bioRxiv Science⌕ Search

Biology subjects

Patil, S.

Publications and source records attributed to Patil, S..

At least 19 recordsLinked to original sources

Super-resolution mapping of platelet α-granules uncovers non-polarized secretion and differential retention of von Willebrand Factor and thrombospondin-1

Platelet -granules contain hundreds of bioactive proteins that regulate thrombosis, inflammation and tissue repair. The interplay between -granule secretion and platelet biomechanics is central to platelet function but remains incompletely understood. Here we combined complementary super-resolution microscopy methods, computational image simulations and quantitative single-cell analysis to investigate -granule nanoscale organization and secretion in tandem with cytoskeletal remodeling in spreading human platelets. We show that P-selectin, thrombospondin-1 (TSP1) and von Willebrand factor (VWF) occupy distinct subgranular domains and that apparent co-localization strongly depends on imaging resolution. We identify ring-like P-selectin staining as a robust signature of intact -granules and demonstrate that -granule secretion in spreading platelets was confined to the platelet cell body rather than the actively remodeling periphery. Quantitative assessment at the single-cell level showed that degranulation coincided with transitions from filopodia-rich to lamellipodial morphologies. Comparisons across adhesive substrates and perturbations by soluble agonists indicated that these processes are coordinated through overlapping signaling networks rather than direct local coupling. Analysis of secreted cargo revealed distinct extracellular fates despite no evidence for polarized secretion. TSP1 accumulated beneath platelets within diffusion barrier-restricted membrane pockets and around platelets following matrix binding, whereas VWF remained predominantly tethered to platelet membranes and formed short VWF strings. Together, our findings redefine the organization and release of platelet -granules, demonstrate an absence of secretion polarity, and establish cargo-specific retention mechanisms that may influence platelet signaling and thrombus architecture.

cell biology↗

Functional deficits of the inhibitory control system in children with ADHD: A task-based fMRI meta-analysis

Inhibitory control deficits have long been proposed as a central neurocognitive mechanism underlying childhood Attention Deficit/Hyperactivity Disorder (ADHD). However, neuroimaging findings remain heterogeneous, partly due to methodological variability across developmental samples and experimental paradigms. The present study aimed to characterize the neural architecture of motor response inhibition in typically developing (TD) children and identify reproducible functional abnormalities associated with pediatric ADHD using stringent, developmentally specific inclusion criteria. We conducted two coordinate-based meta-analyses using Activation Likelihood Estimation (ALE). Following a systematic literature search (up to August 2026), we identified 23 task-based fMRI studies reporting inhibitory-control-related activation in TD children (237 foci) and 17 studies comparing children with ADHD and TD peers (114 foci) during the Stop-Signal Task or Go/No-Go Task. All participants were younger than 18 years of age. Statistical significance was determined using cluster-level family-wise error (FWE) correction. In TD children, ALE revealed a robust inhibitory-control network encompassing the bilateral anterior insula (AI), inferior frontal gyrus (IFG), and the midline pre-supplementary motor area (preSMA) and anterior cingulate cortex (ACC). This spatial organization closely resembled the canonical inhibitory-control network consistently observed in adults, suggesting that the core neural architecture supporting motor inhibition is already detectably organized during development. In the between-group analysis, children with ADHD exhibited significant hypoactivation primarily within the preSMA. Notably, this region demonstrated striking spatial overlap with the preSMA cluster reliably recruited in TD children during motor inhibition. These findings provide convergent support for inhibitory-control models of ADHD and identify altered preSMA recruitment as one of the most consistent functional abnormalities associated with pediatric ADHD. While the neural infrastructure supporting inhibitory control is broadly established during childhood, children with ADHD exhibit reduced recruitment of a key cortical node within this network during motor inhibition demands.

neuroscience↗

Reversible, Sexually Dimorphic Sympathetic Aging: Distal Axon Withdrawal Shaped by Prepubertal Gonadal Influences

