bioRxiv : the preprint server for biology最新文献

{"title":"Glutamate indicators with increased sensitivity and tailored deactivation rates.","authors":"Abhi Aggarwal, Adrian Negrean, Yang Chen, Rishyashring Iyer, Daniel Reep, Anyi Liu, Anirudh Palutla, Michael E Xie, Bryan J MacLennan, Kenta M Hagihara, Lucas W Kinsey, Julianna L Sun, Pantong Yao, Jihong Zheng, Arthur Tsang, Getahun Tsegaye, Yonghai Zhang, Ronak H Patel, Benjamin J Arthur, Julien Hiblot, Philipp Leippe, Miroslaw Tarnawski, Jonathan S Marvin, Jason D Vevea, Srinivas C Turaga, Alison G Tebo, Matteo Carandini, L Federico Rossi, David Kleinfeld, Arthur Konnerth, Karel Svoboda, Glenn C Turner, Jeremy Hasseman, Kaspar Podgorski","doi":"10.1101/2025.03.20.643984","DOIUrl":"https://doi.org/10.1101/2025.03.20.643984","url":null,"abstract":"<p><p>Identifying the input-output operations of neurons requires measurements of synaptic transmission simultaneously at many of a neuron's thousands of inputs in the intact brain. To facilitate this goal, we engineered and screened 3365 variants of the fluorescent protein glutamate indicator iGluSnFR3 in neuron culture, and selected variants in the mouse visual cortex. Two variants have high sensitivity, fast activation (< 2 ms) and deactivation times tailored for recording large populations of synapses (iGluSnFR4s, 153 ms) or rapid dynamics (iGluSnFR4f, 26 ms). By imaging action-potential evoked signals on axons and visually-evoked signals on dendritic spines, we show that iGluSnFR4s/4f primarily detect local synaptic glutamate with single-vesicle sensitivity. The indicators detect a wide range of naturalistic synaptic transmission, including in the vibrissal cortex layer 4 and in hippocampal CA1 dendrites. iGluSnFR4 increases the sensitivity and scale (4s) or speed (4f) of tracking information flow in neural networks <i>in vivo</i> .</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974752/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomics and reproductive biology of <i>Leptopilina malgretoutensis</i> Buffington, Lue, Davis & Tracey sp. nov. (Hymenoptera: Figitidae): An asexual parasitoid of Caribbean <i>Drosophila</i>.","authors":"Amelia Ri Lindsey, Chia-Hua Lue, Jeremy S Davis, Lydia J Borjon, Stephanie E Mauthner, Laura C Fricke, Lauren Eads, Molly Murphy, Melissa K Drown, Christopher Faulk, Matthew L Buffington, W Daniel Tracey","doi":"10.1101/2025.03.28.645512","DOIUrl":"https://doi.org/10.1101/2025.03.28.645512","url":null,"abstract":"<p><p><i>Drosophila</i> and parasitic wasps in the genus <i>Leptopilina</i> have long been a model for understanding host-parasite interactions. Indeed, parasitic wasps are important drivers of ecological and evolutionary processes broadly, but we are generally lacking information about the diversity, natural history, and evolution of these relationships. We collected insects from the Caribbean Island of Saint Lucia, home to the eastern Caribbean ' <i>dunni</i> ' subgroup of <i>Drosophila</i> : a clade long appreciated for its recent patterns of speciation and adaptation. Here we present an integrative approach that incorporates natural history, taxonomy, physiology, and genomics to describe <i>Leptopilina malgretoutensis</i> Buffington, Lue, Davis & Tracey sp. nov. (Hymenoptera: Figitidae), a virulent parasitoid of <i>dunni</i> group flies, especially <i>Drosophila antillea. Leptopilina malgretoutensis</i> is nested within an early-branching clade of <i>Leptopilina</i> , offering insights into the evolution of this important genus of <i>Drosophila</i> parasitoids. We present a high-quality assembly for this wasp's 1Gbp genome, and for its bacterial endosymbiont: <i>Wolbachia</i> strain \" <i>w</i> Lmal\". Furthermore, we show that <i>w</i> Lmal induces parthenogenesis in the wasp, and that these wasps are reliant upon their <i>Wolbachia</i> infections to produce female offspring. Finally, comparison to historical museum specimens indicate that <i>Leptopilina malgretoutensis</i> had been collected approximately 40 years prior from the nearby island of Guadeloupe and were also asexually reproducing. This work represents one of only a handful of studies in which field biology, taxonomy, systematics, genomics, and experimental biology are integrated into a species description: showcasing the possibilities for biodiversity research in the genomic era.