Biology subjects

Suzuki, A.

Publications and source records attributed to Suzuki, A..

At least 19 recordsLinked to original sources

bioRxiv2026

SPATNIC enables H&E-grounded cancer-cell identification across spatial and single-cell transcriptomic modalities in colorectal cancer

Tumors contain diverse non-cancer cells that constitute the tumor microenvironment; thus, identifying which cells are cancerous is a foundational and critical first step in cancer research. However, to our knowledge, no transcriptome-based classifier has been trained using pathologist-defined annotations from matched H&E images at single-cell resolution. Moreover, few tools can be shared across diverse platforms. Here, we present SPATNIC, a variational autoencoder that classifies individual cells as cancer or normal, trained on Xenium cells labeled by a pathologist review of matched H&E images. It matches or exceeds the performance of existing tools in primary colorectal tumors and liver and lung metastases. SPATNIC generalizes zero-shot across Visium, Visium HD, CosMx, Xenium, MERSCOPE, and single-cell RNA sequencing. In public single-cell atlases, it identified a rare POU2F3 tuft-like cancer stem cell population missed by existing annotations and associated with worse survival. In rectal cancer profiled before and after chemoradiotherapy, it separated cancer from normal epithelium in tissue, thus enabling per-patient screening of antibody-drug conjugate (ADC) targets.

cancer biology↗

bioRxiv2026

Structural characterization of a pseudaminic acid-modified lateral flagellar filament from Vibrio alginolyticus

Bacterial flagellar filaments are often modified by glycans, but the structural basis and physiological significance of flagellin glycosylation remain poorly understood in many species. Vibrio alginolyticus produces lateral flagella for surface-associated motility in viscous environments, with LafA forming its filament as flagellin. A maf homolog encoding a putative flagellin glycosylation factor is located immediately downstream of lafA, suggesting that the lateral filament is glycosylated. To investigate this possibility, we purified the lateral flagellar filament from V. alginolyticus and determined the structure at 2.37 [A] resolution by electron cryomicroscopy. Upon model building of LafA in the map, we identified additional densities connected to five serine residues, possibly corresponding to O-linked pseudaminic acid modifications. Mass spectrometric analyses identified these modifications as pseudaminic acid attached to Ser148, Ser173, Ser183, Ser189, and Ser197. Deletion of maf abolished lateral flagella formation and motility, and these defects were restored by complementation with maf. These results demonstrate that the Vibrio lateral flagellar filament is extensively modified by pseudaminic acid and that Maf is required for filament formation. Our findings provide the first structural insight into the glycosylation of Vibrio lateral flagellar filament and establish a framework for understanding the role of flagellin glycosylation in surface-associated motility.

microbiology↗

bioRxiv2026

Interstitial macrophages drive chronic lung allograft dysfunction

Despite immunosuppressive regimens targeting adaptive immunity, chronic lung allograft dysfunction (CLAD) remains the major obstacle to durable lung allograft survival. Here, we identify colony-stimulating factor 1 receptor (CSF1R)-expressing interstitial macrophages as critical orchestrators of CLAD. Using lung tissue from patients with CLAD and a mouse model of mismatched lung transplantation, we show that both donor-derived tissue-resident and recipient- monocyte-derived interstitial macrophages spatially co-localize within peribronchial immune aggregates in patients with CLAD. These interstitial macrophages express distinct cytokine programs that include those implicated in the recruitment of T and B cells. Pharmacological inhibition of CSF1R after lung transplantation in mice reduced interstitial macrophage abundance and attenuated CLAD pathology. Our findings identify donor- and recipient-derived interstitial macrophages as upstream regulators of CLAD and suggest CSF1R as a therapeutic target for its prevention and treatment.

