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Lee, S.

Publications and source records attributed to Lee, S..

At least 127 records · Page 7Linked to original sources

Efficient task generalization and humanlike face perception in models that learn to discriminate face geometry

Artificial deep neural networks (DNNs) can excel at face recognition from 2D photographs where both shape and appearance cues abound; however, DNNs have rarely been challenged to recognize faces strictly based on face geometry. Here, we show that DNNs, even those fine-tuned on face photographs, had almost no generalization performance to a new geometry-based face task, while in the opposite direction, networks fine-tuned only on geometrically defined, textureless faces readily generalized to textured faces. To learn geometry in a more practical setting with colored and textured faces, we trained discrimination on face emotion in addition to face identity, which resulted in less texture bias and generalized well across face tasks. Learning in this way from just four individuals and their expressions generalized to unseen individuals, even exceeding standard models which are trained on classifying hundreds of face identities. Compared to standard models, emotion and identity trained models developed more humanlike errors in the identities or emotions that they confused. This novel method learns in a humanlike manner using only a few individuals but enriched with expressions that widely vary face geometry - similar to early human experience during child-parent interactions. Thus, this bioinspired work has broad implications for how moving toward humanlike learning of geometry in artificial vision can be both highly sample efficient and highly performing.

neuroscience↗

Ab initio prediction of RNA structure ensembles with RNAnneal

RNA utilizes three-dimensional structure in addition to sequence to carry out diverse functions in gene expression and disease. Much like well-folded proteins, RNAs adopt specific three-dimensional structures to carry out their function. Yet comparatively few RNA structures have been solved by atomic resolution structural techniques, in part because unlike structured proteins, RNAs fold into heterogeneous ensembles of interconverting structures that pose a challenge for high-resolution structure probing methods. In this work, we introduce RNAnneal as a method for RNA structural ensemble prediction that seamlessly integrates generative deep learning with statistical physics and molecular dynamics modeling. Given the primary sequence, RNAnneal uses ab inito (i.e., first principles) modeling to sample an ensemble of 3D structures, which, in turn, are used to train an ensemble of unsupervised deep learning models. The RNAnneal score, representing the consensus of the deep learning models, is then used to evaluate the 3D structures. We evaluated RNAnneal structures against 16 experimentally-resolved conformations (ERCs) of riboswitch RNAs and found that pseudoknot-free (PK-free) ERCs were well-reproduced by RNAnneal, with clear avenues for improving performance even on PK-comprising structures. Furthermore, we found that the RNAnneal score outperforms the Rosetta score and a state-of-the-art RNA forcefield on the task of classifying ERCs from decoys. We then introduce the interaction entropy as a measure of conformational heterogeneity within an ensemble and use it to assess our predictions. RNAnneal thus provides a generalizable framework for predicting RNA structural ensembles that will accelerate RNA-targeted drug discovery and the design of functional RNA molecules.

biophysics↗

Label-free quantitative phenotyping of hepatic stellate cell activation using holotomography with AI-enabled subcellular segmentation

Hepatic stellate cell (HSC) activation is a central driver of liver fibrosis, yet its quantitative characterization in living cells remains limited by endpoint assays that rely on fixation and labeling. Here we introduce a label-free framework that combines three-dimensional holotomography (HT) with automated, AI-assisted analysis to study HSC activation dynamics in live cells. Using refractive index tomography, we non-invasively visualize hallmark structural features of HSC activation, including lipid droplet depletion, cytoskeletal remodeling, and changes in cellular morphology. Correlative fluorescence imaging validates the biological relevance of HT-derived features, while longitudinal imaging reveals continuous activation trajectories at single-cell resolution. Automated segmentation of whole cells and subcellular organelles enables scalable extraction of multi-parametric biophysical descriptors, defining a quantitative phenotypic fingerprint that distinguishes quiescent and activated states. Together, this work establishes holotomography-based quantitative phenotyping as a powerful approach for studying HSC activation and, more broadly, dynamic cell-state transitions in living systems.

