Funding Opportunity PA-17-308 from the NIH Guide for Grants and Contracts. This funding opportunity announcement (FOA) encourages applications for administrative supplements from the Children's Health Exposure Analysis Resource (CHEAR) grantees in order to support the offering of CHEAR analytical services to meet the needs of the NIH Environmental influences on Children's Health Outcomes (ECHO) program.

Related Articles

High-content drug screening for rare diseases.

J Inherit Metab Dis. 2017 Jun 07;:

Authors: Bellomo F, Medina DL, De Leo E, Panarella A, Emma F

Abstract
Per definition, rare diseases affect only a small number of subjects within a given population. Taken together however, they represent a considerable medical burden, which remains poorly addressed in terms of treatment. Compared to other diseases, obstacles to the development of therapies for rare diseases include less extensive physiopathology knowledge, limited number of patients to test treatments, and poor commercial interest from the industry. Recently, advances in high-throughput and high-content screening (HTS and HCS) have been fostered by the development of specific routines that use robot- and computer-assisted technologies to automatize tasks, allowing screening of a large number of compounds in a short period of time, using experimental model of diseases. These approaches are particularly relevant for drug repositioning in rare disease, which restricts the search to compounds that have already been tested in humans, thereby reducing the need for extensive preclinical tests. In the future, these same tools, combined with computational modeling and artificial neural network analyses, may also be used to predict individual clinical responses to drugs in a personalized medicine approach.

PMID: 28593466 [PubMed - as supplied by publisher]

Related Articles

Kawasaki Disease at 50 Years.

JAMA Pediatr. 2016 Nov 01;170(11):1093-1099

Authors: Cohen E, Sundel R

Abstract
Importance: Kawasaki disease (KD) is the most recognized vasculitis of childhood. The condition's characteristic high fever, rash, mucositis, conjunctivitis, lymphadenopathy, and extremity changes are superficially unexceptional, and resolve spontaneously within a mean of 12 days. It is the acuity and the potential for life-changing damage to the coronary arteries that distinguish KD from conditions that mimic it and exemplify the unique aspects and challenges of vascular inflammation in children.
Observations: Although KD is an orphan disease, its role as a leading cause of acquired heart disease in children has led to significant efforts to determine its etiology, optimize diagnosis, and customize treatment according to individuals' needs. The result is that KD can now be controlled without sequelae in more than 95% of cases. Furthermore, advances in stratifying patients according to measurable risk factors allow therapy to be personalized in increasingly effective ways. High-risk patients, such as infants younger than 6 months, those with early evidence of coronary artery dilatation, and those with extreme abnormalities in laboratory test results, are often identified at presentation. This early identification allows them to be treated with corticosteroids in addition to intravenous immunoglobulin to improve their outcomes. Children with similar findings on laboratory tests and echocardiography may be treated based on algorithms for managing "incomplete KD" despite falling short of fulfilling classic diagnostic criteria. Children who do not respond to intravenous immunoglobulin are the focus of trials to minimize the duration of inflammation and thereby protect their coronary arteries in ways never before considered.
Conclusions and Relevance: Kawasaki disease is a hybrid condition at the junction of infectious diseases, immunology, rheumatology, and cardiology. Rather than being left an orphan disease, KD is bringing disciplines together to identify its genetic, pathophysiological, and hemodynamic features. In turn, this work promises to shed light on many other inflammatory conditions as well.

PMID: 27668809 [PubMed - indexed for MEDLINE]

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NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

J Biomed Semantics. 2017 Jun 07;8(1):21

Authors: Martínez-Romero M, Jonquet C, O'Connor MJ, Graybeal J, Pazos A, Musen MA

Abstract
BACKGROUND: Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms.
METHODS: We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data.
RESULTS: Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios.
CONCLUSIONS: Ontology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available (both via the user interface at http://bioportal.bioontology.org/recommender , and via a Web service API).

PMID: 28592275 [PubMed - in process]

A smartphone-based chloridometer for point-of-care diagnostics of cystic fibrosis.

