Understanding cancer lineage plasticity: reversing therapeutic resistance in metastatic prostate cancer.

Pharmacogenomics. 2017 05;18(7):597-600

Authors: Ellis L

PMID: 28468521 [PubMed - indexed for MEDLINE]

Transcriptomic analysis of longitudinal Burkholderia pseudomallei infecting the cystic fibrosis lung.

Microb Genom. 2018 Jul 10;:

Authors: Price EP, Viberg LT, Kidd TJ, Bell SC, Currie BJ, Sarovich DS

Abstract
The melioidosis bacterium, Burkholderia pseudomallei, is increasingly being recognised as a pathogen in patients with cystic fibrosis (CF). We have recently catalogued genome-wide variation of paired, isogenic B. pseudomallei isolates from seven Australasian CF cases, which were collected between 4 and 55 months apart. Here, we extend this investigation by documenting the transcriptomic changes in B. pseudomallei in five cases. Following growth in an artificial CF sputum medium, four of the five paired isolates exhibited significant differential gene expression (DE) that affected between 32 and 792 genes. The greatest number of DE events was observed between the strains from patient CF9, consistent with the hypermutator status of the latter strain, which is deficient in the DNA mismatch repair protein MutS. Two patient isolates harboured duplications that concomitantly increased expression of the β-lactamase-encoding gene penA, and a 35 kb deletion in another abolished expression of 29 genes. Convergent expression profiles in the chronically-adapted isolates identified two significantly downregulated and 17 significantly upregulated loci, including the resistance-nodulation-division (RND) efflux pump BpeEF-OprC, the quorum-sensing hhqABCDE operon, and a cyanide- and pyocyanin-insensitive cytochrome bd quinol oxidase. These convergent pathoadaptations lead to increased expression of pathways that may suppress competing bacterial and fungal pathogens, and that enhance survival in oxygen-restricted environments, the latter of which may render conventional antibiotics less effective in vivo. Treating chronically adapted B. pseudomallei infections with antibiotics designed to target anaerobic infections, such as the nitroimidazole class of antibiotics, may significantly improve pathogen eradication attempts by exploiting this Achilles heel.

PMID: 29989529 [PubMed - as supplied by publisher]

Killing Many Birds With Two Stones: Hypoxia and Fibrosis Can Generate Ectopic Beats in a Human Ventricular Model.

Front Physiol. 2018;9:764

Authors: Sachetto R, Alonso S, Dos Santos RW

Abstract
During cardiac diseases many types of anatomical and functional remodeling of cardiac tissue can occur. In this work, we focus on two conditions: hypoxia and fibrosis, which are part of complex pathological modifications that take place in many cardiac diseases (hypertrophic cardiomyopathy, hypertensive heart disease, and recurrent myocardial infarction) and respiratory diseases (obstructive pulmonary disease, obstructive sleep apnea, and cystic fibrosis). Using computational models of cardiac electrophysiology, we evaluate if the interplay between hypoxia and fibrosis is sufficient to trigger cardiac arrhythmia. We study the mechanisms behind the generation of ectopic beats, an arrhythmic trigger also known as premature ventricular contractions (PVCs), in regions with high hypoxia and fibrosis. First, we modify an electrophysiological model of myocytes of the human left ventricle to include the effects of hypoxia. Second, diffuse fibrosis is modeled by randomly replacing cardiac myocytes by non-excitable and non-conducting cells. The Monte Carlo method is used to evaluate the probability of a region to generate ectopic beats with respect to different levels of hypoxia and fibrosis. In addition, we evaluate the minimum size of three-dimensional slabs needed to sustain reentries for different stimulation protocols. The observed mechanism behind the initiation of ectopic beats is unidirectional block, giving rise to sustained micro-reentries inside the region with diffuse fibrosis and hypoxia. In summary, our results suggest that hypoxia and fibrosis are sufficient for the creation of a focal region in the heart that generates PVCs.

PMID: 29988469 [PubMed]

Air-Liquid Interface Culture of Human and Mouse Airway Epithelial Cells.