cell biology↗

A computational framework for designing micron-scale crisscross DNA megastructures

Crisscross polymerization enables the assembly of hundreds of unique DNA origami slats into micron-sized structures with nanoscale precision. To design these megastructures, thousands of handle sequences from a fixed library must be assigned to individual slats to encode the desired binding architecture. This complexity presents two major challenges: handles must be selected to minimize parasitic interactions that compete with desired assembly, and the fabrication of hundreds of unique slats creates a substantial logistical burden. Here, we develop a unified framework that standardizes the design and fabrication of crisscross megastructures. We use an evolutionary algorithm to optimize handle assignment and minimize parasitic binding between slats, paired with a graph-based algorithm that expands the handle library. Together, these algorithms enable the assembly of large, multi-layered megastructures that otherwise would be produced at negligible yields. We have released this framework as #-CAD, an open-source graphical application that integrates these algorithms, streamlines laboratory workflows, and makes crisscross DNA origami more broadly accessible.

synthetic biology↗

Bright calcium-modulated bioluminescent indicators for activity imaging and red photon-assisted synaptic transmission

Bioluminescent calcium sensors have unique uses in neuroscience and neuroengineering, enabling noninvasive imaging of neuronal activity and contactless activation of opsin-expressing neurons. However, the speed, range, and robustness of non-invasive imaging and rewiring or neuronal activity are limited by the radiance and dynamic range of existing bioluminescent calcium sensors. Here, we report the stepwise engineering of improved cyan-excitable red fluorescent proteins (mCyRFP4 and dCyRFP4), an improved red bioluminescent protein based on NanoLuc and CyRFP4 (Antares3), and an improved bioluminescent calcium sensor based on Antares3 (CaMBI3). Antares3 is 3-fold brighter than its predecessor, while CaMBI3 responds with an overall dynamic range of 24-fold, enabling high-sensitivity detection of calcium dynamics in muscle and neuronal tissues in vivo. Finally, a CaMBI3 variant and a red-shifted opsin ChRmine enabled red photon-assisted synaptic transmission in C. elegans. CaMBI3 thus facilitates genetically targeted non-invasive imaging and rewiring of neural activity in living animals.

neuroscience↗

Deep Plasma Proteomics Coupled with Functional Genomics Reveals Drivers of Parkinson's Disease Progression and Levodopa Response

Parkinsons disease (PD) is a progressive neurodegenerative disorder lacking disease-modifying therapies, and its clinical management is limited by the absence of accessible biomarkers for tracking disease progression and treatment response. To map these complex disease trajectories, we implemented an ultra-deep plasma proteomics workflow integrating Mag-Net extracellular vesicle enrichment with Orbitrap Astral mass spectrometry to profile longitudinal samples from PD patients. This approach quantified 6,481 plasma proteins at unprecedented depth in PD studies, revealing distinct signatures directly associated with disease duration and dopaminergic therapy exposure. Candidate biomarkers were subsequently validated in an independent cohort using ELISA, demonstrating robust predictive utility in AI-driven prediction models. To uncover the mechanistic drivers underlying these systemic changes, we intersected our proteomic data with novel proteome-wide gene overexpression perturbation screens designed to identify regulators of alpha-synuclein pre-formed fibril (PFF) uptake and PFF-induced neuronal toxicity. Finally, an integrative network analysis combining three independent proteome-wide assays revealed that key pathological hubs, such as CD14, IFNG, and PLAT, are targets of currently approved pharmacological agents. Collectively, these findings provide a comprehensive, systems-level map for PD biomarker discovery and highlight druggable pathways to advance precision medicine strategies.

neuroscience↗

Real world data based evaluation of a novel target-mediated drug disposition approximation model

