Biology subjects

Lee, E. J.

Publications and source records attributed to Lee, E. J..

At least 19 recordsLinked to original sources

bioRxiv2026

The Desmoplakin Hinge Domain Confers a Reversible Conformational Change in Response to Acute External Force

Desmosomes provide mechanical integrity to tissues that experience strain, yet how mechanical force is sensed and distributed within the desmosomal plaque remains poorly understood. Here we identify the hinge within the desmoplakin (DP) head domain is required for repositioning the DP tail in response to acute uniaxial mechanical stretch. This repositioning occurs within 30 seconds of applied stretch and reverses with release, indicating a dynamic reversible switch rather than a stable structural transition. We show this hinge-dependent repositioning correlates with the propagation of mechanical force to the desmosomal cadherins, consistent with the hinge's role in buffering tension at the cadherin interface during mechanical loading. Deletion or shortening of the hinge abolishes the stretch-induced response and compromises desmosome mechanical integrity. The repositioning of the DP tail in the calcium-dependent to hyper-adhesive transition was not impacted by alterations to the hinge, demonstrating that DP repositioning due to acute force or adhesive state is mechanistically distinct. Together, these findings define a reversible, hinge-dependent mechanotransduction pathway through which DP senses and relays mechanical force within the desmosome. This mechanism could act as a mechanical buffer by reducing the impulse of forces on the cadherins, and play a central role in mechanical resilience.

cell biology↗

bioRxiv2026

Pseudomonas aeruginosa R-bodies deliver an ADP deaminase toxin

Diverse bacteria produce proteinaceous polymeric coils called R-bodies (refractile bodies), which extend into ~10 m-long needles in response to environmental triggers. It has been proposed that R-bodies deliver toxins intracellularly after such bacteria are ingested by eukaryotes, but intra-host extension of R-bodies has not been directly observed and these toxins remain unidentified. We use Pseudomonas aeruginosa PA14 and Dictyostelium discoideum to show that R-bodies extend within amoebae. We also identify a novel toxin, DeaR (deaminase associated with the R-body), which contributes to predation resistance and forms a near-megadalton dodecamer with ADP deaminase activity that alters purine metabolism. Our findings elucidate the molecular basis of R-body-mediated toxicity during PA14 infection and provide a paradigm for understanding the potential of cytotoxic effectors delivered by R-bodies (CEDRs) in interkingdom interactions.

microbiology↗

bioRxiv2026

Pirfenidone improves adipose dysfunction and obesity-driven steatohepatitis via mTORC1 signaling

Obesity-driven metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH) are shaped by depot-specific adipose tissue dysfunction, including maladaptive expansion and visceral adipose tissue (VAT) fibrosis. Pirfenidone, an anti-fibrotic agent, improves experimental liver disease. However, its actions on adipose depots and adipose-liver crosstalk remain unclear. Here, we identify pirfenidone as a modulator of mechanistic target of rapamycin complex 1 (mTORC1)-dependent adipose tissue remodeling with divergent outputs in subcutaneous and visceral fat. In diet-induced obese MASH mice, pirfenidone decreased subcutaneous adipose tissue (SAT), inhibiting mTORC1-driven lipogenesis and enhancing oxidative lipid metabolism. Pirfenidone attenuated VAT fibrosis by suppressing an mTORC1-mothers against decapentaplegic homolog 3 (SMAD3)-yes-associated protein (YAP) axis and extracellular matrix gene programs. Pirfenidone also lowered hepatic triglycerides, improved steatosis and fibrosis, reduced hepatic mTORC1 activity. Conditioned medium from fibrotic adipocytes induced lipogenic, inflammatory, and pro-fibrotic programs in AML12, which effects that were blunted by pirfenidone. These data reveal adipose tissue-centered actions of pirfenidone that link mTORC1 remodeling to improved obesity-associated liver disease.

molecular biology↗

bioRxiv2025

Mechanical Cues Regulate Cargo Sorting and Export at the Golgi

The secretory pathway is a sophisticated endomembrane machinery designed to transport and deliver proteins and lipids to intracellular organelles and the extracellular space. While the molecular components of the secretory pathway are well understood, less is known about their regulation, especially by mechanical cues. Here, we report that substrate stiffness stimulates conventional secretion. We have unravelled a molecular pathway that links a mechanical cue through Src and FAK kinases to promote the trafficking of secretory proteins out of the Golgi apparatus and prevent their post-Golgi lysosomal degradation. Phosphoproteomic analysis revealed the Golgi-specific Brefeldin A resistance factor 1 (GBF1) as a key downstream mechano-responsive regulator, whose phosphorylation state orchestrates post-Golgi cargo sorting, directing proteins either toward secretion or to lysosomes. Finally, we identified AMPK as a stiffness-dependent upstream regulator of GBF1 phosphorylation. Together, our data reveal a molecular regulatory loop in which matrix stiffness positively regulates cellular secretion via the Src-FAK-AMPK-GBF1 axis, which can have relevant medical implications in conditions like cancer and fibrosis and their treatment.

