Biology subjects

Patel, P.

Publications and source records attributed to Patel, P..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Metastatic dissemination of breast cancer stem cells requires MenaINV for lung extravasation but not survival

Cancer stemness is a pivotal driver of tumor initiation, treatment resistance, and tumor cell survival. Cancer stem cells (CSCs), though constituting only a small fraction of primary tumor cells, are progressively enriched during metastatic progression: from circulating tumor cells traveling in the bloodstream, to disseminated tumor cells lodged in the lung vasculature, to extravasated tumor cells that have entered tissue parenchyma. However, whether CSCs have an intrinsic advantage for extravasation over cancer non-stem cells (CnSCs), or simply their increased representation in circulation renders them more likely to extravasate, remains unresolved. MenaINV, an invasive isoform of the actin regulatory protein Mena, promotes tumor cell transendothelial migration in primary and secondary sites, yet the direct mechanistic link between stemness and MenaINV in lung metastasis remains unresolved. Here, using a validated fluorescent stemness reporter (SORE6) to identify CSCs, we found that CSCs display elevated MenaINV expression relative to CnSCs. High-resolution intravital imaging showed that CSCs extravasate efficiently into lung parenchyma and survive at higher levels, robustly forming metastatic lesions, while CnSCs show limited extravasation, low survival, and poor colonization. Mechanistically, MenaINV disruption in CSCs specifically impaired extravasation without affecting survival, demonstrating that MenaINV is the key extravasation effector downstream of stemness, whereas stemness-associated factors independently confer survival advantages. Moreover, reintroduction of MenaINV in CnSCs restores their extravasation ability upon which extravasated CnSCs reactivate stem program and form metastases. Overall, we discovered a hierarchical framework where stemness regulates both survival and extravasation capacity, with MenaINV as the key CSC extravasation effector. Significance: This study reveals how breast cancer stem cells achieve metastatic dominance through separable pathways: MenaINV-dependent extravasation and MenaINV-independent survival, providing rationale for targeting stem program to improve patient outcome.

cancer biology↗

bioRxiv2026

Neural Decoding of Musical Engagement Reveals Tension-Release Dynamics

Music listening is one of the most compelling and rewarding activities humans engage in spontaneously. But what exactly catches people"s attention when listening to music remains unclear. Musicologists have argued that tension-release dynamics in music constitute crucial features of the listening experience. They arise from the intertwining of different low-level and high-level features and sit at the core of music enjoyment by engaging listeners dynamically. This study aims to characterize the relationship between tension dynamics and engagement during naturalistic music listening. Using canonical correlation analysis, we decoded the music envelope from EEG and ECoG responses and found that musical tension patterns, as reported by listeners, were predictive of fluctuations in the coupling between the music and the neural response. Importantly, tension dynamics were significantly correlated with neural measures of envelope tracking even after controlling for loudness and musical expectations, confirming the specific and crucial role of musical tension in engaging listeners. These results shed new light on how musical structure gives rise to internal response modulations that, in turn, dynamically reflect musical engagement. This interplay may underlie the pervasive and emotionally rewarding nature of music. Significance StatementThis work addresses a fundamental question in cognition: how engagement dynamically modulates complex auditory input processing. We investigate this issue within the well-controlled yet ecologically valid context of music perception. At the core of the musical experience lies the perception of tension - the shifting sense of expectancy, instability, and resolution that guides listening across time. We show that fluctuations in musical tension, shaped by musical structure, reliably predict modulations of auditory engagement, thereby illuminating an understudied phenomenon: what makes music engaging.

neuroscience↗

bioRxiv2025

Mammary Fibroblasts Secrete Damage Associated Molecular Patterns through Extracellular Vesicles in Response to Ionizing Radiation

