Therapeutic Strategies for Targeting CDKN2A Loss in Melanoma

Loss of the tumor suppressor gene CDKN2A, encoding p16 and p14, is a frequent event driving melanoma progression. Therefore, therapeutic strategies aimed at CDKN2A loss hold great potential to improve melanoma treatment. Pharmacological inhibition of the p16 targets CDK4/6 is a prime example of such a strategy. Other approaches exploit cell cycle deregulation, target metabolic rewiring, epigenetically restore expression, act on dependencies resulting from co-deleted genes, or are directed at the effects of CDKN2A loss on immune responses. This review explores these therapeutic strategies targeting CDKN2A loss, which potentially open up new avenues for precision medicine in melanoma

A NOTCH3 transcriptional module induces cell motility in neuroblastoma

Neuroblastoma is a childhood tumor of the peripheral sympathetic nervous system with an often lethal outcome due to metastatic disease. Migration and epithelial-mesenchymal transitions have been implicated in metastasis but they are hardly investigated in neuroblastoma. Cell migration of 16 neuroblastoma cell lines was quantified in Transwell migration assays. Gene expression profiling was used to derive a migration signature, which was applied to classify samples in a neuroblastoma tumor series. Differential expression of transcription factors was analyzed in the subsets. NOTCH3 was prioritized, and inducible transgene expression studies in cell lines were used to establish whether it functions as a master switch for motility. We identified a 36-gene expression signature that predicts cell migration. This signature was used to analyse expression profiles of 88 neuroblastoma tumors and identified a group with distant metastases and a poor prognosis. This group also expressed a known mesenchymal gene signature established in glioblastoma. Neuroblastomas recognized by the motility and mesenchymal signatures strongly expressed genes of the NOTCH pathway. Inducible expression of a NOTCH intracellular (NOTCH3-IC) transgene conferred a highly motile phenotype to neuroblastoma cells. NOTCH3-IC strongly induced expression of motility- and mesenchymal marker genes. Many of these genes were significantly coexpressed with NOTCH3 in neuroblastoma, as well as colon, kidney, ovary, and breast tumor series. The NOTCH3 transcription factor is a master regulator of motility in neuroblastoma. A subset of neuroblastoma with high expression of NOTCH3 and its downstream-regulated genes has mesenchymal characteristics, increased incidence of metastases, and a poor prognosi

An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae

The exchange of mobile genomic islands (MGIs) between microorganisms is often mediated by phages, which may provide benefits to the phage’s host. The present study started with the identification of Enterobacter cloacae, Klebsiella pneumoniae and Escherichia coli isolates with exceptional cephalosporin and carbapenem resistance phenotypes from patients in a neonatal ward. To identify possible molecular connections between these isolates and their β-lactam resistance phenotypes, the respective bacterial genome sequences were compared. This unveiled the existence of a family of ancient MGIs that were probably exchanged before the species E. cloacae, K. pneumoniae and E. coli emerged from their common ancestry. A representative MGI from E. cloacae was named MIR17-GI, because it harbors the novel β-lactamase gene variant blaMIR17. Importantly, our observations show that the MIR17-GI-like MGIs harbor genes associated with high-level resistance to cephalosporins. Among them, MIR17-GI stands out because MIR17 also displays carbapenemase activity. As shown by mass spectrometry, the MIR17 carbapenemase is among the most abundantly expressed proteins of the respective E. cloacae isolate. Further, we show that MIR17-GI-like islands are associated with integrated P4-like prophages. This implicates phages in the spread of cephalosporin and carbapenem resistance amongst Enterobacteriaceae. The discovery of an ancient family of MGIs, mediating the spread of cephalosporinase and carbapenemase genes, is of high clinical relevance, because high-level cephalosporin and carbapenem resistance have serious implications for the treatment of patients with enterobacteriaceal infections

Optimization of the k2’ parameter for the pharmacokinetic modelling of dynamic PIB scans using SRTM2

