Profiling Protein Sâ Sulfination with Maleimideâ Linked Probes

Cysteine residues are susceptible to oxidation to form Sâ sulfinyl (Râ SO2H) and Sâ sulfonyl (Râ SO3H) postâ translational modifications. Here we present a simple bioconjugation strategy to label Sâ sulfinated proteins by using reporterâ linked maleimides. After alkylation of free thiols with iodoacetamide, Sâ sulfinated cysteines react with maleimide to form a sulfone Michael adduct that remains stable under acidic conditions. Using this sequential alkylation strategy, we demonstrate differential Sâ sulfination across mouse tissue homogenates, as well as enhanced Sâ sulfination following pharmacological induction of endoplasmic reticulum stress, lipopolysaccharide stimulation, and inhibitors of the electron transport chain. Overall, this study reveals a broadened profile of maleimide reactivity across cysteine modifications, and outlines a simple method for profiling the physiological role of cysteine Sâ sulfination in disease.Maleimide, but not iodoacetamide, reacts with aryl and alkyl sulfinic acid standards and Sâ sulfinated proteins to give a sulfonylâ succinimide adduct that is stable under acidic conditions. This sequential alkylation strategy can be used for selective sulfinic acid labeling in biological samples. This study reveals a broadened profile of maleimide reactivity across cysteine modifications in proteins.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138861/1/cbic201700137_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138861/2/cbic201700137.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138861/3/cbic201700137-sup-0001-misc_information.pd

Discovery of a potent deubiquitinase (DUB) small molecule activity‐based probe enables broad spectrum DUB activity profiling in living cells

Deubiquitinases (DUBs) are a family of >100 proteases that hydrolyze isopeptide bonds linking ubiquitin to protein substrates. This leads to reduced substrate degradation through the ubiquitin proteasome system. Deregulation of DUB activity has been implicated in many diseases, including cancer, neurodegeneration and auto-inflammation, and several have been recognized as attractive targets for therapeutic intervention. Ubiquitin-derived covalent activity-based probes (ABPs) provide a powerful tool for DUB activity profiling, but their large recognition element impedes cellular permeability and presents an unmet need for small molecule ABPs which can account for regulation of DUB activity in intact cells or organisms. Here, through comprehensive chemoproteomic warhead profiling, we identify cyanopyrrolidine (CNPy) probe IMP-2373 (12) as a small molecule pan-DUB ABP to monitor DUB activity in physiologically relevant live cells. Through proteomics and targeted assays, we demonstrate that IMP-2373 quantitatively engages more than 35 DUBs across a range of non-toxic concentrations in diverse cell lines. We further demonstrate its application to quantification of changes in intracellular DUB activity during pharmacological inhibition and during MYC deregulation in a model of B cell lymphoma. IMP-2373 thus offers a complementary tool to ubiquitin ABPs to monitor dynamic DUB activity in the context of disease-relevant phenotypes

Sister Mary Joseph's Nodule at a University Teaching Hospital in Northwestern Tanzania: A Retrospective Review of 34 cases.

Sister Mary Joseph's nodule is a metastatic tumor deposit in the umbilicus and often represents advanced intra-abdominal malignancy with dismal prognosis. There is a paucity of published data on this subject in our setting. This study was conducted to describe the clinicopathological presentation and treatment outcome of this condition in our environment and highlight challenges associated with the care of these patients, and to proffer solutions for improved outcome. This was a retrospective study of histologically confirmed cases of Sister Mary Joseph's nodule seen at Bugando Medical Centre between March 2003 and February 2013. Data collected were analyzed using descriptive statistics. A total of 34 patients were enrolled in the study. Males outnumbered females by a ratio of 1.4:1. The vast majority of patients (70.6%) presented with large umbilical nodule > 2 cm in size. The stomach (41.1%) was the most common location of the primary tumor. Adenocarcinoma (88.2%) was the most frequent histopathological type. Most of the primary tumors (52.9%) were poorly differentiated. As the disease was advanced and metastatic in all patients, only palliative therapy was offered. Out of 34 patients, 11 patients died in the hospital giving a mortality rate of 32.4%. Patients were followed up for 24 months. At the end of the follow-up period, 14(60.9%) patients were lost to follow-up and the remaining 9 (39.1%) patients died. Patients survived for a median period of 28 weeks (range, 2 to 64 weeks). The nodule recurred in 6 (26.1%) patients after complete excision. Sister Mary Joseph's nodule of the umbilicus is not rare in our environment and often represents manifestation of a variety of advanced intra-abdominal malignancies. The majority of the patients present at a late stage and many with distant metastases. The patient's survival is very short leading to a poor outcome. Early detection of primary cancer at an early stage may improve the prognosis