Peripheral innervation declines with age, but whether this process is sexually dimorphic and whether it reflects neuronal degeneration or deterioration of nerve-target interactions remain unclear. Using mouse skin as a defined neuroeffector system, we show that sympathetic aging is strongly sexually dimorphic, with greater denervation in aged males. Skin-projecting sympathetic neurons remain intact, indicating that denervation reflects distal axon withdrawal rather than neuronal loss. Nerve-target interactions and the arrector pili muscle niche deteriorate with age, predominantly in males. Aged sympathetic neurons retain NGF responsiveness, and restoring NGF within arrector pili muscles promotes sympathetic reinnervation and hair regeneration in aged males. Genetic and endocrine models show that divergent aging trajectories are associated with gonadal rather than chromosomal sex and are attenuated by early gonadectomy. Together, these findings identify sympathetic aging as a reversible, sexually dimorphic distal axonopathy shaped by the target environment and gonadal influences.

developmental biology↗

Cell Mechanics Regulate Membrane Tubulation-Driven Trogocytosis in Adherent Cells

Trogocytosis is a widespread and physiologically important process in which one cell ingests fragments of another. It has been observed in diverse biological contexts, such as in Entamoeba histolytica, a human enteric parasite that nibbles host intestinal cells via trogocytosis, thereby invading the tissue and leading to lethal extra-intestinal disease, and in macrophages on interaction with adherent tumor monolayers. Despite its physiological relevance, knowledge of trogocytosis with adherent cells remains elusive. Here, we established a monolayer-based trogocytosis assay and uncovered a distinct membrane-tube-mediated trogocytic mechanism operative in adherent cells. We characterized it into four sequential events: contact, membrane tubulation, stretching, and scission. By targeting the proteic constituents of target cell stiffness, we show that trogocytic output exhibits a non-monotonic dependence on the viscoelastic properties of the target cell, with maximal uptake occurring in an intermediate mechanical regime. Further, we integrated live-cell trogocytosis observations with a viscoelastic model-based theoretical framework to propose a tube-breaking mechanism across distinct mechanical subtypes. Finally, using micropatterning, we demonstrated that target cell shape influences trogocytosis kinetics. This work suggests that trogocytosis is sensitive to the mechanical state of the target cell.

cell biology↗

Brain Organoids, Lessons from Fetal Neocortex Formation, and Rational Design for Quality Control

Recent widespread adoption of cerebral organoid protocols has led to many new studies assessing the human-specific features of neural diseases. However, not all organoid studies employ proper quality control, which limits the physiological relevance of their findings. Here, we discuss the stages of in vivo neocortex formation and how those stages are recapitulated in organoid protocols. We then present the first guide for real-time operator removal of maldeveloped organoids in shaking culture. Finally, we show preliminary work on an organoid imaging and mesofluidic control platform for automated quality control of organoid development. Taken together, this approach for assessing the morphological features of organoids will improve the rigor and reproducibility of organoid studies, increase effect sizes of physiologically relevant disease etiology, and pave the way for cortical organoid GMP in high-throughput. Clinical RelevanceThis establishes high-throughput, visual brain organoid quality control for disease studies and preclinical testing.

neuroscience↗

Dietary Microplastics Engage Gut Mechanosensory-Endocrine Signaling to Disrupt Bone Homeostasis

