Biology subjects

Lee, D.

Publications and source records attributed to Lee, D..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Slow running benefits: Boosts in mood and facilitation of prefrontal cognition even at very light intensity

Although running upright has been reported to have positive effects on both physical and mental health, the minimum running intensity/speed that would benefit mood and prefrontal cognition is not yet clear. For this reason, we aimed to investigate the acute effect of very slow running, which is classified as a very light intensity exercise, on mood, executive function (EF), and their neural substrates in the prefrontal cortex (PFC). Twenty-four healthy participants completed a 10-minute very slow running session on a treadmill at 35% [Formula] and a resting control session in randomized order. EF was measured using the Stroop task and the mood state was measured using the Two-Dimensional Mood Scale (TDMS) before and after both sessions. Cortical hemodynamic changes while performing the task were monitored using functional near-infrared spectroscopy (fNIRS). The results show that ten minutes of very slow running significantly enhanced mood, reduced Stroop interference time (i.e., enhanced EF), and elicited left lateral PFC activation. Moreover, head acceleration, the magnitude of up-and-down oscillations, was measured during running, and a significant positive correlation with pleasant mood was found. Head acceleration is a remarkable characteristic of running and may be one of the factors related to a pleasant mood induced by very slow running. In conclusion, the current study reveals that a single bout of running, even at very slow speed, elicits a pleasant mood and improved executive function with enhancing activation in prefrontal subregions. This shed light on the slow running benefits to brain health.

neuroscience↗

bioRxiv2024

Beta-cell adaptation to metabolic stresses requires prolactin receptor signaling

The role of prolactin receptor (PRLR) signaling in {beta}-cell adaptation to maternal insulin resistance of pregnancy has been well demonstrated. Using transgenic mice with an inducible {beta}-cell-specific Prlr deletion ({beta}Prlr-/-), we found that intact PRLR, as found in {beta}Prlr+/+ mice, were protected from developing glucose intolerance during pregnancy, and the main mechanism responsible for this PRLR-mediated effect is the up regulation of {beta}-cell proliferation and insulin synthesis. Interestingly, studies in male mice and humans have found a link between diminished PRLR signaling and abnormal {beta}-cell function. We aimed to determine whether PRLR has a role in regulating {beta}-cell function outside of pregnancy, protecting {beta}-cell against exposure to metabolic stressors. In this study, we found that {beta}-cell-specific PRLR reduction resulted in impaired glucose tolerance in multiparous female mice challenged with a 12-week course of high-fat diet (HFD). Unlike in pregnancy, where PRLR signaling up regulates {beta}-cell proliferation resulting in a greater {beta}-cell mass, we observed no difference in {beta}-cell mass between the wild type ({beta}Prlr+/+) and mutant ({beta}Prlr-/-) mice. In vitro glucose-stimulated insulin secretion using isolated islets from wild type ({beta}Prlr+/+) and mutant ({beta}Prlr-/-) mice showed comparable insulin response, but {beta}Prlr-/- mice showed blunted first-phase insulin release in vivo, although only when challenged with glucose orally and not intraperitoneally, suggesting an impairment of the incretin effect. In support of the observed defect in incretin action, we found a reduction in expression of both incretin hormone receptors, Gipr and Glp-1r, and several of their upstream regulators, such as E2f1, Nkx6.1, Pax6, Ppar{gamma}, and Tcf7l2. Islets from the mutant mice also have a lower insulin content and reduced levels of genes that regulate glucose metabolism. Together, these results suggested that PRLR signaling plays an important role in preserving {beta}-cell function in mice exposed to metabolic stress by maintaining incretin receptor expression and insulin secretory capacity in {beta} cells.

physiology↗

bioRxiv2024

Single dopaminergic neuron DAN-c1 in Drosophila larval brain mediates aversive olfactory learning through D2-like receptors

