Biology subjects

Li, Y.

Publications and source records attributed to Li, Y..

At least 289 records · Page 16Linked to original sources

bioRxiv2026

Organoid modeling of tumor-associated macrophages reveals phagocytosis checkpoint blockade-induced conversion to an immunosuppressive SPP1+ phenotype

Tumor-associated macrophages (TAM) exert essential functions during the immune response to cancer. However, investigations of TAM within a native human tumor microenvironment (TME) have been impeded by a lack of appropriate model systems. Here, patient-derived organoids (PDO) from air-liquid interface (ALI)-grown tumor fragments, containing a human TME that encompassed stroma and immune subsets, robustly preserved TAM that were maintained by endogenous CSF-1 and appropriately responded to polarization signals. Antibody blockade of the CD47 regulatory checkpoint in organoids stimulated phagocytosis and remodeled TAM cytokine secretion profiles that were confirmed in anti-CD47 phase I trial patients. Amongst PDO histologies screened, anti-CD47 tumor killing was notable in clear cell renal cell carcinoma (ccRCC) which was associated with increased TAM infiltration. PDO contained diverse previously described TAM subsets; however, anti-CD47 reprogrammed organoid TAM toward an immunosuppressive SPP1+ phenotype, highlighting a negative feedback mechanism. Our findings uncover a resistance circuit engaged by macrophage checkpoint blockade and position ALI PDO as a robust translational platform for dissecting human macrophage biology and informing precision immunotherapy.

cancer biology↗

bioRxiv2026

Understanding the mechanisms of lateral parietalmemory modulation in Mild Cognitive Impairment

The application of transcranial magnetic stimulation (TMS) to lateral parietal cortex has shown promise in improving episodic memory in older adults with Mild Cognitive Impairment (MCI). Previous work has suggested that such improvements are achieved by activating hippocampus at a distance with TMS, though this explanation is incomplete. We hypothesized that the mnemonic benefits arise from an additional mechanism: the modulation of semantic representations. Nineteen participants with amnestic MCI received either active intermittent theta-burst stimulation (iTBS) to angular gyrus or control vertex stimulation over three consecutive days while viewing object stimuli and completing relational memory encoding tasks during fMRI, followed by conceptual and perceptual recognition memory tests. We found that active TMS (relative to control TMS) significantly modulated conceptual memory performance. Using Representational Similarity Analysis with semantic embeddings derived from a large language model, we examined how TMS affects neural representations in inferior parietal lobule and hippocampus. We found that TMS enhanced semantic representational strength in inferior parietal lobule and reduced representational strength in hippocampus. Surprisingly, both effects supported successful memory. Neural pattern similarity analyses suggested that reduced hippocampal similarity supported successful memory, perhaps by promoting pattern separation mechanisms. These findings demonstrate that parietal TMS modulates semantic processing in a region-specific manner, by strengthening semantic integration at the stimulation site while promoting representational differentiation in medial temporal regions. This work advances our mechanistic understanding of memory neuromodulation and has implications for the optimization of therapeutic interventions in age-related memory disorders. Significance StatementTranscranial Magnetic Stimulation (TMS) applied to parietal cortex can improve memory in patients with Mild Cognitive Impairment (MCI), a population at high risk for Alzheimers Disease, yet the mechanisms underlying this benefit remain poorly understood. Using fMRI and Representational Similarity Analysis (RSA), we examined how TMS alters the neural representation of semantic stimulus information in parietal cortex and hippocampus during memory encoding. Our results show that TMS selectively modulates semantic representations at the stimulation site and in hippocampus, and that these representational changes predict memory improvement. These findings advance our mechanistic understanding of parietal memory neuromodulation and lay the groundwork for more targeted and effective TMS-based interventions for age-related memory disorders.

neuroscience↗

bioRxiv2026

A massively parallel reporter assay of MECP2 cis-regulatory elements reveals genetic candidates for male-biased autism

