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Gao, T.

Publications and source records attributed to Gao, T..

At least 19 recordsLinked to original sources

SAIL: Sparse Autoencoders for Interpretable Alignment of Human Vision and Multimodal Large Language Models

Alignment between human high-level visual representations and those of multimodal large language models (MLLMs) offers a quantitative framework for understanding information processing in human vision. However, similarities between model and brain representations do not directly reveal the semantic content underlying their correspondence, as this content is difficult to isolate in entangled MLLM representations. Here, we introduce SAIL, an interpretable framework that formulates voxel interpretation as a multi-unit sparse semantic correspondence problem between MLLMs and human vision. First, we train unified cross-layer sparse autoencoders (SAEs) on MLLM representations of Natural Scenes Dataset images and captions, and align each brain voxel with multiple SAE units. Second, we quantify semantic similarity between their top-response image sets to map semantic alignment across the cortex. We project multiple semantic labels back onto the cortex to interpret the content of this alignment. Finally, we assess these correspondences using category responses measured in independent fLoc experiments. Compared with SAEs trained independently at each layer, SAIL exhibits lower redundancy in SAE unit response profiles and higher semantic alignment. We find that semantic alignment is organized along the human ventral visual pathway across the models and subjects examined. The projected labels reveal semantic preferences within canonical visual regions, while fLoc experiments show agreement between predicted and measured category response patterns. Exploratory analyses further reveal cortical distributions of action-related semantics consistent with established functional accounts of lateral occipitotemporal and posterior parietal cortex. Overall, SAIL provides an interpretable account of the semantic correspondences between MLLM representations and human visual responses.

neuroscience↗

Divergent amyloid trajectories distinguish normal aging from Alzheimer's disease progression

Aging is the greatest risk factor for Alzheimer's disease (AD), yet how and when AD-related pathological progression diverges from aging remains poorly understood. This distinction is particularly difficult at early stages, when clinically and biomarker-defined populations contain individuals following fundamentally different trajectories. Here, we model AD progression as a deviation from aging using longitudinal amyloid PET and a self-supervised trajectory-learning framework. In ADNI, the learned trajectory revealed a shared early path that bifurcated into an aging branch and an AD-related branch. The two branches showed distinct profiles in amyloid burden, cognitive decline, risk of progression to AD dementia, and genetic risk. Unseen participants from the independent NACC cohort were projected onto the trajectory without retraining, further reproducing key branch-specific biological and genetic patterns. Together, the bifurcating trajectory provides a biologically grounded framework for resolving early-stage heterogeneity and enabling risk stratification beyond binary amyloid status.

neuroscience↗

Structural mechanism governing radiationless energy transfer in Renilla bioluminescence

The nonradiative transport of electronic excitation from one chromophore to another, known as resonance energy transfer, lies at the root of photochemical processes in biology. Unlike photosynthesis, bioluminescence converts chemical energy into light through an enzymatic oxygenation of an energy-rich luciferin. In glowing cnidarians, the energy is relocated from an excited oxyluciferin to a fluorescent protein, shifting the colour and enhancing the quantum yield of a photogenic reaction. How protein-chromophore complexes assemble during this interplay in real space, and what this association entails for function, are unknown. Here, we report co-crystal structures of a 120-kilodalton energy-transfer complex from the luminescent soft coral Renilla reniformis. We find a heterotetrameric 2:2 assembly composed of two coelenteramide-loaded luciferases (RrLuc) docked at opposite sides of a head-to-tail dimer of green fluorescent protein (RrGFP). The edge-to-edge distance between donor and acceptor chromophores is below 3 nm, favouring the Forster-type radiationless energy transfer. Furthermore, RrGFP serves not only as a colour-switchable antenna and luminescence amplifier but also tunes the efficiency of luciferase catalysis by controlling its inherent dynamics. Our results provide detailed spatial information about intermolecular dipole-dipole coupling in Renilla bioluminescence, including the arrangement of donor-acceptor pairs that secure excited-state energy transfer with exquisite precision.

biochemistry↗

Cross-Regional Trajectory Analysis Reveals Distinct Temporal Progression of Shared Proteomic Programs in Alzheimer's Disease

