Biology subjects

Cai, R.

Publications and source records attributed to Cai, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Cyclic-thiourea ionizable lipids program multilamellar mRNA-LNPs for sustained expression, frozen-storage stability and potent vaccine immunotherapy

Lipid nanoparticles (LNPs) are the leading delivery vehicles for mRNA therapeutics, yet transient expression and limited formulation stability constrain their broader therapeutic application. Here we report the phenotype-driven discovery of an ionizable lipid (HI-62) bearing a 1,3,5-triazinane-2-thione (cyclic-thiourea) headgroup that reproducibly assemble mRNA into onion-like multilamellar nanoparticles. Cryogenic electron microscopy revealed ordered internal lamellae, while molecular-dynamics simulations supported a cooperative assembly model involving pH-responsive electrostatics, headgroup preorganization and short-range directional interactions. The lead HI-62 formulation maintained greater than 95% mRNA encapsulation across N/P ratios of 3-7, prolonged reporter expression for substantially longer durations than benchmark formulations following intravenous and intramuscular delivery, and retains physicochemical integrity and in vivo potency after repeated freeze-thaw cycles and 18 months of storage at -20. In the tumor models, HI-62 elicits robust cellular responses and achieved significant inhibition of tumor growth. These findings establish cyclic-thiourea headgroup chemistry as a design principle for programming lipid-RNA organization into multilamellar architecture, and provide a design principle for next-generation LNPs platform with durable protein expression and superior stability. The HI-62-based formulation has been utilized in mRNA cancer vaccine program which will enter clinical development in months.

bioengineering↗

bioRxiv2026

Selective GRAB sensors reveal distinct endocannabinoid dynamics in vivo

The endocannabinoid system modulates diverse physiological processes via two endogenous lipid ligands, 2-arachidonoylglycerol (2-AG) and anandamide (AEA); however, their specific spatiotemporal dynamics remain poorly understood owing to the lack of selective probes. Here, we developed GRAB2-AG2.0 and GRABAEA2.0, two genetically encoded fluorescent sensors that selectively detect 2-AG and AEA, respectively. Both sensors exhibited high apparent affinity and molecular specificity for their respective ligands, enabling the real-time detection of 2-AG and AEA release evoked by electrical stimulation in cultured neurons and acute brain slices. In freely behaving mice, these sensors revealed ligand- and context-specific eCB dynamics: aversive stimulation preferentially evoked 2-AG, whereas psychoactive drugs produced distinct 2-AG and AEA responses. Notably, {Delta}9-THC elicited a sustained 2-AG signal in the nucleus accumbens shell, and local deletion of Dagla markedly attenuated both this signal and {Delta}9-THC-induced hypolocomotion. These sensors therefore enable detecting 2-AG and AEA signaling seperately and reveal an endogenous 2-AG component of the behavioral response to {Delta}9-THC.

neuroscience↗

bioRxiv2026

SRPK3 regulates back-splicing of pre-MYOCD through Phosphorylating SRSF10 to modulate cardiac hypertrophy

Cardiac hypertrophy represents a hallmark of pathological remodeling in heart failure, involving complex molecular networks that remain incompletely defined. While post-transcriptional regulation is increasingly recognized as a key control layer, the role of splicing kinases in this process requires further elucidation. This study identifies serine/arginine-rich protein kinase 3 (SRPK3) as a central regulator of myocardial hypertrophy through its control of circular RNA (circRNA) biogenesis. We observed marked SRPK3 upregulation in phenylephrine/angiotensin II-treated cardiomyocytes, transverse aortic constriction (TAC) rats, and human heart failure datasets. Gain- and loss-of-function studies demonstrated that SRPK3 overexpression exacerbates hypertrophic phenotypes, including increased cell surface area and upregulation of markers (ANP, BNP, Myh7). Conversely, siRNA knockdown or pharmacological inhibition with the pan-SRPK inhibitor MSC-1186 effectively attenuated these pathological features. Mechanistically, SRPK3 interacts with and phosphorylates the splicing factor SRSF10 at specific serine residues (S129, S131, and S133). This phosphorylation event inhibits the back-splicing of pre-MYOCD, resulting in reduced cardioprotective circ-MYOCD levels and a concomitant increase in linear MYOCD expression. The depletion of circ-MYOCD relieves its competitive inhibition on linear splicing, driving the transcriptional activation of pro-hypertrophic signaling pathways. Crucially, restoring circ-MYOCD expression reversed SRPK3-driven pathology, confirming its protective role. These findings establish the SRPK3-SRSF10-circ-MYOCD axis as a critical regulatory circuit in cardiac remodeling. By bridging kinase activity with splicing dynamics, this study highlights RNA processing as a vital therapeutic target. Targeting this axis via SRPK3 inhibition or circ-MYOCD delivery represents a promising dual-modality strategy for treating heart failure.

