Biology subjects

Reid, A.

Publications and source records attributed to Reid, A..

17 recordsLinked to original sources

bioRxiv2026

Depletion of the isocitrate dehydrogenase 3 subunit IDHA-1 licenses germ cell-to-neuron direct reprogramming in C. elegans

Direct reprogramming (DR) converts one differentiated cell identity into another and is a promising strategy for regenerative approaches when cells are lost because of injury or disease. Transcription factors (TFs) that specify a given cell type can drive DR, but inhibitory mechanisms restrict this conversion in most cell types. To identify such barriers in vivo, we use Caenorhabditis elegans and the zinc finger TF CHE-1, which is required to specify the glutamatergic taste neuron fate of ASE neurons. Ectopic CHE-1 expression can induce DR of different cell types to ASE neurons upon RNAi-mediated depletion of barrier genes. Here we characterize the subunit of the mitochondrial isocitrate dehydrogenase 3 complex (IDH3), IDHA-1, as a barrier to DR of germ cells into neurons. RNAi against idha-1 produced consistent ASE fate reporter expression, accompanied by morphological changes to neuron-like structures in the germline upon ectopic CHE-1 expression. Using different neuronal gene expression reporters, single-molecule FISH, and antibody staining, we confirm that this germ cell conversion (GeCo) produces neuron-like cells. We found that loss of IDH3 activity causes metabolic perturbations that result in a variety of direct and indirect effects on DR of germ cells. One arm implicates the hypoxia-inducible factor HIF-1, which promotes GeCo. Its loss causes a significant decrease, while the vhl-1 mutant background, in which HIF-1 protein is stabilized, leads to enhanced GeCo. Another arm implicates epigenetic changes leading to a detectable loss of the repressive histone marks H3K27me3 and H3K9me3 upon idha-1 depletion. Furthermore, stable-isotope-resolved metabolomics shows strong citrate accumulation without a noteworthy drop in -Ketoglutarate (KG) levels, indicating that compensatory pathways maintain KG levels. Genetics and metabolomics analyses confirmed that Glutamate anaplerosis contributes to compensating for the loss of IDHA-1. Additionally, we found that depletion of glucose transporter FDGT-2 nearly doubles GeCo efficiency. Overall, our findings define the TCA cycle as an in vivo safeguard of germ cell identity and show that multiple metabolic inputs converge to keep germ cells refractory to TF-induced DR to neuronal cells.

biochemistry↗

bioRxiv2026

The histone code of love: epigenetics of maturation of gonads in the human blood fluke Schistosoma mansoni

Schistosoma mansoni is a parasitic flatworm that has two, genetically determined, sexes. We used aggregated data of 8 posttranslational histone modifications (ChIP-Seq), chromatin accessibility (ATAC-Seq), transcription (RNA-Seq) and genome feature annotations to decipher the histone code of genes involved in the differentiation of schistosome gonads (i.e. female ovaries and male testes). We show schistosome gonads express at least two classes of protein coding genes: H3K4me3-positive genes that display canonical features of eukaryotic protein-coding genes such as peaks of H3K4me3 at the transcription start sites (TSS) and increases in histone acetylation marks towards the transcription end site (TES), but also a non-canonical H3K9/27me3 plateau just upstream of the TSS. H3K4me3 enrichment at the TSS is highly predictive for transcription strength in these genes compared to a second class of protein coding genes (H3K4me3-negative genes) that do not display this pattern and is characterised by absence of the investigated histone marks at TSS and TES. This is indicative of the existence of hitherto unknown, potentially schistosome-specific histone marks in these genes. The absence of H3K4me3 at the TSS is not associated with inducible or stable gene expression in the gonads. Instead, gene ontology analysis indicates that H3K4me3-positive genes are related to functions which typically govern processes such as metabolism or signal transduction while H3K4me3-negative genes are dedicated to cell communication or immune responses. Second, individual histone modifications and their combinations are associated with functional features of the schistosome genome, known as "chromatin colours". In H3K4me3-positive genes, there is clear co-linearity of 3 colours, which strongly suggests a functional role for histone modifications in the control of transcription pre-initiation, promotor release, and transcription termination. Third, there are striking chromatin structure changes during maturation of the gonads in all genomic features including protein-coding and non-protein coding genes as well as repetitive sequences. The nature of these changes is different in both sexes. H3K36me3 and H3K9me3, as well as H3K23ac and H3K9ac show the strongest variations. Last, we show that pharmacological inhibition of histone demethylation activity by IOX1 leads to a concentration-dependent separation ("divorce") of schistosome couples confirming the importance of H3K36/H3K9 methylation for pairing maintenance and indicating histone demethylases as a potential drug target family. Collectively, our findings offer unprecedented insights into histone codes and chromatin dynamics governing the reproductive development of S. mansoni gonads.

