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Biology subjects

Ma, T.

Publications and source records attributed to Ma, T..

At least 19 recordsLinked to original sources

Multiplexed mammalian gene control via modular splicing riboswitches

Precise, multiplexed gene regulation in mammalian cells remains constrained by a heavy reliance on heterologous protein regulators, whose associated immunogenicity and strict cargo-size limits impede clinical translation. Here, we introduce SpliceRACER (Splice-based Riboswitch Array for Combinatorial Expression Regulation), a multiplexed RNA switch platform that achieves scalable, orthogonal, and combinatorial control of gene expression in mammalian cells through alternative splicing, eliminating the need for exogenous protein co-expression. SpliceRACER independently orchestrates three orthogonal channels to regulate fluorescent reporter outputs, yielding 27 discrete combinatorial expression states, vastly exceeding the capacity of conventional binary gene switches. Furthermore, we engineered three generalizable strategies to effectively suppress the basal leakage inherent to synthetic riboswitches, thereby enabling tight OFF-state control of the potent pyroptotic effector GSDMD-NT for precise cell-death induction. This work offers broad utility in synthetic biology and therapeutic applications.

bioengineering↗

GENIE: a multi-agent system for closed-loop autonomous microscopy

Microscopy is foundational to biology, enabling direct observation of otherwise inaccessible cellular structures and processes. Artificial intelligence has advanced microscopy through acquisition control, image analysis, and natural language instrument operation. No system has unified these steps into a complete experimental loop. We introduce an autonomous multi-agent system that turns plain language goals into measurements and statistically tested answers, gating and executing every action in deterministic code. This sets the groundwork for extending microscopy from biological observation to autonomous investigation.

biophysics↗

Mice navigate complex landscapes by learning a sparse vocabulary of paths

Effective navigation is critical for survival, but how animals contend with the scale, complexity, and self-similarity of natural landscapes is unknown. Here, we investigate spontaneous exploratory mouse behavior, both outdoors and in dark self-similar landscapes made from tens to hundreds of tiles of varying heights. Within 2 hours of exploration, mice detected small covert changes to the landscape and jumped across ledges to invisible landing spots, revealing detailed spatial knowledge. In this process, mice converged on a sparse set of memorized paths. These routes depended on prior experience and increased the compressibility of sensory information over time. Our results demonstrate that mice rapidly learn sparse internal representations of their surroundings and suggest that animals use structured behavioral sequences to reduce the complexity of natural navigation.

animal behavior and cognition↗

Inferotemporal cortex stimulation is perceived before its onset

Neural response latency measures when stimulus-evoked activity becomes detectable, but it does not reveal when the brain assigns the causal contribution of that activity to events in the external world. We define this temporal adjustment as projected delay and measure it in the macaque inferotemporal cortex using optogenetic stimulation and behavior. Two rhesus macaques performed a cortical perturbation detection task in which a visual masker appeared at different times relative to stimulation. Detection was selectively impaired when the masker began 200 ms before stimulation. We then tested this timing using Perceptography, a method that optimizes image perturbations to mimic stimulation-evoked visual events. Image perturbations presented 200 ms before stimulation elicited higher false-alarm rates than perturbations presented at stimulation onset. Here, we show that stimulation-evoked visual events in inferotemporal cortex depend preferentially on visual information originating approximately 200 ms before the cortical perturbation. This projected delay exceeds typical inferotemporal response latencies and suggests temporally extended readout mechanisms relevant to causal models of visual perception and the timing of cortical visual prostheses.

neuroscience↗

An Excelled Trifluorinated Probe for GPCR Conformational Quantification

G protein-coupled receptors (GPCRs) represent the largest membrane protein family in the human body and the major targets of FDA-approved medications. Unlike some other physiological proteins, GPCRs are highly plastic and often exist as collections of conformational ensembles in the environment to exert their function. Therefore, understanding how a GPCR adopts different conformational ensembles in response to ligands and signaling partners is essential for drug development. 19F-NMR has emerged as one of the most promising tools in this regard; however, a well-established 19F-labeling system is still lacking, including an effective 19F probe that meets both environmental susceptibility and NMR sensitivity requirements, even though progress has been made dramatically in recent years. Thus, this manuscript reports a novel conformational probe (4-(bromomethyl)-ethoxy-2-(trifluoromethyl)benzene, BTMB) that offers paramount benefits for future GPCR conformational dynamics studies. To rationalize the mechanism behind BTMB's superiority for future probe development, we performed MD simulations, referenced to the current state-of-the-art probe, BTFMA. Our study suggests that the spatial proximity of aromatic residues significantly influences the chemical shift dispersion and linewidths of related 19F-probe-profiled conformational states, as well as the rigidity and compactness of -CF3 in the target protein.