cell biology↗

bioRxiv2025

Early postpartum development of pup urine preference in mothers

The transition to motherhood involves profound physiological and neural changes, including adaptations in the sensory systems that support infant care.1,2 While the olfactory system plays a critical role in guiding maternal behaviors such as pup retrieval and nesting,3,4 how olfactory processing itself is reshaped during motherhood remains poorly understood. Here, we show that first-time mothers develop a selective preference for pup urine following parturition and early postpartum care, a preference not observed for other social or neutral odors. Using odor preference assays combined with liquid and gas chromatography-mass spectrometry, we identify specific volatile compounds in pup urine that may contribute to this maternal attraction. Disruption of olfactory input or restriction of contact chemosensation abolished the preference, indicating that both volatile and non-volatile sensory modalities contribute, likely through combined input from the main olfactory epithelium (MOE) and vomeronasal organ (VNO).5,6 Notably, this preference is absent in late-pregnant females, in mothers separated from pups at birth, and in virgins cohoused with pups or exposed to pup urine-highlighting that pup urine preference depends on the convergence of internal hormonal signals and external chemosensory cues.7,8 These findings reveal a previously unrecognized specificity in maternal olfactory behavior and provide insight into how motherhood modulates the sense of smell to support offspring recognition and care. In BriefMaternal pup urine preference depends on both hormonal changes and chemosensory cues associated with motherhood. HighlightsO_LIPup urine specifically attracts postpartum mothers but not virgin females C_LIO_LIPup urine contains distinct volatile and non-volatile metabolites C_LIO_LIPup urine preference requires both pup experience and the hormonal priming of motherhood C_LI

neuroscience↗

bioRxiv2025

A two-dimensional space of linguistic representations shared across individuals

Our ability to extract meaning from linguistic inputs and package ideas into word sequences is supported by a network of left-hemisphere frontal and temporal brain areas. Despite extensive research, previous attempts to discover differences among these language areas have not revealed clear dissociations or spatial organization. All areas respond similarly during controlled linguistic experiments as well as during naturalistic language comprehension. To search for finer-grained organizational principles of language processing, we applied data-driven decomposition methods to ultra-high-field (7T) fMRI responses from eight participants listening to 200 linguistically diverse sentences. Using a cross-validation procedure that identifies shared structure across individuals, we find that two components successfully generalize across participants, together accounting for about 32% of the explainable variance in brain responses to sentences. The first component corresponds to processing difficulty, and the second--to meaning abstractness; we formally support this interpretation through targeted behavioral experiments and information-theoretic measures. Furthermore, we find that the two components are systematically organized within frontal and temporal language areas, with the meaning-abstractness component more prominent in the temporal regions. These findings reveal an interpretable, low-dimensional, spatially structured representational basis for language processing, and advance our understanding of linguistic representations at a detailed, fine-scale organizational level.

neuroscience↗

bioRxiv2025

Identification of genetic variation associated with high-temperature tolerance in cowpea

Heat tolerance is an important trait in cowpea, a crop that constitutes the primary protein source for a large portion of the human population in sub-Saharan Africa. Cowpea grows across this region, with cultivated, landrace, semi-wild, and wild cowpeas germplasm growing across diverse climatic conditions. This study used environmental association (envGWAS) and allele frequency outlier approaches in a panel of 580 gene bank accessions to identify genomic regions associated with heat and limited precipitation. Because allele frequency outliers are detected independent of potential selection factors driving differentiation, we used a ranking-based approach to identify the climate variables most associated with variants among outliers. Precipitation-related variables dominated the signals we identified for envGWAS and allele frequency outliers. We found variants on all eleven chromosomes putatively associated with the adaptation of cowpea to higher-temperature environments. The considerable overlap between variants associated with low precipitation and high temperature suggests that these traits may be inextricably linked in cowpea. The Sahel region is the source of many accessions with derived variants associated with high temperature, suggesting the potential for accessions from this region to contribute to heat tolerance alleles for cowpea improvement.

