Drug Repositioning for Noonan and LEOPARD Syndromes by Integrating Transcriptomics With a Structure-Based Approach

Noonan and LEOPARD syndromes (NS and LS) belong to a group of related disorders called RASopathies characterized by abnormalities of multiple organs and systems including hypertrophic cardiomyopathy and dysmorphic facial features. There are no approved drugs for these two rare diseases, but it is known that a missense mutation in PTPN11 genes is associated with approximately 50% and 70% of NS and LS cases, respectively. In this study, we implemented a hybrid computational drug repositioning framework by integrating transcriptomic and structure-based approaches to explore potential treatment options for NS and LS. Specifically, disease signatures were derived from the transcriptomic profiles of human induced pluripotent stem cells (iPSCs) from NS and LS patients and reverse correlated to drug transcriptomic signatures from CMap and L1000 projects on the basis that if disease and drug transcriptomic signatures are reversely correlated, the drug has the potential to treat that disease. The compounds that were ranked top based on their transcriptomic profiles were docked to mutated and wild-type 3D structures of PTPN11 by an adjusted Induced Fit Docking (IFD) protocol. In addition, we prioritized repositioned candidates for NS and LS by a consensus ranking strategy. Network analysis and phenotypic anchoring of the transcriptomic data could discriminate the two diseases at the molecular level. Furthermore, the adjusted IFD protocol was able to recapitulate the binding specificity of potential drug candidates to mutated 3D structures, revealing the relevant amino acids. Importantly, a list of potential drug candidates for repositioning was identified including 61 for NS and 43 for LS and was further verified from literature reports and on-going clinical trials. Altogether, this hybrid computational drug repositioning approach has highlighted a number of drug candidates for NS and LS and could be applied to identifying drug candidates for other diseases as well.

Opportunities for use of one species for longer-term toxicology testing during drug development: A cross-industry evaluation

An international expert working group representing 37 organisations (pharmaceutical/biotechnology companies, contract research organisations, academic institutions and regulatory bodies) collaborated in a data sharing exercise to evaluate the utility of two species within regulatory general toxicology studies. Anonymised data on 172 drug candidates (92 small molecules, 46 monoclonal antibodies, 15 recombinant proteins, 13 synthetic peptides and 6 antibody-drug conjugates) were submitted by 18 organisations. The use of one or two species across molecule types, the frequency for reduction to a single species within the package of general toxicology studies, and a comparison of target organ toxicities identified in each species in both short and longer-term studies were determined. Reduction to a single species for longer-term toxicity studies, as used for the development of biologicals (ICHS6(R1) guideline) was only applied for 8/133 drug candidates, but might have been possible for more, regardless of drug modality, as similar target organ toxicity profiles were identified in the short-term studies. However, definition and harmonisation around the criteria for similarity of toxicity profiles is needed to enable wider consideration of these principles. Analysis of a more robust dataset would be required to provide clear, evidence-based recommendations for expansion of these principles to small molecules or other modalities where two species toxicity testing is currently recommended.

African-Caribbean Cancer Consortium Scientific and Training Conference 2017

The sixth International African-Caribbean Cancer Consortium (AC3) Conference was held 6-9 October 2017 in Miami, Florida, U.S.A. The conference was open to all researchers, trainees, clinical and public health professionals, and community members, and served as an international hub for the United States, the Caribbean, and Africa. Sessions included AC3 collaboration meetings, cancer surveillance and research skills training workshops, and a community cancer prevention conference.

Potential for children with intellectual disability to engage in cognitive behaviour therapy: the parent perspective

BACKGROUND

This study aimed to obtain the opinions of parents and carers of children with intellectual disability (ID) as to whether cognitive behaviour therapy (CBT) could be useful for their children.

METHODS

A mixed qualitative and quantitative method was employed. Twenty-one carers of children aged 10 to 17 having borderline to moderate intellectual functioning responded to an online questionnaire. Participants were provided with information about CBT and asked to respond to open-ended questions. Quantitative data pertained to questions about their child's ability to identify and describe thoughts, feelings and behaviours. Thematic analysis of responses was conducted using an inductive method of identifying themes from the qualitative data collected.