Target-mediated drug disposition (TMDD) models have been widely used to describe nonlinear pharmacokinetic profiles driven by high-affinity, low-capacity drug-target binding. A pTMDD model, derived by applying the Pade approximation of the quasi-steady-state (QSS) model (qTMDD) was previously proposed. Although pTMDD model showed a comparable estimation accuracy while maintaining computational efficiency, further validation in realistic clinical scenarios and comprehensive performance evaluations have been needed to assess its practical applicability. Here, we evaluated the pTMDD model using five clinical datasets and extended the previous study that focused on simulations. Using the full TMDD as a reference, the approximation models were compared in terms of the parameter estimation results (parameter estimates, relative standard error values and model diagnostics) and computational efficiency (estimation and bootstrap runtimes). The pTMDD model, previously validated in simulation settings, also preserved the estimation accuracy while reducing the computation time of the clinical data. Both pTMDD and qTMDD remained close to the full TMDD model, whereas Michaelis-Menten TMDD (mTMDD) model showed substantial discrepancies especially at low doses, including biased estimates for key TMDD-related parameters (e.g., kdeg, kint, krec, and kup) and higher objective function values. Moreover, pTMDD was faster than qTMDD in four of the five cases compared to the full TMDD. The time savings were particularly pronounced for larger datasets, supporting the computational efficiency of pTMDD. Q2PCONV, an R Shiny application that converts NONMEM code from qTMDD to pTMDD, was also developed, thereby making this new approximation more accessible to researchers. The findings support pTMDD as a practical alternative to existing TMDD approximation models. Author SummaryTarget-mediated drug disposition (TMDD) models describe a high-affinity, low-capacity binding between drug and its target. To avoid overparameterization, approximation models have been used. The two primary models are Michaelis-Menten model (mTMDD), which is accurate only at high doses, and Quasi-steady-state (qTMDD), which is accurate in wider ranges but requires longer runtime. We have proposed a new approximation model named pTMDD. Here, we evaluated pTMDD using five real clinical trial datasets to assess its practical usefulness. pTMDD produced parameter estimates closer to those from the full TMDD model and showed lower uncertainty than both the full TMDD and mTMDD models. In terms of computational efficiency, pTMDD reduced estimation time by an average of 11% and bootstrap time by an average of 6% relative to qTMDD across cases. In addition, we also developed an R shiny application to help researchers apply pTMDD in practice. Our work supports pTMDD as a practical and efficient tool for TMDD modeling in drug development.

pharmacology and toxicology↗

Monitoring Gene Expression in Retina with Synthetic Serum Markers

Gene expression underlies retinal development, function, and pathogenesis. However, monitoring retinal gene expression in vivo is challenging. In this study, we apply synthetic serum markers, called Released Markers of Activity, or RMAs, to quantify gene expression in an intact retina through a simple blood test. We show that RMAs can quantify transduction of multiple retinal cell-types and monitor cell implantation or cell loss. We found RMAs are sensitive enough to measure transduction of rare cell populations, such as retinal ganglion cells and could detect transplantation of as few as 100 stem cells. Expression of RMAs showed no evidence of cell loss or immune activation in the retina. Overall, these findings demonstrate that RMAs are highly sensitive, tissue non-destructive gene expression reporters that can continuously track gene delivery and cell survival in intact retina through a simple blood test.

bioengineering↗

Neonatal Enteric Infection Disrupts the Microbiota-Gut-Brain Axis Through Pattern Recognition Receptors and Altered Neuroimmune Signaling