evolutionary biology↗

bioRxiv2024

A 3.5-minute-long reading-based fMRI localizer for the language network

The field of human cognitive neuroscience is increasingly acknowledging inter-individual differences in the precise locations of functional areas and the corresponding need for individual-level analyses in fMRI studies. One approach to identifying functional areas and networks within individual brains is based on robust and extensively validated localizer paradigms--contrasts of conditions that aim to isolate some mental process of interest. Here, we present a new version of a localizer for the fronto-temporal language-selective network. This localizer is similar to a commonly-used localizer based on the reading of sentences and nonword sequences (Fedorenko et al., 2010) but uses speeded presentation (200ms per word/nonword). Based on a direct comparison between the standard version (450ms per word/nonword) and the speeded versions of the language localizer in 24 participants, we show that a single run of the speeded localizer (3.5 min) is highly effective at identifying the language-selective areas: indeed, it is more effective than the standard localizer given that it leads to an increased response to the critical (sentence) condition and a decreased response to the control (nonwords) condition. This localizer may therefore become the version of choice for identifying the language network in neurotypical adults or special populations (as long as they are proficient readers), especially when time is of essence.

neuroscience↗

bioRxiv2024

Linguistic inputs must be syntactically parsable to fully engage the language network

Human language comprehension is remarkably robust to ill-formed inputs (e.g., word transpositions). This robustness has led some to argue that syntactic parsing is largely an illusion, and that incremental comprehension is more heuristic, shallow, and semantics-based than is often assumed. However, the available data are also consistent with the possibility that humans always perform rule-like symbolic parsing and simply deploy error correction mechanisms to reconstruct ill-formed inputs when needed. We put these hypotheses to a new stringent test by examining brain responses to a) stimuli that should pose a challenge for syntactic reconstruction but allow for complex meanings to be built within local contexts through associative/shallow processing (sentences presented in a backward word order), and b) grammatically well-formed but semantically implausible sentences that should impede semantics-based heuristic processing. Using a novel behavioral syntactic reconstruction paradigm, we demonstrate that backward- presented sentences indeed impede the recovery of grammatical structure during incremental comprehension. Critically, these backward-presented stimuli elicit a relatively low response in the language areas, as measured with fMRI. In contrast, semantically implausible but grammatically well-formed sentences elicit a response in the language areas similar in magnitude to naturalistic (plausible) sentences. In other words, the ability to build syntactic structures during incremental language processing is both necessary and sufficient to fully engage the language network. Taken together, these results provide strongest to date support for a generalized reliance of human language comprehension on syntactic parsing. Significance statementWhether language comprehension relies predominantly on structural (syntactic) cues or meaning- related (semantic) cues remains debated. We shed new light on this question by examining the language brain areas responses to stimuli where syntactic and semantic cues are pitted against each other, using fMRI. We find that the language areas respond weakly to stimuli that allow for local semantic composition but cannot be parsed syntactically--as confirmed in a novel behavioral paradigm--and they respond strongly to grammatical but semantically implausible sentences, like the famous Colorless green ideas sleep furiously sentence. These findings challenge accounts of language processing that suggest that syntactic parsing can be foregone in favor of shallow semantic processing.

neuroscience↗

bioRxiv2024

Precision fMRI reveals that the language network exhibits adult-like left-hemispheric lateralization by 4 years of age

In adults, left hemisphere (LH) damage often leads to aphasia, but many cases of early damage leave linguistic processing intact, with a functional language system developing in the right hemisphere. To explain this early apparent equipotentiality of the two hemispheres for language, some have proposed that the language system is more bilateral during early development and becomes increasingly left-lateralized with age. We examined language lateralization using fMRI in two large developmental cohorts (total n=273 children aged 4-16 years; n=107 adults). Strong, adult-like LH lateralization (in response magnitude and activation volume) was evident by age 4, although other features of the LH language network showed protracted development, including the magnitude of language response and the strength of functional connectivity. Thus, although the RH can take over language function in some cases of early brain damage, this plasticity occurs in spite of adult-level LH bias present by age 4 years.

neuroscience↗

bioRxiv2024

Neuron-derived Prox1 suppresses injury-induced reprogramming of Muller glia to proliferative retinal progenitor cells

