Biology subjects

Qiu, Q.

Publications and source records attributed to Qiu, Q..

At least 19 recordsLinked to original sources

bioRxiv2026

A Measurable Systemic Immune Phenotype Links Circulating Myeloid Dysfunction to Tumour Spatial Organization in Gastroesophageal Adenocarcinoma

Background: Both static and longitudinal measures of circulating neutrophil-to-lymphocyte ratio (cNLR) are prognostic markers across solid malignancies, including gastroesophageal adenocarcinoma (GEA). Despite this consistency, cNLR remains poorly integrated into clinical decision-making and is generally regarded as a nonspecific inflammatory or disease-burden signal rather than a defined biological state. Analysis of a large, prospectively assembled GEA cohort showed that cNLR was only weakly associated with tumour burden or pathological response, yet both baseline and postoperative cNLR independently predicted outcome. Methods: These observations prompted a retrospective biological investigation of what host biology cNLR captures. Using available clinically linked biospecimens, we performed multiscale analyses across complementary patient subsets encompassing peripheral-blood immune function and soluble signalling, tumour single-cell transcriptional programmes, and spatial myeloid organization within tissue. Results: High baseline cNLR was associated with reduced circulating cytotoxic and immune-trafficking mediators, elevated angiogenesis-associated factors, neutrophil-mediated suppression of lymphocyte proliferation, impaired tumour-cell killing, and enhanced spontaneous neutrophil extracellular trap formation. Single-cell profiling identified coordinated transcriptional differences across tumour compartments, including innate, cytokine and myeloid programmes. Spatial profiling showed that myeloid abundance and organization varied across anatomical compartments; greater tumour-periphery PDL1 positive myeloid clustering was associated with inferior recurrence-free survival. Baseline cNLR showed little relationship with static myeloid abundance, whereas pretreatment cNLR dynamics were associated with altered cross-compartment spatial relationships between CD8 positive cells and myeloid cells. Notably, higher early postoperative cNLR was associated with greater PDL1 positive myeloid clustering at the tumour periphery, linking the spatial architecture of the resected tumour with a systemic myeloid phenotype persisting after surgery. Conclusions: The data identify a prognostic, multilevel myeloid-associated host phenotype in GEA that is incompletely explained by tumour burden. Integrating systemic immune function, tumour single cell transcriptomics and spatial myeloid organization demonstrates that these biological domains provide distinct, yet convergent views of the host immune phenotype captured by cNLR. These findings establish a biological framework for the clinical utility of cNLR and highlight myeloid-associated immune processes as promising targets for therapeutic intervention.

cancer biology↗

bioRxiv2026

Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain

Spatial and activity-dependent gene regulation in the mammalian brain requires coordinated control of RNA synthesis and degradation 1,2, yet spatially resolved measurement of RNA turnover kinetics in complex tissues remains technically challenging 3. Here, we present spatial NT-seq, an approach that integrates transgenesis-free metabolic RNA labeling with in situ chemical recoding to spatially co-map RNA abundance and turnover kinetics in the mouse brain. By distinguishing newly synthesized from pre-existing RNAs, this method reveals spatially resolved transcriptional and post-transcriptional responses to electroconvulsive stimulation (ECS), a treatment for refractory depression. We uncover pronounced spatial heterogeneity in RNA turnover, with the dentate gyrus (DG) exhibiting elevated basal RNA turnover and robust ECS-induced responses. These findings reveal a "kinetics scaling" mechanism of coordinated regulation of RNA synthesis and decay, by which DG cells can rapidly remodel their transcript pools in responses to external stimuli or differentiation signals 4,5. Machine learning applied to in vivo RNA kinetics landscapes further identifies sequence features and post-transcriptional regulators underlying region-and cell-type-specific control of mRNA stability. Together, this integrated experimental and computational framework, in vivo Timescope, enables transcriptome-wide mapping of RNA turnover kinetics and the regulatory architecture of RNA stability across spatial and cellular contexts, providing new insights into the spatiotemporal regulation of RNA dynamics in brain function and disease.