The intricate relationship between the dopaminergic system and olfactory associative learning in Drosophila has been an intense scientific inquiry. Leveraging the formidable genetic tools, we conducted a screening of 57 dopaminergic drivers, leading to the discovery of DAN-c1 driver, uniquely targeting a pair of dopaminergic neurons (DAN) in the larval brain. While the involvement of excitatory D1-like receptors is well-established, the role of D2-like receptors (D2Rs) remains underexplored. Our investigation reveals the expression of D2Rs in both DANs and the mushroom body (MB) of third instar larval brains. Silencing D2Rs in DAN-c1 via microRNA disrupts aversive learning, further supported by optogenetic activation of DAN-c1 during training, affirming the inhibitory role of D2R autoreceptor. Intriguingly, D2R knockdown in the MB impairs both appetitive and aversive learning. These findings elucidate the distinct contributions of D2Rs in diverse brain structures, providing novel insights into the molecular mechanisms governing associative learning in Drosophila larvae.

neuroscience↗

bioRxiv2023

Spatial dissection of cellular heterogeneity and functional crosstalk in the tumor microenvironments of gastric cancers

Spatial transcriptomics offers unprecedented challenges in characterizing tumor ecosystems, encompassing tumor cells and their surrounding tumor microenvironments (TME) along with cellular interactions therein. Here, we conducted Visium-based spatial transcriptomics on nine primary gastric cancers (GC) to translate the spatial organization of GC ecosystems into the functional landscape of cellular crosstalk across malignant, stromal and immune cells. We identified three distinct GC subtypes of 3 immunogenic, 3 epithelial and 3 stromal GCs with elevated infiltration of immune, malignant cells and fibroblasts reflecting the heterogeneity of the cell types and their interactions in GC TME. GC spatial architecture was further delineated into 6 regional compartments with varying degree of TME infiltration, among which the fibroblast-enriched TME was associated with the upregulation of epithelial-to-mesenchymal transformation (EMT) and immune response in malignant and immune cells, respectively. Cell type-specific transcriptional dynamics representing cellular crosstalk between TME cells were further identified, e.g., the infiltration of malignant and endothelial cells promote the cellular proliferations of TME cells whereas the fibroblasts and immune cells are associated with pro-cancer and anti-cancer immunity, respectively. Ligand-receptor analysis further revealed that CCL2-expressing fibroblasts promote the pro-cancer signaling of immune cells including JAK-STAT3 signaling and inflammatory response in tumor-infiltration macrophages. The CCL2+fibroblasts and macrophages with activated JAK-STAT3 signals are co-localized in spatial GC architecture and their co-abundance was associated with unfavorable clinical outcomes. Taken together, GC spatial transcriptomes can be regionally and functionally delineated into functional cellular crosstalk involving multiple cell types with potential clinical relevance, particularly the interaction between CCL2+ fibroblasts and JAK-STAT3+macrophages contributing to cancer-favoring immune contexture in GC TME.

cancer biology↗

bioRxiv2023

Human disease-specific cell signatures in non-lesional tissue in Multiple Sclerosis detected by single-cell and spatial transcriptomics

Recent investigations of cell type changes in Multiple Sclerosis (MS) using single-cell profiling methods have focused on active lesional and peri-lesional brain tissue, and have implicated a number of peripheral and central nervous system cell types. However, an important question is the extent to which so-called "normal-appearing" non-lesional tissue in individuals with MS accumulate changes over the lifespan. Here, we compared post-mortem non-lesional brain tissue from donors with a pathological or clinical diagnosis of MS from the Religious Orders Study or Rush Memory and Aging Project (ROSMAP) cohorts to age- and sex-matched brains from persons without MS (controls). We profiled three brain regions using single-nucleus RNA-seq: dorsolateral prefrontal cortex (DLPFC), normal appearing white matter (NAWM) and the pulvinar in thalamus (PULV), from 15 control individuals, 8 individuals with MS, and 5 individuals with other detrimental pathologies accompanied by demyelination, resulting in a total of 78 samples. We identified region- and cell type-specific differences in non-lesional samples from individuals diagnosed with MS and/or exhibiting secondary demyelination with other neurological conditions, as compared to control donors. These differences included lower proportions of oligodendrocytes with expression of myelination related genes MOBP, MBP, PLP1, as well as higher proportions of CRYAB+ oligodendrocytes in all three brain regions. Among microglial signatures, we identified subgroups that were higher in both demyelination (TMEM163+/ERC2+), as well as those that were specifically higher in MS donors (HIF1A+/SPP1+) and specifically in donors with secondary demyelination (SOCS6+/MYO1E+), in both white and grey matter. To validate our findings, we generated Visium spatial transcriptomics data on matched tissue from 13 donors, and recapitulated our observations of gene expression differences in oligodendrocytes and microglia. Finally, we show that some of the differences observed between control and MS donors in NAWM mirror those previously reported between control WM and active lesions in MS donors. Overall, our investigation sheds additional light on cell type- and disease-specific differences present even in non-lesional white and grey matter tissue, highlighting widespread cellular signatures that may be associated with downstream pathological changes.

