Biology subjects

Xu, E.

Publications and source records attributed to Xu, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Synaptic microRNA dysregulation orchestrates aberrant glutamatergic transmission in a human neuronal model of 22q11.2 deletion syndrome

22q11.2 Deletion Syndrome (22q11DS), the most prevalent chromosomal microdeletion disorder in humans (incidence ~1 in 4,000 live births), arises from hemizygous deletions of a 1.5-3.0 Mb region on chromosome 22. Notably, 20-30% of individuals with 22q11DS develop schizophrenia (SCZ) by early adulthood, making 22q11DS one of the strongest genetic risk factors for SCZ. However, the mechanisms by which the 22q11.2 deletion perturbs neuronal function and drive psychotic manifestations in 22q11DS remain poorly defined. In this study, we generated human 2D cortical neurons and 3D cortical organoids from induced pluripotent stem cells (iPSCs) derived from clinically well-characterized individuals with 22q11DS. Cellular and electrophysiological analyses revealed that 22q11DS neurons exhibit hyperexcitability, reduced glutamatergic synaptic transmission, and impaired homeostatic synaptic plasticity, which are pathophysiological hallmarks that may be relevant to the clinical, cognitive, and psychophysiological profiles of patients. Transcriptomic profiling of neurons and synaptosomes from 22q11DS cortical organoids uncovered dysregulated immune pathways and synaptic gene networks. Integrative mRNA-microRNA network analysis identified synergistic downregulation of hsa-miR-185-5p and hsa-miR-128-3p at synapses, driving aberrant regulation of immune and synaptic transcripts. Experimental knockdown of these microRNAs in control neurons recapitulated the molecular and functional phenotypes of 22q11DS neurons, thereby establishing a mechanistic link to synaptic dysfunction and impaired plasticity. Collectively, these findings delineate a multimodal mechanistic framework that bridges genetic vulnerability, synaptic pathology, and psychosis penetrance in 22q11DS, positioning dysregulated synaptic microRNAs as nodal regulators of neurodevelopmental networks and potential therapeutic targets.

neuroscience↗

bioRxiv2026

Molecular Basis of Histone H3 Reading and Writing by Legionella pneumophila SET Domain Lysine Methyltransferases

RomA and its highly conserved strain ortholog LegAS4 are SET and ankyrin domain-containing effector proteins of the intracellular bacterial pathogen Legionella pneumophila. These enzymes are secreted into host cells, where they translocate to the nucleus and methylate Lys14 in histone H3 (H3K14), a novel post-translation modification (PTM) that reprograms gene expression and promotes bacterial replication. To elucidate their H3K14 substrate specificity, we determined the crystal structures of LegAS4 and RomA bound to histone H3 peptides and characterized nucleosome binding and methylation by the enzymes. The results reveal a distinctive bipartite engagement of the histone H3 N-terminal tail by the enzymes SET and ankyrin domains. Further, the ankyrin domain distinguishes different PTMs at H3R2 and H3K4, which is crucial for nucleosome engagement and H3K14 methylation. Together, these studies yield new insights into histone H3 reading and writing by the L. pneumophila histone lysine methyltransferases during host cell infection.

biochemistry↗

bioRxiv2026

Haplotype-resolved centromeric chromatin organization from a complete diploid human genome

Centromeres ensure proper chromosome segregation during cell division, yet the organization and regulation of centromeric chromatin within satellite DNA arrays remain incompletely understood. Here, we leverage the complete diploid human genome benchmark (T2T-HG002) to provide a detailed study of centromeric sequence and chromatin architecture on individual haplotypes. Using adaptive-sampling-enriched, ultra-long-read DiMeLo-seq, we achieve single-molecule chromatin profiling across all centromeres, revealing that along single chromatin fibers, CENP-A, the histone variant specifying centromere identity, forms multiple discrete subdomains within hypomethylated centromere dip regions (CDRs) that are flanked by H3K9me3-enriched heterochromatin. Despite underlying sequence variation, CDRs localize to sequence-homogeneous domains and maintain relatively balanced CENP-A dosage and aggregate length across all chromosomes and between haplotypes. Further, we show that bidirectional changes to centromeric and pericentromeric DNA methylation are accompanied by changes to centromeric chromatin architecture. In passaged cells with centromeric hypomethylation, subdomain boundaries are eroded, and adjacent CENP-A domains tend to merge and expand. Conversely, in pluripotent stem cells with centromeric hypermethylation, CDRs are fundamentally reorganized, such that discrete hypomethylated domains are frequently consolidated into broader contiguous tracts. These methylation-associated CDR restructuring events suggest that DNA methylation acts as a principal regulator of human centromere organization, with implications for understanding centromere plasticity, epigenetic inheritance, and chromosomal instability in development and disease.

