Biology subjects

Brooks, T.

Publications and source records attributed to Brooks, T..

11 recordsLinked to original sources

bioRxiv2026

p63 regulates stem cell maintenance and age-associated functional decline in human airway basal cells

Age is a principal risk factor for chronic respiratory diseases. During aging, the airway epithelium undergoes structural and functional changes, including a reduced regenerative capacity. Basal cells act as stem/progenitor cells within the airway epithelium and are known to acquire age-dependent intrinsic defects, such as genomic mutations, transcriptomic changes and declining stem cell potential. However, the molecular mechanisms bridging transcriptomic change and stem cell function are unknown. Here we show that the transcription factor p63, a key regulator of epithelial cell identity, controls airway basal cell progenitor function in vitro and declines in expression with aging. We found impaired in vitro 2D colony and 3D organoid formation potential, as well as reduced culture longevity in primary human nasal basal cells isolated from older adults (>70 years) compared to those from pediatric (<10 years) donors. p63 protein expression was lower in basal cells from older adults and p63-regulated genes were enriched among genes whose expression changed with aging. Overexpression of p63 in older adult basal cells partially rescued progenitor cell functions, while gene knockdown in pediatric cells caused functional deficits. Integrative transcriptomic analyses revealed the network of p63-regulated genes in basal cells and demonstrated similarities in pathway engagement between TP63-knockdown cells and aged epithelium. Thus, while exogenous p63 expression alone could not rejuvenate older adult epithelial cells, p63 has an influential role in declining epithelial stem cell function during airway aging. Defining the upstream mechanisms controlling p63 decline during epithelial aging may reveal novel targets to promote healthy aging and reduce the burden of chronic lung disease.

cell biology↗

bioRxiv2026

Gut-derived serine protease reduces sleep but extends lifespan

Sleep has historically been viewed through a brain-centric lens with little known about the contribution of the periphery. Through a targeted screen of secreted peptides from the fat body, gut, and body wall muscle in Drosophila, we identified CG11037, a trypsin-like serine endopeptidase secreted from midgut enterocytes, as a previously unrecognized regulator of sleep. Loss of CG11037 reduces daily sleep, as well as sleep following injury/infection, although recovery is enhanced suggesting reduced need for sleep during sickness. Proteomic analysis of flies with reduced CG11037 revealed altered oxidative stress response pathways including cytochrome P450-related proteins. Indeed, gut-specific knockdown of Cyp6a2 or Cyp28d1 phenocopies CG11037 sleep defects, and loss of CG11037 or P450 elevates reactive oxygen species (ROS) selectively in the gut without affecting brain ROS. Rescue of sleep by antioxidant treatment demonstrates that peripheral ROS accumulation drives the behavioral phenotype. Strikingly, despite physiological dysfunction and reduced sleep, CG11037 or Cytochrome P450 knockdown extends lifespan in a ROS-dependent manner, suggesting that stress adaptation of these knockdowns allows them to live longer. Together, these findings uncover a mechanism for the unexpected association of reduced sleep and extended lifespan.

genetics↗

bioRxiv2025

Developmental wave of programmed ganglion cell death in human retinal organoids

The delicate and complex structure of the neural retina that enables proper visual function is achieved during embryonic development through a precise balance of proliferation, differentiation, and cell death. Retinal ganglion cells (RGC), the only output neurons of the retina, show a steady increase in numbers during development except for two conserved waves of developmental cell death. However, the mechanisms responsible for these phenomena in the human retina are incompletely understood. In this work, we took advantage of human induced pluripotent stem cell (hiPSC)-derived retinal organoids to explore these questions. Using different markers and quantitative techniques in three different hiPSC lines, we found a consistent decrease in RGC numbers at week 8 of differentiation, corresponding to the timing of the early developmental wave described in other vertebrates. This decrease coincided with a peak in caspase 3 activation and TUNEL(+) staining, suggesting an apoptotic mechanism. Notably, this occurred without caspase 9 activation or an increased BAX/BCL2 ratio, but with elevated caspase 8 activation, indicating involvement of the extrinsic apoptotic pathway. Together, these results show for the first time the intrinsic ability of the human retina to regulate RGC numbers through programmed cell death, providing insight into conserved developmental mechanisms and informing the use of retinal organoids in basic and translational research.

