Biology subjects

Kwon, J.

Publications and source records attributed to Kwon, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Benchmarking Generalizability in Deep Learning-Based White Matter Tract Segmentation

Summary paragraphWhite matter tracts (WMTs) are the brains structural foundation for information transfer, underlying essential cognitive and behavioral functions. While diffusion MRI and tractography enable non-invasive mapping of these pathways, automated segmentation often lacks generalizability across diverse data sources. We conducted a systematic, cross-dataset evaluation of four state-of-the-art deep learning architectures, benchmarking their performance across independent datasets with varying acquisition protocols and populations. CNN-based models such as TractSeg achieved the highest within-domain accuracy, but performance dropped sharply under domain shift, most severely when we applied adult-trained models to pediatric data. To address this degradation, we introduce Ensemble White Matter Tract Segmentation (EWMTS), which combines complementary models to partially recover accuracy under domain shift, although performance still falls short of within-domain levels. By openly releasing this benchmark and a reproducible processing pipeline, we provide the neuroimaging community with a framework to develop and benchmark segmentation models across the heterogeneity of real-world neuroimaging data.

neuroscience↗

bioRxiv2026

Attenuated adaptive growth of interpersonal synchrony in autism

During social interactions, people continuously align their movements and rhythms, a process known as interpersonal synchrony that supports rapport, mutual understanding, and smooth communication. In autism spectrum disorder (ASD), previous studies have often reported atypical or reduced synchrony, but most have relied on aggregate or session-averaged measures that may miss how coordination develops over time. It therefore remains unclear whether interactional differences in autism reflect a general reduction in synchrony or altered temporal dynamics of interpersonal coordination. We examined the temporal dynamics of head-movement synchrony during a structured face-to-face communication task, comparing non-autistic dyads (two typically developing [TD] partners) with mixed-neurotype dyads (one TD speaker paired with one autistic listener), using gyroscope-based tracking and time-resolved trajectory modelling. Phase-based synchrony, indexed by the phase-locking value (PLV), was lower overall in mixed-neurotype dyads. Critically, time-resolved analyses revealed a marked group difference in synchrony trajectories: non-autistic dyads showed progressive, adaptive growth in synchrony over the interaction, whereas mixed-neurotype dyads showed a significantly attenuated, flatter pattern. These findings suggest that autism may involve altered temporal organization of social coordination rather than simply reduced synchrony overall. Lay AbstractWhen we talk with someone, we often naturally match their body language and rhythms without even realizing it. This physical "syncing up" helps us feel connected, builds trust and shared understanding, and makes communication flow easily. Research shows that autistic people might sync their movements differently during conversations compared to non-autistic people. However, past studies usually just measured an overall average of this syncing across a whole interaction. This approach misses how human interactions actually unfold over time. We wanted to know: do autistic people just sync less overall, or does their syncing change differently as the conversation goes on? To find out, we used small motion sensors to track the head movements of adults having structured face-to-face conversations and compared two types of pairs: non-autistic pairs, where both people were non-autistic, and mixed-neurotype pairs, where one non-autistic speaker talked to one autistic listener. We found a notable difference in how the two groups interacted over time. For the non-autistic pairs, the physical syncing grew progressively stronger as the conversation progressed; they progressively "tuned in" to each other. In contrast, mixed-neurotype pairs showed a flatter pattern--their level of syncing stayed relatively constant from start to finish without that same gradual build-up. These findings are important because they suggest that differences in autistic communication are not simply a "lack" or "deficit" in social coordination. Instead, autistic individuals have a distinct style of interacting--one that maintains social engagement without relying on the progressive build-up of physical syncing that non-autistic people use. Taken together, our results highlight the importance of examining how interactions evolve over time to better understand the different ways autistic and non-autistic people communicate.

