Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy

In digenic inheritance, pathogenic variants in two genes must be inherited together to cause disease. Only very few examples of digenic inheritance have been described in the neuromuscular disease field. Here we show that predicted deleterious variants in SRPK3, encoding the X-linked serine/argenine protein kinase 3, lead to a progressive early onset skeletal muscle myopathy only when in combination with heterozygous variants in the TTN gene. The co-occurrence of predicted deleterious SRPK3/TTN variants was not seen among 76,702 healthy male individuals, and statistical modeling strongly supported digenic inheritance as the best-fitting model. Furthermore, double-mutant zebrafish (srpk3-/-; ttn.1+/-) replicated the myopathic phenotype and showed myofibrillar disorganization. Transcriptome data suggest that the interaction of srpk3 and ttn.1 in zebrafish occurs at a post-transcriptional level. We propose that digenic inheritance of deleterious changes impacting both the protein kinase SRPK3 and the giant muscle protein titin causes a skeletal myopathy and might serve as a model for other genetic diseases.

Transcriptional profiling of zebrafish identifies host factors controlling susceptibility to Shigella flexneri

Shigella flexneri is a human-adapted pathovar of Escherichia coli that can invade the intestinal epithelium, causing inflammation and bacillary dysentery. Although an important human pathogen, the host response to S. flexneri has not been fully described. Zebrafish larvae represent a valuable model for studying human infections in vivo. Here, we use a Shigella-zebrafish infection model to generate mRNA expression profiles of host response to Shigella infection at the whole-animal level. Immune response-related processes dominate the signature of early Shigella infection (6 h post-infection). Consistent with its clearance from the host, the signature of late Shigella infection (24 h post-infection) is significantly changed, and only a small set of immune-related genes remain differentially expressed, including acod1 and gpr84. Using mutant lines generated by ENU, CRISPR mutagenesis and F0 crispants, we show that acod1- and gpr84-deficient larvae are more susceptible to Shigella infection. Together, these results highlight the power of zebrafish to model infection by bacterial pathogens and reveal the mRNA expression of the early (acutely infected) and late (clearing) host response to Shigella infection.

Bilateral adrenal haemorrhage in antiphospholipid syndrome and a short review of the literature

Antiphospholipid syndrome (APS) is an uncommon autoantibody-mediated condition characterised by acquired thrombophilia resulting in recurrent arterial and venous thrombosis. An inciting factor allows for the exposure of endothelial phospholipids, causing antigen formation and subsequent creation of antibodies. A woman in her 70s presented after vehicular trauma, suffering broken ribs, pneumothorax and incidentally discovered left adrenal haemorrhage. Two weeks later she presented with acute-onset abdominal pain and was found to have a right adrenal gland haemorrhage on CT imaging without interval trauma occurring. The patient had antiphospholipid antibody laboratory studies drawn and was given intravenous heparin with a bridge to warfarin at discharge. Laboratory results returned positive for lupus anticoagulant, beta-2 glycoprotein and anticardiolipin antibodies indicating triple positivity, with repeated laboratory tests positive in 12 weeks' time, confirming the diagnosis. Bilateral adrenal haemorrhage, rather than traditional venous thromboembolism, was the presenting pathology in this patient's diagnosis of APS.

Efficacy and dose-response relationship of oral treprostinil in PAH patients on monotherapy or dual background therapy

Background

FREEDOM-C and FREEDOM-C2 were randomized, placebo-controlled, double-blinded international, multicenter studies investigating the use of oral treprostinil (TRE) in subjects on mono or dual background pulmonary arterial hypertension (PAH) therapies. Both had a primary endpoint of change in 6-minute walk distance (6MWD) at Week 16 vs baseline. Previous post-hoc analyses combining mono and dual therapy subjects (PDE-5i and/or ERA) from these studies revealed a TRE dose-dependent increase in 6MWD. (1. White & Rao, 2016)

Purpose

This post-hoc analysis was performed to determine if subjects from FREEDOM-C and FREEDOM-C2 derive improvements in 6MWD with increasing doses of TRE when stratified by mono or dual background therapy and to determine if PAH background therapies (mono or dual) impacted 6MWD.

Methods

All active subjects (n=331) from FREEDOM-C and FREEDOM-C2 were grouped into TRE dose tertiles (low-dose: ≤2 mg BID, mid-dose: >2 mg to ≤3.5 mg BID, and high-dose: >3.5 mg BID). Placebo subjects (n=329) were in a separate 0 mg dose group. No data imputation was implemented.

Comparisons of 6MWD change at Weeks 4, 8, 12, and 16 between mono and dual therapy subgroups at any dose group were performed using a two-sample t-test or nonparametric Wilcoxon rank-sum test. The nonparametric Kruskal-Wallis test was conducted with subsequent pairwise comparisons of 6MWD change at Week 16 between the four dose groups through Dunn's approach. Additionally, the Jonckheere-Terpstra test was used to assess the linear trend for 6MWD improvement with higher doses of TRE.

Results

Baseline characteristics of the combined intention to treat (ITT) population and summary of 6MWD for subjects with both baseline and Week 16 data are in Table 1. 6MWD change improved steadily to Week 16 in subjects at higher TRE doses, regardless of the number of PAH background therapies (Figure 1). No statistical differences were found between mono and dual therapy at any time point or for any dose group. At Week 16, there was a significant difference in 6MWD change between the placebo group and high dose group within both mono and dual background therapy subjects. The difference between the low- and high-dose groups was significant for subjects on dual background therapy. There was a significant positive linear trend for TRE doses in 6MWD improvement at Week 16 for both monotherapy subjects (one-sided p-value = 0.0002) and dual therapy subjects (one-sided p-value = 0.0242).

Conclusions

6MWD improved in PAH patients regardless of their background therapy (monotherapy or dual background) and derive greater 6MWD improvements with higher doses of TRE. The observed dose-dependent 6MWD increase supports the use of TRE in sequential combination with background therapies (mono or dual).