Molecular Biology↗

bioRxiv2025

Mechanoresilience of lysosomes conferred by TMEM63A

Lysosomes are subject to perturbations that can cause damage to their limiting membrane. Osmotic shifts, pore-forming toxins, and the growth of luminal polymers or pathogens all stand to increase lysosomal membrane tension and/or disrupt the bilayer. In some contexts, this leads to lysosomal rupture and cell death. Here we describe a mechanism that enables lysosomes to sense and respond to acute increases in tension of their limiting membrane. We report that the lysosome-resident non-selective cation channel, TMEM63A, can drive the directional flux of monovalent cations, major osmoticants, out of the lumen when gated by mechanical tension on the organelle. This results in the ability for lysosomes to relieve hydrostatic pressure and, proportionally, membrane tension, affording lysosomes the time to acquire additional lipids. Lysosomes without this mechanism -either because TMEM63A is deleted or in the case when cells express disease-causing variants of TMEM63A- are an order of magnitude more sensitive to lysis upon increases to their membrane tension when compared to their wildtype counterparts. These findings suggest that lysosomes are capable of regulating hydrostatic pressure and volume in response to high tension.

cell biology↗

bioRxiv2025

A neural circuit for female-specific defensive homeostasis in risk assessment

HighlightsSC CB1R+ neurons encode visual survival threats and initiate risk assessment in both sexes CB1R+ SC-LHb GABAergic circuit maintains defensive homeostasis in risk assessment in females eCBs gate this circuit by disinhibiting presynaptic GABA release exclusively in females Disruption of this mechanism female-specifically impairs risk assessment and stress coping In BriefLiu et al. identify a female-specific subcortical circuit in which eCB signaling, via CB1R on GABAergic terminals in the SC, suppresses transmission to the LHb to maintain precise defensive homeostasis in risk assessment. These findings uncover the circuit and neuronal mechanisms that contribute to the sexually dimorphic maintenance of defensive homeostasis. Risk assessment in defensive behavior is an adaptive mechanism shaped by natural selection, enabling individuals to evaluate potential threats and thereby maintain defensive homeostasis. However, it remains unknown whether specific neural circuits maintain their behavioral homeostasis in a sex-specific manner. To address this, we investigated its neural basis by hierarchical behavior analysis framework with neural circuit dissection. In mice of both sexes, visual survival threats activated cannabinoid 1 receptor (CB1R)-expressing neurons in the superior colliculus (SC) to initiate consistent risk assessment. Deletion of CB1R in SC GABAergic neurons female-specifically impairs risk assessment by disinhibiting GABA release in SC-lateral habenula (LHb) projections, resulting in shortened risk assessment. This disruption furthermore increases the occurrence of abnormal spontaneous behavior following chronic stress exclusively in females. We identified a female-specific SC-LHb GABAergic circuit gated by CB1R maintains defensive homeostasis in risk assessment. Our findings reveal how a conserved neuromodulatory system sex-specifically gates a subcortical circuit to orchestrate distinct survival strategies.

neuroscience↗

bioRxiv2025

Acetaminophen inhibits diacylglycerol lipase synthesis of 2-arachidonoyl glycerol: implications for nociception