Methods Mol Biol. 2018;1809:91-109

Authors: Jiang D, Schaefer N, Chu HW

Abstract
Air-liquid interface culture enables airway epithelial cells to differentiate into a pseudostratified cell layer, consisting of ciliated cells, goblet/secretory cells, and basal cells (Ghio et al., Part Fibre Toxicol 10:25, 2013). This technique is critically important for in vitro studies of lung diseases such as asthma, chronic obstructive pulmonary disease, and cystic fibrosis, since differentiated airway epithelial cells are more representative of the in vivo lung environment than non-differentiated cells (Derichs et al., FASEB J 25:2325-2332, 2011; Hackett et al., Am J Respir Cell Mol Biol 45:1090-1100, 2011;Schneider et al., Am J Respir Crit Care Med 182: 332-340, 2010). Here we describe the process of isolating and expanding human and mouse airway epithelial cells, as well as differentiation of airway epithelial cells by air-liquid interface culture.

PMID: 29987785 [PubMed - in process]

Overall and differentiated sensory responses to cardiopulmonary exercise test in patients with cystic fibrosis: kinetics and ability to predict peak oxygen uptake.

Eur J Appl Physiol. 2018 Jul 09;:

Authors: Gruet M, Mely L, Vallier JM

Abstract
PURPOSE: We evaluated the validity of predicting peak oxygen uptake ([Formula: see text]O2peak) from submaximal ratings of perceived exertion (RPE) during incremental cardiopulmonary exercise test (CPET) in patients with cystic fibrosis (CF) and compared the predictive accuracy between overall and differentiated RPE scores.
METHODS: Thirty-five adults with CF (FEV1 = 58 ± 23%) performed a CPET on cycle ergometer with gas exchange measurements. Leg, chest and overall RPE were collected every minute throughout the test. Linear regressions between [Formula: see text]O2 and RPE ≤ 15 were extrapolated to maximal theoretical RPE (i.e. RPE18 and RPE19) to predict [Formula: see text]O2peak. Agreements between measured and all predicted [Formula: see text]O2peak were tested using Bland-Altman Plots, for the whole group and for subjects presenting significant exercise intolerance (n = 24).
RESULTS: Leg, chest and overall RPE increased similarly with exercise intensity. No differences were found between predicted [Formula: see text]O2peak and measured [Formula: see text]O2peak with RPE18 as maximal RPE, for both overall and differentiated RPE (P range 0.94-0.98). Ranges for Pearson correlations and limits of agreements were 0.88-0.91 and 380-461 mL min-1 for the whole group and 0.92-0.94 and 269-365 mL min-1 for subjects with significant exercise intolerance. The greatest association and narrowest limits of agreements were obtained from chest RPE scores.
CONCLUSIONS: Submaximal RPE scores obtained during CPET can provide acceptable estimate of [Formula: see text]O2peak in adults with CF, particularly in those having significant exercise intolerance. Future studies should assess whether the prediction can be improved, particularly by encouraging the regular use of RPE scales during physical activities/exercise rehabilitations sessions.

PMID: 29987367 [PubMed - as supplied by publisher]

Silencing of the Hsp70-specific nucleotide-exchange factor BAG3 corrects the F508del-CFTR variant by restoring autophagy.

J Biol Chem. 2018 Jul 09;:

Authors: Hutt DM, Mishra SK, Roth DM, Larsen MB, Angles F, Frizzell RA, Balch WE

Abstract
The protein chaperones heat shock protein 70 (Hsp70) and Hsp90 are required for de novo folding of proteins and protect against misfolding-related cellular stresses by directing misfolded or slowly folding proteins to the ubiquitin/proteasome system (UPS) or autophagy/lysosomal degradation pathways. Here, we examined the role of the BCL2-associated athanogene (BAG) family of Hsp70-specific nucleotide-exchange factors in the biogenesis and functional correction of genetic variants of the cystic fibrosis transmembrane conductance regulator (CFTR) whose mutations cause cystic fibrosis (CF). We show that siRNA-mediated silencing of BAG1 and -3, two BAG members linked to the clearance of misfolded proteins via the UPS and autophagy pathways, respectively, leads to functional correction of F508del-CFTR and other disease-associated CFTR variants. BAG3 silencing was the most effective, leading to improved F508del-CFTR stability, trafficking, and restoration of cell-surface function, both alone and in combination with the FDA-approved CFTR corrector, VX-809. We also found that the BAG3 silencing-mediated correction of F508del-CFTR restores the autophagy pathway, which is defective in F508del-CFTR-expressing cells, likely because of the maladaptive stress response in CF pathophysiology. These results highlight the potential therapeutic benefits of targeting the cellular chaperone system to improve the functional folding of CFTR variants contributing to CF and possibly other protein-misfolding-associated diseases.

