Biology subjects

Burke, R.

Publications and source records attributed to Burke, R..

18 recordsLinked to original sources

bioRxiv2026

Cellular uptake of folate-olaparib conjugates via folate receptor-mediated endocytosis: Potential for selective delivery of DNA damage response inhibitors into tumour cells

The folate receptor (FR) is overexpressed in a range of human tumours including ovarian cancer cells. We propose that the overexpression of the FR on the surface of ovarian tumour cells could be exploited for the selective delivery of a DNA damage response inhibitor (DDRi) in the form of an intact folate drug conjugate (FDC). This approach would improve the therapeutic index of the parent DDRi facilitating combination studies of the DDRi-based FDC with DNA damaging chemotherapy. FR-mediated cellular uptake of the proposed folate drug conjugates is requisite for FDC selective delivery into tumours. In this study, we synthesised a series of olaparib-based folate conjugates that maintained the biochemical PARP1 inhibition associated with olaparib and showed binding affinity for the folate receptor. Significantly, we identified compounds 10b and 11 that selectively enter FR overexpressing tumour cells via folate receptor-mediated endocytosis in their intact form and engage with their target as demonstrated by the potent inhibition of PARylation (KB cells, PARylation IC50 = 5.7 and 3.9 nM; respectively).

biochemistry↗

bioRxiv2026

Fibroblast response to burn injury in larval zebrafish mirrors developmental maturation and is inhibited by infiltrating neutrophils

Fibroblasts mediate tissue repair after damage, but aberrant fibroblast behavior in response to injury can result in impaired wound healing. Severe burn injury often results in tissue scarring, but the underlying mechanisms by which fibroblasts respond to burn injury and the role of inflammation in fibrosis are not well understood. Here we developed fluorescent reporters of collagen expressing mesenchymal cells enabling real time imaging of fibroblasts during homeostatic development and in response to burn injury using larval zebrafish. We find that fibroblasts derived from the mesenchyme respond to burn injury by engaging in a maturation process, characterized by the expression of vimentin, which is reminiscent of larval development. In burned tissue, fibroblast maturation is perturbed by prolonged neutrophil infiltration, resulting in disorganized extracellular matrix (ECM) and delayed ECM remodeling, which can be rescued by neutrophil depletion. This work adds to our understanding of fibroblast development in zebrafish and shows that collagen expressing mesenchymal cells regulate ECM remodeling in coordination with immune cells during burn wound healing. Summary StatementVimentin-positive fibroblasts are required for normal wound healing in larval zebrafish, but the presence of inflammatory neutrophils after burn injury impairs fibroblast maturation and collagen remodeling.

Developmental Biology↗

bioRxiv2025

Dietary Zn governs protein: carbohydrate regulation of fecundity and lifespan in Drosophila melanogaster

Recent work has shown that dietary zinc (Zn) restriction has a strong effect to limit egg production in female Drosophila, while also producing a variable, but beneficial, effect on lifespan. This combination of phenotypes is interesting because it is consistent with the disposable soma theory of ageing, and phenocopies the well-studied effects of reducing the dietary protein-to-carbohydrate (P:C) ratio. Thus, Zn restriction may be a key precision nutrition intervention to extend lifespan. To investigate this, we decided to assess the interactive effects of dietary Zn and P:C ratios on reproduction and lifespan. We found that the interventions interact, producing equally strong, but not additive, effects to modify female reproduction and lifespan. Specifically, both Zn restriction and lowering the P:C ratio reduced reproduction and benefited lifespan, but only when the other nutrient was maintained at high levels. When either Zn or P:C was at intermediate or low levels, adjusting the other nutritional component varied reproduction, but did so independently of lifespan, which remained fixed at a high level. Disrupting the Zn transporter, white, modified the magnitude of some effects, but not their direction. Thus, the micronutrient Zn modifies life-history outcomes to the same extent as altering the macronutrient (P:C) ratio, indicating its nutritional availability is likely to be a key determinant of fitness for Drosophila.

evolutionary biology↗

bioRxiv2025

Modulation of temporal prediction by STN-DBS in Parkinson's disease: Links between behavior and cortical oscillations