Autism affects males four times more often than females, yet the basis of this sex bias remains unclear. One hypothesis is that hypomorphic variants in X-linked genes--genes where loss-of-function alleles cause syndromic neurodevelopmental disorders (NDDs) predominantly in females--produce milder, non-syndromic phenotypes in hemizygous males. We tested this by investigating cis-regulatory elements (CREs) of MECP2, a dosage-sensitive X-linked gene. Using a massively parallel reporter assay in human neurons, we mapped transcription factor binding sites within MECP2 CREs and tested autism-associated variants for functional impact. We identified two noncoding variants that change CRE activity, each with a male-biased phenotype. One of these, a promoter variant, disrupts NFY binding and reduces MECP2 expression by [~]30%, a magnitude that produces autism-like phenotypes in mice. These findings suggest noncoding MECP2 variants can cause non-syndromic, male-biased autism, and provide a framework for uncovering regulatory variants in other X-linked NDD genes that may contribute to autisms missing heritability.

genetics↗

bioRxiv2026

Scalable longitudinal imaging and transcriptomics of cells in dynamic enclosures

Dynamic transitions between cell states underlie both normal physiology and disease. However, most single-cell technologies capture only static snapshots. To address this gap, we developed a platform that integrates light-guided hydrogel polymerization with computer vision to generate on-demand compartments around live cells, enabling longitudinal imaging of cellular behavior paired with whole-transcriptome profiling of the same cells at scale. These data link dynamic phenotypes with molecular programs, enabling deeper characterization of cellular states. This approach revealed an adaptive, drug-resistant state in lung cancer cells characterized by potassium channel upregulation and p53-dependent quiescence. In models of adipogenesis and microglial phagocytosis, joint analysis of imaging and transcriptomic data identified key drivers of cellular function that were missed by transcriptomic clustering alone. These results establish the value of paired functional and transcriptomic analysis to resolve molecular drivers of complex cellular behaviors.

systems biology↗

bioRxiv2026

CXCL13-CXCR5 Signaling in CD8⁺ T Cell Recruitment and Lymphoid Immune Organization in Clear Cell Renal Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC) exhibits heterogeneity in immune infiltration and clinical outcomes, but the mechanisms governing recruitment and organization of tumor-reactive CD8 T cells remain incompletely defined. We investigated the role of the CXCL13-CXCR5 axis in shaping CD8 T cell recruitment, differentiation, and immune organization in high-risk, non-metastatic ccRCC. Human tumor, plasma, and matched adjacent kidney specimens were analyzed using ELISA, quantitative PCR, migration assays, multiplex immunofluorescence, single-cell RNA sequencing, spatial transcriptomics, and a syngeneic mouse model. CXCL13 was among the most upregulated chemokines in ccRCC relative to matched normal kidney and was embedded within a CD8 T cell-associated inflammatory transcriptional program. In transwell and microphysiological system (MPS) assays, CXCL13 promoted CD8 T cell migration, enriched CXCR5 cells among migrating CD8 T cells and showed reduced migration after CXCL13 or CXCR5 blockade. Single-cell analyses identified CXCR5 expression within stem-like CD8 T cell states associated with TCF7 and IL7R, whereas CXCL13 associated with later cytotoxic/exhausted states along a continuous differentiation landscape. Spatial transcriptomics demonstrated that stem-like CD8 T cells localized within structured lymphoid aggregates enriched for B cells, coordinated CXCL13/CXCR5 expression, and signaling programs. In vivo, tumor-derived CXCL13 suppressed tumor growth, increased intratumoral CD8 T cell infiltration, and enriched CXCR5TCF1CD8 stem-like T cells. In human tumors, higher CXCL13 expression correlated with increased CXCR5CD8 T cell infiltration and improved recurrence-free survival. These findings identify CXCL13 as a regulator of immune recruitment and niche organization and support the CXCL13-CXCR5 axis as a biomarker and possible therapeutic target in ccRCC.

cancer biology↗

bioRxiv2026

Retroelement Hypomethylation Links Hypoxia Signaling, Immune Phenotypes, and Survival in Clear Cell Renal Cell Carcinoma

