Literature Watch
Comprehensive mapping of Cystic Fibrosis mutations to CFTR protein identifies mutation clusters and molecular docking predicts corrector binding site.
Comprehensive mapping of Cystic Fibrosis mutations to CFTR protein identifies mutation clusters and molecular docking predicts corrector binding site.
Proteins. 2018 Mar 23;:
Authors: Molinski SV, Shahani VM, Subramanian AS, MacKinnon SS, Woollard G, Laforet M, Laselva O, Morayniss LD, Bear CE, Windemuth A
Abstract
Cystic Fibrosis (CF) is caused by mutations in the CFTR gene, of which over 2000 have been reported to date. Mutations have yet to be analyzed in aggregate to assess their distribution across the tertiary structure of the CFTR protein, an approach that could provide valuable insights into the structure-function relationship of CFTR. In addition, the binding site of Class I correctors (VX-809, VX-661, C18) is not well understood. In this study, exonic CFTR mutations and mutant allele frequencies described in three curated databases (ABCMdb, CFTR1 and CFTR2, comprising >130,000 data points) were mapped to two different structural models: a homology model of full-length CFTR protein in the open-channel state, and a cryo-electron microscopy core-structure of CFTR in the closed-channel state. Accordingly, residue positions of six high-frequency mutant CFTR alleles were found to spatially co-localize in CFTR protein, and a significant cluster was identified at the NBD1:ICL4 interdomain interface. In addition, immunoblotting confirmed the approximate binding site of Class I correctors, demonstrating that these small molecules act via a similar mechanism in vitro, and in silico molecular docking generated binding poses for their complex with the cryo-electron microscopy structure to suggest the putative corrector binding site is a multi-domain pocket near residues F374-L375. These results confirm the significance of interdomain interfaces as susceptible to disruptive mutation, and identify a putative corrector binding site. The structural pharmacogenomics approach of mapping mutation databases to protein models shows promise for facilitating drug discovery and personalized medicine for monogenetic diseases. This article is protected by copyright. All rights reserved.
PMID: 29569753 [PubMed - as supplied by publisher]
Future directions in pharmacogenomics discovery in cardiovascular disease.
Future directions in pharmacogenomics discovery in cardiovascular disease.
Pharmacogenomics. 2018 Mar 23;:
Authors: Friede KA, Voora D
PMID: 29569527 [PubMed - as supplied by publisher]
Pharmacogenetics and the treatment of chronic myeloid leukemia: how relevant clinically? An update.
Pharmacogenetics and the treatment of chronic myeloid leukemia: how relevant clinically? An update.
Pharmacogenomics. 2018 Mar 23;:
Authors: Ankathil R, Azlan H, Dzarr AA, Baba AA
Abstract
Despite the excellent efficacy and improved clinical responses obtained with imatinib mesylate (IM), development of resistance in a significant proportion of chronic myeloid leukemia (CML) patients on IM therapy have emerged as a challenging problem in clinical practice. Resistance to imatinib can be due to heterogeneous array of factors involving BCR/ABL-dependent and BCR/ABL-independent pathways. Although BCR/ABL mutation is the major contributory factor for IM resistance, reduced bio-availability of IM in leukemic cells is also an important pharmacokinetic factor that contributes to development of resistance to IM in CML patients. The contribution of polymorphisms of the pharmacogenes in relation to IM disposition and treatment outcomes have been studied by various research groups in numerous population cohorts. However, the conclusions arising from these studies have been highly inconsistent. This review encompasses an updated insight into the impact of pharmacogenetic variability on treatment response of IM in CML patients.
PMID: 29569526 [PubMed - as supplied by publisher]
Genetic analysis of sick sinus syndrome in a family harboring compound CACNA1C and TTN mutations.
Genetic analysis of sick sinus syndrome in a family harboring compound CACNA1C and TTN mutations.