BACKGROUNDAccurate temporal prediction is essential for adaptive behavior and relies on coordinated neural activity within cortico-basal ganglia circuits. Parkinsons disease (PD), with the main hallmark of dopaminergic depletion and abnormal neural synchrony, impairs this ability. Deep brain stimulation deep brain stimulation (DBS) of the subthalamic nucleus (STN) is a widely used treatment for reducing motor symptoms in PD, but its effects on temporal prediction remain not fully understood. OBJECTIVESThis study aimed to investigate how STN-DBS influences temporal prediction performance and its underlying oscillatory dynamics in PD patients, with a particular focus on beta-band power and delta-band inter-trial phase consistency (ITPC). METHODS13 PD patients (5 female, age: 64 {+/-} 5.7 years; disease duration: 11.8 {+/-} 1.8 years) with STN-DBS performed a temporal prediction task with (DBS ON) and without (DBS OFF) stimulation, while 64-channel-electroencephalography (EEG) was recorded. 20 age-matched healthy controls completed the same task. Behavioral performance was assessed using psychometric function slopes. Time-frequency analyses and source-level EEG measures examined beta power and delta ITPC. RESULTSPD patients showed impaired temporal prediction performance compared to controls, reflected in shallower psychometric slopes. DBS significantly improved performance to a level comparable to those of controls. EEG revealed reduced beta suppression in PD patients during DBS OFF, while beta suppression in DBS ON was comparable to controls. Both DBS OFF and ON exhibited reduced delta ITPC compared to controls. In DBS ON, source-level delta ITPC was positively correlated with temporal prediction accuracy. CONCLUSIONSTN-DBS improves temporal prediction performance in PD, likely through modulation of beta and delta oscillatory activity. While beta power suppression is partially restored, deficits in delta phase alignment persist, suggesting frequency-specific DBS effects on temporal prediction processes.

neuroscience↗

bioRxiv2025

Differential contributions of low-frequency phase and power in crossmodal temporal prediction: A MEG study

BACKGROUNDOur representation of time is embedded within multisensory perception, based on sight, sound, or touch. However, despite being a crucial aspect of daily life, the neural dynamics of cross-modal temporal predictions remain elusive. The objective of this study was to investigate neural correlates of tactile-to-visual influences on temporal prediction using magnetencephalography (MEG). We hypothesized to observe increased inter-trial phase consistency (ITPC) in the low-frequency delta range (0.5-4 Hz) due to their involvement in temporal prediction. In addition, stronger ITPC values should correlate with a steeper slope of the psychometric function, indicating phase alignments as a likely cause of more consistent temporal predictions. METHODSThe study was conducted within one MEG session employing a modified version of the time prediction task by Roth et al. [2013] and Daume et al. [2021]. Participants (N=23) observed a visual stimulus moving towards an occluder. Shortly before reaching the occluder, the visual stimulus faded in luminance to make the visual offset less informative. Instead, participants received a brief tactile stimulus to the ipsilateral hand at the time point of disappearance, generating a temporal expectation regarding its reappearance on the opposite side of the occluder. After variable time intervals, a visual stimulus reappeared, and participants had to indicate whether this was too early or too late compared to the movement before disappearance. A non-predictive control condition involved participants judging the variable luminance of the reappearing visual stimulus compared to its initial luminance at the beginning of the trial. Psychometric curves were fitted to the behavioral data of each participant and condition, and MEG recordings were analyzed using time-frequency representations obtained by wavelet convolution. To compare spectral power and ITPC estimates between conditions within frequency bands showing significant differences to the pre-stimulus baseline, we used cluster-based permutation statistics. Pearsons correlations were used to examine the relationship between ITPC or power estimates and the steepness of each participants psychometric function. RESULTSITPC analysis revealed strong increases in the delta range around stimulus disappearance and reappearance. Delta ITPC was significantly stronger during temporal prediction compared to the control condition. Only delta ITPC, but not delta power, correlated with the consistency of temporal prediction. Furthermore, temporal prediction led to increased alpha power in the dorsolateral and medial prefrontal cortex, as well as the right superior temporal sulcus and middle temporal gyrus, whereas beta power did not show differences between conditions. CONCLUSIONOur findings suggest that increased delta ITPC is likely caused by phase resets driven by the temporal prediction process rather than evoked neural activity. Furthermore, our findings indicate that phase alignments occur during crossmodal visuo-tactile-to-visual temporal predictions, even with a combination of non-rhythmic and discrete stimulation. This highlights the broad applicability of phase resets of neural oscillations as a mechanism for predicting timing across various types of stimuli.