Background and AimsMicroplastics are pervasive environmental contaminants increasingly detected in food and water supplies; however, their effects on gastrointestinal physiology and systemic health remain poorly understood. We investigated whether chronic dietary microplastic exposure alters colonic neuroendocrine signaling and skeletal health. MethodsFemale and male C57BL/6J mice were fed purified basal, high-fat/high-cholesterol, or high-fiber diets with or without a physiological relevant polystyrene microplastic mixture ([~]1.7 mg/kg; particle sizes 0.49 - 5.0 {micro}m) for 12 weeks. Colonic cellular responses were evaluated using ELISA, histology, immunofluorescence, and single-nuclei RNA sequencing. Fecal microbiota transplantation was performed to assess microbial contributions to microplastic-induced phenotypes. Bone microarchitecture was assessed by micro-computed tomography. Human bone specimens were analyzed for microplastic content, and primary osteoblast mineralization assays were performed. ResultsDietary microplastic exposure increased chromogranin A-positive enteroendocrine cells and enhanced serotonergic signaling in the colon without evidence of intestinal inflammation or lineage reprogramming. Single-nuclei transcriptomic analysis identified compartment-specific serotonergic and mechanosensory adaptations in epithelial and enteric neuronal populations. Transfer of microbiota from microplastic-exposed donors to control recipients recapitulated increased enteroendocrine cell abundance. Chronic microplastic ingestion induced sex- and diet-dependent reductions in trabecular bone loss and architecture without systemic inflammatory activation. Microplastics were detected in human mineralized bone, and microplastic exposure impaired osteoblast mineralization in a donor-dependent manner. ConclusionsChronic ingestion of microplastics remodels gut neuroendocrine signaling through microbiota-dependent mechanisms and impairs skeletal homeostasis in the absence of overt inflammation. These findings identify a previously unrecognized gut-bone pathway through which dietary microplastic exposure may influence host physiology.

physiology↗

MERFISH 2.0, an ultra-sensitive single-cell spatial transcriptomics imaging chemistry across diverse tissue types

Spatial transcriptomics has emerged as a transformative approach for elucidating tissue architecture, cellular heterogeneity, and disease mechanisms by preserving the spatial context of gene expression in cells. Despite these advances, many spatial transcriptomic methods underperform in archival or clinically relevant specimens, particularly formalin-fixed, paraffin-embedded (FFPE) tissues, where RNA degradation and crosslinking hinder transcript detection. To address these challenges, we developed Multiplexed Error Robust Fluorescence In Situ Hybridization 2.0 (MERFISH 2.0), an optimized spatial transcriptomic imaging chemistry to enhance profiling of fragmented and highly crosslinked RNA. Across diverse human and mouse tissues preserved as fresh-frozen, fixed-frozen, and FFPE specimens, MERFISH 2.0 substantially increased transcript detection sensitivity by up to [~]8-fold relative to MERFISH 1.0 while preserving quantitative concordance (Pearson r [≥] 0.8 across tissues). In archived fresh-frozen human brain samples, MERFISH 2.0s enhanced sensitivity improved transcript recovery, enhanced cell type resolution and spatial analyses. In low quality archival FFPE human breast cancer specimen, MERFISH 2.0 revealed additional cell populations, novel cell clusters, refined tumor-immune architecture, and increased detection of gene-gene and cell-cell interactions relative to MERFISH 1.0, underscoring the impact of improved sensitivity on downstream spatial analysis. By substantially expanding robust transcript detection to degraded and archival samples, MERFISH 2.0 enables scalable, cohort-level spatial transcriptomic analysis across clinically relevant tissue collections.

genomics↗

HOXA10 is a Temporal Switch in Controlling Decidual Inflammation and Its Dysregulation is Associated with Early Pregnancy Loss

Successful implantation requires precisely timed endometrial inflammation. Although an initial inflammatory burst is essential for implantation, this response must be rapidly resolved for placentation and pregnancy to progress. The mechanisms that coordinate this temporal switch remain poorly understood. Here, we identify the transcription factor HOXA10 as a key regulator of inflammatory transitions in decidual stromal cells and examine how its dysregulation contributes to implantation failure and early pregnancy loss. In mice, HOXA10 expression decreases transiently at implantation and rises again post-implantation. Silencing HOXA10 in human decidualized stromal cells induced a robust pro-inflammatory state, altered integrin and cytoskeletal gene expression, and impaired stromal substrate adhesion. In non-pregnant Hoxa10 hypomorphs, stromal cells exhibited elevated IL1β and TXNIP, activation of the NLRP3/ASC inflammasome, and dysregulation of receptivity markers. During pregnancy, persistent HOXA10 deficiency prevented the resolution of inflammation, resulting in disorganized decidua, defective placentation, infertility, or progressive reproductive decline. To assess translational relevance, we analyzed publicly available bulk and single-cell RNA-seq datasets from first-trimester human decidua and from women with recurrent pregnancy loss (RPL). Single-cell analysis revealed that HOXA10 is selectively low in inflammatory decidual stromal cell clusters, which display concordant upregulation of IL1B, PYCARD, TXNIP, and inflammasome components. Consistently, both bulk and single-cell datasets from women with RPL showed reduced HOXA10 accompanied by increased inflammatory gene expression. Overall, HOXA10 functions as a temporal switch that enables the initial inflammatory activation required for implantation and subsequently suppresses inflammation to support decidual organization, adhesion, and placentation. Loss of this switch leads to persistent decidual inflammation and is associated with pregnancy loss in both mouse models and humans. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/691844v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@ee81b6org.highwire.dtl.DTLVardef@85d84eorg.highwire.dtl.DTLVardef@13c1b6aorg.highwire.dtl.DTLVardef@12bed9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