genomics↗

bioRxiv2026

Multiplexed cellular and tissue imaging via plasmonic heating activated signal exchange of DNA probes

Fluorescence microscopic methods are critical for spatial profiling of multiple biological targets in cells and tissues to study cell and tissue functions, but their multiplexity was limited to 3[~]5 targets under a conventional setup using different fluorescent channels because of spectra overlap. Here, we introduce a simple, rapid, multiplexed fluorescence imaging method in cells and tissues, termed DNA based plasmonic heating activated signal exchange reaction (PHASER). PHASER uses infrared light-induced plasmonic heating of gold bipyramid nanoparticles to sequentially activate thermodynamically calibrated DNA thermal probes in situ for rapid and multiplexed fluorescent imaging of biological targets. We showed that the signal exchange per round between biological targets in PHASER can be completed within 30 seconds, and that 5 irradiation pulses of photothermal heating can activate DNA thermal probes with 5 different signal temperatures in cells and tissues. To demonstrate its practical use, we applied PHASER to profile the subcellular spatial organization of different organelles in cultured cells and resolved different protein spatial expression profiles in mouse brain tissue with dimensions of millimeters in a single fluorophore channel. PHASER is expected to have broad biotechnical applications with multiplexed fluorescence imaging for a wide variety of biological targets across diverse samples.

bioengineering↗

bioRxiv2026

Microglial Lag3 Drives α-Synuclein--induced Neurotoxic Activated (A1) Astrocytes and Neurodegeneration

BackgroundNeuroinflammation and pathologic -synuclein (-syn) aggregation cooperate to drive dopaminergic neurodegeneration in Parkinsons disease, but the glial receptors that couple extracellular -syn to inflammatory cascades remain incompletely defined. Microglia express higher levels of lymphocyte activation gene 3 (Lag3) than neurons, yet the contribution of microglial Lag3 to -syn recognition, glial crosstalk, and neurodegeneration is unknown. MethodsBiochemical binding assays, live-cell imaging, cytokine profiling, and neuron-microglia-astrocyte co-culture paradigms were used to define Lag3-dependent -syn preformed fibril (PFF) binding, uptake, and microglial activation. To interrogate in vivo function, microglia-specific Lag3 conditional knockout mice (Lag3L/L-Cx3cr1CreER) and littermate controls received unilateral intrastriatal -syn PFF injections, followed by histological, biochemical, and behavioral assessments of -syn pathology, gliosis, nigrostriatal integrity, and motor performance. Results-syn PFFs bound microglial Lag3 with high specificity and nanomolar affinity and required Lag3 for efficient fibril internalization and induction of proinflammatory cytokines. Microglial Lag3 deficiency markedly blunted -syn PFF-evoked microglial activation, prevented cytokine-driven conversion of astrocytes into neurotoxic reactive A1 astrocytes, and abolished astrocyte-dependent neuronal death in vitro. In vivo, microglia-specific Lag3 deletion reduced cortical, striatal, and substantia nigra pS129 -syn pathology, suppressed microgliosis and A1 astrocyte induction, preserved substantia nigra dopaminergic neurons and striatal dopamine transporter/tyrosine hydroxylase expression, and ameliorated -syn PFF-induced motor deficits. ConclusionsThis study identifies microglial Lag3 as a key receptor linking extracellular -syn PFF recognition to inflammatory amplification, neurotoxic reactive A1 astrocyte conversion, and dopaminergic neurodegeneration. Together with prior work on neuronal Lag3, these findings support a cell-type-specific dual-axis model in which neuronal Lag3 mediates -syn propagation while microglial Lag3 drives glia-dependent neurotoxicity, positioning Lag3 as a promising precision therapeutic target in -synucleinopathies.

