteins and have limited coverage of proteome from some organelles such as the classical secretory pathway. Due to the central role of this pathway in protein and lipid metabolism, organelle biogenesis, cell cycle, apoptosis and proliferation, and to be recognized as a bottleneck for protein secretion in mammalian cells, its characterization through subcellular proteomics represents a promising strategy for identification of key targets. In fact, over-expression of some proteins from endoplasmic reticulum and Golgi Apparatus has increased the Qp of HEK293 and CHO cells producing different RP. Recently, proteomic reports of subcellular compartments from a variety of cells have been extensively used to study the protein composition of organelles, protein dynamics and discovering of novel proteins involved in the secretion pathway. Thus, this approach was applied to the secretory pathway of CHO cells to identify novel proteins linked to Qp in the present study. Differential proteomics from all remaining compartments was also carried out, giving new lights over other cellular mechanisms associated to the higher producer phenotype. The novel differentially expressed proteins (DEP) found will improve the engineering strategies of CHO cells that will have a positive impact on titer and quality of RP. Cell lines CHO DP-12 clone #1933 CRL-12444 and clone #1934 CRL-12445, which secrete a mAb against human interleukin 8 (IL-8), were used as cell models of recombinant CHO cell lines producing the same RP at different Qp. Our goal is that the processing of raw proteomics data and the identification and classification of DEP belonging to the classical secretory pathway will allow to propose a model by which the increase in the productivity of CHO cells has been associated with the deregulation of proteins from this pathway that show differential expression among the clones under study. This strategy of subcellular proteomics allowed us to identify a large number of new targets and cell pathways with respect to previous whole cell proteomic studies, which can improve the understanding of the molecular mechanisms behind RP production and provide the basis to design new sub-lines with stronger capabilities.
HostingRepository	PRIDE
AnnounceDate	2021-05-04
AnnouncementXML	Submission_2021-05-03_22:37:46.389.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Saumel Perez Rodriguez
SpeciesList	scientific name: Cricetulus griseus; NCBI TaxID: 10029;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-19 23:34:24	ID requested
⏵ 1	2021-05-03 22:37:46	announced

Dataset with its publication pending

submitter keyword: Chinese hamster ovary cell, Subcellular fractionation, Proteomics, Classical secretory pathway

Norma Adriana Valdez Cruz
contact affiliation	Laboratorio C036, Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Ciudad de México, México
contact email	adrivaldez1@gmail.com
lab head
Saumel Perez Rodriguez
contact affiliation	Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México
contact email	saumel840217@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021014
     1. Label: PRIDE project
     2. Name: Compartmentalized proteomic profiling outlines the crucial role of the Classical secretory pathway during recombinant protein production in Chinese hamster ovary cells