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974902/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polygenic Associations between Motor Behaviour, Neuromotor Traits, and Active Music Engagement in Four Cohorts.","authors":"T L Henechowicz, P L Coleman, D E Gustavson, Y N Mekki, S Nayak, R Nitin, A C Scartozzi, E S Tio, R van Klei, D Felsky, M H Thaut, R L Gordon","doi":"10.1101/2025.03.27.645667","DOIUrl":"https://doi.org/10.1101/2025.03.27.645667","url":null,"abstract":"<p><p>Phenotypic investigations have shown that actively engaging with music, i.e., playing a musical instrument or singing may be protective of motor decline in aging. For example, music training associated with enhanced sensorimotor skills accompanied by changes in brain structure and function. Although it is possible that the benefits of active music engagement \"transfer\" to benefits in the motor domain, it is also possible that the genetic architecture of motor behaviour and the motor system structure may influence active music engagement. This study investigated whether polygenic scores (PGS) for five behavioural motor traits, 12 neuromotor structural brain traits, and seven rates of change in brain structure traits trained from existing discovery genome-wide association studies (GWAS) predict active music engagement outcomes in four independent cohorts of unrelated individuals of European ancestry: the Canadian Longitudinal Study on Aging (CLSA; N=22,198), Wisconsin Longitudinal Study (WLS; N=4,605), Vanderbilt's BioVU Repository (BioVU; N=6,150), and Vanderbilt's Online Musicality study (OM; N=1,559). Results were meta-analyzed for each PGS main effect across outcomes and cohorts, revealing that PGS for a faster walking pace was associated with higher amounts of active music engagement. Within CLSA, a higher PGS for walking pace was associated with greater odds of engaging with music. Findings suggest a shared genetic architecture between motor function and active music engagement. Future intervention-based research should consider the genetic underpinnings of motor behavior when evaluating the effects of music engagement on motor function across the lifespan.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Two-photon activation, deactivation, and coherent control of melanopsin in live cells.","authors":"Carlos A Renteria, Jiho Kahng, Brian Tibble, Rishyashring R Iyer, Jindou Shi, Haya Algrain, Eric J Chaney, Edita Aksamitiene, Yuan-Zhi Liu, Phyllis Robinson, Tiffany Schmidt, Stephen A Boppart","doi":"10.1101/2025.03.26.645437","DOIUrl":"https://doi.org/10.1101/2025.03.26.645437","url":null,"abstract":"<p><p>Intrinsically photosensitive retinal ganglion cells are photoreceptors discovered in the last 20 years. These cells project to the suprachiasmatic nucleus of the brain to drive circadian rhythms, regulated by ambient light levels. The photopigment responsible for photoactivation in these cells, melanopsin, has been shown to exhibit many unique activation features among opsins. Notably, the photopigment can exist in three states dependent on the intensity and spectrum of ambient light, which affects its function. Despite increasing knowledge about these cells and melanopsin, tools that can manipulate their three states, and do so with single-cell precision, are limited. This reduces the extent to which circuit-level phenomena, and studying the implications of melanopsin tri-stability in living systems, can be pursued. In this report, we evoke and modulate calcium transients in live cells and intrinsically photosensitive retinal ganglion cells from isolated retinal tissues following two-photon excitation using near-infrared light pulses. We demonstrate that two-photon activation of melanopsin can successfully stimulate melanopsin-expressing cells with high spatio-temporal precision. Moreover, we demonstrate that the functional tri-stability of the photopigment can be interrogated by multiphoton excitation using spectral-temporal modulation of a broadband, ultrafast laser source.