Biology subjects

Chen, J. X.

Publications and source records attributed to Chen, J. X..

9 recordsLinked to original sources

bioRxiv2026

Intranasal photobiomodulation: an energy efficient paradigm for cortical and subcortical stimulation

Previous studies have shown the hemodynamic response to transcranial photobiomodulation (tPBM) in localized cortical regions during and after forehead irradiation. However, it is unclear if tPBM can reach deeper regions such as subcortical tissue. It is also unclear whether the manner of regional neurovascular coupling predominantly studied using tPBM extends to all brain regions. As an alternative to forehead delivery, intranasal PBM (iPBM) uses the pathway of the cribriform plate, which is thin and directly leads to the orbitofrontal cortex, rather than the prefrontal cortex in the case of forehead PBM. Thus, it is possible that iPBM can stimulate the brain more efficiently (i.e. with less power). In this study, healthy young adults underwent different iPBM protocols differing in wavelength, frequency and irradiance. We utilized functional magnetic resonance imaging (fMRI) to quantify regional blood oxygenation (BOLD) and perfusion. We further model the neurovascular interactions underlying the fMRI response. We uncovered three distinct temporal signatures, varying by brain region. Specifically, a significant response in the thalamus was observed, with a time-locked BOLD response. Overall, iPBM was found to be associated with much higher efficiency at eliciting BOLD fMRI responses than its forehead (tPBM) counterpart. Lastly, in addition to the expected dose dependence, there were extensive sex differences in the fMRI response to iPBM, surpassing those observed for tPBM. Collectively, these findings highlight the feasibility and efficacy of iPBM and establish a foundation for personalizing PBM protocols for optimal outcomes.

neuroscience↗

bioRxiv2026

Functional and sensitivity profiling of theKITMutation Landscape in Melanoma

Melanoma in Asia presents a unique epidemiological profile, with a higher prevalence of acral and mucosal subtypes compared to Western populations. While KIT mutations are found in up to 15% of Asian melanoma cases, clinical outcomes with KIT inhibitors have been modest due to heterogeneous mutation profiles and a lack of specific patient selection criteria. This study characterizes the landscape of KIT mutations in melanoma using the GENIE database, identifying 86 recurrent hotspots, many of which are variants of unknown significance (VUS). We validated drug sensitivities for key mutations using in vitro and in vivo models. Our results indicate that while the L576P mutation is highly sensitive to multiple inhibitors, the N822K mutation shows resistance to imatinib but responds to sunitinib, nilotinib, and nintedanib. These findings highlight the necessity of genotype-guided therapeutic strategies and provide a rationale for future clinical trials combining broad-spectrum KIT inhibitors with immune checkpoint inhibitors. Translational SignificanceMelanoma subtypes prevalent in Asia, specifically acral and mucosal melanoma, frequently harbor KIT mutations but show poor response rates (23-26%) to the standard-of-care inhibitor, imatinib. This study challenges the current clinical practice of treating all KIT-mutated melanomas uniformly. We demonstrate that specific recurrent mutations, such as N822K, are intrinsically resistant to imatinib but highly sensitive to broad-spectrum inhibitors like sunitinib and nintedanib. By establishing a comprehensive "lookup table" of drug sensitivities for both common and previously uncharacterized KIT variants, this work provides the evidence base required to transition from a "one-size-fits-all" approach to a genotype-guided precision medicine strategy. Furthermore, validating these targets informs the design of next-generation clinical trials, particularly those combining optimal KIT inhibitors with immune checkpoint blockade to improve survival in currently underserved patient populations.

cancer biology↗

bioRxiv2026

Mutation-Resolved Drug Sensitivity Atlas Reveals Broad RAS(ON) Inhibitor Vulnerabilities and a STAT3 Co-Dependency in NRAS-Mutant Melanoma