developmental biology↗

bioRxiv2025

Evaluating Microglial Contributions to the Neurovascular Unit in Health and Neurodegeneration Using Human In Vitro Models

BackgroundMicroglia are emerging as critical regulators of neurovascular function in health and Alzheimers disease (AD), yet their interactions with the human neurovascular unit (NVU), particularly brain endothelial cells, remain incompletely understood. Current in vitro NVU platforms typically exclude microglia and lack perfusable vascular networks with physiologically relevant architecture. Here, we established complementary two-dimensional (2D) and three-dimensional (3D) NVU models to investigate microglia-endothelial and microglia-neurovascular interactions. MethodsHuman induced pluripotent stem cell derived-neurons (iNs), astrocytes (iAs), and microglia-like cells (iMGLs) were incorporated into a soft-lithography based engineered microvessel system to establish a multicellular neuroimmune-vascular model. To specifically evaluate iMGL-endothelial cell (EC) interactions, iMGL were co-cultured with primary human brain microvascular endothelial cells (HBMECs) and junctional protein localization was evaluated using immunofluorescence. The barrier integrity of engineered microvessels containing iMGL was evaluated using dextran permeability. Our 2D and 3D systems were stimulated with tumor necrosis factor- (TNF) to evaluate whether iMGL would promote or attenuate EC inflammation and barrier breakdown. ResultsIncorporation of iNs, iAs, and iMGLs into a perfusable vascular model enabled a more complete representation of NVU cellular diversity and promoted neuronal health. In monolayer co-culture with iMGL, HBMECs enhanced the junctional localization of tight and adherens junction proteins through both contact-dependent and paracrine mechanisms. Following an inflammatory challenge, iMGLs reduced endothelial inflammatory activation, suggesting a protective role in response to AD-relevant inflammatory conditions. Finally, when embedded in 3D collagen matrices surrounding perfusable endothelialized lumen networks, iMGLs reduced dextran permeability and preserved endothelial barrier integrity following TNF challenge. ConclusionsTogether, these findings establish a 3D perfusable neuroimmune-vascular model that enables the dissection of microglial contributions to neurovascular function in health and disease.

cell biology↗

bioRxiv2025

TREM2 macrophages are associated with enhanced response to PD-1 blockade in human hepatocellular carcinoma

Macrophages are known to dampen tumor immunity. However, identifying druggable targets that modulate these cells to improve existing immunotherapies has been limited by a dearth of studies identifying macrophages that associate with pathological response to immune checkpoint blockade. To fulfill this unmet clinical need, we leveraged transcriptional and spatial profiling of specimens collected from a Phase II clinical trial studying neoadjuvant PD-1 blockade in patients with hepatocellular carcinoma (HCC). We determined that the intratumoral abundance of TREM2-expressing macrophages and serological levels of soluble TREM2 are elevated in patients who responded to PD-1 blockade, compared to non-responders. We validated these findings in a second HCC cohort and in the IMbrave150 trial. These highlight the robust potential for TREM2 macrophages to predict therapeutic responses of HCC to immunotherapy. Therefore, our study provides a novel basis for the use of TREM2 macrophages to strategize treatment for patients with HCC to maximize therapeutic benefit.

immunology↗

bioRxiv2025

Ghosts of symbionts past: The hidden history of the dynamic association between filarial nematodes and their Wolbachia endosymbionts

