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Phosphorylation of proteins on tyrosine (Tyr) residues evolved in metazoan organisms as a mechanism of coordinating tissue growth1. Multicellular eukaryotes typically have more than 50 distinct protein Tyr kinases that catalyse the phosphorylation of thousands of Tyr residues throughout the proteome1–3. How a given Tyr kinase can phosphorylate a specific subset of proteins at unique Tyr sites is only partially understood4–7. Here we used combinatorial peptide arrays to profile the substrate sequence specificity of all human Tyr kinases. Globally, the Tyr kinases demonstrate considerable diversity in optimal patterns of residues surrounding the site of phosphorylation, revealing the functional organization of the human Tyr kinome by substrate motif preference. Using this information, Tyr kinases that are most compatible with phosphorylating any Tyr site can be identified. Analysis of mass spectrometry phosphoproteomic datasets using this compendium of kinase specificities accurately identifies specific Tyr kinases that are dysregulated in cells after stimulation with growth factors, treatment with anti-cancer drugs or expression of oncogenic variants. Furthermore, the topology of known Tyr signalling networks naturally emerged from a comparison of the sequence specificities of the Tyr kinases and the SH2 phosphotyrosine (pTyr)-binding domains. Finally we show that the intrinsic substrate specificity of Tyr kinases has remained fundamentally unchanged from worms to humans, suggesting that the fidelity between Tyr kinases and their protein substrate sequences has been maintained across hundreds of millions of years of evolution.An atlas of the substrate specificities for the human tyrosine kinome reveals diversity of motif specificities and enables identification of kinase–substrate relationships and kinase regulation in phosphoproteomics experiments. [ABSTRACT FROM AUTHOR]

Brain metastases (BrMs) are a common occurrence in lung cancer with a dismal outcome. To understand the mechanism of metastasis to inform prognosis and treatment, here we analyze primary and metastasized tumor specimens from 44 non-small cell lung cancer patients by spatial RNA sequencing, affording a whole transcriptome map of metastasis resolved with morphological markers for the tumor core, tumor immune microenvironment (TIME), and tumor brain microenvironment (TBME). Our data indicate that the tumor microenvironment (TME) in the brain, including the TIME and TBME, undergoes extensive remodeling to create an immunosuppressive and fibrogenic niche for the BrMs. Specifically, the brain TME is characterized with reduced antigen presentation and B/T cell function, increased neutrophils and M2-type macrophages, immature microglia, and reactive astrocytes. Differential gene expression and network analysis identify fibrosis and immune regulation as the major functional modules disrupted in both the lung and brain TME. Besides providing systems-level insights into the mechanism of lung cancer brain metastasis, our study uncovers potential prognostic biomarkers and suggests that therapeutic strategies should be tailored to the immune and fibrosis status of the BrMs.Brain metastases (BrMs) in non-small cell lung cancer (NSCLC) are associated with dismal outcomes, and are possibly sustained by the brain microenvironment. Here, the authors analyse NSCLC BrMs using Digital Spatial Profiling and reveal fibrosis, immune suppression, and cell reprogramming in the BrM microenvironment. [ABSTRACT FROM AUTHOR]

Pancreatoscopy plays a significant role in the diagnosis and treatment of pancreatic diseases. However, the risk of pancreatoscopy is remarkably greater than that of other endoscopic procedures, such as gastroscopy and bronchoscopy, owing to its severe invasiveness. In comparison, virtual pancreatoscopy (VP) has shown notable advantages. However, because of the low resolution of current computed tomography (CT) technology and the small diameter of the pancreatic duct, VP has limited clinical use. In this study, an optimal path algorithm and super-resolution technique are investigated for the development of an open-source software platform for VP based on 3D Slicer. The proposed segmentation of the pancreatic duct from the abdominal CT images reached an average Dice coefficient of 0.85 with a standard deviation of 0.04. Owing to the excellent segmentation performance, a fly-through visualization of both the inside and outside of the duct was successfully reconstructed, thereby demonstrating the feasibility of VP. In addition, a quantitative analysis of the wall thickness and topology of the duct provides more insight into pancreatic diseases than a fly-through visualization. The entire VP system developed in this study is available at https://github.com/gaoyi/VirtualEndoscopy.git. [ABSTRACT FROM AUTHOR]