neuroscience↗

bioRxiv2025

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

Pedigree analysis remains the gold standard for rare disease diagnostics, yet whole genome sequencing studies typically omit critical regions like centromeres, telomeres, and acrocentric chromosome p-arms. Here, we present telomere-to-telomere (T2T) reference genomes for four self-identified African American individuals of admixed ancestry spanning three generations. Our parent-of-origin assigned, chromosome-level assemblies revealed precise meiotic recombination breakpoints in previously inaccessible regions, including recombination events across acrocentric and subtelomeric sequences. Centromeric regions were highly stable, with multi-megabase arrays inherited intact across three generations, while the position of kinetochore assembly sites remained consistent and predominantly associated with the p-arm proximal region. The relative lengths of telomeres on individual chromosomes were maintained across generations. Using a targeted rDNA assembly approach, we reconstructed a complete megabase-scale ribosomal DNA (rDNA) array corresponding to the paternal chromosome 14. This openly available pedigree provides a benchmark dataset for studying recombination and genetic and epigenetic variation across the complete genome.

genomics↗

bioRxiv2025

A tailored in vivo CRISPR screen identifies BAP1 as a potent tumor suppressor of soft tissue sarcoma

Undifferentiated pleomorphic sarcoma (UPS) is one of the most common soft tissue sarcomas (STS) in adults. Despite decades of research, therapeutic advancements for STS, including UPS, have remained limited. The genetic complexity of UPS, characterized by the absence of recurrent driver oncogene mutations, has hindered the development of effective targeted therapies beyond conventional chemotherapy and immunotherapy. To address this challenge, we conducted a customized in vivo CRISPR/Cas9 screen in mice to systematically identify potential tumor suppressors involved in UPS development. Our screen revealed BRCA1-associated protein 1 (Bap1) as a potent tumor suppressor in STS. Using total RNA sequencing, multiplex immunohistochemistry, and flow cytometry, we found that Bap1-deficient mouse sarcomas exhibit significant immune suppression. Further analysis indicated that polo-like kinase 1 (Plk1) is essential for the survival of Bap1-deficient sarcomas. Treatment with volasertib, a Plk1 inhibitor, markedly inhibited tumor growth in both syngeneic and spontaneous mouse models of Bap1-loss sarcoma. In conclusion, our findings suggest that PLK1 inhibition, or combined with immunotherapy, may represent a promising targeted therapeutic strategy for tumors lacking BAP1.

cancer biology↗

bioRxiv2025

Longitudinal Changes in Cortical Response Dynamics with Deep Brain Stimulation to the Subcallosal Cingulate for Treatment-Resistant Depression

Deep brain stimulation (DBS) of the subcallosal cingulate cortex (SCC) is a promising intervention for treatment-resistant depression, yet objective biomarkers that track recovery remain limited. This study examined longitudinal changes in stimulation-evoked potentials (SEPs) to characterize how SCC-driven cortical communication evolves during treatment. Ten patients across three SCC-DBS trials underwent high-density EEG recordings at 4 and 24 weeks. SEP features were extracted from source-localized SCC signals and related to clinical outcomes and fractional anisotropy (FA) of midcingulate cingulum. Cortical responses showed a consistent reduction in latency and an increase in magnitude over time, indicating faster and stronger electrocortical signaling with chronic stimulation. Higher baseline midcingulate FA predicted greater latency acceleration, linking SEP timing to white-matter integrity. These findings identify temporal SEP dynamics as candidate mechanistic biomarkers that reflect circuit engagement during SCC-DBS and offer a pathway toward physiology-guided optimization of neuromodulation for depression. HighlightsO_LIReduced latency of stimulation evoked potential after 6 months of DBS C_LIO_LILarger cortical evoked response to single pulse perturbation after 6 months of DBS C_LIO_LIBaseline myelin integrity in MCC predicts magnitude of change in EP latency C_LI

neuroscience↗

bioRxiv2025

Programmable orthogonal and rapid DNA strand displacement for fluidic-exchange-free highly multiplexed fluorescent imaging