Biosens Bioelectron. 2017 May 27;97:164-168

Authors: Zhang C, Kim JP, Creer M, Yang J, Liu Z

Abstract
Chloride in sweat is an important diagnostic marker for cystic fibrosis (CF), but the implementation of point-of-care systems for diagnosis is hindered by the prohibitive costs of existing chloride sensors. To enable low cost diagnostic solutions, we recently established a citrate-derived synthesis platform for the development of new fluorescence sensors with high selectivity for chloride. As a next step, we herein designed a smartphone operated chloridometer that optimizes the analytical performance of the citrate-derived sensor materials for the detection of chloride in sweat. The sensor material demonstrated a wide linear range of 0.8-200mM chloride and a diffusion-limited response time; sweat chloride levels corresponded to measurable changes in fluorescence emission that was captured by a smartphone. Clinical validation was performed with sweat from individuals with and without CF, demonstrating convenient sweat diagnostics with reliable detection of cystic fibrosis. To our knowledge, this is the first clinical study of a smartphone-based chloride sensor, paving the way for point-of-care diagnostic systems for CF.

PMID: 28595077 [PubMed - as supplied by publisher]

The Meanings of Helping: An Analysis of Cystic Fibrosis Patients' Reasons for Participating in Biomedical Research.

J Empir Res Hum Res Ethics. 2017 Jun 01;:1556264617713098

Authors: Christofides E, Stroud K, Tullis DE, O'Doherty K

Abstract
Research participants often report wanting to help as a reason for participation, but who they want to help and why is rarely explored. We examined meanings associated with helping among 21 adults with cystic fibrosis (CF)-a group with high participation in research. Meanings included helping to advance research, helping others with CF, helping as their job, helping themselves, helping because they are special, and helping to give back. While some meanings were primarily oriented toward helping others, some also involved hoping for benefits for oneself, and some included feelings of responsibility. Despite indicating that they understood that research is not designed to help them directly, participants nevertheless hoped that it might. We discuss implications for research ethics oversight.

PMID: 28593817 [PubMed - as supplied by publisher]

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Erratum to: The evidence on tiotropium bromide in asthma: from the rationale to the bedside.

Multidiscip Respir Med. 2017;12:17

Authors: Radovanovic D, Santus P, Blasi F, Mantero M

Abstract
[This corrects the article DOI: 10.1186/s40248-017-0094-3.].

PMID: 28593046 [PubMed - in process]

Related Articles

Bacterial Sphingomyelinase is a State-Dependent Inhibitor of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR).

Sci Rep. 2017 Jun 07;7(1):2931

Authors: Stauffer BB, Cui G, Cottrill KA, Infield DT, McCarty NA

Abstract
Sphingomyelinase C (SMase) inhibits CFTR chloride channel activity in multiple cell systems, an effect that could exacerbate disease in CF and COPD patients. The mechanism by which sphingomyelin catalysis inhibits CFTR is not known but evidence suggests that it occurs independently of CFTR's regulatory "R" domain. In this study we utilized the Xenopus oocyte expression system to shed light on how CFTR channel activity is reduced by SMase. We found that the pathway leading to inhibition is not membrane delimited and that inhibited CFTR channels remain at the cell membrane, indicative of a novel silencing mechanism. Consistent with an effect on CFTR gating behavior, we found that altering gating kinetics influenced the sensitivity to inhibition by SMase. Specifically, increasing channel activity by introducing the mutation K1250A or pretreating with the CFTR potentiator VX-770 (Ivacaftor) imparted resistance to inhibition. In primary bronchial epithelial cells, we found that basolateral, but not apical, application of SMase leads to a redistribution of sphingomyelin and a reduction in forskolin- and VX-770-stimulated currents. Taken together, these data suggest that SMase inhibits CFTR channel function by locking channels into a closed state and that endogenous CFTR in HBEs is affected by SMase activity.

PMID: 28592822 [PubMed - in process]

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The added value of exhaled breath temperature in respiratory medicine.

