NR3C1 gene polymorphisms are associated with steroid resistance in patients with primary nephrotic syndrome.

Pharmacogenomics. 2018 Jan;19(1):45-60

Authors: Liu J, Wan Z, Song Q, Li Z, He Y, Tang Y, Xie W, Xie Y, Zhang J

Abstract
AIM: The aim of this study was to investigate the role of SNPs of genes involved in the glucocorticoid pathway in the development of steroid resistance in patients with primary nephrotic syndrome.
METHODS: Sequenom MassARRAY method was used to sequence 25 SNP genotypes in 154 patients. The frequency distribution of the genotypes was compared between patients with steroid-sensitive nephrotic syndrome and those with steroid-resistant nephrotic syndrome.
RESULTS: NR3C1 rs6196 G allele carriers had a decreased risk of steroid resistance compared with that of the A allele carriers. The presence of rs10052957 and rs258751 A alleles could reduce the incidence of steroid resistance compared with that with G allele. Haplotype analysis showed AAG and GGA haplotypes that contain NR3C1 rs10052957, rs258751 and rs6196 were associated with steroid resistance.
CONCLUSION: NR3C1 gene polymorphisms are significantly associated with the response to glucocorticoids in patients with primary nephrotic syndrome.

PMID: 29207898 [PubMed - indexed for MEDLINE]

Recent trends on the role of epigenomics, metabolomics and noncoding RNAs in rationalizing mood stabilizing treatment.

Pharmacogenomics. 2018 Jan;19(2):129-143

Authors: Pisanu C, Katsila T, Patrinos GP, Squassina A

Abstract
Mood stabilizers are the cornerstone in treatment of mood disorders, but their use is characterized by high interindividual variability. This feature has stimulated intensive research to identify predictive biomarkers of response and disentangle the molecular bases of their clinical efficacy. Nevertheless, findings from studies conducted so far have only explained a small proportion of the observed variability, suggesting that factors other than DNA variants could be involved. A growing body of research has been focusing on the role of epigenetics and metabolomics in response to mood stabilizers, especially lithium salts. Studies from these approaches have provided new insights into the molecular networks and processes involved in the mechanism of action of mood stabilizers, promoting a systems-level multiomics synergy. In this article, we reviewed the literature investigating the involvement of epigenetic mechanisms, noncoding RNAs and metabolomic modifications in bipolar disorder and the mechanism of action and clinical efficacy of mood stabilizers.

PMID: 29199496 [PubMed - indexed for MEDLINE]

A genomic characterization of the influence of silver nanoparticles on bone differentiation in MC3T3-E1 cells.

J Appl Toxicol. 2018 Feb;38(2):172-179

Authors: Qing T, Mahmood M, Zheng Y, Biris AS, Shi L, Casciano DA

Abstract
Silver nanoparticles (AgNPs) have been widely used in a variety of biomedical applications. Previous studies demonstrated that AgNPs significantly enhanced bone cell mineralization and differentiation in MC3T3-1 cells, a model in vitro system, when compared to several other NPs. This increased bone deposition was evaluated by phenotypic measurements and assessment of the expression of miRNAs associated with regulation of bone morphogenic proteins. In the present study, we used RNA-seq technology, a more direct measurement of gene expression, to investigate further the mechanisms of bone differentiation induced by AgNP treatment. Key factors associated with the osteoclast pathway were significantly increased in response to AgNP exposure including Bmp4, Bmp6 and Fosl1. In addition, genes of metabolism and toxicity pathways were significantly regulated as well. Although this study suggests the potential for AgNPs to influence bone morphogenesis in injury or disease applications, further investigation into the efficacy and safety of AgNPs in bone regeneration is warranted.

PMID: 28975650 [PubMed - indexed for MEDLINE]

Structural constraints and importance of caffeic acid moiety for anti-hyperglycemic effects of caffeoylquinic acids from chicory.

