Exome Sequencing Diagnoses X-Linked Moesin-Associated Immunodeficiency in a Primary Immunodeficiency Case.

Front Immunol. 2018;9:420

Authors: Bradshaw G, Lualhati RR, Albury CL, Maksemous N, Roos-Araujo D, Smith RA, Benton MC, Eccles DA, Lea RA, Sutherland HG, Haupt LM, Griffiths LR

Abstract
Background: We investigated the molecular etiology of a young male proband with confirmed immunodeficiency of unknown cause, presenting with recurrent bacterial and Varicella zoster viral infections in childhood and persistent lymphopenia into early adulthood.
Aim: To identify causative functional genetic variants related to an undiagnosed primary immunodeficiency.
Method: Whole genome microarray copy number variant (CNV) analysis was performed on the proband followed by whole exome sequencing (WES) and trio analysis of the proband and family members. A >4 kbp deletion identified by repeated CNV analysis of exome sequencing data along with three damaging missense single nucleotide variants were validated by Sanger sequencing in all family members. Confirmation of the causative role of the candidate gene was performed by qPCR and Western Blot analyses on the proband, family members and a healthy control.
Results: CNV identified our previously reported interleukin 25 amplification in the proband; however, the variant was not validated to be a candidate gene for immunodeficiency. WES trio analysis, data filtering and in silico prediction identified a novel, damaging (SIFT: 0; Polyphen 1; Grantham score: 101) and disease-causing (MutationTaster) single base mutation in the X chromosome (c.511C > T p.Arg171Trp) MSN gene not identified in the UCSC Genome Browser database. The mutation was validated by Sanger sequencing, confirming the proband was hemizygous X-linked recessive (-/T) at this locus and inherited the affected T allele from his non-symptomatic carrier mother (C/T), with other family members (father, sister) confirmed to be wild type (C/C). Western Blot analysis demonstrated an absence of moesin protein in lymphocytes derived from the proband, compared with normal expression in lymphocytes derived from the healthy control, father and mother. qPCR identified significantly lower MSN mRNA transcript expression in the proband compared to an age- and sex-matched healthy control subject in whole blood (p = 0.02), and lymphocytes (p = 0.01). These results confirmed moesin deficiency in the proband, directly causative of his immunodeficient phenotype.
Conclusion: These findings confirm X-linked moesin-associated immunodeficiency in a proband previously undiagnosed up to 24 years of age. This study also highlights the utility of WES for the diagnosis of rare or novel forms of primary immunodeficiency disease.

PMID: 29556235 [PubMed]

High-throughput sequencing of nodal marginal zone lymphomas identifies recurrent BRAF mutations.

Leukemia. 2018 Feb 28;:

Authors: Pillonel V, Juskevicius D, Ng CKY, Bodmer A, Zettl A, Jucker D, Dirnhofer S, Tzankov A

Abstract
Nodal marginal zone lymphoma (NMZL) is a rare small B-cell lymphoma lacking disease-defining phenotype and precise diagnostic markers. To better understand the mutational landscape of NMZL, particularly in comparison to other nodal small B-cell lymphomas, we performed whole-exome sequencing, targeted high-throughput sequencing, and array-comparative genomic hybridization on a retrospective series. Our study identified for the first time recurrent, diagnostically useful, and potentially therapeutically relevant BRAF mutations in NMZL. Sets of somatic mutations that could help to discriminate NMZL from other closely related small B-cell lymphomas were uncovered and tested on unclassifiable small B-cell lymphoma cases, in which clinical, morphological, and phenotypical features were equivocal. Application of targeted gene panel sequencing gave at many occasions valuable clues for more specific classification.

PMID: 29556019 [PubMed - as supplied by publisher]

Beyond Gene Panels: Whole Exome Sequencing for Diagnosis of Congenital Heart Disease.