genomics↗

bioRxiv2026

Abalone genomics reveals an ancient asymmetry axis and the multifunctionality of the mantle

Gastropod diversification represents one of the most spectacular evolutionary radiations, underpinned by a fundamentally asymmetric body plan and diverse pigmentation patterns. To understand the genetic underpinnings of these cardinal traits, we constructed a chromosome-level genome assembly for the rainbow abalone, Haliotis iris. Integrating systematic genomics, histoembryology, and molecular assays, we uncover an ancient regulatory axis, conserved for over 544 million years, in which the long non-coding RNA lncRNA1 functions as a competing endogenous RNA to shield pitx transcripts from miRNA-mediated degradation, thereby driving the establishment of asymmetric body patterning, including the mantle. Furthermore, we identify a wnt-mitf-tyr cascade as the driver of melanogenesis and demonstrate that the mantle is the primary site of melanin synthesis. Concurrently, we reveal the mantle as a multifunctional organ possessing mechanosensory capabilities. These findings elucidate the ancient genetic toolkit governing trait evolution in gastropods. TeaserA deeply conserved RNA switch directs gastropod body plans and reveals the mantles hidden talents.

genomics↗

bioRxiv2025

Per- and Polyfluoroalkyl Substances Induces Salt-Sensitive Hypertension by Upregulating Epithelial Sodium Channel - The First Experimental Evidence Supporting Causality

Per- and polyfluoroalkyl substances (PFAS) are synthetic chemicals found in the plasma of 98% of Americans. Epidemiological studies associate PFAS exposure with hypertension and kidney dysfunction, but causality and mechanisms remain unclear. We examined the effects of a mixture of 4 PFAS commonly detected in humans, including PFOA, PFOS, PFHxS, and PFNA, on blood pressure, salt sensitivity, and renal injury in 129S6 mice. Exposure to a lower dose for 3 weeks produced plasma PFAS levels in mice resembling occupational and regional environmental exposures; while a upper dose achieved levels similar to PFAS production workers. PFAS induced dose-dependent pressor effects in male but not female mice on a 0.4% low salt diet. During 4% high salt feeding, PFAS induced greater salt-sensitive hypertension in male mice, accompanied by glomerulopathy, interstitial fibrosis, and a trend towards increased albuminuria. Pressor effects were independent of plasma norepinephrine. Single-cell RNA sequencing of kidneys revealed most transcriptional changes in proximal tubule, thick ascending limb, and collecting duct, with enrichment of pathways in cholesterol synthesis, mitochondria respiration, ATP production, and transmembrane transporter activity. PFAS markedly increased the mRNA and protein of the pore-forming subunit of epithelial sodium channel (ENaC), with no change in {beta}ENaC and a slight reduction in {gamma}ENaC protein. Elevated ENaC coincided with a 30% decrease in Nedd4-2 phosphorylation (Ser448), suggesting reduced ENaC ubiquitination and degradation. However, protein expression of 1 Na+-K+-ATPase and serum- and glucocorticoid-regulated kinase 1 (SGK1) as well as SGK1 phosphorylation (Ser78) were unaltered. Amiloride abolished salt-induced hypertension in lower-dose mice but only partially corrected hypertension in the upper dose group. Taken together, our results provide causal evidence that PFAS exposure promotes hypertension, salt sensitivity, and kidney injury via renal epithelial mechanisms, supporting and extending human epidemiologic observations. Translational StatementOur findings establish four PFAS as causal drivers of salt-sensitive hypertension and kidney injury through convergent effects on ENaC and other tubular sodium transporters. These results not only provide a mechanistic explanation for epidemiologic associations but also identify PFAS as environmental amplifiers of dietary sodium risk. Given the ubiquity of human exposure, reducing PFAS burden alongside salt reduction may represent a complementary strategy to curb the global epidemic of hypertension and kidney disease.