Mol Nutr Food Res. 2017 Sep;61(9):

Authors: Jackson KMP, Rathinasabapathy T, Esposito D, Komarnytsky S

Abstract
SCOPE: Chicory (Cichorium intybus L.) is a perennial herb often consumed as a vegetable, whereas the ground and roasted roots are blended as a coffee substitute. Caffeoylquinic or chlorogenic acids (CQA), the abundant intermediates of lignin biosynthesis in chicory, have been reported to improve glucose metabolism in humans, but the functional group in their structure responsible for this effect has not been yet characterized.
METHODS AND RESULTS: Here, we showed that three di-O-caffeoylquinic acids suppressed hepatic glucose production in H4IIE rat hepatoma cells by reducing expression of glucose-6-phosphatase (G6Pase) and phosphoenolpyruvate carboxykinase (PEPCK), two key enzymes that regulate hepatic gluconeogenesis. Direct comparisons between CQAs and their metabolites (3-caffeoylquinic, caffeic, and quinic acids) revealed the caffeic acid moiety alone was responsible for the observed effects. Further analysis suggested the activation of PI3K and MAPK pathways as a method of controlling gene expression was shared between caffeoylquinic and caffeic acids. These compounds promoted increased mitochondrial respiration and cellular metabolism, in part by inducing oxidative phosphorylation and proton leak.
CONCLUSION: We concluded that the caffeic acid moiety was important for suppression of hepatic gluconeogenesis and hyperglycemia, ultimately strengthening the link between dietary interventions based on caffeic acid-containing plant foods and healthy glucose metabolism.

PMID: 28371117 [PubMed - indexed for MEDLINE]

Presence of pldA and exoU in mucoid Pseudomonas aeruginosa associated with high risk of exacerbations in non-CF bronchiectasis patients.

Clin Microbiol Infect. 2018 Jul 20;:

Authors: Luo RG, Miao XY, Luo LL, Mao B, Yu FY, Xu JF

Abstract
OBJECTIVE: We aimed to explore the association between the virulence genes, exoU and pldA, in isolated mucoid Pseudomonas aeruginosa and the clinical outcomes of patients with non-cystic fibrosis (CF) bronchiectasis.
METHODS: A prospective, observational cohort study was performed in the Shanghai Pulmonary Hospital from Oct 2012 to Jan 2015. We consecutively enrolled all non-CF bronchiectasis patients with mucoid Pseudomonas aeruginosa isolates from bronchoalveolar lavage fluid or sputum. The exposure variable was the presence of virulence gene, exoU or pldA, in the strains. The primary outcome was exacerbation of bronchiectasis. Logistic regression analysis was performed to evaluate the association between virulence genes and exacerbation.
RESULTS: The final analysis included 147 patients (mean (SD) age 57.86 (11.43) years, 101 females) with follow-up (median (IQR) of 18 (13-26) months). The following factors were relative to exacerbations: BMI≤18.5 kg/m2 (odds ratio (OR) 5.05, 95% confidence interval (CI) 1.37-18.57), length of stay ≥ 8 days (OR 2.65, 95% CI 1.14-6.19), either virulence gene positive (OR 6.80, 95% CI 1.47-31.37). The gene positive group had more exacerbations per year (mean 2.37, SD 2.10, n=33 vs. mean 0.79, SD 0.83, n=114) and a higher proportion of patients with exacerbation (31/33, 93.94% vs. 74/114, 64.91%). The proportion of patients being exoU or pldA positive ascended as the exacerbation frequency of bronchiectasis increased.
CONCLUSIONS: The virulence genes exoU and pldA in mucoid Pseudomonas aeruginosa are significant risk factors for exacerbations in patients with non-CF bronchiectasis.

PMID: 30036669 [PubMed - as supplied by publisher]

Nasal Potential Difference to Quantify Trans-epithelial Ion Transport in Mice.

