Biology subjects

Huang, Y.-C.

Publications and source records attributed to Huang, Y.-C..

At least 19 recordsLinked to original sources

bioRxiv2026

Transcriptome-wide Differential Expression and Splicing in Inflammatory Bowel Disease Patients

The inflammatory bowel diseases (IBD), comprising mainly Crohn's disease (CD) and ulcerative colitis (UC), are characterized by chronic intestinal inflammation driven in part by complex genetic and gene regulatory mechanisms. Although transcriptomic studies have defined broad expression changes in IBD, the contribution of alternative splicing to disease-associated molecular variation remains less clear. We therefore integrated differential expression (DE) and differential splicing (DS) analyses in macroscopically uninvolved colonic mucosal biopsies from patients with either CD or UC along with non-IBD controls to define gene expression and intron-usage changes across disease subtypes. We identified 491 DS and 316 DE genes in CD vs. non-IBD, and 1,298 DS and 1,107 DE genes in UC vs. non-IBD. DS and DE genes were nearly mutually exclusive, with no overlapping genes in CD and 16 in UC. Consistent with this result, pathway analysis showed that differentially expressed and differentially spliced genes were associated with related but distinct biological programs. DE genes were involved in chromatin organization, transcriptional regulation, and metabolic pathways for glycans and drugs, whereas DS genes were enriched for splicing, cellular signaling, and lipid metabolism. We found substantial similarity in enriched pathways across CD and UC with some notable exceptions, including increased enrichment of DS and DE genes involved in extracellular vesicles and exosomes in CD and enrichment of DS genes in ER-to-Golgi trafficking and stress granules in UC. Direct comparisons of CD and UC patients additionally show differential splicing usage in genes involved in cell adhesion pathways. These findings identify alternative splicing as a major contributor to transcriptomic changes in IBD that is largely distinct from changes in expression level and provide a broader view of molecular contributors to IBD.

genomics↗

bioRxiv2026

The hypothalamic paraventricular nucleus mediates vagus nerve stimulation-enhanced gastric emptying

Background: Vagus nerve stimulation (VNS) improves gastrointestinal (GI) motility, but its central regulatory mechanisms remain unclear. The hypothalamic paraventricular nucleus (PVN) regulates autonomic and neuroendocrine functions. We investigated whether PVN centrally regulates the prokinetic effects of VNS. Methods: Cervical VNS was applied to rats with intestinal manipulation (IM)-induced gastroparesis. GI motility was assessed by gastric emptying (GE) and geometric center (GC) of fluorescein isothiocyanate-dextran. PVN activation during VNS was evaluated by extracellular neuronal firing recording and c-Fos immunostaining. PVN electrical stimulation and muscimol inhibition assessed its causal role. Serum levels of GI motility-related hormones ghrelin and motilin, inflammatory markers TNF-, interleukin (IL)-6, and corticosterone, and gut expression of motilin receptor (MTLR) and myeloperoxidase (MPO), a neutrophil marker, were assessed as potential downstream mediators. Results: IM impaired GE and GC and increased TNF- and IL-6. Cervical VNS enhanced GE and GC, reduced TNF-, IL-6, and MPO, and activated the dorsal motor nucleus of the vagus, nucleus of tractus solitarius, and PVN. PVN neuronal firing increased during VNS in a stimulation-strength dependent manner. Direct PVN stimulation at VNS-evoked firing frequencies enhanced GE, MTLR expression, and serum motilin, which positively correlated with GE. PVN stimulation also reduced IL-6 and MPO. Conversely, PVN inhibition attenuated VNS-enhanced GI motility, and MTLR expression and reduced its anti-inflammatory effects on IL-6 and MPO, although IL-6 was not correlated with GE. Conclusion: PVN acts as a central regulator within the vagal circuit, activated by VNS and gating VNS-enhanced vagal efferent output for gastric emptying and anti-inflammatory effects.

neuroscience↗

bioRxiv2026

Live Imaging of Epithelial Phagocyte Differentiation in the Drosophila Ovary RevealsTransient and Novel Behaviors