Introduction: In Alzheimer’s disease (AD), quantitative measures of amyloid-β (Aβ) deposition in the brain can be assessed by the analysis of dynamic 11C-labelled Pittsburgh Compound B (PIB) scans. To this end, pharmacokinetic modelling of the data is required, with the most frequent approach being the simplified reference tissue model 2 (SRTM2). However, this method was originally developed for the analysis of neuroreceptor binding, thus it expects a well-defined receptor-rich region. This assumption might be violated in the case of PIB, especially in healthy subjects, which are not expected to have Aβ deposition. Therefore, the aim of this study was to explore the consequences of violating this assumption and, if possible, to define an optimal brain region for estimating k2’ (i.e. transfer of the tracer from the reference tissue back to plasma), which is used and fixed in the second iteration of SRTM2. Materials and Methods: Thirty subjects underwent a dynamic PIB PET scan and were then classified by visual inspections as PIB positive (+) or PIB negative (-), with a total of fifteen per group. A set of regions were used to estimate the median value of the k2’ parameter for SRTM2: seven anatomical regions derived from the Hammer’s atlas (grey matter, frontal lobe, parietal lobe, temporal lobe, white matter, brainstem, and the combination of white matter and brainstem), one SPM voxel-based comparison of statistical differences between the groups, and three using different binding potential (BPND) thresholds (0.01, 0.05, 0.1). A sensitivity analysis was also made by fixing a range of k2’ values (from 0.03 to 0.09) and assessing the effects of these changes on estimated BPND. Results: The different regions used to estimate k2’ resulted in distinct values for this parameter. In general, values from grey matter and statistical regions showed a larger difference between the groups, an average difference of 32%. The method that presented the smallest difference was the one where the brainstem was used for the estimation (2% difference between groups), but the estimated median values were, in general, higher than for the other methods. Distribution of median k2’ values showed that the most common estimation is 0.05 for this set of subjects. The method that presented the lowest difference between groups and was the closest to this estimated value was the threshold approach using BPND equal to 0.1. Sensitivity analysis of the effects of different k2’ estimation on BPND showed that the larger the k2’ value, the smaller the change in BPND. Discussion: The large difference between k2’ estimations between groups suggests that grey matter VOI based methods and the one based on statistical differences between groups might not be acceptable. Threshold based approaches guarantee that only regions with some binding will be considered when estimating k2’. Preliminary analysis of the data showed that since the relationship between k2’ and BPND is not linear, an overestimation of k2’ value might result in a smaller bias in BPND estimation than an underestimation. Therefore the best method for estimating the k2’ is by using a threshold on the BPND

Mesenchymal Neuroblastoma Cells Are Undetected by Current mRNA Marker Panels: The Development of a Specific Neuroblastoma Mesenchymal Minimal Residual Disease Panel

PURPOSE Patients with neuroblastoma in molecular remission remain at considerable risk for disease recurrence. Studies have found that neuroblastoma tissue contains adrenergic (ADRN) and mesenchymal (MES) cells; the latter express low levels of commonly used markers for minimal residual disease (MRD). We identified MES-specific MRD markers and studied the dynamics of these markers during treatment. PATIENTS AND METHODS Microarray data were used to identify genes differentially expressed between ADRN and MES cell lines. Candidate genes were then studied using real-time quantitative polymerase chain reaction in cell lines and control bone marrow and peripheral blood samples. After selecting a panel of markers, serial bone marrow, peripheral blood, and peripheral blood stem cell samples were obtained from patients with high-risk neuroblastoma and tested for marker expression; survival analyses were also performed. RESULTS PRRX1, POSTN, and FMO3 mR NAs were used as a panel for specifically detecting MES mRNA in patient samples. MES mRNA was detected only rarely in peripheral blood; moreover, the presence of MES mRNA in peripheral blood stem cell samples was associated with low event-free survival and overall survival. Of note, during treatment, serial bone marrow samples obtained from 29 patients revealed a difference in dynamics between MES mRNA markers and ADRN mRNA markers. Furthermore, MES mRNA was detected in a higher percentage of patients with recurrent disease than in those who remained disease free (53% v 32%, respectively; p= .03). CONCLUSION We propose that the markers POSTN and PRRX1, in combination with FMO3, be used for real-time quantitative polymerase chain reaction-based detection of MES neuroblastoma mRNA in patient samples because these markers have a unique pattern during treatment and are more prevalent in patients with poor outcome. Together with existing markers of MRD, these new markers should be investigated further in large prospective studies. (C) 2019 by American Society of Clinical Oncolog

Mesenchymal-Type Neuroblastoma Cells Escape ALK Inhibitors

Cancer therapy frequently fails due to the emergence of resistance. Many tumors include phenotypically immature tumor cells, which have been implicated in therapy resistance. Neuroblastoma cells can adopt a lineage-committed adrenergic (ADRN) or an immature mesenchymal (MES) state. They differ in epigenetic landscape and transcription factors, and MES cells are more resistant to chemotherapy. Here we analyzed the response of MES cells to targeted drugs. Activating anaplastic lymphoma kinase (ALK) mutations are frequently found in neuroblastoma and ALK inhibitors (ALKi) are in clinical trials. ALKi treatment of ADRN neuroblastoma cells with a tumor-driving ALK mutation induced cell death. Conversely, MES cells did not express either mutant or wild-type ALK and were resistant to ALKi, and MES cells formed tumors that progressed under ALKi therapy. In assessing the role of MES cells in relapse development, TRAIL was identified to specifically induce apoptosis in MES cells and to suppress MES tumor growth. Addition of TRAIL to ALKi treatment of neuroblastoma xenografts delayed relapses in a subset of the animals, suggesting a role for MES cells in relapse formation. While ADRN cells resembled normal embryonal neuroblasts, MES cells resembled immature precursor cells, which also lacked ALK expression. Resistance to targeted drugs can therefore be an intrinsic property of immature cancer cells based on their resemblance to developmental precursors. SIGNIFICANCE: In neuroblastoma, mesenchymal tumor cells lack expression of the tumor-driving ALK oncogene and are resistant to ALKi, but dual treatment with ALKi and mesenchymal cell-targeting TRAIL delays tumor relapse

Associations of Relative Fat Mass, a New Index of Adiposity, with Type-2 Diabetes in the General Population

Supplemental material for manuscript "Associations of Relative Fat Mass, a New Index of Adiposity, with Type-2 Diabetes in the General Population"