Biology subjects

Zhang, H.

Publications and source records attributed to Zhang, H..

At least 433 records · Page 24Linked to original sources

bioRxiv2025

Superinfection with intact HIV-1 results in conditional replication of defective proviruses and nonsuppressible viremia in people living with HIV-1

During replication of some RNA viruses, defective particles can spontaneously arise and interfere with wild-type (WT) virus replication. Recently, engineered versions of these defective interfering particles (DIPs) have been proposed as an HIV-1 therapeutic. However, DIPs have yet to be reported in people with HIV-1 (PWH). Here, we find DIPs in PWH who have a rare, polyclonal form of non-suppressible viremia (NSV). While antiretroviral therapy (ART) rapidly reduces viremia to undetectable levels, some individuals experience sustained viremia due to virus production from cell clones harboring intact or defective proviruses. We characterized the source of NSV in two PWH who never reached undetectable viral load despite ART adherence. Remarkably, in each participant, we found a diverse set of defective viral genomes all sharing the same fatal deletions. We found that this paradoxical accumulation of mutations by viruses with fatal defects was driven by superinfection with intact viruses, resulting in mobilization of defective genomes and accumulation of additional mutations during untreated infection. We show that these defective proviruses interfere with WT virus replication, conditionally replicate, and, in one case, have an R0 > 1, enabling in vivo spread. Despite this, clinical outcomes show no evidence of a beneficial effect of these DIPs.

microbiology↗

bioRxiv2025

Object categorization based on abstract concepts by monkeys, humans, and vision models

Humans categorize objects at multiple levels of abstraction--animate versus inanimate, big versus small, and many other attributes. Despite its apparent challenge, the advent of deep neural networks (DNNs) has demonstrated that complex visual processing alone can support such classification without language or human-specific knowledge. This raises a natural question: to what extent can non-human primates, without language, perform such categorization? Although basic object-recognition behavior in monkeys such as similarity judgment has been extensively studied, their ability to classify objects across diverse rules remains poorly characterized. Here, we developed a task paradigm that enabled us to train monkeys on a large battery of binary classification tasks using natural object images, spanning more than 10 rules, such as animate versus inanimate, natural versus man-made objects, and mammalian versus non-mammalian animals. Monkeys acquired each rule in a few days, generalized the learned rules to new images, and exhibited error patterns consistent with human judgments. At the same time, their classification performance correlated more strongly with that of visual DNNs trained without language input, whereas human performance was better explained by language-informed DNNs. These results provide an important benchmark for the capacity of biological neural networks to perform image classification without language and human-specific knowledge.

neuroscience↗

bioRxiv2025

The sialylation pattern of dietary glycopeptides is vital for inhibiting pathogens and modulating gut microbiota in elderly individuals

N-glycosylation is a post-translational modification of proteins that can influence the structure and function of glycoproteins. Edible birds nest (EBN) contains highly sialylated mucins with N-glycans and O-glycans, while casein glycomacropeptide (CGMP) is modified with only O-glycans. We prepare EBN sialoglycopeptides through sequential protease treatment and their inhibitory effects on pathogens, including Candida albicans, Helicobacter pylori, and avian influenza virus (AIV), as well as their modulation of gut microbiota in elderly individuals, were compared with CGMP. N-glycan analysis revealed the presence of multiantenna N-glycans, characterized by sialylation and bisecting GlcNAc in the EBN glycopeptides. EBN glycopeptides significantly inhibited C. albicans and H. pylori. However, the removal of terminal sialic acid from EBN glycopeptides resulted in a marked reduction of this inhibitory effect. Using Maackia Amurensis Lectin II as an AIV mimic, EBN glycopeptides effectively inhibited AIV adhesion to MDCK cells. In vitro fecal fermentation using fecal samples from elderly individuals revealed that the EBN glycopeptide group exhibited remarkable probiotic effects on the gut microbiota, increasing the relative abundance of beneficial bacteria such as Lactobacillus and Roseibacterium, while decreasing the relative abundance of harmful bacteria such as Escherichia-Shigella and Klebsiella. Overall, EBN glycopeptide, rich in sialylated N-glycans and O-glycans, strongly inhibited pathogenic microorganisms and showed superior probiotic properties compared to CGMP with sole O-glycosylation.

