Biology subjects

Cheng, S.

Publications and source records attributed to Cheng, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

A mitochondrial program encodes brain vascular reserve

Brain resilience depends on collateral vessels whose geometries preserve blood flow when primary arteries are perturbed. How these protective vascular architectures are developmentally established remains unknown. Using longitudinal in vivo imaging in zebrafish, we show that mitochondrial state in embryonic angiogenic tip cells encodes the topology of basal and surface brain collateral networks. Mechanistically, microRNA-125a establishes the bioenergetic and redox balance of endothelial tip-cell mitochondria through conserved repression of the metabolic regulator PGC1a. Disruption of the microRNA-125a-PGC1a axis uncouples mitochondrial capacity from redox buffering in developing brain tip cells, redirecting their migration toward sparse, incompletely connected collateral network topologies and increasing adult cerebrovascular vulnerability. Consistent with this mechanism, humans with subclinical cerebrovascular injury exhibit reduced circulating microRNA-125a levels associated with incomplete basal collateral configurations. Together, these findings identify mitochondrial state as an instructive and conserved developmental program that encodes brain vascular reserve.

developmental biology↗

bioRxiv2026

Experience-driven reallocation of sensory and mnemonic representations during working memory

Mastering fine perceptual skills requires maintaining precise visual information while simultaneously processing new inputs. In the visual cortex, sensory and mnemonic representations coexist through region-wide multiplexing, yet how perceptual experience reshapes these neural codes remains unknown. Here, combining five days of intensive perceptual training with fMRI and multivariate pattern analyses, we tracked how perceptual learning reformats mnemonic neural representations in a motion-direction discrimination task. Learning improved motion-direction discrimination sensitivity and reshaped the distribution of sensory- and mnemonic-format codes across the visual hierarchy. Sensory-format maintenance was enhanced in V1, and the magnitude of this enhancement closely tracked the behavioral learning effect across individuals, whereas mnemonic-format coding was reduced in V3A. Within V1, learning further increased temporal coupling between sensory and mnemonic codes while leaving their near-orthogonal coding geometry largely unchanged. Our results suggest that perceptual learning reformats working memory codes along a reverse visual hierarchy, strengthening high-fidelity sensory-like representations while preserving the separable organization of multiplexed codes. These findings identify reverse-hierarchy reformatting as a hallmark of experience-driven working memory plasticity.

neuroscience↗

bioRxiv2026

The first step is not always the hardest: A change-point analysis of predictive learning

The progress of learning is usually quantified by averaging responses across participants and/or multiple trials within a block. However, such approaches obscure the trial-by-trial progress of learning, which has been shown recently to express a rich variety of dynamics. An alternative approach which does not suffer from this problem is the detection and analysis of points of behavioral change, i.e., change-point analysis. Using change-point analysis, we reanalyzed data from human participants in different predictive learning tasks in which learned contingencies underwent reversal. We find that responses of individual participants were more accurately characterized by behavioral change points than the average learning curve. Importantly, change points significantly shifted to later trials during reversal learning indicating that reversal learning is more difficult than the initial learning. In a computational model based on deep reinforcement learning, we show that the change point shift required the replay of previous experiences, which in turn depends on the hippocampus. This finding is consistent with studies showing that lesions of the hippocampus yield faster reversal learning. In summary, we reaffirm the importance of the analysis of single participant responses, show that phenomenological learning rates are slower during reversal learning, and provide a theoretical account for this difference.

neuroscience↗

bioRxiv2026

Streak-Aware Localization Microscopy Enables High-Throughput Brain Imaging Across Platforms

