Biology subjects

Ma, J.

Publications and source records attributed to Ma, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Bexobrutideg: A Selective, Catalytic Degrader of Bruton's Tyrosine Kinase Overcomes Inhibitor Resistance and Suppresses Autoantibody-Mediated Disease

Brutons tyrosine kinase (BTK) transduces B-cell receptor (BCR), Toll-like receptor (TLR), and Fc receptor (FcR) signaling, and overactivation of these pathways drives B-cell malignancies and antibody-mediated autoimmune disease. Small molecule inhibitors block the enzymatic functions of BTK, but this inhibition is undermined by resistance mutations, several of which abolish BTKs kinase activity yet promote oncogenic signaling through BTK scaffolding functions. We report the discovery and characterization of bexobrutideg (NX-5948), a heterobifunctional degrader that recruits cereblon (CRBN) to selectively degrade BTK while sparing molecular glue neosubstrates. We demonstrate that bexobrutideg acts catalytically, degrading thousands of copies of BTK per molecule per hour, and this event-driven pharmacology renders it resilient to mutations that confer resistance to both covalent- and noncovalent-inhibitors. Bexobrutideg is orally bioavailable, driving deep and durable BTK degradation across species. Bexobrutideg demonstrates strong efficacy in wild-type and ibrutinib-resistant lymphoma models and robustly suppresses pathway activation in models of autoimmune disease.

cancer biology↗

bioRxiv2026

High glucose confers senescence resistance via GLUT1 epigenetic rewiring to blunt immunotherapy responses in esophageal squamous cell carcinoma

Therapeutic resistance and undefined predictive biomarkers severely hinder the clinical popularization of immunotherapy in esophageal squamous cell carcinoma (ESCC). Herein, we identify the glucose transporter 1 (GLUT1) as a critical determinant of immunotherapy resistance. Elevated expression of GLUT1 correlates with poor immunotherapy response and unfavorable prognosis in ESCC patients. GLUT1 deletion or inhibition enhances CD8 T cell infiltration and cytotoxicity, and sensitizes ESCC tumors to anti-PD-1 (-PD1) therapy. Importantly, dietary glucose restriction exhibits equivalent antitumor efficacy to GLUT1 inhibition when combined with -PD1. Mechanistically, GLUT1 establishes a positive feedback loop with HAT1 and FOXM1, which epigenetically remodels chromatin accessibility to suppress tumor cell senescence, thereby impeding CD8 T cell-mediated antitumor immunity. Our findings highlight GLUT1 as a predictive biomarker of immunotherapy resistance and suggest dietary glucose restriction as a viable strategy to potentiate immunotherapy efficacy in ESCC. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/738372v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@c2c5d5org.highwire.dtl.DTLVardef@14a34c7org.highwire.dtl.DTLVardef@cf05e4org.highwire.dtl.DTLVardef@18bc354_HPS_FORMAT_FIGEXP M_FIG C_FIG SHORT SUMMARYDong et al. identify glucose transporter 1 (GLUT1) as a predictor of poor response to immunotherapy in esophageal squamous cell carcinoma. GLUT1 promotes immune evasion by forming a positive feedback loop with the HAT1/FOXM1 anti-senescence axis, thereby epigenetically remodeling chromatin accessibility. GLUT1 inhibition or dietary glucose restriction restores CD8 T-cell-mediated antitumor immunity and improves the efficacy of anti-PD-1 therapy in preclinical models.

cancer biology↗

bioRxiv2026

Integrative computational toxicology reveals PFOS and PFHxS associated inflammatory keratinocyte niches in psoriasis through exposure transcriptomics, single-cell spatial mapping and token-aware virtual perturbation

Per- and polyfluoroalkyl substances (PFAS) are persistent toxicants with immunological, metabolic and epithelial effects, but their relevance to inflammatory skin disease remains unclear. We developed a computational toxicology framework to test whether perfluoroalkyl sulfonate programs, especially perfluorooctanesulfonic acid (PFOS) and perfluorohexanesulfonic acid (PFHxS), converge with psoriasis-associated keratinocyte inflammation. Exposure transcriptomes were derived from GSE236956, in which human embryonic stem cell-derived epithelial-lineage models were exposed to 10 M PFAS for 8-16 days. Six PFAS were prioritized using descriptors, Tanimoto similarity, toxicology evidence, adverse outcome pathway (AOP)-like key events, exposure differentially expressed gene burden and read-across support. PFAS signatures were integrated with psoriasis bulk transcriptomes, single-cell RNA sequencing, keratinocyte-state mapping, regulator and communication inference, spatial transcriptomics and token-aware Geneformer-compatible virtual perturbation. PFOS ranked highest in integrated prioritization, followed by PFHxS and perfluorooctanoic acid. PFHxS produced a smaller but directionally informative signature within a PFOS-dominant perfluoroalkyl sulfonate footprint. The shared PFOS and PFHxS program converged with psoriasis through inflammatory keratinocyte, epidermal-stress, cytoskeletal and lipid-related modules. Single-cell and spatial analyses localized the program to activated keratinocytes and inflammatory epidermal niches, with strong spatial co-localization with inflammatory keratinocyte and epidermal stress scores. Virtual perturbation prioritized S100A9, S100A8, KRT16, IL36G, CCL20, CXCL8, FABP5, KRT17, FOS, JUN and NFKBIZ as candidate effectors. These findings support an exposure-informed, experimentally testable hypothesis linking persistent perfluoroalkyl sulfonate programs to keratinocyte inflammatory niches in psoriasis.

bioinformatics↗

bioRxiv2026

IgGM2: An All-Atom Foundation Model for Adaptive Immune Receptor Design

Accurate immune receptor design requires modeling the coupled variation of aminoacid sequence, full-atom conformation, and target-binding geometry across antibodies, nanobodies, and T-cell receptors (TCRs). Existing methods often address only part of this problem, either by separating structure generation from sequence design, relying on fixed-backbone inverse folding, or focusing on a single receptor class. We introduce IgGM2, a unified all-atom generative framework for immune receptor structure prediction and CDR sequence-structure co-design. IgGM2 follows a structure-to-design strategy: it first learns how immune receptors are positioned around fixed target structures, and then transfers this target-conditioned structural prior to CDR design. Unlike modular design pipelines, IgGM2 jointly generates CDR residue identities and full-atom receptor structures, allowing frame-work geometry to adapt to designed CDRs without separate inverse folding or external sidechain packing. Unlike continuous residue encodings based on virtualatom geometry, IgGM2 keeps sequence prediction explicit while using atom14 placeholders only for full-atom representation. On structure prediction benchmarks, IgGM2 better captures receptor-target spatial relationships than AlphaFold3 on FoldBench and achieves strong performance on TCR-pMHC modeling. On sequence design benchmarks, IgGM2 achieves competitive amino-acid recovery and improves Rosetta-based interface preference metrics, suggesting more favorable generated binding interfaces. These results support IgGM2 as a unified all-atom framework for adaptive immune receptor structure prediction and design.

bioinformatics↗

bioRxiv2026

Germline hypomethylation shapes dynamic CpG reservoirs in ape genomes

Telomere-to-telomere (T2T) genome assemblies resolve DNA methylation of complete ape genomes, including repetitive and satellite-rich compartments that were largely inaccessible in previous primate reference genomes. Here, integrating complete ape genome assemblies with long- and short-read germline and somatic DNA methylomes, we demonstrate dual roles of germline DNA methylation. While solidifying germline DNA methylation as a major driver of genome-wide long-term CpG erosion, we report an unexpected reservoir of hypomethylated CpGs that exist in previously inaccessible regions. Specifically, peri/centromeric satellites are markedly hypomethylated in sperm across great apes, despite their heterochromatic context and rapid sequence turnover. Moreover, we found their hypomethylation extends into adjacent non-satellite DNA at the boundaries of satellite-rich heterochromatic sequences and adjacent euchromatic sequences, forming centromeric hypomethylated extension domains, or CHEDs. CHEDs are enriched in recently duplicated genes, and CHED-associated genes show reproducible, enriched expression in the brain and testis. Extending our analyses to other structurally dynamic regions, including lineage-specific insertions, recent segmental duplications and structurally divergent regions, we show that these regions are also CpG-rich and relatively hypomethylated in sperm. Together, our results reveal a unique germline hypomethylation landscape in ape genomes in which structurally dynamic regions act not only as substrates of rapid genome evolution, but also as transient reservoirs of CpG-rich sequence contexts, promoting evolutionary innovations involving new genes and tissue-biased expression.

genomics↗

bioRxiv2026

FALCON: Closed-Loop Multi-Objective Optimization of Lipid Nanoparticles for Cell-Selective mRNA Delivery

Efficient, cell type-selective delivery of genetic payloads remains a central challenge in the development of gene and cell therapies. Lipid nanoparticles (LNPs) offer a versatile delivery platform, but their optimization is hindered by reliance on brute-force screening methods that are laborious, resource-intensive, and focus on single targets. Here, we present FALCON (Framework for Active Learning-driven Compositional Optimization of Nanoparticles), a closed-loop pipeline that leverages iterative screening, surrogate modeling, and multi-objective optimization to accelerate LNP compositional design. In B cell-targeted validation experiments, FALCON-optimized LNPs achieved a 1.8-fold increase in splenic B cell transfection in vivo compared with reference compositions. When optimized for selectivity, FALCON LNPs displayed an 84-fold improvement in selective transfection of splenic B cells over off-target liver populations and enabled spleen-tropic behavior across factorial panels of varying ionizable and helper lipid chemistries. In vaccine studies, these LNPs induced higher IgG2c antibody titers and a more Th1-biased immune profile. FALCON was also deployed to optimize LNPs for myeloid cell-selective delivery, achieving enhanced in vivo selectivity following systemic administration both across and within spleen and liver compartments. Our results establish FALCON as a useful tool for data-driven design of LNP compositions for precision gene delivery.

bioengineering↗

bioRxiv2026

A fatal plant toxicosis described more than a century ago is caused by a bacterial endophyte

Gousiekte ( quick disease) is a fatal plant toxicosis affecting livestock in South Africa. Gousiekte is characterized by the sudden death of animals following the ingestion of leaves of several species of Rubiaceae, most notably Vangueria pygmaea, Pavetta harborii, P. schumanniana and Fadogia homblei. The toxin causing gousiekte is pavettamine, a hydroxylated polyamine pavettamine for which no biosynthetic pathway is known. Interestingly, all plants known to contain pavettamine also feature obligate endophytes of the Burkholderiaceae family, in particular belonging to the Caballeronia and Paraburkholderia genera. We identified a cluster of three genes conserved in all Burkholderia s.l. endophytic symbionts of plants containing pavettamine. Constitutive expression the pavABC gene cluster in a strain of Paraburkholderia caledonica isolated from leaves of Fadogia homblei resulted in detectable levels of pavettamine in cultures, and targeted gene deletions showed the involvement of all three genes in its biosynthesis. Genomes of important animal and human pathogens of the Burkholderia pseudomallei complex encode functional homologs of the pavABC genes, indicating a potentially unrecognized role of pavettamine in disease or complications from infections. Significance statementGousiekte is a fatal disease of livestock caused by plants containing the toxin pavettamine, yet the origin of this compound has remained a mystery. We demonstrate that pavettamine is synthesized not by the plants themselves, but by their obligate bacterial endophytes via a conserved three-gene cluster, pavABC. Crucially, these genes were likely acquired via horizontal gene transfer from an ancestor of the Burkholderia pseudomallei complex, a group of significant human and animal pathogens. This discovery identifies the genetic basis of a potent toxin and suggests a previously unrecognized role for pavettamine in human infectious diseases. This work emphasizes the preeminent role of horizontal gene transfer and secondary metabolism for host-microbe interactions.

microbiology↗

bioRxiv2026

Validation of MHPC512: A Publicly Available Special-Purpose Supercomputer for Molecular Dynamics Simulations of Biomolecular Systems

MHPC512 is a massively parallel, special-purpose supercomputer designed primarily for atomic-level molecular dynamics (MD) simulations of biomolecular systems. It comprises 512 processor units interconnected by a high-speed three-dimensional torus network and employs a custom chip architecture that uses 35-bit fixed-point arithmetic to accelerate computation while controlling precision loss within an acceptable margin. The preprocessor is compatible with GROMACS and AMBER input formats and supports widely used biomolecular force fields (including CHARMM, AMBER, and OPLS/AA), the Neutral Territory method for short-range nonbonded interactions, the k-space Gaussian Split Ewald method for long-range electrostatics, and multiple thermostats, barostats, and integrators. We present a three-tier validation protocol--comparing static energy and virial components, examining ensemble distributions (NVE, NVT, NPT), and evaluating long-time statistical properties--demonstrating that MHPC512 reproduces results consistent with GROMACS and AmberTools. Application examples, including bulk water, dipeptide conformational sampling, folding of fast-folding peptides, membrane-protein systems, lipid self-assembly, and GPCR conformational transitions, further confirm its reliability. MHPC512 has been deployed at multiple supercomputing centers and is publicly accessible, representing a significant advance in high-throughput, large-scale biomolecular MD simulations.

Molecular Biology↗

bioRxiv2026

Transient suppression of the ECM1 gatekeeper is essential for HGF/c-MET-driven liver regeneration

Hepatocyte growth factor (HGF) is a multifunctional cytokine stored in the extracellular matrix as an inactive precursor and is essential for tissue repair. How HGF activity is dynamically regulated during regeneration remains unclear. Here, we identify extracellular matrix protein 1 (ECM1) as a physiological inhibitor of active HGF during liver regeneration. Following 70% partial hepatectomy, active HGF rapidly increases in parallel with a sharp decline in ECM1, and preventing this downregulation delays liver mass recovery. Mechanistically, ECM1 directly binds the active HGF -subunit through a mechanism dependent on residue R392, thereby suppressing c-MET-ERK-MYC signaling and hepatocyte proliferation. Loss of ECM1 permits activation of this pathway, whereas MYC overexpression rescues ECM1-mediated growth inhibition. In patients, proliferative hepatocytes localize to ECM1-negative regions. Supported by transcriptomic analyses and computational modeling, these findings identify ECM1 as an extracellular gatekeeper whose transient downregulation enables HGF-driven tissue repair. HighlightsO_LIECM1 is temporally downregulated during liver regeneration, while forced ECM1 expression delays liver mass recovery after 70% PHx by suppressing hepatocyte proliferation. C_LIO_LIRapid and transient ECM1 downregulation permits HGF-c-Met-ERK-MYC signaling to drive hepatocyte cell-cycle entry and expansion. C_LIO_LIECM1 directly binds the active HGF -subunit with residue R392 playing a critical role, revealing a novel extracellular mechanism for growth factor inhibition. C_LIO_LILoss of ECM1 marks proliferative hepatocytes in human liver repair, identifying ECM1 as a tunable regulator of regenerative capacity. C_LI

cell biology↗

bioRxiv2026

Deciphering the limitations of immortalized hepatocyte cell lines for the study of liver cis-regulatory elements

Immortalized cell lines are widely used in biological research despite their known differences from their tissues and cell types of origin. Such cell lines are especially popular for testing hypotheses regarding the activity of cis-regulatory elements (CREs) that regulate gene expression. Previous investigations of blood and skin cell lines revealed many differences between the transcriptional regulatory networks of the cell lines and the associated primary cells. Similar comparisons for other tissues have been limited. Here, we used ATAC-seq to profile CREs in four immortalized liver cell lines and found many differences between each cell lines CREs and primary liver tissue, including differences in the transcription factors that are likely to bind them and differences in the genes that they are likely to regulate. Modifying cell culture conditions based on recommendations in the literature did not improve the similarity with primary liver tissue. Our results suggest that differences between the transcriptional regulatory networks in cell lines and primary tissue should be considered when designing and interpreting cell line experiments.

genomics↗

bioRxiv2026

Accurate de novo design of peptides from programming biophysical landscape

Peptides regulate virtually every cellular process and emerge as transformative modalities in bioengineering and therapeutics. However, the de novo design of functional peptides remains challenging, as peptide-protein interactions are governed by delicate and dynamic biophysics that are difficult to model, and experimental datasets are scarce. Here we present NeoPep, a generative deep-learning framework that encodes biophysical principles to accurately design functional peptides de novo. By integrating over 5 million peptide-protein complexes spanning experimentally determined, sequence mimics, and structure ensembles, NeoPep learns the complex biophysical landscape governing peptide function and enables its programmable control. In prospective application across 10 diverse and challenging targets, NeoPep generated potent peptide binders, agonists, and antagonists with hit rates of 12.5-66.7%, even in the absence of defined binding sites or structure information. Beyond de novo co-design, NeoPep supports standalone structure or sequence redesign, readily discriminating subtle context differences. In the structure redesign mode, it generates highly selective peptides with atomic-level conformational accuracy (C RMSD < 2.0 [A] to our solved cryo-EM structure). This structural precision circumvents the need for experimental structure determination, further accelerating iterative sequence redesign to yield a 43.3-fold improvement in potency. These findings establish a general framework for translating biophysical principles into actionable peptide functions, with broad implications for basic research, bioengineering, and medicine.

molecular biology↗

bioRxiv2026

Immune repertoire profiling reveals extensive clonal expansion of T and B cells in CXCL9-rich niches in sinonasal cancer

Sinonasal cancer (SNC) is a rare and aggressive head and neck cancer with limited therapeutic options and an incompletely defined immune microenvironment. Although histopathology remains central to clinical tumor evaluation, immune profiling typically requires tissue dissociation and therefore loses the spatial relationships that shape antitumor immunity. Here, we combined single-cell RNA-sequencing approaches, spatial transcriptomics and Spatial V(D)J, a technique we recently pioneered, to analyse the cellular, spatial, and clonal architecture of SNC. We found that SNC tumors were marked by a robust T cell infiltration, including substantial proportions of classical tissue resident memory (TRM) and exhausted (TExh) CD8+ T cells. This inflamed phenotype was accompanied by an immense infiltration of suppressive regulatory T (Treg) cells, which differentiated towards a Tbet+CXCR3+ phenotype. Spatially, expanded Treg, CD8 T and B cell clones concentrated within specialized peritumoral immune niches enriched for cancer-associated fibroblasts, CXCL9 tumor-associated macrophages and LAMP3IDO1 dendritic cells. T cell clones occupying these niches were clonally related to those infiltrating epithelial tumor regions, linking lymphoid hubs to the broader tumor immune response. Together, these data identify SNC as an inflamed but highly immunoregulatory tumor type and reveal a spatially organized clonal architecture in which suppressive and cytotoxic lymphocyte states coexist within CXCL9 myeloid niches.

immunology↗

bioRxiv2026

Candida albicans reprograms host inosine metabolism to drive immunosuppressive macrophage polarization and gastric cancer carcinogenesis

Gastric cancer (GC) is strongly associated with changes in the gastric microbiome. However, the direct contribution of individual pathogenic species to tumor initiation and progression remains poorly defined. Here, we identified Candida albicans (C. albicans), a fungus that ranks as the most significantly enriched taxon in GC tissues, can directly promote gastric carcinogenesis. We found that when C. albicans alone was colonized into the gastric mucosa of mice, it induced the complete sequence of GC-associated preneoplastic lesions, including chronic gastritis, mucinous metaplasia, and atypical hyperplasia, with 16% of colonized animals progressing to low-grade intraepithelial dysplasia. In K19-C2mE transgenic mice, a model of spontaneous GC formation, infection with C. albicans significantly accelerated GC formation, with synergistic effects observed upon co-infection with the well-known gastric carcinogen, Helicobacter pylori. Mechanistically, C. albicans upregulated inosine levels in both gastric tissues and circulation. This inosine promoted polarization of macrophages toward an M2-like phenotype by activating the adenosine A2a receptor (A2aR), creats an immunosuppressive microenvironment that protects GC cells from the tumoricidal effects of anti-tumor immunity. Depletion of M2 macrophages or pharmacological inhibition of A2aR attenuated C. albicans-mediated tumorigenesis. Clinically, elevated inosine levels correlated with prior C. albicans exposure and poorer outcomes of GC patients. Our findings establish C. albicans as a direct pro-tumorigenic pathogen in GC and highlight the inosine-A2aR-M2 macrophage axis as a promising target for therapeutic intervention.

cancer biology↗

bioRxiv2026

The single nucleotide polymorphism rs1053230 modulates kynurenine 3-monooxygenase stability and is associated with cognitive and mood phenotypes

BackgroundThe single nucleotide polymorphism (SNP) rs1053230 within the kynurenine 3-monooxygenase (KMO) gene encodes either an arginine (CGC) or cysteine (TGC) at amino acid residue 452. The rs1053230 genotype is associated with alterations in KMO expression and activity, and impaired cognition. Additionally, KMO intronic SNP rs2275163 is associated with schizophrenia endophenotypes. However, the direct functional consequences of these SNPs on KMO function have never been investigated. MethodsHere we performed the first in vitro cell-based examination of the rs1053230 genotype on KMO expression, activity, cellular localisation and KMO-protein interactions, as well as examination of the effects of rs1053230 on schizophrenia-relevant clinical measures. We also examined the effects of rs2275163 genotype on KMO pre-mRNA stability and alternative splicing. ResultsHEK293T cells expressing KMO-Arg452 or KMO-Cys452 with a red fluorescent protein (RFP) tag produced equivalent levels of KMO mRNA, protein and enzymatic activity, and localised to mitochondria to the same extent. However, cycloheximide-mediated inhibition of protein translation revealed a striking reduction in protein stability of KMO-Arg452-RFP. KMO-RFP-trap pull-down followed by tandem liquid-chromatography-mass spectrometry (LC-MS/MS) identified dramatic differences in protein partners between KMO variants. Indeed, gene ontology-term enrichment analysis revealed that terms associated with synaptic function were more highly enriched amongst KMO-Cys452 interacting proteins. rs1053230 genotype was found to associate with chronic, trait-like depressive mood symptoms in patients. rs2275163 genotype had no effect on KMO pre-mRNA. ConclusionsDifferences in protein stability and protein-protein interactions may underlie the mechanisms by which the KMO rs1053230 genotype influences neuronal function, leading to cognitive differences in psychiatric conditions.

molecular biology↗

bioRxiv2026

ProtmRNA: Cross-Modal Knowledge Transfer from Proteins to Messenger RNA

MotivationAccording to the central dogma of molecular biology, messenger RNA (mRNA) sequences are directly translated into amino acid sequences, positioning mRNA as the fundamental intermediary between genetic information and functional proteins. This natural correspondence suggests that mRNA sequence analysis could greatly benefit from the rich evolutionary and functional representations learned by large-scale protein language models. ResultsProtmRNA repurposes the pre-trained ESM-2 protein language model for mRNA sequence processing via cross-modal transfer learning. Evaluated on mRNA- and protein-related datasets, along with eight additional benchmarks compiled in this study, ProtmRNA achieves performance comparable or superior to state-of-the-art mRNA language models while using less than half the pre-training computational resources. This work establishes the potential of cross-modal transfer learning between biological sequences by demonstrating that protein-derived knowledge can be efficiently transferred to mRNA, offering a resource-efficient paradigm for advancing mRNA sequence understanding. Availability and ImplementationThe pre-trained ProtmRNA model and the eight CDS-region regression benchmarks curated in this study are publicly available at https://github.com/pesenteur/ProtmRNA.

bioinformatics↗

bioRxiv2026

Functional consequences of centromeric satellite array asymmetry in female meiosis.