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): United Therapeutics Corporation

Loss of slc39a14 causes simultaneous manganese hypersensitivity and deficiency in zebrafish

Manganese neurotoxicity is a hallmark of hypermanganesemia with dystonia 2, an inherited manganese transporter defect caused by mutations in SLC39A14. To identify novel potential targets of manganese neurotoxicity, we performed transcriptome analysis of slc39a14-/- mutant zebrafish that were exposed to MnCl2. Differentially expressed genes mapped to the central nervous system and eye, and pathway analysis suggested that Ca2+ dyshomeostasis and activation of the unfolded protein response are key features of manganese neurotoxicity. Consistent with this interpretation, MnCl2 exposure led to decreased whole-animal Ca2+ levels, locomotor defects and changes in neuronal activity within the telencephalon and optic tectum. In accordance with reduced tectal activity, slc39a14-/- zebrafish showed changes in visual phototransduction gene expression, absence of visual background adaptation and a diminished optokinetic reflex. Finally, numerous differentially expressed genes in mutant larvae normalised upon MnCl2 treatment indicating that, in addition to neurotoxicity, manganese deficiency is present either subcellularly or in specific cells or tissues. Overall, we assembled a comprehensive set of genes that mediate manganese-systemic responses and found a highly correlated and modulated network associated with Ca2+ dyshomeostasis and cellular stress. This article has an associated First Person interview with the first author of the paper.

Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants

In model organisms, RNA-sequencing (RNA-seq) is frequently used to assess the effect of genetic mutations on cellular and developmental processes. Typically, animals heterozygous for a mutation are crossed to produce offspring with different genotypes. Resultant embryos are grouped by genotype to compare homozygous mutant embryos to heterozygous and wild-type siblings. Genes that are differentially expressed between the groups are assumed to reveal insights into the pathways affected by the mutation. Here we show that in zebrafish, differentially expressed genes are often over-represented on the same chromosome as the mutation due to different levels of expression of alleles from different genetic backgrounds. Using an incross of haplotype-resolved wild-type fish, we found evidence of widespread allele-specific expression, which appears as differential expression when comparing embryos homozygous for a region of the genome to their siblings. When analysing mutant transcriptomes, this means that the differential expression of genes on the same chromosome as a mutation of interest may not be caused by that mutation. Typically, the genomic location of a differentially expressed gene is not considered when interpreting its importance with respect to the phenotype. This could lead to pathways being erroneously implicated or overlooked due to the noise of spurious differentially expressed genes on the same chromosome as the mutation. These observations have implications for the interpretation of RNA-seq experiments involving outbred animals and non-inbred model organisms.

Behavioral and Gene Regulatory Responses to Developmental Drug Exposures in Zebrafish

Developmental consequences of prenatal drug exposure have been reported in many human cohorts and animal studies. The long-lasting impact on the offspring-including motor and cognitive impairments, cranial and cardiac anomalies and increased prevalence of ADHD-is a socioeconomic burden worldwide. Identifying the molecular changes leading to developmental consequences could help ameliorate the deficits and limit the impact. In this study, we have used zebrafish, a well-established behavioral and genetic model with conserved drug response and reward pathways, to identify changes in behavior and cellular pathways in response to developmental exposure to amphetamine, nicotine or oxycodone. In the presence of the drug, exposed animals showed altered behavior, consistent with effects seen in mammalian systems, including impaired locomotion and altered habituation to acoustic startle. Differences in responses seen following acute and chronic exposure suggest adaptation to the presence of the drug. Transcriptomic analysis of exposed larvae revealed differential expression of numerous genes and alterations in many pathways, including those related to cell death, immunity and circadian rhythm regulation. Differential expression of circadian rhythm genes did not correlate with behavioral changes in the larvae, however, two of the circadian genes, arntl2 and per2, were also differentially expressed at later stages of development, suggesting a long-lasting impact of developmental exposures on circadian gene expression. The immediate-early genes, egr1, egr4, fosab, and junbb, which are associated with synaptic plasticity, were downregulated by all three drugs and in situ hybridization showed that the expression for all four genes was reduced across all neuroanatomical regions, including brain regions implicated in reward processing, addiction and other psychiatric conditions. We anticipate that these early changes in gene expression in response to drug exposure are likely to contribute to the consequences of prenatal exposure and their discovery might pave the way to therapeutic intervention to ameliorate the long-lasting deficits.

Total Nucleic Acid Extraction from Single Zebrafish Embryos for Genotyping and RNA-seq

RNA sequencing allows for the quantification of the transcriptome of embryos to investigate transcriptional responses to various perturbations (e.g., mutations, infections, drug treatments). Previous protocols either lack the option to genotype individual samples, or are laborious and therefore difficult to do at a large scale. We have developed a protocol to extract total nucleic acid from individual zebrafish embryos. Individual embryos are lysed in 96-well plates and nucleic acid is extracted using SPRI beads. The total nucleic acid can be genotyped and then DNase I treated to produce RNA samples for sequencing. This protocol allows for processing large numbers of individual samples, with the ability to genotype each sample, which makes it possible to undertake transcriptomic analysis on mutants at timepoints before the phenotype is visible. Graphic abstract: Extraction of total nucleic acid from individual zebrafish embryos for genotyping and RNA-seq.