Multiplexed fluorescent imaging methods are essential for studying cellular function by visualization of biomolecules in cells and tissues with high-resolution spatial information, but most suffer from limitations such as low multiplexity because of spectral overlap between the used fluorophores. Fluidic exchange based sequential multiplexed imaging overcomes this limitation but requires time-consuming incubation and washing steps. We introduce a novel multiplexed fluorescent imaging method that uses rapid, orthogonal DNA strand displacement reactions to enable unlimited multiplexed fluorescent imaging without fluidic exchange. The signal switching between targets is achieved by strand displacement with added non-fluorescent DNA displacer strands, no fluidic washing step is required for sequential multiplexed imaging. We experimentally screened a set of rapid and orthogonal DNA displacement sequences for probe design and applied it for RNA imaging, which takes less than 30 seconds per round to complete in fixed cells. Because of the vast sequence design space of DNA probes, theoretically unlimited multiplexity can be achieved. Using 25 developed rapid orthogonal probes, we achieved 25-plex RNA imaging in a single fluorophore channel in fixed cells within 20 minutes. To further demonstrate robustness and practical usage of DIRSE-based imaging, we showed 24-plex RNA imaging with the method in retinal tissues and resolved different cell types. This DIRSE mechanism significantly simplifies the high-plex fluorescent imaging process with pre-programmed DNA probes and has broad biotechnical applications for future medicine and diagnostics.

bioengineering↗

bioRxiv2024

α-Synuclein Strain Dynamics Correlate with Cognitive Shifts in Parkinson's Disease

-Synuclein (-syn) strains can serve as discriminators between Parkinsons disease (PD) and related -synucleinopathies. The relationship between -syn strain dynamics and clinical performance as patients transition from normal cognition (NC) to cognitive impairment (CI) is not known. Here, we show that the biophysical properties and neurotoxicity of -syn strains change as PD cognitive status transitions from NC to mild cognitive impairment (PD-MCI) and dementia (PD-D). Both cross-sectional and longitudinal analyses reveal distinct -syn strains in PD patients correlating to their level of cognitive impairment. Machine learning (ML) was employed to achieve high classification accuracy. The combination of thioflavin T (ThT) maximal fluorescence intensity (mfi), max slope of rise curve (forming rate), lag time (tlag), 20% time (t20), and half-time (t50), dynamic light scattering (DLS) (peak number, [1/2] peak size, [1/2] peak intensity) and neurotoxicity together with demographic variables for model training yielded superior performance (89[~]99% accuracy in the 4- and 2- classification schema) compared to individual features alone in classifying cognitive status. For the longitudinal study, DLS peak number emerged as the strongest predictor of cognitive transition (HR = 0.12, P = 0.002), with the optimal predictive model combining DLS peak number, sex, education, DLS peak 1 size, and DLS peak 2 polydispersity achieving high accuracy (C-index of [~]93%). This study presents evidence that individuals with PD have different -syn strains correlating to their cognitive status and highlights the potential of -syn strain dynamics to guide future diagnosis, management, and stratification of PD patients. One Sentence SummaryDistinct features of -syn strains change with cognitive decline in Parkinsons disease and AI-based analysis incorporating these combined characteristics serves as a powerful tool for PD clinical stratification.

neuroscience↗

bioRxiv2024

Modular Nano-Scaffold Biocatalysis for Superior PET Depolymerization and Valorization

The global crisis of polyethylene terephthalate (PET) waste demands new strategies for sustainable management. Biocatalytic recycling offers a promising route, but direct depolymerization under moderate conditions is often limited by kinetic constrains of individual enzyme. Here, we engineer and optimize modular protein scaffolds that utilize orthogonal interaction domains, including the cohesin-dockerin pairs from bacterial cellulosomes and the SH3 ligand/domain pair from mouse Crk, to assemble complementary hydrolases (PETase, MHETase, and ICCG) into a synergistic multi-enzyme cascade. This architecture overcomes intermediate inhibition, efficiently converting PET hydrolysis products into the final monomers, terephthalic acid (TPA) and ethylene glycol (EG), outperforming previous multi-enzyme systems. The systems application is further evaluated by stability enhancement via immobilization on metal-organic frameworks (MOFs), coupling depolymerization to the valorization of EG into glycolic acid (GA), and adapting the system for scalable whole-cell biocatalysis. This scaffold-based multi-enzyme approach provides a new strategy for developing integrated biocatalytic systems to advance a circular PET economy.