BackgroundRetrotransposable elements (RE) comprise approximately 45% of the human genome and are typically repressed by DNA methylation to preserve genomic integrity. In cancer, global DNA hypomethylation can lead to RE derepression, resulting in genomic instability and activation of innate immune pathways through viral mimicry. While individual RE classes have been examined in clear cell renal cell carcinoma (ccRCC), the integrated epigenetic landscape of multiple RE families and their clinical relevance remain incompletely characterized. MethodsWe performed a genome-wide prediction of DNA methylation across three major RE classes (Alu, LINE-1, and LTR elements) using a validated computational framework applied to Illumina methylation array data from two independent ccRCC tumor cohorts. Integrated unsupervised clustering of RE methylation profiles was used to define the epigenetic subtypes. Associations with clinicopathologic variables, tumor immune microenvironment composition (DNA Methylation-derived), hypoxia signaling, innate immune activation, and overall survival were evaluated. Prognostic relevance was assessed using multivariable Cox regression models adjusting for age, sex, AJCC stage or AUA risk group, and immune and angiogenic tumor microenvironment features. Key findings were then externally validated in CPTAC-ccRCC and independently replicated in an institutional Dartmouth Cancer Center (DCC) cohort with matched methylation and RNA-sequencing data. ResultsIntegrated clustering identified three reproducible RE methylation subtypes, Repressed, Transient, and Active. In the discovery cohort, the Active subtype showed significantly worse overall survival than the Repressed subtype, with a graded survival pattern across RE methylation states that persisted after multivariable adjustment. RE hypomethylation was associated with reduced EPAS1 (HIF2A) expression, increased immune infiltration, elevated PD-1 expression, and heightened cGAS-STING and interferon signaling, consistent with an immune-inflamed yet immunosuppressed tumor state. In the external CPTAC validation cohort, RE methylation subtypes recapitulated key molecular features and showed supportive survival trends. In the independent DCC replication cohort, an Active RE state was again associated with poorer survival, lower EPAS1 expression, increased PD-1 expression, greater CD8 T-cell and Treg infiltration, and elevated T-cell exhaustion signatures, supporting the reproducibility of the prognostic and immune-exhausted phenotype across cohorts. ConclusionsWe identified RE methylation subtypes with distinct molecular, immunologic, and prognostic features in ccRCC. External validation in CPTAC and independent replication in DCC support the robustness of this RE methylation framework across large-scale and institutional cohorts. These findings highlight the prognostic potential of RE methylation profiles and support their integration into molecular classification strategies to improve risk stratification in ccRCC.

cancer biology↗

bioRxiv2026

Coordinated acetylcholine release and adaptation of neuronal representations in the retrosplenial cortex during contextual uncertainty

Accurate learning underpins optimal predictions and requires the brain to navigate uncertainty, identifying important information and distinguishing between expected and unexpected uncertainties. Theoretical models propose that the neuromodulator acetylcholine positively correlates with expected uncertainty, priming neuronal networks for learning. We tested this hypothesis by measuring acetylcholine release and neuronal representations in the retrosplenial cortex of mice whilst challenging them with expected and unexpected uncertainties of reward location. Acetylcholine release did not directly correlate with expected or unexpected uncertainty but instead increased with changes in expected uncertainty. In tandem, increased expected uncertainty shifted neuronal representations from a positional reference frame to focus on salient landmarks, such as reward location. Transitions in expected uncertainty also accelerated remapping of neuronal representations and behavioural adaptation when unexpected uncertainty was experienced. Thus, we demonstrate acetylcholine release in retrosplenial cortex discerns types of uncertainty and correlates with learning speed in uncertain environments.

neuroscience↗

bioRxiv2026

Hippocampal Glucuronyl C5-epimerase promotes stress resilience by directly engaging PI3K through a non-enzymatic mechanism

Major depressive disorder (MDD) seriously affects human physical and mental health and causes global socioeconomic burdens. Stress-induced depressive etiology is linked to dendritic atrophy in the hippocampus, however, the underlying mechanism was poorly understood. Here, we identify that glucuronyl C5-epimerase (Glce), a heparan sulfae-modifying enzyme, as a critical regulator of hippocampal dendritic integrity and stress resilience. Genetic ablation of Glce in the hippocampal excitatory neurons is sufficient to induce dendritic atrophy and depressive-like behaviors, whereas its restoration rescues these deficits. Notably, Glce levels are reduced in the plasma of depressed individuals. We further find that Glce functions independently of its enzymatic activity, instead binding directly to and activating PI3K (p85/p110), thereby triggering an Akt/CREB/BDNF signaling cascade. Together, our findings uncover a non-canonical role for Glce and establish that Glce-PI3K-BDNF axis is essential for maintaining hippocampal structure and behavioral resilience, thereby highlighting a critical role of Glce in the pathophysiology of depression.