J Breath Res. 2017 Jun 08;:

Authors: Popov TA, Kralimarkova T, Labor M, Plavec D

Abstract
Recognition of the huge economic burden chronic respiratory diseases pose for society motivated fundamental and clinical research leading to insight into the role of airway inflammation in various disease entities and their phenotypes. However, no easy, cheap and patient-friendly methods to assess it have found a place in routine clinical practice. Measurement of exhaled breath temperature (EBT) has been suggested as a non-invasive method to detect inflammatory processes in the airways as a result of increased blood flow within the airway walls. As EBT values are within a narrow range, the thermometers designed for the purpose of assessing it need to be precise and very sensitive. EBT increases linearly over the pediatric age range and seems to be influenced by gender, but not by height and body weight. In non-smoking individuals with no history of respiratory disease EBT has a natural circadian peak about noon and increases with food intake and physical exercise. When interpreting EBT in subjects with alleged airway pathology, the possibilities of tissue destruction (chronic obstructive pulmonary disease, cystic fibrosis) or excessive bronchial obstruction and air trapping (severe asthma) need to be considered, as these conditions drive (force) EBT down. A prominent advantage of the method is to assess EBT when patients are in a steady state of their disease and to use this "personal best" to monitor them and guide their treatment. Individual devices outfitted with microprocessors and memory have been created, which can be used for personalized monitoring and disease management by telemedicine.

PMID: 28592704 [PubMed - as supplied by publisher]

Related Articles

Linaclotide activates guanylate cyclase-C/cGMP/protein kinase-II-dependent trafficking of CFTR in the intestine.

Physiol Rep. 2017 Jun;5(11):

Authors: Ahsan MK, Tchernychev B, Kessler MM, Solinga RM, Arthur D, Linde CI, Silos-Santiago I, Hannig G, Ameen NA

Abstract
The transmembrane receptor guanylyl cyclase-C (GC-C), expressed on enterocytes along the intestine, is the molecular target of the GC-C agonist peptide linaclotide, an FDA-approved drug for treatment of adult patients with Irritable Bowel Syndrome with Constipation and Chronic Idiopathic Constipation. Polarized human colonic intestinal cells (T84, CaCo-2BBe) rat and human intestinal tissues were employed to examine cellular signaling and cystic fibrosis transmembrane conductance regulator (CFTR)-trafficking pathways activated by linaclotide using confocal microscopy, in vivo surface biotinylation, and protein kinase-II (PKG-II) activity assays. Expression and activity of GC-C/cGMP pathway components were determined by PCR, western blot, and cGMP assays. Fluid secretion as a marker of CFTR cell surface translocation was determined using in vivo rat intestinal loops. Linaclotide treatment (30 min) induced robust fluid secretion and translocation of CFTR from subapical compartments to the cell surface in rat intestinal loops. Similarly, linaclotide treatment (30 min) of T84 and CaCo-2BBe cells increased cell surface CFTR levels. Linaclotide-induced activation of the GC-C/cGMP/PKGII signaling pathway resulted in elevated intracellular cGMP and pVASP(ser239) phosphorylation. Inhibition or silencing of PKGII significantly attenuated linaclotide-induced CFTR trafficking to the apical membrane. Inhibition of protein kinase-A (PKA) also attenuated linaclotide-induced CFTR cell surface trafficking, implying cGMP-dependent cross-activation of PKA pathway. Together, these findings support linaclotide-induced activation of the GC-C/cGMP/PKG-II/CFTR pathway as the major pathway of linaclotide-mediated intestinal fluid secretion, and that linaclotide-dependent CFTR activation and recruitment/trafficking of CFTR from subapical vesicles to the cell surface is an important step in this process.

PMID: 28592587 [PubMed - in process]

Related Articles

Knockdown of CFTR enhances sensitivity of prostate cancer cells to cisplatin via inhibition of autophagy.

Neoplasma. 2017 Jun 08;:

Authors: Zhu Q, Li H, Liu Y, Jiang L

Abstract
Prostate cancer is one of the most lethal diseases in men worldwide. Although the survival rate of men diagnosed with prostate cancer has increased with the improvement of treatments, drug resistance still remains a big challenge for improving overall survival. Cystic fibrosis transmembrane conductance regulator (CFTR), a cAMP-activated anion channel, has been reported to have a pivotal role in the pathogenesis of various cancers, but its role in chemoresistance of prostate cancer cells is poorly understood. In our study, we found that CFTR expression was significantly increased in prostate cancer tissues associated the chemoresistance, and in the cisplatin-resistant cell line LNCaP/CP compared with their respective parental cells. Cisplatin treatment inhibited CFTR expression in a concentration-dependent manner, which was correlated with a decrease in cell viability. Moreover, inhibition of CFTR by transfection of small interfering RNA enhanced cisplatin-induced the decrease of cell viability. Autophagy was dramatically increased in LNCaP/CP cells, as evidenced by autopaphgic markers as well as fluorescence microscopy analysis of GFP-LC3, MDC and AO staining. Of note, inhibiting autophagy by 3MA induced LNCaP/CP cell apoptosis, showed by MTT assay and Hoechst 33258 staining. In addition, blockade of CFTR also inhibited LNCaP/CP cell viability and autophagy. Furthermore, the dephosphorylation of AKT and mTOR was reversed by CFTR inhibition, indicating the knockdown of CFTR might inhibit autophagy in LNCaP/CP cells via activation of AKT/mTOR signaling. Altogether, these results provide a novel understanding of the mechanism for acquired cisplatin. Inhibition of CFTR may be a useful strategy to increase the efficacy of cisplatin to treat prostate cancer by preventing the protective response of autophagy.

PMID: 28592122 [PubMed - as supplied by publisher]

Related Articles

Keratin 8 knockdown leads to loss of the chloride transporter DRA in the colon.

Am J Physiol Gastrointest Liver Physiol. 2016 Jun 01;310(11):G1147-54

Authors: Asghar MN, Priyamvada S, Nyström JH, Anbazhagan AN, Dudeja PK, Toivola DM

Abstract
Keratins (K) are intermediate filament proteins important in protection from stress. The roles of keratins in the intestine are not clear, but K8 knockout (K8(-/-)) mice develop a Th2-type colonic inflammation, epithelial hyperproliferation, and mild diarrhea caused by a keratin level-dependent decrease in short-circuit current and net sodium and chloride absorption in the distal colon. The lack of K8 leads to mistargeting or altered levels of membrane proteins in colonocytes; however, the main transporter responsible for the keratin-related ion transport defect is unknown. We here analyzed protein and mRNA levels of candidate ion transporters CFTR, PAT-1, NHE-3, and DRA in ileum, cecum, and proximal and distal colon. Although no differences were observed for CFTR, PAT-1, or NHE-3, DRA mRNA levels were decreased by three- to fourfold and DRA protein was almost entirely lost in K8(-/-) cecum and proximal and distal colon compared with K8(+/+), whereas the levels in ileum were normal. In K8(+/-) mice, DRA mRNA levels were unaltered, while decreased DRA protein levels were detected in the proximal colon. Immunofluorescence staining confirmed the loss of DRA in K8(-/-) distal colon, while K8(+/-) displayed a similar but more patchy apical DRA distribution compared with K8(+/+) DRA was similarly decreased when K8 was knocked down in Caco-2 cells, confirming that K8 levels modulate DRA levels in an inflammation-independent manner. Taken together, the loss of DRA in the K8(-/-) mouse colon and cecum explains the dramatic chloride transport defect and diarrheal phenotype after K8 inactivation and identifies K8 as a novel regulator of DRA.

PMID: 27125276 [PubMed - indexed for MEDLINE]

Identification of a rare LAMB4 variant associated with familial diverticulitis through exome sequencing.

Hum Mol Genet. 2017 Jun 08;:

Authors: Coble JL, Sheldon K, Yue F, Salameh T, Harris L, Deiling S, Ruggiero F, Eshelman M, Yochum GS, Koltun WA, Gerhard GS, Broach JR

Abstract
Diverticulitis is a chronic disease of the colon in which diverticuli, or outpouching through the colonic wall, become inflamed. Although recent observations suggests that genetic factors may play a significant role in diverticulitis, few genes have yet been implicated in disease pathogenesis and familial cases are uncommon. Here, we report results of whole exome sequencing performed on members from a single multi-generational family with early onset diverticulitis in order to identify a genetic component of the disease. We identified a rare single nucleotide variant in the laminin β 4 gene (LAMB4) that segregated with disease in a dominant pattern and causes a damaging missense substitution (D435N). Targeted sequencing of LAMB4 in 148 non-familial and unrelated sporadic diverticulitis patients identified two additional rare variants in the gene. Immunohistochemistry indicated that LAMB4 localizes to the myenteric plexi of colonic tissue and patients harboring LAMB4 variants exhibited reduced LAMB4 protein levels relative to controls. Laminins are constituents of the extracellular matrix and play a major role in regulating the development and function of the enteric nervous system. Reduced LAMB4 levels may therefore alter innervation and morphology of the enteric nervous system, which may contribute to colonic dysmotility associated with diverticulitis.

