Biology subjects

Choi, H.

Publications and source records attributed to Choi, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Transcutaneous auricular Vagus nerve stimulation for working memory enhancement: A comparative study of electrical and ultrasound stimulation

ObjectivesTranscutaneous auricular vagus nerve stimulation (taVNS) is a non-invasive neuromodulation technique that has shown potential to enhance cognitive function, including working memory. This study investigated the acute effects of both electrical (E-taVNS) and ultrasound (U-taVNS) modalities on working memory using a 3-back task in healthy young adults. We hypothesized that active taVNS would enhance working memory performance relative to sham, and that both stimulation modalities would engage similar neuromodulatory mechanisms. Materials and MethodsFifty-nine participants underwent a single-blind, sham-controlled, within-subject design study, with working memory performance assessed using a 3-back task before and after stimulation. Primary performance measures included correct rejection rate, error false alarm, and sensitivity (d'). Statistical analyses compared pre- and post-stimulation performance across modalities. ResultsE-taVNS significantly enhanced working memory performance through an increase in correct rejection rate and sensitivity (measured by d), alongside a reduction in error of false alarm. U-taVNS showed a similar directional trend across performance measures, although these effects did not reach statistical significance. Baseline anxiety levels significantly predicted individual responsiveness to taVNS. In terms of tolerability, a higher proportion of participants receiving E-taVNS reported skin irritation compared to those receiving U-taVNS. ConclusionsE-taVNS can acutely enhance working memory performance, while U-taVNS may offer a comparable, better tolerated alternative. Our findings highlight the potential of taVNS to support memory function, while showing the importance of further research to clarify modality-specific effects and optimize stimulation parameters.

neuroscience↗

bioRxiv2026

Comparing Electrical and Ultrasound Transcutaneous Vagus Nerve Stimulation (taVNS) on Associative Memory

Associative memory, the ability to bind and retrieve relationships between unrelated elements, is a cornerstone of human cognition and a primary target for neurorehabilitation. Vagus nerve stimulation (VNS) has emerged as a promising method to modulate the locus coeruleus-norepinephrine (LC-NE) system and hippocampal-prefrontal circuits essential for memory. However, the comparative efficacy of non-invasive modalities such as electrical (E-taVNS) and the emerging field of ultrasound (U-taVNS) remains poorly understood in the context of active recall. In this study, participants performed a crossmodal video-word associative memory task before and after receiving either E-taVNS or U-taVNS in active and sham conditions. We investigated whether these modalities enhance cued recall accuracy and retrieval reaction time. Our results revealed that neither E-taVNS nor U-taVNS significantly improved recall accuracy. However, E-taVNS significantly accelerated response times specifically for correctly recalled items. These findings suggest that while taVNS may not increase the likelihood of recalling associative memories, electrical stimulation may enhances the efficiency in which we do so. These findings suggest that electrical taVNS is a viable tool for facilitating memory search processes, though further research is required to optimize ultrasound parameters and validate mechanistic pathways through physiological monitoring.

neuroscience↗

bioRxiv2026

Getting over ANOVA: Estimation graphics for multi-group comparisons

Data analysis in experimental science mainly relies on null-hypothesis significance testing, despite its well-known limitations. A powerful alternative is estimation statistics, which focuses on effect-size quantification. However, current estimation tools struggle with the complex, multi-group comparisons common in biological research. Here we introduce DABEST 2.0, an estimation framework for complex experimental designs, including shared-control, repeated-measures, two-way factorial experiments, and meta-analysis of replicates.