immunology↗

bioRxiv2026

The sympathetic nervous system initiates liver regeneration

Within hours of injury to the liver, signals from damaged hepatocytes activate Kupffer cells, inducing the production of inflammatory cytokines and proliferation of quiescent hepatocytes to regenerate the liver1,2. In humans, liver regenerative capacity declines with age3,4. However, the nature of the initial signals of liver regeneration and how they are affected during aging remain unclear. In this study, we leveraged "neuro-aging mice", in which neuronal function declines with age5, and discovered an essential role for intrahepatic sympathetic nerves in the early phase of liver regeneration. Upon liver injury in wild-type mice, there was a rapid, transient production of noradrenaline (NA) in the liver. This was abolished in neuro-aging mice who instead exhibited decreased metabolic capacity and fatal liver regeneration failure. NA coordinated the activity of multiple cell types by inducing expression of acute-response genes in hepatocytes and stimulating production of inflammatory cytokines such as IL-6 in Kupffer cells. These results identify a crucial role for the sympathetic nervous system and NA in liver regeneration. Further, they suggest that aging-related loss of this sympathetic nerve-NA regulatory axis reduces liver regenerative capacity.

physiology↗

bioRxiv2026

CATaN maps gene regulatory programs that shape genetic risk across complex diseases

Causal variants of complex traits are enriched at transcription factor (TF) binding sites and are thought to contribute to pathology by disrupting TF activity and thereby causing transcriptome dysregulation. However, existing approaches typically address TF-mediated gene regulatory networks (TF-GRNs) and transcriptomes separately, and methods that jointly leverage both to systematically assess disease heritability remain limited. We aimed to develop a framework that jointly leverages TF-GRNs and transcriptomes to assess disease heritability. Here, we constructed a matrix encoding TF-GRNs and developed an unsupervised analytical pipeline, Canonical correlation Analysis of Transcriptome and TF-gene regulatory Networks (CATaN). CATaN applies canonical correlation analysis (CCA) to extract canonical correlation (CC) components, i.e., shared variation components between transcriptomes and TF-GRNs, and converts them into genome-wide functional annotation scores connected to stratified LD score regression (S-LDSC) for heritability analysis. We applied CATaN to eight datasets, including 19,198 bulk samples and 611,772 single cells from human and mouse sources, identifying 588 CC components that are significantly enriched for SNP heritability across 69 complex traits. Notably, functional annotation tracks based on these TF-GRNs are distinct from transcriptome signatures prioritized by LDSC-SEG, with greater heritability enrichment for a subset of traits. Finally, we suggest that CATaN may help prioritize candidate causal variants for experimental fine-mapping using genome editing. Together, integrating TF-GRNs with transcriptomes reveals disease-relevant regulatory programs that are not fully captured by transcriptome-based analyses alone.

genetics↗

bioRxiv2026

Single-cell spatial multiomics identifies POSTN+ CAFs mediating chemoradiotherapy resistance in rectal cancer

Neoadjuvant chemoradiotherapy (CRT) is standard for locally advanced rectal cancer (LARC), yet many patients retain residual disease. To resolve CRT-associated remodeling of the tumor microenvironment, we generated a multimodal spatial atlas from serial sections of paired pretreatment and post-treatment specimens from 24 patients using Xenium single-cell spatial transcriptomics and PhenoCycler multiplex proteomics, profiling 2.8 million cells; matched Visium HD datasets were generated on adjacent serial sections. Resistance was most strongly associated with fibroblast and myeloid programs adjacent to residual tumor. We identify a periostin (POSTN)-expressing CAF subset selectively enriched around residual tumor cells in non-responders, displaying a myofibroblastic phenotype and activating extracellular matrix remodeling, noncanonical WNT signaling, and immunosuppressive pathways. Tumor cells neighboring POSTN+ CAFs show consistent epithelial-mesenchymal transition signatures. Together, this atlas enables interrogation of CRT-induced spatial remodeling and nominates POSTN+ CAFs as key mediators and targets of CRT resistance, with direct relevance to CRT-based combination strategies.

cancer biology↗

bioRxiv2026

Spatial profiling of CAR protein organization reveals in vivo remodeling during CAR-T therapy