The transformation of epithelial cells into Non-Professional Phagocytes (NPPs) is a conserved and versatile adaptation that occurs in response to immune challenges, tissue remodeling, and apoptotic debris clearance. In the Drosophila melanogaster ovary, follicle cells (FCs) acquire phagocytic capabilities under stress, providing a powerful model to study this process. Using time-lapse live imaging, we captured dynamic behaviors associated with FC-to-NPP differentiation that are too transient to detect by static imaging. Our approach confirmed established features, including germline cell death, cytoplasmic expansion, and debris engulfment, and revealed previously unrecognized capabilities. These include a gradual increase in JNK pathway activation, after which NPPs exhibit collective migration toward dying germline cells, epithelial delamination, long-range target capture through pseudopodial extensions, and the engulfment of neighboring FCs. These findings demonstrate that epithelial-derived NPPs can perform complex phagocytic tasks typically attributed to professional phagocytes such as macrophages. Our work establishes the Drosophila ovary as a robust in vivo system to uncover conserved and novel aspects of epithelial plasticity and phagocytic function, particularly those involving transient behaviors missed by fixed-sample analyses.

cell biology↗

bioRxiv2026

Leptin Acts as a Peripheral Tropic Signal to Tune Steroidogenesis

The integration of metabolic status with reproductive and developmental timing is a cornerstone of animal physiology, yet how steroidogenesis rapidly adapts to abrupt environmental changes remains poorly understood. Here, we identify a peptide hormone circuit in which leptin or its analogs act as peripheral tropic signals, directly coupling systemic metabolic state to steroid hormone production through dynamic remodeling of intracellular lipid pools. Mechanistically, spatiotemporal fluctuations in leptin activate JAK/STAT signaling within steroidogenic tissues to reprogram the balance among lipid droplets, cholesteryl esters, and free cholesterol, thereby tuning the amplitude and timing of steroid hormone pulses via hormone-sensitive lipase (Hsl), a rate-limiting determinant of steroidogenic flux. Cross-species analyses in Drosophila melanogaster, Blattella germanica, and Mus musculus suggest a partially conserved leptin-JAK/STAT-lipase axis that functions as a metabolic "sterol rheostat", enabling rapid modulation of steroidogenesis in response to systemic metabolic and stress cues. These findings reveal a metabolic-endocrine mechanism by which leptin can act directly on steroidogenic organs to regulate hormonal output.

developmental biology↗

bioRxiv2026

Dendritic excitations primarily mediate back-propagation in CA1 pyramidal neurons during behavior

Dendrites integrate synaptic inputs to trigger action potentials, and dendrites carry back-propagating action potentials (bAPs) to synapses where these signals contribute to plasticity. Despite strong evidence for a rich repertoire of nonlinear dendritic excitations, the in vivo roles of these excitations in dendritic integration and back-propagation remain uncertain. Here, we used high-speed voltage imaging through a chronically implanted microprism to map membrane potential dynamics from basal to apical dendrites of CA1 neurons in mice navigating in a virtual reality environment. Despite complex dendritic branch morphology, the dynamics were largely captured by 2 or 3 electrical compartments: basal, soma, and apical. Fast dendritic spikes almost always started from bAPs, indicating that dendritic spikes are primarily a consequence rather than a cause of somatic spiking. These fast spikes sometimes triggered slower apical dendritic plateau depolarizations, which drove complex spikes at the soma. We found that the biophysics of dendritic excitability determined the distribution of simple and complex spikes across a place field. Our results show how CA1 pyramidal neurons convert synaptic inputs to spiking outputs and suggest a primary role of dendritic nonlinearities in mediating activity-dependent plasticity.

neuroscience↗

bioRxiv2025

An Atlas of Extrachromosomal DNA Structures Illuminates Its Evolution and Biogenesis in Cancer

