Biology subjects

Shen, J.

Publications and source records attributed to Shen, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Pansoma, a machine learning tool for identifying somatic variants using pangenome graphs

Somatic variant calling, the identification of mutations in non-germline cells acquired over an individuals lifetime, is critical for studying diseases, including cancer, and for developing precision oncology strategies. Traditional somatic variant calling methods rely on linear reference genomes, which do not adequately capture human genetic diversity and result in reference bias, compromising the accuracy of somatic variant detection. Recently developed graph-based human pangenome reference represents diverse genetic variants across human populations and has promised to drive advances in many genetics and genomics studies. In this study, we introduced Pansoma, a novel pangenome-native and machine learning-based tool specifically designed for somatic variant calling using a pangenome graph reference. Pansoma performs somatic variant detection from both short- and long-read sequencing data by learning tensor representations of alignment on graph nodes rather than on a linear reference. Pansoma outputs variant representations anchored to the pangenome graph paths and conventional somatic variant calls remapped to the linear reference. Additionally, we provide accompanying bioinformatics tools tailored for graph-based genomic data management and variant calling results analysis. Benchmarking shows that Pansoma not only improves tumor-only somatic variant detection but also preserves graph-specific variant representations that are not directly recoverable from linear- reference outputs.

genomics↗

bioRxiv2026

MeCP2 is Necessary in Cerebellar Purkinje Cells for Precise Network Dynamics During Associative Motor Learning

Loss-of-function variants of MECP2 cause Rett syndrome; however, their impact on cerebellar computations for learning remains poorly understood. Here, we show that Mecp2 deletion specifically in Purkinje cells does not broadly disrupt cerebellar-dependent behaviors but selectively compromises those that require precise timing, coordination, and associative updating in the cerebellar cortex. Mecp2 loss altered the emergence of learning-related Purkinje cell activity in vivo and disrupted their intrinsic and synaptic properties that support adaptive cerebellar output. These findings identify MeCP2 as a critical player in Purkinje cell function to regulate cerebellar learning signals and suggest that Rett syndrome-related motor dysfunction reflects impaired adaptive computation rather than a generalized loss of motor capacity.

neuroscience↗

bioRxiv2026

Basal gland localization and focal distribution of OLFM4-expressing cells in increasing severity of gastric intestinal metaplasia

Patients with gastric intestinal metaplasia (GIM), a precancerous lesion, are at high risk for progressing to gastric cancer. Identifying these patients is critical to enable gastric cancer interception. Current approaches rely primarily on histologic evaluation of GIM severity and extent, which may be improved by incorporating molecular features that distinguish high-risk lesions. Our prior single-cell and spatial transcriptomics study identified differentially expressed genes associated with the highest-risk category of GIM. They included ANPEP expressed in enterocytes and CPS1 and OLFM4 expressed in intestinal stem-like or progenitor cells. We evaluated the protein expression and localization of these three markers to understand the cellular features associated with GIM risk and their spatial distribution within metaplastic tissues. Using multiplex immunofluorescence, whole slide image analysis and confocal microscopy, we examined protein expression from 100 tissue biopsies annotated for metaplasia severity using the Operative Link on Gastric Intestinal Metaplasia Assessment (OLGIM) system. Tissue samples included control gastric tissue, GIM, dysplasia and adenocarcinoma. Quantitative whole slide image analysis demonstrated that CPS1 expression had a modest association with disease severity. Although ANPEP was strongly associated with GIM severity, it was also frequently expressed in stromal regions outside epithelial glands. In contrast, OLFM4 expression was largely restricted to epithelial glands and showed a strong association with increased OLGIM severity. These OLFM4-positive epithelial cells were present in discrete glandular foci that expanded with increasing severity of metaplasia. Within individual metaplastic glands, OLFM4 expression was highest at the gland base with decreased expression toward the gland surface. Overall, these findings identified OLFM4 as a protein marker associated with high-risk GIM. The spatial organization of OLFM4-expressing cells at the base of metaplastic glands and their focal expansion within tissues suggest the presence of a stem cell-like epithelial compartment that may contribute to the progression of GIM towards gastric cancer.