A point mutation decouples the lipid transfer activities of microsomal triglyceride transfer protein

Apolipoprotein B-containing lipoproteins (B-lps) are essential for the transport of hydrophobic dietary and endogenous lipids through the circulation in vertebrates. Zebrafish embryos produce large numbers of B-lps in the yolk syncytial layer (YSL) to move lipids from yolk to growing tissues. Disruptions in B-lp production perturb yolk morphology, readily allowing for visual identification of mutants with altered B-lp metabolism. Here we report the discovery of a missense mutation in microsomal triglyceride transfer protein (Mtp), a protein that is essential for B-lp production. This mutation of a conserved glycine residue to valine (zebrafish G863V, human G865V) reduces B-lp production and results in yolk opacity due to aberrant accumulation of cytoplasmic lipid droplets in the YSL. However, this phenotype is milder than that of the previously reported L475P stalactite (stl) mutation. MTP transfers lipids, including triglycerides and phospholipids, to apolipoprotein B in the ER for B-lp assembly. In vitro lipid transfer assays reveal that while both MTP mutations eliminate triglyceride transfer activity, the G863V mutant protein unexpectedly retains ~80% of phospholipid transfer activity. This residual phospholipid transfer activity of the G863V mttp mutant protein is sufficient to support the secretion of small B-lps, which prevents intestinal fat malabsorption and growth defects observed in the mttpstl/stl mutant zebrafish. Modeling based on the recent crystal structure of the heterodimeric human MTP complex suggests the G865V mutation may block triglyceride entry into the lipid-binding cavity. Together, these data argue that selective inhibition of MTP triglyceride transfer activity may be a feasible therapeutic approach to treat dyslipidemia and provide structural insight for drug design. These data also highlight the power of yolk transport studies to identify proteins critical for B-lp biology.

Predictors of chemotherapy and its effects in early stage squamous cell carcinoma of the larynx

BACKGROUND

Squamous cell carcinoma (SCC) of larynx is a common head and neck cancer. For cases that are node negative, the role of definitive concurrent chemoradiation is unclear and not supported by guidelines but used at provider discretion. To address this knowledge gap, we examined the oncological outcomes with additional chemotherapy and factors correlated with the chemotherapy administration.

METHODS

We queried the National Cancer Database for patients with early stage (T2N0M0) laryngeal SCC treated nonsurgically. Multivariable logistic regression identified predictors of chemotherapy. Multivariable Cox regression evaluated predictors of survival. Propensity matching accounted for indication biases.

RESULTS

We identified 7181 patients meeting the eligibility criteria, of which 1568 (22%) patients received chemotherapy in addition to radiation. Predictors of chemotherapy use included younger age, Caucasian race, more remote year of treatment, higher grade, sites other than glottis, treatment at a community cancer center, and use of intensity-modulated radiation therapy. Median overall survival was not significantly different in the two arms analyzed-65 months (95% confidence interval [CI] 60, 72months) with chemotherapy compared to 70 months without chemotherapy (95% CI 66, 75 months, P<.37). Predictors for survival on propensity-matched multivariable analysis were increased age, male sex, less education, lower income, higher comorbidity score, receipt of treatment at a community center, and nonglottic sites.

CONCLUSIONS

This study shows no clear survival benefit with chemotherapy in early stage disease. Although this implies that chemotherapy should not be routinely delivered, individualized judgment and prospective studies are recommended as the biology behind this interesting finding is undefined.

LEVEL OF EVIDENCE

2C (Outcomes Research).

Modular Methodology for Determination of Poly chlorinated Biphenyls in Soil as Aroclors and Individual Congeners

A comprehensive screening and confirmatory method was developed for monitoring polychlorinated biphenyls (PCBs), both as Aroclors and as individual congeners. This approach incorporates extraction, extract cleanup, and analysis modules designed to match cost, time, and data quality requirements. Soxhlet, sonication, supercritical fluid, and accelerated solvent extractions were evaluated. Carbon chromatographic cleanup procedures were used for separation of congeners on the basis of ortho substitutions, which permitted calculation of toxicity equivalents. Individual congener determinations, congener total histograms, and peak comparison techniques for Aroclor identification were elaborated by using high and low resolution mass spectrometricdata. A screening procedure based on immunoassay using the Ohmicron PCB RaPID AssayTM kit gave results comparable to those obtained by gas chromatography with electron capture detection in the range 0.40-230 ppm, when the appropriate Aroclor calibrator was used.

Common and distinct transcriptional signatures of mammalian embryonic lethality

The Deciphering the Mechanisms of Developmental Disorders programme has analysed the morphological and molecular phenotypes of embryonic and perinatal lethal mouse mutant lines in order to investigate the causes of embryonic lethality. Here we show that individual whole-embryo RNA-seq of 73 mouse mutant lines (>1000 transcriptomes) identifies transcriptional events underlying embryonic lethality and associates previously uncharacterised genes with specific pathways and tissues. For example, our data suggest that Hmgxb3 is involved in DNA-damage repair and cell-cycle regulation. Further, we separate embryonic delay signatures from mutant line-specific transcriptional changes by developing a baseline mRNA expression catalogue of wild-type mice during early embryogenesis (4-36 somites). Analysis of transcription outside coding sequence identifies deregulation of repetitive elements in Morc2a mutants and a gene involved in gene-specific splicing. Collectively, this work provides a large scale resource to further our understanding of early embryonic developmental disorders.

The gene regulatory basis of genetic compensation during neural crest induction

The neural crest (NC) is a vertebrate-specific cell type that contributes to a wide range of different tissues across all three germ layers. The gene regulatory network (GRN) responsible for the formation of neural crest is conserved across vertebrates. Central to the induction of the NC GRN are AP-2 and SoxE transcription factors. NC induction robustness is ensured through the ability of some of these transcription factors to compensate loss of function of gene family members. However the gene regulatory events underlying compensation are poorly understood. We have used gene knockout and RNA sequencing strategies to dissect NC induction and compensation in zebrafish. We genetically ablate the NC using double mutants of tfap2a;tfap2c or remove specific subsets of the NC with sox10 and mitfa knockouts and characterise genome-wide gene expression levels across multiple time points. We find that compensation through a single wild-type allele of tfap2c is capable of maintaining early NC induction and differentiation in the absence of tfap2a function, but many target genes have abnormal expression levels and therefore show sensitivity to the reduced tfap2 dosage. This separation of morphological and molecular phenotypes identifies a core set of genes required for early NC development. We also identify the 15 somites stage as the peak of the molecular phenotype which strongly diminishes at 24 hpf even as the morphological phenotype becomes more apparent. Using gene knockouts, we associate previously uncharacterised genes with pigment cell development and establish a role for maternal Hippo signalling in melanocyte differentiation. This work extends and refines the NC GRN while also uncovering the transcriptional basis of genetic compensation via paralogues.