SUMMARYThough acetaminophen is a ubiquitous analgesic, its mechanism of action remains unknown. Thus, even though acetaminophen causes ∼500 deaths each year in the US it has not been possible to design safer alternatives. Because endocannabinoids may have a role in acetaminophen action, we examined interactions between the two. We now report that acetaminophen inhibits the activity of diacylglycerol lipase α (DAGLα), but not DAGLβ, decreasing production of the endocannabinoid 2-arachidonoyl glycerol. This gave rise to the counterintuitive hypothesis that decreasing endocannabinoid production by DAGLαinhibitionmay be antinociceptive in certain settings. Supporting this hypothesis, we find that DAGL inhibition by RHC80267 is antinociceptive in wildtype but not CB1 knockout mice in the hotplate test. We propose 1) that activation of DAGLα may exacerbate some forms of nociception and 2) a novel mechanism for the antinociceptive actions of acetaminophen whereby acetaminophen inhibits a DAGLα/CB1-based circuit that plays a permissive role in at least one form of nociception.

neuroscience↗

bioRxiv2025

Identity-by-descent mapping using multi-individual IBD with genome-wide multiple testing adjustment

We present an identity-by-descent mapping approach to test the association between genome-wide loci and complex traits. Our method evaluates whether levels of genetic similarities at specific genomic locations, captured by local relatedness matrices derived from multi-individual IBD sharing, are associated with phenotypic variation in complex traits. In addition, we propose an approach to adjust for multiple testing in genome-wide IBD mapping scans based on the correlation structure between test statistics across the genome. Through simulation studies, we demonstrate that our test has a well-controlled genome-wide type-I error rate and superior power to detect rare and untyped variants compared to standard single-variant tests. We applied our method to systolic blood pressure data from White British individuals in the UK Biobank.

genetics↗

bioRxiv2025

Intracellular tension relaxation engineered through D-enantiomeric hydrogel maneuvers neurogenesis and immunomodulation to facilitate spinal cord repair

Microenvironmental mechanics regulate morphogenesis and post-injury inflammation, however, the fragile mechanical strength and oxidative physiological environment hinder precise and consistent mechanical management after spinal cord injury (SCI). Here, we engineered self-assembling hydrogels of enantiomeric peptides with neural tissue- matching mechanical properties to persistently manipulate mechanosensing and mechanotransduction through stereo conformational recognition and consequent protein affinity difference. While hindering proliferation and morphogenesis in non-neural cells, D-hydrogel-induced intracellular tension relaxation triggered neurogenesis and ECM remolding in astrocytes, while simultaneously suppressing pro-inflammation and promoting pro-regeneration in microglia, which together enable neuroprotection from degeneration and enhance functional recovery in severe SCI rat models. These effects are mediated through neurogenic morphology changes resulting from cytoskeletal tension relaxation, leading to the opening of mechanosensitive ion channels in the cellular membrane, chromatin unfolding, and YAP nuclear translocation. This exclusive D- hydrogel-dependent neurogenesis, triggered by intracellular tension relaxation, revealed a neural-specific response to mechanical cues and provided a targeted tissue repair strategy for nerve injury. TeaserIntracellular tension relaxion activates morphogenesis specifically in neural cells through reversing neurogenic cellular morphology.

neuroscience↗

bioRxiv2024

Red-shifted GRAB acetylcholine sensors for multiplex imaging in vivo

The neurotransmitter acetylcholine (ACh) is essential in both the central and peripheral nervous systems. Recent studies highlight the significance of interactions between ACh and various neuromodulators in regulating complex behaviors. The ability to simultaneously image ACh and other neuromodulators can provide valuable information regarding the mechanisms underlying these behaviors. Here, we developed a series of red fluorescent G protein-coupled receptor activation-based (GRAB) ACh sensors, with a wide detection range and expanded spectral profile. The high-affinity sensor, rACh1h, reliably detects ACh release in various brain regions, including the nucleus accumbens, amygdala, hippocampus, and cortex. Moreover, rACh1h can be co-expressed with green fluorescent sensors in order to record ACh release together with other neurochemicals in various behavioral contexts using fiber photometry and two-photon imaging, with high spatiotemporal resolution. These new ACh sensors can therefore provide valuable new insights regarding the functional role of the cholinergic system under both physiological and pathological conditions.