developmental biology↗

bioRxiv2024

The transcriptomic landscape of monosomy X (45,X) during early human fetal and placental development

Monosomy X (45,X) is associated with Turner syndrome and pregnancy loss in humans, but the underlying mechanisms remain unclear. We therefore analyzed the transcriptomic landscape of clinically relevant human fetal 45,X tissues (including pancreas, liver, kidney, skin, placenta) with matched 46,XX and 46,XY control samples between 11-15 weeks post conception (n=78). Although most pseudoautosomal region 1 (PAR1) genes were lower in monosomy X tissues, we also found reduced expression of several key genes escaping X inactivation (e.g., KDM5C and KDM6A), and potentially clinically important transcripts such as genes implicated in ascending aortic aneurysm. In contrast, higher expression of an autosomal, long non-coding RNA (OVCH1-AS1) was seen in all 45,X tissues. In the placenta, lower expression of CSF2RA was demonstrated, likely contributing to immune dysregulation. Taken together, these findings provide novel insights into the biological consequences of a single X chromosome during early human development and potential insights in genetic mechanisms in Turner syndrome.

genetics↗

bioRxiv2024

Sex differences in early human fetal brain development

The influence of sex chromosomes and sex hormones on early human brain development is poorly understood. We therefore undertook transcriptomic analysis of 46,XY and 46,XX human brain cortex samples (n=64) at four different time points between 7.5 and 17 weeks post conception (wpc), in two independent studies. This developmental period encompasses the onset of testicular testosterone secretion in the 46,XY fetus (8wpc). Differences in sex chromosome gene expression included X-inactivation genes (XIST, TSIX) in 46,XX samples; core Y chromosome genes (n=18) in 46,XY samples; and two Y chromosome brain specific genes, PCDH11Y and RP11-424G14.1. PCDH11Y (protocadherin11 Y-linked) regulates excitatory neurons; this gene is unique to humans and is implicated in language development. RP11-424G14.1 is a novel long non-coding RNA. Fewer differences in sex hormone pathway-related genes were seen. The androgen receptor (AR, NR4A2) showed cortex expression in both sexes, which decreased with age. Global cortical sex hormone effects were not seen, but more localized AR mechanisms may be important with time (e.g., hypothalamus). Taken together, our data suggest that limited but potentially important sex differences occur during early human fetal brain development.

developmental biology↗

bioRxiv2023

Single-nucleus RNA-sequencing reveals novel potential mechanisms of ovarian insufficiency in 45,X Turner Syndrome