Mol Med Rep. 2018 Mar 16;:
Authors: Zhu YB, Luo JW, Jiang F, Liu G
Abstract
Sick sinus syndrome (SSS) is a sinus node dysfunction characterized by severe sinus bradycardia. SSS results in insufficient blood supply to the brain, heart, kidneys, and other organs and is associated with the increased risk of sudden cardiac death. Bradyarrhythmia appears in the absence of any associated cardiac pathology and displays a genetic legacy. The present study identified a family with primary manifestation of sinus bradycardia (five individuals) along with early repolarization (four individuals) and atrial fibrillation (one individual). Targeted exome sequencing was used to screen exons and adjacent splice sites of 61 inherited arrhythmia‑associated genes, to detect pathogenic genes and variant sites in the proband. Family members were sequenced by Sanger sequencing and protein functions predicted by Polyphen‑2 software. A total of three rare variants were identified in the family, including two missense variants in calcium voltage‑gated channel subunit alpha1 C (CACNA1C) (gi:193788541, NM_001129843), c.1786G>A (p.V596M) and c.5344G>A (p.A1782T), and one missense variant in titin (TTN) c.49415G>A (p.R16472H) (gi:291045222, NM_003319). The variants p.V596M and p.R16472H were predicted to be deleterious and resulted in alterations in the amino acid type and sequence of the polypeptide chain, which may partially or completely inactivate the encoded protein. The comparison of literature, gene database, and pedigree phenotype analysis suggests that p.V596M or p.R16472H variants are pathogenic. The complex overlapping variants at three loci lead to a more severe phenotype in the proband, and may increase the susceptibility of individuals to atrial fibrillation. The simultaneous occurrence of V596M and R16472H may increase the severity of early repolarization. Various family members may have carried heterozygous mutants of p.A1782T and p.R16472H due to genetic heterogeneity, however did not exhibit clinical signs of cardiac electrophysiological alterations, potentially attributable to the low vagal tone. To the best of the author's knowledge, this is the first study to suggest the involvement of the novel missense CACNA1C c.1786G>A and TTN c.49415G>A variants in the inheritance of symptomatic bradycardia and development of SSS.
PMID: 29568937 [PubMed - as supplied by publisher]
Evaluation of CYP2C9- and VKORC1-based pharmacogenetic algorithm for warfarin dose in Gaza-Palestine.
Evaluation of CYP2C9- and VKORC1-based pharmacogenetic algorithm for warfarin dose in Gaza-Palestine.
Future Sci OA. 2018 Mar;4(3):FSO276
Authors: Ayesh BM, Abu Shaaban AS, Abed AA
Abstract
Aim: To evaluate applicability of CYP2C9*2, *3 and VKORC1-1639G > A based algorithm to predict warfarin stable dose (WSD) in a group of Palestinian patients.
Patients & methods: Warfarin doses were retrospectively calculated for 101 Palestinian patients under warfarin therapy using three models. Performance of the three models was assessed in 47 patients found to take WSD.
Results: Frequency of CYP2C9*2, *3 and VKORC1-1639G > A alleles is 13.6, 0.0 and 46.5% respectively. The international warfarin pharmacogenetics consortium algorithm was more reliable (MAE = 8.9 ± 1.4; R2 = 0.350) than both the clinical algorithm (MAE = 10.4 ± 1.4; R2 = 0.128;) and the fixed-dose algorithm (MAE = 11.1 ± 1.7).
Conclusion: The international warfarin pharmacogenetics consortium algorithm can be reliably applied for predicting the WSD in Palestinian population.
PMID: 29568565 [PubMed]
Genome-wide Analyses Identify KIF5A as a Novel ALS Gene.
Genome-wide Analyses Identify KIF5A as a Novel ALS Gene.
Neuron. 2018 Mar 21;97(6):1268-1283.e6