Ionizing radiation (IR) is an integral component of cancer therapy. Cellular exposure to IR typically leads to major biological consequences including cell death and senescence. Furthermore, tissue injury in known to involve the release of damage-associated molecular patterns (DAMPs) into the extracellular space, which trigger inflammation and wound healing. However, DAMP release in the context of radiation injury remains to be fully characterized. Evidence suggests that extracellular vesicle (EV) secretion and associated cargo components are part of the cellular response to IR, but the mechanisms integrating cellular damage and EV secretion post-IR are largely unexplored. In this study, we show that acute IR-induced damage in mammary fibroblasts results in a senescence-like phenotype and substantially increased EV secretion. Quantitative proteomic analysis revealed that IR-induced EVs are enriched with extracellular and intracellular DAMPs, along with other pro-inflammatory mediators. We show that knockdown of the GTPase Rab27a abrogates IR-induced EV secretion and inhibits the enrichment of key DAMPs in EVs. By examining the integration of cellular damage and senescence with the release of inflammatory signals, this study elucidates a potentially critical role for EV-associated proteins in the radiation response.

cancer biology↗

bioRxiv2025

Evolutionary convergence of a Pyroptosis-Apoptosis crosstalk drives non-canonical inflammasome signalling.

The coordination of efficient immune responses to infections is essential to enable pathogen clearance and host survival. Cell death modalities are a crucial component of the innate immune system and are key to controlling intracellular and extracellular infections. Human caspase-4 and -5 are cysteine proteases activated upon intracellular detection of bacterial lipopolysaccharide (LPS) and triggers pyroptosis, a lytic and pro-inflammatory form of cell death. However, the interaction between these caspases and other cell death modalities remains poorly understood. Here, we build on evidence that caspase-4 can engage in crosstalk with the apoptotic executioner caspases-3 and -7. Our work validated caspase-3 and -7 as direct substrates of caspase-4 and -5, and demonstrated that this specificity was regulated by exosite interactions as opposed to the tetrapeptide. Using AlphaFold, we generated an interaction model between caspase-4 and executioner caspases-3 and -7. From this, we experimentally validated the importance of a hydrophobic interface on caspase-3 and -7 that engaged the caspase-4 exosite, enabling their recognition and cleavage. Importantly, this interface is not used by the apoptotic initiator caspase-8, which cleaved caspase-3 in a tetrapeptide-dependent manner. Our work highlights that inflammatory caspases have evolved a novel mechanism to coordinate crosstalk between pyroptotic and apoptotic signalling, and suggests that these pathways may synergise for the efficient amplification of cell death pathways.

biochemistry↗

bioRxiv2025

Androgens Drive SOX9 Upregulation in Injured Proximal Tubular Cells

IntroductionSex influences susceptibility, recovery, and long-term outcomes after acute kidney injury (AKI) in humans. Rodent models have been invaluable for elucidating AKI mechanisms; however, most studies have focused on males, assuming direct applicability to females, an assumption that remains largely untested. In males, the transcription factor SOX9 regulates injury-associated proximal tubule cell states, supporting survival during injury but also contributing to maladaptive repair. Given the well-described role of SOX9 in sex determination during development and its emerging importance in AKI, we investigated whether it mediates sex-specific tubular responses in the adult kidney. MethodsWe first optimized differential ischemic and cisplatin conditions in males and females to generate injury-matched models. We then used these models to ask whether proximal tubular cell responses, particularly Sox9 upregulation, are sex dependent. Tubule-specific knockout models of Sox9, Sox4, Sox11, Vgf, Zfp24, and the androgen receptor (Ar), along with gonadectomy and hormone replacement studies, combined with gene and protein analyses, were used to define regulatory networks. ResultsIn both ischemic and nephrotoxic AKI, SOX9 expression was markedly blunted in females, with levels more than fivefold lower than in males. While injury biomarkers such as NGAL and KIM1 were equally induced in both sexes, Sox9 and its downstream target Vgf showed markedly reduced induction in females, whereas the upstream regulator Zfp24 was functionally relevant only in males. Deletion of Sox9, Zfp24, or Vgf worsened injury in males but not in females. In contrast, Sox4 and Sox11 were equally upregulated and protective in both sexes. Castration or proximal tubule-specific deletion of Ar in males abolished Sox9 induction, establishing a testosterone-dependent regulatory axis. ConclusionsThese findings define a hormone-driven, male-specific tubular repair program and demonstrate that injury and recovery pathways differ fundamentally between sexes, underscoring the need for sex-inclusive therapeutic strategies for AKI. Translational StatementSex influences susceptibility and outcomes after AKI, but the molecular basis remains unclear. SOX9, a transcription factor recently identified as one of the most highly upregulated genes in proximal tubular cells during AKI in both mice and humans, has been presumed to mediate a universal protective program. Using injury-matched murine models of AKI, we now demonstrate that this response is restricted to males, driven by testosterone and androgen receptor signaling, while SOX9 induction is markedly blunted and functionally dispensable in females. These findings reveal that tubular protective pathways differ fundamentally between sexes despite equivalent injury severity. Because SOX9 activation confers epithelial protection in males, therapeutic targeting of this pathway may have clinical relevance primarily in male patients. These data underscore the importance of incorporating biological sex into mechanistic, translational, and clinical studies of kidney injury and recovery.