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Material Damage to Multielectrode Arrays after Electrolytic Lesioning is in the Noise.","authors":"Alice Tor, Stephen E Clarke, Iliana E Bray, Paul Nuyujukian","doi":"10.1101/2025.03.26.645429","DOIUrl":"https://doi.org/10.1101/2025.03.26.645429","url":null,"abstract":"<p><p>1The quality of stable long-term recordings from chronically implanted electrode arrays is essential for experimental neuroscience and brain-computer interfaces. This work uses scanning electron microscopy (SEM) to image and analyze eight 96-channel Utah arrays previously implanted in motor cortical regions of four subjects (subject H = 2242 days implanted, F = 1875, U = 2680, C = 594), providing important contributions to a growing body of long-term implant research leveraging this imaging technology. Four of these arrays have been used in electrolytic lesioning experiments (H = 10 lesions, F = 1, U = 4, C = 1), a novel electrolytic perturbation technique using small direct currents. In addition to surveying physical damage, such as biological debris and material deterioration, this work also analyzes whether electrolytic lesioning created damage beyond what is typical for these arrays. Each electrode was scored in six damage categories, identified from the literature: abnormal debris, metal coating cracks, silicon tip breakage, parylene C delamination, parylene C cracks, and shank fracture. This analysis confirms previous results that observed damage on explanted arrays is more severe on the outer-edge electrodes versus inner electrodes. These findings also indicate that are no statistically significant differences between the damage observed on normal electrodes versus electrodes used for electrolytic lesioning. This work provides evidence that electrolytic lesioning does not significantly affect the quality of chronically implanted electrode arrays and can be a useful tool in understanding perturbations to neural systems. Finally, this work also includes the largest collection of single-electrode SEM images for previously implanted multielectrode Utah arrays, spanning eleven different intact arrays and one broken array. As the clinical relevance of chronically implanted electrodes with single-neuron resolution continues to grow, these images may be used to provide the foundation for a larger public database and inform further electrode design and analyses.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974832/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Single-Cell Atlas of RNA Alternative Splicing in the Glioma-Immune Ecosystem.","authors":"Xiao Song, Deanna Tiek, Minghui Lu, Xiaozhou Yu, Runxin Wu, Maya Walker, Qiu He, Derek Sisbarro, Bo Hu, Shi-Yuan Cheng","doi":"10.1101/2025.03.26.645511","DOIUrl":"https://doi.org/10.1101/2025.03.26.645511","url":null,"abstract":"<p><p>Single-cell analysis has refined our understanding of cellular heterogeneity in glioma, yet RNA alternative splicing (AS)-a critical layer of transcriptome regulation-remains underexplored at single-cell resolution. Here, we present a pan-glioma single-cell AS analysis in both tumor and immune cells through integrating seven SMART-seq2 datasets of human gliomas. Our analysis reveals lineage-specific AS across glioma cellular states, with the most divergent AS landscapes between mesenchymal- and neuronal-like glioma cells, exemplified by AS in <i>TCF12</i> and <i>PTBP2</i> . Comparison between core and peripheral glioma cells highlights AS-redox co-regulation of cytoskeleton organization. Further analysis of glioma-infiltrating immune cells reveals potential isoform-level regulation of protein glycosylation in regulatory T cells and a link between <i>MS4A7</i> AS in macrophages and clinical response to anti-PD-1 therapy. This study emphasizes the role of AS in glioma cellular heterogeneity, highlighting the importance of an isoform-centric approach to better understand the complex biological processes driving tumorigenesis.