Biology subjects

Kemp, J. P.

Publications and source records attributed to Kemp, J. P..

10 recordsLinked to original sources

bioRxiv2026

NSAIDs impair fracture healing by disrupting neutrophil-mediated repair

Neutrophils are among the first immune cells recruited to fractures, yet their contribution to bone repair remains poorly understood. Using live imaging and neutrophil perturbation in adult zebrafish, we show that neutrophils establish the early fracture microenvironment. Neutrophils rapidly accumulated at fractures, underwent NETosis, and exhibited transcriptional programmes associated with matrix remodelling. Compromising neutrophil recruitment, via ibuprofen treatment or orthogonal perturbations, increased fracture non-union, delayed osteoblast differentiation, impaired mineralisation, and altered callus architecture. Mechanistically, neutrophils actively interacted with extracellular matrix proteins, including laminin, fibronectin, and collagen I, through uptake, trafficking and secretion-associated pathways. Together, our findings reveal that neutrophils establish a provisional emergency fracture matrix that templates subsequent bone repair, providing a mechanistic link between early non-steroidal anti-inflammatory drug (NSAID) exposure and impaired skeletal regeneration.

immunology↗

bioRxiv2026

Differential control of both cell cycle-regulated and quantitative histone mRNA expression by Drosophila Mute

Coupling histone gene expression to S phase of the cell cycle is essential for genome duplication and stability. Activation of Cyclin E/Cdk2 at the G1-S transition stimulates high-level expression of histone genes during S phase, but how histone genes are turned off at the end of S phase is not understood. Here we demonstrate that the essential Drosophila gene mute functions to repress inappropriate histone mRNA accumulation outside of S phase by counteracting Cyclin E/Cdk2-dependent phosphorylation of Mxc, which activates histone gene expression. Additionally, Mute plays contrasting roles in histone gene expression during S phase by promoting high levels of H1, H2a and H2b expression but not H3 and H4. Although Mute is present only at replication-dependent histone genes, its loss leads to 801 differentially regulated genes, primarily those involved in muscle related processes in late-stage embryos. Thus, disruptions of histone gene expression control alters the transcriptome resulting in developmental defects.

cell biology↗

bioRxiv2025

The genetic architecture of trabecular bone score and association with fracture: a genome-wide association and meta-analysis

BackgroundTrabecular bone score (TBS) is a texture-based measurement derived from DXA scans, which describes the distribution of mineral across the vertebral bodies. Identifying its genetic determinants is crucial for enhancing understanding of its biological basis and clarifying its relationship with fracture risk. MethodsWe conducted a large-scale genome-wide association study (GWAS) of TBS from 44,767 participants (95.08% European ancestry). Sex heterogeneity was assessed through sex-stratified GWAS. Post-GWAS analyses included functional annotation, gene-set enrichment analysis, and cis-expression quantitative trait locus (cis-eQTL) colocalization. Two-sample and multivariable Mendelian randomization (MR) were employed to investigate the causal effect of TBS on fractures. FindingsWe identified 33 independent variants associated with TBS, which explained 4.06% of TBS phenotypic variance. All the discovered signals map to previously identified BMD-associated loci. Additionally, we identified genetic variants in the RAB11FIP3 locus that exhibited a sex-heterogeneous effect, being associated with TBS exclusively in males. Functional annotation and colocalization identified functional genes related to TBS. The two-sample and multivariable MR analyses indicated that TBS potentially has an independent causal effect on fracture risk. InterpretationOur study unveiled 33 independent loci associated with TBS, all in BMD-associated loci. One locus was further identified as associated with TBS only in males. MR results suggested that genetically derived TBS may be causally associated with fracture risk at different sites, potentially beyond BMD. This study provides insights into the TBS genetic architecture and uncovers its potential clinical applications in fracture risk prediction. FundingAll funding information can be found in the Acknowledgements section. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSOsteoporosis is a common disease prevalent in older adults, mainly diagnosed by low bone mineral density and disruption of bone architecture. While the genetic determinants of bone mass have been well studied, the genetic architecture of bone features beyond BMD remains largely unknown. Added value of this studyThis study presents a large genome-wide association meta-analysis of the trabecular bone score (TBS), a measurement of trabecular distribution of bone mineralization across vertebral bodies. Our study identified 33 independent variants associated with TBS and one association signal only in males. Functional annotation highlighted crucial genes related to TBS. The two-sample and multivariable Mendelian randomization (MR) analyses suggested that TBS may be causally linked with fracture risk, potentially independent of BMD. Implications of all the available evidenceOur study represents an expansion of the traditional bone density phenotype used in most previous skeletal genetic studies. Based on the findings that all of the significant loci for TBS have been previously identified in GWAS of BMD, we conclude that TBS-associated variants have pleiotropic effects affecting not only mineral density but also the distribution patterns of minerals in the cancellous bone. Continuing to perform genetic studies of new skeletal phenotypes beyond BMD could ultimately impact the management and prediction of osteoporosis patients.