Authors: Nicolas A, Kenna KP, Renton AE, Ticozzi N, Faghri F, Chia R, Dominov JA, Kenna BJ, Nalls MA, Keagle P, Rivera AM, van Rheenen W, Murphy NA, van Vugt JJFA, Geiger JT, Van der Spek RA, Pliner HA, Shankaracharya, Smith BN, Marangi G, Topp SD, Abramzon Y, Gkazi AS, Eicher JD, Kenna A, ITALSGEN Consortium, Mora G, Calvo A, Mazzini L, Riva N, Mandrioli J, Caponnetto C, Battistini S, Volanti P, La Bella V, Conforti FL, Borghero G, Messina S, Simone IL, Trojsi F, Salvi F, Logullo FO, D'Alfonso S, Corrado L, Capasso M, Ferrucci L, Genomic Translation for ALS Care (GTAC) Consortium, Moreno CAM, Kamalakaran S, Goldstein DB, ALS Sequencing Consortium, Gitler AD, Harris T, Myers RM, NYGC ALS Consortium, Phatnani H, Musunuri RL, Evani US, Abhyankar A, Zody MC, Answer ALS Foundation, Kaye J, Finkbeiner S, Wyman SK, LeNail A, Lima L, Fraenkel E, Svendsen CN, Thompson LM, Van Eyk JE, Berry JD, Miller TM, Kolb SJ, Cudkowicz M, Baxi E, Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium, Benatar M, Taylor JP, Rampersaud E, Wu G, Wuu J, SLAGEN Consortium, Lauria G, Verde F, Fogh I, Tiloca C, Comi GP, Sorarù G, Cereda C, French ALS Consortium, Corcia P, Laaksovirta H, Myllykangas L, Jansson L, Valori M, Ealing J, Hamdalla H, Rollinson S, Pickering-Brown S, Orrell RW, Sidle KC, Malaspina A, Hardy J, Singleton AB, Johnson JO, Arepalli S, Sapp PC, McKenna-Yasek D, Polak M, Asress S, Al-Sarraj S, King A, Troakes C, Vance C, de Belleroche J, Baas F, Ten Asbroek ALMA, Muñoz-Blanco JL, Hernandez DG, Ding J, Gibbs JR, Scholz SW, Floeter MK, Campbell RH, Landi F, Bowser R, Pulst SM, Ravits JM, MacGowan DJL, Kirby J, Pioro EP, Pamphlett R, Broach J, Gerhard G, Dunckley TL, Brady CB, Kowall NW, Troncoso JC, Le Ber I, Mouzat K, Lumbroso S, Heiman-Patterson TD, Kamel F, Van Den Bosch L, Baloh RH, Strom TM, Meitinger T, Shatunov A, Van Eijk KR, de Carvalho M, Kooyman M, Middelkoop B, Moisse M, McLaughlin RL, Van Es MA, Weber M, Boylan KB, Van Blitterswijk M, Rademakers R, Morrison KE, Basak AN, Mora JS, Drory VE, Shaw PJ, Turner MR, Talbot K, Hardiman O, Williams KL, Fifita JA, Nicholson GA, Blair IP, Rouleau GA, Esteban-Pérez J, García-Redondo A, Al-Chalabi A, Project MinE ALS Sequencing Consortium, Rogaeva E, Zinman L, Ostrow LW, Maragakis NJ, Rothstein JD, Simmons Z, Cooper-Knock J, Brice A, Goutman SA, Feldman EL, Gibson SB, Taroni F, Ratti A, Gellera C, Van Damme P, Robberecht W, Fratta P, Sabatelli M, Lunetta C, Ludolph AC, Andersen PM, Weishaupt JH, Camu W, Trojanowski JQ, Van Deerlin VM, Brown RH, van den Berg LH, Veldink JH, Harms MB, Glass JD, Stone DJ, Tienari P, Silani V, Chiò A, Shaw CE, Traynor BJ, Landers JE
Abstract
To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.
PMID: 29566793 [PubMed - in process]
Contractile reserve and the response to cardiac resynchronization therapy.
Contractile reserve and the response to cardiac resynchronization therapy.
Int J Cardiol. 2018 02 01;252:234-235
Authors: Bristow MR
PMID: 29249434 [PubMed - indexed for MEDLINE]
Impact of BCL2 polymorphisms on survival in transitional cell carcinoma of the bladder.
Impact of BCL2 polymorphisms on survival in transitional cell carcinoma of the bladder.
J Cancer Res Clin Oncol. 2017 Sep;143(9):1659-1670
Authors: Hess J, Stelmach P, Eisenhardt A, Rübben H, Reis H, Schmid KW, Bachmann HS
Abstract
PURPOSE: To evaluate the impact of three BCL2 single-nucleotide polymorphisms, i.e., c.-938C>A (rs2279115), c.21G>A (rs1801018), and c.*2203A>G (rs4987853) on survival in patients with transitional cell carcinoma of the bladder.
METHODS: We analyzed 179 patients who underwent surgical treatment for bladder cancer at the Clinic of Urology, University Hospital Essen, Germany. Genomic DNA was extracted and genotyped for the polymorphisms. For all polymorphisms, linkage analysis was performed. Kaplan-Meier and Cox regression analyses were used to determine the putative impact of the three polymorphisms on outcome.
RESULTS: c.-938C>A and c.21G>A, but not c.*2203A>G, are in strong linkage disequilibrium (D' 0.96). We found a significant association between c.-938C>A and relapse-free survival (p = 0.024) with an allele dose effect. In the same way, c.21G>A had a significant impact on both relapse-free survival (p = 0.009) and progression-free survival (p = 0.012), as well as a pronounced allele dose effect. Regression analysis proved c.21G>A and c.-938C>A, to be an independent risk factor in univariate and multivariable analyses.
