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Plasma proteomic signature of human longevity.
No full textThe identification of protein targets that exhibit anti-aging clinical potential could inform interventions to lengthen the human health span. Most previous proteomics research has been focused on chronological age instead of longevity. We leveraged two large population-based prospective cohorts with long follow-ups to evaluate the proteomic signature of longevity defined by survival to 90 years of age. Plasma proteomics was measured using a SOMAscan assay in 3067 participants from the Cardiovascular Health Study (discovery cohort) and 4690 participants from the Age Gene/Environment Susceptibility-Reykjavik Study (replication cohort). Logistic regression identified 211 significant proteins in the CHS cohort using a Bonferroni-adjusted threshold, of which 168 were available in the replication cohort and 105 were replicated (corrected p value <0.05). The most significant proteins were GDF-15 and N-terminal pro-BNP in both cohorts. A parsimonious protein-based prediction model was built using 33 proteins selected by LASSO with 10-fold cross-validation and validated using 27 available proteins in the validation cohort. This protein model outperformed a basic model using traditional factors (demographics, height, weight, and smoking) by improving the AUC from 0.658 to 0.748 in the discovery cohort and from 0.755 to 0.802 in the validation cohort. We also found that the associations of 169 out of 211 proteins were partially mediated by physical and/or cognitive function. These findings could contribute to the identification of biomarkers and pathways of aging and potential therapeutic targets to delay aging and age-related diseases
Enhancing the Small-Scale Screenable Biological Space beyond Known Chemogenomics Libraries with Gray Chemical Matter─Compounds with Novel Mechanisms from High-Throughput Screening Profiles
No full textPhenotypic assays have become an established approach to drug discovery. Greater disease relevance is often achieved through cellular models with increased complexity and more detailed readouts, such as gene expression or advanced imaging. However, the intricate nature and cost of these assays impose limitations on their screening capacity, often restricting screens to well-characterized small compound sets such as chemogenomics libraries. Here, we outline a cheminformatics approach to identify a small set of compounds with likely novel mechanisms of action (MoAs), expanding the MoA search space for throughput limited phenotypic assays. Our approach is based on mining existing large-scale, phenotypic high-throughput screening (HTS) data. It enables the identification of chemotypes that exhibit selectivity across multiple cell-based assays, which are characterized by persistent and broad structure activity relationships (SAR). We validate the effectiveness of our approach in broad cellular profiling assays (Cell Painting, DRUG-seq, and Promotor Signature Profiling) and chemical proteomics experiments. These experiments revealed that the compounds behave similarly to known chemogenetic libraries, but with a notable bias toward novel protein targets. To foster collaboration and advance research in this area, we have curated a public set of such compounds based on the PubChem BioAssay dataset and made it available for use by the scientific community
Recommendations for measuring and standardizing light for laboratory mammals to improve welfare and reproducibility in animal research.
No full textLight enables vision and exerts widespread effects on physiology and behavior, including regulating circadian rhythms, sleep, hormone synthesis, affective state, and cognitive processes. Appropriate lighting in animal facilities may support welfare and ensure that animals enter experiments in an appropriate physiological and behavioral state. Furthermore, proper consideration of light during experimentation is important both when it is explicitly employed as an independent variable and as a general feature of the environment. This Consensus View discusses metrics to use for the quantification of light appropriate for nonhuman mammals and their application to improve animal welfare and the quality of animal research. It provides methods for measuring these metrics, practical guidance for their implementation in husbandry and experimentation, and quantitative guidance on appropriate light exposure for laboratory mammals. The guidance provided has the potential to improve data quality and contribute to reduction and refinement, helping to ensure more ethical animal use
Applying the Estimand Framework to Non-inferiority Trials
No full textMost published applications of the estimand framework have focused on superiority trials. However, non-inferiority trials present specific challenges compared to superiority trials. The ICH E9(R1) addendum on estimands and sensitivity analysis in clinical trials notes there may be special considerations to the implementation of estimands in clinical trials with a non-inferiority objective yet provides little guidance.
This paper discusses considerations that trial teams should make when defining estimands for a clinical trial with a non-inferiority objective. We briefly introduce non-inferiority trials and discuss how the pre-ICH E9(R1) way of establishing non-inferiority can be embraced by the estimand framework. We discuss the use of the Per Protocol analysis set given the ICH E9(R1) guidance and how the estimand can be constructed for a non-inferiority objective. We examine what clinical questions of interest can be formulated in the context of non-inferiority trials and outline why it is not sensible to describe an estimand as “conservative”.
Key considerations in non-inferiority trials are whether trials should have more than one primary estimand and the choice of non-inferiority margin. Other important issues relate to assay sensitivity, switching from non-inferiority to superiority and estimation. We conclude by providing a list of recommendations, and important considerations for defining estimands for trials with a non-inferiority objective
A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction.
No full textSickle cell disease (SCD) is a prevalent, life-threatening condition attributable to a heritable mutation in β-hemoglobin. Therapeutic induction of fetal hemoglobin (HbF) can ameliorate disease complications and has been intently pursued. However, safe and effective small-molecule inducers of HbF remain elusive. We report the discovery of dWIZ-1 and dWIZ-2, molecular glue degraders of the WIZ transcription factor that robustly induce HbF in erythroblasts. Phenotypic screening of a cereblon (CRBN)-biased chemical library revealed WIZ as a previously unknown repressor of HbF. WIZ degradation is mediated by recruitment of WIZ(ZF7) to CRBN by dWIZ-1, as resolved by crystallography of the ternary complex. Pharmacological degradation of WIZ was well tolerated and induced HbF in humanized mice and cynomolgus monkeys. These findings establish WIZ degradation as a globally accessible therapeutic strategy for SCD
Unlocking the Potential: A systematic review of Master Protocol in Pediatrics
No full textImportance: The use of master protocols allows for innovative approaches to clinical trial designs, potentially enabling new approaches to operations and analytics and creating value for patients and drug developers.
