Biology subjects

Yu, H.

Publications and source records attributed to Yu, H..

At least 163 records · Page 9Linked to original sources

bioRxiv2025

Simultaneous measurement of intrinsic promoter and enhancer potential reveals principles of functional duality and regulatory reciprocity

Accumulating evidence indicates that both promoters and enhancers are capable of exerting promoter and enhancer functions; however, the relationship between these two activities within individual elements and the determinants of this dual functionality remain poorly understood. We developed a massively parallel dual reporter assay that enables simultaneous assessment of the intrinsic promoter and enhancer potential exerted by the same sequence. Parallel quantification for thousands of elements reveals that canonical human promoters and enhancers can act as both promoters and enhancers under the same contexts, and that promoter activity may be necessary but not sufficient for enhancer function. Perturbations to element transcription factor binding motifs lead to disruptions in both activities, implicating a shared syntax for the two regulatory functions. Combinations of elements with different minimal promoters reveal reciprocal activity modulation, which, together with a strong correlation between promoter and enhancer functions, imply a bidirectional feedback loop to sustain environments of high transcriptional activity. Finally, we validate this reciprocity and correlation in situ using CRISPR activation at the human {beta}-globin locus. Our approach reveals that the functional convergence between promoters and enhancers arises from a shared regulatory logic and sequence syntax, advancing a unified model for regulatory element biology.

genomics↗

bioRxiv2025

The sialome of the retina, alteration in age-related macular degeneration (AMD) pathology and potential impacts on Complement Factor H

PurposeLittle is known about sialic acids of the human retina, despite their integral role in self/non-self-discrimination by complement factor H (CFH), the alternative complement pathway inhibitor. MethodsA custom sialoglycan microarray was used to characterize the sialic acid-binding specificity of native CFH or recombinant molecules where IgG Fc was fused to CFH domains 16-20 (contains a sialic acid-binding site), domains 6-7 (contains a glycosaminoglycan-binding site) or the CFH-related proteins (CFHRs) 1 and 3. We analyzed macular and peripheral retinal tissue from post-mortem ocular globes for amount, type, and presentation (glycosidic linkage type) of sialic acid in individuals with age-related macular degeneration (AMD) and age-matched controls using fluorescent lectins and antibodies to detect sialic acid and endogenous CFH. Released sialic acids from neural retina, retinal pigmented epithelium (RPE) cells and the Bruchs membrane (BrM) were labelled with 1,2-diamino-4,5-methylenedioxybenzene-2HCl (DMB), separated and quantified by high-performance liquid chromatography (DMB-HPLC). ResultsBoth native CFH and the recombinant CFH domains 16-20 recognized Neu5Ac and Neu5Gc that is 2-3-linked to the underlying galactose. 4-O-Actylation of sialic acid and sulfation of GlcNAc did not inhibit binding. Different linkage types of sialic acid were localized at different layers of the retina. The greatest density of 2-3-sialic acid, which is the preferred ligand of CFH, did not colocalize with endogenous CFH. The level of sialic acids at the BrM/choroid interface of macula and peripheral retina of individuals with AMD were significantly reduced. ConclusionsThe sialome of the human retina is altered in AMD. This can affect CFH binding and consequently, alternative complement pathway regulation.

biochemistry↗

bioRxiv2025

Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning

The sky islands of Southwest China, characterized by dramatic topographical and climatic variations, are prominent hotspots of biodiversity and endemism. Organisms inhabiting middle-to-high elevation habitats in this region are geographically isolated within distinct mountain chains, which over geological time have been subjected to isolation-by-distance and isolation-by-environment. These processes have led to profound allopatric diversification and strong phylogeographic structuring, resulting in a plethora of genetically distinct cryptic species, as is becoming increasingly evident for many small mammal families. However, morphological conservatism can pose significant challenges in delineating these clades within species complexes. In this study, we leverage artificial intelligence technologies to unravel the hidden species diversity of moles (family Talpidae) in Southwest Chinas sky islands. We first employed ultraconserved elements (UCEs) to investigate the evolutionary history of talpid moles, conducted molecular species delimitation using mitochondrial and multi-locus genes, and utilized both traditional and geometric morphometrics to examine their morphological disparity. To address the challenges of morphology based cryptic species identification, we developed a deep learning Hierarchical Identification of Species NETwork (HIS-NET) to create an image-based model that analyzes four different views of the skull/mandible to distinguish genera and species hierarchically. HIS-NET not only achieved expert-level accuracy in species identification but also effectively distinguished between cryptic and known species, aiding in the identification of key morphological variation intervals. Our results support the recognition of allopatrically distributed taxa in Euroscaptor and Parascaptor as full species, thereby confirming that species diversity in this region remains underestimated. Beyond advancing our understanding of speciation in this unique and fragile ecosystem, our study serves as a proof-of-concept, demonstrating the power of deep learning in unraveling hidden biodiversity within this and other species complexes.