Embryonic development is an intricate process that requires genes to be active at the right time and place. Organisms have evolved mechanisms that ensure faithful execution of developmental programmes even if genes fail to function. For example, in a process called genetic compensation, one or more genes become activated in response to loss of function of another. In this work we use the zebrafish model to investigate how two related genes, tfap2a and tfap2c, interact to ensure establishment of the neural crest, a vertebrate-specific cell type that contributes to many different tissues. Losing tfap2a activity causes mild morphological defects and losing tfap2c has no visible effect. Yet when both are inactive, embryos are severely abnormal due to lack of neural crest-derived tissues. Here we show that loss of tfap2a triggers upregulation of tfap2c which prevents the loss of neural crest tissue. However, the genes normally regulated by tfap2a respond differently to tfap2c allowing us to identify the first tier of the Ap2 network and new players in neural crest biology. Our work demonstrates that the expression signature of partial, but morphologically sufficient, genetic compensation provides an opportunity to dissect gene regulatory networks.

Anal adenocarcinoma: Treatment outcomes and trends in a rare disease entity

Importance

Primary Adenocarcinoma of the anus is a rare disease with a poor prognosis and thus tends to have a more aggressive treatment algorithm, typically involving a surgical approach. Prior to 2001, a few retrospective studies outlined improved outcomes with the incorporation of surgery with chemoradiation. However, since the publication of these studies, advancement in radiotherapy modalities and imaging have left the question of improved outcomes while reserving surgery for salvage.

Objective

We conducted this National Cancer Database (NCDB)‐driven retrospective study to analyze treatment trends and outcomes in the current time from 2004 to 2015 with respect to chemoradiation and surgery.

Design

Retrospective NCDB tumor registry data review—using propensity score‐adjusted multivariable analyses for survival.

Setting

Database review.

Participants

We selected for patients listed in the NCDB with AJCC stage 1‐3 anal adenocarcinoma diagnosed between 2004 and 2015 and selected out patients with undocumented/stage 4 disease, those with radiation outside the pelvis, not treated with systemic therapy and patients lost to follow‐up.

Exposure(s)

None.

Main outcomes and measures

Overall survival and use of surgery in the up‐front management of anal adenocarcinoma.

Results

Of the 1729 patients eligible in this study, 1028 were treated with surgery as up‐front management and 701 had definitive chemoradiation. Median overall survival for all patients was 55 months with a 5‐year survival rate of 55%. Patients treated without surgery had worse overall survival, median survival of 45 months compared to 87 months (P < 0.0001) with 5‐year survival rates of 42% and 55% in favor of incorporation of surgery. Analysis across patients treated with surgery alone, surgery followed by adjuvant chemoradiation, neoadjuvant chemoradiation followed by surgery, and chemoradiation alone had median survival rates of 78, 83, 92, and 46 months, respectively. Propensity score‐adjusted multivariable analysis identified older age, grade 3, high comorbidity score, and lack of surgery as predictive of worse outcome.

Conclusions and Relevance

The results of the NCDB analysis indicate improved overall survival with the incorporation of surgery into the initial management of anal adenocarcinoma when compared to chemoradiation alone, despite the omission of surgery in up to 50% of the cases logged. Our results corroborate earlier studies published prior to the year 2000 for surgery to be included in the definitive management of anal adenocarcinoma.

Trends in intensity-modulated radiation therapy use for rectal cancer in the neoadjuvant setting: a National Cancer Database analysis

PURPOSE

Traditionally, three-dimensional conformal radiation therapy (3D-CRT) is used for neoadjuvant chemoradiation in locally advanced rectal cancer. Intensity-modulated radiation therapy (IMRT) was later developed for more conformal dose distribution, with the potential for reduced toxicity across many disease sites. We sought to use the National Cancer Database (NCDB) to examine trends and predictors for IMRT use in rectal cancer.

MATERIALS AND METHODS

We queried the NCDB from 2004 to 2015 for patients with rectal adenocarcinoma treated with neoadjuvant concurrent chemoradiation to standard doses followed by surgical resection. Odds ratios were used to determine predictors of IMRT use. Univariable and multivariable Cox regressions were used to determine potential predictors of overall survival (OS). Propensity matching was used to account for any indication bias.

RESULTS

Among 21,490 eligible patients, 3,131 were treated with IMRT. IMRT use increased from 1% in 2004 to 22% in 2014. Predictors for IMRT use included increased N stage, higher comorbidity score, more recent year, treatment at an academic facility, increased income, and higher educational level. On propensity-adjusted, multivariable analysis, male gender, increased distance to facility, higher comorbidity score, IMRT technique, government insurance, African-American race, and non-metro location were predictive of worse OS. Of note, the complete response rate at time of surgery was 28% with non-IMRT and 21% with IMRT.

CONCLUSION

IMRT use has steadily increased in the treatment of rectal cancer, but still remains only a fraction of overall treatment technique, more often reserved for higher disease burden.

The age of heterozygous telomerase mutant parents influences the adult phenotype of their offspring irrespective of genotype in zebrafish

Background: Mutations in proteins involved in telomere maintenance lead to a range of human diseases, including dyskeratosis congenita, idiopathic pulmonary fibrosis and cancer. Telomerase functions to add telomeric repeats back onto the ends of chromosomes, however non-canonical roles of components of telomerase have recently been suggested.

Methods: Here we use a zebrafish telomerase mutant which harbours a nonsense mutation in tert to investigate the adult phenotypes of fish derived from heterozygous parents of different ages. Furthermore we use whole genome sequencing data to estimate average telomere lengths.

Results: We show that homozygous offspring from older heterozygotes exhibit signs of body wasting at a younger age than those of younger parents, and that offspring of older heterozygous parents weigh less irrespective of genotype. We also demonstrate that tert homozygous mutant fish have a male sex bias, and that clutches from older parents also have a male sex bias in the heterozygous and wild-type populations. Telomere length analysis reveals that the telomeres of younger heterozygous parents are shorter than those of older heterozygous parents.