PMID: 29986884 [PubMed - as supplied by publisher]

A Survey of the Common Mutations and IVS8-Tn Polymorphism of Cystic Fibrosis Transmembrane Conductance Regulator Gene in Infertile Men with Nonobstructive Azoospermia and CBAVD in Iranian Population

Iran Biomed J. 2018 Jul 10;

Authors: Asadi F, Mirfakhraie R, Mirzajani F, Khedri

Abstract
Background: Studies have revealed a strong association between mutations of CFTR gene and the congenital bilateral absence of the vas deferens (CBAVD), but the role of this gene in other types of male infertility is still unclear. The purpose of the this study was to investigate the frequency of the most common mutations of the CFTR gene (DF508, G542X, N1303K, G551D, and W1282X) in a population of infertile men with nonobstructive azoospermia (NOA) and CBAVD in Iran.
Methods: Blood samples were obtained from 50 NOA, 50 CBAVD, and 100 normal males (control). Genomic DNA was isolated from whole blood leukocytes, and the presence of common mutations of the CFTR gene was assessed by an amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). Restriction fragment length polymorphism (PCR-RFLP) was also used to analyze IVS8-Tn polymorphism.
Results: It was found that 16%, 8%, and 8% of patients with CBAVD were heterozygote for DF508, G542X, and N1303K, respectively. The frequency of the 5T allele was 34% and higher than the normal group (p < 0.001). None of the common CFTR gene mutations were detected in NOA patients, and no significant difference was found in the distribution of the 5T allele between the NOA patients and the control group (5 vs. 3 p = 0.721).
Conclusion: Based on the present case-control study, the CFTR gene mutations and IVS8-Tn polymorphisms are correlated with CBAVD; however, extensive investigations are necessary to determine the exact relationship between the gene mutations and other forms of male infertility.

PMID: 29986553 [PubMed - as supplied by publisher]

Expanding Phenotype of Nephronophthisis-Related Ciliopathy: an Elderly Patient with Homozygous RPGRIP1L Mutation.

Nephron. 2018 Jul 10;:1-5

Authors: Kawaguchi T, Yoshida T, Hirahashi J, Uehara T, Takenouchi T, Kosaki K, Itoh H, Hayashi M

Abstract
Nephronophthisis-related ciliopathies (NPHP-RC) are autosomal recessive disorders characterized by renal corticomedullary cysts with the extrarenal symptoms. Typically, patients with NPHP-RC reach end-stage kidney disease (ESKD) before the age of 30 years. We herein report a Japanese woman with NPHP-RC who had unusually delayed progression to ESKD after 6 decades. She exhibited liver dysfunction at the age of 23 years. She also showed mild renal dysfunction at the age of 43 years. Ultrasonography revealed bilateral multiple renal cysts with loss of corticomedullary differentiation. Her liver and renal functions gradually deteriorated. She was diagnosed with liver fibrosis as a result of biopsy, and initiated the maintenance hemodiafiltration therapy for ESKD at the age of 61 years. Because of a unique combination of multiple renal cysts and liver fibrosis, ciliopathy was suspected and medical exome analysis was performed. A novel homozygous missense mutation was identified in RPGRIP1L (c.1810G>A p.Glu604Lys), a causative gene for NPHP-RC. To the best of our knowledge, this patient is the oldest one who progressed to ESKD in NPHP-RC. Our case illustrates that NPHP-RC should be included in the differential diagnosis of the patient with corticomedullary polycystic kidneys accompanied by the extrarenal organ involvements, even if the patient is elderly.

PMID: 29991045 [PubMed - as supplied by publisher]

A novel SLC1A4 homozygous mutation causing congenital microcephaly, epileptic encephalopathy and spastic tetraparesis: a video-EEG and tractography - case study.

