Biology subjects

Park, A.

Publications and source records attributed to Park, A..

At least 19 recordsLinked to original sources

bioRxiv2026

RAPPL-Seq Enables Rapid, High-Sensitivity Ribosome Profiling of Scarce Samples

Ribosome profiling is a powerful method for transcriptome-wide monitoring of translation activity in vivo, but its use is limited by lengthy protocols, reliance on specialized equipment and inefficient recovery of ribosome-protected fragments (RPFs). To overcome these challenges, we developed RAPPL-Seq, a magnetic bead-based affinity capture method that enables fast and efficient RPF isolation. RAPPL-Seq achieves high recovery efficiency, short processing time, and robust performance with limited input material. It is broadly applicable across multiple sample types, including cell lines, primary tissues, and human biospecimens. RAPPL-Seq can also be paired with translation inhibitors to characterize inhibitor- and tissue-specific mRNA translation. RAPPL-Seq efficiently captured translatomes of glioblastoma (GBM) and adjacent non-tumor brain tissues from patient biopsies. Together, these findings establish RAPPL-Seq as a straightforward, easily accessible, and highly sensitive approach that extends translatome studies to scarce experimental and clinical samples, opening new avenues for mechanistic insight and therapeutic discovery.

molecular biology↗

bioRxiv2026

Hunger reconfigures a reward learning circuit into a memory competent mode

Internal states such as hunger dynamically reshape activity across circuits to support resource seeking. Neuromodulation provides a means of controlling such physiological properties of neurons, but how this flexibility regulates memory networks remains unclear. Here, we describe how hunger reconfigures a dopaminergic food-reward circuit between two physiological modes that support memory formation, in Drosophila. Starvation suppresses baseline dopaminergic activity through peptidergic signalling, enabling reward-evoked, large-amplitude dopamine neuron spikes to reinforce learning. This spiking mode can be engaged by sugar consumption and persists beyond feeding, reflecting the fly's satiety state. Persistent dopaminergic large-amplitude spiking reinforces learning and transitions the memory network into a mode that prioritizes consolidation of recently acquired memories. The transition from hunger to satiation is also reflected in the activity of postsynaptic output neurons that shift from a tonic, decorrelated mode that is responsive to dopamine into a bursting, correlated mode in which further dopaminergic modulation is occluded. Therefore, nutrient deprivation reconfigures the memory circuit into a learning competent dopamine-receptive mode, which persistent reinforcing dopamine then switches into a satiated mode driving memory consolidation. Together these processes mechanistically intertwine state-dependent reward-signalling with subsequent memory stabilization through transitions in physiological mode.

neuroscience↗

bioRxiv2026

Focal radiotherapy improves CAR T cell therapy targeting prostate cancer

Chimeric antigen receptor (CAR) T cell therapy has limited efficacy against solid tumors such as prostate cancer due to the immunosuppressive tumor microenvironment (TME). Combining CAR T cells with existing therapies that remodel the TME and promote endogenous immune responses, such as radiation therapy and chemotherapies, may strengthen antitumor responses. Here, we assessed the potency of combining focal radiotherapy (RT), cyclophosphamide (Cy) preconditioning, and prostate stem cell antigen (PSCA)-CAR T cells against syngeneic prostate cancer models. Focal RT alone increased T cell and dendritic cell infiltration and activation in the irradiated tumor. Furthermore, the combination of all three therapies was critical for enhanced antitumor responses and survival across multiple subcutaneous, bone-metastatic, and multifocal disease models. This combination, in the irradiated TME and tumor-draining lymph nodes (tdLN), led to greater antigen presentation by myeloid cells and endogenous T cell activation and cytotoxicity. Our study demonstrates the potency of combining focal RT with PSCA-CAR T cells, significantly improving therapeutic responses in the irradiated tumor and contributing to a more robust systemic immune response against metastatic burden in prostate cancer.