Conclusions: These data indicate that the phenotypes observed in offspring from older parents cannot be explained by telomere length. Instead we propose that Tert functions outside of telomere length maintenance in an age-dependent manner to influence the adult phenotypes of the next generation.

A high-resolution mRNA expression time course of embryonic development in zebrafish

We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.

KDM2A integrates DNA and histone modification signals through a CXXC/PHD module and direct interaction with HP1

Functional genomic elements are marked by characteristic DNA and histone modification signatures. How combinatorial chromatin modification states are recognized by epigenetic reader proteins and how this is linked to their biological function is largely unknown. Here we provide a detailed molecular analysis of chromatin recognition by the lysine demethylase KDM2A. Using biochemical approaches we identify a nucleosome interaction module within KDM2A consisting of a CXXC type zinc finger, a PHD domain and a newly identified Heterochromatin Protein 1 (HP1) interaction motif that mediates direct binding between KDM2A and HP1. This nucleosome interaction module enables KDM2A to decode nucleosomal H3K9me3 modification in addition to CpG methylation signals. The multivalent engagement with DNA and HP1 results in a nucleosome binding circuit in which KDM2A can be recruited to H3K9me3-modified chromatin through HP1, and HP1 can be recruited to unmodified chromatin by KDM2A. A KDM2A mutant deficient in HP1-binding is inactive in an in vivo overexpression assay in zebrafish embryos demonstrating that the HP1 interaction is essential for KDM2A function. Our results reveal a complex regulation of chromatin binding for both KDM2A and HP1 that is modulated by DNA- and H3K9-methylation, and suggest a direct role for KDM2A in chromatin silencing.

The age of heterozygous telomerase mutant parents influences the adult phenotype of their offspring irrespective of genotype in zebrafish

Background: Mutations in proteins involved in telomere maintenance lead to a range of human diseases, including dyskeratosis congenita, idiopathic pulmonary fibrosis and cancer. Telomerase functions to add telomeric repeats back onto the ends of chromosomes, however non-canonical roles of components of telomerase have recently been suggested.Methods: Here we use a zebrafish telomerase mutant which harbours a nonsense mutation intertto investigate the adult phenotypes of fish derived from heterozygous parents of different ages. Furthermore we use whole genome sequencing data to estimate average telomere lengths.Results: We show that homozygous offspring from older heterozygotes exhibit signs of body wasting at a younger age than those of younger parents, and that offspring of older heterozygous parents weigh less irrespective of genotype. We also demonstrate thatterthomozygous mutant fish have a male sex bias, and that clutches from older parents also have a male sex bias in the heterozygous and wild-type populations. Telomere length analysis reveals that the telomeres of younger heterozygous parents are shorter than those of older heterozygous parents.Conclusions: These data indicate that the phenotypes observed in offspring from older parents cannot be explained by telomere length. Instead we propose that Tert functions outside of telomere length maintenance in an age-dependent manner to influence the adult phenotypes of the next generation.

Baseline Characteristics of the Median Nerve on Ultrasound Examination

Background: Previous studies using ultrasound for diagnosis of carpal tunnel syndrome have reported on relatively small series of patients, leading to large standard deviations and/or confidence intervals for the mean cross-sectional area of the median nerve. The purpose of this study is to define the CSA of the median nerve in a large cohort of patients. Methods: Patients (n = 175) without history of carpal tunnel release were recruited. All participants were evaluated using the Carpal Tunnel Syndrome-6 questionnaire, a validated clinical diagnostic tool, with a score of 12 or greater considered positive for CTS. Ultrasound examination was performed on both wrists of all participants using a 13-6 MHz linear array transducer. Results: The mean median nerve CSA was significantly larger (P < .001) for patients with a positive (mean = 11.16, SD = 2.51) versus negative CTS-6 result (mean = 6.91, SD = 2.06). There was a significant correlation (.527, P < .001, n = 349) between CSA and CTS-6 score. Logistic regression analysis determined that a CSA of 10 mm2 optimized sensitivity and specificity at 80% and 88%, respectively. Accuracy was 87.9%. Conclusions: A significant difference in mean CSA was found between patients with and without CTS. Median nerve CSA showed a statistically significant positive correlation with CTS-6. Similar to prior studies, a CSA of 10 mm2 was determined to be the optimal cutoff. In this large series of patients, ultrasound was a sensitive, specific, and accurate test for confirmation of a clinical diagnosis of CTS.

Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafish

BACKGROUND

The CRISPR/Cas9 system is a prokaryotic immune system that infers resistance to foreign genetic material and is a sort of 'adaptive immunity'. It has been adapted to enable high throughput genome editing and has revolutionised the generation of targeted mutations.

RESULTS

We have developed a scalable analysis pipeline to identify CRISPR/Cas9 induced mutations in hundreds of samples using next generation sequencing (NGS) of amplicons. We have used this system to investigate the best way to screen mosaic Zebrafish founder individuals for germline transmission of induced mutations. Screening sperm samples from potential founders provides much better information on germline transmission rates and crucially the sequence of the particular insertions/deletions (indels) that will be transmitted. This enables us to combine screening with archiving to create a library of cryopreserved samples carrying known mutations. It also allows us to design efficient genotyping assays, making identifying F1 carriers straightforward.

CONCLUSIONS

The methods described will streamline the production of large numbers of knockout alleles in selected genes for phenotypic analysis, complementing existing efforts using random mutagenesis.

High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping

BACKGROUND

We present a genome-wide messenger RNA (mRNA) sequencing technique that converts small amounts of RNA from many samples into molecular phenotypes. It encompasses all steps from sample preparation to sequence analysis and is applicable to baseline profiling or perturbation measurements.

RESULTS

Multiplex sequencing of transcript 3' ends identifies differential transcript abundance independent of gene annotation. We show that increasing biological replicate number while maintaining the total amount of sequencing identifies more differentially abundant transcripts.