zoology↗

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↗

bioRxiv2025

Multi-platform evaluation and optimization of single-cell RNA isoform sequencing

Long-read transcriptomics enables isoform identification and quantification at single-cell resolution, but analysis is complicated by artifacts introduced during library preparation. We characterize the distinct artifact profiles of three popular single-cell platforms and demonstrate their impact on isoform identification. We introduce a new method for the identification of a wide range of artifacts in cDNA libraries and novel biochemical and bioinformatic strategies to significantly reduce their impact on downstream applications. Finally, we provide a comprehensive framework for RNA isoform sequencing analysis and interpretation as the field continues to develop.

genetics↗

bioRxiv2025

Excavating Podocyte-Protective Targets of phloroglucinol-terpene hybrids Utilizing AI Models and Omics Analysis

Lupus nephritis (LN) is a multifactorial autoimmune inflammatory disorder, with podocyte dysfunction or structural abnormalities playing a pivotal role in its pathogenesis. Eucalyptus leaves, traditionally employed in folk medicine, have demonstrated notable efficacy in managing non-infectious inflammations. Eucarbwenstols D (R14) is a novel phloroglucinol-terpene that has been isolated from Eucalyptus robusta. To further refine potential targets, we utilized an AI scoring system and successfully identified the epidermal growth factor receptor (EGFR) as the novel target of R14. This discovery was built upon the foundation of transcriptome and connectivity mapping (CMap) analysis. Molecular docking and molecular dynamics simulations were employed to analyze the interaction between R14 and EGFR, surface plasmon resonance (SPR) and homogeneous time-resolved fluorescence (HTRF) assays were utilized to accurately quantify the binding affinity between R14 and EGFR. Western blot (WB) and immunofluorescence assays were then conducted to explore the downstream signaling pathways initiated by EGFR, specifically the PI3K/AKT/mTOR pathway. These assays demonstrated that R14 modulates the expression of apoptotic proteins Bax and Bcl-2 through this pathway, thereby exerting a protective effect on podocytes from undergoing apoptosis. The modulation of key podocyte proteins, nephrin and podocin, further substantiates this protective effect. Overall, we have applied a novel AI algorithm model that transcends bioinformatics analysis to precise identification of the novel podocyte target of R14. In this study, R14 was identified for the first time as a novel scaffold compound for EGFR inhibition. Moreover, R14 has demonstrated its capacity to inhibit podocyte apoptosis, thereby protecting these critical cells. This discovery establishes a robust theoretical foundation for the use of phloroglucinol-terpene hybrids (PTHs) in the treatment of LN.

cell biology↗

bioRxiv2025

Partially differentiated enterocytes in ileal and distal-colonic human F508del-CF-enteroids 1 secrete fluid in response to forskolin and linaclotide.

Constipation causes significant morbidity in Cystic Fibrosis (CF) patients. Using CF patient (F508del) derived ex vivo ileal and distal colonic/rectal enteroids as a model and the Forskolin Induced Swelling Assay (FIS), we compared CFTR mediated fluid secretion in human enterocytes across the crypt-villus axis. CFTR expression and FIS decreased as enterocytes differentiated from crypt to become partially differentiated and then mature villus cells. While there was no FIS response in undifferentiated (crypt enterocytes) F508del-CF enteroids, partially differentiated F508del-CF enteroids had a swelling response to forskolin (cAMP) and linaclotide (cGMP) which was [~]48%, and [~]67% of the response in healthy enteroids, respectively and was prevented by a CFTR inhibitor. Also, linaclotide and a general PDE inhibitor independently enhanced combined CFTR-modulator-induced FIS response from partially differentiated F508del-CF enteroids. These findings demonstrate that partially differentiated ileal and distal colonic F508del-CFTR enteroids can be stimulated to secrete fluid by cAMP and cGMP.