Many, but not all, parasitic filarial nematodes (Onchocercidae) carry intracellular, maternally-transmitted Wolbachia symbionts, and these alphaproteobacteria are targets for anti-filarial chemotherapeutic interventions for human disease. The symbionts of Onchocercidae derive from four of the major supergroups (C, D, F and J) defined within the genus Wolbachia. Using twenty-two whole genome sequences of filarial nematodes and genome sequences of their Wolbachia partners, we have explored the evolutionary history of the nematode-Wolbachia symbiosis. We screened the nuclear genome sequences of all the nematodes for nuclear Wolbachia transfers (NUWTs), fragments of the Wolbachia genome that have been integrated into the nuclear genome. Six species have no current Wolbachia infection. Setaria labiatopapillosa had no validated NUWTs and we interpret this to mean that this species was never infected with Wolbachia. In the other five species (Acanthocheilonema viteae, Cercopithifilaria (Ce.) johnstoni, Elaeophora elaphi, Loa (Lo.) loa and Onchocerca flexuosa) we found NUWTs, implying they have previously had and have now lost Wolbachia infections. For each NUWT locus, we identified the supergroup membership of the Wolbachia from which it originated, and found that the five Wolbachia-free species carried NUWTs derived from multiple supergroups, including a high shared rate of sequences derived from supergroup C. In Dirofilaria repens we identified a sample that carried two Wolbachia symbionts, one from supergroup C and one from supergroup F. In Dirofilaria immitis where live infection with a supergroup C Wolbachia is found, we identified NUWTs derived from an F Wolbachia, confirming that the F association predated the divergence of these Dirofilaria species. The supergroup D lineage of Wolbachia, as present in the human parasites Wuchereria bancrofti and Brugia malayi, derives from a replacement event. Madathamugadia (Md.) hiepei shows signs of multiple recent repeated endosymbiont replacement. From these data we infer that the history of Wolbachia in onchocercid nematodes includes not only cospeciation (as present in the Onchocerca-Dirofilaria group in association with supergroup C Wolbachia) and loss (in the five Wolbachia-free species), but also frequent symbiont replacement and dual infection. This dynamic pattern is challenging to models that assume host-symbiont mutualism.

genomics↗

bioRxiv2025

Spatial transcriptomic profiling reveals distinct signatures in acute versus chronic wounds through hypergraph modelling and transcriptomic entropy analysis.

IntroductionThe financial burden of wounds to healthcare systems continues to increase, with little progression on advanced treatment options. Single cell RNA sequencing studies have predominantly focused on phenotypically different cell types and are generally descriptive in their analyses. Coordination within the transcriptome can be modelled using hypergraphs, which quantify higher order interactions (coordination between two or more genes) in transcriptomic data. Hypergraph modelling and analysis of transcriptomic entropy of wound samples will further elucidate differences between healing and non-healing wounds. MethodsSpatial transcriptomic analysis (Visium Spatial Gene Expression) was performed on three acute wounds, three chronic wounds and two healthy, unwounded skin samples. Standard transcriptomic analyses were performed in Python using the packages Scanpy and Squidpy. Hypergraph modelling and transcriptomic entropy analyses were performed in R. ResultsAcross the samples, twenty-nine Leiden clusters were defined, with keratinocytes, fibroblasts and adipocytes subclusters present. Fifteen marker genes for acute and chronic wounds were identified, with pathway analysis identifying immune responses and cellular homeostasis present in acute wounds, whilst in chronic wounds, pathways included immune responses and extracellular matrix structure. Spatial transcriptomics allowed for a descriptive analysis of the Leiden clusters within the samples, with each tissue sample being divided up into upper, middle and lower layer for this purpose. Hypergraph analyses of the whole transcriptome from the pathology groups and the independent transcriptomic Leiden clustering, revealed differences in underlying transcriptomic coordination. The top 1000 highly connected genes from each pathology group were analysed by Over Representation Analysis, with integrated stress response signalling, maintenance of cell number and myeloid and mononuclear cell differentiation pathways present in acute samples (all FDR <0.05) compared to regulation of vasculature development, mononuclear cell differentiation and epithelial cell proliferation (all FDR <0.05) in the chronic samples. Analysis of transcriptomic entropy identified further differences between acute and chronic wounds, with decreasing entropy from control to acute to chronic samples (all p-adjusted <0.001). When comparing Leiden clusters that were present in at least two sample groups, there was a statistically significant difference in entropy, although Leiden clusters varied in high or low entropy between acute and chronic wound samples (all p< 2.2 x 10-16). By mapping high and low entropy values to spatial images of each sample, lower transcriptomic entropy within the wound bed was identified compared to the rest of the tissue sample. ConclusionsSpatial transcriptomic analysis allowed for distinct spatial patterning to be observed which delineated acute and chronic wounds. Analysis of higher order interactions within the wound sample transcriptome identified key pathways that were not identified using traditional analyses. Transcriptomic entropy analysis further highlighted the differences between the wound samples. This work has implications for the future development of biomarkers of chronic wounds.