Scale invariance and universality of force networks in static granular matter

Force networks form the skeleton of static granular matter. They are the key ingredient to mechanical properties, such as stability, elasticity and sound transmission, which are of utmost importance for civil engineering and industrial processing. Previous studies have focused on the global structure of external forces (the boundary condition), and on the probability distribution of individual contact forces. The disordered spatial structure of the force network, however, has remained elusive so far. Here we report evidence for scale invariance of clusters of particles that interact via relatively strong forces. We analyzed granular packings generated by molecular dynamics simulations mimicking real granular matter; despite the visual variation, force networks for various values of the confining pressure and other parameters have identical scaling exponents and scaling function, and thus determine a universality class. Remarkably, the flat ensemble of force configurations--a simple generalization of equilibrium statistical mechanics--belongs to the same universality class, while some widely studied simplified models do not.Comment: 15 pages, 4 figures; to appear in Natur

Polymeric Nanoparticle PET/MR Imaging Allows Macrophage Detection in Atherosclerotic Plaques

Author Manuscript 2013 March 02.Rationale: Myeloid cell content in atherosclerotic plaques associates with rupture and thrombosis. Thus, imaging of lesional monocytes and macrophages could serve as a biomarker of disease progression and therapeutic intervention. Objective: To noninvasively assess plaque inflammation with dextran nanoparticle (DNP)-facilitated hybrid positron emission tomography/magnetic resonance imaging (PET/MRI). Methods and Results: Using clinically approved building blocks, we systematically developed 13-nm polymeric nanoparticles consisting of cross-linked short chain dextrans, which were modified with desferoxamine for zirconium-89 radiolabeling ([superscript 89]Zr-DNP) and a near-infrared fluorochrome (VT680) for microscopic and cellular validation. Flow cytometry of cells isolated from excised aortas showed DNP uptake predominantly in monocytes and macrophages (76.7%) and lower signal originating from other leukocytes, such as neutrophils and lymphocytes (11.8% and 0.7%, P<0.05 versus monocytes and macrophages). DNP colocalized with the myeloid cell marker CD11b on immunohistochemistry. PET/MRI revealed high uptake of [superscript 89]Zr-DNP in the aortic root of apolipoprotein E knock out (ApoE[superscript −/−]) mice (standard uptake value, ApoE[superscript −/−] mice versus wild-type controls, 1.9±0.28 versus 1.3±0.03; P<0.05), corroborated by ex vivo scintillation counting and autoradiography. Therapeutic silencing of the monocyte-recruiting receptor C-C chemokine receptor type 2 with short-interfering RNA decreased [superscript 89]Zr-DNP plaque signal (P<0.05) and inflammatory gene expression (P<0.05). Conclusions: Hybrid PET/MRI with a 13-nm DNP enables noninvasive assessment of inflammation in experimental atherosclerotic plaques and reports on therapeutic efficacy of anti-inflammatory therapy.National Heart, Lung, and Blood InstituteNational Institutes of Health (U.S.). Dept. of Health and Human Services (HHSN268201000044C)National Institutes of Health (U.S.). Dept. of Health and Human Services (R01-HL096576)National Institutes of Health (U.S.). Dept. of Health and Human Services (R01-HL095629)National Institutes of Health (U.S.). Dept. of Health and Human Services (T32-HL094301

Partial clustering prevents global crystallization in a binary 2D colloidal glass former

A mixture of two types of super-paramagnetic colloidal particles with long range dipolar interaction is confined by gravity to a flat interface of a hanging water droplet. The particles are observed by video microscopy and the dipolar interaction strength is controlled via an external magnetic field. The system is a model system to study the glass transition in 2D, and it exhibits partial clustering of the small particles. This clustering is strongly dependent on the relative concentration $\xi$ of big and small particles. However, changing the interaction strength $\Gamma$ reveals that the clustering does not depend on the interaction strength. The partial clustering scenario is quantified using Minkowski functionals and partial structure factors. Evidence that partial clustering prevents global crystallization is discussed