CONCLUSIONS: In our cohort, both c.-938C>A and c.21G>A showed a significant impact on outcome with TCC of the bladder. Due to the linkage disequilibrium of both SNPs, maybe, only one of them could mediate this effect. In multivariable analysis, however, both proved to be independently associated with overall survival. Contrary to other findings which found the c.-938C>A mainly influencing outcome, our data may suggest that the main effect on TCC could be due to the c.21G>A polymorphism.
PMID: 28417194 [PubMed - indexed for MEDLINE]
Comprehensive mapping of Cystic Fibrosis mutations to CFTR protein identifies mutation clusters and molecular docking predicts corrector binding site.
Comprehensive mapping of Cystic Fibrosis mutations to CFTR protein identifies mutation clusters and molecular docking predicts corrector binding site.
Proteins. 2018 Mar 23;:
Authors: Molinski SV, Shahani VM, Subramanian AS, MacKinnon SS, Woollard G, Laforet M, Laselva O, Morayniss LD, Bear CE, Windemuth A
Abstract
Cystic Fibrosis (CF) is caused by mutations in the CFTR gene, of which over 2000 have been reported to date. Mutations have yet to be analyzed in aggregate to assess their distribution across the tertiary structure of the CFTR protein, an approach that could provide valuable insights into the structure-function relationship of CFTR. In addition, the binding site of Class I correctors (VX-809, VX-661, C18) is not well understood. In this study, exonic CFTR mutations and mutant allele frequencies described in three curated databases (ABCMdb, CFTR1 and CFTR2, comprising >130,000 data points) were mapped to two different structural models: a homology model of full-length CFTR protein in the open-channel state, and a cryo-electron microscopy core-structure of CFTR in the closed-channel state. Accordingly, residue positions of six high-frequency mutant CFTR alleles were found to spatially co-localize in CFTR protein, and a significant cluster was identified at the NBD1:ICL4 interdomain interface. In addition, immunoblotting confirmed the approximate binding site of Class I correctors, demonstrating that these small molecules act via a similar mechanism in vitro, and in silico molecular docking generated binding poses for their complex with the cryo-electron microscopy structure to suggest the putative corrector binding site is a multi-domain pocket near residues F374-L375. These results confirm the significance of interdomain interfaces as susceptible to disruptive mutation, and identify a putative corrector binding site. The structural pharmacogenomics approach of mapping mutation databases to protein models shows promise for facilitating drug discovery and personalized medicine for monogenetic diseases. This article is protected by copyright. All rights reserved.
PMID: 29569753 [PubMed - as supplied by publisher]
Cellular mechanism for herbal medicine Junchoto to facilitate intestinal Cl-/water secretion that involves cAMP-dependent activation of CFTR.
Cellular mechanism for herbal medicine Junchoto to facilitate intestinal Cl-/water secretion that involves cAMP-dependent activation of CFTR.
J Nat Med. 2018 Mar 22;:
Authors: Numata T, Sato-Numata K, Okada Y, Inoue R
Abstract
Constipation is a common symptom frequently compromising the quality of daily life. Several mechanistically different drugs have been used to mitigate constipation, including Japanese herbal (Kampo) medicines. However, the mechanisms of their actions are often not well understood. Here we aimed to investigate the molecular mechanisms underlying the effects of Junchoto (JCT), a Kampo medicine empirically prescribed for chronic constipation. Cl- channel activity was measured by the patch-clamp method in human cystic fibrosis transmembrane conductance regulator (CFTR)-expressing HEK293T cells and human intestinal Caco-2 cells. cAMP was measured by a luciferase-based assay. Cell volume change was measured by a particle-sizing and particle-counting analyzer and video-microscopic measurement. In both CFTR-expressing HEK293T and Caco-2 cells, JCT dose-dependently induced whole-cell currents showing typical biophysical and pharmacological features of CFTR. Robust expression of CFTR was confirmed by RT-PCR and Western blotting in Caco-2 cells. Luciferase-based measurement revealed that JCT increases intracellular cAMP levels. Administration of the adenylate cyclase inhibitor SQ22536 or CFTR inhibitor-172, or treatment with small interfering RNAs (siRNA) targeting CFTR, abolished JCT-induced whole-cell currents, suggesting that elevated intracellular cAMP by JCT causes activation of CFTR in Caco-2 cells. Finally, blockade of CFTR activity by CFTR inhibitor-172 or siRNA-knockdown of CFTR or application of SQ22536 markedly reduced the degree of cell volume decrease induced by JCT. JCT can induce a Cl- efflux through the CFTR channel to promote water secretion, and this effect is likely mediated by increased cAMP production.
PMID: 29569221 [PubMed - as supplied by publisher]
CT features of diffuse lung disease in infancy.
CT features of diffuse lung disease in infancy.