Optical, ultrasound, and optoacoustic localization microscopy based on microparticle tracking has enabled surpassing the resolution limits imposed by ultrasound diffraction and optical diffusion in tissues. However, its reliance on high-speed (kilohertz) data acquisition systems for precise emitter localization and tracking substantially increases methodological complexity and data storage demands, limiting scalability and applicability beyond specialized benchtop platforms. Here, we present streak-aware localization microscopy (SALM) that employs localization- and tracking-free deep learning model to convert motion-blurred streaks originating from low frame rate recordings of flowing emitters into super-resolved structural and functional readouts. In optical implementations, SALM exploits streaks captured by low-speed cameras to recover capillary-level cerebrovascular maps across a variety of benchtop, miniaturized, and second near-infrared preclinical imaging platforms, achieving over 30-fold reduction in the reconstruction time compared to conventional localization pipelines. We further introduce three coded excitation strategies that embed finer time-varying vectorial flow signatures into individual streaks, enabling single-frame velocimetry and video-rate hemodynamic imaging. Extending SALM to ultrasound imaging enables high-fidelity vascular imaging with centimeter-scale penetration in rhesus macaque and rat brains while reducing plane-wave compounding frame rates by up to one order of magnitude. By overcoming long-standing trade-offs between spatiotemporal resolution and hardware complexity, SALM offers a flexible and scalable framework for next-generation super-resolution microscopy.

neuroscience↗

bioRxiv2026

Therapeutic targeting inflammation linking periodontitis and atherosclerotic comorbidities using cell-free DNA-capturing nanomaterials

Periodontitis-associated systemic inflammation makes it a great challenge to explore therapeutic options applicable to periodontitis and atherosclerotic comorbidities. Here, we identify the crucial role of cell-free DNA (cfDNA) that underlies these comorbidities. Hypothesizing cfDNA as a therapeutic target, we engineer polyamidoamine dendrimer-functionalized nanomaterials to modulate such local-systemic inflammatory crosstalk. Periodontium-originated DNA can be systemically captured by cationic nanomaterials, and capturing cfDNA, whether locally or systemically, alleviates both periodontitis and atherosclerosis prior to severe atherosclerotic development in vivo. The transcriptomic and single-cell RNA sequencing analyses together reveal that cfDNA-capturing nanomaterials regulate inflammatory foam cell transformation in macrophages by modulating the expression of lipid-related foamy markers Spp1 and Fabp4. This study provides a proof of concept for cfDNA-driven periodontitis-atherosclerosis crosstalk, and offers a cfDNA-capturing nanoplatform for therapeutic intervention targeting periodontitis and atherosclerotic comorbidities in a holistic fashion.

immunology↗

bioRxiv2026

Cell-Autonomous AR Dependence in Luminal Prostatic Epithelium Governs Survival and Lineage Plasticity

Prostate cancer resembles differentiated secretory luminal cells and shows cell-autonomous dependence on androgen receptor (AR) signaling, yet normal luminal cells are often considered dependent on paracrine stromal AR signaling. To resolve this, we conditionally deleted Ar in luminal acinar cells in vivo. Ar-deleted luminal cells persisted short-term, in contrast to the rapid regression observed after castration, but were impaired in regeneration and progressively lost. Their depletion was accompanied by replacement through basal-to-luminal differentiation of AR intact basal cells. Transcriptomic and chromatin profiling showed cell-autonomous suppression of the secretory program with induction of stemness, inflammatory, and epithelial-to-mesenchymal transition signatures after AR loss. Mechanistically, the MAP kinase pathway and downstream AP-1 transcription factors were activated and functionally validated, and MAP kinase inhibition selectively depleted AR-deleted luminal cells, indicating a compensatory survival pathway. These findings define intrinsic roles for luminal AR in maintaining differentiation, restraining plasticity, and sustaining regeneration and homeostatic turnover, providing a mechanistic basis for AR dependence in prostate cancer.

cell biology↗

bioRxiv2025

A linear regression model predicts human brain ageing and reveals differential neuronal biological ageing relevant for Parkinson's disease susceptibility

Biological brain ageing is a major risk factor for neurodegenerative diseases, which are characterized by selective degeneration of particular neuron types. We analyzed the impact of ageing on the transcriptome of neurons in the ventral tegmental area (VTA), substantia nigra pars compacta (SNc) and locus coeruleus (LC), that show differential vulnerabilities to Parkinsons disease. Neurons were isolated from human post mortem brain tissues originating from 48 individuals ranging from 17 to 102 years of age and subjected to Smart-seq2 RNA sequencing. We identified 2,764 genes that were correlated with chronological ageing. This gene expression data was used to develop a feature selection-based Time Traversal algorithm, utilizing functionally grouped gene sets, GO terms, with high predictive accuracy of biological brain ageing. We identified 59 GO terms that can predict biological age using a linear regression model, where leave-one-out cross validation demonstrated a strong correlation between chronological age and predicted biological age (Pearson correlation coefficient = 0.946; adjusted R{superscript 2} = 0.771). The algorithm was validated on five independent datasets with high predictive performance, demonstrating shared ageing features across the human brain. Nonetheless, our analysis also highlights brain region and neuron type specificity in particular ageing features. Resilient neurons showed a weaker association with age-related transcriptional changes, indicating that they age slower than their vulnerable counterparts, thus revealing targets that may be used to slow down ageing and prevent disease development.

neuroscience↗

bioRxiv2025

Benchmark for simple and complex genome inversions

BackgroundInversions represent a consequential yet under-characterized form of structural variation, with roles in genomic disorders, evolution, and genome instability. However, their detection remains technically challenging, particularly within repeat-dense regions and for complex multi-breakpoint events. A lack of dedicated, high-quality benchmarks has hindered algorithmic improvement, performance comparison, and robust biological interpretation. ResultsHere, we present a comprehensive, multi-genome benchmark for simple and complex inversions derived from Strand-seq and phased long-read based assemblies across five reference samples, with breakpoint refinement using haplotype-resolved long-read assemblies. This tiered resource spans a broad spectrum of inversion classes, sizes, and zygosity states, and captures challenging genomic contexts including segmental duplications, inverted repeats, and composite rearrangements. We used this benchmark to systematically assess leading structural variant callers and alignment strategies across short-read, PacBio HiFi, and Oxford Nanopore data. Performance varied substantially by inversion class and genomic context: simple inversions were recovered with high sensitivity at sufficient coverage, whereas complex and heterozygous events remained difficult. Sniffles2 and Severus achieved the strongest recall for complex inversions, despite increased false-positive rates. We additionally benchmarked two commonly used long-read alignment pipelines (Minimap2 and VACmap), demonstrating that the mapper choice has a substantial impact on inversion detection in repetitive regions. ConclusionTogether, this work provides the first unified, high-resolution inversion benchmark and reveals clear strengths and limitations of current methods across platforms. Our resource establishes a foundation for principled tool development, evaluation, and tuning, enabling the community to more accurately resolve inversion variation and its biological and clinical consequences.

bioinformatics↗

bioRxiv2025

An ancient transcription factor functions as the master regulator of primary cilia formation

How ancient transcription factors are repurposed during evolution to drive the functional diversification of conserved organelles remains a fundamental question in biology. Although highly conserved in basic morphology, eukaryotic cilia vary extensively in their sizes and functions. Previously, we showed that an evolutionarily ancient transcription factor, X chromosome-associated protein 5 (Xap5), controls motile ciliogenic transcriptional programs during mouse spermatogenesis (Wang et al., 2025). Here we show that Xap5 functions as the master regulator of primary ciliogenesis. Xap5 associates with the nuclear protein Non-POU domain-containing octamer-binding protein (Nono) to form a regulatory module that directly binds and activates the transcription factors Sox5 and Sox9. Genetic ablation of Xap5 or Nono impairs primary ciliogenesis, and loss of Sox5 disrupts the downstream ciliogenic program, consistent with the established role of Sox9. Collectively, our results provide new insight into how complex ciliary transcription factor networks determine ciliary diversity during evolution, and suggest that defects in this regulatory axis may contribute to the etiology of human ciliopathies.

cell biology↗

bioRxiv2025

Graded Notch Signaling Functions as a Rheostat of Lineage Plasticity and Therapy Resistance in Prostate Cancer

Resistance to androgen receptor (AR)-targeted therapies such as enzalutamide in castration-resistant prostate cancer (CRPC) often arises through lineage plasticity, yet the molecular mechanisms that define this process remain incompletely understood. While previous studies reported that Notch1 and Notch2 exert distinct and sometimes opposing effects in prostate cancer differentiation, the integrated role of Notch pathway activity has not been systematically explored. Here, we identify Notch signaling as a graded Rheostat that governs prostate cancer cell fate transitions. Integrative transcriptomic and functional analyses revealed that intermediate Notch activity maintains a stem-like progenitor state, whereas reduced or elevated signaling drives divergent differentiation trajectories toward luminal or neuroendocrine lineages, respectively. During CRPC progression and enzalutamide resistance, Notch signaling becomes dynamically rewired, peaking in progenitor-like populations that sustain plasticity and survival. Both CRISPR-mediated knockout and pharmacologic inhibition of Notch signaling depleted these progenitor cells and restored enzalutamide sensitivity. These findings demonstrate that the level, rather than the binary presence, of Notch signaling dictates lineage directionality and therapeutic response in CRPC, establishing it as a tunable and actionable driver of resistance.

cancer biology↗

bioRxiv2025

Emergence of mutHV76G among longitudinal carbapenem resistant Klebsiella pneumoniae causing long-term colonization and recurrent infection disrupts DNA mismatch repair and results in a hypermutator phenotype

Although hypermutation due to Mut protein mutations that disrupt DNA mismatch repair has been characterized in some bacteria, its mechanisms and consequences in Klebsiella pneumoniae remain poorly defined. We analyzed 11 longitudinal KPC-3 carbapenemase-producing, ST258 K. pneumoniae isolates collected over [~]4 years from an immunocompromised patient with chronic colonization and recurrent infections. After [~]3.3 years, isolates developed ceftazidime-avibactam (CZA)-resistance with restored carbapenem susceptibility, coinciding with emergence of a V76G substitution in a highly-conserved motif in the core of MutH endonuclease. Compared with earlier isolates, mutHV76G-carrying isolates showed greater within-host genomic diversification (69-179 vs. 2-12 SNP differences) and acquired blaKPC-3L169P, encoding an KPC {Omega}-loop substitution that mediates CZA resistance and re-establishes carbapenem susceptibility. mutHV76G isolates exhibited stepwise increases in meropenem-vaborbactam (MVB) and cefiderocol minimum inhibitory concentrations, plausibly linked to substitutions in KPC, OmpK36 porin, CirA iron transporter and/or EnvZ kinase. Clinical mutHV76G isolates and CRISPR-engineered mutHV76G mutants were hypermutators based on rifampin mutational frequencies. Using isogenic mutant and parent strains, we confirmed that mutHV76G accelerated evolution of CZA and MVB resistance in vitro and in vivo, promoted transfer and uptake of resistance plasmids, and improved bacterial fitness during mouse infections. Resistance evolution in mice recapitulated clinical trajectories, with blaKPC-3 and ompK36 mutations emerging under CZA and MVB exposure, respectively. Phenotypes of mutHV76G and mutH-null strains were comparable, indicating that the V76G substitution largely abrogates MutH function. Our findings reveal MutH-mediated hypermutation as an adaptive mechanism in K. pneumoniae, enabling rapid antibiotic resistance development and plasmid acquisition without fitness cost. ImportanceHypermutator bacteria pose a formidable clinical threat by rapidly evolving antibiotic resistance and adapting within the human host. Klebsiella pneumoniae is a major cause of multidrug-resistant infections, yet the contribution of hypermutation to its evolution remains poorly characterized. Analyzing K. pneumoniae isolates collected over [~]4 years from a chronically infected/colonized patient, we demonstrate that emergence of a mutation in mutH (mutHV76G), a DNA mismatch repair gene, results in hypermutation phenotypes and rapid accumulation of gene mutations. Both clinical and lab-engineered mutHV76G mutant strains rapidly acquire resistance or reduced susceptibility to new antibiotics like ceftazidime-avibactam, meropenem-vaborbactam and cefiderocol, due to mutations in carbapenemase (blaKPC-3), porin (ompK36) and other genes. mutHV76G-driven hypermutation also enhances horizontal transfer of resistance plasmids and improves K. pneumoniae fitness during mouse infections. This study is important for understanding K. pneumoniae hypermutation as a potent mediator of antibiotic resistance and other phenotypes relevant to human infections.

microbiology↗

bioRxiv2025

High-Concordance Validation of Droplet Digital PCR and Next-Generation Sequencing for EGFR Mutation Detection Across Diverse Biospecimens in a Large-scale NSCLC Cohort Study

BackgroundsNext-generation sequencing (NGS) and droplet digital PCR (ddPCR) are both established methods for detecting EGFR mutations in non-small cell lung cancer (NSCLC). However, comprehensive validation of their concordance in mutation detection and variant allele frequency (VAF) quantification across heterogeneous sample types remains limited. Inconsistent results from different sample types (e.g., cfDNA, FFPE) pose a significant challenge to clinical decisions. This is particularly critical for advanced NSCLC patients, who often rely on liquid biopsy, yet the concordance between liquid and tissue-based testing lacks validation in large-scale studies. Another issue in clinical practice is that many tumor samples are limited in quantity, making it difficult to meet testing requirements. Therefore, it is worth exploring whether pre-capture NGS libraries can serve as substitutes for original DNA. MethodsIn this study, we first developed three assays to detect EGFR L858R, exon 19 deletions (Ex19del) and T790M, respectively using ddPCR platform. Their Limit of Detection (LOD) could reach 0.01% at 100 ng of input DNA. Subsequently, we conducted a large retrospective clinical study to systematically compare the detection performance of ddPCR and NGS across three mutation types using approximately 1,000 EGFR-positive samples, including cell-free DNA (cfDNA), pre-capture NGS libraries of cfDNA (cfDNA-prePCR), FFPE-derived DNA (ffpeDNA), pre-capture NGS libraries of FFPE-derived DNA (ffpeDNA-prePCR), fresh tumor tissue DNA (ttDNA), pre-capture NGS libraries of ttDNA (ttDNA-prePCR), pleural effusion supernatants DNA (peDNA), and pre-capture NGS libraries of peDNA (peDNA-prePCR). They were analyzed for detection concordance and VAF correlation. Especially, we made comparisons of the tumor DNA, including ctDNA and tumor tissue DNA, with their paired pre-capture NGS library. ResultsKey findings demonstrated excellent overall agreement between NGS and ddPCR. The mutation detection concordance rates were 98.72% (overall), with subtype-specific rates of 98.93% (L858R), 99.23% (Ex19del), and 97.14% (T790M). VAF measurements between ddPCR and NGS showed exceptional correlation (Pearsons r = 0.975, P<0.001). Notably, pre-capture NGS libraries showed remarkable VAF concordance with their source materials (0.993 for cfDNA libraries vs cfDNA; 0.998 for tumor tissue libraries vs tumor DNA with EGFR L858R; 0.991 for tumor tissue libraries vs tumor DNA with EGFR Ex19del). ConclusionsNGS and ddPCR demonstrate high concordance in EGFR mutation detection and VAF quantification, supporting their complementary roles in clinical testing. Using pre-capture libraries as an alternative to source samples can avoid repeat biopsies and enables subsequent testing for patients with inadequate FFPE sample quantity. These findings establish an evidence base for integrated diagnostic paradigms leveraging NGSs multiplexing power and ddPCRs sensitivity.

cancer biology↗

bioRxiv2025

The impact of incomplete taxon sampling on inference of gene flow by Bayesian and summary methods using genomic sequence data

Interspecific gene flow is commonly inferred using genomic data under the multispecies coalescent (MSC) model. The rate of gene flow is measured by the expected proportion of immigrants in the recipient population at the time of hybridization/introgression. Incomplete taxon sampling can impact inference of gene flow in multiple ways. First unsampled ghost lineages that are sources of introgression may mislead inference of gene flow in analysis of genomic data from modern species. Second incomplete taxon sampling causes merges of branches on the species phylogeny, which represent populations of different sizes, and complicates the definition and estimation of the introgression probability. We use mathematical analysis and computer simulation to examine the impact of incomplete taxon sampling on inference of gene flow and estimation of its rate using genomic data. We introduce a Bayesian testing approach to select models of gene flow for a species triplet (such as inflow, outflow, and ghost introgression), using the Savage-Dickey density ratio to calculate Bayes factors. We show that the approach has excellent power and specificity. We find that genomic data allow reliable estimation of the proportion of immigrants (rather than the number of immigrants), even when the assumed demographic model is incorrect due to incomplete taxon sampling. When population size differs among species, assuming the same size may lead to seriously biased estimates of the rate of gene flow. The f -branch approach is found to be effective in reducing the number of significant gene-flow events from triplet analyses, providing useful hypotheses for rigorous testing, but often to produce underestimates of the rate of gene flow. Our results highlight the need for improving summary methods to accommodate different population sizes and to infer gene flow between sister lineages.

genomics↗

bioRxiv2025

Competition Between Memory Updating and Differentiation Emerges from Intrinsic Network Dynamics

When an event occurs that is similar to a previous experience, the original episodic memory can be modified with new information (updating) or a new memory can be encoded (differentiation). Prediction errors, the deviation between expected and actual stimuli, are believed to mediate the competition between updating and differentiation, but the underlying mechanisms remain unclear. Here, we present a new analysis of experimental studies (Boeltzig, Liedtke, & Schubotz, 2025; Liedtke et al., 2025) that examine recognition memory and cued recall of similar conversations. The original version was recognized more confidently than the modified version, and the recognition confidence for modified versions showed a U-shaped dependence on the prediction error. Furthermore, the larger the prediction error, the more frequently participants retrieved two versions during cued recall. To account for these results, we propose a computational model based on a modified Hopfield network, which encodes the original and modified versions sequentially and weights the encoding of new patterns by the prediction error. The model shows that (1) similar new memories interfere with previous ones (updating) while dissimilar ones are stored separately (differentiation), (2) interference from similar representations leads to reduced memory accuracy and lower-confidence recognition, and (3) the encoding weight must be modulated by the prediction error to account for the experimental data. Our modeling results show that prediction-error-driven competition between updating and differentiation can emerge from intrinsic network dynamics alone.

neuroscience↗

bioRxiv2025

Assembly of two functionally-distinct protein import complexes in the outer membrane of plant chloroplasts

The TOC translocon delivers thousands of nucleus-encoded proteins to chloroplasts and related non-photosynthetic plastids. It comprises the {beta}-barrel channel, Toc75, and multiple isoforms of receptor GTPases, Toc33 and Toc159. However, exactly how TOC complexes are assembled in different plastid types is unknown. Here, we present detailed characterization of two distinct TOC complexes, TOC-P and TOC-N, from photosynthetic chloroplasts and non-photosynthetic plastids, respectively. The assembled complexes are distinguished by having different sets of receptors, but both possess Toc75 which we identify as a central hub in TOC biogenesis: assembly is driven by TOC75 expression, with the Toc33 and Toc159 being added sequentially thereafter. Integrative structural analysis revealed a modular architecture for TOC-P comprising a cytosolic GTPase receptor module linked flexibly to a membrane {beta}-barrel channel module. TOC-N has a similar overall architecture, albeit with some clear differences that likely account for observed functional differences related to client specificity.

cell biology↗

bioRxiv2025

Neutrophil extracellular traps-mediated thrombosis drive pyrrolizidine alkaloid-induced hepatic sinusoidal obstruction syndrome

