Loss of the PTCH1 tumor suppressor defines a new subset of plexiform fibromyxoma.

BackgroundPlexiform fibromyxoma (PF) is a rare gastric tumor often confused with gastrointestinal stromal tumor. These so-called "benign" tumors often present with upper GI bleeding and gastric outlet obstruction. It was recently demonstrated that approximately one-third of PF have activation of the GLI1 oncogene, a transcription factor in the hedgehog (Hh) pathway, via a MALAT1-GLI1 fusion protein or GLI1 up-regulation. Despite this discovery, the biology of most PFs remains unknown.MethodsNext generation sequencing (NGS) was performed on formalin-fixed paraffin-embedded (FFPE) samples of PF specimens collected from three institutions (UCSD, NCI and OHSU). Fresh frozen tissue from one tumor was utilized for in vitro assays, including quantitative RT-PCR and cell viability assays following drug treatment.ResultsEight patients with PF were identified and 5 patients' tumors were analyzed by NGS. An index case had a mono-allelic PTCH1 deletion of exons 15-24 and a second case, identified in a validation cohort, also had a PTCH1 gene loss associated with a suspected long-range chromosome 9 deletion. Building on the role of Hh signaling in PF, PTCH1, a tumor suppressor protein, functions upstream of GLI1. Loss of PTCH1 induces GLI1 activation and downstream gene transcription. Utilizing fresh tissue from the index PF case, RT-qPCR analysis demonstrated expression of Hh pathway components, SMO and GLI1, as well as GLI1 transcriptional targets, CCND1 and HHIP. In turn, short-term in vitro treatment with a Hh pathway inhibitor, sonidegib, resulted in dose-dependent cell killing.ConclusionsFor the first time, we report a novel association between PTCH1 inactivation and the development of plexiform fibromyxoma. Hh pathway inhibition with SMO antagonists may represent a target to study for treating a subset of plexiform fibromyxomas

Endothelium-Derived Netrin-4 Supports Pancreatic Epithelial Cell Adhesion and Differentiation through Integrins α2β1 and α3β1

BACKGROUND: Netrins have been extensively studied in the developing central nervous system as pathfinding guidance cues, and more recently in non-neural tissues where they mediate cell adhesion, migration and differentiation. Netrin-4, a distant relative of Netrins 1-3, has been proposed to affect cell fate determination in developing epithelia, though receptors mediating these functions have yet to be identified. METHODOLOGY/PRINCIPAL FINDINGS: Using human embryonic pancreatic cells as a model of developing epithelium, here we report that Netrin-4 is abundantly expressed in vascular endothelial cells and pancreatic ductal cells, and supports epithelial cell adhesion through integrins α2β1 and α3β1. Interestingly, we find that Netrin-4 recognition by embryonic pancreatic cells through integrins α2β1 and α3β1 promotes insulin and glucagon gene expression. In addition, full genome microarray analysis revealed that fetal pancreatic cell adhesion to Netrin-4 causes a prominent down-regulation of cyclins and up-regulation of negative regulators of the cell cycle. Consistent with these results, a number of other genes whose activities have been linked to developmental decisions and/or cellular differentiation are up-regulated. CONCLUSIONS/SIGNIFICANCE: Given the recognized function of blood vessels in epithelial tissue morphogenesis, our results provide a mechanism by which endothelial-derived Netrin-4 may function as a pro-differentiation cue for adjacent developing pancreatic cell populations expressing adhesion receptors α2β1 and α3β1 integrins

Genome Sequence and Comparative Genome Analysis of Lactobacillus casei: Insights into Their Niche-Associated Evolution

Lactobacillus casei is remarkably adaptable to diverse habitats and widely used in the food industry. To reveal the genomic features that contribute to its broad ecological adaptability and examine the evolution of the species, the genome sequence of L. casei ATCC 334 is analyzed and compared with other sequenced lactobacilli. This analysis reveals that ATCC 334 contains a high number of coding sequences involved in carbohydrate utilization and transcriptional regulation, reflecting its requirement for dealing with diverse environmental conditions. A comparison of the genome sequences of ATCC 334 to L. casei BL23 reveals 12 and 19 genomic islands, respectively. For a broader assessment of the genetic variability within L. casei, gene content of 21 L. casei strains isolated from various habitats (cheeses, n = 7; plant materials, n = 8; and human sources, n = 6) was examined by comparative genome hybridization with an ATCC 334-based microarray. This analysis resulted in identification of 25 hypervariable regions. One of these regions contains an overrepresentation of genes involved in carbohydrate utilization and transcriptional regulation and was thus proposed as a lifestyle adaptation island. Differences in L. casei genome inventory reveal both gene gain and gene decay. Gene gain, via acquisition of genomic islands, likely confers a fitness benefit in specific habitats. Gene decay, that is, loss of unnecessary ancestral traits, is observed in the cheese isolates and likely results in enhanced fitness in the dairy niche. This study gives the first picture of the stable versus variable regions in L. casei and provides valuable insights into evolution, lifestyle adaptation, and metabolic diversity of L. casei

Anti-KIT DNA Aptamer for Targeted Labeling of Gastrointestinal Stromal Tumor.