cell biology↗

bioRxiv2025

Peripheral Neuropathy After Chronic Alcohol Exposure in Mice: Impact of sex, total intake and duration and alcohol metabolism.

Alcohol induced peripheral neuropathy (AIPN) is a neurodegenerative disease caused by chronic alcohol intake and is associated with peripheral nerve damage and somatosensory symptoms, such as allodynia. Current treatments lack efficacy and do not target underlying pathology emphasizing the need for preclinical models of AIPN to elucidate mechanisms and novel targets. Thus, we performed a detailed characterization of a mouse model of AIPN and candidate mechanistic associations including the role of neuroinflammation and acetaldehyde. Our studies showed chronic alcohol induced mechanical and cold hypersensitivity and deficits in spontaneous behaviors in EtOH concentration-, time- and sex-dependent manners. Female mice drank more alcohol and developed more rapid and severe hypersensitivity but less robust deficits of spontaneous behaviors. The grimace test demonstrated chronic alcohol promoted spontaneous pain independent of sex. Duration of intake impacted alcohol-induced deficits in peripheral nerve electrophysiology amplitude and intra-epidermal nerve fiber density. We characterized an extensive time-course of chronic alcohol-induced neuroinflammation in the DRG and spinal cord and found significant time, sex and tissue effects. Polymorphisms of ALDH2 have been associated with alcohol-induced neuroinflammation, alcohol-related pain, and alcohol-induced peripheral neuropathy. We investigated the role of acetaldehyde, via inhibition of ALDH2, in the development of AIPN and showed that ALDH2 inhibition accelerated and exacerbated development of chronic alcohol-induced hypersensitivity in male and female mice. Overall, our studies in a well-controlled model of AIPN strongly point to neuroinflammation and inflammatory modulators such as acetaldehyde as important mechanistic targets for possible intervention in AIPN.

pharmacology and toxicology↗

bioRxiv2025

The role of aging on endothelial cell-cell junctions and pulmonary microvascular permeability

Lung injury leads to pulmonary microvascular endothelial cell (PMVEC) damage, disruption of cell-cell junctions, and increased permeability. Previously, we demonstrated in a mechanical ventilation-induced model of lung injury that aging exacerbated pulmonary microvascular permeability. Based on this, we hypothesized that aging was associated with increased PMVEC barrier dysfunction due to impaired cell-cell junction integrity. PMVEC were isolated from young and aged mice and cultured to confluence in vitro. Barrier function and cell-cell junction integrity were assessed through electric cell-substrate impedance sensing, XPerT permeability assay, immunofluorescence, and western blot analysis. Further studies were conducted to examine alterations in the proteome, markers of inflammation, and actin cytoskeleton organization. To model injurious conditions, PMVEC were stimulated with inflammatory cytokines; permeability and actin cytoskeletal alterations were subsequently assessed. We observed increased basal permeability in PMVEC from aged mice, which was associated with disrupted cell-surface localization of the adherens junction protein, vascular endothelial (VE)-cadherin. Protein abundance of VE-cadherin was significantly increased with age; however, levels of the adapter protein,{gamma} -catenin, and the tight junction protein, claudin-5, were decreased. Measures of inflammation, including cytokine expression and cell surface abundance of adhesion molecules, did not differ with age. Alterations in actin cytoskeleton organization, characterized by augmented presence of actin stress fibers, were observed in aged PMVEC. Under inflammatory conditions, permeability and actin stress fiber formation were exacerbated with age. It is concluded that aging predisposes PMVEC to elevated injury, due to inherent deficiencies in cell-cell junctions and barrier function, potentially mediated through altered actin cytoskeleton organization. New and NoteworthyCompared with pulmonary microvascular endothelial cells (PMVEC) from young mice, PMVEC isolated from aged mice had higher permeability, which was directly associated with impairments in cell-cell junctions. The higher permeability in aged PMVEC was not associated with augmented inflammatory signaling but was associated with actin cytoskeletal alterations. Following an inflammatory insult, PMVEC from aged mice had further exacerbated permeability. These findings may begin to highlight why older patients exhibit higher mortality during lung injury.