Hepatic sinusoidal obstruction syndrome (HSOS) caused by pyrrolizidine alkaloid (PA) is a life-threatening disease with limited treatments, yet the initiating vascular event remains undefined. Neutrophil extracellular traps (NETs), as key driver of immunothrombosis in various thromboinflammatory diseases, may represent a critical yet uncharacterized component in the pathogenesis of PA-HSOS. Rats and mice were separately administered monocrotaline (MCT) or senecionine (SEN) via gavage to induce HSOS. Human hepatic sinusoidal endothelial cell (HHSEC) and primary human neutrophil treated with MCT, SEN, or corresponding metabolites were used as in vitro models. In separate experiments, animals received a neutrophil elastase (NE) inhibitor or neutrophil-depleting antibody to evaluate the contribution of NETs. We detected NETs within the sinusoids of necrotic liver lobes, as evidenced by robust immunostaining for NETs markers, accompanied with elevated level of circulating cell-free DNA, and hepatic citrullinated histone H3. Sinusoidal microthrombi containing VWF, CD41, and fibrin(ogen) were also stained positive for neutrophils in PA-HSOS models. Treatment with NE inhibitor or neutrophil depletion markedly attenuated PA-induced liver injury by concomitantly suppressing NETs formation and intrahepatic thrombogenesis. In vitro, conditioned medium from HHSEC exposed to MCT or SEN metabolites potently induced NETs formation. HHSEC injured by PA metabolites released CXCL8. Furthermore, hepatic mRNA and protein levels of CXCL1 and CXCL2 (murine homologous to human CXCL8) were up-regulated in PA-HSOS models, accompanied by a parallel elevation of their high-affinity receptors, CXCR1 and CXCR2. Our study identifies NETs-mediated immunothrombosis as a key driver in HSOS, which provides a promising target for PA-HSOS treatment.

pharmacology and toxicology↗

bioRxiv2025

RUNX1T1-HDAC Reprogramming of the HOX Code Signaling Drives a Targetable Pan-Cancer Lineage Plasticity

Cancer remains a leading cause of death worldwide, with lineage plasticity emerging as a hallmark that drives therapy resistance and tumor progression by enabling cancer cells to alter identity and evade targeted therapies. Although genomic and transcriptomic aberrations correlate with lineage plasticity, the absence of pan-cancer markers to rapidly identify plastic subtypes has limited predictive utility. Homeobox (HOX) genes encode transcription factors that define tissue identity through distinct expression patterns, or HOX codes, in specific lineages. By analyzing multi-omics data, including 39 HOX genes from over 80,000 RNA-seq samples across 114 cancer types, we discovered that HOX code expression robustly represents cancer cell lineages and reveals multiple previously unrecognized lineage-plastic subtypes in prostate cancer, lung cancer, and acute myeloid leukemia (AML), each displaying altered HOX patterns compared to non-plastic subtypes. Differential analysis further identified RUNX1T1 as a novel and consistent marker of plasticity, elevated across all three cancer types and correlating with HOX code and lineage-plastic marker genes. We validated these correlations in bulk and single-cell RNA-seq from extensive preclinical and clinical cohorts and provided direct functional evidence that RUNX1T1 is required for lineage-plastic programs in prostate cancer. Using AI-based modeling, we identified NCOR/HDAC as RUNX1T1 binding partners forming a co-repressor complex that regulates HOX codes and plasticity. Finally, pharmacologic HDAC inhibition selectively suppressed the growth of plastic cells, revealing a novel therapeutic vulnerability. These findings establish ectopic RUNX1T1 as a pan-cancer biomarker and critical mediator of lineage plasticity and identify the RUNX1T1-HDAC complex as a druggable target.

cancer biology↗

bioRxiv2025

Comprehensive Transcriptome Annotation of Thousands of HIV-1 Genomes

Alternative splicing in HIV-1 has been a central focus of decades of research, uncovering key mechanisms of viral gene regulation, immune evasion, and therapeutic response - yet, no reference resource has existed to support transcriptome-wide analysis, limiting adoption of modern computational methods. We present HIV Atlas (https://ccb.jhu.edu/HIV_Atlas), the first reference-quality annotation of HIV-1 and SIV transcriptional diversity. We manually curated transcriptomes for HIV-1HXB2 and SIVmac239 and developed Vira, an automated annotation-transfer method specifically designed to address unique challenges of viral genome biology, to generate high-quality annotations for 2,077 complete HIV-1 genomes. Using the resources presented in our work, we evaluated conservation of splice sites, revealing near-perfect preservation of major donors and acceptors. Furthermore, using several public datasets, we demonstrate how HIV Atlas enhances methodology, improves the quality and novelty of results, and opens novel avenues for research, supporting more accurate and comprehensive analyses of bulk, single-cell, and spatial RNA-seq in HIV-1 studies.

genomics↗