physiology↗

bioRxiv2025

Evolutionary patterns and repeated adaptive strategies of deep-sea anemones

Sea anemones occupy the full depth of the oceans, yet their evolutionary patterns and adaptive strategies to the enigmatic deep sea have remained contentious and poorly resolved. Here, we assemble genomes (n = 13) and transcriptomes for 15 species collected between 432 and 6,000 m and integrate them with all publicly available actiniarian data. Phylogenomic analyses reveal a mosaic topology among deep-sea and shallow-water clades. Using a novel framework that contrasts convergent gene-loss patterns, we show that a large number of light-associated gene families-- including the complete circadian toolkit--were independently deleted after lineages entered the aphotic realm, whereas comparable loss in shallow taxa is negligible, providing decisive support for a shallow-water origin followed by multiple descents. Intriguingly, some deep-sea lineages further streamline energy budgets by recurrent loss or pseudogenisation of key meiotic genes (e.g., Meiosin, Ythdc2, Spo11, Rad21, Mlh3), indicating a shift towards asexual reproduction. Despite this extensive genomic erosion, deep-sea anemones exhibit sophisticated molecular tuning: specific amino-acid substitutions enhance protein stability and activity under deep-sea conditions, while selective expansions of gene families related to neural excitability, membrane systems, etc., likely mitigate the suppressive environmental effects on vital physiological processes. Enzyme activity assays in the yeast system confirm that the deep-sea variants exhibit superior activity and enhanced growth at 4{degrees}C. These results define a "loss-optimization-innovation" triad that underlies bathymetric adaptations and may apply to other deep-sea fauna worldwide.

evolutionary biology↗

bioRxiv2025

Highly sensitive and scalable time-resolved RNA sequencing in single cells with scNT-seq2

Understanding gene expression dynamics requires resolving newly synthesized RNAs from pre-existing pools at single-cell resolution. Here, we present scNT-seq2, a highly sensitive and scalable method for time-resolved single-cell RNA sequencing. By systematically optimizing the second-strand cDNA synthesis (2nd SS) step, we substantially improved read alignment rates, reduced background mutations, and enhanced library complexity compared to the original scNT-seq 1. Benchmarking in 4sU-labeled K562 cells demonstrated that scNT-seq2 accurately quantifies newly synthesized transcripts and preserves the gene level RNA turnover. The enhanced sensitivity enables robust detection of dynamic, cell-cycle state specific genes, such as S-phase regulators. Together, scNT-seq2 provides an efficient and versatile tool for dissecting transcriptional dynamics across diverse biological systems at single-cell resolution.

genomics↗

bioRxiv2025

Role of DEPDC1 in Glioblastoma Malignant Phenotype and Radiosensitivity

Radiotherapy has significantly improved survival outcomes in glioblastoma (GBM) patients, particularly when combined with tumor resection and temozolomide chemotherapy. However, radioresistance remains a major obstacle, limiting further advances in prognosis and potential cure. DEPDC1, a gene implicated in various malignant phenotypes, has not yet been investigated for its role in GBM radioresistance, despite suggestive evidence from previous studies. In this study, analysis of the cancer database and GBM tissue microarrays revealed that DEPDC1 expression is significantly elevated in GBM tissues compared to normal brain tissues. Using GBM cell lines with DEPDC1 knockdown, we observed markedly reduced proliferation and motility. Notably, DEPDC1 downregulation significantly enhanced radiosensitivity, as demonstrated by increased radiation-induced apoptosis, G2/M phase arrest, DNA damage, and impaired DNA repair post-radiation, resulting in lower survival rates in clonogenic assays. Mechanistically, these effects may be mediated through DEPDC1-driven upregulation of NF-{kappa}B, supported by tumor sample analysis from our xenograft mouse model. Collectively, our findings suggest that DEPDC1 is not only involved in GBM malignancy but also represents a promising therapeutic target for overcoming radioresistance and developing effective radiosensitizers.

cancer biology↗

bioRxiv2025

Exploring Population Differences in the Human Gut Microbiome: from Microbial Abundance to Single Nucleotide Polymorphisms