bioinformatics↗

bioRxiv2026

Generative single-cell transcriptomics via large language models

Single-cell and spatial transcriptomics have generated vast atlases of cellular states, yet these data are almost exclusively used for analysis rather than generation. Here we introduce the LLM-based model PGL, Portraying Gene Language, a framework that reframes single-cell transcriptomes as a language generation modeling problem. PGL represents each cell as a long sequence of gene-expression tokens and uses a large language model to synthesize complete single-cell RNA-seq profiles from metadata alone, such as tissue and disease context. PGL-generated cells recapitulate dataset-specific transcriptomic structure, align with known cancer subtype biology, and mix coherently with real single-cell datasets. Notably, generated cells can be used as effective references for spatial transcriptomics, enabling accurate cell-type mapping without matched single-cell atlases. By shifting single-cell modeling from representation learning to cell generation, PGL enables virtual cohort construction, hypothesis generation, and reference-on-demand analysis, positioning generative language models as foundational tools for in silico single-cell biology.

bioinformatics↗

bioRxiv2026

mRNAbow: A versatile gene expression system for multiplexed fluorescent imaging using optimized in vitro transcribed mRNA

Messenger RNA (mRNA) transfection enables rapid, transient protein expression without nuclear entry, providing a powerful alternative to DNA or viral delivery in post-mitotic and otherwise difficult-to-transfect cells. Although in vitro transcribed (IVT) mRNAs have revolutionized therapeutic applications, their adoption in experimental biology remains limited by challenges in synthesis, variability across cell types, and concerns about cytotoxicity. Here, we define design principles that maximize IVT mRNA performance across diverse cellular and organismal systems. Through systematic comparison of capping strategies and base modifications, including N1-methyl-pseudouridine, 5-methylcytidine, and 5-methoxyuridine, we identify modifications that enhance translation while minimizing activation of cellular stress responses. Optimized transcripts drive robust protein expression within four hours, persist for up to one week, and support multiplexed expression of structurally and functionally distinct proteins in mammalian cells, including cancer cell lines, iPSC-derived systems, primary cells, and organoids, as well as in vivo in zebrafish embryos and in less genetically tractable models such as Danionella cerebrum and sea urchin embryos. To further expand accessibility for community use, we developed mRNAbow, a platform for generating low-toxicity mRNAs encoding organelle-targeted fluorescent proteins and biosensors for multiplex imaging, with corresponding plasmids made publicly available. Together, these advances establish a generalizable framework for IVT mRNA design and expand experimental access to synthetic mRNA technologies for dissecting cellular architecture and dynamics.

cell biology↗

bioRxiv2025

MRMhub: one-stop solution for automated processing of large-scale targeted metabolomics data

Data processing and quality control are essential for complex targeted mass spectrometry (MS) assays in large-scale metabolomics studies. However, existing software solutions have significant gaps in robustness and scalability. We report MRMhub, a one-stop solution for streamlined processing of large-scale targeted MS data. MRMhub consists of a novel peak integration engine with unique algorithmic design to address the scalability challenge and a comprehensive collection of post-acquisition data processing and analytical quality control tools. The ensemble facilitates rapid and consistent processing of complex chromatograms, quantification, drift and batch correction, quality assessment and control, feature filtering, and data/workflow sharing and reporting. MRMhub can process data from highly complex assays in population-scale studies within minutes, with full digital footprints warranting reproducibility and traceability. We demonstrate its performance using two large-scale lipidomics data sets. We distribute the source code and data sets freely for community development.

bioinformatics↗

bioRxiv2025

Smooth muscle LRRC8A knockout reduces superoxide influx, inflammation, senescence and atherosclerosis

