Kinase inhibitors are important cancer therapeutics. Polypharmacology is commonly observed, requiring thorough target deconvolution to understand drug mechanism of action. Using chemical proteomics, we analyzed the target spectrum of 243 clinically evaluated kinase drugs. The data revealed previously unknown targets for established drugs, offered a perspective on the "druggable" kinome, highlighted (non)kinase off-targets, and suggested potential therapeutic applications. Integration of phosphoproteomic data refined drug-affected pathways, identified response markers, and strengthened rationale for combination treatments. We exemplify translational value by discovering SIK2 (salt-inducible kinase 2) inhibitors that modulate cytokine production in primary cells, by identifying drugs against the lung cancer survival marker MELK (maternal embryonic leucine zipper kinase), and by repurposing cabozantinib to treat FLT3-ITD-positive acute myeloid leukemia. This resource, available via the ProteomicsDB database, should facilitate basic, clinical, and drug discovery research and aid clinical decision-making.

Cancer cell invasion takes place at the cancer-host interface and is a prerequisite for distant metastasis. The relationships between current biological and clinical concepts such as cell migration modes, tumour budding and epithelial-mesenchymal transition (EMT) remains unclear in several aspects, especially for the 'real' situation in human cancer. We developed a novel method that provides exact three-dimensional (3D) information on both microscopic morphology and gene expression, over a virtually unlimited spatial range, by reconstruction from serial immunostained tissue slices. Quantitative 3D assessment of tumour budding at the cancer-host interface in human pancreatic, colorectal, lung and breast adenocarcinoma suggests collective cell migration as the mechanism of cancer cell invasion, while single cancer cell migration seems to be virtually absent. Budding tumour cells display a shift towards spindle-like as well as a rounded morphology. This is associated with decreased E-cadherin staining intensity and a shift from membranous to cytoplasmic staining, as well as increased nuclear ZEB1 expression.

Our results identify and validate a BAL signature that predicts mortality in IPF and improves the accuracy of outcome prediction based on clinical parameters. The BAL signature associated with mortality unmasks a potential role for airway basal cells in IPF.

Preoperative stratification of patients regarding risk for POPF by simple clinical parameters is feasible. Pancreatic texture, as evaluated intraoperatively by the surgeon, is the strongest single predictive factor of POPF. The findings of the study may have important implications for perioperative risk assessment and patient care, as well as for the choice of anastomotic techniques.

Recently, a new human polyoma virus has been identified in Merkel cell carcinomas (MCC). MCC is a highly aggressive neuroendocrine nonmelanoma skin cancer (NMSC) associated with immunosuppression. Clonal integration of this virus which was termed Merkel cell polyoma virus (MCPyV) was reported in a number of MCC. Squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) are also NMSC and are the most frequent cancers in the setting of immunosuppression. A unique group of 56 NMSC from 11 immunosuppressed patients and 147 NMSC of 125 immunocompetent patients was tested for MCPyV by DNA PCR, targeting the Large T Antigen and the structural Viral Protein 1. NMSC included SCC, BCC and Bowen's disease (BD). In addition, normal skin and 89 colorectal cancers were tested. MCPyV specific sequences were significantly more frequently found in NMSC of immunosuppressed patients compared to immunocompetent patients (p < 0.001). In particular BD and BCC revealed a significant increased association of MCPyV of immunosuppressed patients (p 5 0.002 and p 5 0.006). Forty-seven of 147 (32%) sporadic NMSC were MCPyV positive. Interestingly, 37.5% (36/96) of sporadic BCC of immunocompetent patients were MCPyV positive. No MCPyV was detected within normal skin and only 3 out of 89 of additionally tested colorectal cancers were MCPyV positive. Our data show that MCPyV is a frequently reactivated virus in immunocompromized patients. How MCPyV contributes to the pathogenesis of NMSC, i.e., BD, SCC and BCC, in immunosuppressed patients and in addition, potentially to the pathogenesis of a subset of sporadic BCC needs further investigations. ' UICCKey words: nonmelanoma skin cancer (NMSC); merkel cell polyoma virus (MCPyV); immunosuppression Squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) are nonmelanoma skin cancers (NMSC) and in this order constitute the most frequent cancers associated with immunosuppression in transplant recipients. [1][2][3][4][5][6] According to the steadily increasing number of transplant operations performed each year in the European Union and the United States, post-transplant skin cancer is a leading medical issue in current transplantation medicine. To date a number of risk factors for the increasing number of NMSC under immunosuppression have been identified. 2 In addition to SCC and BCC, other NMSC, i.e., sebaceous cancers, cutaneous lymphomas and Merkel cell carcinomas (MCC) occur more frequently in post-transplant patients. 7,8 MCC has been described relatively recently and is a rare but very aggressive malignant neuroendocrine skin cancer of the elderly and immunosuppressed. [8][9][10] Very recently, Feng et al. reported the identification of a new human polyoma virus which was designated Merkel cell polyomavirus (MCPyV) based on its detection in MCC by digital transcriptome subtraction technique. 11 They reported the presence of MCPyV in 8 of 10 human MCC and also clonal integration of the viral DNA in 6 of 8 MCPyV-positive MCC. Analyzing the first large number patient cohort of MCC by PCR...

