Biology subjects

Muto, Y.

Publications and source records attributed to Muto, Y..

11 recordsLinked to original sources

bioRxiv2026

Macrophage SLC9A1 Links Endocytic Trafficking to Innate Immune Activation in Myocardial Injury

Excessive innate immune activation drives adverse remodeling after myocardial infarction (MI), yet the upstream mechanisms by which macrophages sense ischemic danger signals remain poorly defined. Here we tested whether macropinocytosis functions as a mediator of post-ischemic inflammation and whether the Na/H exchanger SLC9A1 links membrane ion transport to innate immune activation in the injured heart. Macropinocytosis was robustly activated in infarct-associated macrophages, which are the predominant cell type with the macropinocytotic activity in the injured heart. Pharmacologic inhibition of macropinocytosis with 5-(N-ethyl-N-isopropyl)amiloride (EIPA) improved cardiac function and attenuated post-MI remodeling. EIPA also attenuated cardiac inflammatory responses induced by systemic lipopolysaccharide and Poly(I:C). To define macrophage-intrinsic mechanisms, we generated monocyte- and monocyte-derived macrophage-specific Slc9a1 knockout mice. Genetic deletion of Slc9a1 recapitulated the cardioprotective effects of EIPA and markedly suppressed interferon-stimulated gene programs in infarct-associated macrophages, as revealed by single-cell RNA sequencing. Mechanistically, SLC9A1 promoted endocytic uptake of Poly(I:C) acid and enhanced endosome-dependent inflammatory signaling. Together, these findings identify macrophage macropinocytosis as a regulator of innate immune activation after MI and reveal SLC9A1 as a previously unrecognized link between membrane ion transport and inflammatory signaling in the injured heart. Targeting SLC9A1-dependent membrane trafficking pathways may therefore represent a strategy to limit maladaptive inflammation in ischemic heart disease.

immunology↗

bioRxiv2025

Cell Type-Specific and Diabetic Kidney Disease-Associated Expression of Long Non-Coding RNAs in Human Kidneys

BackgroundLong non-coding RNAs (lncRNAs) play essential roles in cellular processes, often exhibiting cell type-specific expression and influencing kidney function. While single-cell RNA sequencing (scRNA-seq) has advanced our understanding of cellular specificity, past studies focus solely on protein-coding genes. We hypothesize that lncRNAs, due to their cell-specific nature, have crucial functions within particular renal cells and thereby play essential roles in renal cell function and disease. MethodsUsing single-nucleus RNA sequencing (snRNA-seq) data from kidney samples of five healthy individuals and six DKD patients, we explored the non-coding transcriptome. Cell type-specific lncRNAs were identified, and their differential expression in DKD was assessed. Integrative analyses included expression quantitative trait loci (eQTL), genome-wide association studies (GWAS) for estimated glomerular filtration rate (eGFR), and gene regulatory networks. Functional studies focused on TARID, a lncRNA with podocyte-specific expression, to elucidate its role in podocyte health. Resultswe identified 349 lncRNAs with cell type-specific expression across kidney cell types. Of these, 104 lncRNAs were differentially expressed in DKD. Integrative analyses, including eQTL data, GWAS results for eGFR and gene regulatory networks, pinpointed TARID, a podocyte-specific lncRNA, as a key candidate upregulated in DKD. Functional studies confirmed TARIDs podocyte-specific expression and revealed its central role in actin cytoskeleton reorganization, a critical process in podocyte health. ConclusionsOur study provides a comprehensive resource of single-cell lncRNA expression in the human kidney and highlights the importance of cell type-specific lncRNAs in kidney function and disease. Specifically, we demonstrate the functional relevance of TARID in podocyte health. This work underscores the utility of integrating scRNA-seq with functional genomics to uncover novel regulatory mechanisms in kidney biology. Key pointsO_LIThis provides a resource for kidney (cell type-specific) lncRNA expression and demonstrates the importance of lncRNAs in renal health. C_LIO_LIWe identified 349 cell type-specific lncRNAs in the human kidney, with 104 showing altered expression in diabetic kidney disease (DKD). C_LIO_LITARID, a podocyte-specific lncRNA upregulated in DKD, is crucial for actin cytoskeleton reorganization in podocytes. C_LI

bioinformatics↗

bioRxiv2024

Multi-omics profiling of mouse polycystic kidney disease progression at a single cell resolution

Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disease and causes significant morbidity, ultimately leading to end-stage kidney disease. PKD pathogenesis is characterized by complex and dynamic alterations in multiple cell types during disease progression, hampering a deeper understanding of disease mechanism and the development of therapeutic approaches. Here, we generate a single nucleus multimodal atlas of an orthologous mouse PKD model at early, mid and late timepoints, consisting of 125,434 single-nucleus transcriptomic and epigenetic multiomes. We catalogue differentially expressed genes and activated epigenetic regions in each cell type during PKD progression, characterizing cell-type-specific responses to Pkd1 deletion. We describe heterogeneous, atypical collecting duct cells as well as proximal tubular cells that constitute cyst epithelia in PKD. The transcriptional regulation of the cyst lining cell marker GPRC5A is conserved between mouse and human PKD cystic epithelia, suggesting shared gene regulatory pathways. Our single nucleus multiomic analysis of mouse PKD provides a foundation to understand the earliest changes molecular deregulation in a mouse model of PKD at a single-cell resolution.

genomics↗

bioRxiv2024

Endogenous retrovirus ERV-DC8 highly integrated in domestic cat populations is a replication-competent provirus

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections in vertebrate genomes and are inherited by offspring. ERVs can produce pathogenic viruses through gene mutations or recombination. ERVs in domestic cats (ERV-DCs) generate feline leukemia virus subgroup D (FeLV-D) through viral recombination. Herein, we characterized the locus ERV-DC8, on chromosome B1, as an infectious replication-competent provirus. ERV-DC8 infected several cell lines, including human cells. Transmission electron microscopy of ERV-DC8 identified the viral release as a Gammaretrovirus. ERV-DC8 was identified as the FeLV-D viral interference group, with feline copper transporter 1 as its viral receptor. Insertional polymorphism analysis showed high ERV-DC8 integration in domestic cats. This study highlights the role, pathogenicity, and evolutionary relationships between ERVs and their hosts.

microbiology↗

bioRxiv2024

A unique subset of pericystic endothelium associates with aberrant microvascular remodelling and impaired blood perfusion early in polycystic kidney disease

Hallmarks of autosomal dominant polycystic kidney disease (ADPKD), the most common hereditary kidney anomaly, include expanding fluid-filled epithelial cysts, inflammation, and fibrosis. Despite previous work showing the potential of vascular-based therapies, renal microvascular alterations in ADPKD, and their timing, are poorly understood. Using single-cell transcriptomics of human kidney microvasculature, we identify a population of endothelial cells adjacent to cysts in ADPKD. This pericystic endothelium, distinguishable by its expression of osteopontin (SPP1), has a distinct molecular profile compared to the common endothelial cell injury signature in other kidney diseases. SPP1+ pericystic endothelium was also present in an orthologous mouse model of ADPKD before overt kidney functional decline. By interrogating geometric, topological and fractal properties from three-dimensional imaging of early ADPKD mouse kidneys, we show that pericystic endothelium associates with disorganisation and non-uniformity of the renal cortical microvasculature. Concurrently, we detected region-specific reductions in cortical blood flow within ADPKD murine kidneys using arterial spin labelling. We conclude that ADPKD kidneys contain a unique subset of endothelium manifesting with aberrant remodelling and impaired blood perfusion. Its detection, prior to renal functional decline, advocates the vasculature as a therapeutic target to modulate or preserve renal function in early ADPKD.

pathology↗

bioRxiv2024

Epigenetic reprogramming driving successful and failed repair in acute kidney injury