PMID: 28595269 [PubMed - as supplied by publisher]

Compound heterozygous mutations in glycyl-tRNA synthetase (GARS) cause mitochondrial respiratory chain dysfunction.

PLoS One. 2017;12(6):e0178125

Authors: Nafisinia M, Riley LG, Gold WA, Bhattacharya K, Broderick CR, Thorburn DR, Simons C, Christodoulou J

Abstract
Glycyl-tRNA synthetase (GARS; OMIM 600287) is one of thirty-seven tRNA-synthetase genes that catalyses the synthesis of glycyl-tRNA, which is required to insert glycine into proteins within the cytosol and mitochondria. To date, eighteen mutations in GARS have been reported in patients with autosomal-dominant Charcot-Marie-Tooth disease type 2D (CMT2D; OMIM 601472), and/or distal spinal muscular atrophy type V (dSMA-V; OMIM 600794). In this study, we report a patient with clinical and biochemical features suggestive of a mitochondrial respiratory chain (MRC) disorder including mild left ventricular posterior wall hypertrophy, exercise intolerance, and lactic acidosis. Using whole exome sequencing we identified compound heterozygous novel variants, c.803C>T; p.(Thr268Ile) and c.1234C>T; p.(Arg412Cys), in GARS in the proband. Spectrophotometric evaluation of the MRC complexes showed reduced activity of Complex I, III and IV in patient skeletal muscle and reduced Complex I and IV activity in the patient liver, with Complex IV being the most severely affected in both tissues. Immunoblot analysis of GARS protein and subunits of the MRC enzyme complexes in patient fibroblast extracts showed significant reduction in GARS protein levels and Complex IV. Together these studies provide evidence that the identified compound heterozygous GARS variants may be the cause of the mitochondrial dysfunction in our patient.

PMID: 28594869 [PubMed - in process]

Analysis of selected genes associated with cardiomyopathy by next-generation sequencing.

J Clin Lab Anal. 2017 Jun 08;:

Authors: Szabadosova V, Boronova I, Ferenc P, Tothova I, Bernasovska J, Zigova M, Kmec J, Bernasovsky I

Abstract
BACKGROUND: As the leading cause of congestive heart failure, cardiomyopathy represents a heterogenous group of heart muscle disorders. Despite considerable progress being made in the genetic diagnosis of cardiomyopathy by detection of the mutations in the most prevalent cardiomyopathy genes, the cause remains unsolved in many patients. High-throughput mutation screening in the disease genes for cardiomyopathy is now possible because of using target enrichment followed by next-generation sequencing. The aim of the study was to analyze a panel of genes associated with dilated or hypertrophic cardiomyopathy based on previously published results in order to identify the subjects at risk.
METHODS: The method of next-generation sequencing by IlluminaHiSeq 2500 platform was used to detect sequence variants in 16 individuals diagnosed with dilated or hypertrophic cardiomyopathy. Detected variants were filtered and the functional impact of amino acid changes was predicted by computational programs.
RESULTS: DNA samples of the 16 patients were analyzed by whole exome sequencing. We identified six nonsynonymous variants that were shown to be pathogenic in all used prediction softwares: rs3744998 (EPG5), rs11551768 (MGME1), rs148374985 (MURC), rs78461695 (PLEC), rs17158558 (RET) and rs2295190 (SYNE1). Two of the analyzed sequence variants had minor allele frequency (MAF)<0.01: rs148374985 (MURC), rs34580776 (MYBPC3).
CONCLUSION: Our data support the potential role of the detected variants in pathogenesis of dilated or hypertrophic cardiomyopathy; however, the possibility that these variants might not be true disease-causing variants but are susceptibility alleles that require additional mutations or injury to cause the clinical phenotype of disease must be considered.