physiology↗

bioRxiv2025

Astrocytic contribution to sensory hypersensitivity in a mouse model of fragile X syndrome

Fragile X syndrome (FXS) is the most common form of inherited intellectual disability and a leading cause of autism spectrum disorder (ASD). FXS is caused by mutations in the fragile X messenger ribonucleoprotein gene 1 (FMR1), which result in complete or partial loss of expression of its protein product, fragile X messenger ribonucleoprotein (FMRP). Neuronal impairments in the absence of FMRP have been extensively characterized. However, much less is known about the impact that loss of FMRP has on the physiology and function of astrocytes and the implications for behavior. A common behavior exhibited by both FXS and ASD patients is hypersensitivity to sensory stimuli, but how astrocytes contribute to hypersensitivity in the context of FXS remains unknown. Using mice with astrocyte-specific reduction of Fmr1 (Fmr1 conditional KO (cKO)) and mice with astrocyte-specific expression of Fmr1 (Fmr1 cON), we demonstrated that reduction of astrocytic FMRP is sufficient but not necessary to confer susceptibility to audiogenic seizures, an indication of auditory hypersensitivity. In addition, reduction of astrocytic FMRP impacts neuronal activity, resulting in spontaneous seizures. In contrast, we assessed tactile hypersensitivity using a whisker stimulation paradigm but did not detect significant differences in Fmr1 cKO mice. Our results reveal that astrocytes lacking FMRP contribute to auditory hypersensitivity and spontaneous seizures.

neuroscience↗

bioRxiv2024

Right posterior theta reflects human parahippocampal phase resetting by salient cues during goal-directed navigation

Animal and computational work indicate that phase resetting of theta oscillations (4-12 Hz) in the parahippocampal gyrus (PHG) by salient events (e.g., reward, landmarks) facilitates the encoding of goal-oriented information during navigation. Although well-studied in animals, this mechanism has not been empirically substantiated in humans. In the present article, we present data from two studies (Study 1: asynchronous EEG-MEG | Study 2: simultaneous EEG-fMRI) to investigate theta phase resetting and its relationship to PHG BOLD activation in healthy adults (aged 18-34 years old) navigating a virtual T-maze to find rewards. In the first experiment, both EEG and MEG data revealed a burst of theta power over right-posterior scalp locations following feedback onset (termed right-posterior theta, RPT), and RPT power and measures of phase resetting were sensitive to the subjects spatial trajectory. In Experiment 2, we used probabilistic tractography data from the human connectome project to segment the anterior and posterior PHG based on differential connectivity profiles to other brain regions. This analysis resulted in a PHG subdivision consisting of four distinct anterior and two posterior PHG clusters. Next, a series of linear mixed effects models based on simultaneous EEG-fMRI data revealed that single-trial RPT peak power significantly predicted single-trial hemodynamic responses in two clusters within the posterior PHG and one in the anterior PHG. This coupling between RPT power and PHG BOLD was exclusive to trials performed during maze navigation, and not during a similar task devoid of the spatial context of the maze. These findings highlight a role of PHG theta phase resetting for the purpose of encoding salient information during goal-directed spatial navigation. Taken together, RPT during virtual navigation integrates experimental, computational, and theoretical research of PHG function in animals with human cognitive electrophysiology studies and clinical research on memory-related disorders such as Alzheimers disease.