Radiol Med. 2018 Mar 22;:
Authors: Toma P, Secinaro A, Sacco O, Curione D, Cutrera R, Ullmann N, Granata C
Abstract
Diffuse lung disease in infancy includes a wide range of very rare and peculiar pulmonary conditions usually not seen in older children, in whom diffuse lung disease has much greater overlap with adult disorders. The acronym chILD (childhood Interstitial Lung Disease) commonly defines these disorders, although air spaces, airways, alveolar epithelium, vasculature, pleura, and pleural spaces can also be involved, besides the pulmonary interstitium. chILD can be caused by diffuse developmental disorders, alveolar growth abnormalities, surfactant dysfunction disorders, and other specific conditions of poorly understood etiology. Chest CT imaging studies play a pivotal role in the evaluation of chILD. In some conditions CT findings can be specific, and thus make it possible avoiding further testing. In other disorders, findings are nonspecific, although they may suggest a diagnostic pattern and guide further testing. Nevertheless, chILD disorders often remain unrecognized on imaging studies, as they are very rare. The aim of this article is to review the CT patterns of lung involvement in a series of infants with chILD.
PMID: 29569218 [PubMed - as supplied by publisher]
Neutrophil extracellular traps promote lipopolysaccharide-induced airway inflammation and mucus hypersecretion in mice.
Neutrophil extracellular traps promote lipopolysaccharide-induced airway inflammation and mucus hypersecretion in mice.
Oncotarget. 2018 Mar 02;9(17):13276-13286
Authors: Zou Y, Chen X, Xiao J, Bo Zhou D, Xiao Lu X, Li W, Xie B, Kuang X, Chen Q
Abstract
Bacterial lipopolysaccharide (LPS) contributes to airway inflammation and mucus hypersecretion in chronic airway inflammatory diseases, such as chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF). Neutrophil extracellular traps (NETs) are extracellular meshworks composed of DNA fibers and antimicrobial proteins. Although NET formation has been detected in COPD and CF patients, how NETs contribute to these diseases is poorly understood. This study was performed to clarify the effects and mechanisms of action of NETs in airway inflammation and mucus hypersecretion. We created a murine model of LPS-induced airway inflammation and mucus hypersecretion, and found that LPS-induced NET formation was degraded by aerosolized DNase I treatment in mice. Degradation of NETs by aerosolized DNase I reduced LPS-induced airway inflammation and mucus hypersecretion in mice, this reduction correlated with suppression of TLR4/NF-κB signaling pathway. More importantly, NETs promoted LPS-induced production of IL-1β, IL-6 and TNF-α in macrophages. These results suggest NET degradation using aerosolized DNase I is a potential new therapeutic strategy for treating COPD and CF.
PMID: 29568356 [PubMed]
The evaluation of selected insomnia predictors in adolescents and young adults with cystic fibrosis.
The evaluation of selected insomnia predictors in adolescents and young adults with cystic fibrosis.
Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2018 Mar 21;:
Authors: Tomaszek L, Cepuch G, Pawlik L
Abstract
AIMS AND BACKGROUND: The purpose of the study was to assess the incidence of insomnia in adolescents and young adults with cystic fibrosis and its impact on the quality of life, and to examine whether demographic and clinical factors and negative emotional states are predictors of insomnia in these patients.
METHODS: The study was conducted among 95 cystic fibrosis patients aged 14-25 years. The study used a personal questionnaire survey, the Athens Insomnia Scale, the Cystic Fibrosis Quality of Life Questionnaire, the Hospital Anxiety and Depression Scale, and the Numeric Rating Scale.
RESULTS: Insomnia was diagnosed in 38% of cystic fibrosis patients. In patients with insomnia, the level of anxiety (Me: 10 vs. 4; P=0.000) and depression (Me: 6.5 vs. 2; P=0.000) was significantly higher than in the good sleep quality group. The risk of insomnia increases as anxiety (OR: 4.31; 95% CI: 2.20 to 8.41) and depressive symptoms exacerbate (OR: 4.98; 95% CI: 1.84 to 13.43). Insomnia significantly worsens the quality of life in cystic fibrosis patients (ß =-0.5, P=0.000).
CONCLUSION: Insomnia affects a large percentage of cystic fibrosis patients, and anxiety and depression are factors that increase the risk of insomnia. Insomnia decreases the quality of life in cystic fibrosis patients.
PMID: 29568122 [PubMed - as supplied by publisher]
Sputum active polymyxin lipopeptides: Activity against Cystic Fibrosis Pseudomonas aeruginosa isolates and their interactions with sputum biomolecules.