neuroscience↗

bioRxiv2025

JNK activation dynamics drive distinct gene expression patterns over time mediated by mRNA stability

c-Jun N-terminal kinase (JNK) plays a major role in the regulation of cell death. Numerous studies have highlighted how the dynamics of this kinase dictate whether cells survive in response to cellular stress or induce cell death mechanisms. However, it is less clear how these dynamics potentially contribute to downstream gene expression patterns through regulated transcription factors like c-Jun. To investigate this question, we used a treatment strategy with the JNK agonist anisomycin to drive specific dynamics; sustained, transient, or pulsed activation, and assessed the impact on downstream gene expression patterns. We observed that multiple gene expression patterns emerged depending on the dynamics of JNK activation. Ordinary Differential Equation (ODE) models suggest that a subset of these clusters are mediated by mRNA stability and supported by measured mRNA decay rates. Specific gene clusters also show enrichment in specific cellular pathways, including cell death and inflammatory signaling, suggesting these dynamics contribute to differential regulation of these pathways. These findings highlight another contribution of JNK dynamics to the regulation of cellular responses to stress stimuli.

systems biology↗

bioRxiv2024

Mammalian heat shock protein A4 family ortholog Hsc70Cb is required for two phases of spermatogenesis in D. melanogaster

Heat shock proteins play essential roles as molecular chaperones, enacting protein folding and preventing of protein aggregation. In a previous study, a predicted damaging homozygous non-synonymous genetic variant was detected in the heat shock protein gene HSPA4L. Here, we used RNA interference in Drosophila melanogaster to explore the role of the heat shock protein A member 4 family (HSPA4) family in male fertility. Expression of the fly orthologue of the mammalian HSPA4 and HSPA4L genes, Hsc70Cb, was ablated in the male germline using two RNAi lines and the Nanos-Gal4 driver. Strong knockdown of Hsc70Cb in male germ cells resulted in male sterility, characterised by the absence of germ cells in testes and the over-proliferation of the testis soma. A less robust knockdown of Hsc70Cb in the male germline resulted in a sperm individualisation defect and a failure of sperm release into the seminal vesicle (analogous to the epididymis). When human HSPA4 or HSPA4L cDNA was introduced into infertile Hsc70Cb mutant flies, a partial rescue was observed, whereby in the robust Hsc70Cb knockdown setting germ cells progressed to the spermatocyte stage before undergoing cell death. Collectively, the absence of sperm in the Hsc70Cb (line 1) is consistent with the infertile man harbouring a homozygous HSPA4L genetic variant, supporting the hypothesis that HSPA4L is required for male fertility in humans and flies and highlighting the utility of the fly as a model of human spermatogenesis. In briefHsc70Cb is essential for spermatogonia survival and sperm individualisation in Drosophila. This study highlights the conserved roles of the HSPA4 family across animals and the utility of flies as a model organism for male fertility research.

genetics↗

bioRxiv2024

Delta phase-dependent modulation of temporal predictions by parietal transcranial alternating current stimulation