Early-life enteric infection can have long-lasting effects on the microbiota-gut-brain (MGB) axis. Using a neonatal Enteropathogenic Escherichia coli (EPEC) model, we show that intestinal epithelial cell (IEC) NOD1 signaling coordinates mucosal immunity, barrier repair, and neuroimmune outcomes throughout early development and into adulthood. Neonates infected at postnatal day (P) 7 exhibited ileal inflammation, as demonstrated by increased expression of inflammatory cytokines (Il1{beta}, Il6, Il12, Il22), chemokines/chemokine receptors (Ccl2, Cxcl1, Ccr2), and barrier-repair genes (Muc2, Slc26a3), with increased monocyte/macrophage infiltration and reduced epithelial proliferation in WT mice that was blunted in Nod1{Delta}IEC mice. Neonatal infection of WT mice induced persistent defects into adulthood (P56), including increased intestinal permeability, sustained inflammatory/repair signatures, hippocampal inflammation, altered neurogenesis, and impaired recognition memory, which were largely absent in Nod1{Delta}IEC mice, establishing a crucial role for IEC NOD1 as a determinant of long-term MGB remodeling. Microbially derived ligands of NOD2, muropeptides, isolated from probiotic Lactobacillus species attenuated EPEC-induced mucosal inflammation and chemokine induction without altering bacterial burden, demonstrating NOD2 host-directed immunomodulation. Together, these findings identify an important role for NOD-dependent signaling axis in the gastrointestinal tract that links early-life infection to enduring gut-brain dysfunction and reveals probiotic-derived muropeptides as candidate microbial therapeutics.

physiology↗

Chronic ER Stress Disrupts Mitochondrial-Associated ER Membrane Integrity in Corneal Endothelial Cells.

PurposeFuchs endothelial corneal dystrophy (FECD) is an age-related degenerative disease of the corneal endothelium cells (CEnCs), affecting 4% of the US population over 40. While Endoplasmic reticulum (ER) and mitochondrial stress have been independently associated with FECD pathogenesis, few studies have examined ER-mitochondrial interactions/ER-mitochondrial contact sites/mitochondria-associated ER membrane (MAM), or MAM proteins, and their contribution to ER and mitochondrial stress in FECD. This study aims to characterize alterations in MAMs and identify key MAM proteins associated with ER and mitochondrial stress in FECD. MethodHuman corneal endothelial cell line (HCEnC-21T) and Fuchs corneal endothelial cell line (F35T) were cultured and subjected to ER stressor tunicamycin (1, 10 g/ml) for 6 and 24 hours. MAM proteins were isolated by subcellular fractionation, and key ER and mitochondrial-damage-sensor proteins, such as PERK and Parkin, respectively, were identified by immunoblotting. ER-mitochondrial contact sites were quantified using the MAM plasmid and transmission electron microscopy (TEM) in normal and Fuchs cell lines, as well as in human tissues under chronic ER stress. ResultsER-mitochondrial contact distance significantly increased in Fuchs tissues compared with normal tissues, and a similar increase was observed in 21T cell line after tunicamycin treatment. There was a significant increase in the intensity of the MAM plasmid upon tunicamycin treatment at 6 hours in the 21T cell line compared to the non-treated control. However, MAM plasmid intensity significantly decreased at 24 hours compared to 6 hours post-tunicamycin treatment in 21T cell line. Analysis of MAM function by quantifying phosphatidylserine synthase 1 (PSS1 [gene PTDSS1]) expression in 21T cells showed a reduction in PTDSS1 expression after 24 hours of tunicamycin treatment. ER stress protein PERK and mitochondria damage sensor protein (Parkin) significantly increased in the MAM fraction after tunicamycin at 24 hours in 21T cell line. ConclusionsFuchs cell lines and tissues demonstrate decreased ER-mitochondrial interactions/MAMs, which are also seen in 21T cell line after chronic ER stress. Under chronic ER stress, ER and mitochondrial stress mediator proteins are translocated to MAM. This study highlights the importance of MAMs as a potential mediator of ER-mitochondria crosstalk in degenerating corneal endothelial cells for FECD.

cell biology↗

YAP activation reverses aging-related visual dysfunction caused by impaired cell-matrix adhesion