BackgroundLeucine Rich Repeat Containing 8A (LRRC8A) anion channels (VRACs) associate with NADPH oxidase 1 (Nox1) and support extracellular superoxide (O2{middle dot}-) production, inflammation, and contractility in vascular smooth muscle cells (VSMCs). We proposed previously that VRACs also support influx of O2{middle dot}- to localize cytoplasmic redox signals. MethodsWe assayed O2{middle dot}- influx, assessed changes in mRNA expression (RNAseq), and tested multiple phenotypes of cultured LRRC8A knockout (KO) VSMCs. Aortic atherosclerotic burden and inflammation, and mesenteric vascular reactivity were compared between wild type (WT) apolipoprotein E null (ApoE-/-) mice and VSMC-specific LRRC8A KO, ApoE-/- mice. ResultsKO cells were less permeable to extracellular O2{middle dot}-, produced less mitochondrial O2{middle dot}-, and experienced less oxidant stress (GSH/GSSG, lipid peroxidation, Nrf2 activity) than WT. RNAseq and reporter assays demonstrated reduced pro-inflammatory (NF-{kappa}B and Hif1) transcription. KO cells also under-expressed multiple senescence markers and had longer telomeres. Inflammation causes a metabolic shift from oxidative phosphorylation (OCR) to glycolysis (ECAR). Both pathways were less active in KO cells, as was expression of glycolytic enzymes. Mitochondrial membrane potential was lower in KO cells, but ADP/ATP and NADP+/NADPH were unaltered, suggesting lower energy demand. Consistent with this, proliferation and migration were both reduced in KO cells. Protein-protein interaction analysis of RNAseq data (PPI Hub) identified Epidermal Growth Factor Receptor (EGFR) signaling. Resting phosphorylation of EGFR (pY1068) and AKT (pS473 and pT308) were all reduced in KO cells, as was and EGF-induced pY1068 and pS308. Following 15 weeks of exposure to a high fat diet (42%) VSMC-specific LRRC8A-/- and 8A+/-, ApoE-/- mice had reduced atherosclerotic lesion area, aortic senescence ({beta}-Gal), inflammation (ICAM, VCAM) and proliferation marker (PCNA) expression compared to WT, ApoE-/- controls. Mesenteric artery vasomotor function was also preserved, and the abundance of MYPT1 and CPI17 was lower in KO vessels. Uptake of oxidized LDL (OxLDL) was significantly reduced in KO VSMCs and impaired by VRAC block in WT cells. ConclusionsLoss of LRRC8A reduced O2{middle dot}- influx, oxidative stress, inflammation and senescence, lowers energy demand, and in the setting of hypercholesterolemia impaired uptake of oxidized LDL and abrogated atherosclerosis. VSMC VRACs may be novel targets of vascular anti-inflammatory therapy. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSO_LIChronically inflamed vascular smooth muscle cells (VSMCs) are critical drivers of atherosclerotic plaque development. C_LIO_LIIn VSMCs, Nox1-derived superoxide drives redox signaling that promotes inflammation, phenotypic switching, and senescence. C_LIO_LILRRC8A family volume-regulated anion channels (VRACs) physically associate with Nox1 and support TNF-induced ROS production, receptor endocytosis, NF-{kappa}B activation, and proliferation. C_LIO_LIHypercholesterolemia causes VSMC inflammation via oxidized LDL (OxLDL) activation of scavenger receptors (e.g., LOX-1, CD36) that stimulate oxidant production and EGFR/PI3K-Akt-NF-{kappa}B signaling. C_LI What New Information Does This Article Contribute?O_LILRRC8A channels support influx of extracellular superoxide which impacts cytosolic redox status, metabolism and Nrf2, HIF-1, and NF-{kappa}B activity. C_LIO_LILoss of LRRC8A reprograms VSMCs into a low-oxidative-stress, low-energy-demand state, characterized by diminished proliferation and migration, attenuated senescence, and preservation of telomere length. C_LIO_LILoss of LRRC8A inhibits EGF-stimulated EGFR and Akt phosphorylation and uncouples oxidant-dependent growth factor signaling from downstream inflammatory and metabolic remodeling. C_LIO_LIVSMC-specific LRRC8A knockout or heterozygosity in hypercholesterolemic ApoE-/- mice reduces aortic inflammation and senescence, reduces atherosclerotic lesion burden, and preserves mesenteric artery vasomotor function. C_LIO_LILRRC8A/VRAC activity is necessary for uptake of oxidized but not native LDL in VSMCs. C_LIO_LILRRC8A is a novel regulator of scavenger receptor-dependent lipoprotein handling and a potential therapeutic target to uncouple oxidant signaling from VSMC lipid overload and inflammation in the vessel wall. C_LI

physiology↗

bioRxiv2025

AKAP1 regulates mitochondrial and synaptic homeostasis to enable neuroprotection and repair in retinal ganglion cell degeneration