biochemistry↗

bioRxiv2025

Allo-PED: Leveraging protein language models and structure features for allosteric site prediction

Allosteric regulation plays a pivotal role in modulating protein function and allosteric sites represent a promising target for drug discovery. However, identifying allosteric sites remains challenging due to their structural and evolutionary diversity. Here, we present AlloPED, a novel framework that combines protein language models and machine learning to predict allosteric sites with high accuracy. AlloPED consists of two modules: AlloPED-pocket, an ensemble model leveraging physicochemical features to predict allosteric pockets; and AlloPED-site, a dilated convolutional neural network (DCNN) augmented with a comprehensive attention mechanism for residue-level prediction. AlloPED-pocket achieves state-of-the-art performance on benchmark datasets, yielding an MCC of 0.544 and an AUC of 0.920, outperforming existing methods such as AllositePro and PARS. AlloPED-site further refines predictions using high-dimensional sequence embeddings from the ProtT5 protein language model, achieving a precision of 0.601, a recall of 0.422, and a specificity of 0.661. These results highlight the effectiveness of integrating ensemble learning and deep learning for allosteric site prediction. AlloPED also identifies critical determinants of allosteric sites, including residue clustering coefficients, van der Waals volume, and hydrophobic microenvironments. In summary, this framework provides a robust tool for advancing our understanding of allosteric regulation and facilitating structure-based drug design.

bioinformatics↗

bioRxiv2025

Disentangling the impact of abiotic and biotic environmental factors and dispersal dynamics on bacterial pangenome fluidity

Understanding how pangenomes originate and evolve is crucial for predicting evolutionary trajectories and uncovering ecological interactions of bacterial pathogens. Pangenome fluidity has been attributed to adaptive evolution, yet the underlying ecological drivers for bacterial pathogens persisting in natural reservoirs remain poorly understood. Listeria monocytogenes (Lm), a foodborne pathogen causing fatal listeriosis, serves as an ideal model for investigating the ecological mechanisms underlying pangenome fluidity in bacterial pathogens due to its high evolutionary divergence, broad ecological versatility, and significant public health concern. Through pangenome analysis of 177 Lm isolates representing three evolutionary lineages (I, II, and III) that we isolated from soils across the United States, we found that substantial genome variation was strongly associated with climatic factors (e.g. precipitation and temperature), soil properties (e.g. aluminum, pH, and molybdenum), and bacterial community composition, particularly Nitrospirae, Planctomycetes, Acidobacteria, and Cyanobacteria. These factors exerted selective pressure across many gene functions, with pronounced effects on genes involved in cell envelope synthesis, defense mechanisms, and replication, recombination, and repair. Among Lm lineages occupying varied habitats, distinct pangenome properties were observed. Lineage III exhibited a highly fluid pangenome, which was attributed to local adaptation to nutrient-limited conditions and strong dispersal limitation. In contrast, lineage I maintained a conserved pangenome, likely due to frequent homogenizing dispersal. Consistent with these dispersal patterns, we identified an elevated risk of soil-to-human transmission in lineage I, evidenced by epidemiological links between three soil-derived and 17 clinical isolates. Collectively, this study reveals the pivotal role of environmental selection imposed by both abiotic factors and bacterial communities in governing the adaptive pangenome evolution in bacterial pathogens. It also highlights significant differences in pangenome flexibility, ecological niches, and transmission dynamics across lineages of the same pathogen species, underscoring the need for tailored source tracking strategies. AUTHOR SUMMARYStudying the full set of genes found in different strains of a bacterium (i.e. pangenome) helps us understand how bacterial pathogens develop and adapt to changes in the environment. Here, we focused on Listeria monocytogenes (Lm), a pathogen capable of spreading through food and surviving in diverse environments, to understand how environmental factors and the way that bacteria move across locations can influence the pangenome content in this important bacterium. By analyzing the genomes of 177 Lm strains representing three evolutionary lineages (I, II, and III) collected from soils across the United States, we found that variation in climate, soil chemistry, and surrounding bacteria (e.g., Nitrospirae) was closely linked to genetic differences among strains. These environmental conditions seemed to affect genes that help build the cell envelop, protect the bacteria from harm, and fix damaged DNA. We also observed different levels of genome flexibility across Lm lineages which were found to be related to how they move across different locations. Lineage III showed evidence of barriers to spreading, which may enhance genetic differentiation across populations, leading to a more flexible pangenome. In contrast, lineage I appeared to spread more readily and was epidemiologically linked to human clinical cases, which may facilitate genetic exchange that reduce pangenome diversity. This study shows that both non-living environmental conditions--like precipitation and pH--and nearby groups of bacteria play a big role in shaping how bacterial pathogens change their genes to survive. It also highlights that different subtypes of the same pathogen can have different gene flexibility and spread in different ways, calling for specific biocontrol measures.

genomics↗

bioRxiv2025

Distal Gene Expression Governed by Lamins and Nesprins via Chromatin Conformation Change

The nuclear lamina is a vital structural component of eukaryotic cells, playing a pivotal role in both physiological processes, such as cell differentiation, and pathological conditions, including laminopathies and cancer metastasis. Lamina associated proteins, particularly lamins and nesprins, are integral to mechanosensing, chromatin organization, and gene regulation. However, their precise contributions to gene regulation remain incompletely understood. This study explores the functions of lamin A, LMNA, and SYNE2 in gene expression, with a particular focus on their influence on distal chromatin interactions and conformational changes. Using inducible shRNA knockdown, RNA-seq analysis, and dCas9-mediated live imaging of chromosomes, we demonstrate that lamin A affects RNA synthesis, LMNA governs chromatin spatial organization, and SYNE2 regulates chromatin modifications. Furthermore, both lamins and nesprins enhance telomere dynamics. These findings elucidate nuclear envelope-associated mechanisms in gene regulation, offering valuable insights into chromatin dynamics under both physiological and pathological contexts.

cell biology↗

bioRxiv2025

Next-Generation saRNA Platforms: Systematic Screening and Engineering Enhances Superior Protein Expression and Organ-Specific Targeting for RNA Therapeutics

Self-amplifying RNA (saRNA), derived from alphaviruses, encodes nonstructural proteins (NSP1-4) that form a replicase complex, enabling prolonged and amplified protein expression at lower doses than conventional mRNA. However, its high immunogenicity and limited replication efficiency require optimization for improved protein expression. Here, we systematically optimized a widely used Venezuelan Equine Encephalitis Virus (VEEV)-based saRNA by refining its capping structure, nucleotide modifications, polyA tail length, and regulatory elements, achieving over 10-fold enhancement in protein expression compared to the wild-type. Additionally, we screened 28 alphavirus-derived saRNA constructs in vitro, selecting the top 3 candidates Everglades virus (EVEV), Mosso das Pedras virus (MDPV), and Rio Negro virus (RNV) for in vivo evaluation using SM102 lipid nanoparticle (LNP) formulations and luciferase reporters. These optimized saRNAs demonstrated sustained expression and distinct extrahepatic tissue-specific biodistribution, notably high spleen targeting compared to conventional mRNA. Such organ-specific expression profiles present novel strategies for targeted RNA therapeutics, and further integration with advanced delivery technologies could enhance the precision, efficacy, and therapeutic potential of mRNA-based treatments. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/644708v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1eed9bdorg.highwire.dtl.DTLVardef@192815org.highwire.dtl.DTLVardef@196a8e9org.highwire.dtl.DTLVardef@2b6e53_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOTOC figureC_FLOATNO C_FIG

molecular biology↗

bioRxiv2025

CompBioAgent: an LLM-powered agent for single-cell RNA-seq data exploration

AO_SCPLOWBSTRACTC_SCPLOWAdvancements in high-throughput biological technologies, particularly single-cell RNA sequencing (scRNA-seq), have generated vast amounts of complex data that offer valuable insights into gene expression, cellular behavior, and disease mechanisms. However, the analysis of such data often requires specialized computational skills and expertise, which can pose a barrier to many researchers. To address this challenge, we developed CompBioAgent, a user-friendly web application designed to democratize access to bioinformatics resources, powered by Large Language Models (LLMs). By integrating with the CellDepot, CompBioAgent allows users to easily query and explore gene expression data related to various diseases, cell types, and experimental conditions. Moreover, the tool employs Cellxgene Visualization In Plugin (Cellxgene VIP) platform to generate a range of intuitive visualizations, including violin plots, UMAP embeddings, heatmaps, etc. With its natural language interface, CompBioAgent automatically converts scientific queries into structured data requests and returns the plot of interest, enabling seamless exploration of biological data without the need for programming expertise. Such integration enhances the ability of researchers to visualize complex biological insights and identify key patterns, making high-level data analysis more accessible and efficient. A demo website and a list of examples are available at https://celldepot.bxgenomics.com/compbioagent, and the source code is released at https://github.com/interactivereport/compbioagent.

bioinformatics↗

bioRxiv2025

Munc13-4 mediates tumor immune evasion by regulating the sorting and secretion of PD-L1 via exosomes

Tumor-derived extracellular vesicles primarily carry PD-L1 via exosomes, which interact with PD-1 receptors on T cells, impacting immune responses in the tumor microenvironment and beyond, leading to a more extensive immunosuppressive landscape. However, the mechanisms governing exosomal PD-L1 sorting and secretion remain elusive. In this study, we identified Munc13-4 as a crucial regulator of exosomal PD-L1 sorting and secretion. Deletion of Munc13-4 in breast tumors enhances T cell-mediated anti-tumor immunity, suppresses tumor growth, and improves the efficacy of immune checkpoint inhibitors. Our results illustrate how Munc13-4 collaborates with HRS, Rab27, and SNAREs to facilitate PD-L1 sorting and secretion via exosomes. The cryo-EM structure of the Munc13-4-Rab27a complex provide new insights into its role in exosome secretion. Importantly, we discovered that Munc13-4 has a novel role in sorting PD-L1 onto exosomes, which relies on the formation of a ternary complex with PD-L1 and HRS. In addition, IFN{gamma} stimulation modifies Munc13-4 and HRS, establishing a dynamic regulatory mechanism that enables tumor cells to adapt to immune pressure by modulating PD-L1 sorting. Using a specially designed peptide to disrupt the Munc13-4-PD-L1 interaction and impede PD-L1 sorting significantly enhances anti-tumor immunity and slows tumor growth in vivo. These results highlight the potential of targeting the Munc13-4-PD-L1 axis to suppress tumor immune evasion.

cell biology↗

bioRxiv2025

Cerebellin-2 positive (Cbln2+) Neurons in the Parafascicular Thalamic Nucleus Regulate Self-Grooming Behavior

Self-grooming represents a stereotyped repetitive behavior which is commonly observed in various neuropsychiatric disorders. Deep brain stimulation (DBS) targeting the centromedian / parafascicular complex (CM/PF) has been shown to alleviate obsessive-compulsive disorder/behavior (OCD/OCB) symptoms in human. However, little is known about the neural circuits of the PF that are involved in the regulation of self-grooming behavior in rodents. Here, we report that cerebellin-2 positive (Cbln2+) neurons in PF bidirectionally encode self-grooming. Chemogenetic activation of Cbln2+ PF neurons significantly reduces both physiological and pathological self-grooming, and chemogenetic inhibition of Cbln2+ PF neurons increases physiological self-grooming. Moreover, activating synaptic excitatory inputs to Cbln2+ PF neurons inhibits self-grooming, while synaptic inhibitory inputs enhance it. Cbln2+ PF neurons independently transmit neural signals to the dorsal and ventral striatum. Activation of PF-dorsal striatum and PF-ventral striatum pathways both inhibit self-grooming behavior. Most excitingly, we alleviate excessive grooming in OCD mice by the activation of PF neurons using non-invasive ultrasound stimulation. Together, these data reveal that Cbln2+ PF neurons are integral components of a brain network involved in self-grooming behavior and highly promising targets in the non-invasive therapy of OCD.

neuroscience↗

bioRxiv2025

Resilience and vulnerabilities of tumor cells under purine shortage stress

Purine metabolism is a promising therapeutic target in cancer; however how cancer cells respond to purine shortage,particularly their adaptation and vulnerabilities, remains unclear. Using the recently developed purine shortage-inducing prodrug DRP-104 and genetic approaches, we investigated these responses in prostate, lung and glioma cancer models. We demonstrate that when de novo purine biosynthesis is compromised, cancer cells employ microtubules to assemble purinosomes, multi-protein complexes of de novo purine biosynthesis enzymes that enhance purine biosynthesis efficiency. While this process enables tumor cells to adapt to purine shortage stress, it also renders them more susceptible to the microtubule-stabilizing chemotherapeutic drug Docetaxel. Furthermore, we show that although cancer cells primarily rely on de novo purine biosynthesis, they also exploit Methylthioadenosine Phosphorylase (MTAP)-mediated purine salvage as a crucial alternative source of purine supply, especially under purine shortage stress. In support of this finding, combining DRP-104 with an MTAP inhibitor significantly enhances tumor suppression in prostate cancer (PCa) models in vivo. Finally, despite the resilience of the purine supply machinery, purine shortage-stressed tumor cells exhibit increased DNA damage and activation of the cGAS-STING pathway, which may contribute to impaired immunoevasion and provide a molecular basis of the previously observed DRP-104-induced anti-tumor immunity. Together, these findings reveal purinosome assembly and purine salvage as key mechanisms of cancer cell adaptation and resilience to purine shortage while identifying microtubules, MTAP, and immunoevasion deficits as therapeutic vulnerabilities.

cancer biology↗

bioRxiv2025

KCa3.1 Contributes to Neuroinflammation and Nigral Dopaminergic Neurodegeneration in Experimental models of Parkinson's Disease

Chronic neuroinflammation and misfolded -synuclein (Syn) have been identified as key pathological correlates driving Parkinsons disease (PD) pathogenesis; however, the contribution of ion channels to microglia activation in the context of -synucleinopathy remains elusive. Herein, we show that KCa3.1, a calcium-activated potassium channel, is robustly upregulated within microglia in multiple preclinical models of PD and, most importantly, in human PD and dementia with Lewy bodies (DLB) brains. Pharmacological inhibition of KCa3.1 via senicapoc or TRAM-34 inhibits KCa3.1 channel activity and the associated reactive microglial phenotype in response to aggregated Syn, as well as ameliorates of PD like pathology in diverse PD mouse models. Additionally, proteomic and transcriptomic profiling of microglia revealed that senicapoc ameliorates aggregated Syn-induced, inflammation-associated pathways and dysregulated metabolism in primary microglial cells. Mechanistically, FYN kinase in a STAT1 dependent manner regulates KCa3.1 mediated the microglial reactive activation phenotype after -synucleinopathy. Moreover, reduced neuroinflammation and subsequent PD-like neuropathology were observed in SYN AAV inoculated KCa3.1 knockout mice. Together, these findings suggest that KCa3.1 inhibition represents a novel therapeutic strategy for treating patients with PD and related -synucleinopathies.

neuroscience↗

bioRxiv2025

Topoisomerase IIIb protects from tumorigenesis and immune dysregulation

Topoisomerase III-beta (Top3b) reduces nucleic acid torsional stress and intertwining generated during RNA and DNA metabolism while protecting the genome from pathological R-loops, which otherwise result in DNA breakage and genome instability. By studying Top3b knockout mice (Top3b-KO), we find that the loss of Top3b accelerates the development of spontaneous lymphoid tumors arising in spleens and lymph nodes, the organs with prominent Top3b expression. Aging Top3b-KO mice also display splenomegaly and systemic immune alterations including neutrophilia and lymphopenia suggestive of chronic inflammation. At the molecular level, Top3b deficiency causes genome-wide R-loop accumulation in splenocytes as measured by CUT&Tag sequencing. Increased R-loops is associated with genomic DNA breaks and activation of immune signaling pathways including the IL-6 signaling, interleukin-7 signaling and cGAS-STING. Moreover, knocking-out Top3b promotes the rapid development of syngeneic EL4 T-cell lymphomas. In conclusion, our work implies that, in addition to its role in preserving the nervous system, Top3b protects from tumorigenesis and immune dysregulations. SignificanceTopoisomerase III-beta (TOP3B) is the only dual RNA-DNA topoisomerase. Its inactivation has previously been shown to be critical for neurodevelopmental disorders in humans and R-loop suppression in cell line models. Here, we demonstrate that loss of Top3b accelerates spontaneous lymphomagenesis and promotes syngeneic lymphoma growth in association with innate immune defects and R-loop accumulation in Top3b-KO mice. These findings provide evidence for a previously unappreciated role of Top3b as a tumor suppressor gene and immune regulator.

cancer biology↗

bioRxiv2025

Chromatin organization controls nuclear stiffness

Cellular differentiation is driven by epigenetic modifiers and readers, including the methyl CpG binding protein 2 (MeCP2), whose level and mutations cause the neurological disorder Rett syndrome. During differentiation, most of the genome gets densely packed into heterochromatin, whose function has been simplistically viewed as gene silencing. However, gene expression changes reported in mutations leading to Rett syndrome have failed to be a predictor of disease severity. Here, we show that MeCP2 increases nuclear stiffness in a concentration dependent manner and dependent on its ability to cluster heterochromatin during differentiation. MeCP2-dependent stiffness increase could not be explained by changes in the expression of mechanobiology-related genes, but we found it is disrupted by Rett syndrome mutations and correlated with disease severity. Our results highlight the impact of chromatin organization in the mechanical properties of the cell as an alternative or complementary mechanism to changes in cytoskeleton components. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/643219v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@cb077dorg.highwire.dtl.DTLVardef@158c0c6org.highwire.dtl.DTLVardef@1d830e3org.highwire.dtl.DTLVardef@719456_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Cryo-ET Analysis Unveils the Minimum Structural Unit and Hierarchical Ultrastructure of Silk Fibers in Silkworm and Spider

Silkworm silk and spider silk are renowned for their exceptional mechanical properties, with the toughness of spider dragline silk exceeding that of silkworm silk and even outperforming high-performance synthetic fibers such as Kevlar and nylon. The mechanical properties of silk fibers are determined by their ultrastructure, including the size, morphology, and arrangement of their fundamental structural units. In this study, we employed the state-of-the-art cryo-electron tomography to investigate the in situ ultrastructure of silkworm silk, spider silk, and artificial silk. Our findings reveal that the fundamental structural unit of silkworm silk is a nanofibril approximately 3.6 nm in diameter, connected by numerous bridges, representing the smallest structural unit currently observable. These nanofibrils are aligned parallel to the fiber axis and organized into a herringbone pattern oriented in a specific direction. Multiple layers of this herringbone pattern stack together to form the final micron-scale fiber. In spider silk, a dense structure featuring nanofibrils is clearly visible, with their long axes tightly aligned parallel to the flow direction, leaving no discernible gaps. By contrast, silkworm silk exhibits larger, regionally varying gaps between nanofibrils, while artificial silk lacks the highly ordered arrangement characteristic of natural silks. Our study provides new insights into silk formation and offers valuable principles for designing ultrastrong silk.

biophysics↗

bioRxiv2025

Multimodal brain cell atlas across the adult macaque lifespan

High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study primate brain aging. Here, we introduce a transcriptomic and chromatin accessibility landscape of 1,985,317 cells from eight brain regions of 13 cynomolgus female monkeys spanning adult lifespan including exceptionally old individuals up to 29-years old. This dataset uncovers dynamic molecular changes in critical brain functions such as synaptic communication and axon myelination, exhibiting a high degree of cell type and brain region specificity. We identify the multicellular networks of the pons and medulla as a previously unrecognized hotspot for aging. Furthermore, comparative analyses with human neurodegeneration datasets highlight both shared and distinct mechanisms contributing to aging and disease. In addition, we uncover transcription factors implicated in monkey brain aging and pinpoint aging-regulated loci linked to longevity and neurodegeneration. This spatiotemporal atlas will advance our understanding of primate brain aging and its broader implications for health and disease.

neuroscience↗

bioRxiv2025

REEP6 deficiency impairs ER and Golgi morphologies and causes retinal degeneration by attenuating the expression of phototransduction proteins