cell biology↗

bioRxiv2025

MYD88 mutations in clonal hematopoiesis promote inflammation and hematopoietic stem cell expansion

Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by expansion of mutant hematopoietic stem and progenitor cells (HSPCs) and an increased risk of chronic diseases and cancers. While mutations in DNMT3A, TET2, and ASXL1 are common in CHIP, the contribution of less frequent gene mutations is not well understood. Here, we report MYD88 mutations, including lymphoma-associated and novel variants in blood cells of the general population and newly diagnosed solid cancer patients. MYD88 CHIP mutations in HSPCs activate NF-{kappa}B, indicating a gain-of-function activity. Modeling MYD88 CHIP in mice, Myd88L252P (equivalent of human L265P) expression resulted in a competitive fitness advantage of HSPCs. Myd88L252P HSPCs exhibit a myeloid cell bias and inflammation, leading to hematologic disease. Single-cell RNA sequencing indicated that Myd88L252P expands distinct hematopoietic and immune cell clusters and activates immune-related pathways in HSPCs. An IRAK1/4 inhibitor suppressed MYD88-dependent NF-{kappa}B activation and reversed Myd88L252P cell expansion. Overall, MYD88 mutations contribute to CHIP by inducing innate immune pathways in HSPCs and inflammatory disease.

cancer biology↗

bioRxiv2025

Disassociating cerebral vasomotion from low frequency spontaneous neurovascular coupling

Vasomotion, vascular oscillations at [~]0.1 Hz, may serve as a biomarker and therapeutic target for neurodegenerative diseases, but its origins, structure across brain vasculature, and correlation with neural activity remain unclear. This study examined the spatiotemporal characteristics of cerebral vasomotion and its relationship to neural activity in anaesthetised Hooded Lister rats using simultaneous recordings of neuronal activity and haemodynamics in motor and whisker barrel cortices. In a subset of rats, tissue oxygen was also measured. Blood pressure was pharmacologically modulated to alter vascular oscillations. We found that vasomotion was driven by the arterial tree. Two prominent activity patterns emerged: global vasomotion across the entire hemisphere and phasic vasomotion seen as a travelling wave running through the surface arteries. Moreover, vasomotion was associated with low tissue oxygen and was largely independent of spontaneous neural activity and therefore not a product of neurovascular coupling.

neuroscience↗

bioRxiv2025

Spatial transcriptomic profiling of human paravertebral sympathetic chain ganglia reveals diabetes-induced neuroplasticity