Circ Genom Precis Med. 2018 Mar;11(3):e002097

Authors: Paige SL, Saha P, Priest JR

PMID: 29555674 [PubMed - in process]

A Screening Approach to Identify Clinically Actionable Variants Causing Congenital Heart Disease in Exome Data.

Circ Genom Precis Med. 2018 Mar;11(3):e001978

Authors: Szot JO, Cuny H, Blue GM, Humphreys DT, Ip E, Harrison K, Sholler GF, Giannoulatou E, Leo P, Duncan EL, Sparrow DB, Ho JWK, Graham RM, Pachter N, Chapman G, Winlaw DS, Dunwoodie SL

Abstract
BACKGROUND: Congenital heart disease (CHD)-structural abnormalities of the heart that arise during embryonic development-is the most common inborn malformation, affecting ≤1% of the population. However, currently, only a minority of cases can be explained by genetic abnormalities. The goal of this study was to identify disease-causal genetic variants in 30 families affected by CHD.
METHODS: Whole-exome sequencing was performed with the DNA of multiple family members. We utilized a 2-tiered whole-exome variant screening and interpretation procedure. First, we manually curated a high-confidence list of 90 genes known to cause CHD in humans, identified predicted damaging variants in genes on this list, and rated their pathogenicity using American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines.
RESULTS: In 3 families (10%), we found pathogenic variants in known CHD genes TBX5, TFAP2B, and PTPN11, explaining the cardiac lesions. Second, exomes were comprehensively analyzed to identify additional predicted damaging variants that segregate with disease in CHD candidate genes. In 10 additional families (33%), likely disease-causal variants were uncovered in PBX1, CNOT1, ZFP36L2, TEK, USP34, UPF2, KDM5A, KMT2C, TIE1, TEAD2, and FLT4.
CONCLUSIONS: The pathogenesis of CHD could be explained using our high-confidence CHD gene list for variant filtering in a subset of cases. Furthermore, our unbiased screening procedure of family exomes implicates additional genes and variants in the pathogenesis of CHD, which suggest themselves for functional validation. This 2-tiered approach provides a means of (1) identifying clinically actionable variants and (2) identifying additional disease-causal genes, both of which are essential for improving the molecular diagnosis of CHD.

PMID: 29555671 [PubMed - in process]

Whole-exome sequencing identified mutational profiles of squamous cell carcinomas of anus.

Hum Pathol. 2018 Mar 16;:

Authors: Shin S, Park HC, Kim MS, Han MR, Lee SH, Jung SH, Lee SH, Chung YJ

Abstract
Anal squamous cell carcinoma (ASCC), either with human papillomavirus (HPV) (+) or (-), is a neoplastic disease with frequent recurrence and metastasis. To characterize ASCC genomes, we attempted to disclose novel alterations of ASCC genomes as well as other genetic features including mutation signatures. We performed whole-exome sequencing and copy number alteration (CNA) profiling for 8 ASCC samples from 6 patients (2 cases with primary and recurrent/metastatic tumors). We found known ASCC mutations (TP53, CDKN2A and PIK3CA) and CNAs (gains on 3q and 19q and losses on 11q and 13q). In addition, we discovered novel mutations in HRAS and ARID1A and CNAs (gain on 8q and losses 5q, 9p, 10q and 19p) that had not been reported in ASCCs. We identified 4 signature patterns of the mutations (signatures 1 and 2 with deamination of 5-methyl-cytosin, signature 3 with APOBEC and signature 4 with mismatch repair) in the ASCCs. While the signatures 1-3 have been detected in other SCCs, the signature 4 was first identified in ASCCs. In addition, we first found that ASCCs harbored chromothripsis, copy-neutral losses of heterozygosity and focal amplification of KLF5 super-enhancer. Analyses of primary and recurrent/metastatic pair genomes revealed that driver events in development and progression of ASCC might not be uniform. Our data indicate that ASCCs may have similar mutation and CNA profiles to other SCCs, but that there are unique genomic features of ASCCs as well. Our data may provide useful information for ASCC pathogenesis as well as for developing clinical strategies for ASCC.