J Neurogenet. 2018 Jul 10;:1-6

Authors: Pironti E, Salpietro V, Cucinotta F, Granata F, Mormina E, Efthymiou S, Scuderi C, Gagliano A, Houlden H, Di Rosa G

Abstract
Biallelic mutations in the SLC1A4 gene have been identified as a very rare cause of neurodevelopmental disorders. l-serine transport deficiency has been regarded as the causal molecular mechanism underlying the neurological phenotype of SLC1A4 mutation patients. To date this genetic condition has been reported almost exclusively in a limited number of Ashkenazi-Jewish individuals and as a result the SLC1A4 gene is not routinely included in the majority of the genetic diagnostic panels for neurological diseases. We hereby report a 7-year-old boy from a Southern Italian family, presenting with epileptic encephalopathy, congenital microcephaly, global developmental delay, severe hypotonia, spasticity predominant at the lower limbs, and thin corpus callosum. Whole exome sequencing identified a novel segregating SLC1A4 gene homozygous mutation (c.1141G > A: p.Gly381Arg) as the likely cause of the disease in our family. In order to deeply characterize the electro-clinical and neurological phenotype in our index patient, long-term systematic video-electroencephalograms (EEG) as well as repeated brain imaging studies (which included tractographic reconstructions) were performed on a regular basis during a 7 years follow-up time. In conclusion, we suggest to carefully considering SLC1A4 biallelic mutations in individuals presenting an early onset severe neurodevelopmental disorder with variable spasticity and seizures, regardless the patients' ethnic background.

PMID: 29989513 [PubMed - as supplied by publisher]

New generation sequencing of targeted genes in the classical and the variant form of hairy cell leukemia highlights mutations in epigenetic regulation genes.

Oncotarget. 2018 Jun 22;9(48):28866-28876

Authors: Maitre E, Bertrand P, Maingonnat C, Viailly PJ, Wiber M, Naguib D, Salaün V, Cornet E, Damaj G, Sola B, Jardin F, Troussard X

Abstract
Classical hairy cell leukemia (HCL-c) is a rare lymphoid neoplasm. BRAFV600E mutation, detected in more than 80% of the cases, is described as a driver mutation, but additional genetic abnormalities appear to be necessary for the disease progression. For cases of HCL-c harboring a wild-type BRAF gene, the differential diagnosis of the variant form of HCL (HCL-v) or splenic diffuse red pulp lymphoma (SDRPL) is complex. We selected a panel of 21 relevant genes based on a literature review of whole exome sequencing studies (BRAF, MAP2K1, DUSP2, MAPK15, ARID1A, ARID1B, EZH2, KDM6A, CREBBP, TP53, CDKN1B, XPO1, KLF2, CXCR4, NOTH1, NOTCH2, MYD88, ANXA1, U2AF1, BCOR, and ABCA8). We analyzed 20 HCL-c and 4 HCL-v patients. The analysis of diagnostic samples mutations in BRAF (n = 18), KLF2 (n = 4), MAP2K1 (n = 3), KDM6A (n = 2), CDKN1B (n = 2), ARID1A (n = 2), CREBBP (n = 2) NOTCH1 (n = 1) and ARID1B (n = 1). BRAFV600E was found in 90% (18/20) of HCL-c patients. In HCL-c patients with BRAFV600E , other mutations were found in 33% (6/18) of cases. All 4 HCL-v patients had mutations in epigenetic regulatory genes: KDM6A (n = 2), CREBBP (n = 1) or ARID1A (n = 1). The analysis of sequential samples (at diagnosis and relapse) from 5 patients (2 HCL-c and 3 HCL-v), showed the presence of 2 new subclonal mutations (BCORE1430X and XPO1E571K ) in one patient and variations of the mutated allele frequency in 2 other cases. In the HCL-v disease, we described new mutations targeting KDM6A that encode a lysine demethylase protein. This opens new perspectives for personalized medicine for this group of patients.

PMID: 29989027 [PubMed]

An Exome-wide Association Study for Type 2 Diabetes-Attributed End-Stage Kidney Disease in African Americans.

Kidney Int Rep. 2018 Jul;3(4):867-878

Authors: Guan M, Keaton JM, Dimitrov L, Hicks PJ, Xu J, Palmer ND, Wilson JG, Freedman BI, Bowden DW, Ng MCY