RESULTS

Five themes emerged from the qualitative analysis: Emotional Attunement (i.e. parent's understanding and recognition of their child's emotions), Role of the Therapist (i.e. ways therapists could facilitate the intervention), Role of the Parent (i.e. ways parents could engage in the therapy process), Anticipated Obstacles (i.e. what may get in the way of the therapy) and Suggested Adaptations for Therapy (i.e. how CBT can be adapted to suit the needs of children with ID). Seventy-six per cent agreed that their child would be able to engage in CBT with assistance.

CONCLUSIONS

The majority of parents believed that CBT is an intervention that children with ID could engage in, provided the therapy is adapted, and the therapist accommodates their needs.

Drug-induced liver injury severity and toxicity (DILIst): binary classification of 1279 drugs by human hepatotoxicity

Drug-induced liver injury (DILI) is of significant concern to drug development and regulatory review because of the limited success with existing preclinical models. For developing alternative methods, a large drug list is needed with known DILI severity and toxicity. We augmented the DILIrank data set [annotated using US Food and Drug Administration (FDA) drug labeling)] with four literature datasets (N >350 drugs) to generate the largest drug list with DILI classification, called DILIst (DILI severity and toxicity). DILIst comprises 1279 drugs, of which 768 were DILI positives (increase of 65% from DILIrank), whereas 511 were DILI negatives (increase of 65%). The investigation of DILI positive-negative distribution across various therapeutic categories revealed the most and least frequent DILI categories. Thus, we consider DILIst to be an invaluable resource for the community to improve DILI research.

Toward Clinical Implementation of Next-Generation Sequencing-Based Genetic Testing in Rare Diseases: Where Are We?

Next-generation sequencing (NGS) technologies have changed the landscape of genetic testing in rare diseases. However, the rapid evolution of NGS technologies has outpaced its clinical adoption. Here, we re-evaluate the critical steps in the clinical application of NGS-based genetic testing from an informatics perspective. We suggest a 'fit-for-purpose' triage of current NGS technologies. We also point out potential shortcomings in the clinical management of genetic variants and offer ideas for potential improvement. We specifically emphasize the importance of ensuring the accuracy and reproducibility of NGS-based genetic testing in the context of rare disease diagnosis. We highlight the role of artificial intelligence (AI) in enhancing understanding and prioritization of variance in the clinical setting and propose deep learning frameworks for further investigation.

Derivatisation of parthenolide to address chemoresistant chronic lymphocytic leukaemia

Parthenolide is a natural product that exhibits anti-leukaemic activity, however, its clinical use is limited by its poor bioavailability. It may be extracted from feverfew and protocols for growing, extracting and derivatising it are reported. A novel parthenolide derivative with good bioavailability and pharmacological properties was identified through a screening cascade based on in vitro anti-leukaemic activity and calculated "drug-likeness" properties, in vitro and in vivo pharmacokinetics studies and hERG liability testing. In vitro studies showed the most promising derivative to have comparable anti-leukaemic activity to DMAPT, a previously described parthenolide derivative. The newly identified compound was shown to have pro-oxidant activity and in silico molecular docking studies indicate a prodrug mode of action. A synthesis scheme is presented for the production of amine 7 used in the generation of 5f.

Toxicogenomics: A 2020 Vision

Toxicogenomics (TGx) has contributed significantly to toxicology and now has great potential to support moves towards animal-free approaches in regulatory decision making. Here, we discuss in vitro TGx systems and their potential impact on risk assessment. We raise awareness of the rapid advancement of genomics technologies, which generates novel genomics features essential for enhanced risk assessment. We specifically emphasize the importance of reproducibility in utilizing TGx in the regulatory setting. We also highlight the role of machine learning (particularly deep learning) in developing TGx-based predictive models. Lastly, we touch on the topics of how TGx approaches could facilitate adverse outcome pathways (AOP) development and enhance read-across strategies to further regulatory application. Finally, we summarize current efforts to develop TGx for risk assessment and set out remaining challenges.

