scholarly journals Variant allele frequency enrichment analysis in vitro reveals sonic hedgehog pathway to impede sustained temozolomide response in GBM

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Nidhan K. Biswas ◽  
Vikas Chandra ◽  
Neeta Sarkar-Roy ◽  
Tapojyoti Das ◽  
Rabindra N. Bhattacharya ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Sonic Hedgehog ◽  
Enrichment Analysis ◽  
Hedgehog Pathway ◽  
Variant Allele ◽  
Sonic Hedgehog Pathway ◽  
Variant Allele Frequency

Global and MYC-Specific Translation Is Enhanced in Activated Chronic Lymphocytic Leukemia Cells Carrying NOTCH1 C.7541_7542delct Mutations

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 970-970 ◽  
Author(s):  
Annalisa D'Avola ◽  
Alison Yeomans ◽  
Samantha Drennan ◽  
Matthew Rose-Zerilli ◽  
Jonathan C. Strefford ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Allele Frequency ◽  
Mrna Translation ◽  
Lymphocytic Leukemia ◽  
Chromosome 9 ◽  
Variant Allele ◽  
Variant Allele Frequency ◽  
Genetic Lesion ◽  
13Q Deletion

Abstract Introduction: mRNA translation is increased in activated tumor cells of the aggressive form of Chronic Lymphocytic Leukemia (CLL), typically unmutated (U) immunoglobulin gene heavy-chain variable region (IGHV) with a strong sIgM signaling capacity (Yeomans et al, Blood 2016). C-MYC protein is a master regulator of cell performance and its expression is controlled at both transcriptional and translational levels. C-MYC protein is over-expressed in the proliferation centers of CLL and high c-MYC mRNA expression is associated with poor prognosis. In leukemic cell lines, c-MYC is an essential mediator and direct target of NOTCH1. Pro-activating c.7541_7542delCTmutations in NOTCH1 PEST domain of chromosome 9 exon 34 (NOTCH1ΔCT) are enriched in U-CLL with high sIgM levels/signaling capacity and associate with poorer prognosis in CLL (D'Avola et al, Blood, 2016), likely due to accumulation of more stable NOTCH1 protein and enhanced signaling in tissue activated CLL cells (Arruga et al, Leukemia, 2014). Aims and Methods: We investigated the consequences of NOTCH1ΔCT on global mRNA and c-MYC translation using a novel flow cytometry-based O-propargyl-puromycin (OPP) incorporation assay ('Click-iT' assay) and by c-MYC-specific immunoblotting in U-CLL. Since prolonged culture of CLL cells in vitro in the absence of stimuli led to spontaneous inactivation of NOTCH1 pathway, CpG-mediated TLR9 induction was used as a tool for activation of CLL cells in vitro. Cycloheximide (CHX) was used as a negative control for mRNA translation. For this study, 2 cohorts were investigated: i) a test "CLLΔCT cohort" of U-CLL with NOTCH1ΔCT (variant allele frequency [VAF] by droplet digital PCR, range 42.6-48.9%, median 47% of the CD19+CD5+ CLL cell population), but no additional genetic lesion other than 13q deletion, and ii) a control "CLLWT cohort" of U-CLL with no NOTCH1ΔCT (VAF<1% in all cases) or additional genetic lesion other than 13q deletion. CLL cells were incubated with 7.5 μg/ml CpG-ODN 2006 for 24 hours and assays were performed at baseline, 3 and 24 hours. NOTCH1 pathway γ-secretase inhibition was performed with DAPT GSi. Results: The CLLΔCT cohort had higher sIgM levels (range 31-372 MFI, median 81 MFI) and signaling capacity (Fab'2 anti-IgM induced intracellular calcium mobilization sIgM [iCa2+] range 47-54%, median 51) than the CLLWT cohort (sIgM levels range 19-288 MFI, median 47 MFI; IgM iCa2+ range 2-78%, median 25%). Following TLR9-mediated cell activation, the CLLΔCT cohort had sustained NICD (NOTCH1-intracellular cleaved domain) protein accumulation for up to 24 hours and expressed higher NOTCH1 target gene HES1 (hairy enhancer of split) transcript levels than in the CLLWT cohort. These data indicated NOTCH1 canonical pathway sustainment in the CLLΔCT upon activation. Global mRNA translation after 24 hours in the presence of CpG was 11.5 fold higher than that without CpG in the CLLΔCT cohort and only 4 fold higher in the CLLWT cohort, revealing significantly higher levels of translation in CLLΔCT than in CLLWT (p=0.03). CpG-induced global mRNA translation in the CLLWT cohort was similar to that in the CLLΔCT cohort treated with CHX. By using CpG-induced global mRNA translation in the presence of CHX inhibitor as background levels for each group, DAPT GSiat 2.5 to 10 μM showed from 47% to 63% inhibition of the residual CpG-induced global translation in CLLΔCT (p<0.05), but no effect in CLLWT. Remarkably, c-MYC mRNA translation after 3 hour culture with CpG was higher in CLLΔCT than in CLLWT (p= 0.02), and a similar trend was maintained in the cases investigated at 24 hour. Treatment of CLLΔCT cells with DAPT GSi decreased expression of c-MYC in a dose-dependent manner. Conclusion: NOTCH1ΔCT mutations associate with a very aggressive clinical behavior in CLL. These results now indicate that pro-activating mutations of NOTCH1 pathway associate with increased global mRNA translation and c-MYC expression. They highlight a mechanism by which NOTCH1 pathway may induce c-MYC overexpression in CLL, likely leading to increased proliferation and survival. The association of increased NOTCH1 variant allele frequency with sIgM levels and signaling capacity indicate that these mechanisms are predominant in the less anergic subgroup of U-CLL and make NOTCH1 mediated c-MYC translation an attractive target for therapeutic inhibition. Disclosures Steele: Portola Pharmaceuticals: Honoraria. Packham:Karus Therapeutics: Other: Share Holder & Founder; Aquinox Pharmaceuticals: Research Funding.

