Diagnostic and Management Considerations in Pediatric Dermatofibrosarcoma Protuberans

BACKGROUND

Dermatofibrosarcoma protuberans (DFSP) is a rare fibrohistiocytic tumor of dermal origin. Six percent of all cases present in children, with a childhood incidence of 1 per million.

METHODS

This is a retrospective review of all cases of pediatric DFSP managed at a single institution over a 23-year period.

RESULTS

Seventeen patients (10 male; mean age, 9.9 years) were managed during the study period. The median follow-up was 29 months. All patients had surgical excision. Three patients required further excision to achieve uninvolved final margins. There were no recurrences observed.

CONCLUSIONS

Pediatric DFSP should be managed by a soft tissue tumor multidisciplinary team, with experienced pathologists and reconstructive surgeons. Where R0 resections are obtained, patients can experience recurrence-free survival.

PRM-LIVE with Trapped Ion Mobility Spectrometry and Its Application in Selectivity Profiling of Kinase Inhibitors

Parallel reaction monitoring (PRM) has emerged as a popular approach for targeted protein quantification. With high ion utilization efficiency and first-in-class acquisition speed, the timsTOF Pro provides a powerful platform for PRM analysis. However, sporadic chromatographic drift in peptide retention time represents a fundamental limitation for the reproducible multiplexing of targets across PRM acquisitions. Here, we present PRM-LIVE, an extensible, Python-based acquisition engine for the timsTOF Pro, which dynamically adjusts detection windows for reproducible target scheduling. In this initial implementation, we used iRT peptides as retention time standards and demonstrated reproducible detection and quantification of 1857 tryptic peptides from the cell lysate in a 60 min PRM-LIVE acquisition. As an application in functional proteomics, we use PRM-LIVE in an activity-based protein profiling platform to assess binding selectivity of small-molecule inhibitors against 220 endogenous human kinases.

A Chemoproteomic Strategy for Direct and Proteome-Wide Covalent Inhibitor Target-Site Identification

Despite recent clinical successes for irreversible drugs, potential toxicities mediated by unpredictable modification of off-target cysteines represents a major hurdle for expansion of covalent drug programs. Understanding the proteome-wide binding profile of covalent inhibitors can significantly accelerate their development; however, current mass spectrometry strategies typically do not provide a direct, amino acid level readout of covalent activity for complex, selective inhibitors. Here we report the development of CITe-Id, a novel chemoproteomic approach that employs covalent pharmacologic inhibitors as enrichment reagents in combination with an optimized proteomic platform to directly quantify dose-dependent binding at cysteine-thiols across the proteome. CITe-Id analysis of our irreversible CDK inhibitor THZ1 identified dose-dependent covalent modification of several unexpected kinases, including a previously unannotated cysteine (C840) on the understudied kinase PKN3. These data streamlined our development of JZ128 as a new selective covalent inhibitor of PKN3. Using JZ128 as a probe compound, we identified novel potential PKN3 substrates, thus offering an initial molecular view of PKN3 cellular activity. CITe-Id provides a powerful complement to current chemoproteomic platforms to characterize the selectivity of covalent inhibitors, identify new, pharmacologically addressable cysteine-thiols, and inform structure-based drug design programs.

Akt Kinase Activation Mechanisms Revealed Using Protein Semisynthesis

Akt is a critical protein kinase that drives cancer proliferation, modulates metabolism, and is activated by C-terminal phosphorylation. The current structural model for Akt activation by C-terminal phosphorylation has centered on intramolecular interactions between the C-terminal tail and the N lobe of the kinase domain. Here, we employ expressed protein ligation to produce site-specifically phosphorylated forms of purified Akt1 that are well suited for mechanistic analysis. Using biochemical, crystallographic, and cellular approaches, we determine that pSer473-Akt activation is driven by an intramolecular interaction between the C-tail and the pleckstrin homology (PH)-kinase domain linker that relieves PH domain-mediated Akt1 autoinhibition. Moreover, dual phosphorylation at Ser477/Thr479 activates Akt1 through a different allosteric mechanism via an apparent activation loop interaction that reduces autoinhibition by the PH domain and weakens PIP3 affinity. These results provide a new framework for understanding how Akt is controlled in cell signaling and suggest distinct functions for differentially modified Akt forms.

Interrogating the hidden phosphoproteome

Postgenomic studies continue to highlight the potential clinical importance of protein phosphorylation signaling pathways in drug discovery. Unfortunately, the dynamic range and variable stoichiometry of protein phosphorylation continues to stymie efforts to achieve comprehensive characterization of the human phosphoproteome. In this study, we develop a complementary, two-stage method for enrichment of cysteine-containing phosphopeptides combined with TMT multiplex labeling for relative quantification. The use of this approach with multidimensional fractionation in mammalian cells yielded more than 7000 unique cys-phosphopeptide sequences, comprising 15-20% novel phosphorylation sites. The use of our approach in combination with pharmacologic inhibitors of the mechanistic target of rapamycin complex 1 and 2 identified several putatively novel protein substrates for the mechanistic target of rapamycin kinase.

mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data

Although not yet truly ‘comprehensive’, modern mass spectrometry-based experiments can generate quantitative data for a meaningful fraction of the human proteome. Importantly for large-scale protein expression analysis, robust data pipelines are in place for identification of un-modified peptide sequences and aggregation of these data to protein-level quantification. However, interoperable software tools that enable scientists to computationally explore and document novel hypotheses for peptide sequence, modification status, or fragmentation behavior are not well-developed. Here, we introduce mzStudio, an open-source Python module built on our multiplierz project. This desktop application provides a highly-interactive graphical user interface (GUI) through which scientists can examine and annotate spectral features, re-search existing PSMs to test different modifications or new spectral matching algorithms, share results with colleagues, integrate other domain-specific software tools, and finally create publication-quality graphics. mzStudio leverages our common application programming interface (mzAPI) for access to native data files from multiple instrument platforms, including ion trap, quadrupole time-of-flight, Orbitrap, matrix-assisted laser desorption ionization, and triple quadrupole mass spectrometers and is compatible with several popular search engines including Mascot, Proteome Discoverer, X!Tandem, and Comet. The mzStudio toolkit enables researchers to create a digital provenance of data analytics and other evidence that support specific peptide sequence assignments.

Leveraging Gas-Phase Fragmentation Pathways for Improved Identification and Selective Detection of Targets Modified by Covalent Probes

The recent approval of covalent inhibitors for multiple clinical indications has reignited enthusiasm for this class of drugs. As interest in covalent drugs has increased, so too has the need for analytical platforms that can leverage their mechanism-of-action to characterize modified protein targets. Here we describe novel gas phase dissociation pathways which yield predictable fragment ions during MS/MS of inhibitor-modified peptides. We find that these dissociation pathways are common to numerous cysteine-directed probes as well as the covalent drugs, Ibrutinib and Neratinib. We leverage the predictable nature of these fragment ions to improve the confidence of peptide sequence assignment in proteomic analyses and explore their potential use in selective mass spectrometry-based assays.

The dust distribution within the inner coma of comet P/Halley 1982i: encounter by Giotto's impact detectors

Analysis of the data from Giotto's Dust Impact Detection System experiment (DIDSY) is presented. These data represent measurement of the size of dust grains incident on the Giotto dust shield along its trajectory through the coma of comet P/Halley on 1986 March 13/14. First detection occurred at some 287000 km distance from the nucleus on the inbound leg; the majority of the DIDSY subsystems remained operational after closest approach (604 km) yielding the last detection at about 202000 km from the nucleus. In order to improve the data coverage (and especially for the smallest grains, to approximately 10(-19) kg particle mass), data from the PIA instrument has been combined with DIDSY data. Flux profiles are presented for the various mass channels showing, to a first approximation, a 1/R2 flux dependence, where R is the distance of the detection point from the cometary nucleus, although significant differences are noted. Deviations from this dependence are observed, particularly close to the nucleus. From the flux profiles, mass and geometrical area distributions for the dust grains are derived for the trajectory through the coma. Groundbased CCD imaging of the dust continuum in the inner coma at the time of encounter is also used to derive the area of grains intercepted by Giotto. The results are consistent with the area functions derived by Giotto data and the low albedo of the grains deduced from infrared emission. For the close encounter period (-5 min to +5 min), the cumulative mass distribution function has been investigated, initially in 20 second periods; there is strong evidence from the data for a steepening of the index of the mass distribution for masses greater than 10(-13) kg during passage through dust jets which is not within the error limits of statistical uncertainty. The fluences for dust grains along the entire trajectory is calculated; it is found that extrapolation of the spectrum determined at intermediate masses (cumulative mass index alpha = 0.85) is not able to account for the spacecraft deceleration as observed by the Giotto Radio Science Experiment and by ESOC tracking operations. Data at large masses (>10(-8) kg) recently analysed from the DIDSY data set show clear evidence of a decrease in the mass distribution index at these masses within the coma, and it is shown that such a value of the mass index can provide sufficient mass for consistency with the observed deceleration. The total particulate mass output from the nucleus of comet P/Halley at the time of encounter would be dependent on the maximum mass emitted if this change in slope observed in the coma were also applicable to the emission from the nucleus; this matter is discussed in the text. The flux time profiles have been converted through a simple approach to modeling of the particle trajectories to yield an indication of nucleus surface activity. There is indication of an enhancement in flux at t approximately -29 s corresponding to crossing of the dawn terminator, but the flux detected prior to crossing of the dawn terminator is shown to be higher than predicted by simple modelling. Further enhancements corresponding to jet activity are detected around +190 s and +270 s.

Zodiacal Dust: Measurements by Mariner IV

Data from the Mariner IV dust-particle experiment reveal an increase by a factor of 5 in the flux of interplanetary dust particles as the heliocentric distance from the sun increases. There is a variation in the slope of the cumulative flux-mass distribution, with the steepest slope for the distribution occurring between the planets. No enhancement of the flux in the vicinity of Mars was detected.