Decrypting drug actions and protein modifications by dose- and time-resolved proteomics.

Although most cancer drugs modulate the activities of cellular pathways by changing posttranslational modifications (PTMs), little is known regarding the extent and the time- and dose-response characteristics of drug-regulated PTMs. In this work, we introduce a proteomic assay called decryptM that quantifies drug-PTM modulation for thousands of PTMs in cells to shed light on target engagement and drug mechanism of action. Examples range from detecting DNA damage by chemotherapeutics, to identifying drug-specific PTM signatures of kinase inhibitors, to demonstrating that rituximab kills CD20-positive B cells by overactivating B cell receptor signaling. DecryptM profiling of 31 cancer drugs in 13 cell lines demonstrates the broad applicability of the approach. The resulting 1.8 million dose-response curves are provided as an interactive molecular resource in ProteomicsDB.

[ARMD reaction patterns in knee arthroplasty : A novel hypothetical mechanism: hingiosis]. / ARMD-Reaktionsmuster bei Kniegelenkendoprothesen : Ein neuer hypothetischer Mechanismus: Hingiose.

BACKGROUND: There are case descriptions of pronounced peri-implant inflammatory reactions and necrosis in non-infectious knee joint replacements with metal-polyethylene pairing. OBJECTIVES: Due to the histopathological similarities to the dysfunctional metal-on-metal (MoM) hip joint replacement, MoM-like reactions in knee joint arthroplasty ("ARMD-KEP") are proposed and a histopathological comparison is made. MATERIALS AND METHODS: This analysis evaluates five cases of "ARMD-KEP" using: (1) the SLIM consensus classification, (2) the particle algorithm, (3) the CD3 focus score and (4) the AVAL score. The comparison groups consist of 11 adverse cases of MoM hip and 20 cases of knee joint arthroplasty without adverse reaction. RESULTS: The ARMD-KEP cases were identified as SLIM type VI. Their median ALVAL score was 10. The CD3 focus score confirmed an adverse reaction. Particle corrosion was found in two of five cases. CONCLUSIONS: This data indicates that, in rare cases, an adverse MoM-like reaction may be present in knee replacements, with inflammatory and immunological expression similar to that of the adverse MoM reaction in the hip. The pathomechanisms can be discussed as follows: (1) secondary metal-metal contact, (2) dysfunctional loading of the coupling mechanism and (3) corrosion of the metal components. Much like trunnionosis in the hip, the term "hingiosis" is proposed for corrosion phenomena in dysfunctional conditions of coupled knee endoprosthetic systems.

A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.

The TP53 gene is frequently mutated in human cancer. Research has focused predominantly on six major "hotspot" codons, which account for only ∼30% of cancer-associated p53 mutations. To comprehensively characterize the consequences of the p53 mutation spectrum, we created a synthetically designed library and measured the functional impact of ∼10,000 DNA-binding domain (DBD) p53 variants in human cells in culture and in vivo. Our results highlight the differential outcome of distinct p53 mutations in human patients and elucidate the selective pressure driving p53 conservation throughout evolution. Furthermore, while loss of anti-proliferative functionality largely correlates with the occurrence of cancer-associated p53 mutations, we observe that selective gain-of-function may further favor particular mutants in vivo. Finally, when combined with additional acquired p53 mutations, seemingly neutral TP53 SNPs may modulate phenotypic outcome and, presumably, tumor progression.

Protein structure determination by combining sparse NMR data with evolutionary couplings.

Accurate determination of protein structure by NMR spectroscopy is challenging for larger proteins, for which experimental data are often incomplete and ambiguous. Evolutionary sequence information together with advances in maximum entropy statistical methods provide a rich complementary source of structural constraints. We have developed a hybrid approach (evolutionary coupling-NMR spectroscopy; EC-NMR) combining sparse NMR data with evolutionary residue-residue couplings and demonstrate accurate structure determination for several proteins 6-41 kDa in size.