PMID: 28594148 [PubMed - as supplied by publisher]

Eosinophil-rich tissue infiltrates in chronic myelomonocytic leukemia patients.

Leuk Lymphoma. 2017 Jun 08;:1-5

Authors: Droin N, Lucas N, Parinet V, Selimoglu-Buet D, Humbert M, Saada V, Lambotte O, Solary E, Noël N

Abstract
Chronic myelomonocytic leukemia (CMML) is a clonal hematopoietic disorder that associates dysplastic and proliferative features. Tissue inflammatory disorders occur in a fraction of CMML patients during the course of their disease. Here, we describe the occurrence of eosinophil-rich tissue inflammation, including eosinophilic pneumonia, chondritis, and cystitis, in CMML patients. Whole exome sequencing of leukemic cells did not identify a recurrent genetic abnormality among these three patients who were clinically improved by local or oral corticosteroids. Hypomethylating drugs were subsequently added in two of them, allowing decreasing corticosteroid doses and further treating their hematopoietic malignancy.

PMID: 28593791 [PubMed - as supplied by publisher]

Molecular diagnostics for hereditary hearing loss in children.

Expert Rev Mol Diagn. 2017 Jun 08;:

Authors: Sommen M, Wuyts W, Van Camp G

Abstract
INTRODUCTION: Hearing loss (HL) is the most common birth defect in industrialized countries with far-reaching social, psychological and cognitive implications. It is an extremely heterogeneous disease, complicating molecular testing. The introduction of next-generation sequencing (NGS) has resulted in great progress in diagnostics allowing to study all known HL genes in a single assay. The diagnostic yield is currently still limited, but has the potential to increase substantially. Areas covered: In this review the utility of NGS and the problems for comprehensive molecular testing for HL are evaluated and discussed. Expert commentary: Different publications have proven the appropriateness of NGS for molecular testing of heterogeneous diseases such as HL. However, several problems still exist, such as pseudogenic background of some genes and problematic copy number variant analysis on targeted NGS data. Another main challenge for the future will be the establishment of population specific mutation-spectra to achieve accurate personalized comprehensive molecular testing for HL.

PMID: 28593790 [PubMed - as supplied by publisher]

Related Articles

Loss of function in ROBO1 is associated with tetralogy of Fallot and septal defects.

J Med Genet. 2017 Jun 07;:

Authors: Kruszka P, Tanpaiboon P, Neas K, Crosby K, Berger SI, Martinez AF, Addissie YA, Pongprot Y, Sittiwangkul R, Silvilairat S, Makonkawkeyoon K, Yu L, Wynn J, Bennett JT, Mefford HC, Reynolds WT, Liu X, Mommersteeg MTM, Chung WK, Lo CW, Muenke M

Abstract
BACKGROUND: Congenital heart disease (CHD) is a common birth defect affecting approximately 1% of newborns. Great progress has been made in elucidating the genetic aetiology of CHD with advances in genomic technology, which we leveraged in recovering a new pathway affecting heart development in humans previously known to affect heart development in an animal model.
METHODS: Four hundred and sixteen individuals from Thailand and the USA diagnosed with CHD and/or congenital diaphragmatic hernia were evaluated with chromosomal microarray and whole exome sequencing. The DECIPHER Consortium and medical literature were searched for additional patients. Murine hearts from ENU-induced mouse mutants and transgenic mice were evaluated using both episcopic confocal histopathology and troponin I stained sections.
RESULTS: Loss of function ROBO1 variants were identified in three families; each proband had a ventricular septal defect, and one proband had tetralogy of Fallot. Additionally, a microdeletion in an individual with CHD was found in the medical literature. Mouse models showed perturbation of the Slit-Robo signalling pathway, causing septation and outflow tract defects and craniofacial anomalies. Two probands had variable facial features consistent with the mouse model.
CONCLUSION: Our findings identify Slit-Robo as a significant pathway in human heart development and CHD.