biophysics↗

Protein hunger-driven nitrogen flow from phospholipids to amino acids inDrosophila

Protein is unique among macronutrients due to its nitrogen content and that its building blocks, essential amino acids, cannot be synthesized by animals. Additionally, animals lack specialized amino acid storage sites, necessitating a continuous dietary intake. In the face of insufficient dietary protein, how do animals manage nitrogen limitation? Using Drosophila, we reveal a previously undocumented nitrogen flow from phospholipids to amino acids, a process enhanced by protein deprivation. Protein restriction triggers the degradation of phosphatidylethanolamine (PE), releasing the nitrogen-containing headgroup, ethanolamine, which subsequently serves a dual function. Ethanolamine stimulates protein intake by activating protein hunger neurons and, remarkably, along with phosphoethanolamine, donates nitrogen for amino acid biosynthesis. This nitrogen transfer is mediated by the microbiome and ethanolamine-phosphate phospho-lyase (ETNPPL) pathway in fly cells. Together, our findings identify phospholipids as a hidden nitrogen reservoir and reveal an unrecognized metabolic plasticity that reallocates nitrogen to maintain protein homeostasis.

physiology↗

Higher-Order Mechanical Neighbourhood Sensing Governs Cell Fate in Complex Tissues

Adult tissues maintain precise architectures composed of multiple interspersed cell types, yet prevailing models of cell fate patterning rely on pairwise interactions between neighbouring cells that generate binary decisions. How local interactions encode higher-order, beyond pairwise, multicellular organization remains unclear. Here, using the Drosophila midgut as a model of adult tissue self-organization, we identify a higher-order neighbourhood-sensing mechanism that couples cell identity, mechanics and stem cell (SC) fate. We show that the receptors Cirl/Latrophilin and Toll-8 are expressed in complementary cellular compartments, restricting their engagement to heterotypic interfaces between progenitors and differentiated enterocytes (ECs). These interactions generate interface-specific myosin II-dependent tension that depends on EC neighbourhood composition and mechanically gates Delta-Notch signalling. Thus, although Delta-Notch acts through pairwise interactions, these fate decisions are modulated by a higher-order mechanical state integrating information from surrounding cell contacts. A mathematical model incorporating this coupling reproduces multicellular tissue architecture from first principles and predicts that loss of higher-order coupling destabilizes progenitor organization. This prediction is consistent with the excessive fate transitions, topological disorganization and regenerative defects observed after Cirl-Toll-8 disruption. These findings establish higher-order mechanical neighbourhood sensing as a general principle by which tissues integrate local cellular identities to maintain and restore complex architectures.

cell biology↗

Hierarchical tissue structure creates history-dependent barriers to clonal invasion

Tissues of higher organisms are maintained by hierarchies of stem and progenitor cell compartments regulated by homeostatic feedback. Somatic mutations generate genetically distinct clones whose evolutionary success depends not only on their fitness but also on the tissue architecture in which they arise. In previous work, we showed that this hierarchical organization creates invasion barriers that prevent advantageous mutants originating in downstream compartments from expanding unless their fitness exceeds a critical threshold. Here, we extend this framework to populations containing multiple competing mutant clones. We derive a general invasion criterion showing that the threshold for mutant expansion is determined by the equilibrium established by the resident clones and therefore depends on the evolutionary history of the system. Established clones modify the invasion barriers encountered by subsequent mutants, making clonal evolution history-dependent. The theory predicts competitive exclusion between clones entering the same compartment and shows that resident clones can prevent the establishment of later mutants. Using a model previously parameterized for murine hematopoiesis, we showed that our framework provides a mechanistic explanation for mutation-order effects involving JAK2 V617F and TET2 mutations in myeloproliferative neoplasms. Our results identify invasion barriers as a principle governing history-dependent clonal evolution in hierarchical tissues.