The paravertebral sympathetic chain ganglia (SCG) are autonomic ganglia critical for regulating the "fight-or-flight" response. Symptoms of sympathetic dysfunction are prevalent in diabetes, affecting up to 90% of patients. The molecular and cellular composition of the human SCG and its alteration in diabetes remains poorly defined. To address this gap, we performed spatial transcriptomic profiling of lumbar SCGs from diabetic and non-diabetic organ donors. We identified 3 three distinct neuronal populations, two noradrenergic (NA1 and NA2) and one cholinergic (CHO), based on tyrosine hydroxylase (TH) and SLC18A3 expression, respectively. We also characterized 9 non-neuronal populations consisting of Schwann cells, immune cells, fibroblasts, adipocytes, and endothelial cells. In diabetic SCGs, we observed a significant loss of myelinating Schwann cells and a phenotypic shift of cholinergic neurons toward a noradrenergic identity. Additionally, diabetes was associated with a significant reduction in the transcripts of vasodilatory neuropeptides, such as VIP and CALCA, suggesting a mechanism for impaired vascular control. Upstream regulator analysis highlighted altered neurotrophic signaling in diabetes, with enhanced NGF/TRKA and diminished BDNF/TRKB activity, potentially driven by target-derived cues. Comparison between SCG and dorsal root ganglia (DRG) neurons revealed ganglia-specific genes, like SCN3A and NPY (SCG) versus SCN10A and GPX1 (DRG), offering specific therapeutic targets for autonomic dysfunction or pain. Our findings provide a transcriptomic characterization of human SCG, revealing molecular signatures that underlie diabetic autonomic dysfunction. This work lays a foundation for the development of therapies to restore sympathetic function and avoid unintended autonomic effects in the development of analgesics. Significance StatementAutonomic dysfunction affects up to 90% of people with diabetes, yet the human sympathetic nervous system remains poorly molecularly defined. To address this gap, we present a spatial transcriptomic profile of the human sympathetic chain ganglia (SCG), revealing how diabetes affects the human autonomic nervous system. We show that diabetes shifts the cholinergic neuronal population to a noradrenergic phenotype and reduces vasodilation neuropeptide expression, potentially explaining impaired vascular control and thermoregulation. Comparative analysis of sympathetic and sensory ganglia reveals distinct gene profiles that may inform novel therapeutic strategies. These findings offer critical insight into the molecular drivers of diabetic autonomic neuropathy and lay the groundwork for safer, more precise treatments that selectively modulate autonomic or sensory function in chronic disease.

neuroscience↗

bioRxiv2025

Towards interpretable molecular and spatial analysis of the tumor microenvironment from digital histopathology images with HistoTME-v2

The tumor microenvironment (TME) is a critical focus for biomarker discovery and therapeutic targeting in cancer. However, widespread clinical adoption of TME profiling is hindered by the high cost and technical complexity of current platforms such as spatial transcriptomics and proteomics. Artificial Intelligence (AI)-based analysis of the TME from routine Hematoxylin & Eosin (H&E)-stained pathology slides presents a promising alternative. Yet, most existing deep learning approaches depend on extensive high-quality single-cell or patch-level annotations, which are labor-intensive and costly to generate. To address these limitations, we previously introduced HistoTME, a weakly supervised deep learning framework that predicts the activity of cell type-specific transcriptomic signatures directly from whole slide H&E images of non-small cell lung cancer. This enables rapid, high throughput analysis of the TME composition from whole slide H&E images (WSI) without the need for segmenting and classifying individual cells. In this work, we present HistoTME-v2, a pan-cancer extension of HistoTME, applied across 25 solid tumor types, substantially broadening the scope of prior efforts. HistoTME-v2 demonstrates high accuracy for predicting cell type-specific transcriptomic signature activity from H&E images, achieving a median Pearson correlation of 0.61 with ground truth measurements in internal cross- validation on The Cancer Genome Atlas (TCGA), encompassing 7,586 WSIs, 6,901 patients, and 24 cancer types, and a median Pearson correlation of 0.53 on external validation datasets spanning 5,657 WSIs, 1,775 patients and 9 cancer types. Furthermore, HistoTME- v2 resolves the spatial distribution of key immune and stromal cell types, exhibiting strong spatial concordance with single-cell measurements derived from multiplex imaging (CODEX, IHC) as well as Visium spatial transcriptomics, spanning 259 WSI, 154 patients, and 7 cancer types. Overall, across both bulk and spatial settings, HistoTME-v2 significantly outperforms baselines, positioning it as a robust, interpretable and cost-efficient tool for TME profiling and advancing the integration of spatial biology into routine pathology workflows.

pathology↗

bioRxiv2025

The abundance of potential B12 producers in gut microbiome is inversely associated with serum vitamin B12 levels: A putative role of Host-microbiome feedback regulation