1.5mile run time and body mass predict 8mile loaded march performance, irrespective of sex

OBJECTIVES

To develop a statistical model to predict 8mile Loaded March (LM) performance and quantify differences in physical characteristics for men and women British Army Personnel.

DESIGN

135 trained soldiers (87 men; 48 women) completed two sessions, seven days apart.

METHODS

Session 1: Participants' stature, body mass, Fat Free Mass (FFM) [by dual-energy X-ray absorptiometry], Single Lift (SL), Water Can Carry (WCC), and 1.5mile run performance were measured. Session 2: Participants completed an 8mile LM, carrying 25kg (4miles paced and 4miles individual best effort). Sex differences were compared using independent samples t-tests and 8mile LM performance time was predicted using various multiple linear regression analysis: hierarchical forced entry multiple ordinary least squares, principal component and ordinary least products.

RESULTS

A combination of 1.5mile run time and body mass were the strongest predictors of 8mile LM time (R²=0.71; SEE=4.17min; p<0.001). Including stature, FFM, sex, SL score, or WCC score did not further improve predictions (p>0.05). Compared to women, men had faster mean 1.5mile run and LM times, greater body mass and total FFM and higher SL and WCC scores (p<0.001), however some women outperformed men.

CONCLUSION

1.5mile run time and body mass predict 8mile LM performance with no further improvement gained in the model by including sex as a variable.

Transcriptional Responses Reveal Similarities Between Preclinical Rat Liver Testing Systems

Toxicogenomics (TGx) is an important tool to gain an enhanced understanding of toxicity at the molecular level. Previously, we developed a pair ranking (PRank) method to assess in vitro to in vivo extrapolation (IVIVE) using toxicogenomic datasets from the Open Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System (TG-GATEs) database. With this method, we investiagted three important questions that were not addressed in our previous study: (1) is a 1-day in vivo short-term assay able to replace the 28-day standard and expensive toxicological assay? (2) are some biological processes more conservative across different preclinical testing systems than others? and (3) do these preclinical testing systems have the similar resolution in differentiating drugs by their therapeutic uses? For question 1, a high similarity was noted (PRank score = 0.90), indicating the potential utility of shorter term in vivo studies to predict outcome in longer term and more expensive in vivo model systems. There was a moderate similarity between rat primary hepatocytes and in vivo repeat-dose studies (PRank score = 0.71) but a low similarity (PRank score = 0.56) between rat primary hepatocytes and in vivo single dose studies. To address question 2, we limited the analysis to gene sets relevant to specific toxicogenomic pathways and we found that pathways such as lipid metabolism were consistently over-represented in all three assay systems. For question 3, all three preclinical assay systems could distinguish compounds from different therapeutic categories. This suggests that any noted differences in assay systems was biological process-dependent and furthermore that all three systems have utility in assessing drug responses within a certain drug class. In conclusion, this comparison of three commonly used rat TGx systems provides useful information in utility and application of TGx assays.

Medical Databases

An entity relationship level design is given for medical information systems. This design is aimed at-conceptual-integration of hospital information systems, patient history record keeping systems, future diagnosis systems, etc. In particular, it lays out a foundation for distributed databases.

Evaluation of Positive Contrast Arthrography in Canine Cranial Cruciate Ligament Disease

Arthrographic and intraoperative evaluations of stifles affected with cranial cruciate disease were compared. Arthrography did not appear to be helpful in predicting cranial cruciate ligament pathology. The caudal cruciate ligament was consistently not visualized in the arthrograms and was normal at surgery. The menisci were visualized consistently in the arthrograms, but conclusions could not be made as to the benefit of arthrography in predicting meniscal pathology. Arthrography was not helpful in predicting joint capsule and femoral articular surface pathology. Survey radiographic evaluation was better than arthrography in evaluating joint pathology. When cruciate injury is suspected, after history and physical examination, survey radiographs are better than positive contrast arthrograms at supporting the diagnosis.