Chimeric antigen receptor (CAR) T cell therapy utilizes genetically engineered patient-derived T cells to target cancer cells. Despite its clinical successes in multiple cancer types, the underlying molecular mechanisms by which molecules on CAR-T cells and surrounding cells interact with other proteins and collectively determine treatment efficacy remain elusive. Most previous studies have relied on transcriptome profiling, which does not fully reflect protein-level organization and interactions. In this study, we developed an antibody-oligonucleotide conjugate targeting the FMC63 region of CAR and integrated it into molecular pixelation (MPX). This approach enabled profiling of the dynamics of CAR molecules on cell surfaces as well as their colocalization with other proteins at the single-cell level. By applying MPX to longitudinal samples from three patients undergoing CAR-T cell therapy, we characterized the dynamic changes in CAR-associated protein organization in both pre-infusion CAR products and post-infusion peripheral blood. While CAR protein abundance and polarization showed limited variation across clinical courses, remodeling of a CAR-centered co-localization network was observed over time, including different retentions of specific molecular associations between patients with different clinical outcomes. Although derived from a limited cohort, our study identifies insights from this methodological framework beyond those gained by conventional omics analyses and offers results of a systematic investigation to predict and enhance CAR therapeutic outcomes. Key pointsO_LIMolecular pixelation was applied for chimeric antigen receptor (CAR) profiling at single-molecule and single-cell resolutions. C_LIO_LIProtein and transcriptome analyses of the CAR molecule showed dynamic remodeling during CAR-T therapy in patients with non-Hodgkin lymphoma. C_LI

genomics↗

bioRxiv2026

Sleep neural code perpetuates the evolving negativity bias under stress

Negativity bias is the distorted cognitive processing of how self-experiences are negatively perceived through rumination and overgeneralization. Despite proposed theories of higher-order emotional representation and the involvement of default mode networks, the biological mechanisms underlying how negative emotional bias is persistently generated remain unknown. Here, we show that under negative emotional state, sleep orchestrates neural dynamics to shape persistent negativity bias. A negative emotional state, induced by repeated social defeat stress (SoD), generates negativity bias in both memory-recall and novel experiences such as fear conditioning. Longitudinal Ca2+ imaging of the hippocampus across days revealed that in emotional states, negative schema-like representations that encode the semantic aspect of negativity across experiences are generated. These negative schema-like representations are continuously processed along with dynamic co-reactivations of distinct emotional experiences during sleep. Closed-loop optogenetic silencing of stress experience-tagged cellular ensembles during sleep, but not during awake, prevents negativity bias in future memory-recall and novel experiences. Finally, sleep-active, but not sleep-nonactive, SoD cells predict and decode emotional behaviours during learned and novel situations. Together, these results reveal the biological emergence of semantic-like representations of emotional experiences and sleep causally coordinate neuronal dynamics to persistently shape negativity in future conscious states. These findings offer a new perspective on how higher-order emotional processing during sleep may determine our emotional interpretation of past and future experiences.

neuroscience↗

bioRxiv2026

CCAN forms the spherical shell-like structure in interphase kinetochores

The kinetochore is an essential structure for the faithful chromosome segregation during mitosis. The 16-protein complex known as the constitutive centromere-associated network (CCAN) localizes the kinetochore throughout the cell cycle and forms the basis of the kinetochore. Although a structural model of an individual CCAN unit has been proposed through cryo-electron microscopy analysis, little is known about how multiple CCAN units are organized within cells. Here, using in silico and in vivo analyses, we demonstrate that multiple CCAN units form a spherical, shell-like structure in interphase DT40 kinetochores. CENP-T and CENP-N localize to the CCAN shell, and the CENP-C cupin domain clusters at the center. Molecular dynamics simulations of CCAN assembly suggest that CENP-C contributes to the orientation of CCAN units, leading to the formation of a spherical shell-like structure via CENP-C oligomerization. Super-resolution imaging reveals the spherical shell-like structure at DT40 kinetochores, and knocking out CENP-C abolishes the structure, supporting the reliability of the predicted models. These findings provide important insights into the spatial organization of functional kinetochores within cells.