Study questionCan single-nuclei and bulk RNA sequencing technologies be used to elucidate novel mechanisms of ovarian insufficiency in Turner Syndrome (TS)? Summary answerUsing single-nucleus and bulk RNA sequencing approaches, we identified novel potential pathogenic mechanisms underlying ovarian insufficiency in TS including and beyond X chromosome haploinsufficiency. What is known alreadyTurner syndrome (TS) is the most common genetic cause of Primary Ovarian Insufficiency (POI) in humans. Morphological analyses of human fetal 45,X ovaries have demonstrated fewer germ cells and marked apoptosis established by 15-20 weeks post conception (wpc); however, we do not understand why POI develops mechanistically in the first instance. Study design, size, durationSingle-nucleus RNA sequencing (snRNA-seq): two 46,XX and two 45,X (TS) human fetal ovaries at 12-13 wpc. Bulk RNA sequencing: 19 human fetal ovary, 20 fetal testis, and 8 fetal control tissue (n=47 total samples; Carnegie Stage 22-16wpc). Participants/materials, setting, methodsTo identify novel potential mechanisms of ovarian insufficiency in TS and to characterise X chromosome gene expression in the 45,X ovary, we performed snRNA-seq of peri-meiotic 46,XX (n=2) and 45,X (n=2) fetal ovaries at 12-13 weeks post conception (wpc); and 2) a bulk RNA sequencing time-series analysis of fetal ovary, testis, and control samples across four developmental timepoints. Main results and the role of chanceGerm and somatic cell subpopulations were mostly shared across 46,XX and 45,X ovaries, aside from a 46XX-specific/45,X-depleted cluster of oogonia ("synaptic oogonia") containing genes with functions relating to sex chromosome synapsis; histone modification; intracellular protein regulation and chaperone systems. snRNA-seq enabled accurate cell counting localised to individual cell clusters; the 45,X ovary has fewer germ cells than the 46,XX ovary in every germ cell subpopulation, confirmed by histopathological analysis. The normal sequence of X-chromosome inactivation and reactivation is disrupted in 45,X ovaries; XIST was not expressed in 45,X somatic cells but was present in germ cell clusters, albeit with lower expression than in corresponding 46,XX clusters. The 45,X ovary has a globally abnormal transcriptome, with low expression of genes with proteostasis functions (RSP4X); cell cycle progression (BUB1B); and OXPHOS mitochondrial energy production (COX6C, ATP11C). Genes with higher expression in 45,X cell populations were enriched for apoptotic functions (e.g., NR4A1). Limitations, reasons for cautionLimitations include the relatively small sample size of the snRNA-seq analysis and the focus on a fixed meiotic timepoint which may overlook a dynamic process over time. Wider implications of the findingsWe characterise the human fetal peri-meiotic 45,X ovary at single-cell resolution and offer insights into novel pathogenic mechanisms underlying ovarian insufficiency in TS. Although asynapsis due to X chromosome haploinsufficiency likely plays a significant role, these data suggest meiotic failure and ovarian insufficiency may be a combinatorial process characterised by periods of vulnerability throughout early 45,X germ cell development Study funding/competing interest(s)This research was funded in whole, or in part, by the Wellcome Trust Grants 216362/Z/19/Z to SMcG-B and 209328/Z/17/Z to JCA. Human fetal material was provided by the Joint MRC/Wellcome Trust (Grant MR/R006237/1) Human Developmental Biology Resource (http://www.hdbr.org). Research at UCL Great Ormond Street Institute of Child Health is supported by the National Institute for Health Research, Great Ormond Street Hospital Biomedical Research Centre (grant IS-BRC-1215-20012).

genomics↗

bioRxiv2023

Mapping the anatomical and transcriptional landscape of early human fetal ovary development

The complex genetic mechanisms underlying human ovary development can give rise to clinical phenotypes if disrupted, such as Primary Ovarian Insufficiency and Differences of Sex Development. Through a clinically-focused lens, we combine single-nuclei RNA sequencing, bulk RNA sequencing, and micro-focus computed tomography to elucidate the anatomy and transcriptional landscape of the human fetal ovary across key developmental timepoints (Carnegie Stage 22 until 20 weeks post conception). We show the marked growth and distinct morphological changes within the fetal ovary at the critical timepoint of germ cell expansion, and demonstrate that the fetal ovary becomes more transcriptomically distinct from the testis with age. We describe novel ovary developmental pathways, relating to neuroendocrine signalling, energy homeostasis, mitochondrial networks, piRNA processes, and inflammasome regulation. We define transcriptional regulators and candidate genes for meiosis within the developing ovary. Together, this work advances our fundamental understanding of human ovary development and clinical ovarian insufficiency phenotypes.