Glaucoma is a leading cause of irreversible blindness, characterized by progressive retinal ganglion cell (RGC) loss and optic nerve degeneration. Mitochondrial dysfunction plays a central role in this neurodegeneration, yet effective targeted therapies remain limited. Here, we identify the mitochondrial scaffold A-kinase anchoring protein 1 (AKAP1) as a critical regulator of RGC resilience and axon regeneration. AKAP1 expression is diminished in human glaucomatous retinas and experimental glaucoma models, correlating with elevated intraocular pressure, disrupted mitochondrial dynamics, oxidative stress, and synaptic instability. Restoration of AKAP1 via adeno-associated virus serotype 2-mediated gene therapy preserves RGC survival, promotes mitochondrial fusion and cristae integrity, enhances ATP production, and mitigates oxidative and apoptotic stress in mouse models of glaucoma and optic nerve injury. Transcriptomic profiling of AKAP1 knockout retinas reveals widespread dysregulation of mitochondrial and synaptic gene networks. Mechanistically, AKAP1 stabilizes synapses by promoting mitochondrial biogenesis, modulating calcium/calmodulin-dependent kinase II and synapsin phosphorylation, maintaining synaptophysin expression, and suppressing complement component C1q expression, thereby preventing early synaptic loss in glaucomatous neurodegeneration. Moreover, restoring AKAP1 expression facilitates axonal regeneration, preserves the central visual pathway, and maintains visual function. Collectively, these findings establish AKAP1 as a master regulator of mitochondrial and synaptic homeostasis and axonal regeneration and a promising therapeutic target for vision preservation in glaucomatous neurodegeneration. One Sentence SummaryAKAP1 protects retinal ganglion cells and preserves vision by restoring mitochondrial and synaptic health in experimental glaucoma models.

neuroscience↗

bioRxiv2025

Computational design of cysteine proteases

Despite advances in de novo enzyme design, success has been largely limited to low energy barrier model reactions. Amide bonds such as those linking amino acids along the peptide backbone are stable for hundreds of years in neutral aqueous solution because of the high energy barrier to hydrolysis. Here we describe the de novo design of enzymes which utilize an activated cysteine nucleophile to hydrolyze the polypeptide backbone in a sequence-dependent manner, with a success rate of 13/69=19% and rate enhancements over the background reaction (kcat/kuncat) of up to 3 x 10^7. The designed proteases have folds very different from proteases in nature (TM score < 0.50), and six crystal structures are very close to the design models (Ca RMSDs < 1.2 A), highlighting the capacity for generalization and the accuracy of the design methodology. Experimental and computational analyses suggest that the remaining gap in activity to the most active native cysteine proteases arises from imperfections in active site preorganization and substrate positioning. The designed proteases efficiently cleave their targets in mammalian cells, opening the door to a wide range of synthetic biology applications.

biochemistry↗

bioRxiv2025

Computational design of metalloproteases

Although significant progress has been made in creating de novo metalloenzymes that hydrolyze activated esters, the energetically demanding cleavage of amide bonds has remained a major challenge for enzyme design: amide bonds are significantly more stable than ester bonds, the amine leaving groups in proteins are not activated, and peptide substrates are flexible making them difficult to bind precisely. Here, we report the de novo design of zinc proteases from minimal catalytic motifs using RoseTTAFold Diffusion 2 for Molecular Interfaces, optimized for both enzyme and protein-protein interaction design. Of 135 computational designs experimentally tested, 36% had activity and cleaved precisely at the intended site. The most active design accelerates peptide bond hydrolysis by more than 10^8-fold relative to the uncatalyzed reaction, and by over 10^10-fold following the introduction of four point mutations that enhanced active-site preorganization4. Building on these capabilities, we designed metalloproteases that specifically cleave human TDP-43, the amyloid-{beta} peptide, and serum amyloid A with rate accelerations up to 9.2x10^8-fold over background. We illustrate the potential of our approach for bio-orthogonal control over cell state by generating caged cytokines and caged receptor antagonists that are selectively unmasked by our designed proteases. These results demonstrate that de novo enzyme design has advanced well beyond model reactions with activated substrates and open the door to design of proficient metallohydrolases for a wide range of applications in medicine and bioremediation.