Individuals with retinal degenerative diseases face significant obstacles in restoring normal vision due to the inability to regenerate degenerated retinal cells. While retinal neurons can be regenerated from Muller glia (MG) in cold-blooded vertebrates, this regenerative ability is lacking in mammals, indicating the limited competence of mammalian MG for retinal regeneration. In this study, we elucidate the role of prospero-related homeobox 1 (Prox1) in rendering the mammalian retina incompetent for MG-derived regeneration. Prox1 accumulates in MG in the degenerating human and mouse retinas but not in those in the regenerating zebrafish retina. Strikingly, Prox1 in mouse MG originated from neighboring retinal neurons through intercellular protein transfer. Consequently, inhibition of Prox1 transfer to MG enables the reprogramming of MG into proliferative retinal progenitor cells in injured mouse retinas. Furthermore, we succeeded in regenerating retinal neurons and delaying vision loss in retinitis pigmentosa disease model in mice by adenoassociated viral gene delivery of an anti-Prox1 antibody that sequesters extracellular Prox1 in the mouse retina. Taken together, our findings highlight the therapeutic potential of anti-Prox1 therapy in restoring the regenerative potential of the mammalian retina.

developmental biology↗

bioRxiv2023

Design of a symmetry-broken tetrahedral protein cage by a method of internal steric occlusion

Methods in protein design have made it possible to create large and complex, self-assembling protein cages with diverse applications. These have largely been based on highly symmetric forms exemplified by the Platonic solids. Prospective applications of protein cages would be expanded by strategies for breaking the designed symmetry, e.g., so that only one or a few (instead of many) copies of an exterior domain or motif might be displayed on their surfaces. Here we demonstrate a straightforward design approach for creating symmetry-broken protein cages able to display singular copies of outward-facing domains. We modify the subunit of an otherwise symmetric protein cage through fusion to a small inward-facing domain, only one copy of which can be accommodated in the cage interior. Using biochemical methods and native mass spectrometry, we show that co-expression of the original subunit and the modified subunit, which is further fused to an outward-facing anti-GFP DARPin domain, leads to self-assembly of a protein cage presenting just one copy of the DARPin protein on its exterior. This strategy of designed occlusion provides a facile route for creating new types of protein cages with unique properties.

biochemistry↗

bioRxiv2023

Interaction between PSD 95 and TRPV4 through PDZ domain controls TRPV4's localization and activity.

The TRPV4 cation channel, is expressed in a broad range of tissues where it participates in generation of Ca2+ signal and/or depolarization of membrane potential. Here, we identified post synaptic density protein 95 (PSD95) as an interacting protein of this epithelial Ca2+ channel using confocal microscopy analysis and immunological assay. Using co-immunoprecipitation assays, we demonstrated that PSD95 was part of the TRPV4 protein complex. PSD95 protein was specifically associated with the C-terminal tail of TRPV4 to form a complex. A TRPV4 tail deletion mutant ({Delta}DAPL871: 4d) exhibited a diminished capacity to bind PSD95. Confocal microscopy analysis suggested that apical localization of TRPV4 required PSD95-TRPV4 interaction. Our data clearly suggest that formation of a complex between TRPV4 and PSD95 can regulate TRPV4 membrane localization. Both TRPV4 Ca2+ channel and its autophagy activity of 4d were reduced by more than 80% compared to those of the TRPV4 wild type. Our observation suggests that PSD95-TRPV4 complex plays crucial roles in routing TRPV4 to the apical plasma membrane and maintaining its authentic Ca2+ channel and biological function. CapsuleO_ST_ABSBackgroundC_ST_ABSTRPV4 contain putative PDZ tail motif (DAPL871). ResultsDeletion of TRPV4 tail PDZ motif fails to interact with PSD95 PDZ III domain. ConclusionTRPV4 tail is an authentic PDZ motif to interact with PSD95. SignificanceInteraction between TRPV4 and PSD95 requires for its proper biological functions.

cell biology↗

bioRxiv2023

An integrated single-cell transcriptome landscape of postnatal mouse hypothalamus

The neural stem cells (NSCs) in the hypothalamus are relatively more narrowly defined than in other neurogenic regions of the postnatal brain. By leveraging single-cell RNA sequencing (scRNA-seq) data, we generated an integrated reference dataset comprising 296,282 cells from postnatal hypothalamic regions and the adjacent region, bed nucleus of the stria terminalis (BNST), and identified 30 hypothalamic neuronal and non-neuronal cell populations. The analyses of their gene expression pattern, and specific differentiation trajectories reveal the presence of NSCs and intermediate progenitor cells (IPCs) that show a continuum of activation and differentiation processes in the hypothalamus after birth. Through comparative analyses of the integrated dataset with our lab-generated Connect-seq data obtained from the whole hypothalamus, we further assessed the technical validity of the dataset presented in this study. Our large-scale unified scRNA-seq dataset with harmonized cell-level metadata can serve as a valuable resource for investigating cell type-specific gene expression and cellular differentiation trajectories in the postnatal mouse hypothalamus.