CONCLUSIONS

This method can be implemented on polyadenylated RNA from any organism with an annotated reference genome and in any laboratory with access to Illumina sequencing.

A systematic genome-wide analysis of zebrafish protein-coding gene function

Since the publication of the human reference genome, the identities of specific genes associated with human diseases are being discovered at a rapid rate. A central problem is that the biological activity of these genes is often unclear. Detailed investigations in model vertebrate organisms, typically mice, have been essential for understanding the activities of many orthologues of these disease-associated genes. Although gene-targeting approaches and phenotype analysis have led to a detailed understanding of nearly 6,000 protein-coding genes, this number falls considerably short of the more than 22,000 mouse protein-coding genes. Similarly, in zebrafish genetics, one-by-one gene studies using positional cloning, insertional mutagenesis, antisense morpholino oligonucleotides, targeted re-sequencing, and zinc finger and TAL endonucleases have made substantial contributions to our understanding of the biological activity of vertebrate genes, but again the number of genes studied falls well short of the more than 26,000 zebrafish protein-coding genes. Importantly, for both mice and zebrafish, none of these strategies are particularly suited to the rapid generation of knockouts in thousands of genes and the assessment of their biological activity. Here we describe an active project that aims to identify and phenotype the disruptive mutations in every zebrafish protein-coding gene, using a well-annotated zebrafish reference genome sequence, high-throughput sequencing and efficient chemical mutagenesis. So far we have identified potentially disruptive mutations in more than 38% of all known zebrafish protein-coding genes. We have developed a multi-allelic phenotyping scheme to efficiently assess the effects of each allele during embryogenesis and have analysed the phenotypic consequences of over 1,000 alleles. All mutant alleles and data are available to the community and our phenotyping scheme is adaptable to phenotypic analysis beyond embryogenesis.

Wound infection, dressings and pain, is there a relationship in the chronic wound?

The focus on quality of life issues in wound care has justly taken a far greater importance. With the acceptance that pain can be a major factor to the patient, and in particular, pain at dressing change comes the opportunity for avoidance and/or reduction strategies. Whilst pain has been associated with wound infection for millennia, it is only much more recently that this has received due attention from research and clinical practice. In this study, the nature of pain, changes in pain and pain associated with infection are the focal points. A Delphi approach, now a frequently used tool in wound care research, has been used to obtain expert opinion on these aspects of management.

Identifying and relating biological concepts in the Catalogue of Life

BACKGROUND

In this paper we describe our experience of adding globally unique identifiers to the Species 2000 and ITIS Catalogue of Life, an on-line index of organisms which is intended, ultimately, to cover all the world's known species. The scientific species names held in the Catalogue are names that already play an extensive role as terms in the organisation of information about living organisms in bioinformatics and other domains, but the effectiveness of their use is hindered by variation in individuals' opinions and understanding of these terms; indeed, in some cases more than one name will have been used to refer to the same organism. This means that it is desirable to be able to give unique labels to each of these differing concepts within the catalogue and to be able to determine which concepts are being used in other systems, in order that they can be associated with the concepts in the catalogue. Not only is this needed, but it is also necessary to know the relationships between alternative concepts that scientists might have employed, as these determine what can be inferred when data associated with related concepts is being processed. A further complication is that the catalogue itself is evolving as scientific opinion changes due to an increasing understanding of life.

RESULTS

We describe how we are using Life Science Identifiers (LSIDs) as globally unique identifiers in the Catalogue of Life, explaining how the mapping to species concepts is performed, how concepts are associated with specific editions of the catalogue, and how the Taxon Concept Schema has been adopted in order to express information about concepts and their relationships. We explore the implications of using globally unique identifiers in order to refer to abstract concepts such as species, which incorporate at least a measure of subjectivity in their definition, in contrast with the more traditional use of such identifiers to refer to more tangible entities, events, documents, observations, etc.

CONCLUSIONS

A major reason for adopting identifiers such as LSIDs is to facilitate data integration. We have demonstrated the incorporation of LSIDs into the Catalogue of Life, in a manner consistent with the biodiversity informatics community's conventions for LSID use. The Catalogue of Life is therefore available as a taxonomy of organisms for use within various disciplines, including biomedical research, by software written with an awareness of these conventions.

Novel therapeutic approaches in pulmonary arterial hypertension: focus on tadalafil

Pulmonary arterial hypertension (PAH) is an enigmatic, often fatal disease of the lung. Excess vasoconstriction and progressive obliteration of the precapillary arterioles combine to reduce the cross-sectional area for blood flow and thus cause chronic elevation in the pulmonary arterial pressures with progressive right heart dysfunction, heart failure and death. In 1995, the FDA approved the first therapy for PAH: epoprostenol, a highly efficacious drug but one that was difficult to use for patients and clinicians alike. Since then, there have been eight additional drugs approved, each offering advantages in terms of convenience over previously available drugs. In 2009, tadalafil (Adcirca®) was approved for PAH. The 405 patients enrolled in the single pivotal trial give this drug the largest initial placebo-controlled dataset of any of the oral PAH therapies; its once-daily dosing and excellent safety profile make it the most convenient of the therapies by a significant margin. After introducing the PAH disease state with references for more interested readers, this paper discusses the nitric oxide pathway as it relates to the pulmonary circulation, provides an overview of clinically available phosphodiesterase inhibitors and discusses tadalafil in relationship to sildenafil (Revatio®), the first phosphodiesterase inhibitor approved for PAH.