NRAS-mutated melanoma remains a major unmet clinical need, with no approved targeted therapy and rapid progression on standard treatment. Tri-complex RAS(ON) inhibitors such as daraxonrasib (RMC-6236) and RMC-7977 have shown early clinical activity, but the mutation-specific sensitivity landscape and adaptive resistance programs in melanoma remain undefined. To address this, we generated an isogenic 3D melanoma platform and performed a saturation mutagenesis screen across 95 NRAS missense variants (>99% of clinically recurrent variants), profiling oncogenic fitness and responses to six RAS-targeting agents in spheroids and xenografts. RMC-6236 and RMC-7977 showed the broadest activity and stratified recurrent NRAS mutants into hypersensitive (G12 variants and Q61R/K/L; [~]95% of cases), moderately sensitive (G13D/R/V; [~]4%), and resistant (G60E and Q61P; [~]1%) classes. Structural analyses supported distinct mechanisms underlying reduced susceptibility in a restricted subset of variants. In sensitive genotypes, RAS(ON) inhibition elicited an adaptive cytokine- and RTK-associated survival program converging on STAT3. Co-inhibition of STAT3 enhanced apoptosis, suppressed MYC, and induced tumor regression in NRAS-mutant melanoma models. Together, these findings define a mutation-resolved therapeutic landscape for NRAS-mutant melanoma and identify adaptive STAT3 signaling as a rational target for combination therapy. Statement of Translational SignificanceNRAS-mutated melanoma lacks effective targeted treatments, and clinical responses to immunotherapy are suboptimal. This study presents the first comprehensive drug sensitivity map across 95 NRAS mutations in melanoma, identifying the pan-RAS(ON) inhibitors RMC-6236 and RMC-7977 as broadly effective agents. Multiple mutants with reduced susceptibility are identified, providing mutation-informed guidance for patient selection and clinical trial stratification. Mechanistic analyses reveal that RTK/cytokine-driven STAT3 activation functions as a key survival pathway under RAS(ON) blockade, and its inhibition markedly enhances the efficacy of pan-RAS(ON) inhibitors. These findings support mutation-guided use of RAS(ON) inhibition and highlight STAT3 co-targeting as a rational strategy to strengthen and prolong therapeutic responses in NRAS-mutated melanoma. Highlights- A functional and therapeutic atlas defines 95 recurrent and nonrecurrent NRAS missense variants in melanoma - RMC-6236 and RMC-7977 show broad but genotype-selective activity across major NRAS mutations - A restricted subset of recurrent NRAS mutants shows reduced susceptibility to RAS(ON) inhibition - RAS(ON) inhibition induces an adaptive STAT3 survival program that is therapeutically targetable

cancer biology↗

bioRxiv2025

The fMRI response to transcranial photobiomodulation: the effect of wavelength, irradiance, frequency and skin tone on the BOLD and CBF response in healthy young adults

BackgroundTranscranial photobiomodulation (tPBM) utilizes near-infrared light to penetrate the skull to stimulate neural tissue. However, the in vivo physiological response and the factors influencing this response in the human brain have yet to be understood. MethodsIn this study, we utilize functional magnetic resonance imaging (fMRI) to evaluate the effect of tPBM on the blood-oxygenation (BOLD) and cerebral blood flow (CBF), while varying stimulation parameters such as wavelength, irradiance, and frequency. We further examine the influence of skin tone and sex. We further model the neurovascular interactions underlying the response. ResultsOur results show that the fMRI responses to tPBM is not restrained to the site of irradiation, but quickly spreads to distal sites. Certain regions display an fMRI response sustained after tPBM cessation. Importantly, the responses are dependent on biological and stimulation parameters. Lastly, biophysical modeling revealed a consistent neurovascular coupling-like behaviour underlying these responses. ConclusionEmpirical characterizations of dose dependence are critically important to brain stimulation methods in general but have yet to be demonstrated in most cases. This is the first tPBM study to do just that, establishing the foundation for precision medicine using tPBM, and sets a valuable precedent for the field of brain stimulation.

bioengineering↗

bioRxiv2025

Real-time spatial evolution of the fMRI response to photobiomodulation in the healthy human brain