Suppressor of cytokine signaling (SOCS)2 protein is a key negative regulator of the growth hormone (GH) and Janus kinase (JAK)-Signal Transducers and Activators of Transcription (STAT) signaling cascade. The central SOCS2-Src homology 2 (SH2) domain is characteristic of the SOCS family proteins and is an important module that facilitates recognition of targets bearing phosphorylated tyrosine (pTyr) residues. Here we identify an exosite on the SOCS2-SH2 domain which, when bound to a non-phosphorylated peptide (F3), enhances SH2 affinity for canonical phosphorylated ligands. Solution of the SOCS2/F3 crystal structure reveals F3 as an α-helix which binds on the opposite side of the SH2 domain to the phosphopeptide binding site. F3:exosite binding appears to stabilise the SOCS2-SH2 domain, resulting in slower dissociation of phosphorylated ligands and consequently, enhances binding affinity. This biophysical enhancement of SH2:pTyr binding affinity translates to increase SOCS2 inhibition of GH signaling. SOCS2 is a key regulator of growth hormone and cytokine signaling, which recognizes phosphotyrosine (pTyr)-modified targets via a central SH2 domain. Here, the authors discover and characterize an exosite on this SH2 domain that can bind a non-phosphorylated peptide to enhance SOCS2:pTyr affinity. [ABSTRACT FROM AUTHOR]

We sought to investigate the utilization of prasugrel and its association with outcomes relative to clopidogrel in three typical subgroups of ACS in a real-world setting. Prasugrel is superior to clopidogrel for reducing risk of ischemic events in acute coronary syndrome (ACS) patients undergoing percutaneous coronary intervention (PCI), but is associated with an increased risk of bleeding complications. PROMETHEUS was a retrospective multicenter observational study of 19,913 ACS patients undergoing PCI from 8 centers in the United States between 2010 and 2013. Major adverse cardiovascular events (MACE) were defined as a composite of all-cause mortality, myocardial infarction, stroke or unplanned revascularization. The study cohort included 3285 (16.5%) patients with ST-segment elevation myocardial infarction (STEMI), 5412 (27.2%) patients with NSTEMI and 11,216 (56.3%) patients with unstable angina (UA). The frequency of prasugrel use at discharge was highest in STEMI and lowest in UA patients, 27.3% versus 22.2% versus 18.9% (p < 0.001). Use of prasugrel vs clopidogrel was associated with a lower rate of MACE in STEMI, NSTEMI, or UA at 1 year, but the differences were attenuated for all groups except for patients with UA (adjusted HR 0.81, 95% CI 0.69–0.94, p = 0.006) after propensity adjusted analysis. After adjustment, there was no difference in bleeding risk between prasugrel and clopidogrel for all groups at 1 year. STEMI patients were more likely to receive prasugrel compared to NSTEMI and UA patients. Prasugrel was associated with reduced adverse outcomes compared with clopidogrel in unadjusted analyses, findings that were largely attenuated upon adjustment and suggest preferential use of prasugrel in low vs high risk patients. [ABSTRACT FROM AUTHOR]

Methylation of Lys and Arg residues on non-histone proteins has emerged as a prevalent post-translational modification and as an important regulator of cellular signal transduction mediated by the MAPK, WNT, BMP, Hippo and JAK-STAT signalling pathways. Crosstalk between methylation and other types of post-translational modifications, and between histone and non-histone protein methylation frequently occurs and affects cellular functions such as chromatin remodelling, gene transcription, protein synthesis, signal transduction and DNA repair. With recent advances in proteomic techniques, in particular mass spectrometry, the stage is now set to decode the methylproteome and define its functions in health and disease. [ABSTRACT FROM AUTHOR]