evolutionary biology↗

ERK signaling integrates multiple mechanisms to drive cortical evolutionary expansion

A critical first step in human evolutionary divergence from chimpanzees and other primates is the production of greatly increased numbers of cortical pyramidal neurons during development and over evolutionary time. This expansion underpins the enlarged human cerebral cortex and, consequently, higher-order cognition and consciousness. However, the cellular and molecular mechanisms driving this progressive increase in cortical neuron number remain incompletely understood. Here we show that elevated ERK signaling in human cortical radial glia (RGs), relative to mouse RGs, arises from evolutionary changes in the developmental expression of existing shared genes. Using the Emx1-Cre line to overexpress MEK1DD, a constitutively active mutant of rat MAP2K1, we found that enhanced ERK signaling in mouse cortical RGs upregulates cAMP-PKA signaling, along with promoting self-renewal, expanding the RG pool, and accelerating cell cycle progression. Conversely, overexpression of PKA signaling in mouse cortical RGs via in utero electroporation of constitutively active PRKACA mutants (L206R or W196G) reduces ERK activity, prolongs the cell cycle, suppresses SHH-SMO and YAP/TAZ pathway activity, and blocks ependymal gliogenesis. Together, our results demonstrate that ERK and PKA signaling in cortical RGs engage a dynamic balance of synergistic and antagonistic interactions. This interplay couples evolutionarily enhanced ERK and PKA activities to increased cortical RG numbers, prolonged cell cycle progression, and an extended neurogenic period, which collectively culminate in a marked increase in neuronal production. We conclude that heightened ERK pathway activity in cortical RGs serves as a central driver of progressive neocortical expansion across mammalian evolution. Significance StatementThe human brains extraordinary cognitive abilities stem from a dramatic increase in cortical neuron numbers during evolution. This study reveals that enhanced ERK signaling in human cortical radial glia neural stem cells, relative to other primates, is a key driver of this expansion. By manipulating this pathway in mice, we demonstrate that ERK coordinates multiple mechanisms--including self-renewal, cell cycle acceleration, and a dynamic interplay with PKA signaling--to boost neuronal output. These findings identify a core molecular axis underlying mammalian cortical evolution and provide a framework for understanding how the human cortex acquired its unique size and, consequently, its remarkable complexity.

developmental biology↗

A principal-stress rule for cell division in epithelia

Dense active materials, from cellular tissues to jammed and glassy systems, must continuously relieve internal mechanical stress to remain structurally stable as they are driven far from equilibrium. In epithelial tissues, this relief occurs through cell division, yet what sets the geometry of this structural remodeling event has, for over a century, been attributed to a purely geometric principle: Hertwigs rule, whereby cells divide along their long axis. We show that as epithelial tissues densify and cell shape anisotropy collapses, this geometric rule is superseded by a mechanical one in which dense epithelia relieve anisotropic stress by cells dividing along their principal axis, independent of the tissues isotropic stress state. Using direct force measurement and stress inference, we show that stress orientation, rather than cell shape, governs the axis of cell division across mechanically distinct systems, from fluid-like to jammed monolayers and structurally heterogeneous organoids, remaining predictive precisely where the classical geometric rule fails. This stress-oriented remodeling is reciprocally coupled to the materials mechanical state: anisotropic stress accelerates the underlying remodeling rate, while each remodeling event locally dissipates the stress that triggered it, closing a negative feedback loop. This "principal-stress rule" recasts epithelial cell division as a stress-relief mechanism intrinsic to dense active matter, providing a general mechanical framework linking internal stress, structural remodeling, and homeostasis in living materials.

