PXD023388

PXD023388 is an original dataset announced via ProteomeXchange.

Title	Chronological mitochondrial proteomics of chemically induced hepatocellular carcinoma in rat
Description	Although disruption of mitochondrial function has been associated with energetic deregulation in cancer, the chronological changes in mitochondria during cancer development remain unclear. With the aim to assess the role of mitochondria throughout cancer development, we analyzed samples chronologically obtained from induced hepatocellular carcinoma (HCC) in rats. In our analyses, we integrated mitochondrial proteomic data, mitochondrial metabolomic data and nuclear genome transcriptomic data. We used pathway over-representation and weighted gene co-expression network analysis (WGCNA) to integrate expression profiles of genes, miRNAs, proteins and metabolite levels throughout HCC development. Our results show that mitochondria are dynamic organelles presenting specific modifications in different stages of HCC development. For carcinogenesis, a modified resistant hepatocyte model was used. Rats were initiated with diethylnitrosamine (DEN) (200 mg/kg of body weight) at day 0. Then, 2-acetylaminofluorene (AAF) was administered (20 mg/kg per dose) at days 7, 8 and 9, followed by 3/5 partial hepatectomy (PH) at day 10. Three control groups of non-treated animals were sacrificed by exsanguination on the first day and at 9 and 18 months after the beginning of the experiment. Treated animals were sacrificed at 1, 7, 11 and 16 days and at 1, 9 and 18 months. Their livers were excised, washed in physiological saline solution, frozen with liquid nitrogen in 2-methyl butane and stored at -80°C. Once selected and separately collected nodular, tumoral and its adjacent tissues, total RNA was isolated using TriPureIsolation Reagent (Roche) according to the manufacturer’s protocol. The microarray analysis was performed using GeneChip Rat Exon 1.0 ST Arrays. Four replicas for each condition and controls were analyzed. This created 11 pairwise contrasts for the differential expression analysis. We grouped all evaluated conditions in three categories: i) early stages, including samples obtained since day one until one month after treatment, these were compared against rats without treatment sacrificed the first day; ii) tumor, nodular and its adjacent tissues obtained from nine months rats were compared against rats without treatment of the same age; and iii) tumor and its adjacent tissues obtained from eighteen months rats were compared against rats without treatment of the same age.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-09_15:57:35.664.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rafael Montiel
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-04 03:59:44	ID requested
⏵ 1	2021-09-09 15:57:36	announced

Garc, í, a-Ch, á, vez JN, V, á, squez-Garz, ó, n VR, L, ó, pez MG, Villa-Trevi, ñ, o S, Montiel R, Integration of chronological omics data reveals mitochondrial regulatory mechanisms during the development of hepatocellular carcinoma. PLoS One, 16(8):e0256016(2021) [pubmed]

submitter keyword: rat, hepatocellular carcinoma, mitochondria, omics integration, chronological study, shotgun proteomics

Rafael Montiel
contact affiliation	Langebio, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
contact email	rafael.montiel@cinvestav.mx
lab head
Rafael Montiel
contact affiliation	LANGEBIO-CINVESTAV
contact email	rafael.montiel@cinvestav.mx
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD023388
     1. Label: PRIDE project
     2. Name: Chronological mitochondrial proteomics of chemically induced hepatocellular carcinoma in rat