neuroscience↗

bioRxiv2026

The contribution of short tandem repeats to splicing variation in the human cortex

BackgroundSplicing disruption has been implicated in a range of heritable phenotypes, including numerous psychiatric and neurological disorders. Recent studies have identified thousands of common genetic variants impacting splicing in brain and other tissues, but have focused largely on single nucleotide polymorphisms or short indels. Despite growing evidence that genetic variation at short tandem repeats (STRs) influences splicing, large-scale studies of STR-mediated splicing in brain have been limited by low sample sizes of available RNA-seq data or exclusion of certain classes of STRs, such as homopolymers which account for around half of all STRs. ResultsIn this study, we leveraged deep RNA-seq and SNP array data from 336 human dorsolateral prefrontal cortex (DLPFC) samples collected by the Human Brain Collection Core (HBCC). We imputed 445,720 STRs into available genotype data and identified 51,343 unique STRs for which copy number is significantly associated with one or multiple alternative splicing events of nearby genes (spliceSTRs). We prioritized and characterized candidate causal spliceSTRs using three orthogonal fine-mapping strategies which identified 1,313 high-confidence fine-mapped spliceSTRs. Our analyses revealed strong associations between copy number of certain repeat units and binding of specific RNA-binding proteins (RBPs), including a previously known relationship between HNRNPL and AC repeat length, suggesting that the functional impact of some spliceSTRs may be mediated through their binding affinity for RBPs. Finally, co-localization analyses using summary statistics from genome-wide association studies (GWAS) for 6 brain-related disorders identified multiple signals that may be driven by spliceSTRs, including a previously identified GTn repeat that is a spliceSTR for PLEKHA1 associated with Alzheimers disease as well as a newly identified AGGn spliceSTR in SEPTIN3 co-localized with schizophrenia. ConclusionsTogether, our findings highlight the role of STRs in regulating alternative splicing in the human brain, suggest a general relationship between STR polymorphism and RBP-mediated splicing events, and identify specific spliceSTRs detected by co-localization analysis as candidate causal variants for brain-related disorders.

genomics↗

bioRxiv2026

Automated behavioral segmentation and markerless pose tracking of mice during spaceflight

The NASA Rodent Habitat aboard the International Space Station enabled long-duration studies of behavioral responses to spaceflight, but video-based behavioral analysis has relied on laborious manual annotation. No study has tested whether deep learning tools can automate this analysis under the demanding imaging conditions of orbital vivaria. We applied pose estimation (SLEAP) and behavioral segmentation (DeepEthogram) to archival footage from the Rodent Research-1 mission. Nine labelers annotated 3,249 pose labels across 2,063 frames, and three behaviorists labeled 411,194 frames across 66 videos. Pose tracking accuracy approximated human inter-annotator variability despite progressive lens soiling, grid occlusions, and spherical aberration. Behavioral classification across eight categories achieved accuracy of 0.86-0.90 and suggests progressive behavioral adaptations to microgravity. Kinematic reconstruction of circling estimated centripetal accelerations periodically approaching 1g. This is the first application of deep learning-based pose estimation and behavioral segmentation to rodents in spaceflight, establishing benchmarks for future monitoring systems. One-Sentence SummaryDeep learning-based pose estimation and behavioral segmentation of ISS video reveal progressive behavioral adaptations of mice to microgravity

neuroscience↗

bioRxiv2026

Discovery of a CI-994 derivative as a dual modulator of class I HDACs and Wnt/β-catenin signaling for Alzheimer's disease therapy