physiology↗

bioRxiv2025

Leopard Cats Occupied Human Settlements in China for 3,500 years before the Arrival of Domestic cats in 600-900 CE around the Tang Dynasty

The earliest cats in human settlements in China were not domestic cats (Felis catus), but native leopard cats (Prionailurus bengalensis). To trace when and how domestic cats arrived in East Asia, we analyzed 22 feline bones from 14 sites across China spanning 5,000 years. Nuclear and mitochondrial genomes revealed that leopard cats began occupying anthropogenic scenes around 5,400 years ago and last appeared in 150 CE. Following several centuries gap of archeological feline remains, the first known domestic cat (706-883 CE) in China was identified in Shaanxi during the Tang Dynasty. Genomic analysis suggested a white or partially white coat and a link to a contemporaneous domestic cat from Kazakhstan, indicating a likely dispersal route via the Silk Road. The two felids once independently occupied ancient anthropogenic environments in China but followed divergent paths and reached different destinations in human-animal interactions.

evolutionary biology↗

bioRxiv2025

Single-cell and spatial transcriptomics reveal the pathogenesis of chronic granulomatous disease in a natural model

Genetic defects in NOX2 can cause chronic granulomatous disease (CGD), characterized by increased susceptibility to infections and pronounced inflammatory responses that lead to granuloma formation. We developed a CGD model using Ncf2-/- mice through controlled environmental exposure. Unlike in specific pathogen-free environment, these mice spontaneously developed pulmonary granulomas under clean-grade conditions. Employing single-cell RNA sequencing, we observed an expansion of neutrophils and monocyte-derived macrophages (MDMs) within the lung tissue, identifying pro-inflammatory NOS2high-neutrophils and a distinct MDMs subset marked by NOS2 and ARG1. Spatial transcriptomics demonstrated that NOS2high-neutrophils were located at the core area, while the MDMs subset was positioned at the periphery, facilitating extracellular matrix remodeling. Pharmacological targeting of MIF, deletion of the pro-survival gene Morrbid, and elimination of Il1r1 all suppressed granuloma formation by mitigating inflammation. This study underscores how environmental control can establish a natural CGD model, elucidates the mechanisms of granuloma formation, and develops potent therapeutic interventions. HighlightsO_LIThrough installing a mutation in a NOX2 subunit gene Ncf2 and changing the husbandry environment, we generated a natural CGD mouse model with progressive pulmonary granuloma formation. C_LIO_LINOS2high neutrophils located in the core region of CGD lung granulomas, exhibit a pro-inflammatory transcriptional profile. C_LIO_LIMonocyte-derived macrophages marked by Nos2 and Arg1 are located at the periphery of granulomas and exhibit a profibrotic transcriptional profile. C_LIO_LIThe transcriptomic studies assist the development of three effective perturbations for treating the rare disease CGD via targeting Il1r1, Morrbid, and Mif respectively. C_LI

immunology↗

bioRxiv2025

Volatile-suppressed peptide signaling enhances volatile responses in plant-plant interactions

Plant volatiles shape plant-plant interactions by acting as defense regulators and response factors. While plant volatile biosynthesis is well understood, how their emission is regulated remains largely elusive. Here, we show that small peptide signaling regulates induced volatile release in maize. Following herbivore attack, green leaf volatiles such as (Z)-3-hexenyl acetate (HAC) are released and induce terpene and indole emissions from neighboring plants. This process is accompanied by reduced expression of the ZmCLE1E9 gene and the ZmBAM1A, ZmBAM1B and ZmBAM3C receptor genes in HAC-exposed plants. Exogenous ZmCLE1E9 peptide inhibits HAC-triggered volatile release by limiting stomatal aperture. This inhibition disappears in the Zmbam1a/Zmbam1b/Zmbam3c triple mutant. Molecular docking supports ZmCLE1E9 and ZmBAMs as ligand-receptor pairs. Furthermore, Zmcle1e9 and Zmbams triple mutants show increased volatile emissions upon HAC exposure. In summary, we show that upon HAC perception, maize plants enhance their capacity to release terpenes and indole via the suppression of CLE1E9 signaling. This behavior allows maize plants to rapidly deploy volatile cues in response to stress volatiles and thus shape the infochemical dynamics of multitrophic environments.

plant biology↗

bioRxiv2025

Impact of cross-validation designs on cattle behavior prediction using machine learning and deep learning models with tri-axial accelerometer data

1Assessing cattle behaviors provides insights into animal health, welfare, and productivity to support on-farm management decisions. Wearable accelerometers offer an alternative approach to traditional human evaluation, providing a more objective and efficient method for predicting cattle behavior. Random cross-validation (CV) is commonly used to evaluate behavior prediction by splitting data into training and testing sets, but it can yield inflated results when records from the same animal are included in both sets. Block CV splits data by block effects, offering a more realistic evaluation but remains underexplored for predicting multi-class imbalanced cattle behavior. Additionally, deep learning (DL) models have not been fully explored for behavior prediction compared to machine learning (ML) models. The objectives of this study were to examine the impact of CV designs on multi-class imbalanced cattle behavior prediction and to compare the performance of ML and DL models. Three ML and two DL models were used to predict the four behaviors of six beef cows from a public tri-axial accelerometer dataset, with model performance evaluated using both hold-out and leave-cow-out CV designs representing random and block CV, respectively. In hold-out CV, ML models achieved accuracies of 0.94 to 0.96 and F1 scores of 0.93 to 0.95, while DL models achieved accuracies of 0.9 to 0.92 and F1 scores of 0.89 to 0.91. In the leave-cow-out CV, ML models obtained accuracies of 0.72 to 0.82 and F1 scores of 0.64 to 0.82, whereas DL models obtained accuracies of 0.76 to 0.82 and F1 scores of 0.64 to 0.76. Generally, ML models outperformed DL models in the hold-out CV, but the multi-layer perceptron DL model demonstrated comparable or superior performance in the leave-cow-out CV. All models performed better with hold-out CV than leave-cow-out CV. Our results suggest that CV designs can affect behavior prediction performance. While a random CV produces seemingly good predictions, these results can be artificially inflated by the data partition. A block CV that strategically partitions data could be a more appropriate design.

animal behavior and cognition↗

bioRxiv2025

ca-circSCN8A promotes HPASMCs ferroptosis via LLPS initiated R-Loop

BACKGROUNDFerroptosis has been implicated in pulmonary hypertension. Chromatin-associated RNAs are linked to ferroptosis. However, their role in pulmonary vascular ferroptosis in PH is unexplored. METHODSBioinformatics, Sanger sequencing, RNase R and others were employed to identify differentially higher expression of ca-circSCN8A. Functional gain and loss assays were employed to unveil the role of ca-circSCN8A in hypoxia-induced redox-dependent ferroptosis in HPASMCs and PH mice model. Interaction between ca-circSCN8A and FUS was detected via RNA immunoprecipitation and pull-down assays. FRAP, CHIRP-qPCR, MDA, GSH and GSSG were conducted to explore the potential molecular mechanism. RESULTSca-circSCN8A was firstly identified and confirmed to be upregulated in PH. Upregulation of ca-circSCN8A can promote hypoxia induced ferroptosis in HPASMCs. Under hypoxic conditions, ca-circSCN8A promoted the lactylation of FUS by recruiting EP300, leading to formation of LLPS of ca-circSCN8A/FUS/EP300. LLPS maintained the stability of the R-Loop formed by ca-circSCN8A and ferroptosis related-gene SLC7A11 promoter that inhibit the transcription of the SLC7A11 gene, further result in the disruption of the redox balance and causes ferroptosis in HPASMCs. CONCLUSIONSca-circSCN8A recruits EP300 to promote the lactylation of FUS, thereby promoting LLPS formation of ca-circSCN8A/EP300/FUS. Further, the LLPS motivates ca-circSCN8A to form R-loop with its non-host SLC7A11 and participating in the regulation of hypoxic induced HPASMCs redox-dependent ferroptosis. This is the first confirmation that circRNAs forming R-loops with non-host genes regulated by LLPS. Our findings indicated that ca-circSCN8A plays an important role in ferroptosis of hypoxic induced HPASMCs and may be a potential target for the treatment of PH.

molecular biology↗

bioRxiv2025

TCR signaling via NFATc1 constrains IL-15-induced NK-like activation of human memory CD8+ T cells

Here we investigated the regulatory mechanisms of TCR-independent bystander activation and NK-like cytotoxicity of human memory CD8+ T cells. We found that TCR signals suppressed characteristic features of IL-15-induced CD8+ T-cell activation, including increased NKG2D expression and upregulation of genes related to NK cytotoxicity and IFN response. Moreover, ionomycin suppressed IL-15-induced bystander activation and NK-like cytotoxicity, indicating that Ca2+-calcineurin signaling is responsible for TCR-mediated suppression of IL-15-induced bystander activation. In detail, NFATc1 suppressed IL-15-induced bystander activation via binding to AP-1 that is necessary for the IL-15-induced upregulation of NK cytotoxicity-related genes. Consistent with these results, calcineurin inhibitors enhanced IL-15-induced NKG2D expression in the presence of TCR signals. Additionally, we defined genes upregulated by IL-15 and downregulated by concurrent TCR signals as an IL-15-induced bystander activation gene set, and found that this gene signature was upregulated in bystander CD8+ T cells from patients with hepatitis A virus infection. This study paves the way for further investigation of bystander CD8+ T-cell activation in various pathological conditions, and its regulation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/632884v2_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1e6c320org.highwire.dtl.DTLVardef@114a23eorg.highwire.dtl.DTLVardef@1a7b9edorg.highwire.dtl.DTLVardef@9faccc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITCR signaling downregulates IL-15-induced transcriptomic features related to NK-like bystander activation of human memory CD8+ T cells via the Ca2+-calcineurin pathway. C_LIO_LINFATc1 suppresses IL-15-induced bystander activation via binding to AP-1, which is responsible for IL-15-induced NK-like cytotoxic activity. C_LIO_LICalcineurin inhibitors cannot suppress IL-15-induced bystander CD8+ T-cell activation, and paradoxically increase IL-15-induced NKG2D expression in the presence of TCR signals. C_LIO_LIGenes upregulated by IL-15 and downregulated by concurrent TCR signals define the gene set of bystander CD8+ T-cell activation, which was validated in disease contexts. C_LI

immunology↗

bioRxiv2025

TCR clonality and TCR clonal expansion in the in situ microenvironment of non-small cell lung cancer

T-cell activation and clonal expansion are essential for the efficacy of immunotherapy in non-small cell lung cancer (NSCLC) patients. Since the distribution of T-cell clones might provide insights into immunogenic mechanisms, we determined the /{beta} TCR clonality using RNA-sequencing from frozen tumor tissue of 182 NSCLC patients and paired the results with extensive in situ image and sequence analyses of the immune microenvironment of NSCLC. TCR clonality (Gini index) patterns ranged from high T-cell clone diversity with high evenness (Gini index low) to clonal dominance with low evenness (Gini index high). TCR clonality in cancer tissue was lower than in matched normal lung (p=0.021). High Gini index correlated strongly with distinct mutations (EGFR, P53), tumor mutation burden (p<0.001), and inflamed tumor phenotypes (PRF1, GZMA, GZMB, INFG) with exhaustion signatures (LAG3, TIGIT, IDO1, PD-1, PD-L1). Correspondingly, PD-1+, CD3+, CD8A+, CD163+, and CD138+ immune cells infiltrated cancer tissue with high TCR clonality. In situ sequencing revealed that dominant T-cell clones were more often of CD8-subtype and tended to approximate the tumor cell compartment (p<0.03). In a checkpoint inhibitor-treated NSCLC patient cohort, high TCR clonality was associated with therapy response (p=0.016) and prolonged survival (p=0.003, median survival 13.8 vs 2.9 months). Our robust analysis pipeline revealed diverse TCR repertoires related to genotypes and immune phenotypes. The in situ positioning of expanded T-cell clones indicated functional impact, which was clinically confirmed in NSCLC patients receiving immunotherapy. One sentence summaryT-cell clone expansion in NSCLC is associated with genetic mutations, immune phenotypes, immunotherapy response, and patient survival.