Acute kidney injury (AKI) causes epithelial damage followed by subsequent repair. While successful repair restores kidney function, this process is often incomplete and can lead to chronic kidney disease (CKD) in a process called failed repair. To better understand the epigenetic reprogramming driving this AKI-to-CKD transition we generated a single nucleus multiomic atlas for the full mouse AKI time course, consisting of [~]280,000 single nucleus transcriptomes and epigenomes. We reveal cell-specific dynamic alterations in gene regulatory landscapes reflecting especially activation of proinflammatory pathways. We further generated single nucleus multiomic data from four human AKI samples including validation by genome-wide identification of NF-kB binding sites. A regularized regression analysis identifies key regulators involved in both successful and failed repair cell fate, identifying the transcription factor CREB5 as a regulator of both successful and failed tubular repair that also drives proximal tubule cell proliferation after injury. Our interspecies multiomic approach provides a foundation to comprehensively understand cell states in AKI.

genomics↗

bioRxiv2022

Predicting regulators of epithelial cell state through regularized regression analysis of single cell multiomic sequencing

Chronic disease processes are marked by cell-specific transcriptomic and epigenomic changes. Single nucleus joint RNA- and ATAC-seq offers an opportunity to study the gene regulatory networks underpinning these changes in order to identify key regulatory drivers. We developed a regularized regression approach, RENIN, (Regulatory Network Inference) to construct genome-wide parametric gene regulatory networks using multiomic datasets. We generated a single nucleus multiomic dataset from seven adult human kidney biopsies and applied RENIN to study drivers of a failed injury response associated with kidney disease. We demonstrate that RENIN is highly effective tool at predicting key cis- and trans-regulatory elements.

genomics↗

bioRxiv2022

Quality assessment and refinement of chromatin accessibility data using a sequence-based predictive model

Chromatin accessibility assays are central to the genome-wide identification of gene regulatory elements associated with transcriptional regulation. However, the data have highly variable quality arising from several biological and technical factors. To surmount this problem, we use the predictability of open-chromatin peaks from DNA sequence-based machine-learning models to evaluate and refine chromatin accessibility data. Our framework, gapped k-mer SVM quality check (gkmQC), provides the quality metrics for a sample based on the prediction accuracy of the trained models. We tested 886 samples with DNase-seq from the ENCODE/Roadmap projects to demonstrate that gkmQC can effectively identify high-quality samples underperforming owing to marginal read depths. Peaks identified in high-quality samples by gkmQC are more accurately aligned at functional regulatory elements, show greater enrichment of regulatory elements harboring functional variants from genome-wide association studies (GWAS), and explain greater heritability of phenotypes from their relevant tissues. Moreover, gkmQC can optimize the peak-calling threshold to identify additional peaks, especially for single-cell chromatin accessibility data as well as bulk data. Here we provide a standalone open-source toolkit (https://github.com/Dongwon-Lee/gkmQC) for such analyses and share improved regulatory maps using gkmQC. These resources will contribute to the functional interpretation of disease-associated regulatory genetic variation.

genomics↗

bioRxiv2022

Multimodal single cell sequencing of human diabetic kidney disease implicates chromatin accessibility and genetic background in disease progression