neuroscience↗

bioRxiv2023

PI4KIII3β inhibition reduces rhinovirus associated cell shedding and ciliary dysfunction

BackgroundPatients with chronic obstructive pulmonary disease (COPD) experience respiratory exacerbations, many of which are associated with rhinoviruses. Current treatment strategies do not target the pathogenic rhinovirus trigger. Research questionWhat is the immediate effect of rhinovirus on the ciliated respiratory epithelium and can viral replication and epithelial toxicity be reduced by targeted PI4KIII{beta} inhibition. MethodsShort (24h) and longer (7 days) rhinovirus infection were explored in primary ciliated airway epithelial cultures from multiple healthy and COPD patients using high-speed video microscopy, viral titration assays and immunofluorescence studies. Ciliated epithelial cultures were pre-treated with a PI4KIII{beta} (GSK533) blocker prior to infection to assess efficacy against rhinovirus. Cytokine and chemokine production were assessed by multiplex immunoassays. ResultsWithin hours of infection rhinovirus co-localised with ciliated cells causing extensive apoptosis-associated shedding of predominantly ciliated cells within 24 hours. Viral replication that peaked at day 1 and cleared by day 7, was associated with dramatic loss of ciliated cells confirmed by reduced ciliary activity and ciliary DNAI2 protein expression. Ciliary beat frequency (CBF) of remaining cilia was significantly reduced by day 7 in cultures from COPD. Infection was partly dependent on PI4KIII{beta} with the GSK533 blocker reducing viral replication while preserving ciliary activity. High levels of pro-inflammatory mediators were secreted by infected cells. ConclusionDecreased ciliation due to rhinovirus infection is likely to impair mucociliary clearance in healthy individuals and COPD patients, contributing to the pathophysiology of COPD exacerbations. PI4KIII{beta} inhibition blocks viral replication, helping to preserve ciliary activity. Take home messageRhinovirus replication in the healthy and COPD respiratory epithelium is mediated by PI4KIII{beta} and intracellular PI4P platform formation. Inhibition of PI4KIII{beta} reduced viral replication and ciliated cell loss.

cell biology↗

bioRxiv2023

Inhibition of hypoxia-inducible factors suppresses subretinal fibrosis

Age-related macular degeneration (AMD) is a common cause of vision loss. The aggressive form of AMD is associated with ocular neovascularization and subretinal fibrosis, representing a responsive outcome against neovascularization mediated by epithelial-mesenchymal transition of retinal pigment epithelium cells. A failure of the current treatment (anti-vascular endothelial growth factor therapy) has also been attributed to the progression of subretinal fibrosis. Hypoxia-inducible factors (HIFs) increase gene expressions to promote fibrosis and neovascularization. HIFs act as a central pathway in the pathogenesis of AMD. HIF inhibitors may suppress ocular neovascularization. Nonetheless, further investigation is required to unravel the aspects of subretinal fibrosis. In this study, we used RPE-specific HIFs or von Hippel-Lindau (VHL, a regulator of HIFs) conditional knockout (cKO) mice, along with pharmacological HIF inhibitors, to demonstrate the suppression of subretinal fibrosis. Fibrosis was suppressed by treatments of HIF inhibitors, and similar suppressive effects were detected in RPE-specific Hif1a/Hif2a- and Hif1a-cKO mice. Promotive effects were observed in RPE-specific Vhl-cKO mice, where fibrosis-mediated pathologic processes were evident. Marine products extracts and their component taurine suppressed fibrosis as HIF inhibitors. Our study shows critical roles of HIFs in the progression of fibrosis, linking them to the potential development of therapeutics for AMD.

molecular biology↗

bioRxiv2023

Tight junction component protein claudin-1 deficiency in retinal pigment epithelium leads to early and intermediate age-related macular degeneration phenotypes in mice.