Alzheimers disease (AD) is a multifactorial disease with mixed pathologies. Consequentially, drugs targeting multiple pathological processes may offer synergistic benefits. While histone deacetylase (HDAC) inhibitors have demonstrated efficacy in alleviating AD-related pathologies in animal models, the neuroprotective Wnt/{beta}-catenin signaling pathway remains compromised in AD brain. CI-994 is a class I HDAC inhibitor containing N-(2-aminophenyl)-benzamide. Our recent studies indicate that CI-994 is also an activator of Wnt/{beta}-catenin signaling by stabilizing Wnt co-receptor LRP6. We herein use CI-994 as a scaffold to develop novel potent dual modulators of class I HDACs and Wnt/{beta}-catenin signaling for AD therapy. Our lead compound, W2A-28, selectively inhibits class I HDAC1, 2 and 3 with IC50 values of 0.51 M, 0.68 M, and 0.22 M, respectively, and shows no inhibitory activities on other HDACs. Furthermore, W2A-28 potently activates Wnt reporter activity with an EC50 value of 1.61 M in Wnt-3A-expressing HEK293 cells. As expected, activation of Wnt/{beta}-catenin signaling by W2A-28 is associated with elevated LRP6 protein level. Importantly, W2A-28 displays excellent microsomal stability in both mouse and human liver microsomal stability assays, alongside high permeability and a lack of active efflux in MDR1-MDCKII models. Critically, W2A-28 treatment significantly enhances histone acetylation, activates Wnt/{beta}-catenin signaling, and suppresses tau phosphorylation in AD patient-specific cerebral organoids carrying APOE {varepsilon}4/{varepsilon}4 or APOE {varepsilon}3/{varepsilon}4 with PSEN1 M146V mutation. Our findings position W2A-28 as a promising multi-target drug candidate for AD therapy.

neuroscience↗

bioRxiv2026

Magnetogenetic control of endogenous calcium signaling via ROS-sensitive ion channels reveals astrocytic regulation of neural circuit activity

Astrocytes exhibit complex calcium signaling proposed to detect, integrate, and modulate neuronal activity; however, their causal contribution to neural circuit function remains unresolved. This is partly due to the lack of tools that recapitulate physiological astrocyte calcium signaling. Here, we show that experimental magnetic control of endogenous calcium signaling in astrocytes is sufficient to modulate neural circuit dynamics. Using pmFeRIC, a magnetogenetic tool for remote, noninvasive, and on-demand activation of endogenous calcium pathways, we demonstrate that selective activation of astrocyte calcium signaling drives neuronal activity. pmFeRIC uses magnetic fields and endogenous ferritin to generate localized reactive oxygen species (ROS) at the plasma membrane, activating native ROS-sensitive ion channels, inducing calcium influx. In hippocampal circuits in vitro, magnetic activation of endogenous astrocytic calcium signaling produced robust, state-dependent changes in neuronal circuit activity, in part by increasing presynaptic release probability, postsynaptic burst firing, and glutamatergic transmission. These effects were mediated by transient receptor potential channels, amplified by intracellular calcium stores, and abolished when astrocyte calcium signaling was disrupted, establishing a causal role in neural circuit dynamics. In vivo, pmFeRIC activates endogenous calcium signaling in astrocytes with kinetics comparable to locomotion-induced activity, enabling control of astrocyte calcium dynamics that resemble physiological behavioral responses. Together, these findings establish that endogenous astrocytic calcium signaling is sufficient to modulate neural circuit function and introduce a broadly applicable platform for cell-specific, wireless, on-demand control of endogenous calcium signaling through magnetic activation of ROS-sensitive ion channels.

neuroscience↗

bioRxiv2026

Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells

Cohesin is crucial for establishing 3D genome organization and functions. However, the in vivo mechanism of cohesin-mediated extrusion remains unsettled. Here, we investigated extrusion directionality using integrated genome mapping coupled with perturbation in human cells. By defining cohesin loading at NIPBL binding loci and anchoring at CTCF sites, we systematically characterized the aggregated and single-molecule trajectories of extrusion "stripes" and contact "dots" from and between individual cohesin loading and anchoring points. Our analyses delineated two dynamic modes of in vivo mechanism in which NIPBL/cohesin initiates extrusion at its loading sites in a one-sided manner; after encountering CTCF, CTCF/cohesin switches its extrusion direction backward and robustly extrude DNA unidirectionally until completing the convergent CTCF loop. Surprisingly, depleting CTCF resulted substantial increase of NIPBL/cohesin-mediated extrusion activity, which is further validated by in silico perturbation. These findings reveal novel mechanistic insights into how cohesin and CTCF orchestrate cohesin-mediated loop extrusion in vivo.