scholarly journals Baicalin Attenuates Alcoholic Liver Injury through Modulation of Hepatic Oxidative Stress, Inflammation and Sonic Hedgehog Pathway in Rats

2016 ◽  
Vol 39 (3) ◽  
pp. 1129-1140 ◽  
Author(s):  
Huifen Wang ◽  
Yanli Zhang ◽  
Ruxue Bai ◽  
Miao Wang ◽  
Shiyu Du
Keyword(s):  
Oxidative Stress ◽  
Liver Injury ◽  
Sonic Hedgehog ◽  
Inflammatory Responses ◽  
Hedgehog Pathway ◽  
Alcoholic Liver Injury ◽  
Sonic Hedgehog Pathway ◽  
Shh Pathway

Background/Aims: Lipid accumulation, inflammatory responses and oxidative stress have been implicated in the pathology of alcoholic liver disease (ALD). Targeting inhibition of these features may provide a promising therapeutic strategy for ALD. Baicalin, a flavonoid isolated from Scutellaria baicalensis Georgi, has been shown to exert a hepatoprotective effect. However, its effects on ALD remain obscure. This study was aimed to investigate the effects of baicalin on alcohol-induced liver injury and its related mechanisms. Methods: For in vivo experiments, rats were supplied intragastrical administration of alcohol continuously for 4 or 8 weeks, and then received baicalin treatment in the latter 4 weeks in the presence / absence of alcohol intake. Liver histology and function, inflammatory cytokines, oxidative mediators, and the components of the Sonic hedgehog pathway were evaluated. For in vitro experiments, alcohol-stimulated human normal liver cells LO2 were used. Results: Baicalin treatment significantly alleviated alcoholic liver injury, improved liver function impaired by alcohol, and inhibited hepatocytes apoptosis. In addition, baicalin decreased the expression levels of proinflammatory cytokines TNF-α, IL-1β, IL-6) and malonyldialdehyde (MDA), and increased the activities of antioxidant enzymes SOD and GSH-Px. Furthermore, baicalin modulated the activation of Sonic hedgehog (Shh) pathway. Administration of baicalin upregulated the expression of sonic hedgehog (Shh), patched (Ptc), Smoothened (Smo), and Glioblastoma-1(Gli-1). Blockade of the Shh pathway in cyclopamine abolished the effects of baicalin in vitro. Conclusion: Both in vivo and in vitro experimental results indicate that baicalin exerts hepatoprotective roles in alcohol-induced liver injury through inhibiting oxidative stress, inflammatory response, and the regulation of the Shh pathway.