The early and intermediate age-related macular degeneration (AMD) is characterized by the presence of drusen and pigmentary abnormalities in the retinal pigment epithelial (RPE) cells which form the outer blood retinal barrier (oBRB). Fluid leakage through the disrupted oBRB from the choroid to the neural retina has been implicated in the pathogenesis of AMD, however; the molecular mechanisms still remain unclear. The family of four transmembrane proteins, claudins are known to form tight junctions (TJs) in the oBRB. Nonetheless, there are few reports showing how they function in the oBRB in vivo. We found that claudin-1 is dominantly expressed in TJs of the mouse RPE. To investigate the role of claudin-1 in the RPE, we generated RPE-specific Cldn1 conditional knockout mice (Best1-Cre+/- Cldn1flox/flox mice: Cldn1 cKO mice). Deficiency of Cldn1 led to age-related lipid deposits such as subretinal drusenoid deposits (SDD), increased lipid droplets in the RPE, basal lamellar deposits (BlamD) and membranous debris in the Bruchs membrane. In addition, pigmentary abnormalities such as RPE hypertrophy, multilayered-RPE cells, and ectopic pigment granules outside the RPE were observed in Cldn1 cKO mice. Our study provides new insights into the possible association of the TJ protein claudin-1 with lipid metabolism and cellular ageing in the RPE contributing to the early onset of AMD.

molecular biology↗

bioRxiv2023

Understanding epistatic networks in the B1 -lactamases through coevolutionary statistical modeling and deep mutational scanning

Over the course of evolution, proteins families undergo sequence diversification via mutation accumulation, with extant homologs often sharing less than 25% sequence identity. The resulting diversity presents a complex view of sequence-structure-function relationships, as epistasis is prevalent, and deleterious mutations in one protein can be tolerated in homologous sequences through networks of intramolecular, compensatory interactions. Understanding these epistatic networks is crucial for understanding and predicting protein function, yet comprehensive analysis of such networks across protein families is limited. In this study, we combine computational and experimental approaches to examine epistatic networks in the class B1 metallo-{beta}-lactamases, a diverse family of antibiotic-degrading enzymes. Using Direct Coupling Analysis, we assess global coevolutionary signatures across the B1 family. We also obtain detailed experimental data from deep mutational scanning on two distant B1 homologs, NDM-1 and VIM-2. There is good agreement between the two approaches, revealing both family-wide and homolog specific patterns that can be associated with 3D structure. However, specific interactions remain complex, and strong epistasis in evolutionarily entrenched residues are not easily compensated for by changes in nearby interactions.

biochemistry↗

bioRxiv2023

Comparative single-cell transcriptomic atlases reveal conserved and divergent features of drosophilid central brains

To explore how brains change upon species evolution, we generated single-cell transcriptomic atlases of the central brains of three closely-related but ecologically-distinct drosophilids: the generalists Drosophila melanogaster and Drosophila simulans, and the noni fruit specialist Drosophila sechellia. The global cellular composition of these species central brains is well-conserved, but we predicted a few cell types (perineurial glia, sNPF and Dh44 peptidergic neurons) with divergent frequencies. Gene expression analysis revealed that distinct cell types within the central brain evolve at different rates and patterns; notably, glial cell types exhibit the greatest divergence between species. Compared to D. melanogaster, the cellular composition and gene expression patterns of the central brain in D. sechellia display greater deviation than those of D. simulans - despite their similar phylogenetic distance from D. melanogaster - that the distinctive ecological specialization of D. sechellia is reflected in the structure and function of its brain. Expression changes in D. sechellia encompass metabolic and ecdysone signaling genes, suggestive of adaptations to its novel ecological demands. Additional single-cell transcriptomic analysis on D. sechellia revealed genes and cell types responsive to dietary supplement with noni, pointing to glia as sites for both physiological and genetic adaptation to novel conditions. Our atlases represent the first comparative analyses of "whole" central brains, and provide a comprehensive foundation for studying the evolvability of nervous systems in a well-defined phylogenetic and ecological framework.