synthetic biology↗

bioRxiv2024

Zebrafish models of human-duplicated gene SRGAP2 reveal novel functions in microglia and visual system development

The expansion of the human SRGAP2 family, resulting in a human-specific paralog SRGAP2C, likely contributed to altered evolutionary brain features. The introduction of SRGAP2C in mouse models is associated with changes in cortical neuronal migration, axon guidance, synaptogenesis, and sensory-task performance. Truncated SRGAP2C heterodimerizes with the full-length ancestral gene product SRGAP2A and antagonizes its functions. However, the significance of SRGAP2 duplication beyond neocortex development has not been elucidated due to the embryonic lethality of complete Srgap2 knockout in mice. Using zebrafish, we show that srgap2 knockout results in viable offspring and that these larvae phenocopy "humanized" SRGAP2C larvae, including altered morphometric features (i.e., reduced body length and inter-eye distance) and differential expression of synapse-, axonogenesis-, and vision-related genes. Through single-cell transcriptome analysis, we demonstrate a skewed balance of excitatory and inhibitory neurons that likely contribute to increased susceptibility to seizures displayed by Srgap2 mutant larvae, a phenotype resembling SRGAP2 loss-of-function in a child with early infantile epileptic encephalopathy. Single-cell data also shows strong endogenous expression of srgap2 in microglia with mutants exhibiting altered membrane dynamics and likely delayed maturation of microglial cells. Microglia cells expressing srgap2 were also detected in the developing eye together with altered expression of genes related to axonogenesis in mutant retinal cells. Consistent with the perturbed gene expression in the retina, we found that SRGAP2 mutant larvae exhibited increased sensitivity to broad and fine visual cues. Finally, comparing the transcriptomes of relevant cell types between human (+SRGAP2C) and non-human primates (-SRGAP2C) revealed significant overlaps of gene alterations with mutant cells in our zebrafish models; this suggests that SRGAP2C plays a similar role altering microglia and the visual system in modern humans. Together, our functional characterization of conserved ortholog Srgap2 and human SRGAP2C in zebrafish uncovered novel gene functions and highlights the strength of cross-species analysis in understanding the development of human-specific features. Abstract (short)SRGAP2C has been implicated in contributing to altered brain features in the evolution of humans. However, the significance of SRGAP2 duplication beyond neocortex development has not been elucidated due to the embryonic lethality of complete Srgap2 knockout in mice. Using zebrafish, we show that srgap2 knockout results in viable offspring that phenocopy "humanized" SRGAP2C larvae. Morphometric, behavioral, and transcriptome analyses collectively suggest srgap2 impacts axonal guidance, synaptogenesis, and seizure susceptibility. Beyond neurons, Srgap2 functions in controlling membrane dynamics and maturation of microglial cells, possibly leading to altered axonogenesis in the developing retina and increased sensitivity to broad and fine visual cues. Comparing relevant transcriptomes between human and nonhuman primates suggests that SRGAP2C similarly impacts microglia and vision in modern humans. Our functional characterization of conserved ortholog Srgap2 and human SRGAP2C in zebrafish uncovered novel gene functions and highlights the strength of cross-species analysis in understanding the development of human-specific features.

genomics↗

bioRxiv2024

Creating anatomically-derived, standardized, customizable, and three-dimensional printable head caps for functional neuroimaging