BackgroundThe human gut microbiome is a natural source of essential micronutrients like B-vitamins, which are utilized by both the host and other community members. The prevalence and abundance of known B-vitamin producers and B-vitamin biosynthesis pathways have already been reported in gut microbiome cohorts of a few countries including India. ObjectiveTo test whether the presence of B-vitamin producers/biosynthetic pathways translates into serum B-vitamin levels, taking B12 as a case example. MethodsFecal samples were collected from non-deficient (serum B12 level > 210 pg/mL, n=29) and B12 deficient (serum B12 level < 210 pg/mL, n=30) children from a tribal region of central India. Whole metagenomic DNA was extracted, sequenced, and analyzed for taxonomic profiling and diversity comparisons. Differentially abundant taxa between two groups were identified. The prevalence and abundance of potential B12 producers were compared, and their association with serum B12 level was established. ResultsA comparison of within-sample diversity between the two groups didnt show any difference; however, between-sample diversity was significantly less in the B12 deficient group. Differential abundance testing also showed different microbiome structure in the B12 deficient group, where an increased abundance of B12 transporter-carrying Bacteroides thetaiotaomicron, a few pathogenic species, and ten known B12 producers was observed. Potential B12 producers were also significantly prevalent and abundant in the deficient group. Their cumulative abundance was also significantly higher in the deficient group and showed a negative association with serum B 12 levels. ConclusionA higher abundance of potential B12 producers in the deficient group suggested an adaptive mechanism by the gut microbiome to meet the communitys B12 requirements, by selectively promoting the growth of B12 producers.

genomics↗

bioRxiv2025

A new Paramoeba Isolate from Florida Exhibits a Microtubule-Bound Endosymbiont Closely Associated with the Host Nucleus

The genera Paramoeba and Neoparamoeba, within the family Paramoebidae (order Dactylopodida), are distinguished by their dactylopodial pseudopodia and the presence of an intracellular eukaryotic symbiont, the Perkinsela-like organism (PLO). Taxonomic classification within these genera has been challenging due to overlapping morphological traits and close phylogenetic relationships. Most species are marine, with some acting as significant parasites, contributing to sea urchin mass mortality and serving as causative agents of Amoebic Gill Disease (AGD). Despite their ecological and economic importance, many aspects of their diversity, biology, evolution, and host interactions remain poorly understood. In this study, we describe a novel amoeba species, Paramoeba daytoni n. sp., isolated from Daytona Beach, Florida. Morphological and molecular analyses confirm its placement within the Paramoeba clade, closely related to P. eilhardi, P. karteshi, and P. aparasomata. Phylogenetic assessments using 18S and COI markers demonstrate the limitations of 18S gene for species delineation, highlighting COI as a more reliable genetic marker for this group. Additionally, observations on PLO morphology, movement, and microtubule association provide insights into the endosymbiotic relationship, reinforcing the need for further research into this unique eukaryote-eukaryote symbiosis.

microbiology↗

bioRxiv2024

The use of iconPCR for 16S library preparation improves data quality and workflow

Polymerase Chain Reaction (PCR) is a cornerstone of contemporary biological research, enabling the amplification of specific DNA sequences for various applications. However, suboptimal cycling conditions often undermine its efficacy, which can generate chimeric products, exacerbate PCR duplication rates, and skew species representation in metabarcoding experiments due to the preferential amplification of dominant populations. To address these limitations, we present iconPCR--Individually Controlled PCR--a novel technology that allows each reaction in a 96-well plate to be cycled independently and programmatically. By setting a predefined fluorescence threshold, iconPCR ensures that all Next Generation Sequencing (NGS) libraries are amplified to equivalent levels, thereby eliminating the risks of over- or under-amplification through a process known as "Auto-Normalization." In this study, we applied iconPCR to generate V3, V4, and full-length 16S rRNA gene libraries using Avidite sequencing. The V1-V9 variable region libraries were also evaluated with HiFi sequencing, which significantly demonstrated its potential to improve microbial community analysis accuracy and reliability.

genomics↗

bioRxiv2024

Selective Targeting of a Defined Subpopulation of Corticospinal Neurons using a Novel Klhl14-Cre Mouse Line Enables Molecular and Anatomical Investigations through Development into Maturity