Zebrafish Fukutin family proteins link the unfolded protein response with dystroglycanopathies

Allelic mutations in putative glycosyltransferase genes, fukutin and fukutin-related protein (fkrp), lead to a wide range of muscular dystrophies associated with hypoglycosylation of α-dystroglycan, commonly referred to as dystroglycanopathies. Defective glycosylation affecting dystroglycan–ligand interactions is considered to underlie the disease pathogenesis. We have modelled dystroglycanopathies in zebrafish using a novel loss-of-function dystroglycan allele and by inhibition of Fukutin family protein activities. We show that muscle pathology in embryos lacking Fukutin or FKRP is different from loss of dystroglycan. In addition to hypoglycosylated α-dystroglycan, knockdown of Fukutin or FKRP leads to a notochord defect and a perturbation of laminin expression before muscle degeneration. These are a consequence of endoplasmic reticulum stress and activation of the unfolded protein response (UPR), preceding loss of dystroglycan–ligand interactions. Together, our results suggest that Fukutin family proteins may play important roles in protein secretion and that the UPR may contribute to the phenotypic spectrum of some dystroglycanopathies in humans.

Wound infection-associated pain

Not only does wound infection and the release of pro-inflammatory modulators result in pain and delayed healing, but pain-related stress reduces the immune response to infection. Treatment of pain and infection should be equal priorites.

Remission and relapse of chronic plaque psoriasis treated once a week with clobetasol propionate occluded with a hydrocolloid dressing versus twice daily treatment with clobetasol propionate alone

BACKGROUND

Many studies have shown the clinical efficiency of occlusion therapy for psoriasis, particularly corticosteroids used under hydrocolloid dressings. However, there are no data from comparative clinical studies evaluating the remission and relapse characteristics of such occlusion therapy compared with orthodox topical steroid monotherapy.

METHODS

In a randomised, open-label, parallel group study from three centres, the remission and relapse characteristics were investigated for the use of a hydrocolloid dressing (HCD) over clobetasol propionate 0.05% lotion once a week compared with the same steroid in ointment formulation used unoccluded twice a day in 61 patients with stable chronic plaque psoriasis.

RESULTS

There was a pronounced treatment difference in favour of the HCD + clobetasol propionate lotion group with respect to time to clearance, but there was little evidence for a difference with respect to time to relapse.

CONCLUSION

The combination of the HCD + clobetasol propionate lotion provides a fast and highly effective remission induction.

How degrading: Cyp26s in hindbrain development

The vitamin A derivative retinoic acid performs many functions in vertebrate development and is thought to act as a diffusible morphogen that patterns the anterior-posterior axis of the hindbrain. Recent work in several systems has led to insights into how the spatial distribution of retinoic acid is regulated. These have shown local control of synthesis and degradation, and computational models suggest that degradation by the Cyp26 enzymes plays a critical role in the formation of a morphogen gradient as well as its ability to compensate for fluctuations in RA levels.

Pain assessment and management in patients with chronic wounds

Pain is a frequent symptom in patients with chronic wounds. It contributes to significant levels of suffering and distress, as well as reduced quality of life. This article considers interventions and procedures for managing pain in patients with chronic wounds.

How global is the global biodiversity information facility?

There is a concerted global effort to digitize biodiversity occurrence data from herbarium and museum collections that together offer an unparalleled archive of life on Earth over the past few centuries. The Global Biodiversity Information Facility provides the largest single gateway to these data. Since 2004 it has provided a single point of access to specimen data from databases of biological surveys and collections. Biologists now have rapid access to more than 120 million observations, for use in many biological analyses. We investigate the quality and coverage of data digitally available, from the perspective of a biologist seeking distribution data for spatial analysis on a global scale. We present an example of automatic verification of geographic data using distributions from the International Legume Database and Information Service to test empirically, issues of geographic coverage and accuracy. There are over 1/2 million records covering 31% of all Legume species, and 84% of these records pass geographic validation. These data are not yet a global biodiversity resource for all species, or all countries. A user will encounter many biases and gaps in these data which should be understood before data are used or analyzed. The data are notably deficient in many of the world's biodiversity hotspots. The deficiencies in data coverage can be resolved by an increased application of resources to digitize and publish data throughout these most diverse regions. But in the push to provide ever more data online, we should not forget that consistent data quality is of paramount importance if the data are to be useful in capturing a meaningful picture of life on Earth.

Symptom overlap in patients with upper gastrointestinal complaints in the Canadian confirmatory acid suppression test (CAST) study: further psychometric validation of the reflux disease questionnaire

BACKGROUND

The reflux disease questionnaire (RDQ) is a short, patient-completed instrument.

AIMS

To investigate the psychometric characteristics of the RDQ in patients with heartburn-predominant (HB) and non-heartburn predominant (NHB) dyspepsia.

METHODS

HB (n = 388) and NHB (n = 733) patients were randomized to esomeprazole 40 mg daily or twice daily for 1 week, followed by 3 weeks of esomeprazole 40 mg daily.

RESULTS

High factor loadings (0.78-0.86) supported the 'regurgitation' dimension of the RDQ. Overlapping factor loadings in the 'heartburn' and 'dyspepsia' dimensions suggested symptom overlap. All dimensions demonstrated high internal consistency (Cronbach's alpha: 0.79-0.90). Intra-class correlation coefficients over 4 weeks were good (0.66-0.85). The RDQ showed good responsiveness over 4 weeks of treatment, with high effect sizes (> or =0.80). Moderate or large symptom improvements were reported by 90% and 77% of HB and NHB patients, respectively, following treatment. Patients who responded to acid suppression also experienced symptom benefits in all RDQ dimensions.

CONCLUSIONS

The RDQ is reliable, valid and responsive to change in HB and NHB patients. The symptom overlap is important but need not play a major role in determining treatment strategy as both patient groups benefited from proton pump inhibitor treatment.

ProgeniDB: a novel cell lineage database for generation associated phenotypic behavior in cell-based assays

ProgeniDB is a web-accessible cell lineage database, which comprises data derived from time-lapse microscopy image sequences, using our novel encoding software tool called ProgeniTRAK. This database provides information on qualitative and quantitative changes in cellular dynamics in response to anti-cancer drugs variation, which is critical for pharmacodynamic modeling and validation. The lineage data for each progenitor cell centers around the construction of a bifurcation map, locating in both space and time critical cellular events such as cell division and cell death. This database provides the opportunity to select a set of lineages based on different experimental constraints and observe the associated phenotypic behavior of progenitor cells. The output generated from this database depicts the cellular dynamic of selected population which can be downloaded to explore and exploit in relation to hypothesis-driven drug discovery. A case study is presented where we interrogate drug-induced perturbations on ensuing cell lineages. The database is available at http://biodiversity.cs.cf.ac.uk/cymart/progenidb.html.