Patterns and flow in frictional fluid dynamics

Pattern-forming processes in simple fluids and suspensions have been studied extensively, and the basic displacement structures, similar to viscous fingers and fractals in capillary dominated flows, have been identified. However, the fundamental displacement morphologies in frictional fluids and granular mixtures have not been mapped out. Here we consider Coulomb friction and compressibility in the fluid dynamics, and discover surprising responses including highly intermittent flow and a transition to quasi-continuodynamics. Moreover, by varying the injection rate over several orders of magnitude, we characterize new dynamic modes ranging from stick-slip bubbles at low rate to destabilized viscous fingers at high rate. We classify the fluid dynamics into frictional and viscous regimes, and present a unified description of emerging morphologies in granular mixtures in the form of extended phase diagrams

Evaluation of the prophylactic use of mitomycin-C to inhibit haze formation after photorefractive keratectomy in high myopia: a prospective clinical study

BACKGROUND: To study the effect of prophylactic application of mitomycin-C on haze formation in photorefractive keratectomy (PRK) for high myopia. METHODS: Fifty-four eyes of 28 myopic patients were enrolled in this prospective study. All eyes were operated by PRK followed by 0.02% mitomycin-C application for two minutes and washed with 20 ml normal saline afterwards. All eyes were examined thoroughly on the first 7 days and one month after surgery; 48 eyes (88.9%) at 3 and 6 months postoperatively. Hanna grading (in the scale of 0 to 4+) was used for assessment of corneal haze. RESULTS: The mean spherical equivalent refraction (SE) was -7.08 diopters (D) ± 1.11 (SD) preoperatively. Six months after surgery, 37 eyes (77.1%) achieved an uncorrected visual acuity (UCVA) of 20/20 or better, all eyes had a UCVA of 20/40 or better and 45 (93.7%) eyes had an SE within ± 1.00D. One month postoperatively, 2 eyes (3.7%) had grade 0.5+ of haze, while at 3 and 6 months after surgery no visited eye had haze at all. All eyes had a best corrected visual acuity (BCVA) of 20/40 or better and there were no lost lines in BCVA by 6 months after surgery. In spatial frequencies of 6 and 12 cycles per degree contrast sensitivity had decreased immediately after PRK and it had increased 1.5 lines by the 6(th )postoperative month compared to the preoperative data. CONCLUSIONS: The results show the efficacy of mitomycin-C in preventing corneal haze after treatment of high myopia with PRK. This method- PRK + mitomycin-C – can be considered an alternative treatment for myopic patients whose corneal thicknesses are inadequate for laser in situ keratomileusis (LASIK). However, the results should be confirmed in longer follow-ups

PTCH1+/− Dermal Fibroblasts Isolated from Healthy Skin of Gorlin Syndrome Patients Exhibit Features of Carcinoma Associated Fibroblasts

Gorlin's or nevoid basal cell carcinoma syndrome (NBCCS) causes predisposition to basal cell carcinoma (BCC), the commonest cancer in adult human. Mutations in the tumor suppressor gene PTCH1 are responsible for this autosomal dominant syndrome. In NBCCS patients, as in the general population, ultraviolet exposure is a major risk factor for BCC development. However these patients also develop BCCs in sun-protected areas of the skin, suggesting the existence of other mechanisms for BCC predisposition in NBCCS patients. As increasing evidence supports the idea that the stroma influences carcinoma development, we hypothesized that NBCCS fibroblasts could facilitate BCC occurence of the patients. WT (n = 3) and NBCCS fibroblasts bearing either nonsense (n = 3) or missense (n = 3) PTCH1 mutations were cultured in dermal equivalents made of a collagen matrix and their transcriptomes were compared by whole genome microarray analyses. Strikingly, NBCCS fibroblasts over-expressed mRNAs encoding pro-tumoral factors such as Matrix Metalloproteinases 1 and 3 and tenascin C. They also over-expressed mRNA of pro-proliferative diffusible factors such as fibroblast growth factor 7 and the stromal cell-derived factor 1 alpha, known for its expression in carcinoma associated fibroblasts. These data indicate that the PTCH1+/− genotype of healthy NBCCS fibroblasts results in phenotypic traits highly reminiscent of those of BCC associated fibroblasts, a clue to the yet mysterious proneness to non photo-exposed BCCs in NBCCS patients