BackgroundPrevious research has shown that temporal prediction processes are associated with phase resets of low-frequency delta oscillations in a network of parietal, sensory and frontal areas during non-rhythmic sensory stimulation. Transcranial alternating current stimulation (tACS) modulates perceptually relevant brain oscillations in a frequency and phase-specific manner, allowing the assessment of their functional qualities in certain cognitive functions like temporal prediction. ObjectiveWe addressed the relation between oscillatory activity and temporal prediction by using tACS to manipulate brain activity in a sinusoidal manner. This enables the investigation of the relevance of low-frequency oscillations phase for temporal prediction. MethodsDelta tACS was applied over the left and right parietal cortex in two separate unimodal and crossmodal experiments. Participants judged either the visual or the tactile reappearance of a uniformly moving visual stimulus, which shortly disappeared behind and occluder. Using an intermittent electrical stimulation protocol, tACS was applied with six different phase shifts relative to sensory stimulation in both experiments while participants performed a temporal prediction task. Additionally, a computational model was developed and analysed to elucidate oscillation-based functional principles for the generation of temporal predictions. ResultsOnly in the unimodal experiment, the application of delta tACS resulted in a phase-dependent modulation of temporal prediction performance. By considering the effect of sustained tACS in the computational model, we demonstrate that the entrained dynamics can phase-specifically modulate temporal prediction accuracy. ConclusionOur findings suggest that phase-specific neuromodulation through delta tACS can influence temporal prediction accuracy in a unimodal context. This provides support to the notion that low-frequency delta oscillations are of causal relevance for temporal prediction.

neuroscience↗

bioRxiv2024

Dietary zinc limitation dictates lifespan and reproduction trade-offs of Drosophila mothers

Dietary metal ions significantly influence the lifespan and reproduction of Drosophila females. In this study, we show that while the depletion of all metal ions from the diet adversely affects reproduction and lifespan, the absence of Zn alone negatively impacts reproduction without adversely altering maternal lifespan, indicating it can dictate resource reallocation between key fitness traits. Although our data show that flies sense varying dietary Zn levels, they apparently do not alter their feeding preferences to optimise egg production when faced with a choice between Zn- depleted or Zn- sufficient food, but they can choose to preferentially oviposit on Zn containing food, perhaps indicating a strategy to assure offspring survival. We also uncovered a role for the white gene in sustaining high levels of egg viability when Zn is diluted in the diet. These insights into the role of dietary metal ions, particularly Zn, point to a central role for these dietary micronutrients to indicate environmental quality and so govern trade-offs between lifespan and reproduction in flies.

evolutionary biology↗

bioRxiv2024

A basic framework governing splice-site choice in eukaryotes

Changes in splicing are observed between cells, tissues, organs, individuals, and species. These changes can mediate phenotypic variation ranging from flowering time differences in plants to genetic diseases in humans. However, the genomic determinants of splicing variation are largely unknown. Here, we quantified the usage of individual splice-sites and uncover extensive variation between individuals (genotypes) in Arabidopsis, Drosophila and Humans. We used this robust quantitative measure as a phenotype and mapped variation in splice-site usage using Genome-Wide Association Studies (GWAS). By carrying out more than 130,000 GWAS with splice-site usage phenotypes, we reveal genetic variants associated with differential usage of specific splice-sites. Our analysis conclusively shows that most of the common, genetically controlled variation in splicing is cis and there are no major trans hotspots in any of the three analyzed species. High-resolution mapping allowed us to determine genome-wide patterns that govern splice-site choice. We reveal that the variability in the intronic hexamer sequence (GT[N]4 or [N]4AG) differentiates intrinsic splice-site strength and is among the primary determinants of splice-site choice. Experimental analysis validates the primary role for intronic hexamer sequences in conferring splice-site decisions. Transcriptome analyses in diverse species across the tree of life reveals that hexamer rankings explains splice-site choices from yeast to plants to humans, forming the basic framework of the splicing code in eukaryotes.

genetics↗

bioRxiv2023

The polyamines spermine and spermidine inhibit or induce programmed cell death in Arabidopsis thaliana in vitro and in vivo in a dose dependent manner.

Polyamines are ubiquitous biomolecules with a number of established functions in eukaryotic cells. In plant cells, polyamines have previously been linked to abiotic and biotic stress tolerance, as well as to the modulation of programmed cell death (PCD), with contrasting reports on their pro-PCD and pro-survival effects. Here, we used two well established platforms for the study of plant PCD; Arabidopsis thaliana suspension cultures cells and the root hair assay, to examine the roles of the polyamines spermine and spermidine in the regulation of PCD. We demonstrate that both polyamines can trigger PCD when applied exogenously at higher doses, whereas at lower concentrations they inhibit PCD induced by both biotic and abiotic stimuli. Furthermore, we show that concentrations of polyamines resulting in inhibition of PCD generated a transient ROS burst in our experimental system, and activated the expression of oxidative stress- and pathogen response-associated genes. Finally, we examined PCD responses in existing Arabidopsis polyamine synthesis mutants, and identified a subtle PCD phenotype in Arabidopsis seedlings deficient in thermo-spermine. The presented data show that polyamines can have a role in PCD regulation, however that role is dose-dependent and consequently they may act as either inhibitors, or inducers, of PCD in Arabidopsis.

