Spatially resolved transcriptomics and the kidney: Many opportunities

Spatially resolved transcriptomic profiling for glomerular and tubulointerstitial gene expression in C3 glomerulopathy

Background

Complement 3 (C3) glomerulopathy (C3G) is a rare but clinically significant glomerulopathy. However, little is known about its transcriptomic profile. We investigated the substructure-specific gene expression profile of C3G using the recently introduced spatial transcriptomics technology.

Methods

We performed spatial transcriptomic profiling using GeoMx Digital Spatial Profiler with formalin-fixed paraffin-embedded kidney biopsy specimens of three C3G cases and seven controls from donor kidney biopsy. Additionally, 41 samples of other glomerulonephritis, including focal segmental glomerulosclerosis, membranous nephropathy and minimal change disease, were included as disease controls. We identified differentially expressed genes (DEGs) specific to C3G, followed by in vitro validation analysis of consistently upregulated DEGs in human glomerular endothelial cells through a co-culture with complement-stimulated macrophages.

Results

We found 229 and 157 highly expressed DEGs in the glomeruli of C3G compared with those of donor and disease controls, respectively, including POSTN, COL1A2 and IFI44L. Protease binding, structural molecule activity and extracellular matrix (ECM) structural constituent were among the top enriched Gene Ontology terms in the glomeruli of C3G. Specifically, genes related to the ECM and interferon activity were the most upregulated, with network analysis suggesting possible interactions between complement C3 and the ECM through CD11c. The in vitro experimental validation using iC3b-stimulated CD11c+ macrophages supported these findings, inducing elevated expression of fibrosis markers and ECM components in glomerular endothelial cells.

Conclusions

Significant disease-specific transcriptomic alterations in C3G, including upregulation of genes related to the ECM, provide potential insights into the pathophysiology.

Novel insights into kidney disease: the scRNA-seq and spatial transcriptomics approaches: a literature review

Over the past decade, single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have revolutionized biomedical research, particularly in understanding cellular heterogeneity in kidney diseases. This review summarizes the application and development of scRNA-seq combined with ST in the context of kidney disease. By dissecting cellular heterogeneity at an unprecedented resolution, these advanced techniques have identified novel cell subpopulations and their dynamic interactions within the renal microenvironment. The integration of scRNA-seq with ST has been instrumental in elucidating the cellular and molecular mechanisms underlying kidney development, homeostasis, and disease progression. This approach has not only identified key cellular players in renal pathophysiology but also revealed the spatial organization of cells within the kidney, which is crucial for understanding their functional specialization. This paper highlights the transformative impact of these techniques on renal research that have paved the way for targeted therapeutic interventions and personalized medicine in the management of kidney disease.

Histopathologic Analysis of Human Kidney Spatial Transcriptomics Data: Toward Precision Pathology

The application of spatial transcriptomics (ST) technologies is booming and has already yielded important insights across many different tissues and disease models. In nephrology, ST technologies have helped to decipher the cellular and molecular mechanisms in kidney diseases and have allowed the recent creation of spatially anchored human kidney atlases of healthy and diseased kidney tissues. During ST data analysis, the computationally annotated clusters are often superimposed on a histologic image without their initial identification being based on the morphologic and/or spatial analyses of the tissues and lesions. Herein, histopathologic ST data from a human kidney sample were modeled to correspond as closely as possible to the kidney biopsy sample in a health care or research context. This study shows the feasibility of a morphology-based approach to interpreting ST data, helping to improve our understanding of the lesion phenomena at work in chronic kidney disease at both the cellular and the molecular level. Finally, the newly identified pathology-based clusters could be accurately projected onto other slides from nephrectomy or needle biopsy samples. Thus, they serve as a reference for analyzing other kidney tissues, paving the way for the future of molecular microscopy and precision pathology.

Spatial Transcriptomics: Integrating Morphology and Molecular Mechanisms of Kidney Diseases

The recent arrival of high-resolution spatial transcriptomics (ST) technologies is generating a veritable revolution in life sciences, enabling biomolecules to be measured in their native spatial context. By integrating morphology and molecular biology, ST technologies offer the potential of improving the understanding of tissue biology and disease and may also provide meaningful clinical insights. This review describes the main ST technologies currently available and the computational analysis for data interpretation and visualization, and illustrate their scientific and potential medical interest in the context of kidney disease. Finally, we discuss the perspectives and challenges of these booming new technologies.

Single-Cell Analysis Provides New Insights into the Roles of Tertiary Lymphoid Structures and Immune Cell Infiltration in Kidney Injury and Chronic Kidney Disease

Chronic kidney disease (CKD) is a global health concern with high morbidity and mortality. Acute kidney injury (AKI) is a pivotal risk factor for the progression of CKD, and the rate of AKI-to-CKD progression increases with aging. Intrarenal inflammation is a fundamental mechanism underlying AKI-to-CKD progression. Tertiary lymphoid structures (TLSs), ectopic lymphoid aggregates formed in nonlymphoid organs, develop in aged injured kidneys, but not in young kidneys, with prolonged inflammation and maladaptive repair, which potentially exacerbates AKI-to-CKD progression in aged individuals. Dysregulated immune responses are involved in the pathogenesis of various kidney diseases, such as IgA nephropathy, lupus nephritis, and diabetic kidney diseases, thereby deteriorating kidney function. TLSs also develop in several kidney diseases, including transplanted kidneys and renal cell carcinoma. However, the precise immunologic mechanisms driving AKI-to-CKD progression and development of these kidney diseases remain unclear, which hinders the development of novel therapeutic approaches. This review aims to describe recent findings from single-cell analysis of cellular heterogeneity and complex interactions among immune and renal parenchymal cells, which potentially contribute to the pathogenesis of AKI-to-CKD progression and other kidney diseases, highlighting the mechanisms of formation and pathogenic roles of TLSs in aged injured kidneys.