neuroscience↗

bioRxiv2024

In vivo multiplex imaging of dynamic neurochemical networks with designed far-red dopamine sensors

Neurochemical signals like dopamine (DA) play a crucial role in a variety of brain functions through intricate interactions with other neuromodulators and intracellular signaling pathways. However, studying these complex networks has been hindered by the challenge of detecting multiple neurochemicals in vivo simultaneously. To overcome this limitation, we developed a single-protein chemigenetic DA sensor, HaloDA1.0, which combines a cpHaloTag-chemical dye approach with the G protein-coupled receptor activation-based (GRAB) strategy, providing high sensitivity for DA, sub-second response kinetics, and an extensive spectral range from far-red to near-infrared. When used together with existing green and red fluorescent neuromodulator sensors, Ca2+ indicators, cAMP sensors, and optogenetic tools, HaloDA1.0 provides high versatility for multiplex imaging in cultured neurons, brain slices, and behaving animals, facilitating in-depth studies of dynamic neurochemical networks.

neuroscience↗

bioRxiv2024

Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps

Quorum sensing is a fundamental chemical communication mechanism that enables microorganisms to coordinate behavior and adapt to environmental conditions. In deep-sea cold seep ecosystems, where diverse microbial communities thrive, quorum sensing is likely a key mechanism driving microbial interactions. However, the distribution, mechanisms, and ecological roles of quorum sensing in cold seeps remain poorly understood. To address this, we analyzed 173 metagenomes, 33 metatranscriptomes, and 18 metabolomes from 17 global cold seep sites. We identified 299,355 quorum sensing genes from the seep non-redundant gene catalog, representing 34 gene types across six quorum sensing systems, with distribution patterns influenced by sediment depth and seep type. These quorum sensing genes were present in 3,576 metagenome-assembled genomes from 12 archaeal and 108 bacterial phyla, revealing a complex network of intraspecies and interspecies communication. Microbial groups involved in key metabolic processes, such as sulfate-reducing bacteria, anaerobic methanotrophic archaea, diazotrophs and organohalide reducers, were extensively regulated by quorum sensing, influencing biogeochemical cycles of carbon, nitrogen, and sulfur. Phylogenetic analysis and protein domain identification highlighted the functional roles of key quorum sensing-related proteins (e.g., PDEs, CahR, RpfC/G and LuxR) in modulating microbial behaviors, such as motility and chemotaxis. Heterologous expression and metabolomic profiling further confirmed the activity of representative LuxI-R pairs and identified inhibitors of quorum sensing in cold seep sediments. Overall, these findings highlight complexity and significance of quorum sensing in microbial interactions, ecological adaptation, and biogeochemical cycling within cold seep ecosystems, advancing our understanding of microbial communication in the deep biosphere.

microbiology↗

bioRxiv2024

NINJ1 is activated by calcium-driven plasma membrane lipid scrambling during lytic cell death

NINJ1 is the terminal executioner of cellular rupture in multiple lytic cell death pathways through its clustering in the plasma membrane. Its activation trigger, however, remains unknown. We found that NINJ1-mediated plasma membrane rupture depends on calcium influx into the cell, which suffices to induce NINJ1-mediated rupture. Using genetic and pharmacologic approaches in macrophages, we show calcium drives membrane rupture through phospholipid scrambling by the calcium-activated scramblase TMEM16F. We next tested whether this calcium-activated NINJ1 mechanism is the elusive pathway by which extracellular ATP stimulates cellular rupture. We show that ATP-stimulation of P2X7R induces NINJ1-mediated cell lysis via calcium influx and TMEM16F lipid scrambling, independently of inflammasomes, pannexins and gasdermin D. Our work reveals the mechanism of NINJ1 activation and solves the long-standing mystery of ATP-induced cytolysis. SummaryElevated cytosolic calcium drives NINJ1-mediated cellular rupture during lytic cell death through plasma membrane lipid scrambling.