Photobiomodulation (PBM) is a non-invasive therapeutic technique that uses low-level near-infrared light to influence mitochondrial metabolism and stimulate neural function. While PBM is increasingly used to improve cognitive and clinical outcomes, its in vivo physiological mechanisms in humans remain poorly characterized. In this study, we used BOLD-fMRI to investigate and quantify the temporal and spatial dynamics of transcranial PBM-induced brain activity in young, healthy adults, while incorporating multiple stimulation parameters (wavelength, irradiance, frequency) and transcranial delivery sites (right forehead and intranasal). A time-lagged correlation analysis revealed distinct spatiotemporal patterns of positive and negative BOLD responses that evolved over tens of seconds across both cortical surface and subcortical regions during stimulation. Notably, these effects propagated across brain regions that are potentially mediated by functional networks, were dose-dependent, and were modulated by individual skin tone. This work provides the first real-time, whole-brain mapping of PBM-induced hemodynamic changes in humans, offering new insights into dose-response characteristics and delivery-specific dynamics underlying PBM neurophysiology.

physiology↗

bioRxiv2025

miniVec: A miniaturized plasmid backbone supporting antibiotic-free and additive-free fermentation with enhanced yield and functionality

Plasmids are a foundational research reagent and a key material in biopharmaceutical manufacturing. Plasmids require a backbone for propagation in E. coli, which typically contains an antibiotic resistance gene alongside a replication origin. As plasmids increasingly enter clinical applications, concerns are raised on the safety risks of antibiotic resistance genes. Additionally, these protein-coding genes occupy long stretches of DNA that incur significant metabolic burdens on host cells, which negatively impacts plasmid manufacturability and functionality, leading to high production cost and compromised clinical efficacy. Here, we describe miniVec, a novel miniaturized plasmid backbone devoid of protein-coding sequence, and instead expresses a small RNA to provide constant selective pressure capable of sustaining high plasmid copy numbers in plain culture media devoid of antibiotics or other chemical additives. This simplifies large-scale fermentation and greatly increases plasmid yield. Notably, miniVec confers enhanced functionality in a variety of applications such as chemical transfection, electroporation, virus packaging, transposon-or CRISPR-mediated genome integration, and in vivo naked DNA transfection and vaccination, while exhibiting no detectable immunogenicity or toxicity. These advantages establish miniVec as the next-generation plasmid platform for clinical applications, featuring improved safety that aligns with regulatory expectations, enhanced manufacturability leading to much higher yield and dramatic cost reduction, and augmented functionality in diverse applications.

bioengineering↗

bioRxiv2025

OriGene: A Self-Evolving Virtual Disease Biologist Automating Therapeutic Target Discovery

Here, we present OriGene, a self-evolving multi-agent system that functions as a virtual disease biologist, systematically identifying original and mechanistically grounded therapeutic targets at scale. OriGenes architecture integrates over 600 specialized tools through a Model Context Protocol (MCP), enabling it to reason across diverse data modalities including genomics, protein networks, pharmacology, clinical records and literature evidence, to generate and prioritize target discovery hypotheses. We implemented a strategy combining a knowledge graph-based Tool RAG with an advanced agent selection mechanism to enable dynamic, context-aware tool deployment. Through a self-evolving framework, OriGene continuously integrates human and experimental feedback to iteratively refine its core thinking templates, tool composition, and analytical protocols, thereby enhancing both accuracy and adaptability over time. To comprehensively evaluate its performance, we established TRQA, an original benchmark comprising over 1,900 expert-level question-answer pairs spanning a wide range of diseases and target classes. OriGene consistently outperforms human experts, leading research agents, and state-of-the-art large language models in accuracy, recall, and robustness, particularly under conditions of data sparsity or noise. Critically, OriGene nominated previously underexplored therapeutic targets for liver (GPR160) and colorectal cancer (ARG2), which demonstrated significant anti-tumor activity in patient-derived organoid and tumor fragment models mirroring human clinical exposures. These findings demonstrate OriGenes potential as a scalable and adaptive platform for AI-driven discovery of mechanistically grounded therapeutic targets, offering a new paradigm to accelerate drug development.

bioinformatics↗

bioRxiv2025

Real-Time EEG Response to Pulsed Transcranial Photobiomodulation in Healthy Young Adults: Effects of Stimulation Parameters and Skin Tone