REEP6 is a member of the REEP family proteins belonging to the YIP superfamily. REEP proteins were membrane proteins involved in regulating membrane curvature. Mutations in REEP6 are associated with retinitis pigmentosa (RP). Mice lacking REEP6 were generated to model human RP. Reep6 mutant mice exhibit progressive retinal degeneration, which is attributed to abnormal trafficking of PDE6 and the absent expression of guanylate cyclases (GCs), due to ER dysfunction. However, the phenotype regarding the failed expression of GCs is questionable. Here, we generated an independent Reep6 knockout mouse model. Our Reep6-deficient mouse line showed progressive retinal degeneration as previously reported. Nevertheless, unlike the previous report, our Reep6 mutant mice had normal trafficking of PDE6. GCs were not absent from the mutant mice, but their expression decreased by approximately one third. Other membrane phototransduction proteins, such as rhodopsin and rhodopsin kinase (GRK1) were also reduced. Attenuated expression of membrane proteins might stem from abnormal ER and Golgi function, as in vitro expression of REEP6 altered the expression of the ER marker and Golgi morphologies. Additionally, RNA-seq revealed that deletion of Reep6 caused reduced expression of multiple phototransduction proteins at the transcription level and activated the inflammation pathway. Thus, retinal degeneration associated with REEP6 mutations is the consequence of reduced expression of phototransduction proteins mediated by ER and Golgi dysfunction and ensuing retinal inflammation.

pathology↗

bioRxiv2025

Transcriptomic splicing analysis reveals a gene-independent form of TE reactivation in tumors representing unrecognized source of oncogenes and neoantigens

Transposable elements (TEs) are reactivated in tumors and serve as significant contributors to tumor transcriptomic complexity and heterogeneity. However, their repetitive nature and diverse transcriptional forms have hindered efforts to characterize TE-derived transcripts independent of host gene contexts. Here, using our self-developed splicing-junction analysis tool ASJA, we systematically interrogated TE transcription across 32 cancer types, identifying transcripts autonomously initiated from and exclusively spliced among TEs with high TE content, termed TEtrans. Our analysis revealed 5,361 TEtrans exhibiting pan-cancer prevalence, tumor-specific expression and features of mature transcripts, including canonical splicing, 5 caps and polyA tails. Mostly unannotated and enriched in intergenic regions, TEtrans are predominantly derived from primate-specific classes with conserved splice pattern. TEtrans burden demonstrates heterogeneous associations with prognosis and immune activity across cancers, while their expression can be epigenetically dual-regulated by stemness- and inflammation-associated transcription factors. Functional studies uncovered that TEtrans could act as oncogenes, exemplified by tsTE1, a HERVH-derived transcript that promotes colorectal cancer proliferation by enhancing TOP1-mediated DNA supercoil relaxation. Remarkably, [~]7.2% of TEtrans are identified to encode tumor neoantigens, including viral proteins and unannotated peptides, which are shared among patients and validated by proteogenomic analysis. These TEtrans-derived neoantigens are immunogenic both in vitro and in vivo, and exceed neoepitopes from genomic alterations in abundance per tumor, particularly in cancers with low mutational burden. Collectively, as a gene-independent form of TE-derived transcripts, TEtrans represents a unique source of oncogenes and tumor neoantigens, expanding the functional repertoire of TEs in cancer biology and offering new avenues for therapeutic targeting. HighlightsO_LITEtrans are tumor-specific transcripts with conserved splicing patterns, predominantly derived from primate TEs in intergenic regions. C_LIO_LITEtrans expression is epigenetically activated and dually regulated by stemness/inflammation transcription factors. C_LIO_LITEtrans function as oncogenes, exemplified by tsTE1 enhancing TOP1-mediated DNA relaxation. C_LIO_LITEtrans encode tumor neoantigens that elicit CD8+ T cell responses, providing targets for immunotherapy, especially in low-mutation tumors. C_LI Abstract figure O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/640928v1_ufig1.gif" ALT="Figure 1"> View larger version (78K): org.highwire.dtl.DTLVardef@1d2d4cforg.highwire.dtl.DTLVardef@918f14org.highwire.dtl.DTLVardef@489465org.highwire.dtl.DTLVardef@1069d17_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