cell biology↗

bioRxiv2024

An octopamine-specific GRAB sensor reveals a monoamine relay circuitry that boosts aversive learning

Octopamine (OA), analogous to norepinephrine in vertebrates, is an essential monoamine neurotransmitter in invertebrates that plays a significant role in various biological functions, including olfactory associative learning. However, the spatial and temporal dynamics of OA in vivo remain poorly understood due to limitations associated with the currently available methods used to detect it. To overcome these limitations, we developed a genetically encoded GPCR activation-based (GRAB) OA sensor called GRABOA1.0. This sensor is highly selective for OA and exhibits a robust and rapid increase in fluorescence in response to extracellular OA. Using GRABOA1.0, we monitored OA release in the Drosophila mushroom body (MB), the flys learning center, and found that OA is released in response to both odor and shock stimuli in an aversive learning model. This OA release requires acetylcholine (ACh) released from Kenyon cells, signaling via nicotinic ACh receptors. Finally, we discovered that OA amplifies aversive learning behavior by augmenting dopamine-mediated punishment signals via Oct{beta}1R in dopaminergic neurons, leading to alterations in synaptic plasticity within the MB. Thus, our new GRABOA1.0 sensor can be used to monitor OA release in real-time under physiological conditions, providing valuable insights into the cellular and circuit mechanisms that underlie OA signaling.

neuroscience↗

bioRxiv2024

Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models

The discovery and functional annotation of CRISPR-Cas systems laid the groundwork for the development of novel CRISPR-based gene editing tools. Traditional similarity- search-based Cas discovery strategies, which rely heavily on local sequence alignment and reference Cas homologs, may overlook a significant number of remote homologs with limited sequence similarity; and it can not be applied directly for functional recognition. With the rapid development of protein large language models (LLMs), protein foundation models are expected to help model Cas systems with limited Cas homologs without extensive task-specific training data; however, the full potential of these models for Cas discovery and functional annotation has yet to be determined. To this end, we present a novel, effective and unified AI framework, CHOOSER (Cas HOmlog Observing and SElf-processing scReening), for alignment-free discovery of novel CRISPR-Cas systems with self-processing precursor CRISPR RNA (pre-crRNA) capability utilizing protein foundation models. CHOOSER successfully retrieved 11 novel homologs of Cas{lambda}, the majority of which are predicted to be able to self-process pre-crRNA, nearly doubling the current catalog. One of the candidates, EphcCas{lambda}, was subsequently experimentally validated for its ability to self-process pre-crRNA, target DNA cleavage, and trans-cleavage and was shown to be a promising candidate for use as a CRISPR-Cas-based pathogen detection system. Overall, our study provides an unprecedented perspective and methodology for discovering novel CRISPR-Cas systems with specific functions using foundation models, underscoring the potential for transforming newly identified Cas homologs into genetic editing tools.

bioinformatics↗

bioRxiv2023

Improved dual-color GRAB sensors for monitoring dopaminergic activity in vivo

Dopamine (DA) plays multiple roles in a wide range of physiological and pathological processes via a vast network of dopaminergic projections. To fully dissect the spatiotemporal dynamics of DA release in both dense and sparsely innervated brain regions, we developed a series of green and red fluorescent GPCR activation-based DA (GRABDA) sensors using a variety of DA receptor subtypes. These sensors have high sensitivity, selectivity, and signal-to-noise properties with subsecond response kinetics and the ability to detect a wide range of DA concentrations. We then used these sensors in freely moving mice to measure both optogenetically evoked and behaviorally relevant DA release while measuring neurochemical signaling in the nucleus accumbens, amygdala, and cortex. Using these sensors, we also detected spatially resolved heterogeneous cortical DA release in mice performing various behaviors. These next-generation GRABDA sensors provide a robust set of tools for imaging dopaminergic activity under a variety of physiological and pathological conditions.

neuroscience↗

bioRxiv2023

Physiological and metabolic insights into the first cultured anaerobic representative of deep-sea Planctomycetes bacteria

