PXD011162-1

PXD011162 is an original dataset announced via ProteomeXchange.

Title	Hepatomasys .
Description	Metabolic alterations can serve as targets for diagnosis and therapy of cancer. Due to the highly complex regulation of cellular metabolism, definite identification of metabolic pathway alterations remains challenging and requires sophisticated experimentation. Here, we applied a comprehensive kinetic model of the central carbon metabolism (CCM) to characterize metabolic reprogramming in murine liver cancer. We show that relative differences of protein abundances of metabolic enzymes obtained by mass spectrometry can be used to scale maximal enzyme capacities. Model simulations predicted tumor-specific alterations of various components of the CCM, a selected number of which were subsequently verified by in vitro and in vivo experiments. Furthermore, we demonstrate the ability of the kinetic model to identify metabolic pathways whose inhibition results in selective tumor cell killing. Our systems biology approach establishes that combining cellular experimentation with computer simulations of physiology-based metabolic models enables a comprehensive understanding of deregulated energetics in cancer.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_10:19:05.304.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Guido Mastrobuoni
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-24 01:12:43	ID requested
⏵ 1	2024-10-07 10:19:06	announced

10.1038/s41416-019-0659-3;

Berndt N, Egners A, Mastrobuoni G, Vvedenskaya O, Fragoulis A, Dugourd A, Bulik S, Pietzke M, Bielow C, van Gassel R, Damink SWO, Erdem M, Saez-Rodriguez J, Holzh, ü, tter HG, Kempa S, Cramer T, Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer. Br J Cancer, 122(2):233-244(2020) [pubmed]

curator keyword: Biomedical

submitter keyword: shotgun proteomics, mass spectrometry, liver cancer,hepatocellular carcinoma

Stefan Kempa
contact affiliation	Berlin Institute for Medical System Biology @ Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association Robert-Rössle-Straße 10, 13125 Berlin, Germany
contact email	stefan.kempa@mdc-berlin.de
lab head
Guido Mastrobuoni
contact affiliation	Berlin Institute for Medical Systems Biology at the Max Delbrueck Centrum for Molecular Medicine
contact email	guido.mastrobuoni@mdc-berlin.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/03/PXD011162

PRIDE project URI

• PRIDE
  1. PXD011162
     1. Label: PRIDE project
     2. Name: Hepatomasys