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Bladder cancer is a genetically heterogeneous disease, and novel therapeutic strategies are needed to expand treatment options and improve clinical outcomes. Here, we identified a unique subset of urothelial tumors with focal amplification of the RAF1 (CRAF) kinase gene. RAF1-amplified tumors had activation of the RAF/MEK/ERK signaling pathway and exhibited a luminal gene expression pattern. Genetic studies demonstrated that RAF1-amplified tumors were dependent upon RAF1 activity for survival, and RAF1-activated cell lines and patient- derived models were sensitive to available and emerging RAF inhibitors as well as combined RAF plus MEK inhibition. Furthermore, we found that bladder tumors with HRAS- or WRAS-activating mutations were dependent on RAF1-mediated signaling and were sensitive to RAF1-targeted therapy. Together, these data identified RAF1 activation as a dependency in a subset making up nearly 20% of urothelial tumors and suggested that targeting RAF1-mediated signaling represents a rational therapeutic strategy., Introduction Bladder cancer accounts for approximately 80,000 new cancer diagnoses and nearly 20,000 deaths annually in the United States (1). Approximately 25% of patients present with muscle-invasive bladder cancer (MIBC), [...]

Context.--The analysis of somatic mutations across multiple genes in cancer specimens may be used to aid clinical decision making. The analytical validation of targeted next-generation sequencing panels is important to assess accuracy and limitations. Objective.--To report the development and validation of OncoPanel, a custom targeted next-generation sequencing assay for cancer. Design.--OncoPanel was designed for the detection of single-nucleotide variants, insertions and deletions, copy number alterations, and structural variants across 282 genes with evidence as drivers of cancer biology. We implemented a validation strategy using formalin-fixed, paraffin-embedded, fresh or frozen samples compared with results obtained by clinically validated orthogonal technologies. Results.--OncoPanel achieved 98% sensitivity and 100% specificity for the detection of single-nucleotide variants, and 84% sensitivity and 100% specificity for the detection of insertions and deletions compared with single-gene assays and mass spectrometry-based genotyping. Copy number detection achieved 86% sensitivity and 98% specificity compared with array comparative genomic hybridization. The sensitivity of structural variant detection was 74% compared with karyotype, fluorescence in situ hybridization, and polymerase chain reaction. Sensitivity was affected by inconsistency in the detection of FLT3 and NPM1 alterations and IGH rearrangements due to design limitations. Limit of detection studies demonstrated 98.4% concordance across triplicate runs for variants with allele fraction greater than 0.1 and at least 50X coverage. Conclusions.--The analytical validation of OncoPanel demonstrates the ability of targeted next-generation sequencing to detect multiple types of genetic alterations across a panel of genes implicated in cancer biology. (Arch Pathol Lab Med. 2017; 141:751-758; doi: 10.5858/arpa.2016-0527-OA), The understanding of cancer as a genomic disease, coupled with the introduction of targeted therapeutic agents to treat cancer, has propelled the genomic profiling of tumor samples to aid in [...]

Synaptojanin is a nerve terminal protein that belongs to the inositol-5-phosphatase family. It has 5-phosphatase activity and an amino-terminal domain that matches the yeast protein Sac1 (Rsd1). Aside from dynamin, synaptojanin is the only other major brain protein that binds the SH3 domain of the presynaptic protein amphiphysin. The results of an analysis indicate a relationship between phosphoinositide metabolism and synaptic vesicle recycling.

A study of subcellular localization of rbSec1A and the interaction between rbSec1A and syntaxin 1 in situ shows that rbSec1 is widely distributed in the cytoplasm of neurons and the function of this protein is not limited to synaptic vesicle exocytosis at the synapse. rbSec1 exists in two spliced isoforms differing in their carboxyl termini and is not associated with syntaxin 1. rbSec1 is not an integral part of the SNARE complex.

Proteins belonging to the Sec1 family interact with syntaxin (a T-SNARE) on membrane fusion, contributing to the formation of a docking-fusion complex core in synaptic vesicle exocytosis. Proteins that resemble Sec1 were identified in the nervous system of Caenorhabditis elegane (UNC18) and Drosophila melanogaster (Rop).