Inhibition of the sonic hedgehog pathway by cyplopamine reduces the CD133+/CD15+ cell compartment and the in vitro tumorigenic capability of neuroblastoma cells

2011 ◽  
Vol 310 (2) ◽  
pp. 222-231 ◽  
Author(s):  
Paula Schiapparelli ◽  
Mehdi H. Shahi ◽  
Mónica Enguita-Germán ◽  
John Inge Johnsen ◽  
Per Kogner ◽  
...  
Keyword(s):  
Sonic Hedgehog ◽  
Neuroblastoma Cells ◽  
Hedgehog Pathway ◽  
Sonic Hedgehog Pathway ◽  
Cell Compartment

scholarly journals Examination of the predicted prevalence of Gitelman syndrome by ethnicity based on genome databases

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Atsushi Kondo ◽  
China Nagano ◽  
Shinya Ishiko ◽  
Takashi Omori ◽  
Yuya Aoto ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Carrier Frequency ◽  
Japanese Population ◽  
Autosomal Recessive ◽  
Disease Prevalence ◽  
Gitelman Syndrome ◽  
Variant Allele ◽  
Variant Allele Frequency ◽  
Genome Databases ◽  
Heterozygous Carriers

AbstractGitelman syndrome is an autosomal recessive inherited salt-losing tubulopathy. It has a prevalence of around 1 in 40,000 people, and heterozygous carriers are estimated at approximately 1%, although the exact prevalence is unknown. We estimated the predicted prevalence of Gitelman syndrome based on multiple genome databases, HGVD and jMorp for the Japanese population and gnomAD for other ethnicities, and included all 274 pathogenic missense or nonsense variants registered in HGMD Professional. The frequencies of all these alleles were summed to calculate the total variant allele frequency in SLC12A3. The carrier frequency and the disease prevalence were assumed to be twice and the square of the total allele frequency, respectively, according to the Hardy–Weinberg principle. In the Japanese population, the total carrier frequencies were 0.0948 (9.5%) and 0.0868 (8.7%) and the calculated prevalence was 0.00225 (2.3 in 1000 people) and 0.00188 (1.9 in 1000 people) in HGVD and jMorp, respectively. Other ethnicities showed a prevalence varying from 0.000012 to 0.00083. These findings indicate that the prevalence of Gitelman syndrome in the Japanese population is higher than expected and that some other ethnicities also have a higher prevalence than has previously been considered.

scholarly journals Mutations of the Sonic Hedgehog Pathway Underlie Hypothalamic Hamartoma with Gelastic Epilepsy

2016 ◽  
Vol 99 (2) ◽  
pp. 423-429 ◽  
Author(s):  
Michael S. Hildebrand ◽  
Nicole G. Griffin ◽  
John A. Damiano ◽  
Elisa J. Cops ◽  
Rosemary Burgess ◽  
...  
Keyword(s):  
Sonic Hedgehog ◽  
Hedgehog Pathway ◽  
Hypothalamic Hamartoma ◽  
Sonic Hedgehog Pathway ◽  
Gelastic Epilepsy

Abstract 569: Correlation of variant allele frequency and mean tumor molecules with tumor burden in patients with solid tumors

2021 ◽  
Author(s):  
Antony Tin ◽  
Vasily Aushev ◽  
Ekaterina Kalashnikova ◽  
Raheleh Salari ◽  
Svetalana Shchegrova ◽  
...  
Keyword(s):  
Solid Tumors ◽  
Allele Frequency ◽  
Tumor Burden ◽  
Variant Allele ◽  
Variant Allele Frequency

Cadmium‐induced neurodegeneration and activation of noncanonical sonic hedgehog pathway in rat cerebellum

2018 ◽  
Vol 33 (4) ◽  
pp. e22274
Author(s):  
Mubeena Mariyath P. M. ◽  
Mehdi H. Shahi ◽  
Mohd Tayyab ◽  
Shirin Farheen ◽  
Nabeela Khanam ◽  
...  
Keyword(s):  
Sonic Hedgehog ◽  
Hedgehog Pathway ◽  
Sonic Hedgehog Pathway ◽  
Rat Cerebellum
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