neuroscience↗

bioRxiv2023

Spatial transcriptomic brain imaging reveals the effects of immunomodulation therapy upon specific regional brain cells in mouse dementia model

Increasing evidence of brain-immune crosstalk raises expectations for the efficacy of novel immunotherapies in Alzheimers disease (AD), but the lack of methods to understand brain tissues make it difficult to examine therapeutics. Here, we investigated the changes of spatial transcriptomic signatures and brain cell type using the 10x Genomics Visium platform in immune modulated AD models by various treatments. To proceed with an analysis suitable for a single spot-based transcriptomics, we first organized a workflow for segmentation of neuroanatomical regions, establishment of appropriate gene combinations, and comprehensive review of altered brain cell signatures. Ultimately, we investigated spatial transcriptomic changes following administration of immunomodulators, NK cell supplements and anti-CD4 antibody, that ameliorate behavior impairment, and designated brain cells and regions showing probable associations with behavior changes. We provided the customized analytic pipeline into an application named STquantool. Thus, we anticipate that our approach can help researchers to interpret real action of drug candidate by simultaneously investigating the dynamics of all transcripts for development of novel AD therapeutics.

neuroscience↗

bioRxiv2022

A view of the pan-genome of domesticated cowpea (Vigna unguiculata Walp.)

Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six sub-populations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4,963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO-terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million SNPs relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea. Article SummaryThis study reports annotated genome assemblies of six cowpea accessions. Together with the previously reported annotated genome of IT97K-499-35, these constitute a pan-genome resource representing six subpopulations of domesticated cowpea. Annotations include genes, variant calls for SNPs and short indels, larger presence or absence variants, and inversions. Noncore genes are enriched for loci involved in stress response and harbor many genic variants with potential effects on coding sequence.

genomics↗

bioRxiv2022

Bi-phasic regulation of AIMP2 and its splice variant in PARP-1- dependent neurodegeneration

Parthanatos is a significant molecular cause of Parkinsons disease, in which AIMP2 aberrantly activates PARP-1 through a physical interaction. Interestingly, AIMP2 has an antagonistic splice variant, named DX2, which compromises AIMP2-induced apoptosis via p53 or inflammatory pathway. Here we suggested that DX2 binds to PARP-1 with a higher affinity than AIMP2, deactivating it and improving synaptic physiology. To deliver DX2 into deep brain areas, miR142 target sequence-embedded adeno-associated virus was designed to avoid unexpected expression in hematopoietic cells. RNAseq analysis revealed that DX2 selectively suppressed cell death-associated pathways, such as p53 and neuroinflammation. Upon a single intracranial injection, both behaviour and motility were mitigated in three animal models of Parkinsonism, induced by MPTP, rotenone, or 6-OHDA. Efficacy was observed in therapeutic model as well as preventive ones. Thus, AIMP2 and DX2 are suggested to act as an ON/OFF switch for PARP-1. In particular, as cell survival properties of DX2 was exerted only when AIMP2 is accumulated abnormally, without its own additional tumorigenicity, DX2 could be a unique therapeutic tool for treating patients with Parkinsons disease.

molecular biology↗

bioRxiv2022

Realtime morphological characterization and sorting of unlabeled viable cells using deep learning

Phenotyping of single cells has dramatically lagged advances in molecular characterization and remains a manual, subjective, and destructive process. We introduce COSMOS, a platform for phenotyping and enrichment of cells based on deep learning interpretation of high-content morphology data in realtime. By training models on an atlas of >1.5 billion images, we demonstrate enrichment of unlabeled cells up to 33,000 fold. We apply COSMOS to multicellular tissue biopsy samples demonstrating that it can identify malignant cells with similar accuracy to molecular approaches while enriching viable cells for functional evaluation. We show high-dimensional embedding vectors of morphology generated by COSMOS without any need for complex sample pre-processing, gating, or bioinformatics capabilities, which enables discovery of cellular phenotypes, and integration of morphology into multi-dimensional analyses. One sentence summaryA novel platform capable of high-throughput imaging and gently sorting cells using deep morphological assessment.

cell biology↗