J Vis Exp. 2018 Jul 04;(137):

Authors: Beka M, Leal T

Abstract
The nasal potential difference test has been used for almost three decades to assist in the diagnosis of cystic fibrosis (CF). It has proven to be helpful in cases of attenuated, oligo- or mono-symptomatic forms of CF usually diagnosed later in life, and of CF-related disorders such as congenital bilateral absence of vas deferens, idiopathic chronic pancreatitis, allergic bronchopulmonary aspergillosis, and bronchiectasis. In both clinical and preclinical settings, the test has been used as a biomarker to quantify responses to targeted therapeutic strategies for CF. Adapting the test to a mouse is challenging and can entail an associated mortality. This paper describes the adequate depth of anesthesia required to maintain a nasal catheter in situ for continuous perfusion. It lists measures to avoid broncho-aspiration of solutions perfused in the nose. It also describes the animal care at the end of the test, including administration of a combination of antidotes of the anesthetic drugs, leading to rapidly reversing the anesthesia with full recovery of the animals. Representative data obtained from a CF and a wild-type mouse show that the test discriminates between CF and non-CF. Altogether, the protocol described here allows reliable measurements of the functional status of trans-epithelial chloride and sodium transporters in spontaneously breathing mice, as well as multiple tests in the same animal while reducing test-related mortality.

PMID: 30035761 [PubMed - in process]

Erratum: "Factors influencing readthrough therapy for frequent cystic fibrosis premature termination codons" Iwona Pranke, Laure Bidou, Natacha Martin, Sandra Blanchet, Aurélie Hatton, Sabrina Karri, David Cornu, Bruno Costes, Benoit Chevalier, Danielle Tondelier, Emmanuelle Girodon, Matthieu Coupet, Aleksander Edelman, Pascale Fanen, Olivier Namy, Isabelle Sermet-Gaudelus and Alexandre Hinzpeter.ERJ Open Res 2018; 4: 00080-2017.

ERJ Open Res. 2018 Jul;4(3):

Authors:

Abstract
[This corrects the article DOI: 10.1183/23120541.00080-2017.].

PMID: 30035115 [PubMed - in process]

Modulators of the Cystic Fibrosis Transmembrane Conductance Regulator Protein.

ACS Med Chem Lett. 2018 Jul 12;9(7):592-593

Authors: Kargbo RB

PMID: 30034584 [PubMed]

Dosing challenges in respiratory therapies.

Int J Pharm. 2018 Jul 02;548(1):659-671

Authors: Yeung S, Traini D, Lewis D, Young PM

Abstract
The pulmonary route of administration has been commonly used for local lung conditions such as asthma and chronic obstructive pulmonary disease (COPD). Recently, with the advent of new technologies available for both formulation and device design, molecules usually delivered at high doses, such as antibiotics and insulin to treat cystic fibrosis (CF) and diabetes, respectively, can now be delivered by inhalation as a dry powder. These molecules are generally delivered in milligrams instead of traditional microgram quantities. High dose delivery is most commonly achieved via dry powder inhalers (DPIs), breath activated devices designed with a formulated powder containing micronized drug with aerodynamic diameters between 1 and 5 µm. The powder formulation may also contain other excipients and/or carrier particles to improve the flowability and aerosol dispersion of the powder. A drawback with high doses is that the formulation contains a great number of fine particles, leading to a greater degree of cohesive forces, producing strongly bound agglomerates. With greater cohesive forces holding fine particles together, higher dispersion forces are needed for efficient de-agglomeration and aerosolisation. This requirement of greater dispersion forces has led to different dry powder formulations and vastly different inhaler designs. The purpose of this review is to evaluate the different formulation types, various DPI devices currently available, and how these affect the aerosolisation process and delivery of high dosed inhalable dry powder formulations to the lungs.

PMID: 30033395 [PubMed - as supplied by publisher]

The Q359K/T360K mutation causes cystic fibrosis in Georgian Jews.