genomics↗

bioRxiv2026

Dynamical Biomarkers of Creative Cognition Across Divergent and Convergent Problem-Solving

Creativity fluctuates markedly from moment to moment, even within the same individual, yet the neural dynamics that determines whether a given attempt produces a highly creative idea remains poorly understood. Prior studies have identified static EEG correlates of creative thinking, but these do not explain how brain activity is dynamically organized before and during successful idea generation. Here, we model creative cognition as trajectories through a neural state space using energy landscape analysis (ELA) of EEG recorded during two complementary problem-solving paradigms: the divergent Alternative Uses Test (AUT) and the convergent, goal-directed Fusion Innovation Test (FIT). Across both tasks, creative success was associated with dissociable dynamical signatures in the resting and ideation stages. Before ideation, greater diversity of resting-state patterns of activity, corresponding to possible attractors, indexed a preparatory substrate of creative potential, showing weak trial-level effects but robust subject-level coupling with performance. During ideation, higher creativity was predicted by how the brain traversed its accessible state space: successful trials were characterized by traversal biased toward sustained exploration within stable attractor basins rather than frequent switching between basins of attraction ({beta} = 0.104, p = 0.004, trial-level). These findings identify a task-invariant, biologically grounded dynamical mechanism of creative cognition and show that creative performance depends not only on which neural states are available, but also on how neural activity traverses that state space.

neuroscience↗

bioRxiv2026

Axonal swelling as a neuron-specific compartment to sequester and expel misfolded proteins

Neurons are long-lived, highly specialized cells with extended neurites, requiring precise control of misfolded proteins over time and space. Yet, where misfolded proteins are directed and how quality-control pathways adapt during aging are still unresolved. Here, we identify a neuron-specific quality-control compartment that emerges in neurites as aggresome function declines with age, which we call SolAS (Soluble Misfolded Proteins-induced Axonal Swellings). These structures not only sequester misfolded proteins but also facilitate their clearance via microvesicles and exophers. During aging, neurite SolAS and soma aggresomes function hierarchically to maintain proteostasis, with aggresomes acting as the primary sequestration sites in young neurons and SolAS taking over this role as their function declines with age. This transition is driven by a shift from a ubiquitin-dominant to a SUMO-dominant balance. Moreover, solid pathogenic amyloids, such as GA50, can be converted into soluble forms and sequestered into SolAS via SUMO fusion, thereby reducing neurotoxicity. Our findings identify a previously unrecognized neuronal quality-control pathway critical for proteostasis during aging.

neuroscience↗

bioRxiv2026

Survivin inhibition induces PD-L1 expression through cGAS stabilization and attenuates antitumor immunity

BackgroundSurvivin is a mitotic regulator frequently overexpressed in human cancers and an attractive therapeutic target. However, how Survivin inhibition influences tumor immune regulation remains incompletely understood. This study aimed to investigate whether Survivin inhibition modulates antitumor immunity and to elucidate the underlying mechanisms. MethodsProgrammed death-ligand 1 (PD-L1) expression was evaluated in multiple tumor cell lines following pharmacological or genetic inhibition of Survivin. Mechanistic studies included RNA sequencing, immunoblotting, flow cytometry, cGAS knockdown, and NF-{kappa}B inhibition. Immune profiling was performed using CD8 T-cell cytotoxicity assays, mass cytometry, flow cytometry, immunofluorescence and single-cell RNA sequencing. Clinical relevance was assessed using patient tumor specimens and public immunotherapy cohorts. ResultsSurvivin inhibition, either by YM155 treatment or genetic depletion, increased PD-L1 expression at both mRNA and protein levels in tumor cells. Mechanistically, Survivin inhibition stabilized cyclic GMP - AMP synthase (cGAS) by reducing its ubiquitination and activated NF-{kappa}B signaling, thereby promoting transcriptional upregulation of PD-L1. Functionally, the induced PD-L1 enhanced PD-1 engagement and suppressed CD8 T-cell cytotoxicity, promoting immune evasion. In immunocompetent ovarian cancer models, pharmacological inhibition of Survivin increased PD-L1 expression in tumor and immune compartments and attenuated cytotoxic immune activity. PD-L1 blockade restored antitumor immunity and significantly enhanced the therapeutic efficacy of Survivin inhibition. In addition, analyses of patient samples and public single-cell datasets revealed an inverse association between Survivin and PD-L1 expression, and high Survivin expression was associated with reduced benefit from PD-1/PD-L1 blockade. ConclusionsThese findings identify a Survivin-cGAS-PD-L1 axis linking mitotic stress to immune suppression and provide a mechanistic rationale for combining Survivin-targeted therapy with immune checkpoint blockade.

