Parental Intervention Program for Preschool children with Rare Diseases - a mixed methods evaluation of parents' experiences and utility.

BACKGROUND: The purpose of this study was twofold: (i) To assess the parents' experiences and perception of participating in a "Parental Intervention Program for Preschool children with Rare Diseases" (PIPP-RDs). (ii) To evaluate which elements of the PIPP-RDs that the parents emphasized as important for improving their health literacy related to facilitating the transition of their children from kindergarten to school. METHOD: A mixed methods evaluation study was conducted ten and eleven months post-intervention, integrating an online quantitative survey combined with individual semi-structured interviews. Twenty-two parents participated in individual interviews, of these 18 also responded to the online questionnaire survey. RESULTS: All parents that participated in this study reported that the information conveyed at the program was of great value and utility, 88% reported significantly alleviated stress associated to their child`s school-start, 84% indicated had improved the school-home collaboration and 84% reported that it had encouraged them to establish contact with the school prior to school commencement. From the qualitative data five main themes emerged: (i) Competence and Knowledge Acquisition, (ii) Becoming more Prepared and Relaxed, (iii) Achieved Realistic Expectations, (iv) Enhanced Communication Skills, (v) Increased Health Literacy and Self-Efficacy. The evaluative findings suggest that this invention program has notably improved the parents' aptitude for school interaction, enhanced the adaptions according to children`s needs for accommodations, and has provided reassurance in the school-home collaboration. Parents also described increased self-confidence and self-efficacy in managing the school start for children with RDs. CONCLUSION: The highly positive response of participating in PIPP-RDs may not only reflect the merits of the program`s content, but also underscore the significant needs for such support during the transition to school for parents of children with RDs. Comparable initiatives, oriented towards enhancing the health literacy and empowering the parents, are anticipated to yield similarly favourable results. We argue that intervention program amalgamate pertinent information, group discourse, and workshops on school-related issues, alongside opportunities for parents to meet other parents in similar situations.

The role of brokers in cultivating an inter-institutional community around open educational resources in higher education.

Brokers are individuals who facilitate transfer of knowledge and resources, and coordinate efforts across boundaries of organizations. They are defined by their role rather than their organizational position. Brokers might be imperative for the formation and maintenance of inter-institutional relationship as they have the responsibility and the necessary structural position to connect otherwise separate groups. In the context of this study, brokers had the role to cultivate an inter-institutional community around open educational resources (OER) by connecting groups of teachers across higher education institutes. OER provide higher education institutes with an aid to face the challenges of improving teaching and learning. Yet most OER users encounter challenges that relate to finding resources that are relevant, up-to-date, and of good quality. Communities could minimize this issue, but many OER initiatives fizzle out as expanding their impact is an arduous task. This qualitative descriptive study draws upon cultural-historical activity theory to understand the complexities associated with the role of brokers in creating sustainable collaboration on OER across 15 higher education institutes in the Netherlands. Data was collected from project documents, process reports, reflections reports, and a retrospective focus group. The findings show that brokers engaged in a wide variety of actions but that a small-scale, personal, and content-oriented approach to encourage teachers to engage with the OER repository and the online community was perceived as the most valuable. Brokers also experienced conflicts due to the demanding context they were operating in, the ambiguity of their role, and the organizational constraints they were confronted with. Practical implications refer to supporting higher education institutes that wish to initiate sustainable collaboration across institutes. Supplementary Information: The online version contains supplementary material available at 10.1007/s10734-022-00876-y.

What's in it for me? A mixed-methods study on teachers' value creation in an inter-institutional community on open educational resources in higher education.

The affordances of Open Educational Resources (OER) have resulted in various initiatives around the world, but most of them cease to exist once the initial project funding stops. Communities might be a means to create sustainable practices, yet, such communities can only function if their members perceive these communities as valuable. We applied the value creation framework of Wenger, Trayner, and De Laat to examine the value teachers ascribe to their engagement with an inter-institutional community on OER. In this community, 15 universities of applied sciences collaborated on sharing knowledge and resources across their institutional barriers. We collected data through user statistics, an online questionnaire, and semi-structured interviews. Major value creation occurred from teachers' personal needs, with dominant immediate and potential values. Findings on applied and realized values denote that it became easier for teachers to connect with peers, and to initiate collaboration projects across institutes. The framework we used is helpful to inform actions to further promote value creation in communities on OER. Recommendations relating to communities' aspirations, its relations with the wider organization, and adoption of OER are formulated to inform sustainable practices of inter-institutional communities.