neuroscience↗

bioRxiv2026

A retinotopic wiring principle of the human brain

Summary paragraphA central challenge in neuroscience is to understand how anatomical connectivity links neural representations to behavior. In sensory systems, cortical areas encode structured maps of the external world, yet it remains unclear whether and how this representational geometry constrains long-range connectivity in the living human brain. Here, we show that structural connectivity in the human visual cortex preserves retinotopic organization, revealing a retinotopic wiring principle; cortical regions representing the same locations in visual space preferentially connect. Across more than 1,700 participants spanning ages 2 to 88 years, we further show that well-known perceptual asymmetries correspond to systematic asymmetries in connectivity within early visual cortex, but not in connections linking visual cortex to the rest of the brain. We introduce a scalable approach to map retinotopic connectivity when tractography alone is unreliable. Together, these findings demonstrate that anatomical connectivity preserves the geometry of neural representations, providing a general principle linking brain structure, function, and behavior.

neuroscience↗

bioRxiv2026

Acute Toxicological Profile of Pharmaceutical-Grade Nicotinamide Riboside: A Route-Dependent Assessment Across Intravenous, Intramuscular, and Subcutaneous Administration

Nicotinamide riboside chloride (NR-Cl) has been studied predominantly by the oral route, while information regarding its toxicity following parenteral administration is limited. To characterize route-dependent acute toxicity and estimate median lethal doses (LD50), pharmaceutical-grade NR-Cl was evaluated following bolus intravenous (IV), intramuscular (IM), and subcutaneous (SC) administration in female Sprague Dawley rats, in three independent studies. All studies were conducted using an adapted OECD Guideline 425 Up-and-Down procedure, modified for parenteral administration, in the absence of standardized route-specific OECD guidance. Animals received a single dose of NR-Cl via the respective administration route and were monitored for mortality, clinical signs, bodyweight changes, and gross pathological findings over a 14-day observation period. Following IM and SC administration, no mortalities were observed at doses up to 2000 mg/kg, and LD50 values for both routes were determined to be greater than 2000 mg/kg. In contrast, IV administration yielded an estimated LD50 of approximately 2000 mg/kg. These findings demonstrate that the acute toxicity of NR-Cl differs by route of administration and establish foundational safety benchmarks to support future research.

pharmacology and toxicology↗

bioRxiv2026

Co-repression of Yap1 and Sox9 Abrogates Established Cholangiocarcinoma by Eliminating Transcriptional Compensation

Background/AimsIntrahepatic cholangiocarcinoma (iCCA) represents an unmet clinical need due to its increasing incidence, aggressive biology, and limited treatment options. The extremely low-response rates to current systemic regimens and the emergence of adaptive resistance to targeted therapies underscore the urgent need for alternative therapeutic strategies. Given that the lineage-defining transcription factors SOX9 and YAP1 are central regulators of cholangiocyte and iCCA identity, we investigated their functional roles as potential therapeutic vulnerabilities across multiple preclinical models. MethodsPatient tissue-microarray (TMA) analysis, Sleeping-Beauty hydrodynamic tail vein injection-based iCCA models, and Cre-mediated inducible gene deletion systems were used to investigate the roles of Sox9 and Yap1. Deep-learning-based prediction, RNA-seq, ChIP-seq and immunohistochemistry analyses were performed to delineate transcriptional networks and downstream effectors associated with SOX9/YAP1 signaling. ResultsDual deletion of Sox9 and Yap1 effectively eradicated advanced iCCA while preserving intrahepatic bile ducts, regardless of oncogenic drivers. Mechanistically, SOX9 and YAP1 transcriptionally compensated for each other when one was absent, and ILF2, MGAT5, and WWTR1 were identified as key downstream effectors mediating this compensatory mechanism. Loss of Ilf2, Mgat5, or Taz suppressed iCCA, whereas overexpression of Ilf2 or Taz following Sox9/Yap1 co-deletion restored tumor development, indicating that ILF2 or TAZ can functionally substitute for YAP1 and SOX9 in sustaining iCCA. ConclusionsCo-targeting SOX9 and YAP1 offers a promising and safe broad-spectrum preventive/therapeutic approach for iCCA, potentially overcoming resistance to YAP1 inhibition. The adaptive resistance mechanism identified may extend to other malignancies, providing insights for addressing the advanced resistant to YAP1-TEAD-directed therapies.