AbstractO_ST_ABSSignificanceC_ST_ABSConsistent and accurate probe placement is a crucial step towards enhancing the reproducibility of longitudinal and group-based functional neuroimaging studies. While the selection of headgear is central to these efforts, there does not currently exist a standardized design that can accommodate diverse probe configurations and experimental procedures. AimWe aim to provide the community with an open-source software pipeline for conveniently creating low-cost, 3-D printable neuroimaging head caps with anatomically significant landmarks integrated into the structure of the cap. ApproachWe utilize our advanced 3-D head mesh generation toolbox and 10-20 head landmark calculations to quickly convert a subjects anatomical scan or an atlas into a 3-D printable head cap model. The 3-D modeling environment of the open-source Blender platform permits advanced mesh processing features to customize the cap. The design process is streamlined into a Blender add-on named "NeuroCaptain". ResultsUsing the intuitive user interface, we create various head cap models using brain atlases, and share those with the community. The resulting mesh-based head cap designs are readily 3-D printable using off-the-shelf printers and filaments while accurately preserving the head topology and landmarks. ConclusionsThe methods developed in this work result in a widely accessible tool for community members to design, customize and fabricate caps that incorporate anatomically derived landmarks. This not only permits person-alized head cap designs to achieve improved accuracy, but also offers an open platform for the community to propose standardizable head caps to facilitate multi-centered data collection and sharing.

neuroscience↗

bioRxiv2024

Microenvironment T-Type calcium channels regulate neuronal and glial processes to promote glioblastoma growth

BackgroundGlioblastoma (GBM) is the most common primary malignant brain tumor. The aim of this study was to elucidate the role of microenvironment and intrinsic T-type calcium channels (Cav3) in regulating tumor growth and progression. MethodsWe grafted syngeneic GBM cells into Cav3.2 knockout mice to assess the role of microenvironment T-Type calcium channels on GBM tumor growth. We performed single-cell RNA-seq (scRNA-seq) of tumors from WT and Cav3.2 KO mice to elucidate the regulation of tumors by the microenvironment. We used neurons from WT and Cav3.2 KO mice in co-culture with GBM stem cells (GSC) to assess the effects of Cav3.2 on neuron/GSC synaptic connections and tumor cell growth. ResultsCav3.2 KO in the microenvironment led to significant reduction of GBM growth and prolongation of animal survival. scRNA-seq showed that microenvironment Cav3.2 regulates neuronal and glial biological processes. Microenvironment Cav3.2 downregulated numerous genes associated with regulating the OPC cell state in GBM tumors such as SOX10 and Olig2. Neuronal Cav3.2 promoted neuron/GSC synaptic connections and GSC growth. Treatment of GSCs with the Cav3 blocker mibefradil downregulated genes associated with neuronal processes. The Cav3 blocker drug mibefradil synergized with temozolomide (TMZ) and radiation to reduce in vivo tumor growth and prolong animal survival. ConclusionsTogether these data reveal a role for microenvironment Cav3 in promoting GBM tumor progression through regulating neuronal and glial processes particularly associated with the OPC-cell state. Targeting both intrinsic and microenvironment Cav3 with the inhibitor mibefradil significantly enhanced the anti-GBM effects of TMZ and radiation. Key PointsO_LIMicroenvironment Cav3.2 promotes GBM progression C_LIO_LIMicroenvironment Cav3.2 promotes neuronal and glial processes C_LIO_LIPharmacological targeting of intrinsic and microenvironment Cav3 synergizes with TMZ/radiation C_LI Importance of the StudyIn this study, we demonstrate for the first time that microenvironment Cav3.2 contributes to GBM progression and growth by regulating neuronal and glial processes. Our findings highlight the importance of T-type calcium channels in the microenvironment as well as the tumor and provides preclinically relevant data for the use of mibefradil to inhibit GBM growth in combination with standard of care therapies.

cancer biology↗

bioRxiv2024

Mouse α-synuclein fibrils are structurally and functionally distinct from human fibrils associated with Lewy body diseases

Short AbstractThe intricate process of -synuclein aggregation and fibrillization hold pivotal roles in Parkinsons disease (PD) and multiple system atrophy (MSA). While mouse -synuclein can fibrillize in vitro, whether these fibrils commonly used in research to induce this process or form can reproduce structures in the human brain remains unknown. Here we report the first atomic structure of mouse -synuclein fibrils, which was solved in parallel by two independent teams. The structure shows striking similarity to MSA-amplified and PD-associated E46K fibrils. However, mouse -synuclein fibrils display altered packing arrangements, reduced hydrophobicity, heightened fragmentation sensitivity, and evoke only weak immunological responses. Furthermore, mouse -synuclein fibrils exhibit exacerbated pathological spread in neurons and humanized -synuclein mice. These findings provide new insights into the structural underpinnings of -synuclein pathogenicity and emphasize a need to reassess the role of mouse -synuclein fibrils in the development of related diagnostic probes and therapeutic interventions.