biochemistry↗

bioRxiv2025

Transcutaneous auricular vagus nerve stimulation enhances emotional bias towards happiness in healthy young adults: A comparative study of electrical and ultrasound stimulation

Transcutaneous auricular vagus nerve stimulation (taVNS) is an emerging neuromodulation technique demonstrating promise in emotional regulation. This study investigated the acute effects of both electrical (E-taVNS) and ultrasound (U-taVNS) modalities on emotional bias using a facial emotion categorization task in healthy young adults. Fifty-nine participants underwent a single-blind, sham-controlled, within-subject design, with emotional bias assessed at pre-, during-, and post-stimulation phases. Our findings revealed that both E-taVNS and U-taVNS significantly enhanced emotional bias scores, shifting the perception of neutral and ambiguous faces towards positive interpretations and reducing negative emotional bias. No significant differences in efficacy were observed between the two stimulation modalities. Furthermore, individual differences in interoceptive awareness were found to be associated with the observed taVNS effects. These results suggest that both electrical and ultrasound taVNS can acutely modulate emotional regulation, highlighting the potential of taVNS as a non-invasive, well-tolerated alternative for interventions targeting emotional bias and mood disorders. HighlightsO_LItaVNS reduces negative emotional bias toward ambiguous stimuli. C_LIO_LIBoth electrical and ultrasound taVNS shifted emotional bias toward more positive interpretations of ambiguous facial expressions. C_LIO_LIUltrasound taVNS (U-taVNS) demonstrated comparable efficacy to electrical taVNS (E-taVNS). C_LIO_LIThe subscale of the Multidimensional Assessment of Interoceptive Awareness predicted individual variability in taVNS-induced emotional bias change. C_LI

neuroscience↗

bioRxiv2025

Telomere-to-Telomere Accurate and Gapless Korean Standard Reference Genome

We present KOREF1-G-TTAGGA, the first Telomere-to-Telomere Accurate and Gapless Genome Assembly, standing as the Korean standard reference genome. The paternal and maternal haplotypes spanned 2.91 and 3.03 Gb. Genome-wide, at least 99.15% of assembled sequences were reliably haplotype-resolved, and over 95% remained accurate even in the most error-prone loci, including centromeric satellite arrays and segmental duplications. Rare-k-mer copy-number concordance within satellite arrays held up 98.9% and 98.8% per haplotype. Bionano optical maps fully spanned all canonical rDNA arrays on the five acrocentric chromosomes. The assembly quality index (AQI) of 99.77 and 99.69 exceeded the reference-quality threshold of 90, and more than 99.99% of gene and cCRE sequence was free of structural error. Both haplotypes further showed high base-level accuracy, with consensus quality value (QV) of 81.19 and 79.03, corresponding to one error per 131 and 80 Mb. KOREF1-G-TTAGGA is among the highest-quality East Asian telomere-to-telomere assemblies. It moreover anchors a decade-spanning multi-ome reference dataset for defining individual molecular states. Together, these resources define the personal referenceome as a foundation for individual biology and precision medicine, with the assemblies, annotations, and all multi-omic data openly available at https://koreanreference.org.