PMID: 29555573 [PubMed - as supplied by publisher]

Family History in the Primary Open-Angle African American Glaucoma Genetics Study Cohort.

Am J Ophthalmol. 2018 Mar 16;:

Authors: O'Brien JM, Salowe RJ, Fertig R, Salinas J, Pistilli M, Sankar PS, Miller-Ellis E, Lehman A, Murphy W, Homsher M, Gordon K, Ying GS

Abstract
PURPOSE: To determine the relationship between positive family history (FH) and primary open-angle glaucoma (POAG) diagnosis and clinical presentation in the Primary Open-Angle African American Glaucoma Genetics (POAAGG) cohort.
METHODS: FH of POAG in first-degree relatives was assessed in 2365 subjects in the POAAGG cohort. A standardized interview was used to assess FH of glaucoma, demographic characteristics, lifestyle choices, and medical and ocular comorbidities.
RESULTS: Positive FH was associated with increased risk of POAG (age-adjusted odds ratio and 95% confidence interval 3.4[2.8, 4.1]). In age-adjusted analysis among POAG cases, positive FH was associated with younger age (P<0.001), female gender (P<.001), hypertension (P=.006), use of hypertension medication (P=.03), and prior glaucoma surgery (P=.02). Cases with positive FH also had thicker retinal nerve fiber layers (P=.03).
CONCLUSIONS: The risk conferred by positive FH suggests strong genetic underpinnings for some patients with this disease, which will be investigated by genome-wide association studies and whole exome sequencing.

PMID: 29555482 [PubMed - as supplied by publisher]

Funding Opportunity PAR-18-717 from the NIH Guide for Grants and Contracts. The purpose of this FOA is to encourage applications for research training programs to strengthen the scientific capacity of institutions in low- and middle-income countries (LMICs) to conduct HIV research relevant to the evolving HIV epidemic in their country

Funding Opportunity PAR-18-716 from the NIH Guide for Grants and Contracts. The overall goal of this initiative is to support the development of a sustainable critical mass of bioethics scholars in low and middle-income country (LMIC) research intensive institutions with the capabilities to conduct original empirical or conceptual ethics research that addresses challenging issues in health research and research policy in these countries as well as provide research ethics leadership to their institutions, governments and international research organizations. FIC will support LMIC-U.S. collaborative institutional bioethics doctoral and postdoctoral research training programs that incorporate didactic, mentored research and training components to prepare a number of individuals with ethics expertise for positions of scholarship and leadership in health research institutions in the LMIC.

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New biologics in the treatment of rare glomerular diseases of childhood.

Curr Opin Pharmacol. 2017 04;33:27-33

Authors: Cravedi P, Angeletti A, Remuzzi G

Abstract
Minimal change disease and focal segmental glomerulosclerosis are rare but important causes of end-stage kidney disease in children. Though their pathogenesis is still unclear, evidence of immune abnormalities provided the background for the use of immunosuppressive drugs, such as corticosteroids, calcineurin inhibitors, antiproliferative and alkylating agents. Unfortunately, these treatments fail to achieve a sustained remission in a significant portion of patients and are burdened by significant toxicities. Recent developments of new biologics, including anti-CD20 monoclonal antibodies rituximab and ofatumumab, offered the opportunity to selectively target immune cell subsets or activation pathways, leading to more effective and safer hypothesis-driven treatments.

PMID: 28456094 [PubMed - indexed for MEDLINE]

Funding Opportunity RFA-FD-18-020 from the NIH Guide for Grants and Contracts. FDA's CDER is seeking a computational modeling approach to study the effects of mucociliary clearance on localized drug absorption in the nasal cavity. The modeling approach would utilize computational fluid dynamics (CFD) simulations of inhalation and droplet/particle transport to provide regional nasal spray deposition data, while the three-dimensional mucociliary clearance model would demonstrate localized drug absorption and indicate the efficacy of drug products that target specific nasal regions. The model should be adaptable to cases of interindividual variability, which may include variations in mucociliary clearance rates, changes in nasal geometry, and the presence of relevant disease states (e.g., nasal inflammation, changes in mucus properties, etc.).