Extrachromosomal circular DNA (ecDNA) is a prevalent driver of oncogene amplification across diverse types of cancers. Leveraging single-molecule long-read sequencing and a de novo circular genome assembler, ecLego3, we charted a comprehensive atlas of ecDNA structures from longitudinal pairs of primary and recurrent glioblastoma (GBM). Our approach resolved 23 ecDNA genomes representing major oncogenes associated with GBM pathogenesis and revealed a dynamic configuration characterized by pronounced structural variation and multi-species co-existence within individual tumors. Evolutionary trajectories were shaped by hierarchical accrual of structural variants, predominated by deletions and inversions, giving rise to novel oncogene isoforms and enhancer repositioning. Such structural plasticity promotes intratumor heterogeneity and tumor fitness. Multiomic analyses at single cell resolution linked ecDNA abundance and structure to transcriptional output, uncovering non-linear scaling and synergistic co-selection among multiple ecDNA species. Comparative profiling revealed locus-dependent configuration, a contraction of ecDNA diversity upon recurrence, and convergent structural architectures across patients, implicating repeat-mediated genomic rearrangements and replication stress in ecDNA biogenesis. These findings elucidate ecDNA-driven mechanisms of tumor adaptation and highlight new molecular vulnerabilities, informing potential biomarkers and therapeutic strategies for high-grade gliomas.

cancer biology↗

bioRxiv2025

Functional heterogeneity and plasticity in naive CD8 T cells drive superior effector and memory responses

While significant progress has been made in defining subsets among antigen-experienced CD8 T cells, the heterogeneity of naive CD8 T cells remains poorly understood. Here, we identify naive CD8 T cell subsets with superior persistence and an enhanced capacity to generate effector and memory cells, leading to more effective protection. These high-quality naive CD8 T cells are marked by IL-18R, CD73, and CXCR3, and functionally less potent naive CD8 T cells can convert into these superior subsets. Their enhanced response to infections is driven by better survival of the progeny effector cells during the T cell expansion phase. This improved survival is mediated by increased Ly6C2 expression on effector cells derived from these high-quality naive cells. Collectively, our findings reveal functional heterogeneity and plasticity among naive CD8 T cells and uncover a mechanism by which high-quality naive subsets drive robust CD8 T cell responses, providing a previously unrecognized layer of immune regulation. SUMMARYOur study reveals functional heterogeneity and plasticity within naive CD8 T cells, identifying high-quality subsets that can emerge from less potent cells and drive superior immune responses through enhanced survival of effector progeny.

immunology↗

bioRxiv2025

Presynaptic Release Probability Determines the Need for Sleep

Sleep is universal among animals with synapses, yet the synaptic functions determining the need for sleep remain elusive. By directly measuring synaptic transmission at anatomically defined synapses in Drosophila, we found that synaptic strength remained stable or declined after sleep deprivation in a circuit-specific manner. In contrast, presynaptic release probability (Pr) consistently decreased with sleep loss across circuits and species, stemming from reduced Ca2+ influx or weakened vesicle-channel coupling at presynaptic terminals, and recovered after sleep. Bidirectional manipulations of Pr altered sleep pressure, establishing a causal relationship between presynaptic function and sleep need. Non-synaptic sleep-regulatory signaling pathways consistently modulate Pr but not synaptic strength. Thus, our findings identify Pr, rather than synaptic strength, as the conserved synaptic substrate underlying sleep need.

neuroscience↗

bioRxiv2025

Sleep Facilitates Pattern Separation through SK Channel-Mediated Sparse Coding

The roles of sleep in priming the brain for associative learning remain unclear. Here, we report that acute sleep deprivation in Drosophila selectively impairs pattern separation--the ability to distinguish between similar stimuli--without affecting classical conditioning. This deficit correlates with disrupted sparse coding in the mushroom body, reflected by an increased number of active Kenyon cells and greater overlap in their odor representations. Electrophysiological analyses reveal that sleep loss enhances small conductance calcium-activated potassium (SK) channel-mediated afterhyperpolarization in GABAergic anterior paired lateral (APL) neurons, leading to reduced levels of feedback inhibition onto Kenyon cells and compromised sparse coding. Targeted knockdown of SK channels in APL neurons reduce their augmented afterhyperpolarization and rescues the pattern separation deficits caused by sleep deprivation. These findings identify a critical role for SK channels in inhibitory interneurons to enable sleep to preserve sparse and decorrelated neural representations, supporting cognitive processes such as pattern separation.