genomics↗

bioRxiv2024

Cell cycle-regulated transcriptional pausing of Drosophila replication-dependent histone genes

Coordinated expression of replication-dependent (RD) histones genes occurs within the Histone Locus Body (HLB) during S phase, but the molecular steps in transcription that are cell cycle regulated are unknown. We report that Drosophila RNA Pol II promotes HLB formation and is enriched in the HLB outside of S phase, including G1-arrested cells that do not transcribe RD histone genes. In contrast, the transcription elongation factor Spt6 is enriched in HLBs only during S phase. Proliferating cells in the wing and eye primordium express full-length histone mRNAs during S phase but express only short nascent transcripts in cells in G1 or G2 consistent with these transcripts being paused and then terminated. Full-length transcripts are produced when Cyclin E/Cdk2 is activated as cells enter S phase. Thus, activation of transcription elongation by Cyclin E/Cdk2 and not recruitment of RNA pol II to the HLB is the critical step that links histone gene expression to cell cycle progression in Drosophila.

cell biology↗

bioRxiv2022

Mandatory coupling of zygotic transcription to DNA replication in early Drosophila embryos

Collisions between transcribing RNA polymerases and DNA replication forks are disruptive. The threat of collisions is particularly acute during the rapid early embryonic cell cycles of Drosophila when S phase occupies the entirety of interphase. We hypothesized that collision-avoidance mechanisms safeguard the onset of zygotic transcription in these cycles. To explore this hypothesis, we used real-time imaging of transcriptional events at the onset of each interphase. Endogenously tagged RNA polymerase II (RNAPII) abruptly formed clusters before nascent transcripts accumulated, indicating recruitment prior to transcriptional engagement. Injection of inhibitors of DNA replication prevented RNAPII clustering, blocked formation of foci of the pioneer factor Zelda, and largely prevented expression of transcription reporters. Knockdown of Zelda or the histone acetyltransferase CBP prevented RNAPII cluster formation except at the replication-dependent (RD) histone gene locus. We suggest a model in which the passage of replication forks allows Zelda and a distinct pathway at the RD histone locus to reconfigure chromatin to nucleate RNAPII clustering and promote transcriptional initiation. The replication dependency of these events defers initiation of transcription and ensures that RNA polymerases transcribe behind advancing replication forks. The resulting coordination of transcription and replication explains how early embryos circumvent collisions and promote genome stability.

cell biology↗

bioRxiv2020

The transcriptome of regenerating zebrafish scales identifies genes involved in human bone disease

Zebrafish scales are mineralised plates that can regenerate involving de novo bone formation. This presents an opportunity to uncover genes and pathways relevant to human musculoskeletal disease relevant to impaired bone formation. To investigate this hypothesis, we defined transcriptomic profiles of ontogenetic and regenerating scales, and identified 604 differentially expressed genes (DEGs) that were enriched for extracellular matrix, ossification, and cell adhesion pathways. Next, we showed that human orthologues of DEGs were 2.8 times more likely to cause human monogenic skeletal diseases (P<8x10-11), and they showed enrichment for human orthologues associated with polygenetic disease traits including stature, bone density and osteoarthritis (P<0.005). Finally, zebrafish mutants of two human orthologues that were robustly associated with height and osteoarthritis (COL11A2) or bone density only (SPP1) developed skeletal abnormalities consistent with our genetic association studies. Col11a2Y228X/Y228X mutants showed endoskeletal features consistent with abnormal growth and osteoarthritis, whereas spp1P160X/P160X mutants had elevated bone density (P<0.05). In summary, we show that transcriptomic studies of regenerating zebrafish scales have potential to identify new genes and pathways relevant to human skeletal disease.

genetics↗

bioRxiv2020

Osteocyte Transcriptome Mapping Identifies a Molecular Landscape Controlling Skeletal Homeostasis and Susceptibility to Skeletal Disease

Osteocytes are master regulators of the skeleton. We mapped the transcriptome of osteocytes from different skeletal sites, across age and sexes in mice to reveal genes and molecular programs that control this complex cellular-network. We define an osteocyte transcriptome signature of 1239 genes that distinguishes osteocytes from other cells. 77% have no previously known role in the skeleton and are enriched for genes regulating neuronal network formation, suggesting this program is important in osteocyte communication. We evaluated 19 skeletal parameters in 733 knockout mouse lines and reveal 26 osteocyte transcriptome signature genes that control bone structure and function. We showed osteocyte transcriptome signature genes are enriched for human orthologs that cause monogenic skeletal disorders (P=2.4x10-22) and are associated with the polygenic diseases osteoporosis (P=1.8x10-13) and osteoarthritis (P=1.6x10-7). Thus, we reveal the molecular landscape that regulates osteocyte network formation and function and establish the importance of osteocytes in human skeletal disease.

systems biology↗

bioRxiv2019

Genome-wide association study identifies 49 common genetic variants associated with handedness.