Funding Opportunity RFA-FD-18-019 from the NIH Guide for Grants and Contracts. The purpose of this project is to incorporate drug product quality attributes into dermal physiologically-based pharmacokinetic models developed for dermatological topical dosage forms and transdermal delivery systems. The developed models will be utilized to identify drug-product specific critical quality attributes (model qualification) and perform virtual bioequivalence assessments between brand name and generic drug products to inform regulatory decisions relating to the development of dermatological drug products.

Notice NOT-HL-18-609 from the NIH Guide for Grants and Contracts

Funding Opportunity PAR-18-715 from the NIH Guide for Grants and Contracts. This FOA invites existing Alzheimer's Disease Patient Registry cooperative agreements that are described in Part 2, Section I to submit revision and or renewal applications. Potential applicants are strongly encouraged to contact their current program officer prior to submission to discuss the application.

Notice NOT-NS-18-041 from the NIH Guide for Grants and Contracts

A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins.

Nat Genet. 2018 Mar 19;:

Authors: Letelier J, de la Calle-Mustienes E, Pieretti J, Naranjo S, Maeso I, Nakamura T, Pascual-Anaya J, Shubin NH, Schneider I, Martinez-Morales JR, Gómez-Skarmeta JL

Abstract
Despite their evolutionary, developmental and functional importance, the origin of vertebrate paired appendages remains uncertain. In mice, a single enhancer termed ZRS is solely responsible for Shh expression in limbs. Here, zebrafish and mouse transgenic assays trace the functional equivalence of ZRS across the gnathostome phylogeny. CRISPR/Cas9-mediated deletion of the medaka (Oryzias latipes) ZRS and enhancer assays identify the existence of ZRS shadow enhancers in both teleost and human genomes. Deletion of both ZRS and shadow ZRS abolishes shh expression and completely truncates pectoral fin formation. Strikingly, deletion of ZRS results in an almost complete ablation of the dorsal fin. This finding indicates that a ZRS-Shh regulatory module is shared by paired and median fins and that paired fins likely emerged by the co-option of developmental programs established in the median fins of stem gnathostomes. Shh function was later reinforced in pectoral fin development with the recruitment of shadow enhancers, conferring additional robustness.

PMID: 29556077 [PubMed - as supplied by publisher]

New drug candidates for treatment of atypical meningiomas: An integrated approach using gene expression signatures for drug repurposing.

PLoS One. 2018;13(3):e0194701

Authors: Zador Z, King AT, Geifman N

Abstract
BACKGROUND: Atypical meningiomas are common central nervous system neoplasms with high recurrence rate and poorer prognosis compared to their grade I counterparts. Surgical excision and radiotherapy remains the mainstay therapy but medical treatments are limited. We explore new drug candidates using computational drug repurposing based on the gene expression signature of atypical meningioma tissue with subsequent analysis of drug-generated expression profiles. We further explore possible mechanisms of action for the identified drug candidates using ingenuity pathway analysis (IPA).
METHODS: We extracted gene expression profiles for atypical meningiomas (12 samples) and normal meningeal tissue (4 samples) from the Gene Expression Omnibus, which were then used to generate a gene signature comprising of 281 differentially expressed genes. Drug candidates were explored using both the Board Institute Connectivity Map (cmap) and Library of Integrated Network-Based Cellular Signatures (LINCS). Functional analysis of significant differential gene expression for drug candidates was performed with IPA.
RESULTS: Using our integrated approach, we identified multiple, already licensed, drug candidates such as emetine, verteporfin, phenoxybenzamine and trazodone. Analysis with IPA revealed that these drugs target signal cascades potentially relevant in pathogenesis of meningiomas, particular examples are the effect on ERK by trazodone, MAP kinases by emetine, and YAP-1 protein by verteporfin.
CONCLUSION: Gene expression profiling and use of drug expression profiles have yielded several plausible drug candidates for treating atypical meningioma, some of which have already been suggested by preceding studies. Although our analyses suggested multiple anti-tumour mechanisms for these drugs, further in vivo studies are required for validation.
IMPORTANCE OF THE STUDY: To our knowledge this is the first study which combines relatively new, yet established computational techniques to identify additional treatments for a difficult to manage cerebral neoplasm. Beyond proposing already approved drug candidates in the management of atypical meningioma the study highlights the promise held by computational techniques in improving our management strategies.