evolutionary biology↗

bioRxiv2023

An injectable in situ crosslinkable platform for ultra-long-acting delivery of hydrophilic therapeutics

Achieving ultra-long-term release of hydrophilic drugs over several months remains a significant challenge for existing long-acting injectables (LAIs). Existing platforms, such as in situ forming implants (ISFI), exhibit high burst release due to solvent efflux and microsphere-based approaches lead to rapid drug diffusion due to significant water exchange and large pores. Addressing these challenges, we have developed an injectable platform that, for the first time, achieves ultra-long-term release of hydrophilic drugs for over six months. This system employs a methacrylated ultra-low molecular weight pre-polymer (polycaprolactone) to create in situ cross-linked depots (ISCD). The ISCDs solvent-free design and dense mesh network, both attributed to the ultra-low molecular weight of the pre-polymer, effectively minimizes burst release and water influx/efflux. In vivo studies in rats demonstrate that ISCD outperforms ISFI by achieving lower burst release and prolonged drug release. We demonstrated the versatility of ISCD by showcasing ultra-long-term delivery of several hydrophilic drugs, including antiretrovirals (tenofovir alafenamide, emtricitabine, abacavir, and lamivudine), antibiotics (vancomycin and amoxicillin) and an opioid antagonist naltrexone. Additionally, ISCD achieved ultra-long-term release of the hydrophobic drug tacrolimus and enabled co-delivery of hydrophilic drug combinations encapsulated in a single depot. We also identified design parameters to tailor the polymer network, tuning drug release kinetics and ISCD degradation. Pharmacokinetic modeling predicted over six months of drug release in humans, significantly surpassing the one-month standard achievable for hydrophilic drugs with existing LAIs. The platforms biodegradability, retrievability, and biocompatibility further underscore its potential for improving treatment adherence in chronic conditions.

bioengineering↗

bioRxiv2023

Batch-effect correction in single-cell RNA sequencing data using JIVE

In single-cell RNA sequencing (scRNA-seq) data analysis, addressing batch effects -- technical artifacts stemming from factors such as varying sequencing technologies, equipment, and capture times -- is crucial. These factors cause unwanted variation in the data and often obfuscate the underlying biological signal of interest. The Joint and Individual Variation Explained (JIVE) method can be used to extract shared biological patterns from multi-source sequencing data while adjusting for individual non-biological variations (i.e., batch effect). However, its current implementation is originally designed for bulk sequencing data, making it computationally infeasible for large-scale single-cell sequencing datasets. In this study, we enhance JIVE for large-scale scRNA-seq data by boosting its computational efficiency and tailoring it to the single-cell context. Additionally, we introduce a novel application of JIVE which we use to perform batch-effect correction on multiple scRNA-seq datasets. Our enhanced JIVE method aims to decompose scRNA-seq datasets into a joint structure capturing the true biological variability and individual structures which capture technical variability within each batch. This joint structure is then suitable for use in downstream analyses. We employed four evaluation metrics and benchmarked the results against two other popular tools, Seurat v3 and Harmony, which were developed for this purpose. We found that JIVE performed best in metrics that consider local neighborhoods (kBET and LISI) and in scenarios in which the original data contained distinct differences between batches and cell types.

bioinformatics↗

bioRxiv2023

AGAMOUS-like 6 and MYB DOMAIN PROTEIN 80 regulate the development of female and male cones in Pinus densiflora S. et Z.

To shorten the long breeding period of forest trees, it is necessary to explore biological factors and key genes involved in reproduction. We compared the transcriptomes of female and male cones and then identified major biological processes and hub genes associated with the development of female and male cones in Pinus densiflora. The reproductive and vegetative tissues of P. densiflora were sampled from various developmental stages and a reference transcriptome was generated. Functional annotation and Gene Ontology enrichment analysis of differentially expressed genes were performed as well as gene co-expression network analysis for identifying the hub genes involved in the cone development. Lignin biosynthesis and cell wall loosening were activated in the early and late female cones, respectively. Metabolism of pollen wall components was predominant in the early male cones compared with the later stage. In addition, phytohormone-related genes were highly expressed in the early female cones in contrast to the early male cones. Finally, we found that AGAMOUS-like 6 and MYB DOMAIN PROTEIN 80 were hub genes of the female and male cone development, respectively. This study suggests that various biological factors contribute to reproductive developmental processes. Furthermore, these data will provide the new insight into biotechnology and breeding methods for improving cone and seed production of P. densiflora.