Cellular senescence of retinal pigment epithelium (RPE) cells drives age-related visual decline, particularly in the pathology of age-related macular degeneration (AMD). While genome-wide association studies (GWAS) have identified genetic risk factors underlying AMD, the molecular mechanisms governing RPE senescence remain unclear. Here, single-cell RNA sequencing of young and old mouse RPE revealed dysregulated cell-matrix adhesion as a key feature of senescence, consistent with transcriptional changes in AMD patients. Hydrogel-based experiments confirmed that impaired integrin-mediated adhesion induces RPE senescence. Yes-associated protein 1 (YAP), a crucial mechanotransducer, mediated the protective effects of cell-matrix adhesion, and its activation alone reversed aging phenotypes in senescent RPE cells. Notably, treatment with TRULI, a small-molecule YAP activator, significantly improved visual function in AMD and naturally aged mice. These findings highlight the integrin-YAP mechanotransduction pathway as a fundamental regulator of RPE senescence and a potential therapeutic target for AMD.

physiology↗

RIG-I RNA agonist activates immunostimulatory macrophages to enhance checkpoint immunotherapy for glioblastoma

Glioblastoma (GBM), the most frequent and aggressive primary brain tumor, remains refractory to all current therapies including surgical resection, chemotherapy, radiotherapy and immunotherapy. Immunosuppressive mechanisms in the GBM tumor microenvironment contribute to the lack of anti-tumor adaptive immunity. We found that a subset of tumor associated macrophages (TAMs) can be repolarized into an anti-tumor phenotype via agonist stimulation of the retinoic acid-inducible gene I (RIGI), a cytosolic double-stranded RNA pattern recognition receptor (PRR). In silico analysis of adult GBM datasets available in the public domain revealed that RIGI expression by a subset of activated TAMs positively correlated with patient survival. Studies in syngeneic mouse models of GBM showed that intratumoral delivery of stem-loop RNA 14 (SLR14), a RIG-I agonist, improved the efficacy of chemotherapy, radiotherapy and immunotherapy treatments, beyond the effects of other nuclei acid sensor agonists. We found that RIGI+ macrophages are the main drivers of SLR14 effect, combining activation of TAMs and priming of functional cytotoxic CD8+ T lymphocytes and NK cells. The anti-GBM effect of SLR14 is opening a significant new avenue for adult GBM treatment.

cancer biology↗

Somatic and germline mutational processes across the tree of life

The characterisation of mutational processes active in somatic and germline cells in vivo has predominantly focused on human cancers1,2, normal tissues3-5 and model organisms6-8. Beyond mammals9, little is known about mutational processes across the tree of life. We developed himut (high-fidelity mutation), an algorithm to identify somatic mutations from circular consensus long-read sequencing data, deploying it on 708 samples from 661 species from Britain and Ireland10. The spectra of somatic mutations, categorised by mutation type and local sequence context, showed considerable between-species divergence but within-species similarity. From normalised spectra across the dataset, we extracted 95 distinct patterns, or signatures, of somatic mutations, together with 18 signatures of germline mutational processes. Only two of the somatic signatures resembled mutational signatures extracted from human cancers1,2. Of the somatic signatures, 22 had significant clustering within the taxonomic classification, with some distributed across an entire kingdom or phylum, while others were restricted to a single family or species. Three somatic signatures were found only in water-dwelling species, with one distributed across multiple clades that might suggest it derives from a water-borne mutagen. Of germline signatures, eight were found in multiple species, showed significant clustering by taxonomic classification and had counterpart somatic signatures with matching mutational spectrum and species distribution. Thus, there is considerably greater diversity of mutational processes across the tree of life than found in human samples, likely reflecting either cell-intrinsic biological processes or environmental exposures (or both) operative within distinct clades.