cancer biology↗

bioRxiv2024

LINC00599 Promotes Pulmonary Hypertension via LLPS with G3BP1 and MYH9

BACKGROUNDPulmonary hypertension (PH) represents a significant cardiovascular disorder marked by both functional and structural alterations within the pulmonary vasculature. Long non-coding RNAs (lncRNAs) have been closely associated with the pathogenesis and progression of PH. Nonetheless, the precise mechanisms by which lncRNAs interact with its downstream target molecules to modulate the disease remain inadequately elucidated. METHODSThe expression levels of LINC00599 were quantified in the lung tissues of mice and pulmonary arterial smooth muscle cells (PASMCs) under hypoxic conditions. The involvement of LINC00599 in the progression of PH and vascular remodeling was evaluated through in vivo studies. To investigate the mechanisms by which LINC00599 influences the proliferation of human PASMCs, small interfering RNA and overexpression plasmids were employed. RESUITSThe expression of LINC00599 is upregulated in the medial layer of pulmonary arteries in experimental models of PH and in hypoxic PASMCs. Administration of a single dose of lentivirus-mediated shRNA targeting LINC00599 effectively reverses hypoxic PH in murine models. LINC00599 plays a critical role in PASMC proliferation by modulating stress granule formation through N6-methyladenosine (m6A) modification and promoting proliferation via liquid-liquid phase separation with myosin heavy chain 9. Furthermore, the expression of LINC00599 is regulated by a super-enhancer, which is mediated by the transcription factor ZNF263. CONCLUSIONSThese findings demonstrate for the first time that LINC00599, involved in liquid-liquid phase separation, facilitates the progression of pulmonary hypertension by enhancing the proliferation of pulmonary artery smooth muscle cells. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/629439v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@7ac192org.highwire.dtl.DTLVardef@13a88b3org.highwire.dtl.DTLVardef@1e4c761org.highwire.dtl.DTLVardef@ddd105_HPS_FORMAT_FIGEXP M_FIG C_FIG What Is New?This study identified LINC00599 as a critical regulator of liquid-liquid phase separation through m6A modification and as a pivotal target in promoting the progression of PH. What Is Relevant?LncRNAs are intricately associated with the pathogenesis and progression of PH through the modulation of downstream target molecules. However, it remains unclear whether lncRNAs contribute to PH by forming specific subcellular structures with these target molecules. Furthermore, some studies have suggested that the increased presence of stress granules in PASMCs is implicated in the pathogenesis of pulmonary arterial hypertension. In this study, we provide evidence that LINC00599 promotes the development of PH by forming stress granules with its target proteins. Our findings indicate that the binding of LINC00599, modified with m6A, to G3BP1 and MYH9 in PASMCs suggests that the regulation of liquid-liquid phase separation by lncRNA m6A modification may represent a significant pathological mechanism underlying PH. What Are the Pathophysiological Implications?We found that LINC00599 levels were elevated in hypoxic PASMCs and experimental PH models. Knockout LINC00599 effectively prevented PH, indicating its potential as both a bomarker and therapeutic target for PH.

physiology↗

bioRxiv2024

CD24-Fc resolves inflammation and rescues CD8 T cells with polyfunctionality during HIV-1 infection under cART