Abstract
Introduction: Compared with European Americans, African Americans (AAs) are at higher risk for developing end-stage kidney disease (ESKD). Genome-wide association studies (GWAS) have identified >70 genetic variants associated with kidney function and chronic kidney disease (CKD) in patients with and without diabetes. However, these variants explain a small proportion of disease liability. This study examined the contribution of coding genetic variants for risk of type 2 diabetes (T2D)-attributed ESKD and advanced CKD in AAs.
Methods: Exome sequencing was performed in 456 AA T2D-ESKD cases, and 936 AA nondiabetic, non-nephropathy control individuals at the discovery stage. A mixed logistic regression model was used for association analysis. Nominal associations (P < 0.05) were replicated in an additional 2020 T2D-ESKD cases and 1121 nondiabetic, non-nephropathy control individuals. A meta-analysis combining 4533 discovery and replication samples was performed. Putative T2D-ESKD associations were tested in additional 1910 nondiabetic ESKD and 219 T2D-ESKD cases, as well as 912 AA nondiabetic non-nephropathy control individuals.
Results: A total of 11 suggestive T2D-ESKD associations (P < 1 x 10-4) from 8 loci (PLEKHN1, NADK, RAD51AP2, RREB1, PEX6, GRM8, PRX, APOL1) were apparent in the meta-analysis. Exclusion of APOL1 renal-risk genotype carriers identified 3 additional suggestive loci (OTUD7B, IFITM3, DLGAP5). Rs41302867 in RREB1 displayed consistent association with T2D-ESKD and nondiabetic ESKD (odds ratio: 0.47; P = 1.2 x 10-6 in 4605 all-cause ESKD and 2969 nondiabetic non-nephropathy control individuals).
Conclusion: Our findings suggest that coding genetic variants are implicated in predisposition to T2D-ESKD in AAs.

PMID: 29989002 [PubMed]

Novel ETFDH mutations in four cases of riboflavin responsive multiple acyl-CoA dehydrogenase deficiency.

Mol Genet Metab Rep. 2018 Sep;16:15-19

Authors: Fan X, Xie B, Zou J, Luo J, Qin Z, D'Gama AM, Shi J, Yi S, Yang Q, Wang J, Luo S, Chen S, Agrawal PB, Li Q, Shen Y

Abstract
Multiple acyl-CoA dehydrogenase deficiency (MADD) is an autosomal recessive disorder of fatty acid, amino acid, and choline metabolism caused by mutations in EFTA, EFTB, or ETFDH. Many MADD patients are responsive to treatment with riboflavin, termed riboflavin-responsive MADD (RR-MADD). Here, we report three novel mutations and one previously reported mutation in ETFDH in four RR-MADD patients who presented at various ages, and characterize the corresponding changes in ETF-QO protein structure. Clinicians should consider MADD in the differential diagnosis when patients present with muscle weakness and biochemical abnormalities. Gene testing plays a critical role in confirming the diagnosis of MADD, and may not only prevent patients from invasive testing, but also allow timely initiation of riboflavin treatment. The novel variants in ETFDH and the corresponding clinical features reported here enrich the allelic heterogeneity of RR-MADD and provide insight into genotype-phenotype relationships.

PMID: 29988809 [PubMed]

A rare loss-of-function variant of ADAM17 is associated with late-onset familial Alzheimer disease.

Mol Psychiatry. 2018 Jul 09;:

Authors: Hartl D, May P, Gu W, Mayhaus M, Pichler S, Spaniol C, Glaab E, Bobbili DR, Antony P, Koegelsberger S, Kurz A, Grimmer T, Morgan K, Vardarajan BN, Reitz C, Hardy J, Bras J, Guerreiro R, Balling R, Schneider JG, Riemenschneider M, AESG

Abstract
Common variants of about 20 genes contributing to AD risk have so far been identified through genome-wide association studies (GWAS). However, there is still a large proportion of heritability that might be explained by rare but functionally important variants. One of the so far identified genes with rare AD causing variants is ADAM10. Using whole-genome sequencing we now identified a single rare nonsynonymous variant (SNV) rs142946965 [p.R215I] in ADAM17 co-segregating with an autosomal-dominant pattern of late-onset AD in one family. Subsequent genotyping and analysis of available whole-exome sequencing data of additional case/control samples from Germany, UK, and USA identified five variant carriers among AD patients only. The mutation inhibits pro-protein cleavage and the formation of the active enzyme, thus leading to loss-of-function of ADAM17 alpha-secretase. Further, we identified a strong negative correlation between ADAM17 and APP gene expression in human brain and present in vitro evidence that ADAM17 negatively controls the expression of APP. As a consequence, p.R215I mutation of ADAM17 leads to elevated Aß formation in vitro. Together our data supports a causative association of the identified ADAM17 variant in the pathogenesis of AD.

PMID: 29988083 [PubMed - as supplied by publisher]

Clonal Hematopoiesis: Somatic Mutations in Blood Cells and Atherosclerosis.