plant biology↗

bioRxiv2023

Targeted inhibition of BET proteins in HPV-16 associated head and neck squamous cell carcinoma reveals heterogeneous transcription response

Integrated human papillomavirus (HPV-16) associated head and neck squamous cell carcinoma (HNSCC) tumors have worse survival outcomes compared to episomal HPV-16 HNSCC tumors. Therefore, there is a need to differentiate treatment for HPV-16 integrated HNSCC from other viral forms. We analyzed TCGA data and found that HPV+ HNSCC expressed higher transcript levels of the bromodomain and extra terminal domain (BET) family of transcriptional coregulators. However, the mechanism of BET protein-mediated transcription of viral-cellular genes in the integrated viral-HNSCC genomes needs to be better understood. We show that BET inhibition downregulates E6 significantly independent of the viral transcription factor, E2, and there was overall heterogeneity in the downregulation of viral transcription in response to the effects of BET inhibition across HPV-associated cell lines. Chemical BET inhibition was phenocopied with the knockdown of BRD4 and mirrored downregulation of viral E6 and E7 expression. Strikingly, there was heterogeneity in the reactivation of p53 levels despite E6 downregulation, while E7 downregulation did not alter Rb levels significantly. We identified that BET inhibition directly downregulated c-Myc and E2F expression and induced CDKN1A expression. Overall, our studies show that BET inhibition provokes a G1-cell cycle arrest with apoptotic activity and suggests that BET inhibition regulates both viral and cellular gene expression in HPV-associated HNSCC.

cancer biology↗

bioRxiv2023

Pre-clinical Evaluation of Biomarkers for Early Detection of Nephrotoxicity Following Alpha-particle Radioligand Therapy

PurposeCancer treatment with alpha-emitter-based radioligand therapies (-RLTs) demonstrates promising tumor responses. Radiolabeled peptides are filtered through glomeruli, followed by potential reabsorption of a fraction by proximal tubules, which may cause acute kidney injury (AKI) and chronic kidney disease (CKD). Because tubular cells are considered the primary site of radiopeptides renal reabsorption and potential injury, the current use of kidney biomarkers of glomerular functional loss limits the evaluation of possible nephrotoxicity and its early detection. This study aimed to investigate whether urinary secretion of tubular injury biomarkers could be used as additional non-invasive sensitive diagnostic tool to identify unrecognizable tubular damage and risk of long-term -RLTs nephrotoxicity. MethodsA bifunctional cyclic peptide, melanocortin ligand-1(MC1L), labeled with [203Pb]Pb-MC1L, was used for [212Pb]Pb-MC1L biodistribution and absorbed dose measurements in CD-1 Elite mice. Mice were treated with [212Pb]Pb-MC1L in a dose escalation study up to levels of radioactivity intended to induce kidney injury. The approach enabled prospective kidney functional and injury biomarker evaluation and late kidney histological analysis to validate these biomarkers. ResultsBiodistribution analysis identified [212Pb]Pb-MC1L reabsorption in kidneys with a dose deposition of 2.8, 8.9, and 20 Gy for 0.9, 3.0, and 6.7 MBq injected [212Pb]Pb-MC1L doses, respectively. As expected, mice receiving 6.7 MBq had significant weight loss and CKD evidence based on serum creatinine, cystatin C, and kidney histological alterations 28 weeks after treatment. A dose-dependent urinary Neutrophil gelatinase-associated lipocalin (NGAL, tubular injury biomarker) urinary excretion the day after [212Pb]Pb-MC1L treatment highly correlated with the severity of late tubulointerstitial injury and histological findings. Conclusionurine NGAL secretion could be a potential early diagnostic tool to identify unrecognized tubular damage and predict long-term -RLT-related nephrotoxicity.