neuroscience↗

bioRxiv2025

Nutrient availability-driven changes in extracellular matrix biochemical and mechanical properties regulate pancreatic cancer cell biology

The extracellular matrix (ECM) provides key biochemical and biomechanical cues that govern fundamental cellular processes, including growth and migration. ECM dysregulation and altered cell-matrix interactions are a driver of cancer progression, exemplified by pancreatic ductal adenocarcinoma (PDAC), where an abnormally dense, collagen-rich, and stiff ECM correlates with poor patient outcomes. The PDAC microenvironment is poorly perfused, resulting in altered nutrient availability, yet how this metabolic stress shapes the ECM and its biological activity remains poorly understood. Herein, we demonstrate that glutamine, a key amino acid depleted in poorly perfused PDAC regions, regulates the biochemical composition, mechanical properties, and biological activity of fibroblast-derived ECM. As glutamine availability increases, fibroblasts shift from producing a basement membrane-like ECM toward an interstitial, mature ECM enriched in fibrillar collagens. The ECM generated under glutamine-rich conditions is stiffer, which limits PDAC cell growth, while simultaneously, the elevated collagen I content promotes migration in a 3D spheroid model. Mechanistically, glutamine-dependent collagen I engages integrin 2 (ITGA2) to activate focal adhesion kinase signaling, driving PDAC cell migration independent of growth. In PDAC patients, glutamine stress inversely correlates with collagen expression in CAFs, with collagen I-ITGA2 as the most enriched ECM receptor interaction pair compared to the normal pancreas. These findings establish nutrient availability as a key regulator of ECM biology and offer new avenues to therapeutically intervene with dysregulated cell-matrix interactions in PDAC.

cell biology↗

bioRxiv2025

Pancreatic α-cells are functionally heterogeneous and sex-dependently regulated by neighboring endocrine cells

Glucose and paracrine regulation on -cells, particularly with respect to sex differences, remains unclear. Hence, we imaged islets of GluCre:GCaMP6ffl/fl mice in pancreatic slices, additionally loaded with a red Ca{superscript 2} dye, to precisely interrogate Ca{superscript 2} dynamics in -cells and the adjacent {beta}- and {delta}-cells. During a glucose ramp (1.8-10.8mM), -cell Ca{superscript 2} oscillations were heterogeneous, antiphasic to {beta}-cells, and inversely correlated with {delta}-cells. Selective inhibition of insulin receptor (InsR) and somatostatin receptor subtypes-2 and 3 (SSTR2/3) shifted the majority of -cells to hyperactivity, delayed the decline of -cell activity and onset of synchronized {beta}-cell Ca{superscript 2} oscillations during the ramp. While female -cells exhibited greater sensitivity to SSTR2/3 inhibition, male -cells were more responsive to InsR blockade. Under complete SSTR2/3 and InsR antagonism, -cells exhibited elevated Ca{superscript 2} oscillations but remained glucose-dependent. We conclude that intra-islet coordination fine-tunes -cell glucose responses, with sex-specific paracrine signaling potentially shaping glucagon profiles in metabolic disease.

physiology↗

bioRxiv2025

Orphan nuclear receptors recruit TRIM28 to promote telomeric H3K9me3 for the alternative lengthening of telomeres pathway

Alternative lengthening of telomeres (ALT) is a telomere maintenance mechanism deployed in embryonic stem cells and cancer cells. High levels of the heterochromatin mark H3 lysine 9 trimethylation (H3K9me3) at telomeres are critical for ALT, but how that is achieved remains unclear. Telomeric association of orphan nuclear receptors (NRs)--such as COUP-TF1, COUP-TF2, TR2, and TR4--has been shown previously to promote ALT activation. Here, we show that orphan NRs regulate telomeric H3K9me3 through TRIM28, a corepressor of ZNF transcription factors, to drive ALT. We report that H3K9me3 is induced by telomeric association of orphan NRs in cultured human fibroblast and ALT cancer cell lines. Moreover, TRIM28 is required for the orphan NR-induced H3K9me3 and ALT phenotypes. Importantly, physical interaction of TRIM28 with orphan NRs facilitates a telomeric localization of TRIM28. A TRIM28 variant defective in orphan NR interaction fails to localize to telomeres and is unable to promote H3K9me3 and ALT phenotypes. These findings indicate that telomeric orphan NRs recruit TRIM28, driving telomeric H3K9me3 and ALT activation, emphasizing the role of changes in chromatin structure in ALT activation.