cancer biology↗

bioRxiv2026

Combinatorial DNA-PAINT

State-of-the-art super-resolution microscopy enables nanometer-resolution imaging of proteins, but its multiplexing capacity has been fundamentally constrained. Here, we present Combi-PAINT, a combinatorial DNA barcoding strategy based on DNA-PAINT, that facilitates superlinear scaling of multiplexing with the number of imaging rounds. Instead of assigning one unique docking strand per target, Combi-PAINT encodes targets as combinations of orthogonal sequences, allowing nonlinear scaling of target number with imaging rounds. Using just six imaging rounds, we resolve 41 targets in a field-of-view of 100 x 100 m2 with [~]2.5 nm localization precision and [~]90% decoding accuracy in under 30 minutes, representing the fastest sub-10 nm super-resolution microscopy acquisition to date. We benchmark decoding fidelity and demonstrate robust in situ performance in mammalian cells, achieving 97% decoding accuracy. Combi-PAINT is compatible with existing DNA-PAINT workflows and speed-enhancing techniques, offering a scalable, accessible platform for high-content, single-molecule spatial proteomics.

biophysics↗

bioRxiv2025

T-Cell Synaptosomes Orchestrate Long-Term Anti-Tumor Immunity via Proliferative and Metabolic Reprogramming

A defining feature of T-cell activation is its dependence on physical contact with antigen-presenting cells (APCs). During this interaction, activated T cells release microvesicles, known as T-cell immunological synaptosomes (TIS), onto the surface of APCs. While TIS are known to activate APCs, their broader in vivo functions remain largely unexplored. Here, we show that TIS are primarily phagocytosed by macrophages and dendritic cells, persist intracellularly for several days, and reprogram these cells in a manner distinct from LPS. TIS upregulate genes involved in metabolism, proliferation, and anti-inflammatory responses, and promote immune cell recruitment, including eosinophils. Notably, TIS induce minimal immune activation upon initial exposure but trigger a rapid and robust response upon secondary administration, indicating a priming effect reminiscent of adaptive immunity. In an MC38 colon cancer model, TIS treatment resulted in near-complete tumor suppression and durable protection upon rechallenge, highlighting their potential as a potent and long-lasting immunotherapeutic platform.

immunology↗

bioRxiv2025

Discovery of A Small Molecule non-IMiD Degrader of ZBTB7A for the Treatment of β-hemoglobinopathies

Sickle cell disease and {beta}-thalassemia, two major {beta}-hemoglobinopathies, pose significant clinical challenges globally. Current treatments often face limitations in efficacy and tolerability. The transcription factor ZBTB7A has emerged as a promising therapeutic target for reactivating fetal hemoglobin expression. Here, we report the discovery and characterization of SH6, a small molecule non-IMiD degrader of ZBTB7A. SH6 induces fetal hemoglobin in erythroid cell lines in a CRBN and ZBTB7A-dependent manner, and it is capable of inducing fetal hemoglobin expression in healthy donor, SCD and {beta}-thalassemia patient CD34+ cell derived erythroid cells. The efficacy of SH6 is confirmed in a xenotransplantation humanized mouse model. SH6 outperforms currently available therapeutic agents in vitro, and shows synergy with hypomethylating agents. SH6 exhibits a favorable in vivo toxicity profile. Our findings establish SH6 as a promising therapeutic lead candidate for further optimization towards clinical development for treatment of sickle cell disease and {beta}-thalassemia.