pharmacology and toxicology↗

bioRxiv2023

A Novel Subtype of Myeloproliferative Neoplasms Driven by a MYC-Alarmin Axis

Despite advances in understanding the genetic abnormalities in myeloproliferative neoplasms (MPNs) and the development of JAK2 inhibitors, there is an urgent need to devise new treatment strategies, particularly for triple negative myelofibrosis (MF) patients whose MPNs lack mutations in the JAK2 kinase pathway and have very poor clinical outcomes. Here we report that MYC copy number gain and increased MYC expression frequently occur in triple negative MF, and that MYC-directed activation of S100A9, an alarmin protein that plays pivotal roles in inflammation and innate immunity, is necessary and sufficient to drive development and progression of MF. Notably, the MYC-S100A9 circuit provokes a complex network of inflammatory signaling that involves various hematopoietic cell types in the bone marrow microenvironment. Accordingly, genetic ablation of S100A9 or treatment with small molecules targeting the MYC-S100A9 pathway effectively ameliorates MF phenotypes, highlighting the MYC-alarmin axis as a novel therapeutic vulnerability for this subgroup of MPNs. SIGNIFICANCEThis study establishes that MYC expression is increased in triple negative MPNs via trisomy 8, that a MYC-S100A9 circuit manifest in these cases is sufficient to provoke myelofibrosis and inflammation in diverse hematopoietic cell types in the BM niche, and that the MYC-S100A9 circuit is targetable in triple negative MPN.

cancer biology↗

bioRxiv2023

Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer

Nuclear speckles are membrane-less bodies within the cell nucleus enriched in RNA biogenesis, processing, and export factors. In this study we investigated speckle phenotype variation in human cancer, finding a reproducible speckle signature, based on RNA expression of speckle-resident proteins, across >20 cancer types. Of these, clear cell renal cell carcinoma (ccRCC) exhibited a clear correlation between the presence of this speckle expression signature, imaging-based speckle phenotype, and clinical outcomes. ccRCC is typified by hyperactivation of the HIF-2 transcription factor, and we demonstrate here that HIF-2 drives physical association of a select subset of its target genes with nuclear speckles. Disruption of HIF-2-driven speckle association via deletion of its speckle targeting motifs (STMs)--defined in this study--led to defective induction of speckle-associating HIF-2 target genes without impacting non-speckle-associating HIF-2 target genes. We further identify the RNA export complex, TREX, as being specifically altered in speckle signature, and knockdown of key TREX component, ALYREF, also compromises speckle-associated gene expression. By integrating tissue culture functional studies with tumor genomic and imaging analysis, we show that HIF-2 gene regulatory programs are impacted by specific manipulation of speckle phenotype and by abrogation of speckle targeting abilities of HIF-2. These findings suggest that, in ccRCC, a key biological function of nuclear speckles is to modulate expression of a specific subset of HIF-2-regulated target genes that, in turn, influence patient outcomes. We also identify STMs in other transcription factors, suggesting that DNA-speckle targeting may be a general mechanism of gene regulation. HIGHLIGHTS- Nuclear speckles shown to reproducibly vary in cancer, predicting patient survival in ccRCC - HIF-2 drives DNA/gene-speckle contacts dependent on identified speckle targeting motifs within HIF-2 - Putative speckle targeting motifs are highly enriched among regulators of gene expression - Partitioning of transcription factor functional programs may be a major biological function of nuclear speckles

cancer biology↗

bioRxiv2023

Programmed Cell Death Modifies Neural Circuits and Tunes Intrinsic Behavior

Programmed cell death (PCD) is a common feature of animal development. During development of the C. elegans hermaphrodite, programmed cell death eliminates 131 cells in stereotyped positions in the cell lineage, mostly in neuronal lineages. Blocking cell death results in supernumerary "undead" neurons. We find that undead neurons can be wired into circuits, can display activity, and can modify specific behaviors. The two undead RIM-like neurons participate in the RIM-containing circuit that computes movement. The presence of these two extra neurons results in animals that initiate fewer reversals and lengthens the duration of those reversals that do occur. We describe additional behavioral alterations of cell-death mutants, including in locomotory turning angle and pharyngeal pumping. These findings indicate that physiological or evolutionary variations in PCD might reveal latent neuronal elements that the nervous system can incorporate to modify nervous system function and animal behavior.

neuroscience↗