genomics↗

bioRxiv2025

Risk reshapes amygdala representation of choice

Modifying behavior in response to changing environmental conditions is a crucial adaptive function. This capacity is exemplified when animals curtail pursuit of a valued outcome that risks being punished by aversive consequences, but the mediating brain mechanisms remain poorly understood. Here, using in vivo cellular-resolution calcium (Ca2+) imaging, optogenetics and chemogenetics, we show that risk of punishment dramatically alters animals choice between a large/risky and small- /safe reward and produces novel, causally necessary, patterns of activity in basolateral amygdala (BLA) neurons. We find that experience of a punished outcome generates a BLA representation that is selectively replayed when animals subsequently abort choice of the large/risky reward option. Additionally, we show that risk leads to the incorporation of newly encoding BLA neurons into the pre-choice representation, which predicts shifting away from the large/risky option. These findings reveal how dynamic reshaping of BLA representations underpins behavioral flexibility in the face of risk.

neuroscience↗

bioRxiv2025

Unfolded protein response signaling promotes myeloid cell production and cooperates with oncogenic mutation

Unfolded protein response (UPR) promotes protein homeostasis under endoplasmic reticulum stress. UPR signaling has numerous functions in metabolism, cancer, immunology, and neurodegenerative diseases. Recent studies also showed that UPR signaling has important roles in hematopoietic stem and progenitor cell biology. However, whether UPR signaling regulates hematopoietic lineage fate decision remains elusive. Here, we found that Fc{gamma}R- MPP3 generates erythroid lineage and Jak2V617F mutation leads to overproduction of erythroid cells by expanding Fc{gamma}R- MPP3. We showed that UPR signaling increases myeloid cell production through promoting Fc{gamma}R- MPP3 transition to granulocyte/macrophage progenitor producing Fc{gamma}R+ MPP3 at the expense of erythroid lineage via the XBP1 pathway. Under a disease condition, UPR signaling cooperates with Jak2V617F mutation and exacerbates disease phenotype in a mouse model of polycythemia vera (PV) through the ATF4 pathway. Activation of UPR signaling also increased myeloid output in healthy donor bone marrow MPP cells while skewing the output towards erythroid lineage in PV patient bone marrow MPP cells. Together, our results identify a novel function of UPR signaling in hematopoietic lineage specification and provide critical insights into targeting UPR signaling in hematological malignancies. Key pointsO_LIUPR signaling promotes myeloid cell production at the expense of erythroid lineage in steady state. C_LIO_LIUPR signaling collaborates with Jak2V617F mutation and increases red blood cell production. C_LI

cell biology↗

bioRxiv2025

Targeted degradation of pathogenic TDP-43 proteins in amyotrophic lateral sclerosis using the AUTOTAC platform

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive loss of motor neurons and the cytoplasmic aggregation of misfolded proteins in the spinal cord, including TAR DNA-binding protein-43 (TDP-43). More than 97% of ALS cases exhibit pathological TDP-43 inclusions, yet therapeutic strategies that can selectively eliminate these aggregates remain yet to be developed. Here, we employed the AUTOTAC (Autophagy-Targeting Chimera) to degrade TDP-43 aggregates via macroautophagy mediated by the N-recognin p62/SQSTM1 of the N-degron pathway. The AUTOTAC degraders ATC141 and ATC142 were designed to bind and link the oligomeric species of misfolded TDP-43 to p62, which induces the targeting of TDP-43 cargoes to phagophores for lysosomal co-degradation, while sparing monomeric TDP-43. ATC142 induced the degradation of pathological TDP-43 A315T species and its cleaved variant, TDP-25, with DC50 values of 1.25-9.6 nM. In ALS model mice expressing TDP-43 A315T in the spinal cord, oral administration of 10 mg/kg ATC141 with 24 doses reduced TDP-43 aggregates as well as GFAP+ astrocytes and Iba1+ microglia. ATC141 also exerted disease-modifying efficacy to reverse the disease progression in neuromuscular coordination and cognitive function. This oral drug is under Phase 1 clinical trials in South Korea with 76 healthy volunteers aiming to treat ALS, Alzheimers diseases (AD), and progressive supranuclear palsy (PSP). We suggest that AUTOTAC provides a novel strategy to treat a broad range of neurodegenerative diseases. TeaserAUTOTAC degraders induce lysosomal degradation of pathogenic TDP-43 aggregates in a mouse model of amyotrophic lateral sclerosis.