Circ Genom Precis Med. 2018 Jul;11(7):e001926

Authors: Natarajan P, Jaiswal S, Kathiresan S

Abstract
The most important prognostic factor for atherosclerotic cardiovascular disease is age, independent of all other recognized risk factors. Recently, exome sequence analyses showed that somatic mutations in blood cells, a process termed clonal hematopoiesis, are common and increase in prevalence with age, with at least 1 in 10 adults older than 70 years affected. Carriers of clonal hematopoiesis have been shown to be not only at heightened risk for hematologic malignancy but also at increased risk for atherosclerotic cardiovascular disease. Here, we review the prior literature of clonal selection and expansion of hematopoietic stem cells and the evidence supporting its causal association with atherosclerotic cardiovascular disease.

PMID: 29987111 [PubMed - in process]

Comprehensive genomic diagnosis of non-syndromic and syndromic hereditary hearing loss in Spanish patients.

BMC Med Genomics. 2018 Jul 09;11(1):58

Authors: Cabanillas R, Diñeiro M, Cifuentes GA, Castillo D, Pruneda PC, Álvarez R, Sánchez-Durán N, Capín R, Plasencia A, Viejo-Díaz M, García-González N, Hernando I, Llorente JL, Repáraz-Andrade A, Torreira-Banzas C, Rosell J, Govea N, Gómez-Martínez JR, Núñez-Batalla F, Garrote JA, Mazón-Gutiérrez Á, Costales M, Isidoro-García M, García-Berrocal B, Ordóñez GR, Cadiñanos J

Abstract
BACKGROUND: Sensorineural hearing loss (SNHL) is the most common sensory impairment. Comprehensive next-generation sequencing (NGS) has become the standard for the etiological diagnosis of early-onset SNHL. However, accurate selection of target genomic regions (gene panel/exome/genome), analytical performance and variant interpretation remain relevant difficulties for its clinical implementation.
METHODS: We developed a novel NGS panel with 199 genes associated with non-syndromic and/or syndromic SNHL. We evaluated the analytical sensitivity and specificity of the panel on 1624 known single nucleotide variants (SNVs) and indels on a mixture of genomic DNA from 10 previously characterized lymphoblastoid cell lines, and analyzed 50 Spanish patients with presumed hereditary SNHL not caused by GJB2/GJB6, OTOF nor MT-RNR1 mutations.
RESULTS: The analytical sensitivity of the test to detect SNVs and indels on the DNA mixture from the cell lines was > 99.5%, with a specificity > 99.9%. The diagnostic yield on the SNHL patients was 42% (21/50): 47.6% (10/21) with autosomal recessive inheritance pattern (BSND, CDH23, MYO15A, STRC [n = 2], USH2A [n = 3], RDX, SLC26A4); 38.1% (8/21) autosomal dominant (ACTG1 [n = 3; 2 de novo], CHD7, GATA3 [de novo], MITF, P2RX2, SOX10), and 14.3% (3/21) X-linked (COL4A5 [de novo], POU3F4, PRPS1). 46.9% of causative variants (15/32) were not in the databases. 28.6% of genetically diagnosed cases (6/21) had previously undetected syndromes (Barakat, Usher type 2A [n = 3] and Waardenburg [n = 2]). 19% of genetic diagnoses (4/21) were attributable to large deletions/duplications (STRC deletion [n = 2]; partial CDH23 duplication; RDX exon 2 deletion).
CONCLUSIONS: In the era of precision medicine, obtaining an etiologic diagnosis of SNHL is imperative. Here, we contribute to show that, with the right methodology, NGS can be transferred to the clinical practice, boosting the yield of SNHL genetic diagnosis to 50-60% (including GJB2/GJB6 alterations), improving diagnostic/prognostic accuracy, refining genetic and reproductive counseling and revealing clinically relevant undiagnosed syndromes.

PMID: 29986705 [PubMed - in process]

The BabySeq project: implementing genomic sequencing in newborns.