Multimodal single cell sequencing is a powerful tool for interrogating cell-specific changes in transcription and chromatin accessibility. We performed single nucleus RNA (snRNA-seq) and assay for transposase accessible chromatin sequencing (snATAC-seq) on human kidney cortex from donors with and without diabetic kidney disease (DKD) to identify altered signaling pathways and transcription factors associated with DKD. Both snRNA-seq and snATAC-seq had an increased proportion of VCAM1+ injured proximal tubule cells (PT_VCAM1) in DKD samples. PT_VCAM1 has a pro-inflammatory expression signature and transcription factor motif enrichment implicated NFkB signaling. We used stratified linkage disequilibrium score regression to partition heritability of kidney-function-related traits using publicly-available GWAS summary statistics. Cell-specific PT_VCAM1 peaks were enriched for heritability of chronic kidney disease (CKD), suggesting that genetic background may regulate chromatin accessibility and DKD progression. snATAC-seq found cell-specific differentially accessible regions (DAR) throughout the nephron that change accessibility in DKD and these regions were enriched for glucocorticoid receptor (GR) motifs. Changes in chromatin accessibility were associated with decreased expression of insulin receptor, increased gluconeogenesis, and decreased expression of the GR cytosolic chaperone, FKBP5, in the diabetic proximal tubule. Cleavage under targets and release using nuclease (CUT&RUN) profiling of GR binding in bulk kidney cortex and an in vitro model of the proximal tubule (RPTEC) showed that DAR co-localize with GR binding sites. CRISPRi silencing of GR response elements (GRE) in the FKBP5 gene body reduced FKBP5 expression in RPTEC, suggesting that reduced FKBP5 chromatin accessibility in DKD may alter cellular response to GR. We developed an open-source tool for single cell allele specific analysis (SALSA) to model the effect of genetic background on gene expression. Heterozygous germline single nucleotide variants (SNV) in proximal tubule ATAC peaks were associated with allele-specific chromatin accessibility and differential expression of target genes within cis-coaccessibility networks. Partitioned heritability of proximal tubule ATAC peaks with a predicted allele-specific effect was enriched for eGFR, suggesting that genetic background may modify DKD progression in a cell-specific manner.

genomics↗

bioRxiv2021

Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis

Autosomal dominant polycystic kidney disease (ADPKD) is the leading genetic cause of end stage renal disease and is characterized by the formation and progressive expansion of kidney cysts. Most ADPKD cases arise from mutations in either the PKD1 or PKD2 gene but the precise downstream signaling pathways driving cyst growth are not well understood, and relatively few studies investigate human cystic kidney due to sample scarcity. In order to better understand the cell types and states driving human ADPKD progression, we analyzed eight ADPKD and five healthy human kidney samples, generating a single cell multiomic atlas consisting of ~100,000 single nucleus transcriptomes and ~50,000 single nucleus epigenomes. The integrated datasets identified 11 primary cell clusters including most epithelial cell types as well as large endothelial and fibroblast cell clusters. Proximal tubular cells from ADPKD kidneys expressed a failed repair transcriptomic signature characterized by profibrotic and proinflammatory transcripts. We identified the G protein-coupled receptor GPRC5A as specifically upregulated in cyst lining cells derived from collecting duct. The principal cell subpopulation enriched for GPRC5A expression also exhibited increased transcription factor binding motif availability for NF-{kappa}B, TEAD, CREB and retinoic acid receptor families and we identified and validated a distal enhancer regulating GPRC5A expression containing these transcription factor binding motifs. This study establishes the single cell transcriptomic and epigenomic landscape of ADPKD, revealing previously unrecognized cellular heterogeneity.

genomics↗

bioRxiv2020

Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney

The integration of single cell transcriptome and chromatin accessibility datasets enables a deeper understanding of cell heterogeneity. We performed single nucleus ATAC (snATAC-seq) and RNA (snRNA-seq) sequencing to generate paired, cell-type-specific chromatin accessibility and transcriptional profiles of the adult human kidney. We demonstrate that snATAC-seq is comparable to snRNA-seq in the assignment of cell identity and can further refine our understanding of functional heterogeneity in the nephron. The majority of differentially accessible chromatin regions are localized to promoters and a significant proportion are closely-associated with differentially expressed genes. Cell-type-specific enrichment of transcription factor binding motifs implicates the activation of NF{kappa}B that promotes VCAM1 expression and drives transition between a subpopulation of proximal tubule epithelial cells. These datasets can be visualized at this resource: http://humphreyslab.com/SingleCell/. Our multi-omics approach improves the ability to detect unique cell states within the kidney and redefines cellular heterogeneity in the proximal tubule and thick ascending limb.

genomics↗