PMID: 28592524 [PubMed - as supplied by publisher]

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Germline CDKN2A/P16INK4A mutations contribute to genetic determinism of sarcoma.

J Med Genet. 2017 Jun 07;:

Authors: Jouenne F, Chauvot de Beauchene I, Bollaert E, Avril MF, Caron O, Ingster O, Lecesne A, Benusiglio P, Terrier P, Caumette V, Pissaloux D, de la Fouchardière A, Cabaret O, N'Diaye B, Velghe A, Bougeard G, Mann GJ, Koscielny S, Barrett JH, Harland M, Newton-Bishop J, Gruis N, Van Doorn R, Gauthier-Villars M, Pierron G, Stoppa-Lyonnet D, Coupier I, Guimbaud R, Delnatte C, Scoazec JY, Eggermont AM, Feunteun J, Tchertanov L, Demoulin JB, Frebourg T, Bressac-de Paillerets B

Abstract
BACKGROUND: Sarcomas are rare mesenchymal malignancies whose pathogenesis is poorly understood; both environmental and genetic risk factors could contribute to their aetiology.
METHODS AND RESULTS: We performed whole-exome sequencing (WES) in a familial aggregation of three individuals affected with soft-tissue sarcoma (STS) without TP53 mutation (Li-Fraumeni-like, LFL) and found a shared pathogenic mutation in CDKN2A tumour suppressor gene. We searched for individuals with sarcoma among 474 melanoma-prone families with a CDKN2A-/+ genotype and for CDKN2A mutations in 190 TP53-negative LFL families where the index case was a sarcoma. Including the initial family, eight independent sarcoma cases carried a germline mutation in the CDKN2A/p16(INK4A) gene. In five out of seven formalin-fixed paraffin-embedded sarcomas, heterozygosity was lost at germline CDKN2A mutations sites demonstrating complete loss of function. As sarcomas are rare in CDKN2A/p16(INK4A) carriers, we searched in constitutional WES of nine carriers for potential modifying rare variants and identified three in platelet-derived growth factor receptor (PDGFRA) gene. Molecular modelling showed that two never-described variants could impact the PDGFRA extracellular domain structure.
CONCLUSION: Germline mutations in CDKN2A/P16(INK4A), a gene known to predispose to hereditary melanoma, pancreatic cancer and tobacco-related cancers, account also for a subset of hereditary sarcoma. In addition, we identified PDGFRA as a candidate modifier gene.

PMID: 28592523 [PubMed - as supplied by publisher]

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The genomic road to invasion-examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples.

Genome Med. 2017 Jun 07;9(1):53

Authors: Wood HM, Daly C, Chalkley R, Senguven B, Ross L, Egan P, Chengot P, Graham J, Sethi N, Ong TK, MacLennan K, Rabbitts P, Conway C

Abstract
BACKGROUND: It is frequently assumed that pre-invasive lesions are simpler precursors of cancer and will contain a limited subset of the genomic changes seen in their associated invasive disease. Driver mutations are thought to occur early, but it is not known how many of these are present in pre-invasive lesions. These assumptions need to be tested with the increasing focus on both personalised cancer treatments and early detection methodologies.
METHODS: We examined genomic copy number changes in 256 pre-invasive and invasive samples from 69 oral cancer patients. Forty-eight samples from 16 patients were further examined using exome sequencing.
RESULTS: Evidence of a shared ancestor of both dysplasia and carcinoma was seen in all but one patient. One-third of dysplasias showed independent copy number events. The remainder had a copy number pattern that was similar to or simpler than that of the carcinoma. All dysplasias examined contained somatic mutations absent in the related carcinoma. Previously observed copy number changes and TP53 mutations were very frequently observed, and almost always shared between dysplasia and carcinoma. Other gene changes were more sporadic. Pathway analysis confirmed that each patient's disease developed in a different way. Examining the numbers of shared mutations and the rate of accumulation of mutations showed evidence that all samples contain a population of sub-clones, with little evidence of selective advantage of a subset of these.
CONCLUSIONS: These findings suggest that most of the genomic changes driving oral cancer occur in the pre-cancerous state by way of gradual random accumulation rather than a dramatic single event.

PMID: 28592326 [PubMed - in process]