Positive contrast arthrography was evaluated as a diagnostic aid in canine cranial cruciate ligament disease. It did not appear to be useful in predicting joint pathology. With arthrography, both menisci could be visualized and evaluated for abnormalities. Joint effusion and presence of osteophytes evaluated on survey radiographs was better than arthrography in evaluating joint pathology.

Bolus Advisors: Sources of Error, Targets for Improvement

Bolus advisors that are designed to improve the accuracy of individual bolus doses relative to a meal's carb content and the current glucose have not substantially changed since they were introduced 15 years ago despite an obvious need for enhancement and innovation. Although some glycemic benefits have been demonstrated, bolus advisors largely ignore the large amounts of clinical data they gather that could have a significant impact on glucose outcomes. Concerns have also been raised regarding the aggressive nature of largely unpublished or poorly explained bolus advisor algorithms. Hypoglycemia and hyperglycemia remain significant risks due to inaccurate bolus advisor settings and the absence of tracking or an inappropriate handling of bolus on board. This review covers common sources for bolus advisor error such as the selection of physiologically inappropriate bolus advisor settings, the use of short duration of insulin action times, poor algorithm logic that tends to cover all carb intake fully, and an excessive reliance on simplistic dosing algorithms. As well as discussing these areas, we provide 21 ways to improve current bolus calculators.

Living with conduct problem youth: family functioning and parental perceptions of their child

Parenting children with conduct problems (CP) is challenging, yet very little is known about the impact of the child's behaviour on family functioning or how parents of children with CP perceive their child. The aim of this research was to examine whether families with children with CP and high vs. low levels of callous-unemotional traits (HCU vs. LCU) experience differences in family functioning and parental perceptions. One hundred and one parents/caregivers of boys aged 11-16 [Typically developing (TD) n = 31; CP/HCU n = 35; CP/LCU n = 35] completed the McMaster Family Assessment Device, measuring multiple domains of family functioning. Parents/caregivers also completed a written statement describing their child, used for qualitative analysis. Families with CP/HCU children had poorer affective involvement than TD (p = 0.00; d = - 1.17) and CP/LCU (p = 0.03; d = - 0.62) families. Families with CP/HCU children showed significantly poorer general family functioning (p = 0.04; d = - 0.63) and more poorly defined family roles (p = 0.005; d = - 0.82) than families with TD children. Qualitative analyses indicated that parents/caregivers of CP/HCU children characterised them as having a dichotomous personality and being superficially charming. CP/LCU children were characterised as cheeky and endearing, with parents reporting good rapport. Families with CP/HCU children presented with specific difficulties in affective involvement and parents described challenges which were in line with the child's specific presentation of lack of empathy and shallow affect. These findings may be used to help clinicians identify targets for family interventions.

The Liver Toxicity Knowledge Base (LKTB) and drug-induced liver injury (DILI) classification for assessment of human liver injury

Drug-induced liver injury (DILI) is challenging for drug development, clinical practice and regulation. The Liver Toxicity Knowledge Base (LTKB) provides essential data for DILI study. Areas covered: The LTKB provided various types of data that can be used to assess and predict DILI. Among much information available, several reference drug lists with annotated human DILI risk are of important. The LTKB DILI classification data include DILI severity concern determined by the FDA drug labeling, DILI severity score from the NIH LiverTox database, and other DILI classification schemes from the literature. Overall, ~1000 drugs were annotated with at least one classification scheme, of which around 750 drugs were flagged for some degree of DILI risk. Expert commentary: The LTKB provides a centralized repository of information for DILI study and predictive model development. The DILI classification data in LTKB could be a useful resource for developing biomarkers, predictive models and assessing data from emerging technologies such as in silico, high-throughput and high-content screening methodologies. In coming years, streamlining the prediction process by including DILI predictive models for both DILI severity and types in LTKB would enhance the identification of compounds with the DILI potential earlier in drug development and risk assessment.