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The anaerobic gut fungal community in ostriches ( <i>Struthio camelus</i> ).","authors":"Julia Vinzelj, Kathryn Nash, Adrienne L Jones, R Ty Young, Casey H Meili, Carrie J Pratt, Yan Wang, Mostafa S Elshahed, Noha H Youssef","doi":"10.1101/2025.03.28.646006","DOIUrl":"https://doi.org/10.1101/2025.03.28.646006","url":null,"abstract":"<p><p>Anaerobic gut fungi (AGF; <i>Neocallimastigomycota</i> ) are essential for plant biomass degradation in herbivores. While extensively studied in mammals, information regarding their occurrence, diversity, and community structure in non-mammalian hosts remains sparse. Here, we report on the AGF community in ostriches ( <i>Struthio camelus</i> ), herbivorous, flightless, hindgut fermenting members of the class <i>Aves</i> (birds). Culture-independent diversity surveys of fecal samples targeting the D2 region of the large ribosomal subunit (28S rRNA) revealed a uniform community with low alpha diversity. The community was mostly comprised of sequences potentially representing two novel species in the genus <i>Piromyces,</i> and a novel genus in the <i>Neocallimastigomycota</i> . Sequences affiliated with these novel taxa were absent or extremely rare in datasets derived from mammalian and tortoise samples, indicating a strong pattern of AGF-host association. One <i>Piromyces</i> strain (strain Ost1) was successfully isolated. Transcriptomics-enabled molecular dating analysis suggested a divergence time of ≈ 30 Mya, a time frame in line with current estimates for ostrich evolution. Comparative gene content analysis between strain Ost1 and other <i>Piromyces</i> species from mammalian sources revealed a high degree of similarity. Our findings expand the range of AGF animal hosts to include members of the birds (class <i>Aves</i> ), highlight a unique AGF community adapted to the ostrich alimentary tract, and demonstrate that - like mammals - coevolutionary phylosymbiosis (i.e. concurrent evolution of AGF and their animal hosts) plays a central role in explaining current AGF distribution patterns in <i>Aves</i> .</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974864/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A minimal CRISPR polymerase produces decoy cyclic nucleotides to detect phage anti-defense proteins.","authors":"Ashley E Sullivan, Ali Nabhani, Kate Schinkel, David M Dinh, Melissa L Duncan, Eirene Marie Q Ednacot, Charlotte R K Hoffman, Daniel S Izrailevsky, Emily M Kibby, Toni A Nagy, Christy M Nguyen, Uday Tak, A Maxwell Burroughs, L Aravind, Aaron T Whiteley, Benjamin R Morehouse","doi":"10.1101/2025.03.28.646047","DOIUrl":"https://doi.org/10.1101/2025.03.28.646047","url":null,"abstract":"<p><p>Bacteria use antiphage systems to combat phages, their ubiquitous competitors, and evolve new defenses through repeated reshuffling of basic functional units into novel reformulations. A common theme is generating a nucleotide-derived second messenger in response to phage that activates an effector protein to halt virion production. Phages respond with counter-defenses that deplete these second messengers, leading to an escalating arms race with the host. Here we discover a novel antiphage system we call Panoptes that detects phage infection by surveying the cytosol for phage proteins that antagonize the nucleotide-derived second messenger pool. Panoptes is a two-gene operon, <i>optSE</i> . OptS is predicted to synthesize a second messenger using a minimal CRISPR polymerase (mCpol) domain, a version of the polymerase domain found in Type III CRISPR systems (Cas10) that is distantly related to GGDEF and Thg1 tRNA repair polymerase domains. OptE is predicted to be a transmembrane effector protein that binds cyclic nucleotides. <i>optSE</i> potently restricted phage replication but mutant phages that had loss-of-function mutations in anti-CBASS protein 2 (Acb2) escaped defense. These findings were unexpected because Acb2 is a nucleotide \"sponge\" that antagonizes second messenger signaling. Using genetic and biochemical assays, we found that Acb2 bound the OptS-synthesized nucleotide, 2',3'-cyclic adenosine monophosphate (2',3'-c-di-AMP); however, 2',3'-c-di-AMP was synthesized constitutively by OptS and inhibited OptE. Nucleotide depletion by Acb2 released OptE toxicity thereby initiating abortive infection to halt phage replication. These data demonstrate a sophisticated immune strategy that hosts use to guard their second messenger pool and turn immune evasion against the virus.