molecular biology↗

bioRxiv2025

Cellular and molecular fine mapping pinpoints new immunopathology of lupus

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with an unknown etiology. To pinpoint new disease-relevant cell states and their molecular profiles, we performed an in-depth investigation of multimodal single-cell datasets comprising [~]2.1 million peripheral blood mononuclear cells from 346 donors. By resolving 123 fine-grained cell states across 27 cell types, we identified previously uncharacterized populations distinctively associated with clinical severity and treatment status, including GZMK+GZMH+HLA-DR+ effector memory CD8+ T cells (double-positive [DP] EMCD8) and FOXO1+ARHGAP15+ T cells. Through extensive statistical frameworks and multimodal approaches, we delineated their aberrant immune signaling networks, transcriptional regulators, key surface proteins, T cell receptor repertoires, and genetic/epigenetic landscapes, underscoring them as candidate drivers of SLE immunopathology. These findings provide new insights into therapeutic target discovery in SLE.

immunology↗

bioRxiv2025

Niche-targeted therapy via YAP/TAZ activation enhances hematopoietic regeneration

The distinctive milieu of the bone marrow (BM), known as the BM niche, supports hematopoietic stem cells (HSCs) and serves as a foundation for hematopoietic regeneration. Myeloablative stress disrupts not only hematopoietic stem and progenitor cells but also essential BM niche components, including endothelial cells (ECs) and mesenchymal stromal cells (MSCs); disruption of the latter impairs efficient hematopoietic recovery. However, therapeutic strategies targeting niche restoration remain largely underdeveloped. Here, we demonstrate that the Hippo pathway effectors YAP/TAZ are critical for enabling ECs and MSCs to respond to BM injury, and that YAP/TAZ activation accelerates BM niche recovery, thereby promoting hematopoietic regeneration. We found that YAP/TAZ are rapidly activated in both MSCs and ECs following myeloablative stress, maintaining MSC multipotency and orchestrating vascular remodeling. Mechanistically, YAP/TAZ function as transcriptional hubs in MSCs, regulating key transcriptional factors such as Ebf1 and Ebf3. This regulation preserves MSC identity by preventing osteogenic and fibrogenic differentiation while promoting the expression of hematopoietic factors such as Cxcl12 and angiogenic factors. In parallel, YAP/TAZ signaling in ECs facilitates pro-angiogenic responses and drives sinusoidal vessel remodeling after injury. These YAP/TAZ-mediated niche responses are essential for HSC retention and hematopoietic regeneration following diverse myelosuppressive therapies. Notably, pharmacological activation of YAP/TAZ enhances BM niche reorganization and augments hematopoietic regeneration following myeloablative therapies. These findings establish YAP/TAZ as central regulators of BM niche resilience, providing a rationale for niche-targeted therapeutic strategies to enhance hematopoietic regeneration. Key points{blacksquare} YAP/TAZ enable BM niche cells to sense injury and restore their structure and function, thereby promoting hematopoietic regeneration. {blacksquare}Pharmacological activation of YAP/TAZ enhances BM niche resilience and accelerates hematopoietic recovery after myelosuppressive therapies.

cell biology↗

bioRxiv2025

Evaluation of Conditional Treatment Effect of Salt Stress on Tomato Sugar Content Using Causal Machine Learning: A Pilot Study

Exposing tomatoes to salt stress has been reported to increase the fruit sugar content ({degrees}Brix); however, this treatments causal impact under varying environmental conditions remains unclear. In this pilot study, a causal inference analysis was conducted using a Causal Tree to analyze the factors that influence the effect of salt-stress treatment on improving the {degrees}Brix in tomatoes. Data were collected from a single greenhouse using one cultivar over multiple cultivation periods, totaling 707 fruits. Propensity score matching was applied to reduce the covariate imbalance between the salt (NaCl) treatment and control groups. Using a Causal Tree, conditional average treatment effects were then estimated to assess heterogeneity in treatment impact based on environmental variables, such as temperature, humidity, and illumination. Treatment with NaCl significantly increased {degrees}Brix compared to the control, but the magnitude of the effect varied depending on the environmental conditions. The Causal Tree analysis based on the accumulated cultivation data identified specific combinations of environmental factors under which the impact of NaCl treatment on {degrees}Brix enhancement was more pronounced. For example, the estimated Conditional Average Treatment Effect (CATE) reached as high as 0.88 when humidity was [≥]75%, illuminance was [≥]8144 lx, and categorical variable C3 was F1 or F2. In contrast, the CATE dropped to as low as 0.036 under low humidity (<79%) and high temperature (<24{degrees}C). These findings highlight humidity as the most influential factor, whose impact was modulated by interactions with temperature and light conditions.