neuroscience↗

bioRxiv2024

An increase in reactive oxygen species underlies neonatal cerebellum repair

The neonatal mouse cerebellum shows remarkable regenerative potential upon injury at birth, wherein a subset of Nestin-expressing progenitors (NEPs) undergoes adaptive reprogramming to replenish granule cell progenitors that die. Here, we investigate how the microenvironment of the injured cerebellum changes upon injury and contributes to the regenerative potential of normally gliogenic-NEPs and their adaptive reprogramming. Single cell transcriptomic and bulk chromatin accessibility analyses of the NEPs from injured neonatal cerebella compared to controls show a temporary increase in cellular processes involved in responding to reactive oxygen species (ROS), a known damage-associated molecular pattern. Analysis of ROS levels in cerebellar tissue confirm a transient increased one day after injury at postanal day 1, overlapping with the peak cell death in the cerebellum. In a transgenic mouse line that ubiquitously overexpresses human mitochondrial catalase (mCAT), ROS is reduced 1 day after injury to the granule cell progenitors, and we demonstrate that several steps in the regenerative process of NEPs are curtailed leading to reduced cerebellar growth. We also provide preliminary evidence that microglia are involved in one step of adaptive reprogramming by regulating NEP replenishment of the granule cell precursors. Collectively, our results highlight that changes in the tissue microenvironment regulate multiple steps in adaptative reprogramming of NEPs upon death of cerebellar granule cell progenitors at birth, highlighting the instructive roles of microenvironmental signals during regeneration of the neonatal brain.

developmental biology↗

bioRxiv2024

Mouse Auditory Cortex Undergoes Asynchronous Maturation in the Right and Left Hemispheres

Despite the significance of lateralized auditory processing in human cognition, there are limited studies in animal models exploring the developmental mechanisms of this cortical specialization. Here, we find that cellular and network signs of maturity in the Auditory Cortex (ACx) appear earlier in the right hemisphere in male mice. We further demonstrate that persistent, experience dependent map reorganization is confined to the hemisphere that is actively maturing and can be differentially engaged by temporally limited manipulations of the sensory environment. Our data suggests that differential timing in hemisphere development could lead to lateralized auditory functioning.

neuroscience↗

bioRxiv2022

Single cell RNA-seq identifies inflammation-induced loss of CFTR-expressing airway ionocytes in non-eosinophilic asthma

Asthma is the most common chronic airways disease worldwide and the severe treatment resistant subtype of asthma is responsible for the majority of disease burden. Asthma is heterogeneous in nature and can be classified according to airway infiltrates as eosinophilic or non-eosinophilic (sometimes referred to as Type 2 low), which is further divided into paucigranulocytic (low levels of granulocytes), or neutrophilic asthma characterized by elevated neutrophils, and mixed Type 1 and Type 17 cytokines in airway tissue, sputum, and bronchoalveolar lavage. Severe non-eosinophilic asthma currently has fewer effective treatment options and many of these patients fail to qualify for newer biologic monoclonal therapies. The cystic fibrosis transmembrane conductance regulator (CFTR) is a key protein whose function is dysregulated in multiple respiratory diseases including cystic fibrosis and chronic obstructive pulmonary disease (COPD) and has proven a valuable therapeutic target. Using human bronchial epithelial cells (hBECs) isolated differentiated at air-liquid interface we demonstrated a reduced function of the CFTR in non-eosinophilic asthma. Characterization of the cell and molecular differences in airway epithelial cells between severe asthma subtypes using single cell RNA-sequencing (scRNAseq) revealed that airway epithelial cells from non-eosinophilic asthma, and in particular neutrophilic asthma patients, fail to differentiate into CFTR-expressing ionocytes compared with eosinophilic asthma or healthy donors. We identified a novel ionocyte transcriptional signature, which was present in both bronchial and tracheal airway epithelial samples indicating conserved anatomical gene regulation. Using protein markers and immunofluorescent quantification loss of ionocytes was confirmed in non-eosinophilic asthma hBECs. Similarly, ioncytes were also diminished in the airways of a murine model of neutrophilic-dominant but not eosinophilic allergen asthma models. Furthermore, treatment of hBECs from healthy donors with a neutrophilic asthma-like inflammatory cytokine mixture, but not IL-13, led to loss of ionocytes primarily due to IFN-{gamma}. Inflammation-induced loss of CFTR-expressing ionocytes in airway cells from non-eosinophilic asthma may represent a key feature of disease pathogenesis and a novel drug target for this difficult-to-treat disease.

cell biology↗

bioRxiv2021

Regulation of skeletal muscle metabolism and contraction performance via teneurin-latrophilin action.