BMC Pediatr. 2018 Jul 09;18(1):225

Authors: Holm IA, Agrawal PB, Ceyhan-Birsoy O, Christensen KD, Fayer S, Frankel LA, Genetti CA, Krier JB, LaMay RC, Levy HL, McGuire AL, Parad RB, Park PJ, Pereira S, Rehm HL, Schwartz TS, Waisbren SE, Yu TW, BabySeq Project Team, Green RC, Beggs AH

Abstract
BACKGROUND: The greatest opportunity for lifelong impact of genomic sequencing is during the newborn period. The "BabySeq Project" is a randomized trial that explores the medical, behavioral, and economic impacts of integrating genomic sequencing into the care of healthy and sick newborns.
METHODS: Families of newborns are enrolled from Boston Children's Hospital and Brigham and Women's Hospital nurseries, and half are randomized to receive genomic sequencing and a report that includes monogenic disease variants, recessive carrier variants for childhood onset or actionable disorders, and pharmacogenomic variants. All families participate in a disclosure session, which includes the return of results for those in the sequencing arm. Outcomes are collected through review of medical records and surveys of parents and health care providers and include the rationale for choice of genes and variants to report; what genomic data adds to the medical management of sick and healthy babies; and the medical, behavioral, and economic impacts of integrating genomic sequencing into the care of healthy and sick newborns.
DISCUSSION: The BabySeq Project will provide empirical data about the risks, benefits and costs of newborn genomic sequencing and will inform policy decisions related to universal genomic screening of newborns.
TRIAL REGISTRATION: The study is registered in ClinicalTrials.gov Identifier: NCT02422511 . Registration date: 10 April 2015.

PMID: 29986673 [PubMed - in process]

Multi-modality analysis supports APOBEC as a major source of mutations in head and neck squamous cell carcinoma.

Oral Oncol. 2017 Nov;74:8-14

Authors: Faden DL, Thomas S, Cantalupo PG, Agrawal N, Myers J, DeRisi J

Abstract
OBJECTIVES: The mutagenic processes underlying head and neck squamous cell carcinoma (HNSCC) are poorly understood. Pan-cancer mutational signature analyses have identified a signature for APOBEC, a cytosine deaminase, in a subset of cancers, including HNSCC. The role of APOBEC activity in HNSCC remains poorly understood. Therefore, we sought to determine the role of APOBEC in HNSCC pathogenesis.
MATERIAL AND METHODS: Utilizing bioinformatic approaches we explored the role of APOBEC mediated mutations in tumor exomes, transcriptomes and germline exomes from 511HNSCC patients in the TCGA.
RESULTS: 58% of HNSCC were statistically enriched for the APOBEC signature. APOBEC3A expression had the highest correlation coefficient with APOBEC mutation rate. Gene specific motif analysis revealed a slight predominance of APOBEC3A mutations. Canonical pathway analysis demonstrated immune pathway upregulation in APOBEC mutation rich samples. Overall mutational burden was positively correlated with APOBEC enrichment.
CONCLUSIONS: APOBEC mediated mutations are highly prevalent in HNSCC. APOBEC3A is the most likely gene to be active in HPV+ HNSCC. APOBEC activity correlates with upregulation of immune signaling pathways, supporting the hypothesis that APOBEC activity could be activated as part of the innate immune response.

PMID: 29103756 [PubMed - indexed for MEDLINE]

Possible associations of personality traits representing harm avoidance and self-directedness with medication adherence in Japanese patients with type 2 diabetes.

J Pharm Health Care Sci. 2018;4:16

Authors: Tominaga Y, Aomori T, Hayakawa T, Kijima N, Morisky DE, Takahashi K, Mochizuki M

Abstract
Background: Insufficient medication adherence in diabetes patients, of which numbers continue to increase globally, remains a critical issue. Medication adherence is multifactorial and determined by interactions among factors including socioeconomic status, health care team and system, condition, therapy, and patient-specific factors. On the other hand, personality traits have been studied in adherence other than to medication. Using the instruments of Temperament and Character Inventory (TCI), Harm Avoidance (TCI-HA) and Self-directedness (TCI-SD) showed distinguishing associations with adherence of health-related programs. However, few studies have been performed to elucidate psychometric properties related to medication adherence. We investigated how TCI-HA and TCI-SD of patients with diabetes are related to medication adherence.
Method: A cross-sectional survey was conducted among type 2 diabetes patients recruited at medical institutions or via an online research company. Medication adherence was measured using the 8-item Morisky Medication Adherence Scale (MMAS-8). Personality traits were assessed using the established scales of TCI-HA and TCI-SD. Univariate and multivariate regression analyses of the MMAS-8 scores were performed in addition to assessing demographic and disease characteristics and TCI-HA and TCI-SD.
Results: A total of 358 responses were analyzed. Multivariate regression analysis of MMAS-8 scores revealed that higher TCI-SD was related to better adherence and experiencing drug-related side effects was related to poor adherence. Aging was significantly associated with better medication adherence in univariate regression analysis but became insignificant in multivariate regression.
Conclusions: In diabetes patients, the anxiety reflected in TCI-HA tends to lower and the self-control reflected in TCI-SD tends to promote medication adherence. TCI-SD has a greater effect than TCI-HA.