PMID: 29558515 [PubMed - in process]

Extensive impact of non-antibiotic drugs on human gut bacteria.

Nature. 2018 Mar 19;:

Authors: Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A

Abstract
A few commonly used non-antibiotic drugs have recently been associated with changes in gut microbiome composition, but the extent of this phenomenon is unknown. Here, we screened more than 1,000 marketed drugs against 40 representative gut bacterial strains, and found that 24% of the drugs with human targets, including members of all therapeutic classes, inhibited the growth of at least one strain in vitro. Particular classes, such as the chemically diverse antipsychotics, were overrepresented in this group. The effects of human-targeted drugs on gut bacteria are reflected on their antibiotic-like side effects in humans and are concordant with existing human cohort studies. Susceptibility to antibiotics and human-targeted drugs correlates across bacterial species, suggesting common resistance mechanisms, which we verified for some drugs. The potential risk of non-antibiotics promoting antibiotic resistance warrants further exploration. Our results provide a resource for future research on drug-microbiome interactions, opening new paths for side effect control and drug repurposing, and broadening our view of antibiotic resistance.

PMID: 29555994 [PubMed - as supplied by publisher]

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Combined application of tenuigenin and β-asarone improved the efficacy of memantine in treating moderate-to-severe Alzheimer's disease.

Drug Des Devel Ther. 2018;12:455-462

Authors: Chang W, Teng J

Abstract
Background: Alzheimer's disease (AD) is a slowly progressive neurodegenerative disease which cannot be cured at present. The aim of this study was to assess whether the combined application of β-asarone and tenuigenin could improve the efficacy of memantine in treating moderate-to-severe AD.
Patients and methods: One hundred and fifty-two patients with moderate-to-severe AD were recruited and assigned to two groups. Patients in the experiment group received β-asarone 10 mg/d, tenuigenin 10 mg/d, and memantine 5-20 mg/d. Patients in the control group only received memantine 5-20 mg/d. The Mini Mental State Examination (MMSE), Clinical Dementia Rating Scale (CDR), and Activities of Daily Living (ADL) were used to assess the therapeutic effects. The drug-related adverse events were used to assess the safety and acceptability. Treatment was continued for 12 weeks.
Results: After 12 weeks of treatment, the average MMSE scores, ADL scores, and CDR scores in the two groups were significantly improved. But, compared to the control group, the experimental group had a significantly higher average MMSE score (p<0.00001), lower average ADL score (p=0.00002), and lower average CDR score (p=0.030). Meanwhile, the rates of adverse events were similar between the two groups. Subgroup analysis indicated that the most likely candidates to benefit from this novel method might be the 60-74-years-old male patients with moderate AD.
Conclusion: These results demonstrated that the combined application of β-asarone and tenuigenin could improve the efficacy of memantine in treating moderate-to-severe AD. The clinical applicability of this novel method showed greater promise and should be further explored.

PMID: 29551889 [PubMed - in process]

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The SPOTS System: An Ocular Scoring System Optimized for Use in Modern Preclinical Drug Development and Toxicology.