Critical colonization--the concept under scrutiny

Infection in chronic wounds presents a major clinical challenge and is a cause of high morbidity rates. Much attention has been dedicated to identifying and managing this problem since the publication of the first article on chronic wound infection criteria in 1994. To illustrate how alteration in wound bioburden impacts pathology, the Wound Infection Continuum has been devised and subsequently modified. One stage in this continuum, critical colonization, is putatively described as a pivotal phase that occurs without inducing an overt host response. Critical colonization suggests that the concept is currently better explained from a microbiological than from a clinical perspective. The status of critically colonized wounds may change in one of several ways: 1) deteriorate to clinical infection, 2) remain in a critically colonized state, or 3) improve following appropriate intervention. Research to clearly define the term and clarify the role of bioburden in the chronic wound is needed to help clinicians recognize and implement appropriate treatment.

Topical antimicrobials in the control of wound bioburden

Bacterial colonization and infection are important factors in compromised wound healing, particularly in chronic wounds. Although "best practice" for controlling these factors currently is not defined, systemic antibiotics are generally accepted as the preferred choice for treating infection, provided ischemia does not reduce their bioavailability. However, widespread use of systemic and topical antibiotics is associated with the emergence of resistant bacterial strains such as methicillin-resistant Staphylococcus aureus. Colonization of wounds presents a double problem--potentially delayed healing and a potential source for cross-contamination. The judicious use of dressings, notably those containing certain antiseptic agents, can be a valuable option to control infection and promote healing. A review of the literature underscores the importance of considering the antiseptic route as part of a concerted approach to wound management and infection control.

The prevalence of Barrett's oesophagus in a cohort of 1040 Canadian primary care patients with uninvestigated dyspepsia undergoing prompt endoscopy

BACKGROUND

The prevalence of Barrett's oesophagus in patients undergoing gastroscopy may be influenced by possible referral bias.

AIM

To present the prevalence of Barrett's oesophagus from the the Canadian Adult Dyspepsia Empirical Therapy Prompt Endoscopy study and to explore potential risk factors for its presence.

METHODS

Patients had not been on treatment for dyspepsia for 2-4 weeks prior to endoscopy, which was performed within 10 working days of presentation.

RESULTS

Barrett's oesophagus was endoscopically suspected in 53 of 1040 cases (5%) and histologically confirmed by the presence of intestinal metaplasia in 25 (2.4%). The prevalence of biopsy-proven Barrett's oesophagus was 4% in patients with dominant reflux-like symptoms. Sixty-four percent with confirmed Barrett's oesophagus had dominant reflux-like symptoms compared with 37% without Barrett's oesophagus. Barrett's oesophagus was more common in patients >50 years of age; 68% of cases were males. The mean duration of symptoms was 10 years, yet 16% had symptoms of <1-year duration. Endoscopic reflux oesophagitis was present in 68% of confirmed Barrett's oesophagus patients.

CONCLUSIONS

Barrett's oesophagus is confirmed on biopsy in about half of endoscopically suspected Barrett's oesophagus patients. Barrett's oesophagus is more common in males, in those with dominant reflux-like symptoms, and in patients with a longer symptom history.

Retinoids signal directly to zebrafish endoderm to specify insulin-expressing β-cells

During vertebrate development, the endodermal germ layer becomes regionalized along its anteroposterior axis to give rise to a variety of organs, including the pancreas. Genetic studies in zebrafish and mice have established that the signaling molecule retinoic acid (RA) plays a crucial role in endoderm patterning and promotes pancreas development. To identify how RA signals to pancreatic progenitors in the endoderm, we have developed a novel cell transplantation technique, using the ability of the SOX32 transcription factor to confer endodermal identity, to selectively target reagents to (or exclude them from) the endodermal germ layer of the zebrafish. We show that RA synthesized in the anterior paraxial mesoderm adjacent to the foregut is necessary for the development of insulin-expressingβ-cells. Conversely, RA receptor function is required in the foregut endoderm for insulin expression, but not in mesoderm or ectoderm. We further show that activation of RA signal transduction in endoderm alone is sufficient to induce insulin expression. Our results reveal that RA is an instructive signal from the mesoderm that directly induces precursors of the endocrine pancreas. These findings suggest that RA will have important applications in the quest to induce islets from stem cells for therapeutic uses.

The evolution of peptide deformylase as a target: contribution of biochemistry, genetics and genomics

Although peptide deformylase (PDF, EC 3.5.1.27) was first described in 1968, the instability of enzyme preparations prevented it from being seriously considered as a target until this problem was finally solved in 1998. PDFs essentiality was first demonstrated in Escherichia coli in 1994. Genomic analyses have shown this enzyme to be present in all eubacteria. PDF homologs have also been found in eukaryotes including Homo sapiens. The function and relevance of the human chromosomal homolog to the safety of PDF inhibitors as therapeutic agents is not clear at this stage. Although there is considerable sequence variation between the different bacterial PDFs, there are three strongly conserved motifs that together constitute a critical metal binding site. The observation that PDF is a metalloenzyme has led to the design of inhibitors containing metal chelating pharmacophores. The most potent of these synthetic inhibitors are active against a range of clinically relevant respiratory tract pathogens in vitro and in vivo, including those resistant to current antibiotics. Mutants resistant to PDF inhibitors have been obtained in the laboratory; these resulted from mutations in the genes for transformylase (EC 2.1.2.9) or PDF. The mechanism involved and its frequency were pathogen-dependent. The two most advanced PDF inhibitor leads, which are both reverse hydroxamates, have progressed to phase 1 clinical trials and were well tolerated.