The corticospinal tract (CST) facilitates skilled, precise movements, which necessitates that subcerebral projection neurons (SCPN) establish segmentally specific connectivity with brainstem and spinal circuits. Developmental molecular delineation enables prospective identification of corticospinal neurons (CSN) projecting to thoraco-lumbar spinal segments; however, it remains unclear whether other SCPN subpopulations in developing sensorimotor cortex can be prospectively identified in this manner. Such molecular tools could enable investigations of SCPN circuitry with precision and specificity. During development, Kelch-like 14 (Klhl14) is specifically expressed by a specific SCPN subpopulation, CSNBC-lat, that reside in lateral sensorimotor cortex with axonal projections exclusively to bulbar-cervical targets. In this study, we generated Klhl14-T2A-Cre knock-in mice to investigate SCPN that are Klhl14+ during development into maturity. Using conditional anterograde and retrograde labeling, we find that Klhl14-Cre is specifically expressed by CSNBC-lat only at specific developmental time points. We establish conditional viral labeling in Klhl14-T2A-Cre mice as a new approach to reliably investigate CSNBC-lat axon targeting and confirm that this identifies known molecular regulators of CSN axon targeting. Therefore, Klhl14-T2A-Cre mice can be used as a novel tool for identifying molecular regulators of CST axon guidance in a relatively high-throughput manner in vivo. Finally, we demonstrate that intersectional viral labeling enables precise targeting of only Klhl14-Cre+ CSNBC-lat in the adult central nervous system. Together, our results establish that developmental molecular delineation of SCPN subpopulations can be used to selectively and specifically investigate their development, as well as anatomical and functional organization into maturity. Significance StatementThe cortex connects to brainstem and spinal targets through subcerebral projection neurons (SCPN), which exhibit molecular diversity during development based on their neocortical location and axonal targets. We generated a novel Klhl14-Cre mouse line to utilize this developmental delineation and drive Cre expression in a specific SCPN subpopulation. This developmental specificity enabled investigation of 1) areal locations of Klhl14+ SCPN in mature cortex, 2) their axonal collateralization at maturity, and 3) which genes can control their axon targeting. Using intersectional tools, we can also selectively label these neurons in the adult CNS. Therefore, developmental molecular delineation of SCPN not only provides prospective identification but also enables molecular analysis during development, as well as anatomical and functional investigations in adulthood.

neuroscience↗

bioRxiv2024

Anti-HIV-1 B cell antigen receptor signaling and structure

The B cell antigen receptor (BCR) complex, comprised of antigen recognition and signaling components, functions in initiating B cell activation. While structural studies have described BCR domain organization, gaps remain in our understanding of its antigen binding domain (Fab, fragment antigen-binding) disposition, and how antigen binding is sensed to initiate signaling. Here, we report antigen affinity and signaling of the immunoglobulin (Ig) class IgM and IgG BCRs and define conformational states of full-length BCRs of two human broadly neutralizing antibodies, the glycan-specific, heavy chain domain-swapped, I-shaped 2G12, and a canonical Y-shaped antibody, CH31, that recognizes the CD4-binding site on the HIV-1 Envelope protein (Env). The BCRs adopted the shapes (I or Y) of their respective soluble antibodies, and both Ig class of BCRs of the same specificity bound Env trimers with similar affinities. We observed antigen-valenc y dependent differential signaling by the 2G12 IgM and IgG BCRs with trimeric Envs. Cryo-electron microscopy of the 2G12 IgG and CH31 IgM BCRs revealed varied Fab orientations. Structural comparisons revealed hinge points and regions of flexibility in the BCRs suggesting a highly dynamic structure of the BCR complex. Taken together, our results provide an integrated understanding of BCR structure, conformation, antigen recognition and signaling, and provide the basis for understanding antigen induced BCR signal transmission. One Sentence SummaryCryo-electron microscopy structures of full-length B cell antigen receptor complex provide a novel dynamic BCR model and a basis for understanding antigen binding induced signal transmission.

immunology↗

bioRxiv2024

Protection against Poly Microbial Sepsis by Chitin oligomersis fine tuned by N-Acetyl D-Glucosamine residues