The persistence of HIV-1 reservoirs during combination anti-retroviral therapy (cART) leads to chronic immune activation and systemic inflammation in people with HIV (PWH), associating with a suboptimal immune reconstitution as well as an increased risk of non-AIDS events. This highlights the needs to develop novel therapy for HIV-1 related diseases in PWH. In this study, we assessed the therapeutic effect of CD24-Fc, a fusion protein with anti-inflammatory properties that interacts with danger-associated molecular patterns (DAMPs) and siglec-10, in chronic HIV-1 infection model using humanized mice undergoing suppressive cART. Our findings show that CD24-Fc treatment significantly reduced inflammation and immune hyperactivation in vivo when combined with cART. CD24-Fc mediated resolution of inflammation was associated with improved recovery of CD4 T cells, reduced immune activation, restored central memory T cells and reversal of immune cell exhaustion phenotype. Notably, CD24-Fc treatment rescued CXCR5+ CD8 central memory T cell (TCM) which correlated with increased polyfunctionality in HIV-specific T cells in humanized mice and in cultured peripheral blood mononuclear cells (PBMCs) from PWH. This restoration of CXCR5+ memory CD8 T cells was associated with HIV replication inhibition, delayed viral rebound and reduced HIV-1 pathogenesis upon cART cessation. This study suggests that CD24-Fc treatment could represent a promising new therapeutic strategy for managing chronic systemic inflammation and associated diseases in PWH. Author summaryCombination antiretroviral therapy (cART) cannot block viral gene expression from activated HIV proviral DNA in reservoir cells, contributing to chronic immune activation and inflammation associated diseases in people with HIV (PWH). The therapeutic treatment of anti-inflammatory fusion protein CD24-Fc in humanized mice during suppressive cART (i) resolves inflammation and chronic HIV-1 immune pathogenesis during suppressive cART, (ii) rescues CXCR5-expressing CD8 memory T cells and enhances antiviral response in humanized mice and PWH PBMCs, (iii) delays virus rebound and reduces viral pathogenesis after cART cessation. Thus, CD24-Fc could provide a novel therapeutic strategy for treating chronic systemic inflammation and associated diseases in PWH.

immunology↗

bioRxiv2024

Assessment of DNA methylation from a single genomic region of ELOV2 is sufficient to predict chronological age

Estimation of chronological age is particularly informative in forensic contexts. Assessment of DNA methylation status allows for the prediction of age, though the accuracy and ease of manipulation may vary across different models. In this study, we started with a carefully designed discovery cohort recruiting more elderly subjects than other age categories, to diminish the effect of epigenetic drifting. We analyzed DNA methylation from a single genomic region of ELOV2, which was sufficient to construct an age-prediction model comprising 15 CpG sites. This model is further validated by an independent cohort as well as a multi-center test using trace dried bloodstains. The nature of our analytical pipeline, when combined the assessment of a single genomic locus with high-throughput sequencing, can easily be scaled up with low cost. Taken together, we propose a new age-prediction model featuring accuracy, ease of manipulation, high-throughput, and low cost. This model can be readily applied in both classic and newly emergent forensic contexts that require age estimation.

genetics↗

bioRxiv2024

Mapping of Multilineage Tumor Cell Populations in Mouse Bladder Cancer

In bladder cancer (BLCA), the cellular expression of lineage markers with predictive biomarker function can have important implications for tumor progression, treatment response, and survival. However, tumor heterogeneity and the coexistence of distinct tumor subpopulations can complicate the utility of using a primary, clinically assigned tumor signature. In this report, we have applied the reference atlas, Tabula Sapiens, and deep learning model, UniCell, to conduct in-depth transcriptional analysis of unique lineage marker-defined cell clusters in a carcinogen (BBN) induced bladder cancer model. UniCell deconvolution has identified tumor populations, including urothelial, adenocarcinoma, squamous cell carcinoma, and mesenchymal tumor populations, each with cell-intrinsic gene expression signatures relevant to human BLCA progression. The identified tumor clusters contain uniquely basal, luminal, stromal, or hybrid cells in cell lineage marker expression. To understand the significance of these populations during progression, we used trajectory and pseudo-time analysis to show that cells uniquely basal are plastic in lineage identity and can evolve to form tumor populations composed of other lineage marker-defined signatures. Finally, pathway and drug enrichment analysis of tumor cell clusters were used to identify therapeutics that may preferentially target the identified tumor cell populations. These data collectively define a molecular template that may uniquely profile molecular plasticity occurring during progression and response to therapy with important implications for human disease. SignificanceTumor heterogeneity is a mechanism for treatment resistance. Our study defines unique tumor subpopulations having differential therapeutic sensitivities and potential for lineage plasticity. Our modeling may impact the treatment of BLCA patients.

cancer biology↗