Handedness, a consistent asymmetry in skill or use of the hands, has been studied extensively because of its relationship with language and the over-representation of left-handers in some neurodevelopmental disorders. Using data from the UK Biobank, 23andMe and 32 studies from the International Handedness Consortium, we conducted the worlds largest genome-wide association study of handedness (1,534,836 right-handed, 194,198 (11.0%) left-handed and 37,637 (2.1%) ambidextrous individuals). We found 41 genetic loci associated with left-handedness and seven associated with ambidexterity at genome-wide levels of significance (P < 5x10-8). Tissue enrichment analysis implicated the central nervous system and brain tissues including the hippocampus and cerebrum in the etiology of left-handedness. Pathways including regulation of microtubules, neurogenesis, axonogenesis and hippocampus morphology were also highlighted. We found suggestive positive genetic correlations between being left-handed and some neuropsychiatric traits including schizophrenia and bipolar disorder. SNP heritability analyses indicated that additive genetic effects of genotyped variants explained 5.9% (95% CI = 5.8% - 6.0%) of the underlying liability of being left-handed, while the narrow sense heritability was estimated at 12% (95% CI = 7.2% - 17.7%). Further, we show that genetic correlation between left-handedness and ambidexterity is low (rg = 0.26; 95% CI = 0.08 - 0.43) implying that these traits are largely influenced by different genetic mechanisms. In conclusion, our findings suggest that handedness, like many other complex traits is highly polygenic, and that the genetic variants that predispose to left-handedness may underlie part of the association with some psychiatric disorders that has been observed in multiple observational studies.

genetics↗

bioRxiv2019

A rare SMAD9 mutation identifies the BMP signalling pathway as a potential osteoanabolic target

To identify targets for novel anabolic medicines for osteoporosis, we recruited a large cohort with unexplained high bone mass (HBM). Exome sequencing identified a rare (minor allele frequency 0.0014) missense mutation in SMAD9 (c.65T>C, p.Leu22Pro) segregating with HBM in an autosomal dominant family. The same mutation was identified in another two unrelated individuals with HBM. In-silico protein modelling predicts the mutation severely disrupts the MH1 DNA-binding domain of SMAD9. Affected individuals have bone mineral density [BMD] Z-Scores +3 to +5, with increased volumetric cortical and trabecular BMD, increased cortical thickness, and low/normal bone turnover. Fractures and nerve compressions are not seen. Both genome-wide, and gene-based association testing of heel estimated-BMD in >362,924 UK-Biobank British subjects showed strong associations with SMAD9 (PGWAS=6x10-16; PGENE =8x10-17). Smad9 is highly expressed in murine osteocytes and zebrafish bone tissue. Our findings support SMAD9 as a novel HBM gene, and a potential novel osteoanabolic target.

genetics↗

bioRxiv2018

An Atlas of Human and Murine Genetic Influences on Osteoporosis

Osteoporosis is a common debilitating chronic disease diagnosed primarily using bone mineral density (BMD). We undertook a comprehensive assessment of human genetic determinants of bone density in 426,824 individuals, identifying a total of 518 genome-wide significant loci, (301 novel), explaining 20% of the total variance in BMD--as estimated by heel quantitative ultrasound (eBMD). Next, meta-analysis identified 13 bone fracture loci in ~1.2M individuals, which were also associated with BMD. We then identified target genes from cell-specific genomic landscape features, including chromatin conformation and accessible chromatin sites, that were strongly enriched for genes known to influence bone density and strength (maximum odds ratio = 58, P = 10-75). We next performed rapid throughput skeletal phenotyping of 126 knockout mice lacking eBMD Target Genes and showed that these mice had an increased frequency of abnormal skeletal phenotypes compared to 526 unselected lines (P < 0.0001). In-depth analysis of one such Target Gene, DAAM2, showed a disproportionate decrease in bone strength relative to mineralization. This comprehensive human and murine genetic atlas provides empirical evidence testing how to link associated SNPs to causal genes, offers new insights into osteoporosis pathophysiology and highlights opportunities for drug development.

genomics↗