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A TRPV4-dependent calcium signaling axis governs lamellipodial actin architecture to promote cell migration.","authors":"Ernest Iu, Alexander Bogatch, Wenjun Deng, Jonathan D Humphries, Changsong Yang, Fernando R Valencia, Chengyin Li, Christopher A McCulloch, Guy Tanentzapf, Tatyana M Svitkina, Martin J Humphries, Sergey V Plotnikov","doi":"10.1101/2025.03.28.646012","DOIUrl":"https://doi.org/10.1101/2025.03.28.646012","url":null,"abstract":"<p><p>Cell migration is crucial for development and tissue homeostasis, while its dysregulation leads to severe pathologies. Cell migration is driven by the extension of actin-based lamellipodia protrusions, powered by actin polymerization, which is tightly regulated by signaling pathways, including Rho GTPases and Ca ²⁺ signaling. While the importance of Ca ²⁺ signaling in lamellipodia protrusions has been established, the molecular mechanisms linking Ca ²⁺ to lamellipodia assembly are unknown. Here, we identify a novel Ca ²⁺ signaling axis involving the mechano-gated channel TRPV4, which regulates lamellipodia protrusions in various cell types. Using Ca ²⁺ and FRET imaging, we demonstrate that TRPV4-mediated Ca ²⁺ influx upregulates RhoA activity within lamellipodia, which then facilitates formin-mediated actin assembly. Mechanistically, we identify CaMKII and TEM4 as key mediators relaying the TRPV4-mediated Ca ²⁺ signal to RhoA. These data define a molecular pathway by which Ca ²⁺ influx regulates small GTPase activity within a specific cellular domain - lamellipodia - and demonstrate the critical role in organizing the actin machinery and promoting cell migration in diverse biological contexts.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974816/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell characterization of the human C2 dorsal root ganglion recovered from C1-2 arthrodesis surgery: implications for neck pain.","authors":"Asta Arendt-Tranholm, Ishwarya Sankaranarayanan, Cathryn Payne, Marisol Mancilla Moreno, Khadijah Mazhar, Natalie Yap, Abby P Chiu, Allison Barry, Pooja P Patel, Nikhil N Inturi, Diana Tavares Ferreira, Anubhav Amin, Mahesh Karandikar, Jeffrey G Jarvik, Judith A Turner, Christoph P Hofstetter, Michele Curatolo, Theodore J Price","doi":"10.1101/2025.03.24.645122","DOIUrl":"https://doi.org/10.1101/2025.03.24.645122","url":null,"abstract":"<p><p>Neurons in the dorsal root ganglion (DRG) receive and transmit sensory information from the tissues they innervate and from the external environment. Upper cervical (C1-C2) DRGs are functionally unique as they receive input from the neck, head, and occipital cranial dura, the latter two of which are also innervated by the trigeminal ganglion (TG). The C2 DRG also plays an important role in neck pain, a common and disabling disorder that is poorly understood. Advanced transcriptomic approaches have significantly improved our ability to characterize RNA expression patterns at single-cell resolution in the DRG and TG, but no previous studies have characterized the C2 DRG. Our aim was to use single-nucleus and spatial transcriptomic approaches to create a molecular map of C2 DRGs from patients undergoing arthrodesis surgery with ganglionectomy. Patients with acute (<3 months) or chronic (≥3 months) neck pain were enrolled and completed patient-reported outcomes and quantitative sensory testing prior to surgery. C2 DRGs were characterized with bulk, single nucleus, and spatial RNA sequencing technologies from 22 patients. Through a comparative analysis to published datasets of the lumbar DRG and TG, neuronal clusters identified in both TG and DRG were identified in the C2 DRG. Therefore, our study definitively characterizes the molecular composition of human C2 neurons and establishes their similarity with unique characteristics of subsets of TG neurons. We identified differentially expressed genes in endothelial, fibroblast and myelinating Schwann cells associated with chronic pain, including <i>FGFBP2, C8orf34</i> and <i>EFNA1</i> which have been identified in previous genome and transcriptome wide association studies (GWAS/TWAS). Our work establishes an atlas of the human C2 DRG and identifies altered gene expression patterns associated with chronic neck pain. This work establishes a foundation for the exploration of painful disorders in humans affecting the cervical spine.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974819/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}