Sputum active polymyxin lipopeptides: Activity against Cystic Fibrosis Pseudomonas aeruginosa isolates and their interactions with sputum biomolecules.
ACS Infect Dis. 2018 Mar 22;:
Authors: Schneider-Futschik EK, Paulin OKA, Hoyer D, Roberts KD, Ziogas J, Baker MA, Karas J, Li J, Velkov T
Abstract
The mucoid biofilm mode of growth of Pseudomonas aeruginosa in the lungs of cystic fibrosis patients makes eradication of infections with antibiotic therapy very difficult. The lipopeptide antibiotics polymyxin B and colistin are currently the last-resort therapies for infections caused by multidrug-resistant P. aeruginosa. In the present study, we investigated the antibacterial activity of a series of polymyxin lipopeptides (polymyxin B, colistin, FADDI-003, octapeptin A3 and polymyxin A2) against a panel of polymyxin-susceptible and polymyxin-resistant P. aeruginosa cystic fibrosis isolates grown under planktonic or biofilm conditions in artificial sputum, and their interactions with sputum component biomolecules. In sputum media under planktonic conditions, the lipopeptides FADDI-003 and octapeptin A3 displayed very promising activity against the polymyxin-resistant isolate FADDI-PA066 (polymyxin B MIC = 32 mg/L), while retaining their activity against the polymyxin-sensitive strains FADDI-PA021 (polymyxin B MIC = 1 mg/L) and FADDI-PA020 (polymyxin B MIC = 2 mg/L). Polymyxin A2 was only effective against the polymyxin-sensitive isolates. However, under biofilm growth conditions, the hydrophobic lipopeptide FADDI-003 was inactive compared to the more hydrophilic lipopeptides, octapeptin A3 and polymyxin A2, polymyxin B and colistin. Moreover, transmission electron micrographs revealed octapeptin A3 reduced the cell numbers in biofilm as well as causing 'anti-biofilm' activity/biofilm disruption. We therefore assessed the interactions of the lipopeptides with the component sputum biomolecules, mucin, DNA, surfactant, f-actin, lipopolysaccharide and phospholipids. We observed the general trend that sputum biomolecules reduce lipopeptide antibacterial activity. Collectively, our data suggests that in the airways, lipopeptide binding to component sputum biomolecules may reduce antibacterial efficacy and is dependent on the physicochemical properties of the lipopeptide.
PMID: 29566483 [PubMed - as supplied by publisher]
Novel putative drivers revealed by targeted exome sequencing of advanced solid tumors.
Novel putative drivers revealed by targeted exome sequencing of advanced solid tumors.
PLoS One. 2018;13(3):e0194790
Authors: Pannuti A, Filipovic A, Hicks C, Lefkowitz E, Ptacek T, Stebbing J, Miele L
Abstract
Next generation sequencing (NGS) is becoming increasingly integrated into oncological practice and clinical research. NGS methods have also provided evidence for clonal evolution of cancers during disease progression and treatment. The number of variants associated with response to specific therapeutic agents keeps increasing. However, the identification of novel driver mutations as opposed to passenger (phenotypically silent or clinically irrelevant) mutations remains a major challenge. We conducted targeted exome sequencing of advanced solid tumors from 44 pre-treated patients with solid tumors including breast, colorectal and lung carcinomas, neuroendocrine tumors, sarcomas and others. We catalogued established driver mutations and putative new drivers as predicted by two distinct algorithms. The established drivers we detected were consistent with published observations. However, we also detected a significant number of mutations with driver potential never described before in each tumor type we studied. These putative drivers belong to key cell fate regulatory networks, including potentially druggable pathways. Should our observations be confirmed, they would support the hypothesis that new driver mutations are selected by treatment in clinically aggressive tumors, and indicate a need for longitudinal genomic testing of solid tumors to inform second line cancer treatment.
PMID: 29570743 [PubMed - in process]
A new nonsense mutation in the POGLUT1 gene in two sisters with Dowling-Degos disease.
A new nonsense mutation in the POGLUT1 gene in two sisters with Dowling-Degos disease.
