Biology subjects

Watson, C. J.

Publications and source records attributed to Watson, C. J..

9 recordsLinked to original sources

bioRxiv2024

Loss of cped1 does not affect bone and lean mass in zebrafish

Human genetic studies have nominated Cadherin-like and PC-esterase Domain-containing 1 (CPED1) as a candidate target gene mediating bone mineral density (BMD) and fracture risk heritability. Recent efforts to define the role of CPED1 in bone in mouse and human models have revealed complex alternative splicing and inconsistent results arising from gene targeting, making its function in bone difficult to interpret. To better understand the role of CPED1 in adult bone mass and morphology, we conducted a comprehensive genetic and phenotypic analysis of cped1 in zebrafish, an emerging model for bone and mineral research. We analyzed two different cped1 mutant lines and performed deep phenotyping to characterize more than 200 measures of adult vertebral, craniofacial, and lean tissue morphology. We also examined alternative splicing of zebrafish cped1 and gene expression in various cell/tissue types. Our studies fail to support an essential role of cped1 in adult zebrafish bone. Specifically, homozygous mutants for both cped1 mutant alleles, which are expected to result in loss-of-function and impact all cped1 isoforms, exhibited no significant differences in the measures examined when compared to their respective wildtype controls, suggesting that cped1 does not significantly contribute to these traits. We identified sequence differences in critical residues of the catalytic triad between the zebrafish and mouse orthologs of CPED1, suggesting that differences in key residues, as well as distinct alternative splicing, could underlie different functions of CPED1 orthologs in the two species. Our studies fail to support a requirement of cped1 in zebrafish bone and lean tissue, adding to evidence that variants at 7q31.31 can act independently of CPED1 to influence BMD and fracture risk. Lay summaryBone mineral density (BMD) is a key indicator for predicting and diagnosing osteoporosis and fracture risk, and it has been estimated that up to 89% of variation in BMD is determined by genetics. Multiple human genetics studies have nominated CPED1 as a potential gene underlying BMD and fracture risk heritability, however the function of CPED1 remains poorly understood. In this study, we examined the role of cped1 in bone by quantifying over 200 morphological measures of vertebral and craniofacial bone size, shape, and density in two different mutant lines of zebrafish in which cped1 function was reduced or eliminated. We also examined lean tissue mass because co-heritability of this trait with BMD has also been hypothesized to involve CPED1. Surprisingly, despite the loss of cped1 function, there were no significant differences between the mutant zebrafish and their respective controls. Our study therefore fails to support a role for cped1 in bone and lean tissue, suggesting that hereditary influence on BMD and fracture risk can occur independently of CPED1.

genetics↗

bioRxiv2022

Tideglusib mitigates dystrophic pathology in skeletal muscle and restores diastolic function in young D2 mdx mice

Introductory paragraphDuchenne muscular dystrophy (DMD) is a severe X-linked muscle wasting disorder that affects 1 in 5,000 males worldwide1. It is caused by the absence of functional dystrophin, which compromises muscle integrity, leading to progressive muscle wasting and weakness2. Glucocorticoids are the standard of care for patients with DMD as they delay the loss of ambulation by an average of 3 years3; however, they are also associated with adverse effects such as insulin resistance and increased risk of type 2 diabetes4. Thus, alternative therapeutic options should be explored. Here, we show that treating the DBA/2J mdx mouse with the glycogen synthase kinase 3 (GSK3) inhibitor, tideglusib, improved skeletal muscle function and insulin sensitivity, while also attenuating the hypermetabolic phenotype previously observed in these mice5. Furthermore, treating mdx mice with the GSK3 inhibitor, lithium, augmented the benefits of voluntary wheel running on insulin sensitivity and skeletal muscle function despite running half of the total distance compared to control-treated mdx mice. This is important given that some patients with DMD may not be able to engage in adequate amounts of physical activity. Thus, GSK3 inhibition alone or in combination with exercise can enhance skeletal muscle function and insulin sensitivity in mdx mice.

physiology↗

bioRxiv2022

Kynurenine metabolism is altered in mdx mice: a potential muscle to brain connection

