PXD012230 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells |
Description | An integrated systems approach was used with bioinformatics tools to understand the the role of aldehyde dehydrogenase 1A1 (ALDH1A1) in human colon cancer cells. We combined transcriptomics, proteomics and untargeted metabolomics to gain insight into the mechanisms affected by the suppression of the ALDH1A1 gene in COLO320 cells. RNA-seq and proteomics analyses revealed 1747 transcripts and 336 proteins that were differentially expressed in cells in which the ALDH1A1 had been suppressed by shRNA transfection. Transcriptomics pathway analysis showed significant signaling pathways, such as Wnt/β-catenin (p=3.47E-6), molecular mechanisms of cancer (7.41E-5) and others relevant to lipid metabolism, such as cholesterol biosynthesis I, II and III (p=1.82E-4). Proteomics pathway analysis identified oxidative phosphorylation to be the most highly significant pathway (p=5.01E-31). Pathway analysis of the genes common to the transcriptomics and proteomics analyses revealed the asparagine biosynthesis (p=3.16E-3) and cholesterol biosynthesis the most statistically significant (p=3.36E-3). Univariate analysis of the untargeted metabolomics dataset revealed 859 ions statistically significant. Network analysis showed alterations in pathways linked to energy and lipid metabolism, such carnitine shuttle (p=5.3E-4) and fatty acid oxidation (p=2.9E-2). A systems biology approach was used to integrate all three datasets and a total of 61 pathways were generated. A direct association between the suppression of ALDH1A1 and the Vitamin A (retinol) metabolism pathway and down-regulation of retinol and the UGT2B17, UGT2A3 and PRDX6 genes was shown. In conclusion, the present results confirm the role of ALDH1A1 in retinol metabolism and shows for the first time the influence of this gene on lipid metabolism pathways that may be crucial for cholesterol synthesis in human colon cancer cells. In addition, they demonstrate how an integrated systems approach using unbiased bioinformatics tools can be used to understand the interplay of cellular pathways. |
HostingRepository | PRIDE |
AnnounceDate | 2021-09-08 |
AnnouncementXML | Submission_2021-09-08_08:35:56.713.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | TuKiet Lam |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue |
Instrument | Orbitrap Fusion |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-01-03 03:53:10 | ID requested | |
⏵ 1 | 2021-09-08 08:35:57 | announced | |
Publication List
Charkoftaki G, Thompson DC, Golla JP, Garcia-Milian R, Lam TT, Engel J, Vasiliou V, Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells. Chem Biol Interact, 304():88-96(2019) [pubmed] |
Keyword List
curator keyword: Biomedical |
submitter keyword: aldehyde dehydrogenase 1A1 |
COLO320 |
transcriptomics |
proteomics |
metabolomics |
colorectal cancer |
mass spectrometry |
Contact List
TuKiet Lam |
contact affiliation | Yale University; Keck MS & Proteomics Resource |
contact email | tukiet.lam@yale.edu |
lab head | |
TuKiet Lam |
contact affiliation | Yale University |
contact email | tukiet.lam@yale.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD012230
- Label: PRIDE project
- Name: Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells