Biology subjects

Li, Z.

Publications and source records attributed to Li, Z..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

NeuroPilot: Longitudinal intravital neural imaging across scales and modalities through an agentic platform

Longitudinal intravital imaging is essential for understanding how neural populations evolve across behavioral states, yet converting large-scale recordings into biological insight remains a fundamental challenge because neural signals are degraded by noise, non-rigid motion, and heterogeneous recording conditions. Here we introduce NeuroPilot, an agentic framework that transforms neural imaging analysis into a closed-loop, context-aware process, integrating a multimodal large language model with callable computational imaging modules to adaptively coordinate workflows from raw recordings to population-level readouts. Across heterogeneous imaging and experimental regimes, NeuroPilot restores motion-degraded recordings and supports consistent neural signal recovery, detection, and tracking in challenging deep-brain, freely moving, and longitudinal settings. These enable neuronal population tracking across spinal stimulation paradigms, deep-brain imaging, and continuous 24-hour mPFC recordings aligned with spontaneous sleep-wake behavior. By converting heterogeneous intravital recordings into stable population activity maps, NeuroPilot supports behavioral decoding and reveals structured neural dynamics across behavioral states and transitions. NeuroPilot establishes a scalable agentic paradigm for neural imaging analysis, expanding experimental access to the measurement, visualization, and interpretation of neural population activity.

neuroscience↗

bioRxiv2026

NeoOmni Atlas: an integrated database for pan-cancer neoantigen derived from proteogenomics analysis

Tumor neoantigens derived from diverse molecular aberrations are important targets for personalized cancer immunotherapy, but existing resources incompletely integrate mass-spectrometry-supported canonical and non-canonical antigen evidence across cancer types. NeoOmni Atlas is an interactive pan-cancer T-cell epitope resource, built via proteogenomic reanalysis of 7,561 immunopeptidomics datasets comprising 511 million raw spectra from 2,341 samples across 26 cancer types. The analysis yielded 872,414 eluted canonical peptides and 198,961 non-canonical peptides spanning 18 molecular alteration classes, along with 759,386 unique ligands presented by 322 human leukocyte antigen (HLA) alleles. Relative to existing repositories, NeoOmni Atlas covers a broader range of cancer types, includes 60 additional HLA alleles, and catalogs 369,781 novel ligands. A computational tumor-specific filtering framework identified 316,126 tumor-associated epitopes and 61,231 tumor-specific epitopes. Tumor-specific epitopes showed stronger predicted binding affinity than tumor-associated epitopes for HLA class I A and B alleles, and 65 conserved tumor-specific epitopes recurrent across more than 10 tumor types represent potential shared antigen candidates. NeoOmni Atlas also prioritizes candidate tumor-associated antigens including PMEL (gp100:209-217) and CSPG4, and supports browsing, searching, and downloading by cancer type, human leukocyte antigen allele, peptide sequence, and source event. NeoOmni Atlas is freely accessible at http://modinfor.com/NeoOmni-Atlas/.

bioinformatics↗

bioRxiv2026

Longitudinal Metaproteomic and Lysine Crotonylation Remodeling Defines Clinical Response to Fecal Microbiota Transplantation in Ulcerative Colitis

Background Fecal microbiota transplantation (FMT) can induce steroid-free clinical remission in a subset of patients with ulcerative colitis (UC), but treatment responses remain heterogeneous and are not fully explained by taxonomic microbiome shifts. To define functional molecular features associated with FMT efficacy, we performed integrated longitudinal fecal metaproteomic and lysine crotonylation (Kcr) profiling. Methods We analyzed 87 fecal samples from 23 patients with active UC collected at baseline and at weeks 1, 8, and 12 after FMT. Patients were classified as responders (n = 13) or non-responders (n = 10) according to steroid-free clinical remission at week 12. Across samples, we identified an average of 3,682 proteins and 562 Kcr sites per sample. Results Responders showed greater metaproteomic and meta-crotonylomic complexity at week 12, sustained enrichment of Prevotella and Faecalibacterium, and eight directionally consistent baseline-altered proteins with candidate prognostic value. After FMT, responders exhibited coordinated microbial functional remodeling, including increased proteins involved in short-chain fatty acid (SCFA) metabolism, acyl-CoA-centered pathways, nutrient transport, and polysaccharide degradation, together with attenuation of host neutrophil-related inflammatory protein and Kcr signatures. Non-responders showed minimal or opposing molecular changes. Conclusions: These findings nominate longitudinal fecal metaproteomic and Kcr remodeling as functional molecular readouts of clinical response to FMT in UC and highlight lysine crotonylation as an underexplored metabolite-sensitive layer linking microbial metabolic restoration with host inflammatory resolution.

microbiology↗

bioRxiv2026

Live imaging reveals oocyte membrane pre-remodeling forming permissive space for asymmetric division

Abstract Successful oocyte maturation requires first polar body (PB1) extrusion, yet how the oocyte prepares for this asymmetric event remains unclear. Live membrane imaging of mouse oocytes reveals pronounced regional heterogeneity in plasma-membrane dynamics, generating an early polarized pattern across the surface. Whereas most of the oocyte surface and its microvilli remain relatively stable, a discrete membrane domain collapses and retracts around germinal vesicle breakdown (GVBD), separating from the zona pellucida to establish a pre-extrusion space (PES). Transient oocyte comb-like protrusions arise within the PES and subsequently collapse, converting the protrusion-filled region into an open cavity before PB1 extrusion. Mechanistically, early ERK28 dependent dissociation of the cortical scaffold ZO-1 is required for this space to form. ERK2 phosphorylates ZO-1, suppresses its phase separation, and promotes its removal from the cortex. Blocking MEK-ERK signaling prevents ZO-1 dissociation, abolishes pre-extrusion space formation, and impairs PB1 extrusion, whereas ERK activation restores these events in aged oocytes. Together, our findings identify a membrane collapse-based pre-remodeling mechanism that licenses PB1 extrusion and reveal ERK-ZO-1 signaling as a key regulator of oocyte maturation.

cell biology↗

bioRxiv2026

Structural Basis of γδ T-Cell Receptor Crosslinking and Activation by a Spontaneously Dimerized Fab

The gamma delta T-cell receptor ({gamma}{delta} TCR) mediates {gamma}{delta} T-cell responses that are crucial for immune defense, tissue surveillance, and homeostasis. While recent studies suggest that {gamma}{delta} TCRs engage ligands multivalently, how multivalent engagement activates the {gamma}{delta} TCR remains elusive. Here, we present the structures of the V{gamma}9V{delta}2 (clone G115) TCR in both the inactive and the agonist-crosslinked active states. In the {gamma}{delta} TCR lipoprotein complex, cholesterol and phospholipids form a "barrier" that isolates CD3{zeta}{zeta} from the other subunits and likely prevents autoactivation. As an agonist, the Fab fragment of the UCHT1 antibody dimerizes upon binding the V{gamma}9V{delta}2 TCR, thereby crosslinking and activating the receptor. Cryo-EM analysis of Fab-crosslinked V{gamma}9V{delta}2 TCR identifies three Fab dimer interfaces, one between the two light chains and the other two between light and heavy chains. These Fab-Fab interfaces, together with the Fab-CD3{epsilon} interface, mediate the assembly of the V{gamma}9V{delta}2 TCR and UCHT1 Fab into 2:2 tetramers. Upon activation, the V{gamma}9V{delta}2 TCR becomes conformationally plastic and loses enriched lipids, including cholesterol and phosphatidylethanolamine. Our findings reveal a dimerization-driven activation mechanism, inform the design of rigid TCR-crosslinking agonists, and suggest multivalency-induced clustering as a general paradigm for {gamma}{delta} TCR activation.

immunology↗

bioRxiv2026

scPRIME-seq uncovers synchronized multimodal molecular collapse facilitated by pre-neoplastic epigenetic burden in prostate cancer

Tumorigenesis involves alterations across the genome, epigenome and transcriptome, yet how these layers interact to drive malignant transformation remains unclear, largely due to the lack of scalable multimodal single-cell approaches. Here, we developed scPRIME-seq, a high-throughput platform for simultaneous single-cell profiling of transcriptome, genome and DNA methylome, and applied it to 436,908 cells from 29 prostate cancers and 15 benign tissues. This multimodal atlas resolved dynamic changes across 30 cell types and a unified tumorigenic trajectory. Integrated analysis revealed a cell-state transition tipping point, where the onset of aneuploidy is temporally coupled with global methylomic alterations and transcriptomic rewiring. Early focal epigenetic alterations, including TMEM106A promoter hypermethylation and the emergence of hypomethylated domains, were present in founder aneuploid clones and benign tissues, indicating a pre-neoplastic origin of epigenetic burden. These pre-neoplastic alterations coincide with transcriptomic changes that affect epithelial interactions with stromal and immune compartments, promoting a putative tumor-permissive microenvironment. scPRIME-seq provides a high-throughput multimodal framework for identifying conserved, cell-intrinsic molecular programs underlying tumorigenesis.

cancer biology↗

bioRxiv2026

Paired single-nucleus and spatial transcriptomics of the lung adenocarcinoma invasion sequence reveal niche domains and candidate reversal compounds

Lung adenocarcinoma (LUAD) develops through a defined morphological sequence from atypical adenomatous hyperplasia (AAH) to invasive adenocarcinoma, but the transcriptional programmes accompanying this transition have mostly been characterised in bulk tissue or in tumour tissue alone. We profiled paired samples spanning the full sequence by single-nucleus RNA sequencing (413,697 nuclei, 23 patients) and spatial transcriptomics (56 Visium sections, 25 patients), asking how the transcriptional state of the tissue changes as invasion proceeds and whether that state can be reversed in silico by known perturbations. The atlas resolves into 39 second-level subtypes and the tissue into seven recurring niche-domain archetypes (K* = 7), six of which are ordinary lung structures and only one of which is restricted to invasive disease. A confound then shaped the remaining analyses: domain identity, marker stability and the apparent stage-dependence of the spatial programmes all scale with sequencing depth, and depth is in these sections a proxy for tissue density rather than a purely technical artefact (rho=-0.89 between a domain's depth and the fraction of its markers surviving depth matching). Several apparently positive results disappeared once depth was matched. The invasive domain's ECM/interstitial identity survives that check: within patients the fibroblast ECM programme is higher in invasive disease in 20 of 22 paired cases (P=0.0033 against random gene sets), and the result is unchanged when the genes added by hand are removed and under every leave-one-out variant. Querying a patient-paired disease axis against the LINCS compound library with three scoring schemes returned 34 compounds in common, dominated by PI3K/mTOR inhibitors, with a split-half reproducibility of rho=0.962 against a permutation null of +/-0.045 and an agreement of rho=0.735 between a single-cell-derived and a spatially derived axis. A positive control, the recovery of known regulators of an official benchmark (TBXT ranked 1st of 8,450), establishes that the pipeline recovers true positives, so the negative results reported here are properties of the data rather than of the method. Those negatives are stated explicitly: single-cell copy-number inference produced no usable malignant/non-malignant separator, the cohort-level spatial copy-number difference did not survive depth matching, a developmental trajectory ran opposite to that of the source study, gene-level prediction returned no signal on the pooled axis and only one perturbation survives compartment-wise gating, and a ligand-level analysis produced no usable pair.

cancer biology↗

bioRxiv2026

Neutrophils orchestrate pre-metastatic immunosuppressive bone marrow remodeling during prostate cancer metastasis

The dynamic reprogramming of the bone marrow (BM) microenvironment during metastatic progression is poorly defined. Through single-cell profiling of BM samples spanning benign conditions, high-risk bone metastatic potential localized prostate cancer (HMP) and established bone metastatic prostate cancer (PCa), we uncovered a primary tumor-to-BM signaling axis that orchestrates niche formation through neutrophil-mediated remodeling. Tumor-associated neutrophils (TANs) emerge during the HMP stage, persist throughout metastatic progression, correlate with poor patient prognosis, and exhibit direct immunosuppressive activity that contributes to a BM environment permissive to metastatic colonization. Functional and genetic studies showed that tumor-associated systemic IGF1 reprogrammed BM neutrophils through IGF1R-MAPK/ERK-KLF4 signaling, with IL-1{beta}, reactive oxygen species and nitric oxide contributing to TAN-mediated T cell suppression. Tumor-cell Igf1 perturbation, IGF1R blockade and neutrophil-specific Igf1r deletion attenuated TAN-associated BM remodeling, and reduced subsequent bone metastatic progression. In bone-metastasis models, combined IGF1R and PD-1 blockade suppressed bone-metastatic progression. Translationally, our investigator-initiated clinical trial (NCT06866548) of teprotumumab plus tislelizumab in patients with established metastatic castration-resistant prostate cancer (mCRPC) provided initial safety data and exploratory clinical observations. Together, these findings identify IGF1R-dependent neutrophil reprogramming as a functionally important component of the evolving PCa bone metastatic microenvironment and provide a rationale for therapeutic targeting of IGF1R signaling together with immune checkpoint blockade.

cancer biology↗

bioRxiv2026

AmbiDose: per-cell removal budgets for ambient RNA contamination

Ambient RNA contamination confounds expression analysis in droplet-based single-cell and single-nucleus RNA sequencing. Here we present AmbiDose, which combines an ambient profile estimated from empty droplets with cell-specific nominal removal budgets and expression-based protection of lineage-enriched genes. Its ambient dose guides count removal rather than estimating a calibrated contamination fraction. In a held-out human-mouse GEM-X mixture, AmbiDose removed 92.0% of cross-species UMIs while retaining 99.6% of same-species UMIs. It reduced off-target marker expression in kidney-tumor and fetal-liver cohorts and yielded the lowest proximal-tubule marker leakage among the tested methods across five strain-mixed kidney libraries. Simulations supported the contribution of cell-specific dose estimates but identified reduced endogenous retention or incomplete removal when ambient and endogenous expression overlapped. AmbiDose is available as a Python package compatible with Scanpy.

bioinformatics↗

bioRxiv2026

YGEP: An Integrated Web Platform for Genomic Evaluation and Intelligent Breeding in Yak

Background: The yak (Bos grunniens) is an essential livestock species in high-altitude alpine ecosystems, serving key roles in meat, milk, and wool production as well as ecological maintenance. However, traditional yak breeding systems face several limitations, including fragmented herd data management, inefficient phenotypic collection, missing pedigree records, and high technical barriers to applying genomic technologies. These factors constrain the widespread application of modern genetic evaluation methods in yak breeding programs. Description: We developed the Yak Genomic Evaluation Platform (YGEP, https://yakbreeding.swun.edu.cn/en/), an integrated digital system for yak genetic selection and herd management. YGEP integrates three core analytical modules: pedigree reconstruction, genotype imputation and genomic breeding value estimation. Benchmarking on 706 yaks showed that GBLUP achieved a prediction accuracy of r = 0.96 for cannon bone circumference (CCB), and KBeagle reached 84.0% imputation accuracy with the combined reference panel. Conclusion: YGEP bridges the gap between advanced genomic analytics and practical yak breeding. By integrating pedigree reconstruction, genotype imputation, and GEBV estimation into a user-friendly cloud platform, YGEP effectively eliminates technical and data bottlenecks. Overall, it provides an accessible, scalable, and standardized solution to advance digital herd management and precision genetic improvement in alpine livestock.

bioinformatics↗

bioRxiv2026

Activation thresholds set the speed of biochemical trigger waves

Trigger waves are positive feedback-mediated traveling waves that propagate without slowing down or diminishing in amplitude, enabling biochemical coordination over distances where diffusion alone would be insufficient. Apoptosis can spread as trigger waves of caspase activity, as demonstrated in Xenopus eggs and egg extracts. We measured apoptotic wave speeds in extracts at two cell cycle states and found that waves propagated more slowly in M-phase arrested cytostatic factor (CSF) extracts than in interphase extracts (21 versus 27 m min-1). Luther's equation, v=2{surd}D{kappa}, predicts wave speed from the diffusion coefficient D and the positive-feedback doubling rate {kappa}. However, D and {kappa} were comparable between the two extracts and could not explain the speed difference. This discrepancy highlighted a key limitation of the classical equation: it does not account for an activation threshold in trigger wave initiation, and in fact the threshold required to trigger apoptosis was found to differ between cell cycle states. We therefore extended Luther's equation to include such a threshold, obtaining v{propto}{surd}(AD/Uc ), where A is the reaction rate and Uc is the activation threshold. Perturbing apoptotic sensitivity confirmed the predicted threshold-speed relationship. These findings establish the activation threshold as a key determinant of trigger wave speed and provide a broadly applicable scaling law for predicting the spread of switch-like biochemical signals.

biophysics↗

bioRxiv2026

Differential Adaptation of Osteocyte Lacunar Morphology at Bone (Re)modeling Sites under Mechanical Loading and Pharmacological Therapies in a Mouse Model of Osteoporosis

Postmenopausal osteoporosis is a highly prevalent disease characterized by low bone mass and structural deterioration of bone tissue leading to increased bone fragility and fracture risk. Osteocytes orchestrate local bone (re)modeling and therefore, characterizing their 3D morphological and spatial distribution across distinct (re)modeling microenvironments is essential for understanding the cellular mechanisms underlying divergent tissue-level responses. To address this, we used a 3D-3D multiscale registration framework mapping endpoint osteocyte lacunae onto dynamic, time-lapsed in vivo (re)modeling sites. Ovariectomized 15-week-old mice were subjected to 4 weeks of anabolic parathyroid hormone (PTH) or anti-catabolic bisphosphonate (BIS) treatment as monotreatment or combined with cyclic mechanical loading (ML). Biweekly in vivo micro-computed tomography (micro-CT) to identify (re)modeling sites and endpoint ultra-high resolution (ultra-HR) micro-CT to characterize osteocyte lacunae was performed. Osteocyte lacunae were characterized by lacunar density, volume and sphericity. Our findings showed that physical and pharmacological therapies differentially regulate the osteocyte lacunar network through distinct perilacunar adaptations across functional microenvironments. While BIS stabilizes local lacunar architecture, PTH drives asymmetrical lacunar expansion (increased volume with reduced sphericity) through perilacunar remodeling that supersedes any added ML effects. Crucially, estrogen loss disrupts the natural spatial maturation gradient by inducing rounding of lacunae in newly formed bone. Therapies counteract this disruption, restoring the healthy gradients in lacunar morphometry between spatially distinct microenvironments. Additionally, despite restoring tissue-level bone volume, physical and pharmacological osteoporosis therapies do not fully recover persistent lacunar density deficits. The overall lacunar morphological spatial signatures confirm active osteocytic tuning to endocrine, physical and matrix cues.

bioengineering↗

bioRxiv2026

Mechanistic Decoding of Pharmacodynamic Intratumoral Heterogeneity: A Pan-Cancer Regulatory Framework

Intratumoral heterogeneity (ITH) drives therapy failure through divergent drug response propensities among coexisting subclones - a phenomenon we term pharmacodynamic intratumoral heterogeneity (PharmITH). While single-cell technologies have catalogued transcriptional heterogeneity, which molecular programs shape differential drug responses remains unresolved. Here we decode PharmITH by linking single-cell transcriptomes from 1,279 samples across 24 cancer types with drug-response profiles for 1,218 compounds. We identify 425 hub genes consistently associated with predicted treatment-response heterogeneity and with potential therapeutic relevance and perform multi-omics network analysis in lung adenocarcinoma (LUAD) integrating transcriptional regulation, somatic mutations, cell-cell communication (CCC), and alternative splicing. This analysis identifies four classes of candidate regulatory associations observed in the LUAD case study: 3 transcription factors establishing pre-existing drug-response programs, 41 genomic alterations amplifying pathway signaling through intermediate networks, 5 ligand-receptor pairs coupling microenvironmental cues to intracellular circuits, and 8 genes producing opposing isoforms via differential splicing. These findings converge on 6 core pathways, revealing that PharmITH arises from tumor-intrinsic mechanisms. Experimental validation and an online platform PharmITH for pan-cancer therapy enable state-resolved drug-response analysis and candidate-gene exploration. This approach transforms ITH from descriptive phenotyping to mechanistic dissection, providing actionable targets to overcome therapy resistance.

cancer biology↗

bioRxiv2026

Cytokine-mediated activation of exhausted T cells

CD8 T cell exhaustion during chronic infection and cancer is marked by impaired effector function and limited responsiveness to stimulation. While memory CD8 T cells can be activated TCR-independently by IL-12 and IL-18, it remains unclear whether exhausted cells, despite diminished TCR responsiveness, retain this cytokine-driven effector capacity. Here, we show that IL-12 and IL-18 stimulation induce robust IFN{gamma} production in exhausted CD8 T cells from chronic LCMV Cl13 infection, exceeding responses to antigen-specific stimulation. This activation does not result in upregulation of Tox, suggesting engagement of transcriptional circuits distinct from those promoting exhaustion. Single-cell transcriptomics revealed an innate acting T cell (TIA)-specific gene signature enriched within exhausted populations in chronic infection and tumor-infiltrating lymphocytes, particularly at the interface of intermediate and terminal exhaustion. Using heterologous Legionella pneumophila infection, we confirmed in vivo bystander responsiveness of exhausted CD8 T cells, reducing bacterial burden, highlighting their functional capacity. Our findings demonstrate that exhausted CD8 T cells retain inducible effector capacity through IL-12 and IL-18 stimulation, providing new insights into possible routes to activate exhausted T cells.

immunology↗

bioRxiv2026

A kinetic-aware approach to infer metabolic variations and flux using transcriptomics and metabolomics data

Assessing metabolic variations and flux quantities enable systematic understandings of metabolic shifts, reprogramming, adaptation and interactions in human diseases. However, omics-based estimation of metabolic flux and its variation remains challenging due to several fundamental limitations: the need for disease and tissue context specific metabolic model; nonlinear enzyme kinetic model that links enzyme and substrate changes to reaction flux; partial, unpaired, and snap-shot measurements across omics modalities; and uncertainty in computational prediction. Here, we present Michaelis-Menten model-based Flux Estimation Analysis (mmFEA), a Monte Carlo framework for estimating condition-specific flux changes by integrating paired or unpaired metabolomics and transcriptomics (or proteomics) data. mmFEA separates each reaction-rate change into enzyme- and substrate-associated components and assess reaction rate using Michaelis-Menten kinetics equation. A baseline metabolite saturation rate is introduced by integrating protein language model predicted kinetic parameters and human baseline level metabolic concentration to enable kinetic-aware integration of unpaired substrate and enzyme level measurements. Distribution of metabolic flux and variations between conditions are further computed using MCMC sampling by treating Michaelis-Menten-derived marginal flux distribution as prior and coherency in flux balance as likelihood. To benchmark mmFEA, we generated an in-house multi-omics data set including transcriptomics, metabolomics, metabolic activity functional assay, and CRISPR screening data using pancreatic cancer cell line system treated by APEX1 inhibitors. We demonstrated that mmFEA could accurately capture experimentally observed metabolic changes and achieved a better performance than all baseline methods. Our analysis revealed the necessity in using both substrate and enzyme modality and kinetic aware model in metabolic flux assessment. Further analysis using independent pancreatic cancer cohorts further validated the robustness of mmFEA, supporting integration of condition-linked unpaired data. Pan-cancer and spatial multi-omic applications demonstrated the use of mmFEA for resolving context-dependent metabolic variation when direct flux measurements are unavailable. Together, mmFEA provides a mechanistically grounded framework for estimating relative metabolic flux changes and their uncertainty from heterogeneous omics data.