cell biology↗

bioRxiv2025

Loss of WNT2B Increases Progression from Dysplasia to Colorectal Cancer

Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer-related deaths in the United States, and upregulation of the WNT pathway is a primary driver in most cases. However, the role of individual WNT proteins in the development of CRC remains poorly understood. Our previous studies demonstrated that WNT2B loss-of-function leads to severe intestinal enteropathy in humans and increases chemically-induced colitis in mice, suggesting a protective function in the colon. Therefore, we investigated how loss of WNT2B affects CRC development. We used azoxymethane (AOM)/dextran sodium sulfate (DSS) to model colitis-associated cancer (CAC) and AOM-induced mutagenesis to model sporadic CRC. We measured the number and size of tumors and performed histopathological and molecular analyses. We also analyzed the Cancer Genome Atlas to evaluate WNT2B expression in human colon cancer. In CAC and CRC mouse models, Wnt2b KO mice showed decreased survival and enhanced tumor burden. Moreover, Wnt2b KO mice had larger tumors and enhanced dysplasia, with a higher frequency of animals progressing from adenomas to adenocarcinomas compared to control littermates. Wnt2b KO animals frequently presented with intestinal bleeding and rectum prolapse, which resembles obstructive CRC. Furthermore, WNT2B expression was downregulated in human CRC samples compared to healthy controls, which predicted a significantly lower patient survival. These findings support the conclusion that WNT2B is required for maximal resistance against tumorigenesis and raise the possibility that selectively increasing WNT2B signaling may be a useful colon cancer prevention strategy. SignificanceWNT2B loss-of-function increases colon cancer tumorigenesis. Targeting WNT2B may represent a novel strategy for intestinal diseases with a high risk of neoplastic transformation, potentially decreasing the progression to cancer development.

cancer biology↗

bioRxiv2025

O-mannosylation and protein maturation check-points represent therapeutic opportunities in BRAF fusion protein oncogenesis

Fusions between protein-coding genes are common oncogenic drivers across cancers, typically pairing a proto-oncogene with partner that does not independently drive cancer. In all therapeutically actionable fusions, the proto-oncogene is the drug target, the contributions to oncogenicity of the fusion partner have largely been ignored. We studied the role of BRAF fusion partners and found that they are necessary for transformation. In the setting of KIAA1549::BRAF, the most common fusion protein across brain tumors, we found that KIAA1549 is necessary for the oncogenicity of KIAA1549::BRAF and engenders a striking and specific dependency on the protein O-mannosyltransferase complex (POMT1/2). Specifically, we show that genetic silencing or pharmacologic inhibition of the protein O-mannosyltransferase complex (POMT1/2) reverses fusion-induced transformation, thereby representing a novel and MAPK independent therapeutic target. Furthermore, POMT1/2 is required to glycosylate and enable maturation of the K::B fusion protein. These findings represent a proof-of-concept for targeting the partners in oncogenic fusions as a potential cancer therapeutic strategy.

cancer biology↗

bioRxiv2025

SALL4 is required for YAP1-dependent malignant and regenerative hepatocyte reprogramming into cholangiocyte lineage

Hepatocytes (HCs), which share a developmental origin with cholangiocytes (CCs), have the capacity to undergo reparative reprogramming into CCs in response to liver injury and, under specific conditions, can also transform malignantly into cholangiocarcinoma (CCA). However, the molecular mechanisms governing HC plasticity in liver diseases remain poorly understood. In this study, we investigated the role of Spalt Like Transcription Factor 4 (SALL4), an oncofetal transcription factor, in both malignant and regenerative HC fate transitions toward the biliary lineage. Using Sleeping Beauty hydrodynamic tail vein injection-mediated murine liver cancer models, we explored HC-to-CCA transformation, while the DDC diet-induced cholestasis model was used to investigate regenerative HC-to-CC reprogramming. Our findings reveal that SALL4 is specifically required for myristoylated Akt (myrAkt)-YAP1S127A (AY)-driven HC-to-CCA transformation, as its loss significantly suppressed malignant reprogramming and clonal expansion. Surprisingly, SALL4 overexpression also prevented AY-driven CCA development while promoting the expansion of liver progenitor cell (LPC)-like fatty HCs. Mechanistically, we propose Bmi1 as a key downstream effector of SALL4 in YAP1-dependent HC- to-CCA transformation. Additionally, in the DDC-fed cholestasis model, Sall4 deletion enhanced HC-to-LPC activation while impairing LPC differentiation into mature CCs. These findings establish SALL4 as a critical regulator of HC plasticity in both malignant and regenerative contexts and highlight its potential as a therapeutic target for specific liver cancer subtypes. SIGNIFICANCEHepatocyte plasticity supports repair but can drive malignancy, acting as a double-edged sword. We identify SALL4 as regulator of YAP1-driven hepatocyte-to-cholangiocyte reprogramming, revealing the YAP1-SALL4- BMI1 axis as a therapeutic target for cholangiocarcinoma.