molecular biology↗

bioRxiv2025

SSNA1 organizes the distal luminal centriolar network and promotes ciliogenesis without microtubule association

The distal lumen of the centriole plays a critical role in ciliogenesis, yet the molecular composition, spatial organization, and targeting hierarchy of distal luminal proteins remain poorly understood. In this study, we identify Sjogrens syndrome nuclear autoantigen 1 (SSNA1) as a bona fide centriolar protein and a key regulator of ciliogenesis in mammalian cells. Using our newly developed knockout (KO)-validated antibody, we show that, contrary to previous reports, SSNA1 does not reside in the nucleus, midbody, or ciliary axoneme. Instead, super-resolution imaging combined with expansion microscopy (ExM) reveals that SSNA1 localizes to the distal lumen of centrioles and the basal bodies of both primary and motile cilia, where it is arranged in a ring-like configuration with 9-fold symmetry and apart from centriolar microtubules. Molecular dissection using tag-free SSNA1, its oligomerization-deficient mutants, and microtubule co-pelleting assays further demonstrates that SSNA1, previously described as a microtubule nucleator, stabilizer, and branching factor, does not bind microtubules in vitro. Interactor screening and KO analysis unveil a hierarchical targeting network involving a C2CD3-SSNA1-LRRCC1 axis in the distal lumen. Functional characterization indicates that although dispensable for cell division, overall centriole organization and duplication, SSNA1 promotes cilia assembly by facilitating CP110 removal. Our findings redefine the physiological role of SSNA1 as part of the distal luminal module contributing to ciliogenesis and provide new insights into the molecular architecture and functional relevance of the distal centriolar lumen. SignificanceCentrioles template the assembly of cilia and flagella, whose dysfunction causes human diseases known as ciliopathies. Key centriolar structures - the cartwheel in the proximal lumen, the inner scaffold in the central lumen, and the distal and subdistal appendages outside the distal lumen - have been extensively characterized. However, the molecular organization and functional relevance of the distal lumen remain largely unexplored. Here, we identify SSNA1 as a novel centriolar component at the distal lumen and an essential regulator of ciliogenesis. Our work challenges the long-held view of SSNA1 as a microtubule-associated protein and provides new insights into the architecture, interaction network, targeting hierarchy, and function of the distal centriolar lumen, exemplifying how it modulates centriolar organization and drives ciliogenesis.

cell biology↗

bioRxiv2025

Polyploidy promotes transformation of epithelial cells into non-professional phagocytes

Removal of dead and damaged cells is critical for organismal health. Under stress conditions such as nutritional deprivation, infection, or temperature shift, the clearance of nonessential cells becomes a universal strategy to conserve energy and maintain tissue homeostasis. Typically, this task is performed by professional phagocytes such as macrophages. However, non-professional phagocytes (NPPs) can also adopt a phagocytic fate under specific circumstances. Similar to professional phagocytes, NPPs undergo transitions from immature to mature states and activation, but the precise cellular and molecular mechanisms governing their maturation, induction and phagocytic execution remain largely unknown. A notable example of stress-induced phagocytosis is the removal of germline cells by follicle cell-derived NPPs during oogenesis in Drosophila. In this study, we report that the transformation of follicle cells into NPPs is dependent on Notch signaling activation during mid-oogenesis. Moreover, Notch overactivation is sufficient to trigger germline cell death and clearance (GDAC). We further show that polyploidy, driven by Notch signaling-induced endoreplication, is essential for the transformation of follicle cells into NPPs. Polyploidy facilitates the activation of JNK signaling, which is crucial for the phagocytic behavior of these cells. Additionally, we show that polyploidy in epidermal cells, another type of NPPs, is important for their engulfment of dendrites during induced degeneration. Together, these findings suggest that polyploidy is a critical factor in the transformation of epithelial cells into NPPs, enabling their phagocytic functions, which are essential for maintaining cellular and organismal homeostasis during stress conditions. SIGNIFICANCEThe ability to remove dead and damaged cells is essential for maintaining tissue homeostasis and organismal health. While this task is typically performed by professional phagocytes such as macrophages, non-professional phagocytes (NPPs) can also acquire phagocytic functions during development or in response to stress conditions. Using Drosophila oogenesis as a model, we reveal that the transformation of follicle cells into NPPs is driven by Notch signaling and is critically dependent on polyploidy. Our findings show that polyploidy, induced through Notch signaling-mediated endoreplication, is required for activating JNK signaling, a pathway essential for the phagocytic behavior of NPPs. Furthermore, we show that polyploidy also facilitates the phagocytic activity of epidermal cells in clearing degenerating dendrites. Together, these results suggest that polyploidy plays an important role in enabling epithelial cells to adopt NPP functions and in maintaining tissue and organismal homeostasis under stress conditions.