Cancer Biology↗

bioRxiv2026

Generative design of intrinsically disordered protein regions with IDiom

Intrinsically disordered protein regions are ubiquitous across all kingdoms of life. These structurally heterogeneous regions play central roles in cellular processes such as transcriptional regulation, cellular signaling, and subcellular organization, yet they have remained largely inaccessible to rational design. Structure-based generative methods are not applicable to proteins that lack a stable fold, and existing sequence-based approaches for disordered regions rely on sampling methods that do not capture the evolutionary statistics of natural disordered regions. Here, we introduce IDiom, an autoregressive protein language model trained on 37 million intrinsically disordered region sequences curated from the AlphaFold Database. Trained using a fill-in-the-middle data augmentation, IDiom generates disordered region sequences conditioned on their surrounding structured context, as well as fully disordered proteins without any context. The model generates diverse sequences that recapitulate biologically relevant sequence features of natural disordered regions, and we demonstrate that post-training via reinforcement learning with a subcellular localization reward model produces sequences with features which are consistent with known sequence determinants of compartment-specific localization. These results establish IDiom as a general platform for the generative design of intrinsically disordered proteins and regions.

bioinformatics↗

bioRxiv2026

GBA1 deficiency differentially affects endolysosomal trafficking in neurons versus astrocytes

Mutations in the gene glucosidase, beta acid 1 (GBA1) are the strongest genetic risk factor for Parkinsons disease (PD) and are associated with faster disease progression. GBA1 is expressed in all cell types of the central nervous system, with some evidence supporting higher expression in glial cells than neurons. To elucidate possible specific functions in neurons versus glia, we differentiated human induced pluripotent stem cells (iPSCs) generated from an individual with PD heterozygous for the GBA1 pathogenic null variant IVS2+1 (GBA1IVS/+), homozygous GBA1 IVS2+1 isogenic to GBA1IVS/+ (GBA1IVS/IVS) and a healthy unaffected age-and sex-matched individual (GBA1+/+). GBA1 expression was reduced in GBA1IVS/+ and GBA1IVS/IVS neurons and astrocytes. Endolysosomal trafficking was significantly altered in GBA1-deficient neurons with enlarged early and recycling endosome and lysosome compartments in neurons but not in astrocytes. High molecular weight oligomerization of -synuclein and phosphorylated Ser129 -synuclein were present in GBA1IVS/+ and GBA1IVS/IVS neurons but not in GBA1+/+ neurons, or in GBA1-deficient or GBA1+/+ astrocytes. Transcriptomic analysis of GBA1-deficient neurons and astrocytes revealed cell-type specific profiles. GBA1 deficiency in neurons downregulated immune response and upregulated cholesterol synthesis pathways, while GBA1 deficiency in astrocytes downregulated genes associated with translation and upregulated genes involved in extracellular matrix biogenesis. Transcriptomic analysis also suggests that GBA1 deficiency induces neurotoxic reactivity in astrocytes. Together, these findings indicate that GBA1 deficiency has cell type-specific effects, with increased neuronal vulnerability to endolysosomal trafficking leading to -synucleinopathy while GBA1 deficiency in astrocytes leads to increased neurotoxic reactivity independent of endolysosomal trafficking and -synucleinopathy. HighlightsO_LIiPSC-derived neurons and astrocytes modeled GBA1 deficiency C_LIO_LIEndolysosomal trafficking defects occurred only in GBA1-deficient neurons C_LIO_LI-synuclein oligomers accumulated in GBA1-deficient neurons, not astrocytes C_LIO_LIAstrocyte GBA1 loss drove neurotoxic reactive gene signatures C_LIO_LIGBA1 deficiency causes cell-type specific pathology C_LI

neuroscience↗

bioRxiv2026

Reactive Astrocytes Drive Extracellular Acidification to Mediate α-Synuclein Neurodegeneration