Microglial metabolic reprogramming drives cognitive decline in heart failure with preserved ejection fraction

Heart failure with preserved ejection fraction (HFpEF) is a rapidly growing public health concern and an emerging contributor to dementia, yet the mechanisms linking cardiometabolic dysfunction to neurodegeneration remain poorly understood. Here, we demonstrate that HFpEF drives a sustained neuroinflammatory state through microglial metabolic reprogramming. Using a clinically relevant murine model of HFpEF, we identified robust induction of HIF-1 signaling in microglia via integrated transcriptomics and metabolomics, coupled with increased glycolytic metabolism revealed by extracellular flux analysis. Conditional deletion of Hif1a in microglia during HFpEF attenuated neuroinflammation, preserved white matter integrity, and rescued cognitive performance. We further identify Sema4D as a HIF-1-dependent, microglia-derived effector linking metabolic stress to white matter injury. These findings establish a mechanistic bridge between cardiovascular disease and cognitive dysfunction and reveal microglial HIF-1 signaling as a tractable therapeutic strategy for preventing cognitive decline in cardiometabolic disease.

immunology↗

In Vivo Production of a Protein via the Delivery of Plasmid DNA by Computationally Designed Polymer Nanoparticles (PNP)

While monoclonal antibodies (mAbs) are a prominent class of pharmaceutical products there remain significant issues of cost, complexity, and especially delivery: concepts that overcome the need to infuse antibodies frequently are a desirable objective. An attractive approach is to deliver non-integrating DNA directly to muscle tissue, allowing the patient to act as their own so-called "protein factory." Demonstrations of this concept have been made using lipid nanoparticles (LNPs) and viral vectors, but these delivery methods face significant challenges, including poor extrahepatic delivery, cargo compatibility, safety, redosability, and cost. Polymer nanoparticles (PNPs) offer a solution to these problems, but face their own challenges, such as the vast number of possible polymer structures, and polyplex formulation conditions. However, advances in machine learning, materials informatics, and high-throughput chemical synthesis techniques provide a foundation for addressing these challenges by efficiently exploring the polymer design space. Our SAYERTM platform utilizes a large computational dataset of plasmid DNA (pDNA) - polymer interactions to facilitate targeting agent discovery and refinement via deep learning, and to drive discovery of novel PNPs for a wide variety of target tissues. In this work, we demonstrate our ability to design PNPs that can deliver pDNA encoding for PGT121, a broadly neutralizing anti-HIV antibody that targets a V3 glycan-dependent epitope site on the HIV-1 envelope glycoprotein. SAYER-designed polymers formed small and stable PNPs with PGT121 plasmids. Intravenous delivery demonstrated strong serum PGT121 protein levels at 1-day post-transfection and higher levels of protein expression when compared to other state-of-the-art DNA-delivery vehicles. More importantly, intramuscular delivery of Nanite PNPs enabled greater than 1.0 {micro}g/mL peak protein expression levels, with meaningful, durable expression levels at > 56 days post-injection. Further, we showed that we can increase antibody levels and durability by redosing. A general trend of lower dose and lower N/P ratio providing higher antibody levels is seen when PNPs were delivered intramuscularly. These parameters, separate from polymer structure, provide different mechanisms to optimize PNP in vivo delivery performance using machine learning techniques. Extension of the concept to the continuous production of other antibodies, proteins or enzymes is possible, suggesting the broad applicability of pDNA depoting via PNPs as a therapeutic modality. Finally, we emphasize that this strategy of delivering a DNA-encoded secreted proteins via a safe and effective PNP in vivo could be applicable to a wide range of other disease modalities.

