Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling by high throughput sequencing of HeLa human cancer cell line

ABSTRACT: Illumina single-end sequencing of Hela_2 (HeLa cell line). While the number and identity of proteins expressed in a single human cell type is currently unknown, this fundamental question can be addressed by advanced mass spectrometry (MS)-based proteomics. On-line liquid chromatography coupled to high resolution MS and MS/MS yielded more than 150,000 unique peptides that identified more than 10,000 different human proteins encoded by more than 9,000 human genes. Deep transcriptome sequencing revealed transcripts for nearly all detected proteins. We show that the abundances of more than 90% of proteins and transcripts fall within a 10,000-fold range, and allocate the proteome to different compartments, complexes and functions. Comparisons of the proteome and the transcriptome, and analysis of protein complex databases and GO categories, suggest that we achieved almost complete coverage of the functional transcriptome and the proteome of a single cell type.

ORGANISM(S): Homo sapiens

SUBMITTER: Janet Kelso

PROVIDER: E-MTAB-823 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Deep proteome and transcriptome mapping of a human cancer cell line.

Nagaraj Nagarjuna N Wisniewski Jacek R JR Geiger Tamar T Cox Juergen J Kircher Martin M Kelso Janet J Pääbo Svante S Mann Matthias M

Molecular systems biology 20111108

While the number and identity of proteins expressed in a single human cell type is currently unknown, this fundamental question can be addressed by advanced mass spectrometry (MS)-based proteomics. Online liquid chromatography coupled to high-resolution MS and MS/MS yielded 166 420 peptides with unique amino-acid sequence from HeLa cells. These peptides identified 10 255 different human proteins encoded by 9207 human genes, providing a lower limit on the proteome in this cancer cell line. Deep t ...[more]

PMID: 22068331

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Project description:Sudden cardiac death (SCD) associated with heart failure (HF) is a multifactorial problem requiring a systems level approach applied to suitable experimental animal models with features of the human disease. Here we examine key regulatory pathways underlying the transition from compensated hypertrophy (HYP) to decompensated HF and SCD by integrated analysis of the transcriptome, proteome and metabolome. In a guinea pig model of acquired long QT syndrome and HF/SCD, relative protein abundances from sham-operated, HYP and HF hearts were assessed using isobaric tags for relative and absolute quantification (iTRAQ), prior to liquid chromatography and tandem mass spectrometry (LC-MS/MS). Metabolites were quantified by LC-MS/MS or gas chromatography coupled to MS (GC-MS). Transcriptome profiles were obtained using DNA microarrays. The guinea pig HF proteome exhibited classic biosignatures of cardiac HYP, left ventricular dysfunction, fibrosis, cellular degeneration, inflammation and extravasation. Fatty acid metabolism, mitochondrial transcription/translation factors, antioxidant enzymes, and other mitochondrial processes, were downregulated in HF, but not HYP. Proteins upregulated in HF are consistent with extracellular matrix remodeling, cytoskeletal remodeling, and acute phase inflammation markers. Among metabolites, downregulation of acyl-carnitines was observed in HYP, while fatty acids accumulated in HF. Levels of the tricarboxylic acid (TCA) cycle metabolite, citrate, and the potent inhibitor, 2-methylcitrate, increased upon transition from HYP to HF. Correlation of the magnitude of transcript and protein changes in HF is weak (R2=0.23), indicating that targeting transcript/proteome may reveal inform post-transcriptional gene regulation in HF. Proteome/Metabolome integration suggests metabolic bottlenecks in fatty acyl-CoA processing by carnitine palmitoyl transferase (CPT1B) as well as TCA cycle inhibition. We present a model in which hallmarks of acute signaling in HF, including Ca2+ dysregulation and low cAMP levels, are coupled to mitochondrial metabolic and antioxidant defects, through a CREB/PGC1-alpha transcriptional axis.

Dataset Information

Transcription profiling by high throughput sequencing of HeLa human cancer cell line

Publications

Deep proteome and transcriptome mapping of a human cancer cell line.

Similar Datasets

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