Astrocytes are increasingly recognized as key players in neurodegeneration1-3, yet the molecular mechanisms by which they drive disease remain elusive. Here, we uncover a fundamental pathway in which reactive astrocytes fuel neurodegeneration in -synucleinopathies--including Dementia with Lewy bodies and Parkinsons disease dementia--by acidifying the brains extracellular environment. We demonstrate that both human patient tissue and a gut-to-brain -synuclein mouse model exhibit accumulation of reactive astrocytes and extracellular acidosis. Mechanistically, we show that astrocytic lysosomal exocytosis releases acidic contents, driving a drop in pH that activates neuronal acid-sensing ion channel 1a (ASIC1a), resulting in neuronal loss and behavioral decline. Blocking this pathway--either by inhibiting astrocytic lysosomal exocytosis or genetically or pharmacologically targeting neuronal ASIC1a--mitigates pathology and rescues neurodegenerative phenotypes in vivo. These findings provide a conceptual advance by establishing a mechanistic link between glial inflammation, acid-base homeostasis, and neuronal vulnerability, and suggest that targeting astrocyte-driven acidification or ASIC1a signaling could offer new avenues for disease modification in -synucleinopathies.

neuroscience↗

bioRxiv2025

Cornichon Homolog-3 (Cnih3) deletion impairs spatial memory, reward-cue association, and fentanyl self-administration behavior.

Opioid misuse remains rampant as new synthetic opioids reach the market. Large-scale genetic tools like the GWAS identify previously unrecognized targets and biomarkers in opioid misuse with hopes of combating the opioid epidemic. One such target is the AMPAR auxiliary protein Cornichon Homolog-3 (human analog: CNIH3, mouse analog: Cnih3), which determines AMPAR subunit composition and kinetics. Though CNIH3 was identified as a gene of interest in OUD, its role in opioid use and accompanying risk factors has not been studied. Using mice with Cnih3 deletion, we assess the role of CNIH3 in risk factors for opioid use, cognition, and opioid use itself. We find that Cnih3 deletion moderately impairs spatial memory, reward-cue association, and reversal learning. Cnih3 deletion also impairs fentanyl-cue association and blunts fentanyl intake during IVSA. We use principal component analysis to pinpoint the dimensions in which Cnih3 deletion impacts behavior in an unbiased manner. Additionally, we identify in previously published human data that single-nucleotide polymorphisms are more protective against progression to daily opioid use in women than in men, suggesting a potential sex-specific role of CNIH3. These findings highlight an important role of CNIH3 in opioid use through learning and memory processes that may differ between males and females.

neuroscience↗

bioRxiv2025

Microbial stem cells support productivity in dedicated factory cells in an asymmetrically dividing E. coli system

A major challenge for many bio-manufacturing operations is that cells are burdened by the high fitness cost of product synthesis, limiting their growth and productivity. A potential solution is to decouple cell reproduction from product synthesis by dividing these conflicting tasks between two differentiated cell types. This work describes the use of an asymmetrically inherited protein cue to differentiate an E. coli culture into reproductive stem cells and fully dedicated factory cells. Cell differentiation is based on the ability to accumulate two factors: a variant of phage-derived T7 RNA polymerase (T7RNAP) and GP2, a peptide that inhibits native host cell RNA polymerase. Activating these two factors in factory cells inhibited growth and focused them on T7RNAP-driven product synthesis. Preventing their accumulation in stem cells allowed this cell type to grow and divide asymmetrically, generating new factory cells in the process. These differentiating cell cultures generated over eight-fold higher target protein titers compared to factory cell-only controls. Because they include a mechanism for preventing leaky T7RNAP-driven gene expression in stem cells and pre-induction cultures, it was possible to generate strains with multiple plasmid-based copies of a cytotoxic target gene, whereas leaky expression made the same plasmid inviable in conventional protein expression strains. This versatile genetic system could be useful for generating higher product titers, particularly in cases where product synthesis causes cytotoxicity.

synthetic biology↗

bioRxiv2025

Comparative single-cell multiomic analysis reveals evolutionarily conserved and species-specific cellular mechanisms mediating natural retinal aging.