systems biology↗

bioRxiv2026

Gene dosage effect and reduced core fucosylation in B lymphocytes of FUT8 heterozygous mice

Core fucosylation (alpha1,6-fucosylation) of N-glycans, catalyzed solely by fucosyltransferase 8 (FUT8), plays important roles in development, immunity, and antibody effector functions. Here we report the generation of Fut8 floxed mice using a CRISPR/Cas9-based Extreme Genome Editing (EGE) system, in which loxP sites flank exon 8 of the Fut8 gene and a LoxP-STOP-LoxP-RFP cassette was knocked in downstream of the promoter, rendering the targeted allele functionally null before Cre-mediated recombination. Crossing floxed mice with CMV-Cre transgenic mice yielded complete knockout mice carrying the Cre-recombined allele. A PCR-based genotyping method was established that unambiguously distinguishes the wild-type, heterozygous, and homozygous genotypes (+/+, delta/+, and delta/delta). Intercrossing of heterozygous mice revealed that homozygous knockout mice die during the early postnatal period, consistent with previous reports, whereas heterozygous mice are viable. Flow cytometric analysis of AAL binding to splenic B cells and AAL lectin blotting both demonstrated markedly reduced core fucosylation in heterozygous mice (60.0 +/- 6.8% and approximately 48% of wild-type levels, respectively). These results show that disruption of a single Fut8 allele substantially reduces core fucosylation, and the mouse model described here provides a practical tool for functional studies of core fucosylation.

immunology↗

bioRxiv2026

Structural streamlining of axonemal doublet microtubules in Plasmodium male gametes

Male gametogenesis in malaria parasites produces up to eight flagellated gametes within approximately 15 min, requiring de novo construction of motile axonemes on an unusually short timescale. Here we combine cellular cryo-electron tomography, high-resolution cryo-EM, proteomics, and parasite genetics to define the molecular architecture and assembly states of the Plasmodium male gamete axoneme. The doublet microtubules retain the principal surface-associated motility modules but contain a markedly reduced luminal microtubule inner protein network. Their inner junction lacks PACRG and is instead organized by CFAP20 and CFAP52, whose combined loss disrupts doublet integrity and exflagellation. We further identify a calmodulin protein at the outer dynein arm docking region and show that outer dynein arms accumulate progressively during gametogenesis. These findings establish distinct form of axonemal remodeling in Plasmodium and reveal the ordered assembly of structural and motor modules during rapid male gamete formation.

cell biology↗

bioRxiv2026

KRAS inhibition drives adaptive surfaceome remodeling and reveals ALPP/ALPPL2 as a targetable vulnerability in pancreatic cancer

KRAS is mutated in over 90% of pancreatic ductal adenocarcinoma (PDAC) and is required for tumor initiation and maintenance. While clinical trials testing mutant-selective and pan-RAS inhibitors (KRASi) have demonstrated significant clinical benefit, genetic and non-genetic mechanisms of resistance limit the long-term efficacy of monotherapy strategies. Here, we used quantitative temporal analysis of the global, phosphorylation, and surface proteome to comprehensively identify non-genetic adaptive pathways and cell surface biomarkers in response to acute and long-term KRAS inhibition in PDAC. Through integrative machine learning analysis of the KRASi-proteome and publicly available datasets, we discovered top priority cell surface targets for combination therapy with KRASi. We identified Placental Alkaline Phosphatase (ALPP) as upregulated in response to KRASi through compensatory JAK2/STAT3 signaling. We developed a novel clinical grade ALPP/ALPPL2 (ALPG)-targeting antibody drug conjugate (ADC) with site-specific MMAE conjugation and demonstrated single agent efficacy in PDAC models, as well as enhanced internalization and anti-tumor efficacy in combination with KRASi. Together, these studies comprehensively define the KRASi-induced proteome and identify ALPP/ALPPL2 as a promising cell surface target for combination with KRASi to enhance response and forestall KRASi resistance.

cancer biology↗