bioengineering↗

Open-Source 3D Active Sample Stabilization for Fluorescence Microscopy

Super-resolution microscopy has enabled imaging at nanometer-scale resolution. However, achieving this level of detail without introducing artifacts that could mislead data interpretation requires maintaining sample stability throughout the entire imaging acquisition. This process can range from a few seconds to several hours, particularly when combining live-cell imaging with super-resolution techniques. Here, we present a 3D active sample stabilization system based on real-time tracking of fiducial markers. To ensure broad accessibility, the system is designed using readily available off-the-shelf optical and photonic components. Additionally, the accompanying software is open-source and written in Python, facilitating adoption and customization by the community. We achieve a standard deviation of the sample movement within 1 nm in both the lateral and axial direction for a duration in the range of hours. Our approach allows easy integration into existing microscopes, not only making prolonged super-resolution microscopy more accessible but also allowing confocal and widefield live-cell imaging experiments spanning hours or even days.

biophysics↗

Discovery of Isobavachin, a natural flavonoid, as an Apolipoprotein E4 (ApoE4) structure corrector for Alzheimer's disease

Alzheimers disease (AD) is a progressive neurodegenerative disease characterized by extensive neurodegeneration and consequent severe memory loss. Apolipoprotein E4 (ApoE4) is the strongest genetic risk factor for AD, with its pathological effects linked to structural instability and altered interactions with lipids and other important disease proteins including amyloid beta (A{beta}) and tau ({tau}). Therefore, correcting and stabilizing the ApoE4 structure has emerged as a promising therapeutic strategy for mitigating its detrimental effects. In this study, we investigated naturally occurring bioavailable flavonoids as ApoE4 stabilizers, focusing on their potential to modulate ApoE4 structure and function. Comprehensive investigation of a focused database using our integrated computational and experimental screening protocol led to the identification of Isobavachin as a potential corrector and stabilizer of ApoE4 structure. In addition, a few other bioavailable flavonoids with similar stabilizing properties were identified, albeit to a much lesser extent as compared to Isobavachin. The findings support the therapeutic potential of flavonoids as ApoE4 modulators and highlight Isobavachin as a lead candidate for further preclinical evaluation. These results provide new insights into the pharmacological targeting of ApoE4 and open avenues for the development of flavonoid-based, ApoE-directed therapies for AD.

neuroscience↗

Cytokine Dynamics and Oxidative Stress in Host Cells Stimulated with Drug-Resistant and Sensitive Mycobacterium tuberculosis Isolates

BackgroundThe immune response to Mycobacterium tuberculosis (M. tuberculosis) is central to the pathogenesis of tuberculosis (TB), yet the immune dynamics induced by drug-resistant strains remain underexplored. Understanding the hosts immune response to both drug-sensitive and drug-resistant M. tuberculosis isolates is crucial for elucidating the mechanisms of pathogenesis and resistance. This study aims to assess the cellular immune responses, including PBMC proliferation, cytokine secretion (IL-4 and IL-17a), and reactive oxygen species (ROS) production in response to live drug-sensitive and drug-resistant M. tuberculosis clinical isolates. MethodsPeripheral blood mononuclear cells (PBMCs) from PPD-negative and PPD-positive healthy volunteers were stimulated with live M. tuberculosis isolates, including MDR, SI-resistant, and sensitive strains. The immune responses were assessed by evaluating cell proliferation, secretion of IL-4 and IL-17a cytokines, and ROS production over a 9-day period. ResultsPBMCs from PPD-positive individuals exhibited a higher proliferative response compared to PPD-negative individuals, indicating more robust immune memory. IL-4 secretion was low but varied among samples, with higher levels observed in response to MDR isolates, suggesting a potential role in immunopathology. IL-17a levels increased over time, particularly in PPD-positive individuals, and MDR strains elicited a stronger response than sensitive isolates. ROS production was significantly elevated in response to resistant strains, reflecting the hosts oxidative defense mechanisms. ConclusionThis study demonstrates distinct immune responses to drug-resistant M. tuberculosis isolates, with variations in cell proliferation, cytokine secretion, and ROS production. These findings provide insights into the immune dynamics during infection with resistant strains and underscore the importance of genotype-environment interactions in TB pathogenesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/626310v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1bb9ad6org.highwire.dtl.DTLVardef@1b268e7org.highwire.dtl.DTLVardef@52800org.highwire.dtl.DTLVardef@85234b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Reprogramming the neuronal secretory and metabolic machinery using correctors for Alzheimer therapy