biophysics↗

Mechanical Tension Actively Triggers RhoA-Mediated Cell Extrusion

Cell extrusion is a fundamental process in tissue homeostasis, morphogenesis, and cancer progression, facilitating the removal of cells either alive or through apoptosis. While biochemical signaling pathways are known to regulate extrusion, recent advances have underscored the importance of mechanical forces in this process. Here, using optogenetic control of RhoA activation in epithelial monolayers combined with Bayesian Inversion Stress Microscopy (BISM) and three-dimensional cell-based modeling, we uncover a counterintuitive mechanism whereby elevated tension, instead of stabilizing the monolayer, actively drives extrusion in highly contractile cells. We show that local RhoA activation enhances myosin II-dependent contractility and F-actin reorganization, which promotes cell stiffening, resulting in localized tension buildup. The ensuing tensile stress amplifies vertical mechanical fluctuations, which in turn trigger cell extrusion. Remarkably, these tension-induced extrusions occur both apically and basally. Furthermore, our findings show that RhoA-mediated contractility is not merely an effector of extrusion but also an active promoter of basal extrusion, independently of caspase activation. Our study demonstrates that tensile stress can directly initiate extrusion events and bias their outcome toward apical or basal fates. By identifying tension as a driver rather than a suppressor of extrusion, this work revises current models of epithelial homeostasis and highlights mechanical control as a targetable axis in disease and regeneration.

cell biology↗

Intra-nanoparticle Drug-protein Interactions Mediate Sequential Therapeutic Release

Controlled drug delivery systems have important implications in many therapeutic applications to improve patient health, but it remains challenging to deliver therapeutics to specific target sites while being released at controlled rates to minimize the off-target accumulation. Here, we report a drug (e.g., vancomycin)-modulating other drug release strategies in human serum albumin (HSA)-based nanoparticles (NPs) to achieve multiple drug encapsulation and controlled release of drugs. Without external stimuli but only with water, the release kinetics of drugs such as sulfasalazine and epidermal growth factor can be modulated by adding vancomycin. The mechanistic study suggests that the release kinetics are related to the secondary structure of albumin through the interactions between drugs and HSA. Our strategy achieved controlled drug delivery through modulating the secondary structure of albumin with a water-soluble drug as a modulator, which provides a promising way to simultaneously deliver multiple drugs while releasing in a predicted and sustained manner.

bioengineering↗

Mitochondrial carrier SLC25A34 links clock, diet, and temperature control of interorganellar lipid cycling

Adipocyte lipid metabolism is coordinated by circadian rhythms, diet, and environmental temperature. Yet how these diverse signals are molecularly integrated remains unknown. Here we show that clock, diet, and temperature cues converge on the orphan mitochondrial transporter, SLC25A34, to orchestrate thermogenic cycling of lipid synthesis and oxidation. During sleep, the clock suppresses Slc25a34 transcription through REV-ERB. Waking, lipid-rich diets, or cold exposure abolish this repression, allowing lipolytic signals to stimulate Slc25a34 expression via PPAR. SLC25A34 then imports oxaloacetate into mitochondria to accelerate the export of substrates used for acetyl-CoA production in the cytosol. This feeds into cytosolic lipid synthesis and transcriptional induction of mitochondrial biogenesis, which collectively promote mitochondrial lipid oxidation. Thus, SLC25A34 confers circadian, dietary, and environmental control of thermogenic metabolism through interorganellar lipid cycling.

molecular biology↗

FM-GPT: Bayesian fine mapping for phenome-wide transcriptome-wide association studies