plant biology↗

bioRxiv2025

Intestinal fructose metabolism/GLP-1/β-cell axis counteracts hyperglycemia after short-term fructose ingestion

Fructose ingestion increases circulating GLP-1 and insulin, yet the specific contributions of these hormonal responses to glycaemic control remain incompletely defined. We hypothesised that fructose metabolism in intestinal L-cells triggers GLP-1 secretion, which then potentiates insulin secretion and counteracts fructose-induced hyperglycaemia. To test this hypothesis, we systematically characterised metabolic responses across multiple mouse strains after 24 h ad libitum fructose ingestion. In both lean (NSY.B6-a/a) and obese diabetic (NSY.B6-Ay/a) mice, fructose elevated plasma insulin, glucagon-like peptide 1 (GLP-1), and glucose-dependent insulinotropic polypeptide (GIP). The insulin response was preserved in GIP receptor-deficient mice (Gipr-/-) but was abolished in proglucagon-deficient mice (Gcg-/-) by pharmacological GLP-1 receptor antagonism, indicating a requirement for GLP-1, but not GIP. Across strains, fructose-induced insulin response correlated with attenuation of post-fructose glycaemia, consistent with insulin being essential for suppressing fructose-induced hyperglycaemia. To explore the mechanism underlying fructose-induced GLP-1 secretion, we combined ATP-sensitive potassium channel-deficient mice (Kcnj11-/-), GLUTag L-cell line, and metabolic tracing of 13C-labelled fructose in freshly isolated intestinal crypts. These complementary approaches support a model in which fructolysis increases the ATP/ADP ratio in L-cells, closes KATP channels, and stimulates GLP-1 secretion. In obese diabetic mice, increased fructolytic flux and a higher ATP/ADP ratio were associated with elevated GLP-1 levels, further corroborating this model. Collectively, our findings indicate that intestinal fructose metabolism drives GLP-1 secretion required to potentiate insulin secretion, thereby establishing a gut-pancreas axis that counter-regulates fructose-induced hyperglycaemia. KEY POINTS SUMMARYO_LIFructose ingestion acutely increases plasma insulin levels, but the underlying mechanisms and physiological significance remain elusive. C_LIO_LIOur study demonstrates that short-term (24h) fructose ingestion in mice elevates both insulin and glucagon-like peptide 1 (GLP-1) levels in the blood, with the plasma insulin response being GLP-1-dependent. C_LIO_LIWe found that fructose metabolism in intestinal L-cells triggered GLP-1 secretion by increasing the ATP/ADP ratio and closing ATP-sensitive K+ channels (KATP channels). C_LIO_LIThis intestinal fructose metabolism/GLP-1/{beta}-cell axis plays a crucial role in preventing fructose-induced hyperglycaemia, an effect that is compromised in obese diabetic mice. C_LIO_LIThese insights highlight the previously unclear metabolic responses following short-term fructose ingestion and their importance in glucose homeostasis. C_LI 1. ABSTRACT FIGURE LEGENDThis study investigated the hormonal effects of short-term fructose consumption in mice, allowing them ad-lib access to fructose solution for 24 h. Fructose metabolism in intestinal L-cells increases the intracellular ATP/ADP ratio, leading to GLP-1 secretion via KATP channel closure and Ca2+ influx. GLP-1 promotes insulin secretion from pancreatic {beta}-cells. The fructose metabolism/GLP-1/insulin pathway is essential for mitigation of fructose-induced hyperglycaemia. Figures were drawn using BioRender.com.

physiology↗

bioRxiv2024

CENcyclopedia: Dynamic Landscape of Kinetochore Architecture Throughout the Cell Cycle