Evaluation of 147 perfluoroalkyl substances for immunotoxic and other (patho)physiological activities through phenotypic screening of human primary cells.

A structurally diverse set of 147 per- and polyfluoroalkyl substances (PFAS) was screened in a panel of 12 human primary cell systems by measuring 148 biomarkers relevant to (patho)physiological pathways to inform hypotheses about potential mechanistic effects of data-poor PFAS in human model systems. This analysis focused on immunosuppressive activity, which was previously reported as an in vivo effect of perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), by comparing PFAS responses to four pharmacological immunosuppressants. The PFOS response profile had little correlation with reference immunosuppressants, suggesting in vivo activity does not occur by similar mechanisms. The PFOA response profile did share features with the profile of dexamethasone, although some distinct features were lacking. Other PFAS, including 2,2,3,3-tetrafluoropropyl acrylate, demonstrated more similarity to the reference immunosuppressants but with additional activities not found in the reference immunosuppressive drugs. Correlation of PFAS profiles with a database of environmental chemical responses and pharmacological probes identified potential mechanisms of bioactivity for some PFAS, including responses similar to ubiquitin ligase inhibitors, deubiquitylating enzyme (DUB) inhibitors, and thioredoxin reductase inhibitors. Approximately 21% of the 147 PFAS with confirmed sample quality were bioactive at nominal testing concentrations in the 1-60 micromolar range in these human primary cell systems. These data provide new hypotheses for mechanisms of action for a subset of PFAS and may further aid in development of a PFAS categorization strategy useful in safety assessment.

Use of a rapid human primary cell-based disease screening model, to compare next generation products to combustible cigarettes.

A growing number of public health bodies, regulators and governments around the world consider electronic vapor products a lower risk alternative to conventional cigarettes. Of critical importance are rapid new approach methodologies to enable the screening of next generation products (NGPs) also known as next generation tobacco and nicotine products. In this study, the activity of conventional cigarette (3R4F) smoke and a range of NGP aerosols (heated tobacco product, hybrid product and electronic vapor product) captured in phosphate buffered saline, were screened by exposing a panel of human cell-based model systems using Biologically Multiplexed Activity Profiling (BioMAP® Diversity PLUS® Panel, Eurofins Discovery). Following exposure, the biological activity for a wide range of biomarkers in the BioMAP panel were compared to determine the presence of toxicity signatures that are associated with specific clinical findings. NGP aerosols were found to be weakly active in the BioMAP Diversity PLUS Panel (≤3/148 biomarkers) whereas significant activity was observed for 3R4F (22/148 biomarkers). Toxicity associated biomarker signatures for 3R4F included immunosuppression, skin irritation and thrombosis, with no toxicity signatures seen for the NGPs. BioMAP profiling could effectively be used to differentiate between complex mixtures of cigarette smoke or NGP aerosol extracts in a panel of human primary cell-based assays. Clinical validation of these results will be critical for confirming the utility of BioMAP for screening NGPs for potential adverse human effects.

Expanding the drug discovery space with predicted metabolite-target interactions.

Metabolites produced in the human gut are known modulators of host immunity. However, large-scale identification of metabolite-host receptor interactions remains a daunting challenge. Here, we employed computational approaches to identify 983 potential metabolite-target interactions using the Inflammatory Bowel Disease (IBD) cohort dataset of the Human Microbiome Project 2 (HMP2). Using a consensus of multiple machine learning methods, we ranked metabolites based on importance to IBD, followed by virtual ligand-based screening to identify possible human targets and adding evidence from compound assay, differential gene expression, pathway enrichment, and genome-wide association studies. We confirmed known metabolite-target pairs such as nicotinic acid-GPR109a or linoleoyl ethanolamide-GPR119 and inferred interactions of interest including oleanolic acid-GABRG2 and alpha-CEHC-THRB. Eleven metabolites were tested for bioactivity in vitro using human primary cell-types. By expanding the universe of possible microbial metabolite-host protein interactions, we provide multiple drug targets for potential immune-therapies.

The future of phenotypic drug discovery.