genomics↗

Cereblon Promotes Influenza Virus Replication through AMPK Ubiquitination

Influenza A and B viruses (IAV and IBV) continually threaten global health, with IAV posing a risk of emerging pandemics. Rapid viral evolution makes current treatments less effective, highlighting the urgent need for broad-spectrum antivirals. Targeting host factors essential for viral replication may offer a highly promising broad-spectrum antiviral strategy. In this context, cereblon (CRBN), a substrate adaptor of the CRL4 E3 ubiquitin ligase complex, is found to promote both IAV and IBV replication as a key pro-viral host factor. Mechanistically, CRBN targets and degrades AMP-activated protein kinase (AMPK) via the proteasome. This CRBN-driven degradation shifts the metabolism of the infected cells toward anabolism, promoting lipid droplet (LD) formation and creating a microenvironment favorable for viral replication. Genetic depletion or inhibition of CRBN stabilizes AMPK, significantly reduces LD formation, and effectively suppresses the replication of various IAV and IBV strains in vivo, demonstrating its broad-spectrum potential. Notably, Crbn knockout mice show marked resistance to lethal IAV infection. CRBN inhibition with immunomodulatory imide drugs--known CRBN inhibitors--significantly decreases IAV replication in vivo. This research underscores CRBN as a crucial regulator of host metabolism during viral infection, revealing the CRBN-AMPK axis as a promising target for host-directed pan-influenza antiviral development. Author SummaryInfluenza A and B viruses are response for recurring seasonal epidemics and occasional pandemics that pose serious global health challenges. Current antiviral drugs often lose effectiveness as influenza viruses rapidly develop resistance through genetic mutations. To overcome this limitation, our study focused on a host factor targeted by influenza viruses-the ubiquitin E3 ligase substrate adaptor cereblon (CRBN). We discovered that influenza viruses exploit CRBN to enhance their replication by altering host cell metabolism. Specifically, CRBN binds to a key energy sensor - AMPK and induces the ubiquitination and degradation of AMPK{gamma}. Consequently, the AMPK suppression shifts the cellular environment from catabolism to anabolism, activating lipogenic enzymes and promoting lipid droplets formation which provide a favorable environment for viral growth. Our study highlight that blocking CRBN either genetically or chemical inhibition (immunomodulatory imide drugs) of CRBN reduces LD formation and strongly suppresses diverse influenza strains replication in vitro and in vivo. These findings reveal not only how viruses hijack host metabolism via the CRBN-AMPK pathway but also present a potential therapeutic for novel broad-spectrum anti-influenza.

microbiology↗

Organelles harbour pH gradients

Organelle pH is critical to organelle identity and function. Resident proteins that define each organelle modify transiting cargo proteins, with both retention and trafficking between organelles governed by pH-dependent mechanisms. For example, lysosomal enzymes bind mannose-6-phosphate receptors at the higher pH ([~]6.5) of the Golgi and dissociate at the lower pH ([~]5.5) of late endosomes1. Proteins that stray from the endoplasmic reticulum (ER) are captured by KDEL receptors in the acidic Golgi and returned into the neutral ER2,3. This pH-tuned trafficking system compartmentalizes organelle function and prevents mis-localization of critical enzymes4. Dysregulated organelle pH disrupts their function and leads to various diseases. Because protons move rapidly in water, the pH within a single organelle is currently assumed to be spatially uniform5. Here, using a reporter sensitive from pH 5.5 - 10.5 to map a spectrum of organelles at high resolution, we discovered that pH gradients exist within single, large or long organelles such as the ER and mitochondria, and in membrane-less organelles without ion-transporting proteins such as the nucleolus. These new findings upend our understanding of organellar pH, prompting new questions about proton diffusion within the cell, and its potential consequences on organelle function.

cell biology↗

A Biologically Grounded Structural Causal Model Enables cfRNA Specific In-Context Learning