Transcriptome-wide association studies (TWAS) integrate genome wide association studies with expression quantitative trait locus reference panels to identify genes associated with traits of interest. However, linkage disequilibrium and correlated gene expression can induce spurious TWAS signals, motivating fine mapping methods to prioritize putatively causal genes within associated loci. The rapid growth of large-scale phenomic resources (e.g. electronic health records (EHRs)) has shifted genetic studies from single-trait analyses to phenome-wide investigations that jointly evaluate many closely related phenotypes. We introduce FM-GPT (Fine-mapping of causal Genes for Phenome-wide Transcriptome-wide association studies), a novel Bayesian fine mapping method for prioritizing causal genes across multiple correlated phenotypes with potentially mixed outcome types (e.g., binary, count or continuous) in phenome-wide TWAS. FM-GPT performs gene-guided dimension reduction of the phenotypes and reveals pleiotropic or phenotype-specific effects of the identified genes. In simulations, FM-GPT identified true causal genes more accurately than other fine mapping methods while controlling false positives. We applied FM-GPT to two applications using data from UK Biobank: a brain-wide genetic analysis of MRI data derived regional cortical thickness measures and a phenome-wide genetic analysis of clinical phenotypes derived from EHR data. FM-GPT greatly narrowed down the set size of putatively causal genes and identified: 1. genes with pleiotropic effects on regional cortical thickness across the cerebral cortex, including five genes BCAS3, LRRC37A, NOS2P3, ARL17B and UBB on chromosome 17 regulating neuronal morphology and cortical organization; and 2. genes that influence multiple medical conditions across the circulatory, metabolic, digestive, respiratory and genitourinary systems, revealing two major axes of variation among these conditions that point to a potential trade-off in gene regulation between immune and metabolic functions. These results highlight FM-GPTs power to disentangle complex gene-phenotype relationships in large-scale phenome-wide studies, uncovering shared biological mechanisms across diverse human traits and advancing translational and comorbidity research. Author SummaryWe developed a novel fine mapping method called FM-GPT, to identify putatively causal genes from correlated noise influencing a wide range of human traits and diseases with potentially mixed outcome types (e.g., binary, count or continuous). The rapid expansion of large-scale phenomic datasets has shifted the single-trait genetic studies to phenome-wide analyses, enabling the study of genetic architecture across many related traits simultaneously. FM-GPT performs gene-guided dimension reduction of the phenotypes and reveals pleiotropic or phenotype-specific effects of the identified causal genes. When applied to the UK Biobank data, FM-GPT greatly narrowed down the set size of putatively causal genes compared to other methods. The tool identified genes with pleiotropic effects on regional cortical thickness that regulate neuronal morphology and cortical organization across the cerebral cortex. It also identified genes that influence multiple medical conditions spanning the circulatory, metabolic, digestive, respiratory, and genitourinary systems. Among these conditions, two major axes of variation emerged, revealing a potential trade-off in gene regulation between immune and metabolic functions. This work provides a clearer picture of shared biological mechanisms across traits and diseases, advancing translational research and the understanding of comorbidity.

bioinformatics↗

Glucose is a ligand-like trigger for secretion of postprandial GLP-1

Glucagon-like peptide 1 (GLP-1) is secreted from the intestinal L cells in a glucose-dependent manner. However, the mechanism underlying how glucose stimulates the secretion remains unclear. Here, we found that glucose at postprandial concentrations near the Km of GK for glucose ([~]10 mM), as well as nonmetabolizable glucose analogs, triggers GLP-1 secretion by intestinal L cells through directly binding to glucokinase (GK), without increasing intracellular ATP levels. We also show that in postprandially high glucose, glucose-bound GK interacts and inhibits KATP, as assessed by immunoprecipitation and FRET-FLIM analyses, as well as patch clamping. In addition, we have utilized GK mutants identified in diabetics, demonstrating that those mutants defective in binding to glucose impair GLP-1 secretion in however high glucose, whereas mutants constitutively bound to glucose with defects in catalysis, promote GLP-1 secretion even in low glucose. Furthermore, the KATP mutant unable to bind to GK blocks GLP-1 secretion in high glucose. We have also provided evidence showing that sodium-glucose cotransporter 1 (SGLT1) plays an important role in the basal secretion of GLP-1, but not in high glucose. We have thus revealed that glucose the molecule itself and GK act as a ligand and the receptor, respectively, to induce GLP-1 secretion in response to high glucose, providing new therapeutic avenues targeting metabolic diseases.

biochemistry↗

Multiple Quality Control Checkpoints Safeguard Small Nuclear RNA Biogenesis and Prevent Assembly of Aberrant Spliceosomes

Defective small nuclear (sn)RNAs are produced from hundreds of human snRNA pseudogenes and mutant snRNA genes associated with human developmental disorders. Machineries that prevent defective snRNAs from disrupting pre-mRNA splicing remain poorly defined. Here, we identify multiple checkpoints in snRNA biogenesis monitored by quality control machineries that subject defective snRNAs to degradation and prevent their assembly into spliceosomes. We show that variant U1 snRNAs produced from human pseudogenes, some at rates approaching the canonical snRNAs, are impaired in 3 cleavage and targeted for degradation by the NEXT-exosome while failures in subsequent protein assembly steps promote NEXT-exosome- or Terminal Uridylyl Transferase 4/7-mediated degradation. These pathways also repress mutant snRNAs associated with human developmental disorders. Impeding snRNA quality control causes formation of aberrant spliceosomes and altered pre-mRNA splicing. These findings define checkpoints in snRNA biogenesis that safeguard pre-mRNA splicing and represent potential therapeutic targets for human disorders associated with snRNA mutations.