DUOXA1/NIP1, originally identified as a Numb-interacting protein, was recently shown to function as a maturation factor for the dual oxidase 1(DUOX1). In this study, we identified DUOXA1/NIP1 expression in breast cancer cells, observed high expression of DUOXA1 in non-invasive MCF7 cells and low expression in highly metastatic cells with impaired p53 functions linking the expression of DUOXA1 with p53. An inhibition of cell proliferation associated with upregulation of p21Cip1/WAF1 was observed in MDA-MB-231 cells following transfection of DUOXA1. The transient DUOXA1 overexpression also inhibited expression of cell-surface integrin αVβ5 and CD9, which is associated with impaired spreading ability. However, there was no difference in expression of these proteins in DUOX1-depleted cells. The observed effects coincided with an increase in reactive oxygen species (ROS) generation. Our data also demonstrate that DUOXA1 transient overexpression affected the cell–cell adhesion by modulating the actin cytoskeleton, and sensitized cells to doxorubicin. [ABSTRACT FROM AUTHOR]

AF2241 is a hypothetical protein from Archaeoglobus fulgidus and it belongs to the PFam domain of unknown function 369 (DUF369). NMR structural determination reveals that AF2241 adopts a cyclophilin-like fold, with a β-barrel core composed of eight β-strands, one α-helix, and one 310 helix located at each end of the barrel. The protein displays a high structural similarity to TM1367, another member of DUF369 whose structure has been determined recently by X-ray crystallography. Structural similarity search shows that AF2241 also has a high similarity to human cyclophilin A, however, sequence alignment and electrostatic potential analysis reveal that the residues in the PPIase catalytic site of human cyclophilin A are not conserved in AF2241 or TM1367. Instead, a putative active site of AF2241 maps to a negatively charged pocket composed of 9 conserved residues. Our results suggest that although AF2241 adopts the same fold as the human cyclophilin A, it may have distinct biological function. [ABSTRACT FROM AUTHOR]

The glomerular filtration barrier in the kidney is formed in part by a specialized intercellular junction known as the slit diaphragm, which connects adjacent actin-based foot processes of kidney epithelial cells (podocytes). Mutations affecting a number of slit diaphragm proteins, including nephrin (encoded by NPHS1), lead to renal disease owing to disruption of the filtration barrier and rearrangement of the actin cytoskeleton, although the molecular basis for this is unclear. Here we show that nephrin selectively binds the Src homology 2 (SH2)/SH3 domain-containing Nck adaptor proteins, which in turn control the podocyte cytoskeleton in vivo. The cytoplasmic tail of nephrin has multiple YDxV sites that form preferred binding motifs for the Nck SH2 domain once phosphorylated by Src-family kinases. We show that this Nck–nephrin interaction is required for nephrin-dependent actin reorganization. Selective deletion of Nck from podocytes of transgenic mice results in defects in the formation of foot processes and in congenital nephrotic syndrome. Together, these findings identify a physiological signalling pathway in which nephrin is linked through phosphotyrosine-based interactions to Nck adaptors, and thus to the underlying actin cytoskeleton in podocytes. Simple and widely expressed SH2/SH3 adaptor proteins can therefore direct the formation of a specialized cellular morphology in vivo. [ABSTRACT FROM AUTHOR]

Src homology 2 (SH2) domains play a critical role in signal transduction in mammalian cells by binding to phosphorylated Tyr (pTyr). Apart from a few isolated cases in viruses, no functional SH2 domain has been identified to date in prokaryotes. Here we identify 93 SH2 domains from Legionella that are distinct in sequence and specificity from mammalian SH2 domains. The bacterial SH2 domains are not only capable of binding proteins or peptides in a Tyr phosphorylation-dependent manner, some bind pTyr itself with micromolar affinities, a property not observed for mammalian SH2 domains. The Legionella SH2 domains feature the SH2 fold and a pTyr-binding pocket, but lack a specificity pocket found in a typical mammalian SH2 domain for recognition of sequences flanking the pTyr residue. Our work expands the boundary of phosphotyrosine signalling to prokaryotes, suggesting that some bacterial effector proteins have acquired pTyr-superbinding characteristics to facilitate bacterium-host interactions. [ABSTRACT FROM AUTHOR]