Cell-free RNA (cfRNA) in human plasma provides a minimally invasive readout of tissue physiology, yet its extreme sparsity, heavy-tailed abundance distributions, and weak but structured correlation patterns create major challenges for machine learning. Conventional tabular foundation models are typically trained on synthetic datasets that assume generic statistical properties, and as a result, they fail to capture the distinctive characteristics of cfRNA. These limitations become even more pronounced in settings where labeled data are scarce. We introduce cfRNA-ICL, a cfRNA-specific in-context learning model trained entirely on tasks generated from a biologically grounded structural causal model (SCM). The SCM produces realistic cfRNA-like scenarios by incorporating empirical measurements of gene-level dropout, overdispersion, tissue-mixture-driven latent factors, compositional variability, and sequencing noise. This synthetic task universe enables cfRNA-ICL to acquire inductive biases that closely reflect the geometry of real cfRNA data. Across multiple cancer classification benchmarks, cfRNA-ICL demonstrates consistently higher performance than tabular ICL models trained on generic synthetic data. The gains are most sub-stantial in few-shot settings, where the model benefits from its exposure to cfRNA-specific statistical regimes during meta-training. Representation-level analyses further show that cfRNA-ICL organizes samples into biologically coherent manifolds, preserving cancer-type identity without the use of supervised constraints. This finding indicates strong alignment between the synthetic prior and real cfRNA structure. Taken together, these results show that domain-aware generative priors can meaningfully enhance in-context learning for biological tabular data. cfRNA-ICL provides a generalizable framework for cfRNA modeling and establishes a practical path toward foundation-scale models that are intrinsically adapted to the statistical landscape of plasma cfRNA.

genomics↗

Analyzing associations and higher-order effects in multi-omics data with double machine learning

MotivationIntegrative omics analyses enhance our understanding of disease mechanisms and biomarkers by investigating relationships among traits, omics measurements, genetic variants, and epidemiological factors. Statistically, these analyses are challenging and require robust, flexible methodologies due to high dimensionality, non-standard data distributions, and potentially complex, non-linear confounding effects. ResultsTo facilitate the integration and analysis of multi-omics data, we introduce the Robust Omics MethodologY (ROMY) framework and its corresponding R implementation, the romy package. ROMY enables users to (a) perform robust association testing between two target variables while incorporating flexible covariate adjustments, (b) examine effects on measurement variances and covariances (e.g., co-expression, co-abundance), and (c) conduct rigorous interaction-effect testing. ROMY builds on recent advances in theoretical statistics and double machine learning to ensure robustness and statistical validity. We illustrate the performance of our framework through simulation studies. Availability and implementationromy is an R package available under the GNU GPLv3 license on GitHub: https://github.com/julianhecker/romy.

bioinformatics↗

Decoding the neural stages from action and object recognition to mentalizing

Higher-level action interpretation, such as inferring underlying intentions and predicting future actions, requires the integration of conceptual action information (e.g. "opening") with semantic knowledge about persons and objects (e.g. "my friend Anna", "pizza box"). However, how the neural systems for action and object recognition and memory interact with each other to form the basis for inferring higher-level mental states remains unclear. Here we use fMRI-based crossmodal multiple regression representational similarity analysis in human female and male participants to elucidate the processing stages from basic action and object recognition to mentalizing. We show that inferring intentions from observed actions or written sentences involves a modality-general network of lateral and medial frontoparietal and temporal brain regions associated with conceptual action and object representation and mentalizing. The representational profiles in these regions are explained by models capturing different types of conceptual information, revealing distinct but partially overlapping networks for action, object, and mental state representation. There was no strict separation of networks for action, object, and mental state representations, arguing against a sequential bottom-up hierarchy from action and object understanding pathways to the mentalizing network. Rather, left-hemispheric regions, specifically ventrolateral prefrontal, inferior parietal and anterior lateral occipitotemporal cortex, showed strong representational overlap, pointing towards a core network for making meaning of action-object structures at a conceptual level. We argue that this core network represents a distributional semantic hub between classic networks for action and object understanding and the mentalizing network. Significance StatementHow does the human brain integrate information from actions, e.g., "open a pizza box", to understand the actions underlying intentions? To do so, the brain needs to combine information from different neural networks--for action and object recognition--and pass them to the mentalizing network for inferring intentions, such as "satisfying hunger". We characterize the interplay of networks using fMRI-based crossmodal multivariate analyses and find that a left-lateralized core network in inferior frontal and parietal cortex and lateral occipitotemporal cortex represents all critical ingredients--conceptual action and object information as well as higher-level mental state representation simultaneously in an overlapping manner. This suggests that this core network is essential for semantic interpretation and functions as bridge between recognition pathways and the mentalizing system.

neuroscience↗