In a considerable number of patients, ILD is stable over years and patients may not need any immunosuppressive treatment. Prednisone treatment is often used as the first-line treatment and studies suggest response to treatment in 50-66% of cases. In progressive disease with lung function impairment, combined immunosuppressive treatment is recommended.

Abstract. Malignant tumors degrade glucose to lactate even in the presence of oxygen via the pentose phosphate pathway (ppp). The non-oxidative part of the ppp is controlled by thiamine-dependant transketolase enzyme reactions. Overexpression of the transketolase-like-1-gene (TKTL1) in urothelial and colorectal cancer is associated with poor patient outcome. We analyzed the expression of the TKTL1 protein in a retrospective institution-based patient cohort with invasive breast cancer by immunohistochemical analysis of 124 paraffin-embedded breast cancer tissues. Our study revealed TKTL1 expression in 86% of breast cancer specimens with 45% showing high expression levels. In contrast, only 29% of corresponding non-neoplastic breast tissues were TKTL1 immunopositive, including 9% with high expression levels. High expression levels of TKTL1 correlated significantly to Her2/neu overexpression (p=0.015). However, TKTL1 expression failed to reach statistical significance for other common prognostic parameters. In contrast to recent data for e.g. colorectal cancer TKTL1 overexpression did not correlate to patient outcome and survival. However, in the context of novel insights into TKTL1-related tumor metabolism and the high proportion of TKTL1 overexpressing breast cancers, this enzyme represents a potential candidate for targeted inhibition of tumor growth in this tumor entity.

Abstract:The technological progress in digitalization of complete histological glass slides has opened a new door in tissue -based diagnosis. The presentation of microscopic images as a whole in a digital matrix is called virtual slide. A virtual slide allows calculation and related presentation of image information that otherwise can only be seen by individual human performance. The digital world permits attachments of several (if not all) fields of view and the contemporary visualization on a screen. The presentation of all microscopic magnifications is possible if the basic pixel resolution is less than 0.25 microns. To introduce digital tissue -based diagnosis into the daily routine work of a surgical pathologist requires a new setup of workflow arrangement and procedures. The quality of digitized images is sufficient for diagnostic purposes; however, the time needed for viewing virtual slides exceeds that of viewing original glass slides by far. The reason lies in a slower and more difficult sampling procedure, which is the selection of information containing fields of view. By application of artificial intelligence, tissue -based diagnosis in routine work can be managed automatically in steps as follows: 1. The individual image quality has to be measured, and corrected, if necessary. 2. A diagnostic algorithm has to be applied. An algorithm has be developed, that includes both object based (object features, structures) and pixel based (texture) measures. 3. These measures serve for diagnosis classification and feedback to order additional information, for example in virtual immunohistochemical slides. 4. The measures can serve for automated image classification and detection of relevant image information by themselves without any labeling. 5. The pathologists' duty will not be released by such a system; to the contrary, it will manage and supervise the system, i.e., just working at a "higher level". Virtual slides are already in use for teaching and continuous education in anatomy and pathology. First attempts to introduce them into routine work have been reported. Application of AI has been established by automated immunohistochemical measurement systems (EAMUS, www.diagnomX.eu). The performance of automated diagnosis has been reported for a broad variety of organs at sensitivity and specificity levels >85%). The implementation of a complete connected AI supported system is in its childhood. Application of AI in digital tissue -based diagnosis will allow the pathologists to work as supervisors and no longer as primary "water carriers". Its accurate use will give them the time needed to concentrating on difficult cases for the benefit of their patients.