plant biology↗

bioRxiv2023

Transcriptional signatures associated with waterlogging stress responses and aerenchyma formation in barley root tissue

The negative impact of soil waterlogging on crop production is expected to increase due higher frequencies of extreme rainfall events arising from climate change. Consequently, understanding the molecular mechanisms that enable plants to mitigate waterlogging stress is critical for breeding programmes, particularly in the case of waterlogging-susceptible crop species, such as barley (Hordeum vulgare). Aerenchyma formation is a key morphological adaptation allowing plants to cope with waterlogging stress and hypoxic conditions, however, the genetic regulation of its development in barley remains largely unresolved. In this study, two barley cultivars with contrasting waterlogging tolerance (Franklin and Yerong) were subjected to waterlogging stress, followed by analysis of phenotypic traits including root aerenchyma formation, and transcriptomic profiling of root tissue samples. Differential expression analyses identified genes transcriptionally responsive to 24 and 72 h of waterlogging in both cultivars, and highlighted metabolic adaptations, regulation of ROS signalling and management of stress responses as key elements of the waterlogging response. The results revealed large intra-individual variations in root aerenchyma formation, and these variations were exploited to isolate 81 candidate aerenchyma-associated genes from the generated RNA-seq datasets. Network analyses suggest the involvement of the DNA damage response gene, DRT100 and cell wall modifying genes, XHT16 and XHT15 as regulatory hub genes in aerenchyma formation. Collectively, the generated data provide insights into transcriptional signatures associated with the barley root responses to waterlogging and aerenchyma formation, informing our understanding of strategies that plants employ to cope with the negative impacts of heavy rainfall.

plant biology↗

bioRxiv2023

Arabidopsis cell suspension culture and RNA sequencing reveal regulatory networks underlying plant programmed cell death.

Programmed cell death (PCD) facilitates targeted elimination of redundant, damaged, or infected cells via genetically controlled pathways. In plants, PCD is often an essential component of normal development and can also mediate responses to abiotic and biotic stress stimuli. However, studying the transcriptional regulation of this fundamental process is hindered by difficulties in sampling small groups of cells undergoing PCD that are often buried within the bulk of living plant tissue. We addressed this challenge by using RNA sequencing (RNA-Seq) of Arabidopsis thaliana suspension cells, a system that allows precise monitoring of PCD activation and progression. The use of three PCD-inducing treatments (salicylic acid, heat and critical dilution), in combination with three cell death modulators (3- methyladenine, lanthanum chloride and conditioned medium), allowed isolation of candidate core and stimuli-specific PCD genes, inference of underlying gene regulatory networks and identification of putative transcriptional regulators. This analysis underscored cell cycle disturbance and the repression of both pro-survival stress responses and mitochondrial retrograde signalling as key elements of the PCD-associated transcriptional signature in plants. Further, phenotyping of twenty Arabidopsis T-DNA insertion mutants in selected candidate genes confirmed a role for several in PCD and stress tolerance regulation, and validated the potential of these generated resources to identify novel genes involved in plant PCD pathways and/or stress tolerance in plants.

plant biology↗

bioRxiv2021

CD4+ T cell lymphopenia and dysfunction in severe COVID-19 disease is autocrine TNF-α/TNFRI-dependent