cancer biology↗

bioRxiv2026

Activation-dependent lentiviruses enable antigen-specific T cell expansion and transduction

Cancer immunotherapies rely on tumor-specific T cells, which arise endogenously in most patients with cancer, but can be low frequency and poorly functional. Methods to specifically identify, expand, and manipulate tumor-specific T cells at the rare frequencies found in peripheral blood would enable new immunotherapeutic strategies. Here, we demonstrate an approach to virally transduce polyclonal tumor-reactive T cells across any MHC haplotype and in the absence of knowing the cognate antigen. By generating lentiviral vectors that selectively transduce cells expressing 4-1BB (CD137), a marker of T cell activation, we can transduce antigen-specific T cells with user-defined genetic cargoes that can selectively expand and track individual clonotypes via single-cell sequencing. Anti-4-1BB lentiviruses (4-1BB LVs) encoding therapeutic cargoes can also enhance antigen-specific T cells to extend survival in a xenograft model of human melanoma and transduce tumor-infiltrating T cells from patients with ovarian cancer. Overall, the 4-1BB LV platform targets antigen-specific T cells in a manner agnostic to both the antigen and presenting MHC, with potential applications in adoptive cell therapy manufacturing and TCR identification. One Sentence SummaryEngineered lentiviral vectors targeting 4-1BB selectively activate, expand, and transduce antigen-specific T cells with immunomodulatory cargo.

immunology↗

bioRxiv2026

Glycosylation-dependent Turnover of Triterpenoid Saponins Controls Insect Deterrence

Background and AimsPlants deploy triterpenoid saponins as chemical defences against herbivores, yet it remains unclear whether insect digestion detoxifies these compounds or generates equally or more active metabolites. Because saponin bioactivity depends strongly on glycosylation patterns, we examined the fate and defensive activity of hederagenin-derived saponins during herbivory. MethodsLarvae of Plutella xylostella were fed leaf discs containing structurally defined hederagenin-derived saponins. Saponin composition in treated leaves and larval frass was analysed by LC- qTOF-ESI-MS/MS. Feeding assays were used to compare the antifeedant activity of mono- and bidesmosidic forms. Key ResultsLarvae selectively metabolized complex hederagenin-derived saponins into simpler forms, with cellobiosides converted into monoglucosides during digestion, resulting in a marked shift in saponin composition between ingested material and frass. Feeding assays showed that monodesmosidic saponins strongly deterrer feeding, whereas bidesmosidic saponins were largely inactive. The loss of activity in bidesmosidic saponins was not explained by differential metabolism, indicating that glycosylation patterns directly determine biological function. ConclusionsInsect herbivores selectively modify saponin structures through deglycosylation, thereby altering their defensive properties. Our findings demonstrate that glycosylation governs both saponin activity and metabolic fate, highlighting insect-driven turnover as a critical component of plant chemical defence during plant-herbivore interactions. Issue SectionOriginal article

biochemistry↗

bioRxiv2026

Petabase-scale Papillomavirus Discovery

Freely available nucleic acid sequencing databases have accumulated to a vast archive of genetic diversity, in excess of 50 petabase-pairs from tens of millions of experiments. Together, these data constitute a digital survey of Earths genome. However, the richness of biological information contained within these repositories remains largely unexplored, in large part owing to the technical challenges of analyzing petabytes of data. Recently, Logan completed the sequence-assembly and compression of 27 million sequencing libraries from the Sequence Read Archive (SRA), and here, we systematically search Logan-SRA to reveal the global diversity of the DNA-based Papillomaviruses (PVs). In a single [~]10-hour alignment-based search against the Logan assemblage, we independently re-identified 65% of the 992 PVs recorded within the NCBI Virus database, a body of work representing over five decades of PV characterization. We further expand the diversity of PVs by 34%, identifying 383 novel PV types spanning 105 associated host species, including taxa with no previously associated PVs, such as rhinoceros, voles, and grey foxes. Through integration of virus phylogeny, sample geography, and ecological metadata, we show that novel PV discovery is not directly proportional to sampling effort, and there are significant hotspots of PV biodiversity in East Africa and South America, and that undersampled biomes can yield disproportionately more novel PVs. Public sequencing repositories contain vast, unrealized biological information that is now accessible through advanced computational infrastructure. Here we lay the foundations for the efficient analysis of petabase-scale datasets for DNA virus discovery, with applications to uncovering all genetic diversity.

bioinformatics↗

bioRxiv2026

Slow Dissociation of Nitazenes from the μ-Opioid Receptor Underlies the Challenge of Overdose Reversal

Nitazenes are driving a wave of overdose deaths in the United States and Europe and often require additional doses of naloxone to reverse. To understand the molecular basis, we conducted a joint experimental and simulation study of three common nitazenes, eto-, etodes-, and protonitazene. Radioligand experiments demonstrated that all three nitazenes display higher receptor affinity and longer dissociation half-lives than fentanyl. Notably, protonitazene dissociates slower than carfentanil and its displacement requires fourfold higher antagonist concentrations. The observed trend in nitazene half-lives is recapitulated by molecular dynamics simulations, which suggest that kinetics is controlled by specific interactions with two receptor subpockets. A newly published cryo-EM structure of fluetonitazene-OR complex confirms the predicted interactions, including a{pi} -hole bond between the nitro group and Tyr1.39, a residue recently shown to modulate OR signaling bias. Our findings suggest slow receptor dissociation as a key factor challenging overdose reversal. The mechanistic insights have implications for understanding opioid toxicity and designing more effective countermeasures.

pharmacology and toxicology↗

bioRxiv2026

Chromosomal rearrangements 1 and sequence similarity drivepreferential allosyndetic introgression from a wild relative into wheat

Recombination in polyploid genomes is generally constrained to homologous or homoeologous chromosomes; however, how chromosomal rearrangements influence recombination between chromosomes remains unclear. Here, we demonstrate that large-scale chromosomal rearrangements in the wild relatives of wheat are associated with recombination involving non-homoeologous chromosomes or arms during alien gene introgression under conditions that permit homoeologous recombination mediated by ph1b. Using a wheat chromosome 6A monosomic-induced 6AS*6CL Robertsonian translocation combined with ph1b-mediated recombination, we generated 17 independent recombinants carrying a new stem rust resistance gene, Sr69, from Aegilops caudata chromosome arm 6CL. Unexpectedly, 94.1% (16 of 17) of recombinants resulted from exchanges with wheat group-7 chromosomes rather than with the homoeologous group-6 chromosome. Comparative sequence- and marker-based analyses identified a 67-Mb rearranged interval on Ae. caudata 6CL that corresponds to telomeric regions of the long arms of wheat group-7 chromosomes. Sequence similarity within this interval was quantitatively associated with recombination frequency, with higher similarity corresponding to more frequent translocations. Physical and optical mapping showed that recombination within the rearranged interval generated compensating 7A/6C, 7B/6C, and 7D/6C translocations, whereas recombination outside this region produced non-compensating 6A/6C exchanges. An independent case involving the powdery mildew resistance gene Pm7C showed a similar correspondence between a rearranged 7CL region and preferential introgression into wheat 7DS. Together, these results indicate that ph1b-mediated recombination involving structurally altered chromosomes is driven by local chromosomal structure and sequence similarity rather than strict homoeologous group identity. This provides a mechanistic basis for harnessing untapped beneficial genes from structurally rearranged alien genomes. Significance StatementAlien gene introgression is a powerful strategy for wheat improvement, typically relying on ph1b-mediated recombination between homoeologous chromosomes. The genomic basis and outcomes of introgression from structurally rearranged alien chromosomes remain unclear. Here, we show that ph1b-induced recombination can efficiently target wheat-allosyntenic blocks in rearranged alien genomes, preferentially transferring genes from structurally altered alien segments into their syntenic regions on wheat chromosomes of different homoeologous groups. Crossover formation is governed by extended sequence similarity within corresponding intervals rather than strict collinearity across entire homoeologous chromosomes. As many wild species exhibit extensive genome rearrangement, these findings and methodologies expand access to underexploited genetic diversity embedded within highly rearranged wild genomes for wheat improvement.

genetics↗

bioRxiv2026

SNAP MRI Reveals Association Between Distal Cerebral Arterial Flow and Cognitive Function in an Aging Population

ObjectiveImpaired blood flow has recently been recognized as a critical contributor to cognitive impairment and dementia. It was reported that cerebral distal arterial flow measured from Simultaneous Non-contrast Angiography and Intraplaque Hemorrhage (SNAP) MRI is associated with post-treatment cognitive function improvement in carotid atherosclerosis patients. In this study, we aim to evaluate the value of SNAP-based measurements in assessing cerebrovascular function in an aging population. Materials and MethodsNeurovascular MRI data were collected on 36 aging participants (22 cognitively unimpaired and 14 impaired; 9 mild cognitive impairment (MCI) and 5 Alzheimers Disease (AD)). Neurovascular MRI measurements, including white matter hyperintensities (WMH) volumes, cerebral blood flow (CBF), and SNAP-based distal cerebral arterial flow (dCAF) index, were quantified. Cognitive function was assessed using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). ResultsSignificant differences in the dCAF index were observed between cognitively unimpaired and impaired groups, and the dCAF index was significantly correlated with the RBANS total score. While CBF was significantly associated with dCAF index, there is no significant correlation of CBF or WMH with the RBANS score in this population. ConclusionOur findings suggest that the dCAF measured with SNAP MRI is valuable for evaluating the cognition-related cerebrovascular condition in an aging population.

neuroscience↗

bioRxiv2026

Clarified an rDNA Gene Unit Pattern with (CTTT)n and (CT)n Microsatellites Aggregation Ahead of and Behind the Gene in Human Genome

BackgroundConventional models of human ribosomal DNA (rDNA) array organization have historically depended on transcription-centric boundaries, partitioning the unit into a [~]13 kb rDNA transcription region and a monolithic [~]31 kb intergenic spacer (IGS). While our previous identification of Duplication Segment Units (DSUs) mapped these arrays based on an intuitive analysis of the microsatellite density landscape of the complete reference human genome, our present deep mining of this landscape has revealed a more accurate rDNA Gene Unit Pattern. Methods & ResultsIn this study, we conducted a deep mining analysis of our previously established microsatellite density landscape of the T2T-CHM13 assembly, focusing specifically on nucleolar organizing regions (NORs). We suggest a more accurate rDNA Gene Unit Pattern containing a (CTTT)n microsatellite aggregation ahead of the rDNA gene and a (CT)n microsatellite aggregation behind the gene, rather than a pattern featuring an IGS region inserted between two rDNA genes. ConclusionsA correct rDNA gene pattern of the human genome probably includes a (CTTT)n microsatellite aggregation ahead of the gene and a (CT)n microsatellite aggregation behind it, which possibly constitute cis- and trans-regulating regions; the (CTTT)n and (CT)n microsatellite aggregations may provide two different local stable DNA structures for regulatory protein binding.

genetics↗

bioRxiv2026

Unbiased Single-Cell Transcriptome-Proteome Co-Profiling Reveals Malignant Dormancy and Post-Transcriptional Buffering of CTCs

Leptomeningeal metastasis is driven by rare cerebrospinal fluid circulating tumor cells (CSF-CTCs). However, the mechanisms underlying their adaptation to chemotherapeutic stress remain elusive, primarily because transcriptomics alone poorly predicts functional protein states. Here, we present scMAPS, a single-cell multi-omics method that employs magnetic-assisted partitioning cell lysates to enable unbiased transcriptome-proteome co-profiling without loss-prone physical splitting and precision device. By coupling scMAPS with our custom CLEAP (CTC Label-free Enrichment and Accurate Picking) system, we performed the first deep multi-omics profiling of rare clinical CSF-CTCs before and after localized chemotherapy, detecting an average of 2,547 proteins and 7,821 genes per cell. The integrated CLEAP-scMAPS pipeline reveals a coordinated prioritizing survival over proliferation malignant dormancy phenotype and identified post-transcriptional buffering as the primary driver of treatment resistance. Our platform enables the comprehensive molecular phenotyping of rare clinical specimens, providing a highly versatile framework for decoding complex post-transcriptional regulatory networks.