J Cyst Fibros. 2018 Jul 19;:

Authors: Mei-Zahav M, Stafler P, Senderowitz H, Bentur L, Livnat G, Shteinberg M, Orenstein N, Bazak L, Prais D, Levine H, Gur M, Khazanov N, Simhaev L, Eliyahu H, Cohen M, Wilschanski M, Blau H, Mussaffi H

Abstract
BACKGROUND: The Q359K/T360K mutation, described in Jewish CF patients of Georgian decent, is of questionable clinical significance.
METHODS: Clinical records of patients with the Q359K/T360K mutation from three CF centers were studied for phenotypic expression and putative mechanism of dysfunction. Computer models of mutant CFTR were constructed.
RESULTS: Nine patients (4 homozygous) of Georgian Jewish origin were included. Age at diagnosis was 9.4 (0.25-38.2) years, median (range). Sweat chloride was 106 ± 13 meq/L, mean ± SD. Nasal Potential Difference performed in three, was abnormal. All had pulmonary symptoms since early childhood and bronchiectasis. Median FEV1 was 88 (40-121)%. Five had chronic mucoid P. aeruginosa. Homozygous patients were pancreatic insufficient. Enzyme supplementation was initiated at 3.8 (1-14.7) years, median (range). Structural models hint at possible interference of this mutation with transmembrane chloride transport.
CONCLUSION: In our cohort, the Q359K/T360K mutation resulted in a severe CF phenotype, although with residual early CFTR function. The CFTR2 database should consider defining this mutation as CF-causing.

PMID: 30033373 [PubMed - as supplied by publisher]

Comparative proteomics of respiratory exosomes in cystic fibrosis, primary ciliary dyskinesia and asthma.

J Proteomics. 2018 Aug 15;185:1-7

Authors: Rollet-Cohen V, Bourderioux M, Lipecka J, Chhuon C, Jung VA, Mesbahi M, Nguyen-Khoa T, Guérin-Pfyffer S, Schmitt A, Edelman A, Sermet-Gaudelus I, Guerrera IC

Abstract
Cystic fibrosis (CF) and primary ciliary dyskinesia (PCD) are pulmonary genetic disorders associated with inflammation and heterogeneous progression of the lung disease. We hypothesized that respiratory exosomes, nanovesicles circulating in the respiratory tract, may be involved in the progression of inflammation-related lung damage. We compared proteomic content of respiratory exosomes isolated from bronchoalveolar lavage fluid in CF and PCD to asthma (A), a condition also associated with inflammation but with less severe lung damage. BALF were obtained from 3 CF, 3 PCD and 6 A patients. Exosomes were isolated from BALF by ultracentrifugations and characterized using immunoelectron microscopy and western-blot. Exosomal protein analysis was performed by high-resolution mass spectrometry using label-free quantification. Exosome enrichment was validated by electron microscopy and immunodetection of CD9, CD63 and ALIX. Mass spectrometry analysis allowed the quantification of 665 proteins, of which 14 were statistically differential according to the disease. PCD and CF exosomes contained higher levels of antioxidant proteins (Superoxide-dismutase, Glutathione peroxidase-3, Peroxiredoxin-5) and proteins involved in leukocyte chemotaxis. All these proteins are known activators of the NF-KappaB pathway. Our results suggest that respiratory exosomes are involved in the pro-inflammatory propagation during the extension of CF or PCD lung diseases.
SIGNIFICANCE: The mechanism of local propagation of lung disease in cystic fibrosis (CF) and primary ciliary dyskinesia (PCD) is not clearly understood. Differential Proteomic profiles of exosomes isolated from BAL from CF, PCD and asthmatic patients suggest that they carry pro-inflammatory proteins that may be involved in the progression of lung damage.

PMID: 30032860 [PubMed - in process]

Emerging antibacterial and antiviral drugs for treating respiratory tract infections.

Expert Opin Emerg Drugs. 2018 Jul 23;:

Authors: Mantero M, Rogliani P, Cazzola M, Blasi F, Di Pasquale M

Abstract
INTRODUCTION: Management of LRTI is becoming more frequently challenging since the emergence of multidrug resistance bacteria and the increase of severe viral infection, reducing the number of available effective drugs. The clinical evaluation of new therapeutic associations is mandatory to cope with the increases in resistance, in association with better infection control and antimicrobial policies. Areas covered: We searched Pubmed in English language of phase I, II, III clinical trials and approved treatments for LRTI, between 2006 and 2016. Expert opinion: Development of new molecules or new combinations regimens are very important for patients with severe infections and in specific subgroups of patients like CF and bronchiectatic patients. Standardized protocols for antibiotic stewardship in difficult-to-treat infections are the next step. Moreover, non-antibiotic treatments and preventive strategies as vaccination need to be part of clinical practice.