Biological age is a major risk factor in the development of common degenerative retinal diseases such as age-related macular degeneration and glaucoma. To systematically characterize molecular mechanisms underlying retinal aging, we performed integrated single- cell RNA- and ATAC-Seq analyses of the retina and retinal pigment epithelium (RPE) across the natural lifespan in zebrafish, mice, and humans. By profiling gene expression and chromatin accessibility, we identified extensive cell type- and species-specific aging-dependent changes, with a much smaller number of broadly expressed and conserved genes that include regulators of inflammation and autophagy. We constructed predictive aging clocks for retinal cell types and observed dynamic, reversible shifts in cellular age following acute injury. Spatial transcriptomic analysis revealed region-specific aging signatures and proximity effects, with Muller glia exhibiting pro-rejuvenating influences on neighboring neurons. Targeted Muller glia-specific induction of Yamanaka factors reduced molecular age in rod photoreceptors and bipolar cells without altering glial age. Our findings define conserved and divergent regulatory and signaling pathways mediating retinal aging, highlighting Muller glia as potential therapeutic targets for combating age-associated retinal dystrophies.

neuroscience↗

bioRxiv2025

Single virus lipid mixing study of Sendai virus provides insight into fusion mechanism

Single virus studies have proven useful to interrogate the entry mechanism for several viral families. Here, we employ a fluorescence microscopy-based single virus assay to study the fusion (lipid mixing) of Sendai virus to model membranes, the first for any paramyxovirus to our knowledge. We find that fusion wait times following binding are exponentially distributed, suggesting a single rate-limiting step. Compared to previously studied viruses, fusion is relatively slow (tens of minutes) and inefficient (only a small fraction of virions undergo fusion). Trypsin treatment of the virus or different viral receptors in the target alter the efficiency, although the wait time distribution remains unchanged in both cases. This provides constraints on the fusion mechanism and the identity of the rate-limiting step. Together, our data paints a picture of Sendai virus as a comparatively inefficient and slow fusion "machine" and sets the stage for investigation of other paramyxoviruses.

biophysics↗

bioRxiv2025

Solid tumor CAR T cells engineered with fusion proteins targeting PDL1 for localized IL-12 delivery

CAR T cell efficacy in solid tumors is limited due in part to the immunosuppressive TME. To improve anti-tumor responses, we hypothesized that enabling CAR T cells to secrete bifunctional fusion proteins consisting of a cytokine modifier (e.g., TGF{beta}trap, IL15, or IL12) combined with an immune checkpoint inhibitor (e.g., PDL1) will provide tumor localized immunomodulation to improve CAR T cell functionality. To that end, we engineered CAR T cells to secrete TGF{beta}trap, IL15, or IL12 molecules fused to PDL1 scFv, and assessed in vitro functionality and in vivo safety and efficacy in prostate and ovarian cancer models. CAR T cells engineered with PDL1-IL12 were superior in safety and efficacy compared to CAR T cells alone and to those engineered with PDL1 fused with TGF{beta}trap or IL15. Further, PDL1-IL12 engineered CAR T cells improved T cell trafficking and tumor infiltration, localized IFN{gamma} production, TME modulation, and anti-tumor responses, with reduced systemic inflammation-associated toxicities. We believe our PDL1-IL12 engineering strategy presents an opportunity to improve CAR T cell clinical efficacy and safety across multiple solid tumor types.

bioengineering↗

bioRxiv2025

Color-neutral and reversible tissue transparency enables longitudinal deep-tissue imaging in live mice