cancer biology↗

bioRxiv2025

Synaptic and intrinsic membrane defects disrupt early neural network dynamics in Down syndrome

Down syndrome, caused by trisomy 21, affects around six million people worldwide and features learning, memory and language deficits. However, the mechanisms underlying trisomy 21 neurophenotypes involving human cortical circuitry are unknown. By characterising developing neural network dynamics and single cell excitability profiles, with synaptic and voltage-dependent ion channel behaviour, using an isogenic induced pluripotent stem cell- derived neuronal model, we show that trisomy 21 impairs the activity and development of cortical circuitry. This is caused by deficient glutamatergic synaptic connectivity and by aberrant intrinsic membrane properties involving K+ and Na+ channels culminating in spike firing defects that weaken neural network activity and disrupt the synchrony of developing neurons. We also identify transiently activated A-type K+ channels, specifically Kv4.3 channels, as a key orchestrator for Down syndrome during neurodevelopment. Overall, these excitability changes will significantly contribute towards the aberrant neurophenotypes observed later on in life.

neuroscience↗

bioRxiv2025

Bringing the Genetically Minimal Cell to Life on a Computer in 4D

We present a whole-cell spatial and kinetic model for the 100 minute cell cycle of the genetically minimal bacterium, JCVI-syn3A. This is the first simulation of a complete cell cycle in 4D including all genetic information processes, metabolic networks, growth, and cell division. Integrating hybrid computational methods, dynamics of the morphological transformations were achieved. Growth is driven by synthesis of lipids and membrane proteins and constrained by new fluorescence imaging data. Chromosome replication and segregation is controlled by essential SMC and topoisomerase proteins in Brownian dynamics simulations with replication rates responding to dNTP pools from metabolism. The model captures the origin to terminus ratio measured in our DNA sequencing and recovers other experimental measurements like doubling time, mRNA half-lives, protein distributions, and ribosome counts. Because of stochasticity, each replicate cell is unique. Not only do we predict average behavior for partitioning to daughter cells, we predict the heterogeneity among them.

biophysics↗

bioRxiv2025

Intercellular communication in the brain via dendritic nanotubular network

Recent studies have identified intercellular networks for material exchange by bridge-like nanotubular structures, yet their existence in neurons remains unexplored within the brain. Here, we identified long, thin dendritic filopodia that establish direct dendrite-to-dendrite contacts, forming dendritic nanotubes (DNTs) in mammalian brains. Using super-resolution microscopy, we characterized their unique molecular composition and dynamics in dissociated neurons, enabling Ca2+ propagation over distances. Utilizing imaging and machine-learning-based analysis, we confirmed the in situ presence of DNTs connecting dendrites to other dendrites whose anatomical features are distinguished from synaptic dendritic spines. DNTs mediate the active transport of small molecules or human amyloid-beta (A{beta}), implicating the role of DNT network in AD pathology. Notably, DNT levels increased prior to the onset of amyloid plaque deposits in the mPFC of APP/PS1 mice. Computational simulations predicted the progression of amyloidosis, providing insight into the mechanisms underlying neurodegeneration through these DNTs. This study unveils a previously unrecognized nanotubular network, highlighting another dimension of neuronal connectivity beyond synapses.

neuroscience↗

bioRxiv2025

High-Throughput Multiomics Profiling of Model Systems Using the AVITI24 Platform

We present a multiomics platform comprising Teton, a detection assay system, and AVITI24, a dual-flowcell instrument that performs both cellular imaging and sequencing readout. Teton integrates a compartmentalized flowcell for cell culture with methods to measure morphology, RNA, and protein at subcellular resolution. The platform quantifies morphological features through cell painting of 6 cellular components, RNA expression of up to 350 transcripts via sequencing of oligonucleotides hybridized to mRNA, and protein expression of up to 200 targets using antibody-linked oligonucleotide sequencing. The flow cell accommodates >1 million cells in a 10 cm squared open-well format or can be subdivided into 12 or 48 wells to support experiments with multiple conditions or time points. We describe and validate the detection methods of the platform and showcase its capabilities by co-culturing three cancer cell lines and elucidating the cellular pathways triggered by various drug treatments as a function of time. Using multiple time points enables us to capture the dynamics of cellular processes including receptor activation and signaling cascades. The results demonstrate how different cancer cells evade TNF-induced apoptosis by activating compensatory signaling programs that maintain survival despite pro-apoptotic cues. Our model system replicates previously published results and highlights the versatility of the platform in enabling rapid, high-throughput analysis of complex cellular responses in varied biological contexts.