ObjectivesTranscranial photobiomodulation (tPBM) modulates cortical activity, but how specific stimulation parameters shape the electrophysiological response remains unclear. We tested whether pulsed forehead tPBM produces frequency band-specific EEG changes, whether pulsation frequency entrains endogenous oscillations, and whether wavelength, pulsation frequency, irradiance, sex, and skin tone significantly modulate the response. Materials and MethodsForty-six healthy young adults (24M/22F, 20-32 years) each completed four 12-minute EEG recordings (256-channel; PRE-DURING-POST, 4 min each) with pulsed NIR light delivered to the right forehead. The parameter space included two wavelengths (808 nm, 1064 nm), two pulsation frequencies (10 Hz, 40 Hz), and three irradiances (100, 150, 200 mW/cm2). Forehead skin tone (ITA) and sex were included as biological moderators. EEG band power (delta through gamma) was expressed as percent change from a pre-stimulus baseline. Spatiotemporal cluster-based permutation tests (10,000 permutations, FWER alpha=0.05) identified significant electrode clusters. Linear mixed-effects models with backward elimination and FDR correction (q=0.05) quantified parameter and biological contributions. ResultstPBM produced bilateral, bidirectional EEG changes: frontal gamma enhancement and posterior theta, alpha, and beta suppression, emerging gradually during stimulation and persisting post-stimulation. Wavelength qualitatively shaped the response: 808 nm drove broadband posterior suppression while 1064 nm selectively enhanced frontal gamma. Contrary to entrainment predictions, 10 Hz pulsation produced significantly larger gamma increases and theta reductions than 40 Hz. Sex was the most consistent biological modulator: females showed greater alpha suppression during stimulation and males showed greater posterior beta and gamma suppression. Irradiance and skin tone were not significant. ConclusionsPulsed forehead tPBM produces robust, parameter-dependent EEG changes that are not consistent with neural entrainment. Wavelength determines the character of the cortical response, pulsation frequency modulates its magnitude, potentially through photobiological rather than oscillatory mechanisms, and sex is a significant biological moderator. These findings contribute toward a human-specific foundation for informing optical tPBM parameter selection.

physiology↗

bioRxiv2025

Modulating cerebrospinal fluid dynamics using pulsed photobiomodulation: feasibility, parameter and skin-colour dependence

The use of photobiomodulation (PBM) to enhance brain health, specifically glymphatic drainage and thus neurotoxic waste clearance, may make it a promising therapeutic tool against neurodegenerative diseases such as Alzheimers disease. This study investigates whether PBM can modulate cerebrospinal fluid (CSF) flow in 45 healthy young adults. We conducted forehead transcranial PBM (tPBM) and intranasal PBM (iPBM) at the nostril level, and measured CSF dynamics using blood-oxygenation level-dependent (BOLD) functional MRI (fMRI). Our data demonstrates 4 min of PBM-induced increases in CSF flow. Our data shows that (1) even a short PBM of 4 min can induce a change in CSF dynamics, in the form of an immediate increase in intracranial CSF volume and a reduction in CSF inflow; (2) skin melanin had a significant effect on the CSF response in tPBM, with lighter skin associated with higher responses; (3) both iPBM and tPBM displayed a dose-dependent effect on CSF dynamics in terms of a irradiance-wavelength interaction; (4) intranasal PBM (iPBM) can be used to produce a significant change in CSF dynamics that is equivalent to forehead transcranial PBM (tPBM) with a small fraction of the irradiance. The most likely explanation for the observed fMRI signal changes in CSF regions of interest for both tPBM and iPBM is an increased CSF outflow pressure due to PBM-induced vasodilation that transiently increases intracranial CSF volume and reduces net CSF inflow. This study establishes that PBM can modulate CSF flow in the healthy human brain in real time. This study also suggests that iPBM may be more efficient in CSF modulation due to the proximity to the olfactory system and the lack of melanin dependence. The influence of melanin on tPBM, the feasibility of iPBM and the dose dependence of both will require further investigation in healthy and patient populations.

physiology↗