Alzheimer's pathology progresses through anatomically distinct brain regions, yet how molecular programs are temporally organized across vulnerable regions remains poorly understood. Here, we reconstructed continuous proteomic trajectories from matched dorsolateral prefrontal cortex (DLPFC) and superior temporal gyrus (STG) proteomes to investigate cross-regional molecular progression in AD. The inferred trajectories closely recapitulated established neuropathological staging while remaining independent of age, sex, and race. Across regions, a mitochondrial bioenergetic protein subset declined substantially earlier in the STG than in the DLPFC, revealing a previously unrecognized regional temporal offset in metabolic dysfunction. In parallel, a broadly shared proteomic program progressed in both regions but more rapidly in the STG, indicating that shared molecular responses differ in their temporal progression despite overall coordination. Together, these findings demonstrate that regional vulnerability in AD is reflected not only by the molecular programs involved but also by their temporal organization during disease progression.

neuroscience↗

Low-heteroplasmy mitochondrial DNA mutations improve clonal reconstruction of human cells

Reconstructing clonal relationships among human cells is fundamental to understanding development, aging, and disease. Somatic mitochondrial DNA (mtDNA) mutations act as endogenous single-cell barcodes measurable alongside cell-state profiles, but lineage tracing has traditionally focused on high-heteroplasmy variants, which are easier to detect but few and potentially shaped by selection. Whether the more abundant lower-heteroplasmy variants encode bona fide lineage information has not been tested against an independent clonal reference. Using lentiviral barcoding of human hematopoietic cells to establish ground-truth clone identities, we show that after stringent molecule-level error filtering, mutation calls below 10% per-cell heteroplasmy account for roughly half of all lineage-informative calls. Retaining the full heteroplasmy spectrum approximately doubled the clonal-assignment area under the precision-recall curve relative to a >10% cutoff, and single-molecule-supported calls improved recovery when retained collectively. These findings establish lower-heteroplasmy mtDNA mutations as an abundant, bona fide record of clonal history, substantially expanding the clonal resolution attainable in human tissues without genetic engineering.

genomics↗

12-plex DiLeu enables robust quantification of the feeding neuropeptidome

Understanding the feeding-induced neuropeptidome cascade requires analytical strategies capable of quantifying low-abundance, highly modified peptides across multiple tissues and time points. Herein, we apply 12-plex N,N-dimethyl leucine (DiLeu) isobaric labeling to perform the first multiplexed, tissue-wide, temporal quantitation of the Cancer borealis feeding neuropeptidome. This approach enabled sensitive measurement of neuropeptides across five tissues over six timepoints, revealing distinct regulatory patterns. The pericardial organ (PO) showed rapid early upregulation followed by suppression aligned with foregut emptying, whereas the thoracic ganglion (TG) displayed inverse and strongly condition-dependent responses, indicating previously unrecognized neuromodulatory roles. Single-residue variants and post-translational modifications, including pyro-Glu formation and amidation, produced markedly different temporal profiles, underscoring the functional specificity of closely related isoforms. We further identify differential regulation of proctolin and its amidated form, suggesting modified variants may contribute uniquely to feeding physiology. Collectively, these results establish multiplexed DiLeu labeling as a powerful platform for quantitative neuropeptidomics and reveal new dimensions of peptide-mediated feeding regulation.

neuroscience↗

Direct probabilistic quantification of mosaic loss of chromosome Y from sequencing data

Loss of chromosome Y (LOY) is the most common aneuploidy in aging men and is increasingly recognized as a marker of aging and genomic instability. Because LOY occurs in mosaic form, its degree reflects the fraction of cells lacking the Y chromosome. Existing SNP-array- and sequencing-based methods rely largely on single genomic features and indirect transformations to estimate this fraction. We developed BaySeq-Y, a Bayesian method that directly estimates LOY mosaicism from sequencing data using VCF files with read depth (DP) and allelic depth (AD). Within a rigorous Bayesian framework, BaySeq-Y integrates complementary LOY-associated genomic features, including decreased read depth and allelic imbalance, and can additionally leverage haplotype phasing to improve precision. In simulations and fluorescence in situ hybridization validation (FISH), BaySeq-Y provided accurate estimates and outperformed existing methods. Applications to ROSMAP and GTEx supported its biological relevance through transcriptomic validation, demonstrating its utility for quantifying LOY across diverse sequencing datasets.