Regular exercise can direct muscle kynurenine (KYN) metabolism toward the neuroprotective branch of the kynurenine pathway thereby limiting the accumulation of neurotoxic metabolites in the brain and contributing to mental resilience. While the effect of regular exercise has been studied, the effect of muscle disease on KYN metabolism has not yet been investigated. Previous work has highlighted anxiety-like behaviors in approximately 25% of patients with DMD, possibly due to altered KYN metabolism. Here, we characterized KYN metabolism in mdx mouse models of Duchenne muscular dystrophy (DMD). Young (8-10 week old) DBA/2J (D2) mdx mice, but not age-matched C57BL/10 (C57) mdx mice, had lower levels of circulating KYNA and KYNA:KYN ratio compared with their respective wild-type (WT) controls. Moreover, only D2 mdx mice displayed signs of anxiety-like behaviour, spending more time in the corners of their cages during a novel object recognition test when compared with WT. Along with this, we found that muscles from D2 mdx mice had less peroxisome proliferator-activated receptor-gamma coactivator 1-alpha and kynurenine amino transferase-1 enzyme content as well as elevated expression of inflammatory cytokines compared with WT muscles. Thus, our pilot work shows that KYN metabolism is altered in D2 mdx mice, with a potential contribution from altered muscle health.

physiology↗

bioRxiv2021

Wnt16 exerts pleiotropic effects on bone and lean mass in zebrafish

Bone and muscle interact through developmental, mechanical, paracrine, and autocrine signals. Genetic variants at the CPED1-WNT16 locus are dually associated with bone- and muscle-related traits. While Wnt16 is necessary for bone mass and strength, this fails to explain pleiotropy at this locus. Here, we show wnt16 is required for spine and muscle morphogenesis in zebrafish. In embryos, wnt16 is expressed in dermomyotome and developing notochord, and contributes to larval myotome morphology and notochord elongation. Later, wnt16 is expressed at the ventral midline of the notochord sheath, and contributes to spine mineralization and osteoblast recruitment. Morphological changes in wnt16 mutant larvae are mirrored in adults, indicating that wnt16 impacts bone and muscle morphology throughout the lifespan. Finally, we show that wnt16 is a gene of major effect on lean mass at the CPED1-WNT16 locus. Our findings indicate that Wnt16 is secreted in structures adjacent to developing bone (notochord) and muscle (dermomyotome) where it affects the morphogenesis of each tissue, thereby rendering wnt16 expression into dual effects on bone and muscle morphology. This work expands our understanding of wnt16 in musculoskeletal development and supports the potential for variants to act through WNT16 to influence bone and muscle via parallel morphogenetic processes. AUTHOR SUMMARYIn humans, genetic variants (DNA sequences that vary amongst individuals) have been identified that appear to influence bone and skeletal muscle mass. However, how single genes and genetic variants exert dual influence on both tissues is not well understood. In this study, we found a gene called wnt16 is necessary for specifying the size and shape of muscle and bone during development in zebrafish. Moreover, we disentangled how wnt16 affects both tissues: distinct cellular populations adjacent to muscle and bone secrete Wnt16, where it acts as a signal this guides the size and shape of each tissue. This is important because in humans, genetic variants near the WNT16 gene have effects on both bone- and muscle-related traits. This study expands our understanding of the role of WNT16 in bone and muscle development, and helps to explain how genetic variants near WNT16 affect traits for both tissues. Moreover, WNT16 is actively being explored as a target for osteoporosis therapies; our study could have implications with regard to the potential to target WNT16 to treat bone and muscle simultaneously.

genetics↗

bioRxiv2020

Synonymous mutations reveal genome-wide driver mutation rates in healthy tissues

Genetic alterations that drive clonal expansions in ostensibly healthy tissues have implications for cancer risk. However, the total rate at which clonal expansions occur in healthy tissues remains unknown. Synonymous passenger mutations that hitchhike to high variant allele frequency due to a linked driver mutation can be used to estimate the total rate of positive selection across the genome. Because these synonymous hitchhikers are influenced by all mutations under selection, regardless of type or location, they can be used to estimate how many driver mutations are missed by narrow gene-focused sequencing panels. Here we analyse the variant allele frequency spectrum of synonymous passenger mutations to estimate the total rate at which mutations driving clonal expansions occur in healthy tissues. By applying our framework to data from physiologically healthy blood, we find that a large fraction of mutations driving clonal expansions occur outside of canonical cancer driver genes. In contrast, analysis of data from healthy oesophagus reveals little evidence for many driver mutations outside of those in NOTCH1 and TP53. Our framework, which generalizes to other tissues, sheds light on the fraction of drivers mutations that remain undiscovered and has implications for cancer risk prediction.

