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In Print: Recent Proteomics Papers of Note: Oct 26, 2012

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In Print: Recent Proteomics Papers of Note

Journal: Cancer Genomics & Proteomics, Sept. 9 [Epub ahead of print]

Title: Identification of markers associated with highly aggressive metastatic phenotypes using quantitative comparative proteomics.

Authors: Terp MG; Lund RR; Jensen ON; Leth-Larsen R; Ditzel HJ.

The authors used LC-MS/MS to compare the proteomes of three human breast cancer cell lines with different metastatic potentials, identifying 44 proteins that showed altered expression between the metastatic and non-metastatic lines.


Journal: PLoS One, Sept. 12 [Epub ahead of print]

Title: Novel effects of hormonal contraceptive use on the plasma proteome.

Authors: Josse AR; Garcia-Bailo B; Fischer K; El-Sohemy A.

The authors used multiple-reaction monitoring mass spec to measure 54 high-abundance proteins in 783 women, comparing expression between users and non-users of hormonal contraceptives, identifying 19 differentially expressed proteins involved in inflammation, innate immunity, coagulation, and blood pressure regulation.


Journal:Proteomics, Sept. 12

Title:Ten years of standardizing proteomic data: a report on the HUPO-PSI spring workshop: April 12-14th, 2012, San Diego, USA.

Authors:Orchard S; Binz PA; Borchers C; Gilson MK; Jones AR; Nicola G; Vizcaino JA; Deutsch EW; Hermjakob H.

The authors report on the 2012 HUPO-PSI spring workshop and particularly on the finalization of standards for capturing the output of mass spec techniques like selected-reaction monitoring and quantitative proteomics.


Journal: Molecular & Cellular Proteomics, Sept. 13 [Epub ahead of print]

Title: High-resolution mapping of linear antibody epitopes using ultrahigh-density peptide microarrays.

Authors: Buus S; Rockberg J; Forsstr Oumlm BO; Nilsson P; Uhlen M; Schafer-Nielsen C.

The authors used ultrahigh-density peptide microarrays featuring several hundred thousand different peptides per array to examine the specificity of a panel of polyclonal antibodies and obtain detailed descriptions of their specificities.


Journal:Methods, Sept. 13 [Epub ahead of print]

Title:Quantitative real-time PCR as a sensitive protein-protein interaction quantification method and a partial solution for non-accessible autoactivator and false-negative molecule analysis in the yeast two-hybrid system.

Authors:Maier RH; Maier CJ; Hintner H; Bauer JW; Onder K.

The authors present a method using detection and readout of mRNA expression instead of proteins or conventional Y2H genetic reporters to identify protein-protein interactions with a higher sensitivity than offered by conventional Y2H techniques.


Journal: Proteomics Clinical Applications, Sept. 24 [Epub ahead of print]

Title: Remarkable temporal stability of high-abundance human plasma proteins assessed by targeted mass spectrometry.

Authors: Randall SA; McKay MJ; Pascovici D; Mahon K; Horvath L; Clarke SJ; Molloy MP.

The authors quantified 31 plasma proteins in healthy volunteers over two time courses to determine between-subject and within-subject biological variance, finding that none of the measured proteins exhibited significant fluctuations over either time course, suggesting the suitability of plasma proteins as disease markers.


Journal: PLoS One, Sept. 25 [Epub ahead of print]

Title: Proteome analysis identified the PPARγ ligand 15d-PGJ2 as a novel drug inhibiting melanoma progression and interfering with tumor-stroma interaction.

Authors: Paulitschke V; Gruber S; Hofstätter E; Haudek-Prinz V; Klepeisz P; Schicher N; Jonak C; Petzelbauer P; Pehamberger H; Gerner C; Kunstfeld R.

The authors used shotgun proteomics along with 2D-gel electrophoresis and immunoprecipitation of A375 melanoma cells treated with 15d-PGJ2, finding evidence that the agent might modify Hsp-90 activity along with several chaperones.


Journal: Genome Biology, Sept. 28 [Epub ahead of print]

Title: Correlation of proteome-wide changes with social immunity behaviors provides insight into resistance to the parasitic mite, Varroa destructor, in the honey bee (Apis mellifera).

Authors: Parker R; Guarna MM; Melathopoulos AP; Moon KM; White R; Huxter E; Pernal SF; Foster LJ.

The authors characterized the proteome-wide changes in larval integument and adult antennae in honey bees, identifying several proteins predictive of hygienic behavior enabling bees to resist various diseases.


Journal: Nature Chemical Biology, Sept. 30 [Epub ahead of print]

Title: Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML.

Authors: Winter GE; Rix U; Carlson SM; Gleixner KV; Grebien F; Gridling M; Müller AC; Breitwieser FP; Bilban M; Colinge J; Valent P; Bennett KL; White FM; Superti-Furga G.

The authors combined phosphoproteomics, transcriptomics, and chemical proteomics to investigate the mechanisms underlying the strong synergy between the kinase inhibitors danusertib and bosutinib affecting CML cells harboring BCR-ABL.

The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.