Phenotypic drug discovery (PDD) uses biological systems directly for new drug screening. While PDD has proved effective in the discovery of drugs with novel mechanisms, for broader adoption, key challenges need resolution: progression of poorly qualified leads and overloaded pipelines due to lack of effective tools to process and prioritize hits; and advancement of leads with undesirable mechanisms that fail at more expensive stages of discovery. Here I discuss how human-based phenotypic platforms are being applied throughout the discovery process for hit triage and prioritization, for elimination of hits with unsuitable mechanisms, and for supporting clinical strategies through pathway-based decision frameworks. Harnessing the data generated in these platforms can also fuel a deeper understanding of drug efficacy and toxicity mechanisms. As these approaches increase in use, they will gain in power for driving better decisions, generating better leads faster and in turn promoting greater adoption of PDD.

The activities of drug inactive ingredients on biological targets.

Excipients, considered "inactive ingredients," are a major component of formulated drugs and play key roles in their pharmacokinetics. Despite their pervasiveness, whether they are active on any targets has not been systematically explored. We computed the likelihood that approved excipients would bind to molecular targets. Testing in vitro revealed 25 excipient activities, ranging from low-nanomolar to high-micromolar concentration. Another 109 activities were identified by testing against clinical safety targets. In cellular models, five excipients had fingerprints predictive of system-level toxicity. Exposures of seven excipients were investigated, and in certain populations, two of these may reach levels of in vitro target potency, including brain and gut exposure of thimerosal and its major metabolite, which had dopamine D3 receptor dissociation constant K d values of 320 and 210 nM, respectively. Although most excipients deserve their status as inert, many approved excipients may directly modulate physiologically relevant targets.

Human Cell-Based in vitro Phenotypic Profiling for Drug Safety-Related Attrition.

Ensuring the safety of new drugs is critically important to regulators, pharmaceutical researchers and patients alike. Even so, unexpected toxicities still account for 20-30% of clinical trial failures, in part due to the persistence of animal testing as the primary approach for de-risking new drugs. Clearly, improved methods for safety attrition that incorporate human-relevant biology are needed. This recognition has spurred interest in non-animal alternatives or new approach methodologies (NAMs) including in vitro models that utilize advances in the culture of human cell types to provide greater clinical relevance for assessing risk. These phenotypic assay systems use human primary and induced pluripotent stem cell-derived cells in various formats, including co-cultures and advanced cellular systems such as organoids, bioprinted tissues, and organs-on-a-chip. Despite the promise of these human-based phenotypic approaches, adoption of these platforms into drug discovery programs for reducing safety-related attrition has been slow. Here we discuss the value of large-scale human cell-based phenotypic profiling for incorporating human-specific biology into the de-risking process. We describe learnings from our experiences with human primary cell-based assays and analysis of clinically relevant reference datasets in developing in vitro-based toxicity signatures. We also describe how Adverse Outcome Pathway (AOP) frameworks can be used to integrate results from diverse platforms congruent with weight-of-evidence approaches from risk assessment to improve safety-related decisions in early discovery.

Assessing bioactivity-exposure profiles of fruit and vegetable extracts in the BioMAP profiling system.

The ToxCast program has generated in vitro screening data on over a thousand chemicals to assess potential disruption of important biological processes and assist in hazard identification and chemical testing prioritization. Few results have been reported for complex mixtures. To extend these ToxCast efforts to mixtures, we tested extracts from 30 organically grown fruits and vegetables in concentration-response in the BioMAP® assays. BioMAP systems use human primary cells primed with endogenous pathway activators to identify phenotypic perturbations related to proliferation, inflammation, immunomodulation, and tissue remodeling. Clustering of bioactivity profiles revealed separation of these produce extracts and ToxCast chemicals. Produce extracts elicited 87 assay endpoint responses per item compared to 20 per item for ToxCast chemicals. On a molar basis, the produce extracts were 10 to 50-fold less potent and when constrained to the maximum testing concentration of the ToxCast chemicals, the produce extracts did not show activity in as many assay endpoints. Using intake adjusted measures of dose, the bioactivity potential was higher for produce extracts than for agrichemicals, as expected based on the comparatively small amounts of agrichemical residues present on conventionally grown produce. The evaluation of BioMAP readouts and the dose responses for produce extracts showed qualitative and quantitative differences from results with single chemicals, highlighting challenges in the interpretation of bioactivity data and dose-response from complex mixtures.