PMID: 30032674 [PubMed - as supplied by publisher]

Toll-like receptor 4: a target for chemoprevention of hepatocellular carcinoma in obesity and steatohepatitis.

Oncotarget. 2018 Jun 29;9(50):29495-29507

Authors: Nguyen J, Jiao J, Smoot K, Watt GP, Zhao C, Song X, Stevenson HL, McCormick JB, Fisher-Hoch SP, Zhang J, Futreal PA, Beretta L

Abstract
The incidence of hepatocellular carcinoma (HCC) associated with non-alcoholic fatty liver disease (NAFLD) is rapidly increasing. We aimed to elucidate the genetic basis of NAFLD-associated HCC and identify candidate targets for chemoprevention. Twenty HCC tumors, distant liver and matched tails from mice with hepatocyte-deletion of Pten (HepPten-) were subjected to whole-exome sequencing. A total of 162 genes with somatic non-synonymous single nucleotide variants or exonic small insertions and deletions in tumors were identified. Ingenuity Pathway Analysis of these 162 genes, further identified Toll-like receptor (TLR) 4, a key mediator of proinflammatory responses, and resatorvid, a TLR4 inhibitor, as the main causal networks of this dataset. Resatorvid treatment strongly prevented HCC development in these mice (p < 0.001). Remarkably, HCC patients with high tumoral TLR4 mRNA expression were more likely to be diagnosed with NAFLD and obese. TLR4 mRNA expression positively correlated with IL-6 and IL-10 mRNA expression in HCC tumors and the correlation was stronger in obese HCC patients. We have identified tumor mutation signatures and associated causal networks in NAFLD-associated HCC in HepPten- mice and further demonstrated the important role of TLR4 in promoting HCC development. This study also identified IL-6 and IL-10 as markers of TLR4 activation in HCC and subjects with NAFLD and obesity as the target population who would benefit from TLR4 inhibition treatment for HCC chemoprevention.

PMID: 30034633 [PubMed]

Whole Genome Sequencing instead of Whole Exome Sequencing is required to identify the Genetic Causes of Polycystic Ovary Syndrome in Pakistani families.

Pak J Med Sci. 2018 May-Jun;34(3):540-545

Authors: Khan MJ, Nazli R, Ahmed J, Basit S

Abstract
Background & Objective: Polycystic Ovary Syndrome (PCOS) is the major cause of infertility in females. PCOS is a complex and multifactorial disease, genetic and environmental factors being important predisposing factors. Diagnosis of PCOS is difficult due to the complexity of this disease; hence, better diagnostic tests are required to improve its management. Aim of the study was to elucidate the genetic causes of PCOS in three Pakistani families.
Methods: Three Pakistani families segregating PCOS in an apparently autosomal recessive mode were recruited. Whole genome Single Nucleotide Polymorphism (SNP) genotyping and Whole Exome Sequencing (WES) were carried out to identify the candidate genes.
Results: SNP genotypes data analyses identified multiple regions of homozygosity on different chromosomes. WES was performed in affected members of the family. Screening for pathogenic mutations in homozygous regions failed to detect any mutation/variant of interest.
Conclusion: PCOS is multifactorial and complex disease so variants in the coding as well as in non-coding regions may be the genetic causes of the disease. To elucidate the genetic cause(s) of the PCOS, Whole Genome Sequencing (WGS) is recommended to cover both coding and non-coding regions of the genome.

PMID: 30034412 [PubMed]

ALS-associated missense and nonsense TBK1 mutations can both cause loss of kinase function.