Planctomycetes bacteria are ubiquitously distributed across various biospheres and play key roles in global element cycles. However, few deep-sea Planctomycetes members have been cultivated, limiting our understanding of Planctomycetes in the deep biosphere. Here, we have successfully cultured a novel strain of Planctomycetes (strain ZRK32) from a cold seep sediment, by using an enriched medium supplemented with rifampicin and different nitrogen sources. Our genomic, physiological and phylogenetic analyses indicate that strain ZRK32 is a novel species, which we propose be named: Poriferisphaera heterotrophicis. We show that strain ZRK32 replicates using a budding mode of division. Based on the combined results from growth assays and transcriptomic analyses, we found that rich nutrients, or supplementation with NO3- or NH4+ promoted the growth of strain ZRK32 by facilitating energy production through the tricarboxylic acid (TCA) cycle and the Embden-Meyerhof-Parnas (EMP) glycolysis pathway. Moreover, supplementation with NO3- or NH4+ induced strain ZRK32 to release a bacteriophage in a chronic manner, without host cell lysis. This bacteriophage then enabled strain ZRK32, and another marine bacterium that we studied, to metabolize nitrogen through the function of auxiliary metabolic genes (AMGs). Overall, these findings expand our understanding of deep-sea Planctomycetes bacteria, while highlighting their ability to metabolize nitrogen when reprogrammed by chronic viruses.

microbiology↗

bioRxiv2023

The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples

In 2015, we launched the mesoSPIM initiative (www.mesospim.org), an open-source project for making light-sheet microscopy of large cleared tissues more accessible. Meanwhile, the demand for imaging larger samples at higher speed and resolution has increased, requiring major improvements in the capabilities of light-sheet microscopy. Here, we introduce the next-generation mesoSPIM ("Benchtop") with significantly increased field of view, improved resolution, higher throughput, more affordable cost and simpler assembly compared to the original version. We developed a new method for testing objectives, enabling us to select detection objectives optimal for light-sheet imaging with large-sensor sCMOS cameras. The new mesoSPIM achieves high spatial resolution (1.5 {micro}m laterally, 3.3 {micro}m axially) across the entire field of view, a magnification up to 20x, and supports sample sizes ranging from sub-mm up to several centimetres, while being compatible with multiple clearing techniques. The new microscope serves a broad range of applications in neuroscience, developmental biology, and even physics.

neuroscience↗

bioRxiv2023

Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast

Variation in gene copy number can alter gene expression and influence downstream phenotypes; thus copy-number variation (CNV) provides a route for rapid evolution if the benefits outweigh the cost. We recently showed that genetic background significantly influences how yeast cells respond to gene over-expression (OE), revealing that the fitness costs of CNV can vary substantially with genetic background in a common-garden environment. But the interplay between CNV tolerance and environment remains unexplored on a genomic scale. Here we measured the tolerance to gene OE in four genetically distinct Saccharomyces cerevisiae strains grown under sodium chloride (NaCl) stress. OE genes that are commonly deleterious during NaCl stress recapitulated those commonly deleterious under standard conditions. However, NaCl stress uncovered novel differences in strain responses to gene OE. West African strain NCYC3290 and North American oak isolate YPS128 are more sensitive to NaCl stress than vineyard BC187 and laboratory strain BY4743. Consistently, NCYC3290 and YPS128 showed the greatest sensitivities to gene OE. Although most genes were deleterious, hundreds were beneficial when overexpressed - remarkably, most of these effects were strain specific. Few beneficial genes were shared between the NaCl-sensitive isolates, implicating mechanistic differences behind their NaCl sensitivity. Transcriptomic analysis suggested underlying vulnerabilities and tolerances across strains, and pointed to natural CNV of a sodium export pump that likely contributes to strain-specific responses to OE of other genes. Our results reveal extensive strain-by-environment interaction in the response to gene CNV, raising important implications for the accessibility of CNV-dependent evolutionary routes under times of stress.

evolutionary biology↗