Skeletal muscle regulation is responsible for voluntary muscular movement in vertebrates. The genes of two essential proteins, teneurins and latrophilins (LPHN), evolving in ancestors of multicellular animals, form a ligand-receptor pair, and are now shown to be required for skeletal muscle function. Teneurins possess a bioactive peptide, termed the teneurin C-terminal associated peptide (TCAP) that interacts with the LPHNs to regulate skeletal muscle contractility strength and fatigue by an insulin-independent glucose importation mechanism. CRISPR-based knockouts and siRNA-associated knockdowns of LPHN-1 and-3 shows that TCAP stimulates an LPHN-mediated cytosolic Ca2+ signal transduction cascade to increase energy metabolism and enhance skeletal muscle function via increases in type-1 oxidative fiber formation and reduce the fatigue response. Thus, the teneurin/TCAP-LPHN system is presented as a novel mechanism likely to regulate the energy requirements and performance of skeletal muscle.

physiology↗

bioRxiv2020

The polybasic cleavage site in the SARS-CoV-2 spike modulates viral sensitivity to Type I IFN and IFITM2

The cellular entry of severe acute respiratory syndrome-associated coronaviruses types 1 and 2 (SARS-CoV-1 and -2) requires sequential protease processing of the viral spike glycoprotein (S). The presence of a polybasic cleavage site in SARS-CoV-2 S at the S1/S2 boundary has been suggested to be a factor in the increased transmissibility of SARS-CoV-2 compared to SARS-CoV-1 by facilitating maturation of the S precursor by furin-like proteases in the producer cells rather than endosomal cathepsins in the target. We investigate the relevance of the polybasic cleavage site in the route of entry of SARS-CoV-2 and the consequences this has for sensitivity to interferons, and more specifically, the IFN-induced transmembrane (IFITM) protein family that inhibit entry of diverse enveloped viruses. We found that SARS-CoV-2 is restricted predominantly by IFITM2 and the degree of this restriction is governed by route of viral entry. Removal of the cleavage site in the spike protein renders SARS-CoV-2 entry highly pH- and cathepsin-dependent in late endosomes where, like SARS-CoV-1 S, it is more sensitive to IFITM2 restriction. Furthermore, we find that potent inhibition of SARS-CoV-2 replication by type I but not type II IFNs is alleviated by targeted depletion of IFITM2 expression. We propose that the polybasic cleavage site allows SARS-CoV-2 to mediate viral entry in a pH-independent manner, in part to mitigate against IFITM-mediated restriction and promote replication and transmission. This suggests therapeutic strategies that target furin-mediated cleavage of SARS-CoV-2 S may reduce viral replication through the activity of type I IFNs. IMPORTANCEThe furin cleavage site in the S protein is a distinguishing feature of SARS-CoV-2 and has been proposed to be a determinant for the higher transmissibility between individuals compared to SARS-CoV-1. One explanation for this is that it permits more efficient activation of fusion at or near the cell surface rather than requiring processing in the endosome of the target cell. Here we show that SARS-CoV-2 is inhibited by antiviral membrane protein IFITM2, and that the sensitivity is exacerbated by deletion of the furin cleavage site which restricts viral entry to low pH compartments. Furthermore, we find that IFITM2 is a significant effector of the antiviral activity of type I interferons against SARS-CoV-2 replication. We suggest one role of the furin cleavage site is to reduce SARS-CoV-2 sensitivity to innate immune restriction, and thus may represent a potential therapeutic target for COVID-19 treatment development.

immunology↗

bioRxiv2019

Engineered full-length Fibronectin-based hydrogels sequester and present growth factors to promote regenerative responses in vitro and in vivo

Extracellular matrix (ECM)-derived matrices such as Matrigel are used to culture numerous cell types in vitro and can recapitulate certain ECM functions that support cell growth and differentiation. However, ECM-derived matrices suffer lot-to-lot variability, undefined composition and lack of controlled physical properties. There is a need to develop rationally designed synthetic matrices that can also recapitulate ECM roles. Synthetic matrices have certain limitations as they use synthetic peptides or fragments whereas the ECM consists of full proteins. Here, we report the development of degradable, PEG-based hydrogels of controlled stiffness that incorporate full-length fibronectin (FN) to enable solid-phase presentation of growth factors in a physiological manner. We demonstrate, in vitro and in vivo, the effect of incorporating vascular endothelial growth factor (VEGF) and bone morphogenetic protein 2 (BMP2), in these hydrogels to enhance angiogenesis and bone regeneration, respectively. We show that the solid-state presentation of growth factors enables very low growth factor doses to achieve regenerative effects.

bioengineering↗

bioRxiv2019

The 14q32.31 DLK1-DIO3 MIR300 tumor suppressor promotes leukemogenesis by inducing cancer stem cell quiescence and inhibiting NK cell anti-cancer immunity.