neuroscience↗

bioRxiv2023

Neural Interoceptive Processing is Modulated by Deep Brain Stimulation for Treatment Resistant Depression

BackgroundA critical advance in depression research is to clarify the hypothesized role of interoceptive processing in neural mechanisms of treatment efficacy. This study tests whether cortical interoceptive processing, as indexed by the heartbeat-evoked potential (HEP), is modulated by deep brain stimulation (DBS) to the subcallosal cingulate (SCC) for treatment resistant depression (TRD). MethodsEight patients with TRD were enrolled in a study of SCC DBS safety and efficacy. Electroencephalography (EEG) and symptom severity measures were sampled in a laboratory setting over the course of a six-month treatment protocol. The primary outcome measure was an EEG-derived HEP, which reflects cortical processing of heartbeat sensation. Cluster-based permutation analyses were used to test the effect of stimulation and time in treatment on the HEP. The change in signal magnitude after treatment was correlated with change in depression severity as measured by the 17-item Hamilton Depression Rating Scale. ResultsHEP amplitude was greater after 24 weeks of treatment (t(7)=-4.40, p=.003, g=-1.38, 95% Cl [-2.3, -0.42]), and this change was inversely correlated with latency of treatment response (rho = -0.75, 95% Cl [-0.95, -0.11], p=.03). An acute effect of DBS was also observed, but as a decrease in HEP amplitude (t(6) =6.66, p<.001, g=2.19, 95% Cl [0.81, 3.54]). HEP differences were most pronounced over left posterior sensors from 405-425 ms post-stimulus. ConclusionBrain-based evidence substantiates a theorized link between interoception and depression, and suggests an interoceptive contribution to the mechanism of treatment efficacy with deep brain stimulation for severe depression.

neuroscience↗

bioRxiv2022

A compact breast shape acquisition system for improving diffuse optical tomography image reconstructions

Diffuse optical tomography (DOT) has been investigated for diagnosing malignant breast lesions but its accuracy relies on model-based image reconstructions which in turn depends on the accuracy of breast shape acquisition. In this work, we have developed a dual-camera structured light imaging (SLI) breast shape acquisition system tailored for a mammography-like compression setting. Illumination pattern intensity is dynamically adjusted to account for skin tone differences while thickness-informed pattern masking reduces artifacts due to specular reflections. This compact system is affixed to a rigid mount that can be installed into existing mammography or parallel-plate DOT systems without the need for camera-projector re-calibration. Our SLI system produces sub-millimeter resolution with a mean surface error of 0.26 mm. This breast shape acquisition system results in more accurate surface recovery, with an average 1.6-fold reduction in surface estimation errors over a reference method via contour extrusion. Such improvement translates to 25% to 50% reduction in mean squared error in the recovered absorption coefficient for a series of simulated tumors 1-2 cm below the skin.

bioengineering↗

bioRxiv2022

Structural and functional landscape of α-synuclein fibril conformations amplified from cerebrospinal fluid

Lewy body dementias are pathologically defined by the deposition of -synuclein fibrils into inclusions throughout the brain. Cerebrospinal fluid(CSF) in disease harbors circulating -synuclein-fibril seeds, and parental -synuclein fibrils can template core structure into amplified fibrils. Using cryo-electron microscopy, we identify six novel -synuclein fibril assemblies amplified from ten CSF samples (3.8[A] to 2.9[A] nominal resolutions). Fibrils are classified based on two types of filament interaction, two types of {beta}-sheet stacking, and two types of hydrophobic pocket. CSF-amplified fibril products have one, two, or three distinct assemblies each. Six of ten samples share a common fibril assembly. Within this classification, the fibrils have distinct profiles in amyloid dye binding, and dramatically different potencies in both seeding new inclusions in neurons and evoked microglial pro-inflammatory responses. However, no single structural feature predicts functional phenotypes. Our results highlight CSF as a valuable resource to identify novel -synuclein assemblies potentially important in disease.

neuroscience↗