The human gut microbiota exhibits significant diversity across populations, influenced by factors such as geography, diet, and lifestyle, particularly between the Han Chinese and non-Chinese populations. While previous studies have predominantly focused on the taxonomic abundance of the gut microbiome, the impact of single nucleotide polymorphisms (SNPs) in driving population-specific differences remains largely underexplored. In this study, we systematically investigated gut microbial differences between the Han Chinese and non-Chinese populations using the Human Gut Microbiome Reference Genome Catalog (HGMRGC). HGMRGC includes 271,480 non-redundant genomes from 5,785 prokaryotic species, which was generated by metagenomic sequencing data from 9,320 publicly available samples across 22 countries and 3,584 newly sequenced samples from Han Chinese individuals across 29 provinces and regions in China. We observed geography was the primary driver of microbial variation of abundance and SNPs. We identified 625 novel population-specific genome clusters from HGMRGC with functional differences in carbohydrate utilization and 126 species exhibiting distinct prevalence related to vitamin biosynthesis, antibiotic resistance, and carbohydrate metabolism. Beta diversity analysis highlighted significant inter-population differences in both microbial abundance and SNPs, while alpha diversity analysis revealed that non-Chinese populations exhibited higher diversity in microbial abundance, and Han Chinese populations displayed greater diversity in SNPs. These results provide valuable insights into population-specific microbial diversity, laying the groundwork for future research on its functional and health implications.

microbiology↗

bioRxiv2025

Integrated single-cell and spatial multiomic analysis reveals widespread reactivation of developmental programs in diseased human hearts

The first organ to develop in utero, the human heart undergoes significant changes during development and must sustain its function over a lifetime. To better characterize molecular changes in human cardiac cell-types across sex, aging, developmental and disease, we analyzed single nucleus RNA sequencing (snRNA-seq) datasets from 299 donors, identifying many more differentially expressed genes (DEGs) across developmental and disease states than by sex and age. In cardiomyocytes and most non-cardiomyocyte cell types, developmental and disease DEGs showed significant overlap. Cardiac development and disease were associated with convergent changes in non-cardiomyocyte intercellular communication, including TGF{beta} signaling, but differences in cell-type proportions. By integrating snRNA-seq with 106 snATAC-seq datasets, we reveal potential transcriptional factors driving fetal reactivation in disease. Finally, using spatial transcriptomics data, we identify that fetal reactivation is highly localized in niches. This work offers the largest multimodal, cell-type resolved interrogation of the human heart, providing insights into convergence in development and disease.

genomics↗

bioRxiv2024

Global and genetic regulation of gene expression in human endothelial and vascular smooth muscle cells

BackgroundThe understanding of genetic and epigenetic regulation of gene expression in endothelial and vascular smooth muscle cells remains fragmented with limited experimental validation. MethodsChromatin conformation (Micro-C), DNA methylation (RRBS), chromatin accessibility (ATAC-seq), and transcriptome profiles (RNA-seq) were mapped in human induced pluripotent stem cell (hiPSC)-derived, isogenic endothelial and vascular smooth muscle cells (iECs and iVSMCs). CTCF and RAD21 were depleted to assess the functional relevance of chromatin architecture, and genome editing was used to evaluate the allelic effect of a blood pressure-associated single nucleotide polymorphism (SNP). ResultsSignificant correlations were identified between gene expression levels and chromatin interactions, chromatin accessibility, and DNA methylation in iECs and iVSMCs, with chromatin interactions showing the strongest association. Chromatin contact regions displayed distinct epigenetic landscapes depending on the types of regulatory element interactions involved. Perturbation of CTCF and RAD21 revealed their differential regulatory effects, particularly on the expression of genes overlapping chromatin contacts, with RAD21 exhibiting a broader regulatory impact. SNPs associated with several vascular traits were enriched in chromatin loops or accessible regions in iECs or iVSMCs. Precise genome editing demonstrated allele-dependent effects of SNP rs9833313 on the expression of SHOX2 located 247.4 kbp away but within the same chromatin loops as the SNP. ConclusionThis study provides an extensive epigenetic landscape of vascular cells that may drive novel research on the role of genetic and epigenetic mechanisms of vascular function and disease as demonstrated by our targeted experiments.