bioinformatics↗

eRNAformer enables genome-wide de novo mapping of enhancer-derived RNA loci

Enhancer-derived RNAs (eRNAs) are critical regulators of gene transcription, yet their genome-wide annotation remains challenging. Here, we present eRNAformer, a multi-modal deep learning framework that integrates convolutional neural networks with transformers, specifically designed to capture long-range genetic features associated with bidirectional transcription. This approach enables de novo mapping of eRNA loci using DNA sequence and aggregated conventional RNA-seq data. When evaluated on ENCODE datasets, eRNAformer demonstrated high sensitivity and specificity in discriminating known eRNA loci from non-eRNA loci. Notably, the newly identified eRNA loci were enriched with evolutionarily constrained variants and genetic risk factors for complex diseases, and exhibit potential relevance for cancer therapy. Applied to GEO datasets, eRNAformer identified a range from 14,219 to 56,451 eRNA loci across multiple hematologic malignancies, facilitating the construction of a comprehensive eRNA database for blood cancers. We further identified and experimentally validated FOXO1e, a cluster of eRNAs located approximately 120 kb upstream of FOXO1, a known oncogene that drives t(8;21) acute myeloid leukemia (AML) preleukemic program. Together, these findings establish eRNAformer as a powerful tool for genome-wide eRNA annotation, provide a valuable resource for eRNA studies in hematologic cancers, and underscore the functional importance of eRNAs in AML pathogenesis.

bioinformatics↗

Bridging genomes and peptidomes: hybrid sequencing reveals conserved bioactive peptides in crustaceans

Endogenous peptides are critical regulators of signaling and immunity but remain difficult to characterize in organisms with incomplete genomic annotation. We developed a hybrid discovery platform that integrates transformer-based de novo sequencing (Casanovo), neuropeptide-focused database searching (EndoGenius), and empirical false discovery rate estimation via NovoBoard. This pipeline enables confident identification of endogenous peptides while expanding coverage beyond conventional database-only or de novo-only approaches. Applied to neuroendocrine tissues from Callinectes sapidus and Cancer borealis, the workflow revealed numerous high-abundance novel peptides and provided structural and genomic support for their biological relevance. Notably, we report the first histone-2A-derived antimicrobial peptide in the C. sapidus and characterize naturally occurring sequence variants. We also identified unexpected peptide homologies between crustaceans and Rattus norvegicus, enabling annotation of conserved housekeeping proteins in sparsely annotated genomes. This hybrid platform establishes a scalable, open-source strategy for advancing neuropeptidomics and endogenous peptide discovery in emerging model organisms.

bioinformatics↗

A functional investigation of antibody Fc-FcRn variant binding guided by *in silico* free energy perturbation methods