evolutionary biology↗

bioRxiv2019

The Evolutionary Dynamics and Fitness Landscape of Clonal Haematopoiesis

Somatic mutations acquired in healthy tissues as we age are major determinants of cancer risk. Whether variants confer a fitness advantage or rise to detectable frequencies by chance, however, remains largely unknown. Here, by combining blood sequencing data from [~]50,000 individuals, we reveal how mutation, genetic drift and fitness differences combine to shape the genetic diversity of healthy blood ( clonal haematopoiesis). By analysing the spectrum of variant allele frequencies we quantify fitness advantages for key pathogenic variants and genes and provide bounds on the number of haematopoietic stem cells. Positive selection, not drift, is the major force shaping clonal haematopoiesis. The remarkably wide variation in variant allele frequencies observed across individuals is driven by chance differences in the timing of mutation acquisition combined with differences in the cell-intrinsic fitness effect of variants. Contrary to the widely held view that clonal haematopoiesis is driven by ageing-related alterations in the stem cell niche, the data are consistent with the age dependence being driven simply by continuing risk of mutations and subsequent clonal expansions that lead to increased detectability at older ages.

genomics↗

bioRxiv2018

Deep Phenotyping Enhances Somatic Mutant Detection and Mosaic Pattern Recognition in the Zebrafish Skeleton

Genetic mosaicism manifests as spatially variable phenotypes, whose detection and interpretation remains challenging. This study identifies biological factors influencing spatial phenotypic patterns in the skeletons of somatic mutant zebrafish, and tests methods for their analysis using deep phenotyping. We explore characteristics of loss-of-function clusters in the skeleton of CRISPR-edited G0 (\"crispant\") zebrafish, and identify a distinctive size distribution shown to arise from clonal fragmentation and merger events. Using microCT-based phenomics, we describe diverse phenotypic manifestations in somatic mutants for genes implicated in monogenic (plod2 and bmp1a) and polygenic (wnt16) bone diseases, each showing convergence with germline mutant phenomes. Finally, we describe statistical frameworks for phenomic analysis which confers heightened sensitivity in discriminating somatic mutant populations, and quantifies spatial phenotypic variation. Our studies provide strategies for decoding spatially variable phenotypes which, paired with CRISPR-based screens, can identify genes contributing to skeletal disease.

genetics↗

bioRxiv2017

ScreenCube: A 3D Printed System For Rapid and Cost-Effective Chemical Screening in Adult Zebrafish

Phenotype-based small molecule screens in zebrafish embryos and larvae have been successful in accelerating pathway and therapeutic discovery for diverse biological processes. Yet, the application of chemical screens to adult physiologies has been relatively limited due to additional demands on cost, space, and labor associated with screens in adult animals. Here, we present a 3D printed system and methods for intermittent drug dosing that enable rapid and cost-effective chemical administration in adult zebrafish. Using pre-filled screening plates, the system enables dosing of 96 fish in {small tilde}3min, with a tenfold-reduction in drug quantity compared to that used in previous chemical screens in adult zebrafish. We characterize water quality kinetics during immersion in the system, and use these kinetics to rationally design intermittent dosing regimens that result in 100% fish survival. As a demonstration of system fidelity, we show the potential to identify two known chemical inhibitors of adult tail fin regeneration, cyclopamine and dorsomorphin. By developing methods for rapid and cost-effective chemical administration in adult zebrafish, this study expands the potential for small molecule discovery in post-embryonic models of development, disease, and regeneration.

pharmacology and toxicology↗

bioRxiv2017

microCT-Based Skeletal Phenomics in Zebrafish Reveals Virtues of Deep Phenotyping at the Whole-Organism Scale

Phenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of measures comprised of morphological and densitometric traits from a large number sites in the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes associated with human brittle bone disease and thyroid stimulating hormone receptor hyperactivity. Finally, we develop allometric models and show their potential to aid in the discrimination of mutant phenotypes masked by alterations in growth. Our studies demonstrate virtues of deep phenotyping in a spatially distributed organ. Analyzing phenotypic patterns may increase productivity in genetic screens, and could facilitate the study of genetic variants associated with smaller effect sizes, such as those that underlie complex diseases.

genetics↗