molecular biology↗

Dual Transcriptional Drivers of Immune Suppression in SACC: NOTCH1 for Cellular and MYB for Humoral Immunity

As a classic immune-"cold" tumor, salivary adenoid cystic carcinoma (SACC) represents a significant clinical challenge. Through sequencing analyses, we identify profound systemic immune dysregulation in SACC, characterized by suppressed hematopoiesis, T-cell exhaustion, compensatory myelopoiesis, and an expanded immature B-cell compartment. While lung metastases exhibit a relatively immune-engaged microenvironment enriched in tissue-resident T cells, these sites remain dominated by immature B cells. Mechanistically, this hematopoietic dysfunction originates from direct disruption of tumor-derived signaling entering the circulation, supported by detection of the SACC-signature MYB-NFIB fusion gene in peripheral plasma and blood cells. At the molecular level, we discover that IL17RB/OLIG1/NOTCH1 signaling pathways engage in multicellular crosstalk via IL33 or TP53 to suppress T-cell activation in primary tumors. Moreover, at lung metastatic sites, the MYB/MYBL2-NOTCH1-CXCL13-CXCR5 axis is blocked through CD24 or IL17RB, thereby inhibiting B-cell maturation. Single-cell transcriptomic profiling further identifies cancer stem cells (CSCs) exhibiting dual characteristics of cell-cycle activity and immune progenitor features, a finding that clarifies the fundamental mechanism by which these cells evade immune surveillance. In conclusion, we propose that stem cell camouflage constitutes the core mechanism underlying bone marrow hematopoietic dysfunction and drives immune evasion in SACC. These findings highlight the IL17RB-NOTCH1 signaling axis as a promising therapeutic target, offering potential to overcome the long-standing challenges associated with NOTCH1-targeted therapies in this malignancy. SignificanceOur novel transcriptomic analysis revealed a key G2M/CLP dual-progenitor state in SACC immunocold tumors. Tracing its origin to hematopoietic differentiation, we uncovered a NOTCH1-mediated dual-hit mechanism: restricting antigen presentation to silence T cells while partnering with MYB to block B-cell maturation. This finding pinpoints a root cause of immune evasion and establishes this pathway as a central therapeutic target. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/688163v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@18c22a2org.highwire.dtl.DTLVardef@135e381org.highwire.dtl.DTLVardef@eb4eadorg.highwire.dtl.DTLVardef@7a51c4_HPS_FORMAT_FIGEXP M_FIG C_FIG Dichotomous gene mapping and single-cell interactome reveal the microenvironmental specificity of NOTCH1/MYB regulation of T/B-cell differentiation and its distinct signaling flows.

immunology↗

Pharmacological Induction of Irreversible Senescence in Drug-Tolerant Persister Cells Prevents Tumor Relapse

Despite substantial advances in targeted therapies, most patients with advanced cancers ultimately relapse. This relapse is frequently seeded by drug-tolerant persister cells (DTPs), which persist as minimal residual disease (MRD) by adopting a reversible quiescent state and later reacquire proliferative capacity under ongoing treatment. To address this, we sought to convert quiescent DTPs into an irreversible, non-proliferative state by pharmacologically inducing senescence. Through large-scale chemical screening and combination optimization, we identified SAHA plus tilorone dihydrochloride (SIC) as a regimen that robustly induces senescence in melanoma DTPs and abolishes their proliferative potential in vitro. Mechanistically, SAHA relieves HDAC1-mediated repression of HMGA2, a key senescence driver, while tilorone synergistically inhibits autophagy to promote a fully senescent state. In a melanoma xenograft mouse model receiving MAPK-targeted therapy, SIC treatment significantly suppressed MRD progression. Importantly, SIC also induced robust senescence across diverse DTP models irrespective of tumor origin, mutational background, or prior treatment. Collectively, these findings provide proof-of-concept that converting DTPs from reversible quiescence to permanent senescence represents an effective strategy to prevent relapse under targeted therapy and position SIC as a broadly applicable pharmacological approach for durable control of residual disease in advanced cancers.

cancer biology↗