Sébastien Joël Dumas

Key Points: Spatial metabolomics revealed persistent injured tissue niches after ischemic injury despite the presence of apparently healthy epithelial cells. Proximal tubule cells residing in injured niches exhibited succinate accumulation and linoleic acid depletion. Integration with spatial transcriptomics showed that injured niches were characterized by dysregulated oxidative and lipid metabolism. Background: The role of the tissue microenvironment in the transition from AKI to CKD remains poorly understood. While the persistence of failed-repair proximal tubule (FR-PT) cells is postulated to hamper kidney regeneration, the spatial metabolic architecture of injured tissue and its effect on regenerative capacity have not been fully characterized. Methods: We analyzed mouse kidneys 14 days after bilateral ischemia-reperfusion injury using a multimodal spatial omics approach. Internal standard–normalized mass spectrometry imaging was used to quantify metabolite abundances, followed by unsupervised spatial domain analysis using the BANKSY algorithm to identify tissue niches on the basis of lipidome profiles. Consecutive sections underwent high-resolution spatial transcriptomics (Stereo-seq), and we applied niche projection to integrate metabolomic and transcriptomic data, enabling comparison of proximal tubule cells in healthy versus injured niches. Results: Unsupervised spatial domain analysis revealed distinct healthy and injured niches, with injured niches exhibiting diffusely spread metabolic abnormalities extending beyond FR-PT cells. Quantitative metabolomics demonstrated that seemingly healthy proximal tubule cells residing in injured niches exhibited elevated succinic acid and depleted linoleic acid compared with cells in healthy niches. Spatial transcriptomics confirmed these metabolic defects at the transcriptional level, revealing downregulation of oxidative phosphorylation and fatty acid β -oxidation pathways in proximal tubule cells within injured microenvironments. Conclusions: Combined spatially resolved analysis of internal standard–normalized mass spectrometry imaging and spatial transcriptomics revealed distinct healthy and injured tissue niches after ischemia-reperfusion injury. Metabolic abnormalities, including defects in oxidative phosphorylation and fatty acid β -oxidation, were not restricted to FR-PT cells but extended into seemingly healthy epithelial cells embedded within injured microenvironments.

Multi-modal spatial data analysis often requires precise physical alignment of consecutive tissue sections, a process that can be challenging and typically relies on shared molecular markers or image recognition techniques. Here, we introduce COAST (Consecutive multi-Omics Alignment of Spatial Tissues), a method to reliably physically align consecutive tissue sections to produce a unified multi-modal molecular dataset suitable for downstream applications. COAST relies exclusively on the images associated with spatial data, eliminating the need for common molecular features or prior annotations. We demonstrate the effectiveness of COAST using spatial transcriptomics slides, where it achieves performance comparable to established uni-modal alignment tools. Applying COAST to spatial transcriptomics and metabolomics/lipidomics tissue sections from a mouse model of ischemia reperfusion injury allowed the investigation of lipid/metabolite features of transcriptionally-defined cell types. Overall, COAST offers a streamlined and integrative solution for multi-modal spatial data alignment.

After acute kidney injury (AKI), the persistence of failed repair proximal tubule (FR-PT) cells is postulated to hamper kidney regeneration and increase the risk of chronic kidney disease. This fibrotic shift likely depends on microenvironmental interactions, which remain largely unstudied. To investigate this, we mapped the spatial metabolic architecture of post-ischemic kidneys using an untargeted semi-quantitative spatial metabolomics (qMSI) approach, integrated with high-resolution spatial transcriptomics. Unsupervised neighborhood clustering of qMSI data revealed distinct microenvironments. Lipidome profiles identified diffusely spread areas with persistent injury markers surrounding FR-PT cells. These niches exhibited decreased linoleic acid and elevated succinic acid levels, even in epithelial cells that appeared otherwise healthy. Corresponding transcriptomic profiles confirmed downregulation of oxidative phosphorylation and fatty acid β-oxidation in these regions. Together, these findings point towards niche-specific metabolic failure and persistent mitochondrial dysfunction in areas considered healthy, underscoring the need to prioritize metabolic resuscitation to prevent long-term consequences of AKI.

