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bioRxiv2026

Structures of MyD88 and its oncogenic mutant reveal DNA binding with implications for cytosolic DNA sensing

MyD88 is a universal adaptor that connects to Toll-like receptors and interleukin-1 receptors through its Toll/IL-1R homology (TIR) domain and activates inflammatory signaling via its death domain (DD). However, how MyD88TIR serves as the platform for these functions and if it has additional functions remain unclear. Here, we report cryogenic electron microscopy (cryo-EM) structures of MyD88TIR and its cancer-specific mutant L252P (previously L265P) mainly in ring and spiral forms, respectively. Both assemblies are formed by antiparallel double-filaments, using canonical TIR interfaces within each strand but unique surfaces between the strands, and position MyD88DD at the same sides of the assemblies for self-oligomerization and pathway activation. Surprisingly, these WT or L252P filaments are bound to dsDNA using the concave sides of the rings and the spirals. In vitro assays and cellular studies establish that MyD88 directly binds dsDNA and promotes inflammatory cytokine expression, particularly pro-IL-1{beta}, following dsDNA transfection or viral infection. Notably, these responses are unaffected by deficiency of UNC93B1, the essential chaperone required for trafficking endosomal nucleic acid-sensing TLRs. Structure-guide MyD88 mutant that disrupts dsDNA binding specifically compromises dsDNA-induced transcriptional program while maintaining TLR signaling. RNA-seq further reveals that MyD88 plays a crucial role in inducing gene expression upon dsDNA sensing and that about half of cGAS-dependent genes are also MyD88-dependent. Together, our structural, biochemical and genetic data support the findings that MyD88 directly engages with cytosolic dsDNA and cooperates with cGAS to promote the full innate immune transcriptional response.

immunology↗
bioRxiv2026

Human infection with an ape Plasmodium vivax-like parasite

An unusually divergent Plasmodium vivax parasite was reported in a Swedish patient with recent travel. Using whole-genome sequencing, we show that the infection was caused by a strain of ape P. vivax-like, providing evidence of the zoonotic potential of these parasites that infect wild gorillas and chimpanzees in central Africa.

genetics↗
bioRxiv2026

Revealing multiscale architecture of the intact human spine using hierarchical phase contrast tomography

Background: Computed tomography (CT) and magnetic resonance imaging (MRI) provide detailed clinical assessment of the human spine; however, their millimeter-scale spatial resolution limits direct visualization of tissue microarchitecture and interfaces. Hierarchical phase-contrast tomography (HiP-CT) enables ex vivo non-destructive, micron-resolution imaging of intact human organs without exogenous contrast agents, extending anatomical assessment to spatial scales inaccessible to conventional clinical imaging. Purpose: To evaluate the capability of HiP-CT to visualize macro- to microanatomy of an intact adult human spine ex vivo. Methods: An intact spine (C1-L5) from a 62-year-old male donor without known skeletal disease was formalin-fixed and imaged by HiP-CT at the European Synchrotron. Whole-spine imaging was performed at 16.26 m isotropic voxels, with selected regions of interest imaged using 2.2 m voxels. Ex vivo MRI using clinical sequences was performed for anatomical comparison. Three-dimensional segmentation and quantitative analyses included intervertebral disc (IVD) grading, annulus fibrosus fiber tracing, and vertebral trabecular micro-morphometry. Results: HiP-CT enabled high spatial-resolution, multiscale imaging of the intact human spine, simultaneously visualizing vertebral bone and endplate, IVDs, spinal cord and meninges, nerve roots and ganglia, vasculature, ligaments, and musculature. Three-dimensional segmentation and virtual sectioning mapped neurovascular anatomy and vertebral vascular supply, without exogenous contrast enhancement, while preserving their relationships with surrounding tissues. Whole-spine images enabled quantitative analysis of annulus fibrosus fiber organization and vertebral trabecular microarchitecture, permitting the detection of focal posterolateral fiber disruption at the L4-L5 IVD and regional differences in trabecular architecture between cervical and lumbar vertebral bodies. Local tomography resolved annulus fibrosus lamellae, vertebral endplate Haversian systems, and facet joint hyaline cartilage at micron resolution. Conclusions: HiP-CT enables non-destructive, multiscale three-dimensional imaging of the intact human spine while preserving tissue relationships across spatial scales and hard-soft tissue boundaries. HiP-CT could provide an ex vivo microanatomical reference for future correlation with clinical imaging investigations of spinal disease and in the development and validation of imaging biomarkers.

bioengineering↗
bioRxiv2026

A preclinical platform for focused ultrasound delivery from microplate to awake brain