J Ocul Pharmacol Ther. 2017 Dec;33(10):718-734

Authors: Eaton JS, Miller PE, Bentley E, Thomasy SM, Murphy CJ

Abstract
PURPOSE: To present a semiquantitative ocular scoring system comprising elements and criteria that address many of the limitations associated with systems commonly used in preclinical studies, providing enhanced cross-species applicability and predictive value in modern ocular drug and device development.
METHODS: Revisions to the ocular scoring systems of McDonald-Shadduck and Hackett-McDonald were conducted by board-certified veterinary ophthalmologists at Ocular Services On Demand (OSOD) over the execution of hundreds of in vivo preclinical ocular drug and device development studies and general toxicological investigations. This semiquantitative preclinical ocular toxicology scoring (SPOTS) system was driven by limitations of previously published systems identified by our group's recent review of slit lamp-based scoring systems in clinical ophthalmology, toxicology, and vision science.
RESULTS: The SPOTS system provides scoring criteria for the anterior segment, posterior segment, and characterization of intravitreal test articles. Key elements include: standardized slit lamp settings; expansion of criteria to enhance applicability to nonrabbit species; refinement and disambiguation of scoring criteria for corneal opacity, fluorescein staining severity, and aqueous flare; introduction of novel criteria for scoring of aqueous and anterior vitreous cell; and introduction of criteria for findings observed with drugs/devices targeting the posterior segment. A modified Standardization of Uveitis Nomenclature (SUN) system is also introduced to facilitate accurate use of SUN's criteria in laboratory species.
CONCLUSIONS: The SPOTS systems provide criteria that stand to enhance the applicability of semiquantitative scoring criteria to the full range of laboratory species, in the context of modern approaches to ocular therapeutics and drug delivery and drug and device development.

PMID: 29239680 [PubMed - indexed for MEDLINE]

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A single center, open label study of intradermal administration of an inactivated purified chick embryo cell culture rabies virus vaccine in adults.

Vaccine. 2017 Aug 03;35(34):4315-4320

Authors: Recuenco S, Warnock E, Osinubi MOV, Rupprecht CE

Abstract
In the USA, rabies vaccines (RVs) are licensed for intramuscular (IM) use only, although RVs are licensed for use by the intradermal (ID) route in many other countries. Recent limitations in supplies of RV in the USA reopened discussions on the more efficient use of available biologics, including utilization of more stringent risk assessments, and potential ID RV administration. A clinical trial was designed to compare the immunogenic and adverse effects of a purified chicken embryo cell (PCEC) RV administered ID or IM. Enrollment was designed in four arms, ID Pre-Exposure Prophylaxis (Pre-EP), IM Pre-EP, ID Booster, and IM Booster vaccination. Enrollment included 130 adult volunteers. The arms with IM administration received vaccine according to the current ACIP recommendations: Pre-EP, three 1mL (2.5 I.U.) RV doses, each on day 0, 7, and 21; or a routine Booster, one 1ml dose. The ID groups received the same schedule, but doses administered were in a volume of 0.1mL (0.25 I.U.). The rate of increase in rabies virus neutralizing antibody titers 14-21days after vaccination were similar in the ID and correspondent IM groups. The GMT values for ID vaccination were slightly lower than those for IM vaccination, for both naïve and booster groups, and these differences were statistically significant by t-test. Fourteen days after completing vaccination, all individuals developed RV neutralizing antibody titers over the minimum arbitrary value obtained with the rapid fluorescent focus inhibition test (RFFIT). Antibodies were over the set threshold until the end of the trial, 160days after completed vaccination. No serious adverse reactions were reported. Most frequent adverse reactions were erythema, induration and tenderness, localized at the site of injection. Multi use of 1mL rabies vaccine vials for ID doses of 0.1 was demonstrated to be both safe and inmunogenic.

PMID: 28688782 [PubMed - indexed for MEDLINE]