Lymphopenia is common in severe COVID-19 disease, yet the mechanisms are poorly understood. In 148 patients with severe COVID-19, we found lymphopenia was associated with worse survival. CD4+ lymphopenia predominated, with lower CD4+/CD8+ ratios in severe COVID-19 compared to recovered, mild disease (p<0.0001). In severe disease, immunodominant CD4+ T cell responses to Spike-1(S1) produced increased in vitro TNF-, but impaired proliferation and increased susceptibility to activation-induced cell death (AICD). CD4+TNF-+ T cell responses inversely correlated with absolute CD4+ counts from severe COVID-19 patients (n=76; R=-0.744, P<0.0001). TNF- blockade including infliximab or anti-TNFRI antibodies strikingly rescued S1-specific CD4+ proliferation and abrogated S1-AICD in severe COVID-19 patients (P<0.001). Single-cell RNAseq demonstrated downregulation of Type-1 cytokines and NF{kappa}B signaling in S1-stimulated CD4+ cells with infliximab treatment. Lung CD4+ T cells in severe COVID-19 were reduced and produced higher TNF- versus PBMC. Together, our findings show COVID-19-associated CD4+ lymphopenia and dysfunction is autocrine TNF-/TNFRI-dependent and therapies targeting TNF- may be beneficial in severe COVID-19. One Sentence SummaryAutocrine TNF-/TNFRI regulates CD4+ T cell lymphopenia and dysfunction in severe COVID-19 disease.

immunology↗

bioRxiv2021

Copper signaling promotes proteostasis and animal development via allosteric activation of ubiquitin E2D conjugases

Nutrient copper supply is critical for cell growth and differentiation, and its disturbance is associated with major pathologies including cancer and neurodegeneration. Although increasing copper bioavailability in late Precambrian facilitated emergence of novel cuproproteins, their intricate regulation by this essential trace element remains largely cryptic. We found that subtle rises in cellular copper strikingly increase polyubiquitination and accelerate protein degradation within 30 minutes in numerous mammalian cell lines. We track this surprising observation to allostery induced in the UBE2D ubiquitin conjugase clade through a conserved CXXXC sub-femtomolar-affinity Cu+ binding motif. Thus, physiologic fluctuation in cytoplasmic Cu+ is coupled to the prompt degradation of UBE2D protein targets, including p53. In Drosophila harboring a larval-lethal knockdown of the nearly identical fly orthologue UbcD1, complementation with human UBE2D2 restored near-normal development, but mutation of its CXXXC Cu+ binding motif profoundly disrupted organogenesis. Nutrient Cu+ emerges as a trophic allosteric modulator of UBE2D activity through a structural motif whose evolution coincides with animal multicellularity. One Sentence SummaryModulation of nutrient copper impacts protein turnover and animal morphogenesis through conserved allostery of ubiquitin E2D conjugases. HilightsO_LINutrient copper supply is critical for cell growth and differentiation C_LIO_LIThe E2D clade of ubiquitin conjugases contains a sub-femtomolar-affinity Cu+ binding motif C_LIO_LIAllosteric activation by Cu+ markedly accelerates protein polyubiquitination C_LIO_LIThis sensor couples physiologic fluctuations in cytoplasmic Cu+ with the degradation rate of E2D targets, including p53 C_LIO_LIThis metazoan signaling mechanism is critical for drosophila morphogenesis C_LI In BriefConserved allostery of ubiquitin E2D conjugases links nutrient copper signaling to protein degradation and animal morphogenesis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/431211v2_ufig1.gif" ALT="Figure 1"> View larger version (76K): org.highwire.dtl.DTLVardef@17009fforg.highwire.dtl.DTLVardef@a07f8eorg.highwire.dtl.DTLVardef@11664c7org.highwire.dtl.DTLVardef@1327ab7_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

biochemistry↗

bioRxiv2021

Targeted therapy for LIMD1-deficient non-small cell lung cancer subtypes.