Neurobiol Aging. 2018 Jun 25;:

Authors: de Majo M, Topp SD, Smith BN, Nishimura AL, Chen HJ, Gkazi AS, Miller J, Wong CH, Vance C, Baas F, Ten Asbroek ALMA, Kenna KP, Ticozzi N, Redondo AG, Esteban-Pérez J, Tiloca C, Verde F, Duga S, Morrison KE, Shaw PJ, Kirby J, Turner MR, Talbot K, Hardiman O, Glass JD, de Belleroche J, Gellera C, Ratti A, Al-Chalabi A, Brown RH, Silani V, Landers JE, Shaw CE

Abstract
Mutations in TANK binding kinase 1 (TBK1) have been linked to amyotrophic lateral sclerosis. Some TBK1 variants are nonsense and are predicted to cause disease through haploinsufficiency; however, many other mutations are missense with unknown functional effects. We exome sequenced 699 familial amyotrophic lateral sclerosis patients and identified 16 TBK1 novel or extremely rare protein-changing variants. We characterized a subset of these: p.G217R, p.R357X, and p.C471Y. Here, we show that the p.R357X and p.G217R both abolish the ability of TBK1 to phosphorylate 2 of its kinase targets, IRF3 and optineurin, and to undergo phosphorylation. They both inhibit binding to optineurin and the p.G217R, within the TBK1 kinase domain, reduces homodimerization, essential for TBK1 activation and function. Finally, we show that the proportion of TBK1 that is active (phosphorylated) is reduced in 5 lymphoblastoid cell lines derived from patients harboring heterozygous missense or in-frame deletion TBK1 mutations. We conclude that missense mutations in functional domains of TBK1 impair the binding and phosphorylation of its normal targets, implicating a common loss of function mechanism, analogous to truncation mutations.

PMID: 30033073 [PubMed - as supplied by publisher]

Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles.

Am J Hum Genet. 2018 Jul 12;:

Authors: Coban-Akdemir Z, White JJ, Song X, Jhangiani SN, Fatih JM, Gambin T, Bayram Y, Chinn IK, Karaca E, Punetha J, Poli C, Baylor-Hopkins Center for Mendelian Genomics, Boerwinkle E, Shaw CA, Orange JS, Gibbs RA, Lappalainen T, Lupski JR, Carvalho CMB

Abstract
Premature termination codon (PTC)-bearing transcripts are often degraded by nonsense-mediated decay (NMD) resulting in loss-of-function (LoF) alleles. However, not all PTCs result in LoF mutations, i.e., some such transcripts escape NMD and are translated to truncated peptide products that result in disease due to gain-of-function (GoF) effects. Since the location of the PTC is a major factor determining transcript fate, we hypothesized that depletion of protein-truncating variants (PTVs) within the gene region predicted to escape NMD in control databases could provide a rank for genic susceptibility for disease through GoF versus LoF. We developed an NMD escape intolerance score to rank genes based on the depletion of PTVs that would render them able to escape NMD using the Atherosclerosis Risk in Communities Study (ARIC) and the Exome Aggregation Consortium (ExAC) control databases, which was further used to screen the Baylor-Center for Mendelian Genomics disease database. This analysis revealed 1,996 genes significantly depleted for PTVs that are predicted to escape from NMD, i.e., PTVesc; further studies provided evidence that revealed a subset as candidate genes underlying Mendelian phenotypes. Importantly, these genes have characteristically low pLI scores, which can cause them to be overlooked as candidates for dominant diseases. Collectively, we demonstrate that this NMD escape intolerance score is an effective and efficient tool for gene discovery in Mendelian diseases due to production of truncated or altered proteins. More importantly, we provide a complementary analytical tool to aid identification of genes associated with dominant traits through a mechanism distinct from LoF.

PMID: 30032986 [PubMed - as supplied by publisher]

Germline mutations in young non-smoking women with lung adenocarcinoma.