cancer biology↗

bioRxiv2026

Eukaryotic domestication of a bacterial immune protein following horizontal transfer

Many components of eukaryotic innate immunity originated from bacterial immune systems. However, it is unclear how eukaryotes acquire these genes and how the components are domesticated into eukaryotic physiology. Here, we discovered a recent instance of bacteria-eukaryote horizontal transfer and used it to characterize the genetic and biochemical changes that accompanied eukaryotic acquisition. We focus on Toll/interleukin-1 receptor (TIR) domains, which are widespread yet potentially costly immune modules associated with inflammation and/or cell death. By generating an atlas of TIR diversity across the tree of life, we phylogenetically categorized the domains and uncovered highly diverged, eukaryotic TIR families. This analysis revealed a horizontal transfer event that created the TirBCD protein family of Dictyostelium amoebae, which is closely related to the bacterial immune protein TIR-STING. While the TIR domain was transferred into amoebae, the genomic locus did not contain known regulatory domains nor other components of a bacterial operon. Nevertheless, TirC retained biochemical and physiological similarities to TIR-STING. TirC is a highly potent NADase, capable of oligomerizing into large complexes and depleting NAD+ even at very low protein concentrations. When expressed in heterologous systems, TirC was spontaneously active and highly toxic. In contrast, the natural amoeba host tolerated expression of full length TirC, showing that the cells can typically regulate its activity and avoid autoimmunity. However, a truncated form of TirC induced rapid rounding and cell lysis. These results suggest that amoebae have used TirC to retool a form of bacterial cell death for use in eukaryotic cells. Overall, this study uncovers recent eukaryotic TIR evolution that captures features of both bacterial and eukaryotic immunity. We also expect that the TIR domain atlas will be useful to researchers across model systems as they explore the vast diversity of TIR molecular and cellular functions.

microbiology↗

bioRxiv2026

linearPOA: A parallel, memory-efficient framework for Partial Order Alignment with linear space complexity

Multiple sequence alignment (MSA) is a fundamental problem in computational bioinformatics, playing a critical role in genome biology, especially in long read sequencing and assembly. One solution for representing and solving MSA is Partial Order Alignment (POA), which employs Directed Acyclic Graphs (DAGs) to represent sequence relationships. However, when facing the ultra-long, error-prone reads (e.g., >100 kbps), existing POA algorithms with quadratic space complexity become impractical due to excessive memory consumption. This paper introduces the linearPOA, which based on divide-and-conquer strategy to solve the POA, aimed at saving memory compared to quadratic space complexity algorithms like SPOA, abPOA and TSTA. Particularly notable is its capability to save up to 102.74 times memory usage when aligning sequences with 100 kbp reads, compared to the abPOA method using non-heuristic methods. The algorithm was implemented within the linearPOA library, providing functionality for POA and foundational support for sequencing analysis, like error correction for reads. The linearPOA algorithm provides memory-efficient algorithms for long-read sequencing, especially in directly assembling long reads like 100 kbp reads. AvailabilityThe linearPOA library is freely available at https://github.com/malabz/linearPOA, and the data underlying this article are available in Zenodo, at https://doi.org/10.5281/zenodo.15637837. Supplementary informationSupplementary information are available at BioRxiv online.

bioinformatics↗