cell biology↗

bioRxiv2026

Sex-Specific Vulnerability to Radiofrequency Electromagnetic Radiation-Induced Reproductive and Neurological Impairment in Mice

Electromagnetic radiation (EMR) constitutes a pervasive environmental stressor, yet the sex-specific vulnerabilities to its biological effects remain inadequately characterized. This study investigated the differential impacts of 3.2 GHz pulsed EMR on reproductive and neurological functions in male and female mice following a four-week exposure regimen. We identified a pronounced sexual dimorphism in systemic and organ-specific responses. Male mice exhibited a primary vulnerability in the reproductive axis, manifesting as severe spermatogenic impairment, including depletion of the spermatogonial stem cell pool, disruption of sperm chromatin remodeling, and consequent declines in sperm quality and quantity. In contrast, exposed females showed preserved ovarian function but displayed marked neurobehavioral deficits, including increased anxiety- and depressive-like behaviors, and cognitive impairment, which were correlated with neurodegeneration in the hippocampus and prefrontal cortex. Proteomic analyses revealed distinct sex-specific biomarker profiles, with serum levels of Mdk, histone H1 variants (H1-1, H1-4, H1-5), Hp1bp3, Ncf2, and Rhoc strongly associated with male testicular dysfunction, while decreased levels of the synaptic motor protein KIF13A in serum and brain tissue were linked to female neurological impairment. Our findings delineate clear sex-divergent pathological pathways that target male spermatogenesis and female neurocognitive function and propose novel circulating protein biomarkers. This work provides a critical foundation for sex-aware risk assessment and the development of targeted preventive strategies against EMR-associated health risks.

pathology↗

bioRxiv2026

Identifying genetic regulations on immune cell type proportions and their impacts on autoimmune diseases

Genetic regulation of immune cell composition plays a crucial role in the etiology of complex diseases, yet remains poorly understood. We propose a unified analytical framework that integrates genome-wide association studies (GWAS) of cell type proportions with cell-type-wide association studies (cWAS) to systematically characterize both the genetic regulation of immune cell composition and its downstream effects on disease risk. Using single-cell RNA sequencing data from the OneK1K cohort, we conducted a GWAS of immune cell-type proportions with a depth-weighted quasi-binomial model designed for bounded, overdispersed traits. We identified 47 genome-wide significant loci influencing eight fine-labeled immune cell subtypes. Leveraging these identified genetic effects, we further imputed genetically regulated proportions (GRPs) using polygenic risk score (PRS)-based imputation and assessed their associations with complex diseases through cWAS. We identified five significant cell type-disease associations, including two with type 1 diabetes, two with Crohns disease, and one with ulcerative colitis. Together, our results demonstrate that cell type proportions observed in scRNA-seq can reveal regulatory loci and offer insights into how genetic variations regulate immune cell type proportions to affect disease risk. Although we focused on immune single-cell data, our framework is applicable to other tissues or cellular compositions as scRNA-seq datasets expand. Author SummaryGenome-wide association studies (GWASs) have uncovered many disease-associated signals, yet most lie in noncoding regions and are difficult to interpret. Mapping GWAS signals to the relevant cell types is therefore important for better understanding the biological mechanisms that drive disease. A major challenge is that observed gene expression and measured cell-type proportions can be influenced by environmental factors and disease status. In contrast, genotypes are less affected by these factors, making them more reliable for interpreting factors of diseases. Moreover, the cell-type proportions are bounded and often skewed, so standard GWAS models that rely on Gaussian assumptions may lose power. To address this, we developed a quasi-binomial approach that better matches the data and improves discovery while controlling false positives. In real data, our method identified more genetic loci associated with cell-type proportions than a traditional linear model. To further investigate how genetic variation regulates immune cell composition to influence disease risk, we integrated our results with disease GWAS summary statistics to identify immune cell types that may contribute to disease susceptibility. Together, our results link disease-associated GWAS signals to specific immune cell types and provide insights into the cellular mechanisms that may underlie these diseases.

genetics↗

bioRxiv2026

Targeted knockout of CYP79A1 reduces cyanogenic potential in grain sorghum

Sorghum bicolor is a climate-resilient C4 crop used for food, forage, and bioenergy, but broader adoption is constrained by accumulation of the cyanogenic glucoside dhurrin, which can release toxic hydrogen cyanide (HCN) upon tissue damage. Dhurrin levels are especially high in juvenile tissues, creating risk for grazing animals and limiting use in mixed crop-livestock systems. Here, we establish a CRISPR-Cas9 genome-editing strategy targeting CYP79A1, which catalyzes the first committed step in dhurrin biosynthesis, in the elite grain sorghum inbred RTx430, yielding transgene-free lines with stable, heritable reduction in cyanogenic potential across early vegetative development. Homozygous cyp79a1 knockouts were negligibly cyanogenic, whereas heterozygous plants exhibited approximately half the cyanogenic potential of unedited nulls. Consistent with established livestock grazing guidelines, only homozygous knockouts fell below thresholds considered hazardous for incidental grazing. This work establishes CYP79A1 as a practical and heritable genome-editing target for reducing sorghum cyanogenesis and provides a clear path for deployment of low-cyanogenic alleles in elite breeding backgrounds.

plant biology↗

bioRxiv2026

Expanding Glycopeptide Identification with Match-Between-Glycans in FragPipe

Glycosylation is one of the most important, but also most complex, post-translational modifications of proteins, playing a pivotal role in various pathological processes. Mass spectrometry-based large-scale glycoproteomics analysis offers a powerful approach to explore the fundamental roles of glycosylation in both physiological and pathological contexts. Traditionally, DDA glycopeptide assignment relies on information-dense MS2 spectra, containing sufficient fragmentation information to identify both the peptide and glycan moieties. Achieving this fragmentation can be difficult, especially for low-abundant glycopeptides and/or large, complex glycans. These glycopeptides are often not assigned using current data analysis software, yet they can be of biological relevance. Here, we introduce a method called match-between-glycans (MBG), which expands glycopeptide identification while maintaining the existing glycoproteome analysis workflow. MBG enables expanding the set of identified glycopeptides to include those without MS2 spectra, or with lower quality MS2 spectra, by looking for MS1 signals displaced from other identified glycopeptides by one or multiple monosaccharide unit(s). MBG can also identify glycans not included in the glycan database, such as those containing adducts or modifications, allowing these glycans to be recovered without a drastic expansion of the search space. Combined with target-decoy FDR control, we show this method is capable of accurately expanding glycopeptide identifications and providing a more complete quantitative profile of glycosylation at each glycosite. MBG is fully integrated into the glycoproteomics workflows in FragPipe, allowing seamless, one-click operation.

bioinformatics↗

bioRxiv2026

Enhanced multi-omic viral profiling from microbial community sequencing with BAQLaVa

Viruses are crucial components of microbial communities, both phage that infect bacterial community members as well as pathogenic and other eukaryotic viruses. However, they remain unobserved by most current technologies, due to combinations of experimental and analytical factors. To address the latter, we developed the BAQLaVa algorithm for high-resolution profiling of >120,000 viral species (viral genome bins, VGBs) via reference-based metagenome (MGX) or metatranscriptome (MTX) alignment to complementary nucleotide markers and proteome sets. In comprehensive benchmarking, BAQLaVa substantially outperformed alternatives, achieving species-level recall and precision regularly over 90%. We applied BAQLaVa to MGX and MTX samples from the HMP2 IBDMDB cohort to identify previously undescribed viral perturbations in inflammatory bowel diseases. Most notably, virome diversity was reduced in tandem with bacterial diversity during inflammation, in contrast to previous findings based on a narrower range of viral detection. A subset of viruses were enriched during IBD, associated with carriage of abortive infection anti-defense systems such as AbiL and PD-{lambda}-2, as well as genes involved in the regulation of lysogeny. Leveraging the corresponding viral profiles, we also inferred phage-host relationships using scalable co-occurrence and covariation signals, even in the absence of host references or genome annotations. By enabling high sensitivity and specificity viral profiling from metagenomes or metatranscriptomes, BAQLaVa provides a scalable framework for virome epidemiology and systematic analysis of virus-host interactions.