Accurate calculation of energy changes upon mutation is a key requirement for the effective use of computational methods in protein design. In this study, we applied free energy perturbation (FEP) calculations to predict the effects of mutations on the binding free energy between the immunoglobulin subtype G (IgG) antibody fragment-crystallizable (Fc) region and the neonatal Fc receptor (FcRn), an interaction that is primarily responsible for antibody half-life. We assembled an extensive experimental dataset of Fc-FcRn binding affinities for wild-type (wt) and mutant complexes, including values from literature and from newly measured results. Starting from a crystal structure of the M252Y/S254T/T256E ("YTE") Fc variant bound to FcRn, we prepared all-atom models of human IgG1-subtype wt and YTE variant Fc-FcRn complexes, adding explicit hydrogens and assigning protonation states for key ionizable residues. Initial results using standard FEP protocols to compute relative binding free energies were promising but exhibited multiple outliers. By accounting for coupling effects for FEP mutations near key histidine residues, we improved the results for several outliers, suggesting such coupling as an important approach for pH-sensitive systems. Further, upon determining new crystal structures of four Fc variants at multiple pH values, we observed subtle conformational changes in unbound Fc; by accounting for these conformational changes in FEP calculations, we additionally improved agreement with experiment. The detailed structural and energetic analyses of the Fc-FcRn system we present here thus provide an accurate energy-calculation framework to enable rational in silico design of novel Fc variants. SignificanceThe ability to determine changes in binding affinity upon mutation is critical to structure-based protein design. In this study, we demonstrate a successful computational approach using free energy perturbation (FEP) calculations on the antibody Fc-FcRn complex, a medically relevant system with implications for both therapeutic and prophylactic antibody use. Our successful calculation of accurate binding energies across a wide range of cases speaks to the power of the FEP methodology in navigating the free energy landscapes of dynamic molecular complexes. Furthermore, we show that accurate Fc-FcRn affinity calculations required careful consideration of conformational flexibility between bound and unbound states, contributing to our functional understanding of a system that will be important for future rational antibody-design efforts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/721095v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@f754d8org.highwire.dtl.DTLVardef@1e366beorg.highwire.dtl.DTLVardef@6e67caorg.highwire.dtl.DTLVardef@602a14_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

Prefrontal Mechanisms of Rule Learning

Rule learning is associated with lasting changes in prefrontal activity. However, experiments typically focus on learning a single set of rules or task and there remains a significant gap regarding how related mechanisms may reflect behavioral improvements in different contexts, especially when examining across different tasks and modalities. We therefore recorded single units from chronic electrode arrays implanted in the prefrontal cortex of four monkeys as they were trained to perform spatial and object working memory tasks with the goal of assessing the resulting activity changes that would be induced by rule learning. Progression of training allowed behavioral improvements to be correlated with a variety of neural effects that could be observed across different task contexts, including increases or decreases of both firing rate and decoding, increases in the proportion of firing rate variance that was unexplained by sensory stimuli and motor actions, and the increased separation of population response trajectories in state space. Our results thus reveal how rule learning induces plasticity of prefrontal cortical activity, and the aspects of neural activity changes that were unique to individual tasks and modalities or common across them. Our results ultimately reveal new patterns of training effects, identifying the generalized prefrontal mechanisms that are responsible for rule learning.

neuroscience↗

Modeling mitochondrial inheritance enables high-precision single-cell lineage tracing in humans

Somatic mutations in mitochondrial DNA (mtDNA) provide natural barcodes that enable engineering-free lineage tracing in human tissues, but the complex dynamics of mtDNA inheritance across cell divisions and incomplete sampling of mtDNA introduce uncertainty in reconstructed lineages. Here, we present MitoDrift, a probabilistic framework that integrates Wright-Fisher drift dynamics with sparse single-cell measurements to produce confidence-refined lineage trees enriched for accurate clonal relationships. Validation with gold-standard lentiviral barcoding and whole-genome sequencing demonstrates that MitoDrift outperforms existing tree reconstruction methods in precision while maintaining high clonal recovery, enabling robust analyses linking lineage to cell state. Applying MitoDrift to human hematopoiesis reveals an age-associated decline in clonal diversity with differential impact across cell types and identifies heritable regulatory programs in hematopoietic stem cells in vivo, linking AP-1/stress-associated programs to clonal expansions. In multiple myeloma, MitoDrift captures therapy-associated clonal remodeling undetectable by copy number analysis, revealing phenotypic transitions and linking gene regulatory programs to differential drug sensitivity. Collectively, MitoDrift enables high-precision lineage tracing at scale and establishes quantitative lineage-state analysis in primary human tissues, linking clonal history to transcriptional and epigenetic programs in tissue homeostasis, aging, and disease.

genomics↗

Microglia Piezo1 aggravates cerebral ischemia and reperfusion injury by chemotactic recruitment of T lymphocytes