Advancing nonclinical innovation and safety in pharmaceutical testing.

Nonclinical tests are considered crucial for understanding the safety of investigational medicines. However, the effective translation from nonclinical to human application is limited and must be improved. Drug development stakeholders are working to advance human-based in vitro and in silico methods that may be more predictive of human efficacy and safety in vivo because they enable scientists to model the direct interaction of drugs with human cells, tissues, and biological processes. Here, we recommend test-neutral regulations; increased funding for development and integration of human-based approaches; support for existing initiatives that advance human-based approaches; evaluation of new approaches using human data; establishment of guidelines for procuring human cells and tissues for research; and additional training and educational opportunities in human-based approaches.

Mechanisms of Skin Toxicity Associated with Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators.

Cutaneous reactions represent one of the most common adverse drug effects observed in clinical trials leading to substantial compound attrition. Three negative allosteric modulators (NAMs) of metabotropic glutamate receptors (mGluRs), which represent an important target for neurological diseases, developed by Pfizer, were recently failed in preclinical development due to delayed type IV skin hypersensitivity observed in non-human primates (NHPs). Here we employed large-scale phenotypic profiling in standardized panels of human primary cell/co-culture systems to characterize the skin toxicity mechanism(s) of mGluR5 NAMs from two different series. Investigation of a database of chemicals tested in these systems and transcriptional profiling suggested that the mechanism of toxicity may involve modulation of nuclear receptor targets RAR/RXR, and/or VDR with AhR antagonism. The studies reported here demonstrate how phenotypic profiling of preclinical drug candidates using human primary cells can provide insights into the mechanisms of toxicity and inform early drug discovery and development campaigns.

Phenotypic chemical biology for predicting safety and efficacy.

Phenotypic assays using in vitro cell cultures to forecast compound effects in people are transforming pharmaceutical research and contribute to alternative methods for chemical safety testing. How these assays are validated for human disease relevance is a critical factor for developing more predictive assays. Chemical biology, using drugs as well as target-selective chemical probes, is a direct and efficient approach for establishing disease relevance. Chemical probes can connect information across assays and associate targets to clinical effects. When applied at scale, phenotypic chemical biology advances our understanding of drug and toxicity mechanisms enabling construction of disease outcome pathways. To improve the physiological relevance of phenotypic assays, standardized testing of a curated set of phenotypic pathway probes can provide a higher level of validation for phenotypic assay best practices.

Identification of a Chemical Probe for Family VIII Bromodomains through Optimization of a Fragment Hit.

The acetyl post-translational modification of chromatin at selected histone lysine residues is interpreted by an acetyl-lysine specific interaction with bromodomain reader modules. Here we report the discovery of the potent, acetyl-lysine-competitive, and cell active inhibitor PFI-3 that binds to certain family VIII bromodomains while displaying significant, broader bromodomain family selectivity. The high specificity of PFI-3 for family VIII was achieved through a novel bromodomain binding mode of a phenolic headgroup that led to the unusual displacement of water molecules that are generally retained by most other bromodomain inhibitors reported to date. The medicinal chemistry program that led to PFI-3 from an initial fragment screening hit is described in detail, and additional analogues with differing family VIII bromodomain selectivity profiles are also reported. We also describe the full pharmacological characterization of PFI-3 as a chemical probe, along with phenotypic data on adipocyte and myoblast cell differentiation assays.

Elucidating mechanisms of toxicity using phenotypic data from primary human cell systems--a chemical biology approach for thrombosis-related side effects.

Here we describe a chemical biology approach for elucidating potential toxicity mechanisms for thrombosis-related side effects. This work takes advantage of a large chemical biology data set comprising the effects of known, well-characterized reference agents on the cell surface levels of tissue factor (TF) in a primary human endothelial cell-based model of vascular inflammation, the BioMAP® 3C system. In previous work with the Environmental Protection Agency (EPA) for the ToxCast™ program, aryl hydrocarbon receptor (AhR) agonists and estrogen receptor (ER) antagonists were found to share an usual activity, that of increasing TF levels in this system. Since human exposure to compounds in both chemical classes is associated with increased incidence of thrombosis-related side effects, we expanded this analysis with a large number of well-characterized reference compounds in order to better understand the underlying mechanisms. As a result, mechanisms for increasing (AhR, histamine H1 receptor, histone deacetylase or HDAC, hsp90, nuclear factor kappa B or NFκB, MEK, oncostatin M receptor, Jak kinase, and p38 MAPK) and decreasing (vacuolar ATPase or V-ATPase) and mTOR) TF expression levels were uncovered. These data identify the nutrient, lipid, bacterial, and hypoxia sensing functions of autophagy as potential key regulatory points controlling cell surface TF levels in endothelial cells and support the mechanistic hypothesis that these functions are associated with thrombosis-related side effects in vivo.

Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms.

Addressing the safety aspects of drugs and environmental chemicals has historically been undertaken through animal testing. However, the quantity of chemicals in need of assessment and the challenges of species extrapolation require the development of alternative approaches. Our approach, the US Environmental Protection Agency's ToxCast program, utilizes a large suite of in vitro and model organism assays to interrogate important chemical libraries and computationally analyze bioactivity profiles. Here we evaluated one component of the ToxCast program, the use of primary human cell systems, by screening for chemicals that disrupt physiologically important pathways. Chemical-response signatures for 87 endpoints covering molecular functions relevant to toxic and therapeutic pathways were generated in eight cell systems for 641 environmental chemicals and 135 reference pharmaceuticals and failed drugs. Computational clustering of the profiling data provided insights into the polypharmacology and potential off-target effects for many chemicals that have limited or no toxicity information. The endpoints measured can be closely linked to in vivo outcomes, such as the upregulation of tissue factor in endothelial cell systems by compounds linked to the risk of thrombosis in vivo. Our results demonstrate that assaying complex biological pathways in primary human cells can identify potential chemical targets, toxicological liabilities and mechanisms useful for elucidating adverse outcome pathways.

Consideration of the cellular microenvironment: physiologically relevant co-culture systems in drug discovery.

There is renewed interest in phenotypic approaches to drug discovery, using cell-based assays to select new drugs, with the goal of improving pharmaceutical success. Assays that are more predictive of human biology can help researchers achieve this goal. Primary cells are more physiologically relevant to human biology and advances are being made in methods to expand the available cell types and improve the potential clinical translation of these assays through the use of co-cultures or three-dimensional (3D) technologies. Of particular interest are assays that may be suitable for industrial scale drug discovery. Here we review the use of primary human cells and co-cultures in drug discovery and describe the characteristics of co-culture models for inflammation biology (BioMAP systems), neo-vascularization and tumor microenvironments. Finally we briefly describe technical trends that may enable and impact the development of physiologically relevant co-culture assays in the near future.

Systems biology in drug discovery and development.

The complexity of human biology makes it challenging to develop safe and effective new medicines. Systems biology omics-based efforts have led to an explosion of high-throughput data and focus is now shifting to the integration of diverse data types to connect molecular and pathway information to predict disease outcomes. Better models of human disease biology, including more integrated network-based models that can accommodate multiple omics data types, as well as more relevant experimental systems, will help predict drug effects in patients, enabling personalized medicine, improvement of the success rate of new drugs in the clinic, and the finding of new uses for existing drugs.

Neoclassic drug discovery: the case for lead generation using phenotypic and functional approaches.

Innovation and new molecular entity production by the pharmaceutical industry has been below expectations. Surprisingly, more first-in-class small-molecule drugs approved by the U.S. Food and Drug Administration (FDA) between 1999 and 2008 were identified by functional phenotypic lead generation strategies reminiscent of pre-genomics pharmacology than contemporary molecular targeted strategies that encompass the vast majority of lead generation efforts. This observation, in conjunction with the difficulty in validating molecular targets for drug discovery, has diminished the impact of the "genomics revolution" and has led to a growing grassroots movement and now broader trend in pharma to reconsider the use of modern physiology-based or phenotypic drug discovery (PDD) strategies. This "From the Guest Editors" column provides an introduction and overview of the two-part special issues of Journal of Biomolecular Screening on PDD. Terminology and the business case for use of PDD are defined. Key issues such as assay performance, chemical optimization, target identification, and challenges to the organization and implementation of PDD are discussed. Possible solutions for these challenges and a new neoclassic vision for PDD that combines phenotypic and functional approaches with technology innovations resulting from the genomics-driven era of target-based drug discovery (TDD) are also described. Finally, an overview of the manuscripts in this special edition is provided.