J Eur Acad Dermatol Venereol. 2018 Mar 23;:
Authors: Duchatelet S, Clerc H, Machet L, Gaboriaud P, Miskinyte S, Kervarrec T, Hovnanian A
Abstract
Dowling-Degos disease (DD) (OMIM: 179850, 615327, 615674, 615696) is a rare autosomal-dominant genetic disorder belonging to the spectrum of reticulated pigmented dermatitis(1). Galli-Galli disease is considered as being a variant of DD, harboring all clinical, histological and genetics features of DD in association with acantholysis (2). In 2006, exome sequencing revealed loss-of-function mutations in KRT5 (cytokeratin 5) (p.Ile140fsAsnfs*39, p.Ser5*) in 8 of 10 DD cases (3). Since then, mutations in POGLUT1, encoding O-glucosylosyltransferase 1 enzyme, were reported in Galli-Galli cases (4). Loss-of-function mutations in POFUT1, encoding fucosyltransferase 1, were identified in cases of DD showing overlap with Kitamura disease (5) and finally, mutations in PSENEN (presenilin enhancer gamma-secretase subunit) were found in DD associated with acne inversa or Hidradenitis suppurativa (6). This article is protected by copyright. All rights reserved.
PMID: 29569780 [PubMed - as supplied by publisher]
Dysosteosclerosis is also caused by TNFRSF11A mutation.
Dysosteosclerosis is also caused by TNFRSF11A mutation.
J Hum Genet. 2018 Mar 22;:
Authors: Guo L, Elcioglu NH, Karalar OK, Topkar MO, Wang Z, Sakamoto Y, Matsumoto N, Miyake N, Nishimura G, Ikegawa S
Abstract
Dysosteosclerosis (DOS) is a form of sclerosing bone disease characterized by irregular osteosclerosis and platyspondyly. Its mode of inheritance is autosomal recessive. SLC29A3 mutations have been reported as the causal gene in two DOS families, however, genetic heterogeneity has been suggested. By whole-exome sequencing in a Turkish patient with DOS, we found a novel splice-site mutation in TNFRSF11A. TNFRSF11A mutations have previously been reported in two autosomal dominant diseases (osteolysis, familial expansile and Paget disease of bone 2, early-onset) and an autosomal recessive disease (osteopetrosis, autosomal recessive 7). The biallelic mutation, c.616+3A>G, identified in our study was located in the splice donor site of intron 6 of TNFRSF11A. Exon trapping assay indicated the mutation caused skipping of exon 6, which was predicted to induce a frame-shift and an early termination codon in all known alternative transcript variants of TNFRSF11A. The predicted effect of the mutation for the isoforms was different from those of the previously reported mutations, which could explain the difference of their phenotypes. Thus, our study identified the second disease gene for DOS. TNFRSF11A isoforms may have the different roles in skeletal development and metabolism.
PMID: 29568001 [PubMed - as supplied by publisher]
Alzheimer disease associated variants in SORL1 accelerate dementia development in Parkinson disease.
Alzheimer disease associated variants in SORL1 accelerate dementia development in Parkinson disease.
Neurosci Lett. 2018 Mar 19;:
Authors: Maple-Grødem J, Chung J, Lunde KA, Tzoulis C, Tysnes OB, Pedersen KF, Alves G
Abstract
OBJECTIVE: Dementia in Parkinson disease (PD) is a common occurrence, and shows a marked overlap at a clinical and pathological level with Alzheimer's disease (AD), suggesting they share underlying disease mechanisms. Genetic variants in SORL1 have been identified in patients with AD, but a possible role in other dementias is unknown. The aim of this study was to investigate whether common polymorphisms in SORL1 affect the risk of developing dementia in a population-based cohort of patients with incident PD.
METHODS: One common, nonsynonymous SORL1 variant (rs2298813; A528T) was identified in whole exome sequencing data from 185 patients with PD from the Norwegian ParkWest study, who had been followed up to the 7-year visit after diagnosis. A528T was tested for association with PD risk, the development of dementia, and in a subset of patients (n = 103) for associations with established AD cerebrospinal fluid (CSF) biomarkers measured at the time of PD diagnosis.
RESULTS: We found an association of A528T carrier status with increased risk of developing PD dementia (HR 2.31; 95% CI 1.09-4.90; p = 0.03) compared to non-carriers. Additionally, A528T carrier status was associated with a reduced ratio of CSF β-amyloid 42 to p-Tau (p = 0.014) but no alterations in absolute AD marker levels (all p > 0.05) at the time of PD diagnosis.
CONCLUSION: Our results show the first association of the AD risk factor SORL1 with incident dementia in PD, providing new evidence that AD related disease mechanisms may contribute to dementia in a subset of patients with PD. Finding support for a shared etiology for AD and PD dementia provides new directions for research into treatments for these diseases.
PMID: 29567423 [PubMed - as supplied by publisher]
Neurogenetic analysis of childhood disintegrative disorder.
Neurogenetic analysis of childhood disintegrative disorder.