genomics↗

bioRxiv2024

A single-cell map of hypertension

Hypertension is a leading risk factor for disease burden and death worldwide. Several organ systems are involved in the development of hypertension, which contributes to stroke, heart disease, and kidney disease. Despite the broad health relevance, our understanding of the molecular landscape in hypertension is limited and lags other major diseases. Here we report an extensive analysis of the molecular landscape in hypertension and its end-organ damage and uncover novel mechanisms linking human genetic variants to the development of these diseases. We obtained single-nucleus RNA-seq (612,984 nuclei), single-nucleus ATAC-seq (179,637 nuclei), or spatial transcriptome data from five organs (hypothalamus, kidney, heart, 3rd order mesenteric artery, middle cerebral artery) in three mouse and rat models under twelve experimental conditions. More than one third of all hypertension research in animal models involves these three models. We identified both model-specific and convergent responses in cell types, genes, and pathways. By integrating our data with human genomic data, we partitioned the blood pressure and end-organ damage traits into cell type-specific transcriptional contributions and cell types common across multiple traits. Using genomic editing in animal models and human induced pluripotent stem cells, we extended key findings and identified new mechanisms linking human genetic variants to the development of hypertension and related renal injury. We anticipate that our rich data sets and findings will broadly drive forward the research of hypertension and hypertensive end-organ damage. Our approach of integrating multi-model and multi-tissue single-cell analysis with human genetic data and in vivo and in vitro genome editing can be applied to investigate other complex traits.

physiology↗

bioRxiv2024

Delineation of Single-cell Altas Provides New Insights for Development of Coronary Artery Lesions in Kawasaki Disease: Bad and Good Signaling Molecules

BackgroundKawasaki Disease (KD) is a vasculitis syndrome featured with a high and persistent fever and mainly affects children under 5 years of age. It is the leading cause of acquired heart disease in the form of coronary artery lesions (CALs) for children in developed countries. Most KD can be relieved with the high-dosage Intravenous immunoglobulin (IVIG) therapy, but a small proportion develop CALs after IVIG treatment. MethodsWe performed the single-cell RNA sequencing for the peripheral blood mononuclear cells (PBMCs) from three KD non-CAL patients whose samples were acquired before and after IVIG treatment and three KD CAL patients whose samples were acquired only after IVIG treatment. Cell-to-cell communication patterns were also analyzed in KD CAL and non-CAL patients ResultsOverall cell expression feature analyses show immunoglobulin and adaptive immunity related genes are upregulated in KD CAL patients while B cell activation related genes are downregulated in them. Pseudo-time analyses demonstrate that both KD non-CAL patients before treatment and KD CAL patients after treatment have a dysregulated B cell developmental trajectory while the former has a mixed T and B lineage and the latter has a mixed monocyte and B lineage. The early elevated expression of SPI1 could partly explain the dysregulated B cell development in KD CAL patients. Cell communication analyses propose a disorder cell communication pattern in KD non-CAL patients before treatment and some persistent bad cell-to-cell signals in KD CAL patients after treatment. There are four signaling molecules, APP, CCL, and MCH-II, whose expression is significantly increased in the CD14 and CD16 monocytes of KD CAL patients, where the expression of RESISTIN is significantly increased in those KD non-CAL patients. ConclusionsOur results suggest that APP, CCL, and MCH-II might be the bad signals for indicating the possible development of CAL while RESISTIN is a good one for protecting from CAL.

immunology↗

bioRxiv2024

Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling

A cells ability to respond and adapt to environmental stimuli relies in part on transcriptional programs controlled by histone proteins. Histones affect transcription through numerous mechanisms including through replacement with variant forms that carry out specific functions. We recently identified the first widely expressed H2B histone variant, H2BE and found that it promotes transcription and is critical for neuronal function and long-term memory. However, how H2BE is regulated by extracellular stimuli and whether it controls activity-dependent transcription and cellular plasticity remain unknown. We used CUT&Tag and RNA-sequencing of primary neurons, single-nucleus sequencing of cortical tissue, and multielectrode array recordings to interrogate the expression of H2BE in response to stimuli and the role of H2BE in activity-dependent gene expression and plasticity. We find that unlike Further, we show that neurons lacking H2BE are unable to mount proper long-term activity-dependent transcriptional responses both in cultured neurons and in animal models. Lastly, we demonstrate that H2BE knockout neurons fail to undergo the electrophysiological changes associated with homeostatic plasticity in neurons after long-term stimulation. In summary, these data demonstrate that H2BE expression is inversely correlated to activity and necessary for long-term activity-dependent responses, revealing the first instance of a histone variant involved in the homeostatic plasticity response in neurons.