Lung Cancer. 2018 Aug;122:76-82

Authors: Donner I, Katainen R, Sipilä LJ, Aavikko M, Pukkala E, Aaltonen LA

Abstract
OBJECTIVES: Although the primary cause of lung cancer is smoking, a considerable proportion of all lung cancers occur in never smokers. Gender influences the risk and characteristics of lung cancer and women are overrepresented among never smokers with the disease. Young age at onset and lack of established environmental risk factors suggest genetic predisposition. In this study, we used population-based sampling of young patients to discover candidate predisposition variants for lung adenocarcinoma in never-smoking women.
MATERIALS AND METHODS: We employed archival normal tissue material from 21 never-smoker women who had been diagnosed with lung adenocarcinoma before the age of 45, and exome sequenced their germline DNA.
RESULTS AND CONCLUSION: Potentially pathogenic variants were found in eight Cancer Gene Census germline genes: BRCA1, BRCA2, ERCC4, EXT1, HNF1 A, PTCH1, SMARCB1 and TP53. The variants in TP53, BRCA1, and BRCA2 are likely to have contributed to the early onset lung cancer in the respective patients (3/21 or 14%). This supports the notion that lung adenocarcinoma can be a component of certain cancer predisposition syndromes. Fifteen genes displayed potentially pathogenic mutations in at least two patients: ABCC10, ATP7B, CACNA1S, CFTR, CLIP4, COL6A1, COL6A6, GCN1, GJB6, RYR1, SCN7A, SEC24A, SP100, TTN and USH2A. Four patients showed a mutation in COL6A1, three in CLIP4 and two in the rest of the genes. Some of these candidate genes may explain a subset of female lung adenocarcinoma.

PMID: 30032850 [PubMed - in process]

Divergent susceptibilities to AAV-SaCas9-gRNA vector-mediated genome-editing in a single-cell-derived cell population.

BMC Res Notes. 2017 Dec 08;10(1):720

Authors: Morsy SG, Tonne JM, Zhu Y, Lu B, Budzik K, Krempski JW, Ali SA, El-Feky MA, Ikeda Y

Abstract
OBJECTIVE: Recombinant adeno-associated virus (AAV)-based vectors are characterized by their robust and safe transgene delivery. The CRISPR/Cas9 and guide RNA (gRNA) system present a promising genome-editing platform, and a recent development of a shorter Cas9 enzyme from Staphylococcus aureus (SaCas9) allows generation of high titer single AAV vectors which carry both saCas9- and gRNA-expression cassettes. Here, we used two AAV-SaCas9 vectors with distinct GFP-targeted gRNA sequences and determined the impact of AAV-SaCas9-gRNA vector treatment in a single cell clone carrying a GFP-expression cassette.
RESULTS: Our results showed comparable GFP knockout efficiencies (40-50%) upon a single low-dose infection. Three consecutive transductions of 25-fold higher doses of vectors showed 80% GFP knockout efficiency. To analyze the "AAV-SaCas9-resistant cell population", we sorted the residual GFP-positive cells and assessed their permissiveness to super-infection with two AAV-Cas9-GFP vectors. We found the sorted cells were significantly more resistant to the GFP knockout mediated by the same AAV vector, but not by the other GFP-targeted AAV vector. Our data therefore demonstrate highly efficient genome-editing by the AAV-SaCas9-gRNA vector system. Differential susceptibilities of single cell-derived cells to the AAV-SaCas9-gRNA-mediated genome editing may represent a formidable barrier to achieve 100% genome editing efficiency by this vector system.

PMID: 29221488 [PubMed - indexed for MEDLINE]

Novel Mutation in FLNC (Filamin C) Causes Familial Restrictive Cardiomyopathy.