Light scattering in biological tissue presents a significant challenge for deep in vivo imaging. Our previous work demonstrated the ability to achieve optical transparency in live mice using intensely absorbing dye molecules, which created transparency in the red spectrum while blocking shorter-wavelength photons. In this paper, we extend this capability to achieve optical transparency across the entire visible spectrum by employing molecules with strong absorption in the ultraviolet spectrum and sharp absorption edges that rapidly decline upon entering the visible spectrum. This new color-neutral and reversible tissue transparency method enables optical transparency for imaging commonly used fluorophores in the green and yellow spectra. Notably, this approach facilitates tissue transparency for structural and functional imaging of the live mouse brain labeled with yellow fluorescent protein and GCaMP through the scalp and skull. We show that this method enables longitudinal imaging of the same brain regions in awake mice over multiple days during development. Histological analyses of the skin and systemic toxicology studies indicate minimal acute or chronic damage to the skin or body using this approach. This color-neutral and reversible tissue transparency technique opens new opportunities for noninvasive deep-tissue optical imaging, enabling long-term visualization of cellular structures and dynamic activity with high spatiotemporal resolution and chronic tracking capabilities. Significance StatementTissue scattering represents a major barrier to deep tissue imaging in vivo. We recently showed that tissue can be rendered transparent in the red spectrum using intensely absorbing dye molecules. Here, we introduce a new, color-neutral and reversible tissue transparency approach. We demonstrate longitudinal structural and functional imaging in the deep tissue of awake mice.

bioengineering↗

bioRxiv2025

Seq-Scope-eXpanded: Spatial Omics Beyond Optical Resolution

Sequencing-based spatial transcriptomics (sST) enables transcriptome-wide gene expression mapping but falls short of reaching the optical resolution (200-300 nm) of imaging-based methods. Here, we present Seq-Scope-X (Seq-Scope-eXpanded), which empowers submicrometer-resolution Seq-Scope with tissue expansion to surpass this limitation. By physically enlarging tissues, Seq-Scope-X minimizes transcript diffusion effects and increases spatial feature density by an additional order of magnitude. In liver tissue, this approach resolves nuclear and cytoplasmic compartments in nearly every single cell, uncovering widespread differences between nuclear and cytoplasmic transcriptome patterns. Independently confirmed by imaging-based methods, these results suggest that individual hepatocytes can dynamically switch their metabolic roles. Seq-Scope-X is also applicable to non-hepatic tissues such as brain and colon, and can be modified to perform spatial proteomic analysis, simultaneously profiling hundreds of barcode-tagged antibody stains at microscopic resolutions in mouse spleens and human tonsils. These findings establish Seq-Scope-X as a transformative tool for ultra-high-resolution whole-transcriptome and proteome profiling, offering unparalleled spatial precision and advancing our understanding of cellular architecture, function, and disease mechanisms.

genomics↗

bioRxiv2024

Nitrogen response and growth trajectory of sorghum CRISPR-Cas9 mutants using high-throughput phenotyping

Inorganic nitrogen (N) fertilizer has emerged as one of the key factors driving increased crop yields in the past several decades; however, the overuse of chemical N fertilizer has led to severe ecological and environmental burdens. Understanding how crops respond to N fertilizer has become a central topic in plant science and plant genetics, with the ultimate goal of enhancing N use efficiency (NUE) in crop production. As one of the most essential macronutrients, N significantly influences crop performance across different developmental stages of plant, phenotypic traits result from the accumulative effects of genetic factors, prevailing environmental conditions (specifically N availability), and their complex interactions. To characterize the targeting N-responsiveness and growth trajectory, we employed CRISPR-Cas9 technique to generate sorghum mutants using CRISPR technology. Using a LemnaTec plant imaging system, we obtained time series imagery data from 29 to 130 days after sowing (DAS) for these CRISPR-edited mutants under high N and low N greenhouse conditions. After imagery data analysis, we extracted a number of morphological and greenness index traits as a proxy of plant growth and N responses. Subsequently, we employed two different methods to model the temporal N-responsive traits, allowing us to estimate seven key parameters from the growth curve. Our findings revealed that the wildtype and the edited sorghum lines exhibited differences in N responses for several of the key growth-related parameters. The high-throughput N phenotyping pipeline paves the way for a better understanding of the N responses of edited lines in a dynamic manner and sheds light on further improvements in crop NUE.

plant biology↗

bioRxiv2024

Turncoat antibodies unmasked in a model of autoimmune demyelination: from biology to therapy