genetics↗

bioRxiv2024

Chromatin interaction maps of human arterioles reveal new mechanisms for the genetic regulation of blood pressure

Arterioles are small blood vessels located just upstream of capillaries in nearly all tissues. The constriction and dilation of arterioles regulate tissue perfusion and are primary determinants of systemic blood pressure (BP). Abnormalities in arterioles are central to the development of major diseases such as hypertension, stroke, and microvascular complications of diabetes. Despite the broad and essential role of arterioles in physiology and disease, current knowledge of the functional genomics of arterioles is largely absent, partly because it is challenging to obtain and analyze human arteriole samples. Here, we report extensive maps of chromatin interactions, single-cell expression, and other molecular features in human arterioles and uncover new mechanisms linking human genetic variants to gene expression in vascular cells and the development of hypertension. Compared to large arteries, arterioles exhibited a higher proportion of pericytes which were strongly associated with BP traits. BP-associated single nucleotide polymorphisms (SNPs) were enriched in chromatin interaction regions in arterioles, particularly through enhancer SNP-promoter interactions, which were further linked to gene expression specificity across tissue components and cell types. Using genomic editing in animal models and human induced pluripotent stem cells, we discovered novel mechanisms linking BP-associated noncoding SNP rs1882961 to gene expression through long-range chromatin contacts and revealed remarkable effects of a 4-bp noncoding genomic segment on hypertension in vivo. We anticipate that our rich data and findings will advance the study of the numerous diseases involving arterioles. Moreover, our approach of integrating chromatin interaction mapping in trait-relevant tissues with SNP analysis and in vivo and in vitro genome editing can be applied broadly to bridge the critical gap between genetic discoveries and physiological understanding.

genomics↗

bioRxiv2024

Origin and stepwise improvement of vertebrate lungs

Lungs, essential for terrestrial vertebrates and present in bony fishes but absent in cartilaginous fishes, provide an ideal model for studying organ origination. Our study analyzed single-cell RNA sequencing data from mature and developing vertebrate lungs, revealing substantial similarities in cell composition, developmental trajectories and gene expression pattern across species. Notably, most lung-related genes are also present in cartilaginous fishes, indicating that gene presence alone does not guarantee lung development. We identified thousands of lung regulatory elements specific to bony fishes, with higher concentrations around genes such as tbx4 and the hoxb gene cluster. These regulatory changes might contribute to lung emergence as well as the unique co-expression patterns in lung epithelial cells, such as those related to pulmonary surfactants and cell morphology. Our research also revealed that AT1 cells are specific to mammals, and we identified a mammal-specific gene, sfta2. Knockout experiments demonstrated that sfta2 deletion causes severe respiratory defects in mice, underscoring its critical role in specialized mammalian lungs. In conclusion, our results demonstrate that the origin and evolution of lungs are driven by a complex interplay of regulatory network modifications and the emergence of new genes, underscoring the multifaceted nature of organ evolution.

evolutionary biology↗

bioRxiv2024

Persistent Neurological Deficits in Mouse PASC Reveal Antiviral Drug Limitations

Post-Acute Sequelae of COVID-19 (PASC) encompasses persistent neurological symptoms, including olfactory and autonomic dysfunction. Here, we report chronic neurological dysfunction in mice infected with a virulent mouse-adapted SARS-CoV-2 that does not infect the brain. Long after recovery from nasal infection, we observed loss of tyrosine hydroxylase (TH) expression in olfactory bulb glomeruli and neurotransmitter levels in the substantia nigra (SN) persisted. Vulnerability of dopaminergic neurons in these brain areas was accompanied by increased levels of proinflammatory cytokines and neurobehavioral changes. RNAseq analysis unveiled persistent microglia activation, as found in human neurodegenerative diseases. Early treatment with antivirals (nirmatrelvir and molnupiravir) reduced virus titers and lung inflammation but failed to prevent neurological abnormalities, as observed in patients. Together these results show that chronic deficiencies in neuronal function in SARS-CoV-2-infected mice are not directly linked to ongoing olfactory epithelium dysfunction. Rather, they bear similarity with neurodegenerative disease, the vulnerability of which is exacerbated by chronic inflammation.

microbiology↗

bioRxiv2024

Physiological role and mechanisms of action for a long noncoding haplotype region

Most common sequence variants associated with human traits are in noncoding regions of the genome, form haplotypes with other noncoding variants, and exhibit small effect sizes in the general population. Determining the physiological roles and mechanisms of action for these noncoding variants, particularly large haplotypes containing multiple variants, is both critical and challenging. To address this challenge, we developed an approach that integrates physiological studies in genetically engineered and phenotypically permissive animal models, precise editing of large haplotypes in human induced pluripotent stem cells (hiPSCs), and targeted chromatin conformation analysis. We applied this approach to examine the blood pressure associated rs1173771 locus, which includes a haplotype containing 11 single nucleotide polymorphisms (SNPs) spanning 17.4 kbp. Deleting the orthologous noncoding region in the genome of the Dahl salt-sensitive rat attenuated the salt-induced increase in systolic blood pressure by nearly 10 mmHg. This attenuation of hypertension appeared to be mediated by upregulation of the adjacent gene Npr3 (natriuretic peptide receptor 3) in arteries, enhancing vasodilation. The blood pressure-elevating and -lowering haplotypes were precisely reconstituted in hiPSCs using an efficient, two-step genome editing technique. The blood pressure-elevating haplotype decreased NPR3 expression in endothelial cells and vascular smooth muscle cells derived from the edited, isogenic hiPSCs. The influence of the haplotype was partially recapitulated by the sentinel SNP rs1173771. Additionally, the blood pressure-elevating haplotype showed significantly greater chromatin interactions with the NPR3 promoter region. This study illustrates the feasibility of ascertaining the physiological roles and mechanisms of action for large noncoding haplotypes. Our efficient, integrated, and targeted approach can be applied to investigate other noncoding variants.

genetics↗

bioRxiv2024

Single-Cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape

Cell differentiation during organogenesis relies on precise epigenetic and transcriptional control. Disruptions to this regulation can result in developmental abnormalities and malignancies, yet the underlying mechanisms are not well understood. Wilms tumors, a type of embryonal tumor closely linked to disrupted organogenesis, harbor mutations in epigenetic regulators in 30-50% of cases. However, the role of these regulators in kidney development and pathogenesis remains unexplored. By integrating mouse modeling, histological characterizations, and single-cell transcriptomics and chromatin accessibility profiling, we show that a Wilms tumor-associated mutation in the chromatin reader protein ENL disrupts kidney development trajectory by rewiring the gene regulatory landscape. Specifically, the mutant ENL promotes the commitment of nephron progenitors while simultaneously restricting their differentiation by dysregulating key transcription factor regulons, particularly the HOX clusters. It also induces the emergence of abnormal progenitor cells that lose their chromatin identity associated with kidney specification. Furthermore, the mutant ENL might modulate stroma-nephron interactions via paracrine Wnt signaling. These multifaceted effects caused by the mutation result in severe developmental defects in the kidney and early postnatal mortality in mice. Notably, transient inhibition of the histone acetylation binding activity of mutant ENL with a small molecule displaces transcriptional condensates formed by mutant ENL from target genes, abolishes its gene activation function, and restores developmental defects in mice. This work provides new insights into how mutations in epigenetic regulators can alter the gene regulatory landscape to disrupt kidney developmental programs at single-cell resolution in vivo. It also offers a proof-of-concept for the use of epigenetics-targeted agents to rectify developmental defects.

cancer biology↗