developmental biology↗

bioRxiv2025

Effects of Arginine Vasopressin on Islet Cells in Pancreatic Tissue Slices: Glucose-Dependent Modulation of IP3 Receptor-Specific Responses

Arginine vasopressin (AVP) is well known for regulating fluid volume, osmotic balance, and vascular tone. Its role in the regulation of pancreatic and {beta} cell function has been reported, yet its effects are not fully understood, particularly regarding its interaction with plasma glucose levels. The osmotic and volume challenges posed by hyper- and hypoglycaemia in diabetes can be a significant complication of effective hormonal regulation of metabolism. In this study, we primarily investigated the effects of AVP and synthetic peptide receptor agonists and antagonists on and {beta} cells in pancreatic tissue slices using live confocal Ca2+ imaging. Our findings demonstrate that AVP exerts glucose-dependent effects on both cell types. At low glucose concentrations, AVP, in combination with physiologically or pharmacologically increased cAMP levels, selectively activated cells without significantly affecting {beta} cells. In contrast, at higher glucose concentrations and pharmacologically elevated cAMP levels, physiological levels of AVP enhanced {beta} cell activity, leading to increased Ca2+ oscillations and insulin release. In both cell types, AVP displayed a bell-shaped concentration dependence, with lower AVP concentrations stimulating hormone release and higher concentrations leading to diminished responses, consistent with inositol trisphosphate receptor (IP3R) activation and inactivation properties. Furthermore, our results indicate that AVP acts primarily through V1b receptors in {beta} cells, with no involvement of V1a, V2 or oxytocin receptors. These findings provide new insights into the modulation of glucose-dependent release of pancreatic hormones by AVP in the context of changed blood osmolality due to hyper- or hypoglycemia in diabetes. Importantly, our results emphasize the potential of targeting AVP signaling pathways as a therapeutic approach in diabetes research, aiming to improve hormone regulation and nutrient homeostasis. HighlightsO_LIHighly spatio-temporally resolved imaging of islet Ca2+ oscillations on pancreatic tissue slices provides an in situ-like model for physiological and pharmacological approaches. C_LIO_LIPhysiological glucose stimulation triggers non-linear {beta} cell collective responses that must be taken into account when interpreting single concentration pharmacological experiments. C_LIO_LIIn a high cAMP context, AVP acts through V1b receptors on islet and {beta} cells, exhibiting a bell-shaped dependence driven by the activation-inactivation properties of IP receptors. C_LIO_LIAVP modulates glucose-dependent effects on and {beta} cells in a physiological concentration range, in the presence of altered blood osmolality or volume due to hyperglycemia, or to the direct effects of hypoglycemia in diabetes. C_LI