Autoantibodies contribute to many autoimmune diseases, yet there is no approved therapy to neutralize them selectively. A popular mouse model, experimental autoimmune encephalomyelitis (EAE), could serve to develop such a therapy, provided we can better understand the nature and importance of the autoantibodies involved. Here we report the discovery of autoantibody-secreting extrafollicular plasmablasts in EAE induced with specific myelin oligodendrocyte glycoprotein (MOG) antigens. Single-cell RNA sequencing reveals that these cells produce non-affinity-matured IgG antibodies. These include pathogenic antibodies competing for shared binding space on MOGs extracellular domain. Interestingly, the synthetic anti-MOG antibody 8-18C5 can prevent the binding of pathogenic antibodies from either EAE mice or people with MOG antibody disease (MOGAD). Moreover, an 8-18C5 variant carrying the NNAS mutation, which inactivates its effector functions, can reduce EAE severity and promote functional recovery. In brief, this study provides not only a comprehensive characterization of the humoral response in EAE models, but also a proof of concept for a novel therapy to antagonize pathogenic anti-MOG antibodies.

immunology↗

bioRxiv2024

Proximity to Explosive Synchronization Determines Network Collapse and Recovery Trajectories in Neural and Economic Crises

When complex systems move away from criticality--a balance between order and chaos--they are no longer optimized. Furthermore, when criticality is lost too quickly, or recovery is delayed, system damage can result. However, the mechanism for these abnormally fast or slow critical transitions remains unknown. Here, we show that the proximity of a complex network to explosive synchronization (ES), a first-order phase transition, determines the trajectories of criticality loss and recovery after perturbations. Our computational models revealed characteristic dynamics based on network proximity to ES, enabling us to infer network phase transition types from empirical data and predict criticality transition patterns. We validated our predictions using empirical data from the human brain under anesthesia and the stock market during an economic crisis, demonstrating that early and prolonged recoveries can be systematically predicted. This study has implications for designing resilient networks that withstand perturbations and recover quickly.

systems biology↗

bioRxiv2024

The Hurst exponent as a marker of inhibition in the developing brain

The maturation of inhibitory neurons is crucial for regulating plasticity in developing brains. Previous work using computational models has suggested that the Hurst exponent, the decay in power over frequency, reflects inhibition, but empirical data supporting this link is sparse. Here, we took a cross-species approach to validating the Hurst exponent of fMRI as a marker of inhibition, then characterized the development of the Hurst exponent in childhood. We found significant spatial correlations between the Hurst exponent and ex vivo parvalbumin mRNA expression in human children and adults, and between the Hurst exponent and parvalbumin-positive cell counts in mice. We identified a plateau in the mRNA expression by late childhood, aligning with the Hurst exponent plateau in both humans and rats. In sum, this work suggests that the Hurst exponent can be used to study the development of inhibition in vivo, and in the future, to understand individual differences in plasticity.

neuroscience↗

bioRxiv2024

Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline

SummaryThe price, quality and throughout of DNA sequencing continue to improve. Algorithmic innovations have allowed inference of a growing range of features from DNA sequencing data, quantifying nuclear, mitochondrial and evolutionary aspects of both germline and somatic genomes. To automate analyses of the full range of genomic characteristics, we created an extensible Nextflow meta-pipeline called metapipeline-DNA. Metapipeline-DNA analyzes targeted and whole-genome sequencing data from raw reads through pre-processing, feature detection by multiple algorithms, quality-control and data- visualization. Each step can be run independently and is supported robust software engineering including automated failure-recovery, robust testing and consistent verifications of inputs, outputs and parameters. Metapipeline-DNA is cloud-compatible and highly configurable, with options to subset and optimize each analysis. Metapipeline-DNA facilitates high-scale, comprehensive analysis of DNA sequencing data. AvailabilityMetapipeline-DNA is an open-source Nextflow pipeline under the GPLv2 license and is available at https://github.com/uclahs-cds/metapipeline-DNA.

bioinformatics↗