Drug-resistance of tumor-initiating cells, impaired NK cell immune-response, PP2A loss-of-function and aberrant miRNA expression are cancer features resulting from microenvironmental- and tumor-specific signals. Here we report that genomic-imprinted MIR300 is a cell context-independent dual function tumor suppressor which is upregulated in quiescent leukemic stem (LSC) and NK cells by microenvironmental signals to induce quiescence and impair immune-response, respectively, but inhibited in CML and AML proliferating blasts to prevent PP2A-induced apoptosis. MIR300 anti-proliferative and PP2A-activating functions are differentially activated through dose-dependent CCND2/CDK6 and SET inhibition, respectively. LSCs escape PP2A-mediated apoptosis through TUG1 lncRNA that uncouples and limits MIR300 functions to cytostasis by regulating unbound-MIR300 levels. Halting MIR300 homeostasis restores NK cell activity and suppresses leukemic but not normal hematopoiesis by eradicating nearly all LSCs. Thus, MIR300 tumor suppressor activity is essential and therapeutically important for LSC-driven leukemias.

cancer biology↗

bioRxiv2018

Prognostic Relevance of CCDC88C (Daple) Transcripts in the Peripheral Blood of Patients with Malignant Melanoma

A loss of balance between G-protein activation and deactivation has been implicated in the initiation of melanomas, and non-canonical Wnt signaling via the Wnt5A/Frizzled (FZD) pathway has been shown to be critical for the switch to an invasive phenotype. Daple [CCDC88C gene], a cytosolic guanine nucleotide exchange factor (GEF) which enhances non-canonical Wnt5A/FZD signaling via activation of trimeric G protein, Gai has been shown to serve opposing roles-- as an inducer of EMT and invasiveness and a potent tumor suppressor -- via two isoforms, V1 (full-length) and V2, respectively. Here we report that the relative abundance of these isoforms in the peripheral circulation, presumably largely from circulating tumor cells (CTCs), is a prognostic marker of cutaneous melanomas. Expression of V1 is increased in both the early and late clinical stages (p<0.001, p=0.002, respectively); V2 is decreased exclusively in the late clinical stage (p=0.011). The two isoforms have opposing prognostic effects: high expression of V2 increases progression-free survival (PFS; p = 0.02), whereas high expression of V1 decreases PFS (p=0.013). Furthermore, these effects are additive, in that melanoma patients with a low V2-high V1 signature carry the highest risk of metastatic disease. We conclude that detection of Daple transcripts in the peripheral blood (i.e., liquid biopsies) of patients with melanoma may serve as a prognostic marker and an effective strategy for non-invasive long-term follow-up of patients with melanoma.

cancer biology↗

bioRxiv2018

High genetic diversity and presence of genetic structure characterise the Corso-Sardinian endemics Ruta corsica and Ruta lamarmorae (Rutaceae)

Corsica and Sardinia form one of the ten areas with highest biodiversity in the Mediterranean and are considered one of the priority regions for conservation in Europe. In order to preserve the high levels of endemism and biological diversity at different hierarchical levels, knowledge of the evolutionary history and current genetic structure of Corso-Sardinian endemics is instrumental. Microsatellite markers were newly developed and used to study the genetic structure and taxonomic status of Ruta corsica and Ruta lamarmorae, rare endemics of Corsica and Sardinia, respectively, and previously considered a single species. Our analyses identified high levels of genetic variation within each species (P=0.883, He=0.543 for R. corsica; P=0.972, He=0.627 for R. lamarmorae). Intrinsic traits of the species (hermaphroditism, proterandry and polyploidy) and island-dependent factors (i.e. age, origin and history of the islands) might explain the detected high levels of genetic variation. We discovered differentiation between R. corsica and R. lamarmorae, and genetic structure within each species, which are consistent with the observation of low dispersal ability for both species. Our genetic results support the recent taxonomic classification of R. corsica and R. lamarmorae as separate species and suggest that they diverge at only few loci. One R. corsica population (SA) strongly differed from all other studied populations and appeared to be the product of hybridization between the two species in STRUCTURE analyses. Our results provide important insights for the conservation of the two rare endemics. Further genetic analyses are recommended for R. lamarmorae and for population SA (R. corsica).

genetics↗