Centromeres are epigenetically specified chromosomal sites that support kinetochore assembly and often embedded within large satellite DNA arrays. Recent telomere to telomere genome assemblies have revealed extensive variation in centromeric satellite arrays between chromosomes and between individuals, but the functional significance of this variation remains unclear. To determine how satellite array size influences centromere function, we generated hybrid mouse models in which homologous chromosomes with different array sizes are paired in meiosis I, creating array size asymmetry across each meiotic bivalent. When an extremely small array is paired with a moderate size array, we find that array size asymmetry leads to functional asymmetry in both centromere chromatin and interactions with spindle microtubules, lagging chromosomes in anaphase I, and increased aneuploidy in MII eggs. In contrast, pairing an extremely large array with a moderate array does not lead to functional centromere asymmetry. Together, these results suggest a threshold model in which centromere array size is tolerated across a broad range, but minimal arrays become functionally limiting when paired with larger arrays in meiosis.

cell biology↗

bioRxiv2026

Large-Scale Assessment of NF1 Single Amino Acid Variants as HLA Class I Neoantigens

Neoantigens are cancer-specific antigens arising from genomic alterations. Single Amino Acid Variants (SAAVs) represent a primary class of these neoantigens. To evaluate the therapeutic potential of Neurofibromin 1 (NF1)-derived SAAVs - given that NF1 is frequently mutated in malignant brain tumors - we prioritized the 40 NF1 SAAVs determined to be HLA-A*02:01 binders using computational prediction coupled with experimental validation. To validate these predicted neoepitopes, we employed a two-tiered experimental approach in HLA-A*02:01 homozygous U87-MG cells. We first synthesized minigene constructs encoding the predicted neoepitopes, introduced them via lentiviral transfection and confirmed their expression by mass spectrometry (MS). Subsequently, we performed endogenous validation using pan-HLA immunoprecipitation mass spectrometry (IP-MS), confirming 4 (10 neoepitopes) of the 40 candidate SAAVs. We observed a discrepancy between in silico predictions and the observed sequences. Our endogenous peptidomics further revealed conserved peptide motifs and demonstrated that peptide selection for HLA presentation is transient. While our study substantiates the therapeutic feasibility of T-cell immunotherapies targeting NF1 mutations, these results underscore a limitation in current computational prediction. Our study highlights the necessity of experimental validation to refine neoantigen prioritization strategies.

immunology↗

bioRxiv2026

Causally validated phase-amplitude coupling enables high-fidelity motor decoding for next-generation brain-computer interfaces

Modern Brain-Computer Interfaces (BCIs) face a fundamental performance plateau due to their reliance on broad spectral power reduction (Event-Related Desynchronization, ERD) as the primary decoding feature. ERD acts as a coarse metabolic proxy for cortical activation, discarding the high-frequency temporal syntax necessary for high-dimensional motor control. Here, we demonstrate that Phase-Amplitude Coupling (PAC)--specifically, the phase-locking of high-gamma (70-150 Hz) firing to residual Beta oscillations--provides a high-fidelity temporal feature for decoding motor intent. Using high-density electrocorticography (HD-ECoG) during motor imagery, we show that incorporating Beta-PAC into machine-learning classifiers (LDA/SVM) significantly outperforms traditional power-based features. To definitively validate the causal robustness of this feature against mathematically-derived artifacts, we leveraged a rare in vivo human structural lesion model. In a patient with focal tumor infiltration of the motor tract, the metabolic gate (ERD) was preserved, yet structural uncoupling completely abolished Beta-PAC, collapsing network topology and reducing single-trial decoding accuracy to chance levels. Our findings causally validate Beta-PAC as a robust, independent control signal, establishing a physiological foundation for next-generation, phase-dependent neuroprostheses.

neuroscience↗