Alzheimer disease (AD) is a neurodegenerative disorder characterized by memory loss and personality changes, leading to dementia. The primary cause of the cognitive decline that characterizes AD is the loss of neurons, hypothesized as being due to secretory defects in neurotransmitter release and synaptic plasticity. There is growing evidence that in Alzheimer there is impaired neuronal metabolism due to an increase in free radicals and mitochondrial fission, leading to loss in ATP synthesis required for neurotransmission. Therefore, impaired metabolism in neurons may lead to the observed defects in neurotransmitter release, resulting in the loss of neuronal function and connections in regions of the brain involved in memory and reasoning. In our earlier studies, peptide inhibitor targeting oligomeric ATAD3A, a protein essential for mitochondrial fission and bioenergetics, were found to partially rescue from AD, both in AD neurons and AD mice. In the current study in AD neurons, neuronal porosome reconstitution combined with either a linear or circular peptide inhibitor of ATAD3A oligomers, was able to restore AD neurons to near normal levels of viability and greatly reduce oxidative stress in mitochondria. Additionally, the peptide and a small molecule considered safe by the FDA and used as a food additive, were also able to greatly increase viability in AD neurons and provide reduction to near normal levels of mitochondrial oxidative stress. Collectively, these results demonstrate great promise as secretory and metabolic correctors for AD therapy.

neuroscience↗

A repository of Ogden syndrome (NAA10) and NAA15 patient derived iPSC lines and isogenic pairs by X-chromosome screening and genome-editing.

Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting 80% of cytosolic proteins in humans. The human essential gene, NAA10, encodes the enzyme NAA10, as the catalytic subunit for the N-terminal acetyltransferase A (NatA) complex, including the accessory protein, NAA15. The first human disease directly involving NAA10 was discovered in 2011, and it was named Ogden syndrome (OS), after the location of the first affected family residing in Ogden, Utah, USA. Since that time, other variants have been found in NAA10 and NAA15. Here we describe the generation of 31 iPSC lines, with 16 from females and 15 from males. This cohort includes CRISPR-mediated correction to the wild-type genotype in 4 male lines, along with editing one female line to generate homozygous wild-type or mutant clones. Following the monoclonalizaiton and screening for X-chromosome activation status in female lines, 3 additional pairs of female lines, in which either the wild type allele is on the active X chromosome (Xa) or the pathogenic variant allele is on Xa, have been generated. Subsets of this cohort have been successfully used to make cardiomyocytes and neural progenitor cells (NPCs). These cell lines are made available to the community via the NYSCF Repository.

genetics↗

Arc/Arg3.1 binds the nuclear polyadenylate-binding protein RRM and regulates neuronal activity-dependent formation of nuclear speckles

Arc is a neuronal activity-induced protein interaction hub with critical roles in synaptic plasticity and memory. Arc localizes to synapses and the nucleus, but its nuclear functions are little known. We show that Arc accumulates in the interchromatin space of dentate granule cell nuclei and the nucleosol subcellular fraction following seizure activity and in vivo dentate gyrus LTP. Proteomic analysis of affinity-purified Arc complexes identified proteins with functions in post-transcriptional mRNA processing. During LTP, Arc undergoes enhanced complex formation with polyadenylate binding protein nuclear 1 (PABPN1) and paraspeckle splicing factor (PSF) in the nucleosol. In vitro peptide binding arrays show selective binding of Arc to the PABPN1 polyA RNA recognition motif. In hippocampal neuronal cultures, Arc knockdown increases formation of PABPN1 nuclear speckles and blocks chemical-LTP associated increases in small PABPN1 foci. These results implicate Arc in basal and neuronal activity-dependent regulation of PABPN1 speckles involved in mRNA processing and polyadenylation.