The kinetochore, an intricate macromolecular protein complex located on chromosomes, plays a pivotal role in orchestrating chromosome segregation. It functions as a versatile platform for microtubule assembly, diligently monitors microtubule binding fidelity, and acts as a force coupler. Comprising over 100 distinct proteins, many of which exist in multiple copies, the kinetochores composition dynamically changes throughout the cell cycle, responding to specific timing and conditions. This dynamicity is important for establishing functional kinetochores, yet the regulatory mechanisms of these dynamics have largely remained elusive. In this study, we employed advanced quantitative immunofluorescence techniques to meticulously chart the dynamics of kinetochore protein levels across the cell cycle. These findings offer a comprehensive view of the dynamic landscape of kinetochore architecture, shedding light on the detailed mechanisms of microtubule interaction and the nuanced characteristics of kinetochore proteins. This study significantly advances our understanding of the molecular coordination underlying chromosome segregation.

cell biology↗

bioRxiv2024

Retinoid-impregnated nanoparticles enable control of bone growth by site-specific modulation of endochondral ossification in mice

Growth-plate (GP) injures in limbs and other sites can impair GP function and cause deceleration of bone growth, leading to progressive bone lengthening imbalance, deformities and/or physical discomfort, decreased motion and pain. At present, surgical interventions are the only means available to correct these conditions by suppressing the GP activity in the unaffected limb and/or other bones in the ipsilateral region. Here, we aimed to develop a pharmacologic treatment of GP growth imbalance that involves local application of nanoparticles-based controlled release of a selective retinoic acid nuclear receptor gamma (RAR{gamma}) agonist drug. When RAR{gamma} agonist-loaded nanoparticles were implanted near the medial and lateral sides of proximal tibial growth plate in juvenile C57BL/6j mice, the GP underwent involution and closure. Overall tibia length was shortened compared to the contralateral element implanted with drug-free control nanoparticles. Importantly, when the RAR{gamma} agonist nanoparticles were implanted on the lateral side only, the adjacent epiphysis tilted toward the lateral site, leading to apical angulation of the tibia. In contrast to the local selectivity of these responses, systemic administration of RAR{gamma} agonists led to GP closure at many sites, inhibiting skeletal growth over time. Agonists for RAR and RAR{beta} elicited no obvious responses over parallel regimens. Our findings provide novel evidence that RAR{gamma} agonist-loaded nanoparticles can control activity, function and directionality of a targeted GP, offering a potential and clinically-relevant alternative or supplementation to surgical correction of limb length discrepancy and angular deformities. Lay summaryGrowth-plates (physes), which are cartilage tissues near the ends of bones, support normal bone growth in children. Growth plate injures in limbs and other sites can impair growth plate function, leading to inhibited or imbalanced bone growth, skeletal deformities, decreased motion, discomfort or pain. At present, surgical interventions are the only means available to correct these conditions. Here, we aimed to develop a pharmacologic treatment for bone growth imbalance. Nanoparticles loaded with a selective agonist for the retinoic acid nuclear receptor gamma were prepared and implanted near the tibial growth plate in juvenile mice. The growth plate underwent involution and closure, and overall tibia length was shortened compared to the contralateral element implanted with drug-free control nanoparticles. Importantly, when the same drug nanoparticles were implanted in only one side of the tibia, the tibia was tilted toward the injection site. Our findings provide novel evidence that retinoic acid receptor gamma agonist-loaded nanoparticles can control activity, function and directionality of a targeted growth plate, offering a potential and clinically-relevant alternative or supplementation to surgical correction of limb length imbalances and deformities.

pharmacology and toxicology↗

bioRxiv2024

Inhibition of p38-MK2 pathway enhances the efficacy of microtubule inhibitors in breast cancer cells