Global population aging is an escalating challenge in modern society, especially as it impairs the function of multiple organs and increases the burden of age-related diseases. The kidneys, in particular, experience function decline, reduced regenerative capacity, and increased susceptibility to injury as they age. As a result, the prevalence of chronic kidney disease (CKD) rises with aging, further contributing to the growing health burden in older populations. One of the key factors in this process is the dysfunction of specialized renal endothelial cells (RECs), which are essential for maintaining kidney health by regulating blood flow and supporting filtration, solute and water reabsorption, and vascular integrity. As the kidneys age, REC dysfunction drives vascular and microenvironmental changes, contributing to the overall decline in kidney function. In this review, we outline the structural and functional effects of aging on the kidney’s macrovascular and microvascular compartments and provide a phenotypic description of the aged endothelium. We particularly focus on the molecular and metabolic rewiring driving and sustaining growth-arrested EC senescence phenotype. We finally give an overview of senotherapies acting on ECs, especially of those modulating metabolism. Given that the pathophysiological processes underlying kidney aging largely overlap with those observed in CKD, REC rejuvenation could also benefit patients with CKD. Moreover, such interventions may hold promise in improving the outcomes of aged kidney transplants. Hence, advancing our understanding of REC and kidney aging will create opportunities for innovations that could improve outcomes for both elderly individuals and patients with CKD.

Background: Long 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. Methods: Using 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. Results: we 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 TARID ’s podocyte-specific expression and revealed its central role in actin cytoskeleton reorganization, a critical process in podocyte health. Conclusions: Our 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 points: This provides a resource for kidney (cell type-specific) lncRNA expression and demonstrates the importance of lncRNAs in renal health. We identified 349 cell type-specific lncRNAs in the human kidney, with 104 showing altered expression in diabetic kidney disease (DKD). TARID , a podocyte-specific lncRNA upregulated in DKD, is crucial for actin cytoskeleton reorganization in podocytes.

A common drawback of metabolic analyses of complex biological samples is the inability to consider cell-to-cell heterogeneity in the context of an organ or tissue. To overcome this limitation, we present an advanced high-spatial-resolution metabolomics approach using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) combined with isotope tracing. This method allows mapping of cell-type-specific dynamic changes in central carbon metabolism in the context of a complex heterogeneous tissue architecture, such as the kidney. Combined with multiplexed immunofluorescence staining, this method can detect metabolic changes and nutrient partitioning in targeted cell types, as demonstrated in a bilateral renal ischemia–reperfusion injury (bIRI) experimental model. Our approach enables us to identify region-specific metabolic perturbations associated with the lesion and throughout recovery, including unexpected metabolic anomalies in cells with an apparently normal phenotype in the recovery phase. These findings may be relevant to an understanding of the homeostatic capacity of the kidney microenvironment. In sum, this method allows us to achieve resolution at the single-cell level in situ and hence to interpret cell-type-specific metabolic dynamics in the context of structure and metabolism of neighboring cells.

Human induced pluripotent stem cell-derived kidney organoids have potential for disease modeling and to be developed into clinically transplantable auxiliary tissue. However, they lack a functional vasculature, and the sparse endogenous endothelial cells (ECs) are lost upon prolonged culture in vitro, limiting maturation and applicability. Here, we use intracoelomic transplantation in chicken embryos followed by single-cell RNA sequencing and advanced imaging platforms to induce and study vasculogenesis in kidney organoids. We show expansion of human organoid-derived ECs that reorganize into perfused capillaries and form a chimeric vascular network with host-derived blood vessels. Ligand-receptor analysis infers extensive potential interactions of human ECs with perivascular cells upon transplantation, enabling vessel wall stabilization. Perfused glomeruli display maturation and morphogenesis to capillary loop stage. Our findings demonstrate the beneficial effect of vascularization on not only epithelial cell types, but also the mesenchymal compartment, inducing the expansion of ´on target´ perivascular stromal cells, which in turn are required for further maturation and stabilization of the neo-vasculature. The here described vasculogenic capacity of kidney organoids will have to be deployed to achieve meaningful glomerular maturation and kidney morphogenesis in vitro.