Cerebral ischemia reperfusion injury (CIRI) is a complex pathophysiological process involving multiple mechanisms. Piezo1, a stretch-activated ion channel, has recently emerged as a potential regulator of cellular responses to ischemic conditions. However, its role in specific cells during ischemic events is not well elucidated. Here, we showed that after experimentally induced CIRI, Piezo1 channel was highly expressed in peri-infarct area, where is upregulated and activated mainly in microglia. Behavioral tests, and infarct volume measurements demonstrated that conditional Piezo1 deficient in microglia markedly ameliorated the neurological deficits and reduced the infarct volumes. Flow cytometry and immunofluorescence staining showed decreased peripheral immune cells, especially T lymphocytes infiltration into the brain in microglia Piezo1 deficient mice after stroke. Multiplex chemokine immunoassay and T cell migration assays screened that Piezo1 deficient microglia blocked the CXC chemokine ligand 10 (CXCL10) release from astrocyte, which lead to the inhibited T cell recruitment in transwell co-cultured system. Furthermore, RNA-Sequencing analysis showed that defective Piezo1 in microglia lead to its polarization towards an anti-inflammatory phenotype in response to cerebral ischemia and reduced the secretion of tumor necrosis factor- (TNF-) and interferon-{gamma} (IFN-{gamma}). Collectively, Piezo1 deficiency inhibited the secretion of TNF- and IFN-{gamma} in microglia. The reduction of these inflammatory cytokines further blocked the CXCL10 release from astrocyte, and ultimately ameliorated the infiltration of peripheral T lymphocytes after stroke. Our results therefore highlight the critical role of Piezo1 in microglia-orchestrated neuroinflammation and suggest a potential means for reducing stroke-induced neurological injury.

neuroscience↗

Normative models of individualized functional brain networks reveal language network expansion in autism

Autism spectrum disorder is a highly heterogeneous neurodevelopmental disorder, hindering mechanistic insights and the identification of biomarkers for clinical diagnosis. Recently, precision functional mapping has been developed to identify abnormalities in brain network topologies associated with various psychiatric disorders, yet its application in autism remains limited. Here, we utilized precision functional mapping and a large, multisite neuroimaging dataset (N = 1,182) to construct individualized functional networks in individuals with autism. We developed normative models using network surface area from healthy controls (n = 628) to characterize typical brain network organization across age, allowing for the quantification of individual-specific deviations in individuals with autism (n = 554). We found widespread and heterogeneous deviations from the normative model, with the language network emerging as the most significantly altered region, thereby emerging as an epicenter of functional disruption in autism. Individuals with autism were clustered into three subtypes involving distinct functional network topologies, associated with behavioral profiles marked by impairments in perception, language processing, or socio-emotional functioning. We further linked these atypical brain features to cortical gene expression patterns, revealing enriched pathways related to neurodevelopment, language, and signaling processes. Together, these findings reveal autism-specific deviations in individualized functional brain networks, offering potential clinical relevance for understanding and stratifying autism.

neuroscience↗

PI-FC: Pre-training Individual-specific Functional Connectome through State-invariant Contrastive Learning

Functional MRI enables non-invasive mapping of brain connectivity, yet its clinical translation remains hindered by uncontrolled state-dependent variability that obscures individual-specific signatures during routine scanning. Here we introduce PI-FC -- a deep learning framework leveraging state-invariant contrastive learning to extract stable individual brain signatures across diverse arousal levels, cognitive states, and temporal scales spanning tens of seconds to hours. PI-FC achieves equivalent phenotypic prediction accuracy using substantially reduced scanning time, and eliminates state-dependent effects varying task demands and brain states. Trained on 36,119 subjects across 8 independent datasets, our model demonstrates superior cross-site generalization and outperforms traditional functional connectome (FC) in predicting neuropsychiatric conditions including schizophrenia, autism, depression, and anxiety. Furthermore, PI-FC enables zero-shot inference of brain age, biological sex, and cognitive ability without site-specific retraining. Overall, PI-FC represents a robust, clinically scalable framework that overcomes fundamental barriers to real-world deployment of precision functional neuroimaging.