neuroscience↗

Array Detection Enables Large Localization Range for Simple and Robust MINFLUX

The MINFLUX concept significantly enhances the spatial resolution of single-molecule localization microscopy (SMLM) by overcoming the limit imposed by the fluorophores photon counts. Typical MINFLUX microscopes localize the target molecule by scanning a zero-intensity focus around the molecule in a circular trajectory, with smaller trajectory diameters yielding lower localization uncertainties for a given number of photons. Since this approach requires the molecule to be within the scanned trajectory, MINFLUX typically relies on a photon-demanding iterative scheme with decreasing trajectory diameters. Although the iterative procedure does not substantially reduce the photon efficiency of MINFLUX, this approach is prone to misplacements of the trajectory and increases the systems complexity. In this work, we introduce ISM-FLUX, a novel implementation of MINFLUX using image-scanning microscopy (ISM) with a single-photon avalanche diode (SPAD) array detector. ISM-FLUX provides precise MINFLUX localization within the trajectory while maintaining conventional photon-limited uncertainty outside it. The robustness of ISM-FLUX localization results in a larger localization range and greatly simplifies the architecture, which may facilitate broader adoption of MIN-FLUX.

bioengineering↗

Tumor Subtype Classification Tool for HPV-associated Head and Neck Cancers

ImportanceMolecular subtypes of HPV-associated Head and Neck Squamous Cell Carcinoma (HNSCC), named IMU (immune strong) and KRT (highly keratinized), are well-recognized and have been shown to have distinct mechanisms of carcinogenesis, clinical outcomes, and potentially differing optimal treatment strategies. Currently, no standardized method exists to subtype a new HPV+ HNSCC tumor. Our paper introduces a machine learning-based classifier and webtool to reliably subtype HPV+ HNSCC tumors using the IMU/KRT paradigm and highlights the importance of subtype in HPV+ HNSCC. ObjectiveTo develop a robust, accurate machine learning-based classification tool that standardizes the process of subtyping HPV+ HNSCC, and to investigate the clinical, demographic, and molecular features associated with subtype in a meta-analysis of four patient cohorts. Data SourcesWe conducted RNA-seq on 67 HNSCC FFPE blocks from University of Michigan hospital. Combining this with three publicly available datasets, we utilized a total of 229 HPV+ HNSCC RNA-seq samples. All participants were HPV+ according to RNA expression. An ensemble machine learning approach with five algorithms and three different input training gene sets were developed, with final subtype determined by majority vote. Several additional steps were taken to ensure rigor and reproducibility throughout. Study SelectionThe classifier was trained and tested using 84 subtype-labeled HPV+ RNA-seq samples from two cohorts: University of Michigan (UM; n=18) and TCGA-HNC (n=66). The classifier robustness was validated with two independent cohorts: 83 samples from the HPV Virome Consortium and 62 additional samples from UM. We revealed 24 of 39 tested clinicodemographic and molecular variables significantly associated with subtype. ResultsThe classifier achieved 100% accuracy in the test set. Validation on two additional cohorts demonstrated successful separation by known features of the subtypes. Investigating the relationship between subtype and 39 molecular and clinicodemographic variables revealed IMU is associated with epithelial-mesenchymal transition (p=2.25x10-04), various immune cell types, and lower radiation resistance (p=0.0050), while KRT is more highly keratinized (p=2.53x10-08), and more likely female than IMU (p=0.0082). Conclusions and RelevanceThis study provides a reliable classifier for subtyping HPV+ HNSCC tumors as either IMU or KRT based on bulk RNA-seq data, and additionally, improves our understanding of the HPV+ HNSCC subtypes.

bioinformatics↗