bioinformatics↗

bioRxiv2026

Macrophage Antigen Presentation Is Unleashed by Pan-RAS Inhibition to Promote Antitumor Immunity

Pan-RAS inhibitors have emerged as potent targeted therapies designed to suppress oncogenic signaling in RAS-mutant tumors. However, whether these inhibitors possess therapeutic utility beyond tumors with intrinsic RAS dependency remains unclear. Here we show that the clinical-stage pan-RAS(ON) inhibitor RMC-6236 (Daraxonrasib) induces robust regression of NRAS-wild-type B16 tumors in immunocompetent mice, a response mediated by a mechanism independent of direct tumor-cell targeting. Instead, RMC-6236 acts by remodeling the tumor microenvironment, specifically enhancing the antigen-presenting capacity of tumor-associated macrophages through upregulated MHC-I expression. This anti-tumor efficacy is abrogated in T cell-deficient hosts, identifying a macrophage-dependent, T cell-mediated mechanism of control. Mechanistically, RMC-6236 does not directly block canonical RAS signaling in macrophages. Rather, it suppresses a Myc-Hdac2 epigenetic program, leading to enhanced histone H4 acetylation at the Nlrc5 locus and subsequent activation of the MHC-I master regulator NLRC5. Together, our findings reveal a macrophage-centered, epigenetically wired immune mechanism for pan-RAS inhibition that broadens the therapeutic scope of targeting the "undruggable" RAS pathway beyond tumor genotype towards systemic immune modulation.

immunology↗

bioRxiv2026

PRDM1 Drives Chemoradiotherapy-associated Enrichment of Adaptive NK Cells in Cervical Cancer

Chemoradiotherapy (CRT) induces not only direct tumor cell death but also extensive remodeling of the tumor immune microenvironment. Adaptive natural killer (aNK) cells, initially characterized in chronic viral infection, are increasingly recognized as functionally relevant immune populations in solid tumors, where they may contribute to antitumor immunity and immune memory. However, how aNK cells dynamically respond to chemoradiotherapy and the regulatory mechanisms underlying their activation in solid tumors remain poorly defined. To address this, we analyzed single-cell RNA sequencing data from cervical cancer patients collected before CRT, after the first CRT fraction, and after the second fraction. Single-cell profiling revealed a significant enrichment of aNK cells following CRT. Differential gene expression and pathway enrichment analyses demonstrated that CRT-associated aNK cells exhibit enhanced virus-defending programs with increased cytotoxicity. Among the differentially expressed genes, the transcription factor PRDM1 was consistently and robustly upregulated in aNK cells after both the first and second rounds of CRT. To investigate the functional role of PRDM1, we applied in silico perturbation analyses using scTenifoldKnk and CellOracle. Virtual knockout of PRDM1 resulted in a marked attenuation of effector programs and disruption of metabolic networks in aNK cells. Moreover, PRDM1 perturbation altered inferred cellular trajectories, reversing the progression toward the aNK cell state, suggesting a requirement for PRDM1 in maintaining aNK identity and functional maturation within the CRT-conditioned tumor microenvironment. Together, these findings identify PRDM1 as a key regulatory factor associated with the enrichment, functional activation, and trajectory stabilization of aNK cells following CRT in cervical cancer, providing insight into innate immune remodeling during CRT and highlighting PRDM1 as a potential target for enhancing radiotherapy-induced antitumor immunity.

immunology↗