physiology↗

bioRxiv2025

Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers

Genes involved in the regulation of chromatin structure are frequently disrupted in cancer, contributing to an aberrant transcriptome and phenotypic plasticity. Yet, therapeutics targeting mutant forms of chromatin-modifying enzymes have yielded only modest clinical utility, underscoring the difficulty of targeting the epigenomic underpinnings of aberrant gene regulatory networks. Here, we sought to identify novel epigenetic vulnerabilities in diffuse large B-cell lymphoma (DLBCL). Through phenotypic screens and biochemical analysis, we demonstrated that inhibition of the H3K9 demethylases KDM4A and KDM4C elicits potent, subtype-agnostic cytotoxicity by antagonizing transcriptional networks associated with B-cell identity and epigenetically rewiring heterochromatin. KDM4 demethylases associated with the KRAB zinc finger ZNF587, and their enzymatic inhibition led to DNA replication stress and DNA damage-induced cGAS-STING activation. Broad surveys of transcriptional data from patients also revealed KDM4 family dysregulation in several other cancer types. To explore this potential therapeutic avenue, we performed high-throughput small molecule screens with H3K9me3 nucleosome substrates and identified novel KDM4 demethylase inhibitors. AI-guided protein-ligand binding predictions suggested diverse modes of action for various small molecule hits. Our findings underscore the relevance of targeting fundamental transcriptional and epigenetic mechanisms for anti-cancer therapy. HIGHLIGHTSO_LIPhenotypic screens identified JIB-04 as a potent anti-cancer agent for multiple subtypes of diffuse large B-cell lymphoma C_LIO_LIJIB-04 binds and inhibits KDM4 demethylases resulting in epigenomic rewiring of heterochromatin C_LIO_LIKDM4 demethylases cooperate with KRAB zinc fingers to limit DNA replication stress, and KDM4 inhibition instigates DNA-damage and cGAS-STING activation in several human cancers C_LIO_LIHigh-throughput small molecule screens with semi-synthetic nucleosome substrates and AI-guided molecular docking simulations identify novel KDM4 inhibitors C_LI

genomics↗

bioRxiv2024

H3.1K27M-induced misregulation of the TSK/TONSL-H3.1 pathway causes genomic instability

The oncomutation lysine 27-to-methionine in histone H3 (H3K27M) is frequently identified in tumors of patients with diffuse midline glioma-H3K27 altered (DMG-H3K27a). H3K27M inhibits the deposition of the histone mark H3K27me3, which affects the maintenance of transcriptional programs and cell identity. Cells expressing H3K27M are also characterized by defects in genome integrity, but the mechanisms linking expression of the oncohistone to DNA damage remain mostly unknown. In this study, we demonstrate that expression of H3.1K27M in the model plant Arabidopsis thaliana interferes with post-replicative chromatin maturation mediated by the H3.1K27 methyltransferases ATXR5 and ATXR6. As a result, H3.1 variants on nascent chromatin remain unmethylated at K27 (H3.1K27me0), leading to ectopic activity of TONSOKU (TSK), which induces DNA damage and genomic alterations. Elimination of TSK activity suppresses the genome stability defects associated with H3.1K27M expression, while inactivation of specific DNA repair pathways prevents survival of H3.1K27M-expressing plants. Overall, our results suggest that H3.1K27M disrupts the chromatin-based mechanisms regulating TSK/TONSL activity, which causes genomic instability and may contribute to the etiology of DMG-H3K27a.

genetics↗

bioRxiv2024

Leveraging Single-Cell RNA-Seq to Generate Robust Microglia Aging Clocks

Biological aging clocks - composite molecular markers thought to capture an individuals biological age - have been traditionally developed through bulk-level analyses of mixed cells and tissues. However, recent evidence highlights the importance of gaining single-cell-level insights into the aging process. Microglia are key immune cells in the brain shown to adapt functionally in aging and disease. Recent studies have generated single-cell RNA sequencing (scRNA-seq) datasets that transcriptionally profile microglia during aging and development. Leveraging such datasets, we develop and compare computational approaches for generating transcriptome-wide summaries to establish robust microglia aging clocks. Our results reveal that unsupervised, frequency-based featurization approaches strike a balance in accuracy, interpretability, and computational efficiency. We further extrapolate and demonstrate applicability of such microglia clocks to readily available bulk RNA-seq data with environmental inputs. Single-cell-derived clocks can yield insights into the determinants of brain aging, ultimately promoting interventions that beneficially modulate health and disease trajectories.

neuroscience↗