Biology subjects

Simpson, D. A.

Publications and source records attributed to Simpson, D. A..

5 recordsLinked to original sources

bioRxiv2023

Global analysis of Poales diversification - parallel evolution in space and time into open and closed habitats

O_LIPoales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test the hypotheses that Poales species are assembled into distinct phyloregions, with centres of high phylogenetic diversity and endemism clustered in tropical regions, and that cosmopolitan families show parallel transitions into open and closed habitats at different times. C_LIO_LIWe sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts. A dated supertree of Poales was constructed. We integrated spatial phylogenetics with regionalization analyses, historical biogeography, ancestral state estimations, and models of contingent evolution. C_LIO_LIDiversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time, space, and traits, most prominently in tropical and southern latitudes. Our results reveal parallel and recurrent patterns of habitat and trait transitions in the species-rich families Poaceae and Cyperaceae, yet other smaller families display unique evolutionary trajectories. C_LIO_LIThe Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats. C_LI

ecology↗

bioRxiv2023

Mapping the daily rhythmic transcriptome in the diabetic retina

Retinal function shows marked changes from day to night. Yet, clinical diagnosis, treatments, and experimental sampling occur during the day, leaving a significant gap in our understanding of the pathobiology occurring at night. While there is evidence that diabetes disrupts the circadian system that optimizes our physiology to the environmental light/dark cycle, the impact of such disruption is not well understood. This study investigates whether diabetes affects the retinas daily rhythm of gene expression to understand the pathobiology of diabetic retinopathy. Ins2Akita/J mice, a model of type 1 diabetes, were kept under a standard 12h:12h light/dark cycle until four months of age. Non-diabetic littermates were used as controls. Bulk mRNA sequencing was conducted in retinas collected every 4 hours throughout the 24 hr light/dark cycle. Computational approaches were used to detect rhythmicity, predict acrophase, identify differential rhythmic patterns, analyze phase set enrichment, and predict upstream regulators. The retinal transcriptome exhibited a tightly regulated rhythmic expression with a clear 12-hr axis of transcriptional rush, peaking at midday and midnight. The functions of day-peaking genes were enriched for DNA repair, RNA splicing, and ribosomal protein synthesis, whereas night-peaking genes were enriched for metabolic processes and growth factor signaling. Although the 12-hr transcriptional axis is retained in the diabetic retina, it was phase advanced by approximately 1-3 hours with a wider distribution. Upstream regulator analysis for the genes that showed phase shifts identified oxygen sensing mechanisms and HIF1alpha as regulators, but not the circadian clock, which remained in phase to the light/dark cycle. We propose a model in which early in diabetes, the retina experiences a jet lag caused by the entrained circadian clock and its output being in one phase and metabolic pathways related to neuronal dysfunction and hypoxia driving advancement of gene expression to a different phase. Further studies are now required to evaluate the chronic implications of such internal jet lag for development of diabetic retinopathy.

bioinformatics↗

bioRxiv2022

Mre11 liberates cGAS from nucleosome sequestration during tumorigenesis

Oncogene-induced replication stress generates endogenous DNA damage that activates cGAS/STING-mediated innate immune signaling and tumor suppression1-3. However, the mechanism for cGAS activation by endogenous DNA damage remains enigmatic, particularly given the constitutive inhibition of cGAS by high-affinity histone acidic patch (AP) binding4-10. Here we report an in vivo CRISPR screen that identified the DNA double strand break sensor Mre11 as a suppressor of mammary tumorigenesis induced by Myc overexpression and p53 deficiency. Mre11 antagonizes Myc-induced proliferation through cGAS/STING activation. Direct binding of the Mre11-Rad50-Nbn (MRN) complex to nucleosomes displaces cGAS from AP sequestration, which is required for DNA damage-induced cGAS mobilization and activation by cytosolic DNA. Mre11 is thereby essential for cGAS activation in response to oncogenic stress, cytosolic DNA transfection, and ionizing radiation. Furthermore, we show Mre11-dependent cGAS activation suppresses Myc-induced proliferation through ZBP1/RIPK3/MLKL-mediated necroptosis. In human triple-negative breast cancer, ZBP1 downregulation correlates with increased genome instability, decreased immune infiltration, and poor patient prognosis. These findings establish Mre11 as a critical link between DNA damage and cGAS activation that regulates tumorigenesis through ZBP1-dependent necroptosis. One-sentence summaryMre11 is required for cGAS activation during oncogenic stress and promotes ZBP1-dependent necroptosis.

cell biology↗

bioRxiv2022

Zinc supplementation induced transcriptional changes in primary human retinal pigment epithelium: a single cell RNA sequencing study to understand age-related macular degeneration

Zinc supplementation had been shown to be beneficial to slow the progression of age-related macular degeneration (AMD). However, the molecular mechanism underpinning this benefit is not well understood. In this study, we used single-cell RNA sequencing to identify transcriptomic changes induced by zinc supplementation in human primary retinal pigment epithelial (RPE) cells in culture. The RPE cells were allowed to mature for up to 19 weeks. After one or 18 weeks in culture, we supplemented the culture medium with 125 M added zinc for one week. During maturation RPE cells developed high transepithelial electrical resistance, extensive, but variable, pigmentation and deposited sub-RPE material similar to the hallmark lesions of AMD. Unsupervised cluster analysis of the combined transcriptome of the cells isolated after two-, nine- and 19 weeks in culture, showed a significant degree of heterogeneity. Clustering based on 234 pre-selected RPE specific genes, identified from the literature, divided the cells into two distinct clusters we defined as more- and less-differentiated cells. The proportion of more differentiated cells increased with time in culture, but appreciable numbers of cells remained less differentiated even at 19 weeks. Pseudotemporal ordering identified 537 genes that could be implicated in the dynamics of RPE cell differentiation (FDR< 0.05). Zinc treatment resulted in the differential expression of 281 of these genes (FDR< 0.05). These genes were associated with several biological pathways including extracellular remodelling, retinoid metabolism and modulation of ID1/ID3 transcriptional regulation, to name a few. Overall, zinc had a multitude of effects on the RPE transcriptome including a number of genes that are involved in pigmentation, complement regulation, mineralisation and cholesterol metabolism processes associated with AMD.

cell biology↗

bioRxiv2020

Hyperactive end joining repair mediates resistance to DNA damaging therapy in p53-deficient cells

TP53 mutations in cancer are associated with poor patient outcomes and resistance to DNA damaging therapies1-3. However, the mechanisms underlying treatment resistance in p53-deficient cells remain poorly characterized. Here, we show that p53-deficient cells exhibit hyperactive repair of therapy-induced DNA double strand breaks (DSBs), which is suppressed by inhibition of DNA-dependent protein kinase (DNA-PK). Single-cell analyses of DSB repair kinetics and cell cycle state transitions reveal an essential role for DNA-PK in suppressing S phase DNA damage and mitotic catastrophe in p53-deficient cells. Yet, a subset of p53-deficient cells exhibit intrinsic resistance to therapeutic DSBs due to a repair pathway that is not sensitive to DNA-PK inhibition. We show that p53 deficiency induces overexpression of DNA Polymerase Theta (Pol {theta}), which mediates an alternative end-joining repair pathway that becomes hyperactivated by DNA-PK inhibition4. Combined inhibition of DNA-PK and Pol {theta} restores therapeutic DNA damage sensitivity in p53-deficient cells. Thus, our study identifies two targetable DSB end joining pathways that can be suppressed as a strategy to overcome resistance to DNA-damaging therapies in p53-deficient cancers.

cell biology↗