Dataset Information

Proteome profiling of ovarian cancer and cirrhosis ascites

ABSTRACT: Proteome-metabolome profiling of ovarian cancer ascites reveals novel components involved in intercellular communication http://www.mcponline.org/content/early/2014/09/30/mcp.M114.041194.full.pdf+html?sid=78e7a955-fa54-4ded-b296-89f1fb6adbec

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Ascites

DISEASE(S): Liver Cirrhosis,Malignant Neoplasm Of Ovary

SUBMITTER: Georgij Arapidi

LAB HEAD: Georgij Arapidi

PROVIDER: PXD001403 | Pride | 2014-10-23

REPOSITORIES: Pride

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Publications

Proteome-metabolome profiling of ovarian cancer ascites reveals novel components involved in intercellular communication.

Shender Victoria O VO Pavlyukov Marat S MS Ziganshin Rustam H RH Arapidi Georgij P GP Kovalchuk Sergey I SI Anikanov Nikolay A NA Altukhov Ilya A IA Alexeev Dmitry G DG Butenko Ivan O IO Shavarda Alexey L AL Khomyakova Elena B EB Evtushenko Evgeniy E Ashrafyan Lev A LA Antonova Irina B IB Kuznetcov Igor N IN Gorbachev Alexey Yu AY Shakhparonov Mikhail I MI Govorun Vadim M VM

Molecular & cellular proteomics : MCP 20140930 12

Ovarian cancer ascites is a native medium for cancer cells that allows investigation of their secretome in a natural environment. This medium is of interest as a promising source of potential biomarkers, and also as a medium for cell-cell communication. The aim of this study was to elucidate specific features of the malignant ascites metabolome and proteome. In order to omit components of the systemic response to ascites formation, we compared malignant ascites with cirrhosis ascites. Metabolome ...[more]

PMID: 25271300

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Project description:DNA sequence is a major determinant of the binding specificity of transcription factors (TFs) for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with highly similar DNA binding motifs but distinct in vivo targets. Currently, it is not well understood how TFs with seemingly identical DNA motifs achieve unique specificities in vivo. Here, we used custom protein binding microarrays to analyze TF specificity for putative binding sites in their genomic sequence context. Using yeast TFs Cbf1 and Tye7 as our case study, we found that binding sites of these bHLH TFs (i.e., E-boxes) are bound differently in vitro and in vivo, depending on their genomic context. Computational analyses suggest that nucleotides outside E-box binding sites contribute to specificity by influencing the 3D structure of DNA binding sites. Thus, local shape of target sites might play a widespread role in achieving regulatory specificity within TF families. Three protein binding microarray (PBM) experiments of Saccharomyces cerevisiae transcription factors were performed. Briefly, the PBMs involved binding GST-tagged yeast transcription factors Cbf1 and Tye7 to double-stranded 44K Agilent microarrays in order to determine their binding specificity for putative DNA binding sites in native genomic context. Briefly, we represent three categories of 30-bp genomic sequences: 1) ChIP-chip bound probes, 2) ChIP-chip unbound probes, and 3) negative control probes. ChIP-chip bound probes corresponded to genomic regions bound in vivo by Cbf1 or Tye7 (ChIP-chip P < 0.005 in rich medium (YPD) (Harbison et al., Nature 2004, PMID 15343339)) contained at least two consecutive 8-mers with universal PBM E-score > 0.35 (Zhu et al., Genome Research 2009, PMID 19158363). All putative binding sites occurred at the same position within the probes on the array. M-bM-^@M-^\ChIP-chip unboundM-bM-^@M-^] probes corresponded to genomic regions with ChIP-chip P > 0.5 and at least two consecutive 8-mers at a more stringent universal PBM E-score threshold of 0.4. Negative control probes corresponded to S. cerevisiae intergenic regions with a maximum 8-mer E-score < 0.3. We also designed probes that contain, within constant flanking regions, all 10-bp sequences that occur within the M-bM-^@M-^\ChIP-chip boundM-bM-^@M-^] probes and contain the E-box CACGTG, but are flanked by synthetic rather than native genomic sequence. Each DNA sequence represented on the array is present in 4 replicate spots. We report the PBM signal intensity for each spot. The PBM protocol is described in Berger et al., Nature Biotechnology 2006 (PMID 16998473).

Dataset Information

Proteome profiling of ovarian cancer and cirrhosis ascites

Publications

Proteome-metabolome profiling of ovarian cancer ascites reveals novel components involved in intercellular communication.

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