PMID: 29988655 [PubMed]

A phase I study of panobinostat in pediatric patients with refractory solid tumors, including CNS tumors.

Cancer Chemother Pharmacol. 2018 Jul 09;:

Authors: Wood PJ, Strong R, McArthur GA, Michael M, Algar E, Muscat A, Rigby L, Ferguson M, Ashley DM

Abstract
PURPOSE: This was an open label, phase I (3 + 3 design), multi-centre study evaluating panobinostat in pediatric patients with refractory solid tumors.
METHODS: Primary endpoints were to establish MTD, define and describe associated toxicities, including dose limiting toxicities (DLT) and to characterize its pharmacokinetics (PK). Secondary endpoints included assessing the anti-tumour activity of panobinostat, and its biologic activity, by measuring acetylation of histones in peripheral blood mononuclear cells.
RESULTS: Nine patients were enrolled and treated with intravenous panobinostat at a dosing level of 15 mg/m2 which was tolerated. Six were evaluable for adverse events. Two (33%) patients experienced Grade 3-4 thrombocytopenia, 1 (17%) experienced Grade 3 anemia, and 2 (33%) experienced Grade 3 neutropenia. Grade 4 drug related pain occurred in 2 (33%) of the patients studied. Two (33%) patients experienced a Grade 2 QTcF change (0.478 ± 0.006 ms). One cardiac DLT (T wave changes) was reported. PK values for 15 mg/m2 (n = 9) dosing were: Tmax 0.8 h, Cmax 235.2 ng/mL, AUC0-t 346.8 h ng/mL and t1/2 7.3 h. Panobinostat significantly induced acetylation of histone H3 and H4 at all time points measured when compared to pre-treatment samples (p < 0.05). Pooled quantitative Western blot data confirmed that panobinostat significantly induced acetylation of histone H4 at 6 h (p < 0.01), 24 h (p < 0.01) and 28-70 h (p < 0.01) post dose.
CONCLUSION: A significant biological effect of panobinostat, measured by acetylation status of histone H3 and H4, was achieved at a dose of 15 mg/m2. PK data and drug tolerability at 15 mg/m2 was similar to that previously published.

PMID: 29987369 [PubMed - as supplied by publisher]

Malaria Prophylaxis Using Naphthoquine-Azithromycin Combination: Randomized, Double-Blind, Placebo-Controlled Studies to Assess Safety and Protective Efficacy in Southeast Asia.

Antimicrob Agents Chemother. 2018 Jul 09;:

Authors: Yang H, Wang J, Liu H, Li X, Nie R, Li C, Wang H, Wang Q, Cao Y, Cui L

Abstract
New prophylactic drugs against malaria infections are urgently needed. We conducted randomized, double-blind, placebo-controlled, phase 2 trials of a new antimalarial drug combination, naphthoquine-azithromycin (NQAZ), to determine its safety and protective efficacy in a low-endemicity area of Southeast Asia. In the first trial, 127 healthy volunteers were randomized to receive two single-doses of either 400 mg of NQAZ (200 mg of each drug), 800 mg of NQAZ (400 mg of each drug), or placebo on day 0 and day 30. Weekly follow-ups were performed for two months, and physical and clinical laboratory exams were done during the second and eighth week. Both drug regimens were well tolerated without any serious adverse events. Four adverse events (transient and slight elevation of serum transaminase concentrations) were found only in the two drug-treated groups and thus might be drug-related. In the second trial, 353 volunteer villagers were randomized into the same three groups as in the first trial, and malaria infections were followed for a month. For the intention-to-treat analysis, both regimens offered greater than 90% prophylactic efficacies against all malaria infections. When the analysis was done according to parasite species, 400 mg and 800 mg NQAZ provided 81.63 and 90.59% prophylactic efficacies, respectively, against Plasmodium falciparum infections, whereas both offered 100% prophylactic efficacy against Plasmodium vivax and Plasmodium ovale These trials showed that NQAZ had a good safety profile and monthly single doses of 400 mg or 800 mg for adults offered excellent prophylaxis against malaria infections, especially the two relapsing species.

PMID: 29987144 [PubMed - as supplied by publisher]