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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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The mammalian target of rapamycin  (mTOR) is a serine/threonine kinase that regulates growth, proliferation, and cell survival in response to hormones, growth factors, or nutrient availability. This kinase exists in two structurally and functionally distinct forms: mTOR complex 1  (mTORC1) and mTOR complex 2  (mTORC2). The first form (mTORC1) is composed of a rapamycin-sensitive Raptor and proline-rich Akt substrate, PRAS40. In contrast,  mTORC2 consists of a...
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The mammalian target of rapamycin or mTOR protein was discovered in 1994 due to its direct interaction with rapamycin. The protein gets its name from a yeast homolog called TOR. The mTOR protein complex in mammalian cells plays a major role in balancing anabolic processes such as the synthesis of proteins, lipids, and nucleotides and catabolic processes, such as autophagy in response to environmental cues, such as availability of nutrients and growth factors.
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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies.

Marie Locard-Paulet1, Oana Palasca1, Lars Juhl Jensen1

  • 1Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark.

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Researchers identified 157 genes linked to cell proliferation rates using high-throughput data. This proliferation signature aids in interpreting complex biological data, such as drug screens and tumor samples, by accounting for cell division changes.

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Area of Science:

  • Genomics
  • Proteomics
  • Systems Biology

Background:

  • High-throughput profiling quantifies thousands of proteins or transcripts for differential gene expression analysis.
  • Applications include characterizing cell lines, tissues, drug mechanisms, and drug resistance.
  • Gene expression changes can be confounded by factors like cell proliferation, which are not always accounted for in experimental design.

Purpose of the Study:

  • To identify a gene signature correlating with cell proliferation rates.
  • To provide a resource for interpreting high-throughput biological data where proliferation changes are a factor.
  • To demonstrate the utility of this signature in analyzing drug screens and tumor samples.

Main Methods:

  • Combined analysis of proteomics and transcriptomics data from 1,076 and 1,040 cell lines.
  • Identification of genes significantly correlated with cell proliferation rates.
  • Development of a 157-gene cell proliferation signature.

Main Results:

  • Identified 157 genes associated with cell proliferation rates.
  • These genes are involved in DNA replication, mitosis, and cell cycle regulation.
  • The identified signature effectively correlates with cell proliferation across different conditions.

Conclusions:

  • The cell proliferation signature is a valuable tool for analyzing high-throughput data.
  • It helps interpret results from in vitro drug screens and tumor samples by accounting for proliferation differences.
  • The signature aids in distinguishing proliferation-driven changes from other biological or experimental effects.