genomics↗

bioRxiv2024

Development of a Multifunctional Extracorporeal Life Support (ECLS) System for Lung and Kidney Support: The Pneuma-K ECLS System

Multi-organ failure (MOF), particularly in the coexistence of acute kidney injury (AKI) and acute lung injury (ALI), presents a significant challenge in intensive care units (ICU) and is associated with exceedingly high mortality rates. Respiratory and renal failures are frequently managed by extracorporeal membrane oxygenation (ECMO) and continuous renal replacement therapy (CRRT), respectively. However, employing these therapies using separate devices requires specialized facilities, adds to complexity, and increases the risks of clotting due to the extensive artificial surface areas involved. Therefore, an integrated device capable of providing simultaneous respiratory and renal support is essential. This paper introduces the Pneuma-K ECLS system, which incorporates a multifunctional detoxifying filter (MDF) capable of performing gas exchange and renal replacement in a single cartridge. Ex-vivo blood tests confirmed the ability of the MDF to oxygenate blood, remove carbon dioxide, and eliminate uremic toxins. In addition, animal experiments demonstrated the considerable clinical potential of this novel integrated extracorporeal life support approach. Integrating respiratory and renal support into a singular device could mitigate risks, conserve resources, and enhance the survival rates of critically ill patients suffering from concurrent lung and kidney failure.

bioengineering↗

bioRxiv2024

Modeling American Kestrel Decline Using Spatiotemporal Subsampling to Improve eBird Data Reliability

American Kestrel (Falco sparverius) numbers have plummeted over 40% since 1980, despite many other raptor species, including the closely related Merlin (Falco columbarius) rebounding in the same period, post the ban on the use of DDT. One plausible reason for this decline is the increase in Coopers Hawks (Astur cooperii), a predatory species. To model the impact of Coopers Hawk on American Kestrels, one can use citizen science data such as eBird. However, eBird contains a heavy sampling bias towards recent data in large cities as it has gained popularity over time. A novel framework testing different spatiotemporal subsampling resolutions was employed in seeing how to make the data more reliable and to enjoy a finer time resolution compared to the Breeding Bird Survey (BBS) standard. The ecological relationship between two species is then modeled using a time-series framework that accounts for both current and past interactions, with the model order determined based on criteria such as BIC. The creation and analysis of synthetic data are also tested to verify that our framework reflects the ground truth of the bird abundance trend. Immediate forecast results based on the eBird data suggests a decline of American Kestrels at the current pace.

ecology↗

bioRxiv2024

Comprehensive structure-function analysis reveals gain- and loss-of-function mechanisms impacting oncogenic KRAS activity

To dissect variant-function relationships in the KRAS oncoprotein, we performed deep mutational scanning (DMS) screens for both wild-type and KRASG12D mutant alleles. We defined the spectrum of oncogenic potential for nearly all possible KRAS variants, identifying several novel transforming alleles and elucidating a model to describe the frequency of KRAS mutations in human cancer as a function of transforming potential, mutational probability, and tissue-specific mutational signatures. Biochemical and structural analyses of variants identified in a KRASG12D second-site suppressor DMS screen revealed that attenuation of oncogenic KRAS can be mediated by protein instability and conformational rigidity, resulting in reduced binding affinity to effector proteins, such as RAF and PI3-kinases, or reduced SOS-mediated nucleotide exchange activity. These studies define the landscape of single amino acid alterations that modulate the function of KRAS, providing a resource for the clinical interpretation of KRAS variants and elucidating mechanisms of oncogenic KRAS inactivation for therapeutic exploitation.

cancer biology↗