An early event in lung oncogenesis is loss of the tumour suppressor gene LIMD1 (LIM domains containing 1); this encodes a scaffold protein, which suppresses tumourigenesis via a number of different mechanisms. Approximately 45% of non-small cell lung cancers (NSCLC) are deficient in LIMD11, yet this subtype of NSCLC has been overlooked in preclinical and clinical investigations. Defining therapeutic targets in these LIMD1 loss-of-function patients is difficult due to a lack of druggable targets, thus alternative approaches are required. To this end, we performed the first drug repurposing screen to identify compounds that confer synthetic lethality with LIMD1 loss in NSCLC cells. PF-477736 was shown to selectively target LIMD1 deficient cells in vitro through inhibition of multiple kinases, inducing cell death via apoptosis. Furthermore, PF-477736 was effective in treating LIMD1-/- tumors in subcutaneous xenograft models, with no significant effect in LIMD1+/+ cells. We have identified a novel drug tool with significant preclinical characterization that serves as an excellent candidate to explore and define LIMD1-deficient cancers as a new therapeutic subgroup of critical unmet need. Significance StatementHere we provide the first proof-of-concept data validating the scope for development of a targeted therapy against the non-small cell lung cancers (NSCLC) subtypes deficient in expression of the LIMD1 tumor suppressor gene. Approximately 45% of NSCLC are deficient in LIMD11 representing at least 1.2 million lung cancer patients worldwide; yet this subtype has been ignored in preclinical and clinical investigations with no targeted therapies available. This seminal study applied synthetic lethality drug screening to target the loss/reduction of LIMD1 in lung cancer and normal cell lines, identifying and validating the multi-kinase inhibitor PF-477736 as a selectively cytotoxic compound towards LIMD1 deficient cells. This study provides rationale for further investigation into targeting LIMD1 loss in lung cancer, thereby addressing a critical unmet need for therapeutic approached to targeting LIMD1-deficent cancer subtypes.

cancer biology↗

bioRxiv2019

Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation

One of the signatures of evolutionarily related cell types is the expression of similar combinations of transcription factors in distantly related animals. Here we present evidence that sea urchin larvae possess bilateral clusters of ciliary photoreceptors that are positioned in the oral/anterior apical neurogenic domain and associated with pigment cells. The expression of synaptotagmin indicates that the photoreceptors are neurons. Immunostaining shows that the sea urchin photoreceptors express an RGR/GO-opsin, opsin3.2, which co-localizes with tubulin on immotile cilia on the cell surface. Furthermore, orthologs of several transcription factors expressed in vertebrate photoreceptors are expressed in sea urchin ciliary photoreceptors, including Otx, Six3, Tbx2/3, and Rx, a transcription factor typically associated with ciliary photoreceptors. Analysis of gene expression during sea urchin development indicates that the photoreceptors derive from the anterior apical neurogenic domain. Thus, based on location, developmental origin, and transcription factor expression, sea urchin ciliary photoreceptors are likely homologous to vertebrate rods and cones. However, we found that genes typically involved in eye development in many animals, including pax6, six1/2, eya, and dac, are not expressed in sea urchin ciliary photoreceptors. Instead, all four genes are co-expressed in the hydropore canal, indicating that these genes operate as a module in an unrelated developmental context. Thus, based on current evidence, we conclude that at least within deuterostomes, ciliary photoreceptors share a common evolutionary origin and express a shared regulatory state that includes Rx, Otx, and Six3, but not transcription factors that are commonly associated with the retinal determination circuit.

developmental biology↗

bioRxiv2019

Exploiting evolutionary herding to control drug resistance in cancer

Drug resistance mediated by clonal evolution is arguably the biggest problem in cancer therapy today. However, evolving resistance to one drug may come at a cost of decreased growth rate or increased sensitivity to another drug due to evolutionary trade-offs. This weakness can be exploited in the clinic using an approach called evolutionary herding that aims at controlling the tumour cell population to delay or prevent resistance. However, recapitulating cancer evolutionary dynamics experimentally remains challenging. Here we present a novel approach for evolutionary herding based on a combination of single-cell barcoding, very large populations of 108-109 cells grown without re-plating, longitudinal non-destructive monitoring of cancer clones, and mathematical modelling of tumour evolution. We demonstrate evolutionary herding in non-small cell lung cancer, showing that herding allows shifting the clonal composition of a tumour in our favour, leading to collateral drug sensitivity and proliferative fitness costs. Through genomic analysis and single-cell sequencing, we were also able to determine the mechanisms that drive such evolved sensitivity. Our approach allows modelling evolutionary trade-offs experimentally to test patient-specific evolutionary herding strategies that can potentially be translated into the clinic to control treatment resistance.

cancer biology↗