Microtubule-targeting agents (MTAs) have been successfully translated from basic research into clinical therapies and have been widely used as first- and second-line chemotherapy drugs for various cancers. However, current MTAs exhibit positive responses only in subsets of patients and are often accompanied by side effects due to their impact on normal cells. This underscores an urgent need to develop novel therapeutic strategies that enhance MTA efficacy while minimizing toxicity to normal tissues. In this study, we demonstrate that inhibition of the p38-MK2 (MAP kinase-activated protein kinase 2) pathway sensitizes cancer cells to MTA treatment. We utilize CMPD1, a dual-target inhibitor, to concurrently suppress the p38-MK2 pathway and microtubule dynamicity. In addition to its established role as an MK2 inhibitor, we find that CMPD1 rapidly induces microtubule depolymerization, preferentially at the microtubule plus-end, leading to the inhibition of tumor growth and cancer cell invasion in both in vitro and in vivo models. Notably, 10 nM CMPD1 is sufficient to induce irreversible mitotic defects in cancer cells, but not in non-transformed normal cells, highlighting its high specificity to cancer cells. We further validate that a specific p38-MK2 inhibitor significantly potentiates the efficacy of sub-clinical concentrations of MTA. In summary, our findings suggest that the p38-MK2 pathway presents a promising therapeutic target in combination with MTAs in cancer treatment.

cancer biology↗

bioRxiv2024

Predicted constrained accessible regions mark regulatory elements and causal variants

Open chromatin regions (OCRs) define cell-type-specific regulatory elements across the genome, yet their functional significance varies, making it challenging to pinpoint biologically essential regions. Here, we introduce CAMBUS (Chromatin Accessibility Mutation Burden Score), a machine-learning framework that identifies active and evolutionarily constrained OCRs by leveraging surrounding DNA sequences. Applying CAMBUS to 29 immune cell types, we identified 66,043 constrained OCRs, which were substantially enriched in the known constraint genome (odds ratio=11.45 (95% confidence interval 9.33-14.05), P=4.7 x 10-68), while 90% of these OCRs were not prioritized by existing constraint metrics. These OCRs were highly enriched for known enhancers and super-enhancers, independent of known epigenetic markers and annotated regions, and overlapped with regulatory elements implicated in immune-mediated diseases and experimentally validated functional variants, including rare variants, particularly in leukocyte-related traits. Furthermore, CAMBUS revealed cell-type-specific transcriptional regulatory landscapes, linking genetic constraint with gene regulation in immune cells and identifying plausible connections between 1,533 causal variants and 70 complex traits. By defining biologically constrained regulatory elements at high resolution, CAMBUS provides a framework for understanding the selective pressures shaping the non-coding genome and its role in human health and disease.

genetics↗

bioRxiv2024

β-adrenergic blockers increase cAMP and stimulate insulin secretion through a PKA/RYR2/TRPM5 pathway in pancreatic β-cells in vitro

{beta}-adrenergic blockers ({beta}-blockers) are extensively used to inhibit {beta}-adrenoceptor activation and subsequent cAMP production in many cell types. In this study, we characterized the effects of {beta}-blockers on mouse pancreatic {beta}-cells. Unexpectedly, high doses (100 M) of {beta}- blockers (propranolol and bisoprolol) led to a 5-10 fold increase in cAMP levels, enhanced intracellular influx, and stimulated a 2-4 fold increase in glucose-and glimepiride-induced insulin secretion in MIN6-K8 clonal {beta}-cells and isolated mouse pancreatic islets. These effects were observed despite minimal expression of {beta}-adrenoceptors in these cells. Mechanistically, cAMP increase led to ryanodine receptor 2 (RYR2) phosphorylation via protein kinase A (PKA), triggering Ca2+-induced Ca2+ release (CICR). CICR then activates transient receptor potential cation channel subfamily M member 5 (TRPM5), resulting in increased Ca2+ influx via voltage-dependent Ca2+ channels. These effects contradict the conventional understanding of the pharmacology of {beta}-blockers, highlighting the variability in {beta}-blocker actions depending on the experimental context. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/618403v3_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@c9ef31org.highwire.dtl.DTLVardef@176a67aorg.highwire.dtl.DTLVardef@abc69aorg.highwire.dtl.DTLVardef@17ba9d4_HPS_FORMAT_FIGEXP M_FIG C_FIG At high concentrations (> 10 M), the {beta}-adrenergic blocker propranolol paradoxically increased intracellular cAMP levels in pancreatic {beta}-cells. This leads to PKA-induced RYR2 phosphorylation and extracellular Ca2+ influx, leading to CICR from the ER. CICR activated TRPM5, which augmented {beta}-cell electrical activity, extracellular Ca2+ influx, and insulin secretion.

cell biology↗