Background. Focused ultrasound (FUS) has broad therapeutic potential, but its mechanisms of action are poorly understood. Preclinical FUS research enables rigorous interrogation of understudied parameters, but fragmented, single-purpose benchtop devices prevent standardized acoustic exposure across models. Objective. To describe a unified preclinical FUS platform for cell culture, ex vivo tissue, and awake stereotaxic in vivo delivery in one lightweight system, validated using glioblastoma as a disease model. Methods. We performed single-well FUS delivery to 96-well microplates, single-well delivery to freshly resected human glioblastoma tissue, and stereotaxic transcranial delivery to awake, head-fixed mice ambulating freely on a floating cage. Output was independently calibrated in free field, with measured microplate insertion loss. Pulsed low-intensity focused ultrasound (pLIFU) was applied to GL261-bearing mice, resected human glioblastoma, and macrophage cell lines. Results. Awake stereotaxic pLIFU produced acute tumor signal attenuation in GL261-bearing mice (mean log2 fold-change -1.66 versus +5.20 controls, p = 0.016) with bioluminescence evidence consistent with focal targeting. Ex vivo pLIFU produced directionally consistent immunophenotypic shifts in human glioblastoma (increased iNOS+, decreased Arg1+ populations). In vitro, pLIFU reduced CD80 on immunosuppressive macrophages to 73% of baseline in RAW 264.7 cells (p = 0.0008, n = 5) and 64% in THP-1 cells (p = 0.0006, n = 2), with MHC II upregulation in RAW 264.7 (ratio 1.65, p = 0.004) and ARG1 reduction in THP-1 (ratio 0.52, p = 0.0025). Conclusions. A unified preclinical FUS platform validated across in vitro, ex vivo, and awake in vivo applications enables stereotaxically guided transcranial FUS in awake, head-fixed mice ambulating in an exploratory manner during sonication, and single-well microplate treatments.

neuroscience↗
bioRxiv2026

CellMethMarker provides an integrated database of human cell- and tissue-type-specific DNA methylation markers

Cell- and tissue-type-specific DNA methylation markers provide epigenetic signatures of cellular identity and are widely used to infer cellular origin from bulk and single-cell methylomes. Existing resources mainly emphasize disease-associated biomarkers, methylome atlases, genomic annotations or RNA-based cell markers, leaving an unmet need for an integrated region-level resource dedicated to such markers. Here we present CellMethMarker (http://gu-zhanglab.hfcas.ac.cn/CellMethMarker), a curated database integrating 347,514 de novo markers derived from uniformly processed whole-genome and reduced-representation bisulfite sequencing datasets, 2,203,507 literature-derived marker records and harmonized metadata for 2,810 samples. CellMethMarker enables cell- and tissue-centered marker retrieval, coordinate-based search, genome-browser visualization, interactive methylation analysis and data download. In an independent single-cell methylome atlas, these markers recover the expected cell-type-associated methylation patterns, and a platform-matched reference built from them lowers the mean deconvolution error from 0.365 to 0.144. CellMethMarker therefore links region-level DNA methylation variation to cellular identity and supports methylome-based cell-type annotation and deconvolution.

bioinformatics↗
bioRxiv2026

A comprehensive identification protocol for postcranial bones of Southeast Asian Ruminantia. Part 2: Morphological criteria for small and medium-sized species

The taxonomic identification of postcranial elements from small and medium-sized ruminants represents a significant challenge in zooarchaeological and Late Quaternary paleontological studies, particularly in biodiversity-rich regions such as continental Southeast Asia. This study presents a comprehensive osteological reference framework for the small and medium-sized Ruminantia of this region, based on a comparative sample of 228 specimens representing 14 species across three families (Bovidae, Cervidae, and Moschidae). Osteological characters were first described on a small initial specimen set and subsequently scored across the full sample. Although a small number of character states were found to be unique to specific taxa, most proved highly variable, limiting their individual identification potential. To address this, a Random Forest and a Naive Bayes classifier were applied to assess the discriminatory power of character combinations across four taxonomic ranks (Family, Subfamily, Genus, and Species) on independent bones. Both approaches performed similarly, achieving mean identification accuracies of 87-86% at the family level, 69% at the subfamily level, 50% at the genus level, and 35-33% at the species level. The Naive Bayes models were further deployed as an interactive web application, allowing users to perform bone identification based on any combination of observable character states from a single anatomical element. Our results highlight the limits of morphological identification of postcranial elements in this taxonomic and biogeographic context, while demonstrating that a transparent, reproducible, and statistically grounded approach can still represent a significant step forward for zooarchaeological and Late Quaternary paleontological studies in Southeast Asia and beyond.

zoology↗
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