neuroscience↗

Molecular trick to reverse SN2 mechanism in hydrolytic enzyme

Hydrolytic haloalkane dehalogenase enzymes catalyze an SN2 nucleophilic substitution to erase halogen substituents in organohalogen compounds. The acid-base-nucleophile triad secures irreversible SN2 displacement of the halogen for the hydroxyl derived from the water. Catalysis relies on the protonatable imidazole ring of the histidine base, and its substitution with an asparagine traps the enzyme in a covalently bound intermediate state, a principle exploited in the widely used HaloTag technology. In contrast, the histidine-to-phenylalanine substitution triggers reversibility of the SN2 mechanism, but the molecular trick by which it reprograms the catalytic pathway remains unknown. Here, we show that the phenylalanine at the site of the histidine base spatially disturbs the adjacent residues, leading to the remodeling of surrounding active-site loops. Consequently, rerouting of the access tunnels imparts distinctive kinetic behavior, featuring a reversible SN2 chemical step that facilitates transhalogenation reactions. This information is crucial for engineering next-generation biocatalysts for sustainable chemistry. HighlightsO_LICatalytic triad (glutamate-histidine-aspartate) secures irreversible SN2 mechanism C_LIO_LIHistidine-to-phenylalanine substitution in the triad leads to a reversible SN2 reaction C_LIO_LIEnzyme active site rerouting is a hallmark of the catalytic reprogramming C_LIO_LIBasis for designing biocatalysts for sustainable transhalogenation chemistry C_LI The bigger pictureHaloalkane dehalogenases catalyze the hydrolytic cleavage of the carbon-halogen bond in halogenated hydrocarbons, a feature used in a wide variety of industrial and biotechnological processes. In HaloTag technology, the catalytic histidine is replaced by an asparagine to enable a stable covalent bonding between a probe and a protein for biological imaging, affinity purification, etc. Remarkably, this originally irreversible SN2 process becomes fully reversible in a histidine-to-phenylalanine mutant. Moreover, halogen ion product is released at this stage, offering a greener alternative for transhalogenation reactions compared to the conventional synthetic approach and a way to recycle environmentally harmful halogenated compounds. However, the optimization of enzymes is needed for applications on an industrial scale. Therefore, we investigated the kinetics of the SN2 step and structural features of these two enzyme mutants, providing a basis for subsequent optimization efforts.

bioengineering↗

An efficient artificial esterase with a dynamic conformation via conformational engineering

The catalytic turnover number (kcat) of current enzyme mimics and de novo designed enzymes is still orders of magnitude lower than that of natural enzymes, because mimicking the fast-dynamic feature of enzyme active centers remains a great challenge. Herein, we created a gold nanoparticle-based artificial esterase, Goldenzyme, by conformational engineering to reconstruct dynamic active centers resembling that of -chymotrypsin. NMR characterization shows that Goldenzyme possesses a fast-dynamic feature, about 6-fold faster than typical -helix. Therefore, Goldenzyme efficiently hydrolyzes p-nitrophenyl acetate with a net kcat of 6.37 s-1 per active center, more than 5-fold of that of -chymotrypsin (1.19 s-1), and Goldenzyme can even hydrolyze some non-activated esters that -chymotrypsin cannot. Our conformational engineering approach demonstrates the possibility of creating artificial enzymes that surpass natural ones.

biochemistry↗

Rac1 Selectively Binds a Specific Lamellipodin Isoform via a Noncanonical Helical Interface

Lamellipodin (Lpd) is a multifunctional adapter protein that regulates cell migration and adhesion by recruiting Ena/VASP proteins to the leading edge and modulating actin polymerization. The interaction of Lpd and Rho family or Ras family GTPases is crucial for regulating actin dynamics. Contrary to previous assumptions that the main Lpd isoform interacts with Rac1, here we show that strong and specific binding to Rac1 is instead mediated by the short isoform Lpds. This interaction is dependent on Rac1s GTPase activity and a short insertion (cs2) within the coiled-coil (CC) region unique to the Lpds isoform. Structural modeling and mutagenesis analyses further reveal that Lpds engages Rac1 through a noncanonical, single-helix binding mode distinct from the classical helical pair configuration. Our results reveal a novel isoform-dependent GTPase:effector binding mode and suggest a critical regulatory pathway that may represent a promising therapeutic target in Rac1-driven cancer progression.

biochemistry↗