Gastrointestinal stromal tumor (GIST), the most common sarcoma, is characterized by KIT protein overexpression, and tumors are frequently driven by oncogenic KIT mutations. Targeted inhibition of KIT revolutionized GIST therapy and ushered in the era of precision medicine for the treatment of solid malignancies. Here, we present the first use of a KIT-specific DNA aptamer for targeted labeling of GIST. We found that an anti-KIT DNA aptamer bound cells in a KIT-dependent manner and was highly specific for GIST cell labeling in vitro Functionally, the KIT aptamer bound extracellular KIT in a manner similar to KIT mAb staining, and was trafficked intracellularly in vitro The KIT aptamer bound dissociated primary human GIST cells in a mutation agnostic manner such that tumors with KIT and PDGFRA mutations were labeled. In addition, the KIT aptamer specifically labeled intact human GIST tissue ex vivo, as well as peritoneal xenografts in mice with high sensitivity. These results represent the first use of an aptamer-based method for targeted detection of GIST in vitro and in vivo

Síndrome de Hurler. Informe de un caso

Se presenta paciente femenina de 5 años con una rara enfermedad metabólica, remitida desde la consulta de genética para su evaluación desde el punto de vista oftalmológico, y luego de su estudio exponemos los hallazgos clínicos y comportamiento  de la afección

Identification of pancreatic cell types expressing Netrin-4.

<p>PCR analysis (<b>A</b>) and Western blotting (<b>B</b>) on select pancreatic cell populations show significant levels of Netrin-4 expression in adult primary ductal cells, ductal cell line CAPAN-1, and fetal pancreatic cells, and low levels in pancreatic islets. Representative of n = 3. SYBR green qPCR (<b>C</b>) for Netrin-4-specific transcripts in primary microvascular endothelial cells (hMEC), fetal and adult pancreatic ductal cells, and intact adult islets. SYBR green qPCR for the endothelial-specific cell adhesion molecule VE-cadherin (<b>D</b>) showing that resident endothelia cells are positioned within fetal and adult islets. Fluorescence-activated cell sorting of a single cell suspension from isolated human fetal islets immunostained for insulin (<b>E</b>), and SYBR green qPCR analysis for insulin, Netrin-4, and VE-cadherin (<b>F</b>). Data presented in C, D, E and F are representative of n = 3, with each SYBR green qPCR reaction performed in duplicate.</p

Netrin-4 supports epithelial cell adhesion through integrin receptors and fosters the expression of islet-specific differentiation genes.

<p>(<b>A</b>) Adhesion of pancreatic epithelial cells to Netrin-1, Netrin-4, LN-1 and Collagen IV. BSA was used as negative control. (<b>B</b>) Cell adhesion to Netrin-4 in the absence (n.t., no treatment) or presence of function-blocking antibodies to select integrin subunits. Note the significant blockade of cell attachment to Netrin-4 in the presence of anti-α2, -α3, -β1, or a combination of anti-α2 and anti α3 function-blocking antibodies. (<b>C</b>) Similar results were obtained when cells were plated on a modified recombinant Netrin-4 (ΔC-Netrin-4) that lacks 155aa from its carboxy terminal domain. Data in <b>A</b> and <b>B</b> are representative of n = 4, and in C of n = 3. *p<0.001 ANOVA followed by post-test Bonferroni's multiple comparison test. (<b>D</b>) Immunoprecipitation using anti-Netrin-4, -α2, -α3, -α5, -β3 or control IgGs, followed by Western blotting for Netrin-4 revels that α2 and α3, but not α5 or β3, integrin subunits selectively interacts with Netrin-4 in live cells. Representative of n = 3. (<b>E</b>) TaqMan PCR analysis for insulin and glucagon mRNAs demonstrates that overnight culture of embryonic pancreatic cells on Netrin-4 promotes the expression of these two islet-specific differentiation genes, when compared to Collagen IV. Culture on Netrin-1, that we reported to engage integrin α3β1 as a receptor <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022750#pone.0022750-Yebra1" target="_blank">[10]</a>, also revealed significantly higher levels of insulin- and glucagon-specific transcripts when compared to Collagen IV (n = 6); statistical significance of differences in insulin (p<0.001) and glucagon (p<0.005) expression between Netrins and Coll. IV overnight cultures was determined by ANOVA followed by post-test Bonferroni's multiple comparison test. (<b>F</b>) Blockade of α2, α3, β1, or α2 and α3 simultaneously, significantly reduced Netrin-mediated pro-differentiative effects on pancreatic cells (n = 4). (G) Specific immunoreactivity for the α3 integrin subunit (green fluorescence) is detected both <i>in situ</i> (G, left panel) and <i>in vitro</i> (G, right panel) in insulin-producing cells (red fluorescence, arrowheads). (H) Insulin content measured in embryonic pancreatic cells cultured on either Collagen IV, Netrin-1, or Netrin-4 (n = 4).</p

Pancreatic cell adhesion to Netrin-4 promotes cell cycle exit and fosters the expression of pro-differentiation genes.

<p>Heatmap of select genes that are either down-regulated (<b>A</b>) or up-regulated (<b>B</b> and <b>C</b>) by an 18-hours exposure of fetal pancreatic cells to Netrin-4. Data are presented as fold increase over time 0′. Note that known negative regulators of the cell cycle such as p57/kip2 and p27/kip1 are up-regulated (<b>A</b>), whereas positive regulators such as cyclins are down-regulated (<b>A</b>). Conversely, a number of genes whose function has been linked to events of cellular differentiation are all up-regulated (<b>B</b>, <b>C</b>). Changes in expression of select genes exemplified in panels <b>A</b> and <b>B</b> were validated by qPCR (<b>D</b>), where a value of 1 is equal to no change in gene expression. Complete array data have been deposited in the EBI Array Express Database (accession number pending). Data presented in <b>D</b> are representative of two independent experiments.</p