Chitin, poly-N Acetyl D-glucosamine, is an abundant polysaccharide produced by fungal cell walls, insect epicuticle and nematodes cuticles. Its immunomodulatory function has curious attributes - paradoxically opposing host responses using different host receptors resulting in immunostimulatory or immunosuppressive propertis depending on the size/length of the oligomers as well as aceytylation levels have been reported in literature. Here we demonstrate that Hepta-N-Acetyl Chitoheptaose (7 mer) is a TLR2 ligand, 8 mer activates immune cells through TLR4 while, 6 mer is a relatively poor ligand for both TLR2 and TLR4 in generating inflammatory host cytokines. Significantly enhanced inflammatory response characterized by increased TNF-a, IL-1b, IL-6 and IL-10 was a feature of only 8 mer while, 6 and 7 mers induced modest activation in both HEK cells (transfected with specific TLRs) and in human THP2 cells in vitro. The translational significance of these features were addressed in an experimental model of Sepsis using Cecal Ligation Puncture (CLP) protocol, a murine model, considered a gold standard for human Sepsis. More significantly, therapeutic rather than prophylactic administration, that simulates real life scenerio of human and animal sepsis, of 7 mer rather than 6 or 8 residues of Chitin oligomer, significantly protected mice against sepsis as shown by decreased mortality and decreased induction of inflammatory cytokines. These findings suggest that modulation of immune response by chitopolysaccarides in-vivo is precisely caliberated.

immunology↗

bioRxiv2024

Joint population coding and temporal coherence link an attended talker's voice and location features in naturalistic multi-talker scenes.

Listeners effortlessly extract multidimensional auditory objects, such as a localized talker, from complex acoustic scenes. However, the neural mechanisms that enable simultaneous encoding and linking of distinct sound features--such as a talkers voice and location--are not fully understood. Using invasive intracranial recordings in neurosurgical patients, we investigated how the human auditory cortex processes and integrates these features during naturalistic multi-talker scenes. We found that cortical sites exhibit a gradient of feature sensitivity, ranging from single-feature sensitive sites (responsive primarily to voice or location) to dual-feature sensitive sites (responsive to both features). At the population level, neural response patterns from both single- and dual-feature sensitive sites jointly encoded the attended talkers voice and location. Notably, single-feature sensitive sites encoded their primary feature with greater precision but also represented coarse information about the secondary feature. Sites selectively tracking a single, attended speech stream concurrently encoded both voice and location features, demonstrating a link between selective attention and feature integration. Additionally, attention selectively enhanced temporal coherence between voice- and location-sensitive sites, suggesting that temporal synchronization serves as a mechanism for linking these features. Our findings highlight two complementary neural mechanisms--joint population coding and temporal coherence-- that enable the integration of voice and location features in the auditory cortex. These results provide new insights into the distributed, multidimensional nature of auditory object formation during active listening in complex environments. SIGNIFICANCE STATEMENTIn everyday life, listeners effortlessly extract individual sound sources from complex acoustic scenes which contain multiple sound sources. Yet, how the brain links the different features of a particular sound source to each other - such as a talkers voice characteristics and location - is poorly understood. Here, we show that two neural mechanisms contribute to encoding and integrating voice and location features in multi-talker sound scenes: (1) some neuronal sites are sensitive to both voice and location and their activity patterns encode these features jointly; (2) the responses of neuronal sites that process only one sound feature - that is, location or voice - align temporally to form a stream that is segregated from the other talker. HIGHLIGHTSO_LIAuditory cortex exhibits a gradient of feature sensitivity, with some sites encoding only voice or location features, while others encode both simultaneously (dual-feature sensitive sites). C_LIO_LIDual-feature sensitive sites integrate voice and location features of an attended talker with equal accuracy, providing a unified representation in multi-talker scenes. C_LIO_LISingle-feature sensitive sites primarily encode their preferred feature with high precision but also represent coarse information about other features, contributing to population-level integration. C_LIO_LITemporal coherence selectively enhances synchronization between voice- and location-sensitive sites, providing another mechanism for integrating an auditory objects features. C_LIO_LIMulti-dimensional auditory object formation relies on complementary neural mechanisms: joint population coding and temporal coherence. C_LI

neuroscience↗