Mol Autism. 2017;8:19
Authors: Gupta AR, Westphal A, Yang DYJ, Sullivan CAW, Eilbott J, Zaidi S, Voos A, Vander Wyk BC, Ventola P, Waqar Z, Fernandez TV, Ercan-Sencicek AG, Walker MF, Choi M, Schneider A, Hedderly T, Baird G, Friedman H, Cordeaux C, Ristow A, Shic F, Volkmar FR, Pelphrey KA
Abstract
BACKGROUND: Childhood disintegrative disorder (CDD) is a rare form of autism spectrum disorder (ASD) of unknown etiology. It is characterized by late-onset regression leading to significant intellectual disability (ID) and severe autism. Although there are phenotypic differences between CDD and other forms of ASD, it is unclear if there are neurobiological differences.
METHODS: We pursued a multidisciplinary study of CDD (n = 17) and three comparison groups: low-functioning ASD (n = 12), high-functioning ASD (n = 50), and typically developing (n = 26) individuals. We performed whole-exome sequencing (WES), copy number variant (CNV), and gene expression analyses of CDD and, on subsets of each cohort, non-sedated functional magnetic resonance imaging (fMRI) while viewing socioemotional (faces) and non-socioemotional (houses) stimuli and eye tracking while viewing emotional faces.
RESULTS: We observed potential differences between CDD and other forms of ASD. WES and CNV analyses identified one or more rare de novo, homozygous, and/or hemizygous (mother-to-son transmission on chrX) variants for most probands that were not shared by unaffected sibling controls. There were no clearly deleterious variants or highly recurrent candidate genes. Candidate genes that were found to be most conserved at variant position and most intolerant of variation, such as TRRAP, ZNF236, and KIAA2018, play a role or may be involved in transcription. Using the human BrainSpan transcriptome dataset, CDD candidate genes were found to be more highly expressed in non-neocortical regions than neocortical regions. This expression profile was similar to that of an independent cohort of ASD probands with regression. The non-neocortical regions overlapped with those identified by fMRI as abnormally hyperactive in response to viewing faces, such as the thalamus, cerebellum, caudate, and hippocampus. Eye-tracking analysis showed that, among individuals with ASD, subjects with CDD focused on eyes the most when shown pictures of faces.
CONCLUSIONS: Given that cohort sizes were limited by the rarity of CDD, and the challenges of conducting non-sedated fMRI and eye tracking in subjects with ASD and significant ID, this is an exploratory study designed to investigate the neurobiological features of CDD. In addition to reporting the first multimodal analysis of CDD, a combination of fMRI and eye-tracking analyses are being presented for the first time for low-functioning individuals with ASD. Our results suggest differences between CDD and other forms of ASD on the neurobiological as well as clinical level.
PMID: 28392909 [PubMed - indexed for MEDLINE]
From global action against malaria to local issues: state of the art and perspectives of web platforms dealing with malaria information.
From global action against malaria to local issues: state of the art and perspectives of web platforms dealing with malaria information.
Malar J. 2018 Mar 21;17(1):122
Authors: Briand D, Roux E, Desconnets JC, Gervet C, Barcellos C
Abstract
BACKGROUND: Since prehistory to present times and despite a rough combat against it, malaria remains a concern for human beings. While evolutions of science and technology through times allowed for some infectious diseases eradication in the 20th century, malaria resists.
OBJECTIVES: This review aims at assessing how Internet and web technologies are used in fighting malaria. Precisely, how do malaria fighting actors profit from these developments, how do they deal with ensuing phenomena, such as the increase of data volume, and did these technologies bring new opportunities for fighting malaria?
METHODS: Eleven web platforms linked to spatio-temporal malaria information are reviewed, focusing on data, metadata, web services and categories of users.
RESULTS: Though the web platforms are highly heterogeneous the review reveals that the latest advances in web technologies are underused. Information are rarely updated dynamically, metadata catalogues are absent, web services are more and more used, but rarely standardized, and websites are mainly dedicated to scientific communities, essentially researchers.
CONCLUSION: Improvement of systems interoperability, through standardization, is an opportunity to be seized in order to allow real time information exchange and online multisource data analysis. To facilitate multidisciplinary/multiscale studies, the web of linked data and the semantic web innovations can be used in order to formalize the different view points of actors involved in the combat against malaria. By doing so, new malaria fighting strategies could take place, to tackle the bottlenecks listed in the United Nation Millennium Development Goals reports, but also specific issues highlighted by the World Health Organization such as malaria elimination in international borders.
PMID: 29562918 [PubMed - in process]
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