Circ Cardiovasc Genet. 2017 Dec;10(6):

Authors: Tucker NR, McLellan MA, Hu D, Ye J, Parsons VA, Mills RW, Clauss S, Dolmatova E, Shea MA, Milan DJ, Scott NS, Lindsay M, Lubitz SA, Domian IJ, Stone JR, Lin H, Ellinor PT

Abstract
BACKGROUND: Restrictive cardiomyopathy (RCM) is a rare cardiomyopathy characterized by impaired diastolic ventricular function resulting in a poor clinical prognosis. Rarely, heritable forms of RCM have been reported, and mutations underlying RCM have been identified in genes that govern the contractile function of the cardiomyocytes.
METHODS AND RESULTS: We evaluated 8 family members across 4 generations by history, physical examination, electrocardiography, and echocardiography. Affected individuals presented with a pleitropic syndrome of progressive RCM, atrioventricular septal defects, and a high prevalence of atrial fibrillation. Exome sequencing of 5 affected members identified a single novel missense variant in a highly conserved residue of FLNC (filamin C; p.V2297M). FLNC encodes filamin C-a protein that acts as both a scaffold for the assembly and organization of the central contractile unit of striated muscle and also as a mechanosensitive signaling molecule during cell migration and shear stress. Immunohistochemical analysis of FLNC localization in cardiac tissue from an affected family member revealed a diminished localization at the z disk, whereas traditional localization at the intercalated disk was preserved. Stem cell-derived cardiomyocytes mutated to carry the effect allele had diminished contractile activity when compared with controls.
CONCLUSION: We have identified a novel variant in FLNC as pathogenic variant for familial RCM-a finding that further expands on the genetic basis of this rare and morbid cardiomyopathy.

PMID: 29212899 [PubMed - indexed for MEDLINE]

Identification of TNFSF13, SPATC1L, SLC22A25 and SALL4 as novel susceptibility loci for atrial fibrillation by an exome‑wide association study.

Mol Med Rep. 2017 Nov;16(5):5823-5832

Authors: Yamada Y, Sakuma J, Takeuchi I, Yasukochi Y, Kato K, Oguri M, Fujimaki T, Horibe H, Muramatsu M, Sawabe M, Fujiwara Y, Taniguchi Y, Obuchi S, Kawai H, Shinkai S, Mori S, Arai T, Tanaka M

Abstract
An exome‑wide association study (EWAS) was performed to identify genetic variants, particularly low‑frequency or rare coding variants with a moderate to large effect size, that confer susceptibility to atrial fibrillation in Japanese. The EWAS for atrial fibrillation was performed with 13,166 subjects (884 patients with atrial fibrillation and 12,282 controls) using an Illumina HumanExome‑12 DNA Analysis BeadChip or Infinium Exome‑24 BeadChip arrays. The association of atrial fibrillation with allele frequencies of 41,243 single nucleotide polymorphisms (SNPs) that passed quality control was examined with Fisher's exact test. Based on Bonferroni's correction, a P<1.21x10‑6 was considered statistically significant. The EWAS for atrial fibrillation revealed that 122 SNPs were significantly associated with this condition. The association of the identified SNPs to atrial fibrillation was further examined by multivariable logistic regression analysis with adjustment for age, sex and the prevalence of hypertension. Eight SNPs were related (P<0.01) to atrial fibrillation, among which three polymorphisms, rs11552708 [G/A (G67R)]of TNF superfamily member 13 (TNFSF13; dominant model; P=9.36x10‑9; odds ratio, 0.58), rs113710653 [C/T (E231 K)] of spermatogenesis and centriole associated 1 like (SPATC1L; dominant model; P=1.09x10‑5; odds ratio, 3.27), and rs11231397 [G/C (R300T)] of solute carrier family 22 member 25 (SLC22A25; additive model; P=3.71x10‑5; odds ratio, 1.77), were significantly (P<1.02x10‑4) associated with this condition. The minor T allele of rs113710653 and the minor C allele of rs11231397 were risk factors for atrial fibrillation, whereas the minor A allele of rs11552708 was protective against this condition. In addition, rs77538589 [C/T (G117R)] of SALL4 exhibited a tendency to be associated with atrial fibrillation (dominant model; P=0.0002; odds ratio, 1.88), with the minor T allele representing a risk factor for this condition. TNFSF13, SPATC1L, SLC22A25 and SALL4 may thus be novel susceptibility loci for atrial fibrillation in the Japanese population.

PMID: 28849223 [PubMed - indexed for MEDLINE]