Objective: Pediatric research has been conducted for many decades, but the use of novel designs such as master protocols are in pediatric research is unclear. We aimed to conduct a systematic review to evaluate the utilization of master protocols in pediatric drug development.
Evidence Review: A systematic search was performed in September 2022 using two data sources (PubMed and ClinicalTrials.gov) and included studies conducted in the last 10 years. General study information was extracted such as study type, study status, therapeutic area, clinical trial phase. Study characteristics that are specific to pediatric studies were also collected such as the minimum and maximum age of the study participants, whether the study is in the same adult master protocol, whether the pediatric drug dosing is the same as adult. Lastly, important study design elements of the master protocol were collected such as number of test drug arms and whether randomization and/or concurrent control was used.
Findings: Thirty-eight studies were included in the final analysis, and 16 (42%) are platform trials, 15 (39%) are basket trials and 7 (18%) are umbrella studies. Oncology (58%) is the largest therapeutic area for the included studies, followed by infectious diseases treating COVID (18%) and HIV (8%). The majority of the studies are early phase trials (60%). The use of master protocol in pediatrics started in 1997 and suddenly increased in 2020, mostly in Oncology disease area. Twenty-six (68%) of the 38 pediatric studies are included in the same adult master protocol, and 12 (32%) studies used the same dosing as adult. Overall, 17 studies (45%) used randomization, among which the majority (13 out of 17, 76%) used concurrent control.
Conclusions and Relevance: Master protocols are starting to be adopted in pediatric clinical research, but on a small scale and could be substantially expanded. Work is still required to further understand the barriers in implementing pediatric master protocols, from setting up infrastructure to interpreting study findings
First Pd-catalyzed C(sp2)–H / C(sp2)–H coupling of Limonene
No full textLimonene undergoes a regioselective Pd(II)-catalyzed C(sp2)–H / C(sp2)–H coupling with acrylic acid esters and amides, ,β-unsaturated ketones, styrenes and allyl acetate, affording novel 1,3-dienes. DFT computations gave results in accord with the experimental results and allowed to formulate a plausible mechanism. The post-functionalization of one of the coupled products was achieved via a large scale Sonogashira reaction conducted under micellar catalysis
mRNA Display Identifies Potent, Paralog-Selective Peptidic Ligands for ARID1B
No full textThe ARID1A and ARID1B subunits are mutually exclusive components of the BAF variant of SWI/SNF chromatin remodeling complexes. Loss of function mutations in ARID1A are frequently observed in various cancers, resulting in a dependency on the paralog ARID1B for cancer cell proliferation. However, ARID1B has never been targeted directly, and the high degree of sequence similarity to ARID1A poses a challenge for the development of selective binders. In this study, we used mRNA display to identify peptidic ligands that bind with nanomolar affinities to ARID1B and showed high selectivity over ARID1A. Using orthogonal biochemical, biophysical, and chemical biology tools, we demonstrate that the peptides engage two different binding pockets, one of which directly involves an ARID1B-exclusive cysteine that could allow covalent targeting by small molecules. Our findings impart the first evidence of the ligandability of ARID1B, provide valuable tools for drug discovery, and suggest opportunities for the development of selective molecules to exploit the synthetic lethal relationship between ARID1A and ARID1B in cancer
Automated ELISA for Potency Measurements of Therapeutic Antibodies and Antibody Fragments
No full textPotency assays are essential for the development and quality control of biopharmaceutical drugs, but they are often a time limiting factor due to manual handling steps and consequently low analytical throughput. On the other hand, automation of potency assays can be challenging due to their complexity and the use of biological materials. ELISA (enzyme-linked immunosorbent assay) is widely used for potency determination and is a good candidate for automation as all ELISA types depend on the same basic steps: coating, blocking, sample incubation, detection, and signal measurement. Nevertheless, potency ELISA methods still require drug-specific development and assay validation thereby complicating automation efforts. To simplify potency testing by ELISA, we first developed a manual protocol generally applicable to different drugs and then adapted this protocol for automated measurements. We describe the critical parameters which had to be adapted to transfer the manual ELISA to an automated liquid handling system and demonstrate that gravimetric sample dilution is unnecessary with the automated protocol. Both manual and automated protocols were validated and compared using multiple biotherapeutics. The automated protocol showed lower variability and higher accuracy than the manual method
Guide for Combining Primary Tumors for Statistical Analysis in Rodent Carcinogenicity Studies.
No full textThe Tumor Combination Guide was created at the request of the U. S. Food and Drug Administration (FDA) by a Working Group of biopharmaceutical experts from international societies of toxicologic pathology, the Food and Drug Administration (FDA), and members of the Standard for Exchange of Nonclinical Data (SEND) initiative, to assist pharmacology/toxicology reviewers and biostatisticians in statistical analysis of nonclinical tumor data. The guide will also be useful to study and peer review pathologists in interpreting the tumor data. This guide provides a higher-level hierarchy of tumor types or categories correlating the tumor names from the International Harmonization of Nomenclature and Diagnostic Criteria (INHAND) publications with those available in the NEOPLASM controlled terminology (CT) code list in SEND. The version of CT used in a study should be referenced in the nonclinical study data reviewer's guide (SDRG) (section 3.1) of electronic submissions to the FDA. The tumor combination guide instructions and examples are in a tabular format to make informed decisions for combining tumor data for statistical analysis. The strategy for combining tumor types for statistical analysis is based on scientific criteria gleaned from the current scientific literature; as SEND and INHAND terminology and information evolve, this guide will be updated