genomics↗

bioRxiv2023

Deep Phenotyping of the Lipidomic Response in COVID and non-COVID Sepsis

Lipids may influence cellular penetrance by pathogens and the immune response that they evoke. Here we find a broad based lipidomic storm driven predominantly by secretory (s) phospholipase A2 (sPLA2) dependent eicosanoid production occurs in patients with sepsis of viral and bacterial origin and relates to disease severity in COVID-19. Elevations in the cyclooxygenase (COX) products of arachidonic acid (AA), PGD2 and PGI2, and the AA lipoxygenase (LOX) product, 12-HETE, and a reduction in the high abundance lipids, ChoE 18:3, LPC-O-16:0 and PC-O-30:0 exhibit relative specificity for COVID-19 amongst such patients, correlate with the inflammatory response and link to disease severity. Linoleic acid (LA) binds directly to SARS-CoV-2 and both LA and its di-HOME products reflect disease severity in COVID-19. AA and LA metabolites and LPC-O-16:0 linked variably to the immune response. These studies yield prognostic biomarkers and therapeutic targets for patients with sepsis, including COVID-19. An interactive purpose built interactive network analysis tool was developed, allowing the community to interrogate connections across these multiomic data and generate novel hypotheses.

systems biology↗

bioRxiv2022

A cell atlas of human adrenal cortex development and disease

The adrenal glands synthesize and release essential steroid hormones such as cortisol and aldosterone, but the mechanisms underlying human adrenal gland development are not fully understood. Here, we combined single-cell and bulk RNA-sequencing, spatial transcriptomics, immunohistochemistry and micro-focus computed tomography to investigate key aspects of adrenal development in the first 20 weeks of gestation. We demonstrate rapid adrenal growth and vascularization, with cell division in the outer definitive zone (DZ). Steroidogenic pathways favor androgen synthesis in the central fetal zone (FZ), but DZ capacity to synthesize cortisol and aldosterone develops with time. Core transcriptional regulators were identified, with a role for HOPX in the DZ. Potential ligand- receptor interactions between mesenchyme and adrenal cortex were seen (e.g., RSPO3/LGR4). Growth-promoting imprinted genes were enriched in the developing cortex (e.g. IGF2, PEG3). These findings reveal new aspects of human adrenal development, and have clinical implications for understanding primary adrenal insufficiency and related postnatal adrenal disorders, such as adrenal tumor development, steroid disorders and neonatal stress.

developmental biology↗

bioRxiv2022

Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection.

We analyzed the dynamics of the earliest T cell response to SARS-COV-2. A wave of TCRs strongly but transiently expand during infection, frequently peaking the same week as the first positive PCR test. These expanding TCR CDR3s were enriched for sequences functionally annotated as SARS-COV-2 specific. Most epitopes recognized by the expanding TCRs were highly conserved between SARS-COV-2 strains, but not with circulating human coronaviruses. Many expanding CDR3s were also present at high precursor frequency in pre-pandemic TCR repertoires. A similar set of early response TCRs specific for lymphocytic choriomeningitis virus epitopes were also found at high frequency in the pre-infection naive repertoire. High frequency naive precursors may allow the T cell response to respond rapidly during the crucial early phases of acute viral infection. One-Sentence SummaryHigh frequency naive precursors underly the rapid T cell response during the crucial early phases of acute viral infection.

immunology↗

bioRxiv2021

Circadian regulation of lung repair and regeneration

Optimal lung repair and regeneration is essential for recovery from viral infections such as that induced by influenza A virus (IAV). We have previously demonstrated that lung inflammation induced by IAV is under circadian control. However, it is not known if the circadian clock exerts its influence on lung repair and regenerative processes independent of acute inflammation from IAV. Here, we demonstrate for the first time that lung organoids have a functional clock as they mature and that the absence of an intact circadian clock impairs regenerative capacity. Using several models of circadian disruption, we show that with the absence of an intact clock lung proliferation is disrupted. Further, we find that the circadian clock acts through direct control of the Wnt/{beta}-catenin pathway. We speculate, that adding the circadian dimension to the critical process of lung repair and regeneration will lead to novel therapies and improve outcomes. Finally, we use data from UK Biobank to demonstrate at the population level, the role of poor circadian rhythms in mediating negative outcomes following lung infection.

cell biology↗