neuroscience↗

bioRxiv2025

Non-canonical Sodium Channel Isoforms Underlie Chamber Specific Cardiac Excitability

Voltage-gated sodium (NaV) channels drive cardiac excitability. While NaV1.5 is the primary cardiac isoform, the composition and functional contributions of non-NaV1.5 isoforms in the heart remain unclear. Here, we developed a chemical-genetic mouse model (NaV1.5-GX) in which NaV1.5 can be selectively and reversibly inhibited by acyl- and aryl-sulfonamide compounds (GX drugs). NaV1.5-GX mice exhibited normal cardiac function at baseline, but acute GX drug administration caused profound conduction defects and arrhythmias. Whole-heart optical mapping revealed dose-dependent chamber-specific sensitivity to NaV1.5 inhibition, with the right ventricle (RV) being the most sensitive, followed by the left ventricle (LV), left atrium (LA), and right atrium (RA). Patch-clamp recordings of isolated cardiomyocytes with application of NaV isoform-selective inhibitors showed that NaV1.5 contributed 93% of sodium current in the LV, 81% in the RV and 78% in the LA. Non-NaV1.5 isoforms were differentially enriched across chambers: NaV1.8 in the LV, NaV1.1/1.3 in the RV, and NaV1.2/1.6/1.7 in the atria. These results reveal a surprising chamber-specific isoform landscape of cardiac sodium currents which may underlie the right ventricular predominant phenotype of Brugada syndrome and highlight non-NaV1.5 isoforms as potential mediators of chamber-specific cardiac pathologies and as pharmacological targets.

physiology↗

bioRxiv2025

Structural basis for the function of long noncoding RNA Pnky in neural stem cells

LncRNA Pnky is a trans-acting regulator of neural stem cell (NSC) differentiation, but the molecular mechanisms by which Pnky regulates neurogenesis is unknown. A fundamental step towards mechanistic understanding is to determine whether a lncRNA has folded structure that underlies biological function. Using chemical probing and high-throughput analysis, we determined the secondary structure of Pnky folded in vitro and in cellulo. Pnky adopts a compact structure in vitro with distinct modules and evidence of tertiary interactions. In cellulo, Pnky structure is remarkably similar to the in vitro conformation. We used locked nucleic acid oligonucleotides to interrogate the entire Pnky transcript for function in NSCs and identified regions that when targeted increased neurogenesis - phenocopying Pnky knockdown - without decreasing transcript abundance. Our findings provide a structural basis for the role of Pnky in neurogenesis and, more broadly, illustrate how structural maps combined with phenotypic data can advance fundamental understanding of lncRNA mechanism. HIGHLIGHTSPnky folds into highly structured conformation in vitro with distinct modules. Pnky is a compact lncRNA with evidence of tertiary interactions. Pnky structure in neural stem cells is similar to its in vitro conformation. LNA ASO perturbations identify structured regions of Pnky involved in neuronal differentiation.

molecular biology↗

bioRxiv2025

The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

Nerves are an integral component of the tumor microenvironment, contributing to cancer progression, metastasis, morbidity, and mortality. In pancreatic ductal adenocarcinoma (PDAC), worse clinical outcomes are associated with perineural invasion (PNI), a process by which cancer cells surround and invade nerves. Here, we employed whole-transcriptome and single-cell spatial transcriptomics to identify candidate tumor-nerve interactions that promote PNI. We discovered that Pdgfd signaling promotes key features of nerve invasion. Mechanistically, Pdgfd stimulated cancer cell invasiveness, neurite outgrowth, and direct physical engagement with glia. Pharmacological blockade of this axis reduced each of these processes in vitro as well as PNI in vivo. Thus, Pdgfd-Pdgfrb signaling mediates PNI by coordinating multifaceted cancer-neuron-glia interactions and represents a promising therapeutic strategy aimed at disrupting harmful cancer-nerve crosstalk.

cancer biology↗