New approaches to acute kidney injury

Acute kidney injury (AKI) is a common and serious clinical syndrome that involves complex interplay between different cellular, molecular, metabolic and immunologic mechanisms. Elucidating these pathophysiologic mechanisms is crucial to identify novel biomarkers and therapies. Recent innovative methodologies and the advancement of existing technologies has accelerated our understanding of AKI and led to unexpected new therapeutic candidates. The aim of this review is to introduce and update the reader about recent developments applying novel technologies in omics, imaging, nanomedicine and artificial intelligence to AKI research, plus to provide examples where this can be translated to improve patient care.

Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease

Kidney injury disrupts the intricate renal architecture and triggers limited regeneration, together with injury-invoked inflammation and fibrosis. Deciphering the molecular pathways and cellular interactions driving these processes is challenging due to the complex tissue structure. Here, we apply single cell spatial transcriptomics to examine ischemia-reperfusion injury in the mouse kidney. Spatial transcriptomics reveals injury-specific and spatially-dependent gene expression patterns in distinct cellular microenvironments within the kidney and predicts Clcf1-Crfl1 in a molecular interplay between persistently injured proximal tubule cells and their neighboring fibroblasts. Immune cell types play a critical role in organ repair. Spatial analysis identifies cellular microenvironments resembling early tertiary lymphoid structures and associated molecular pathways. Collectively, this study supports a focus on molecular interactions in cellular microenvironments to enhance understanding of injury, repair and disease.

Multi-Omics Reveals the Effects of Spirulina platensis Powder Replacement of Fish Meal on Intestinal Metabolism and Stress in Zig-Zag Eel (Mastacembelus armatus)

The booming aquaculture industry has created a strong demand for fishmeal and increased environmental pressures. Spirulina, as a potential alternative to fishmeal, has been shown to have growth-promoting and animal health-enhancing properties. In this study, 600 large spiny loaches, divided into five experimental groups, F0, F1, F2, F3, and F4, were reared for 10 weeks using Spirulina platensis powder (SPP) as a substitute for 0%, 5%, 10%, 15%, and 20% of fishmeal, respectively. The results of intestinal physiological indexes showed that superoxide dismutase was lower than F0 in all treatment groups, and the activity of F3 was significantly lower than F0 (p < 0.05). The activity of malondialdehyde was significantly higher than that of F0 in all groups except F3 (p < 0.05). The addition of SPP also led to a decrease in the activity of acid phosphatase in the intestine, which was significantly lower in all treatment groups compared to the F0 group (p < 0.05). The results of serum physiology showed that the activity of superoxide dismutase in serum gradually increased with the increase in the percentage of SPP addition, and the F3 group produced a significant difference from the F0 group (p < 0.05). The transcriptomics results showed that DEGs in the low percentage substitution group (<15%) were mostly enriched in metabolism-related pathways, such as bile secretion; DEGs in the high percentage substitution group (>15%) were mostly enriched in inflammation-related pathways, such as complement p and coagulation cascades. Metabolomics confirmed that nicotinate and nicotinamide metabolism and glycerophospholipid metabolism were the two pathways that were significantly enriched in the treatment groups of fishmeal replacement by SPP. The present study demonstrated that a low percentage (<15%) of fishmeal replacement by SPP in feed mobilized MA digestive metabolism, whereas a high percentage (>15%) of replacement induced intestinal stress. Considering the health and farm efficiency aspects, the proportion of SPP in feed formulation for MA should be less than 15%.

High resolution spatial profiling of kidney injury and repair using RNA hybridization-based in situ sequencing

Emerging spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ at cellular resolution. We apply direct RNA hybridization-based in situ sequencing (dRNA HybISS, Cartana part of 10xGenomics) to compare male and female healthy mouse kidneys and the male kidney injury and repair timecourse. A pre-selected panel of 200 genes is used to identify cell state dynamics patterns during injury and repair. We develop a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting dataset allows us to resolve 13 kidney cell types within distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. At late timepoints after injury, C3+ leukocytes are enriched near pro-inflammatory, failed-repair proximal tubule cells. Integration of snRNA-seq dataset from the same injury and repair samples also allows us to impute the spatial localization of genes not directly measured by dRNA HybISS.

Glomerular spatial transcriptomics of IgA nephropathy according to the presence of mesangial proliferation

Mesangial proliferation is a diagnostic feature and a prognostic predictor of immunoglobulin A nephropathy (IgAN). We aimed to investigate the gene expression profiles of IgAN glomerulus according to the presence of mesangial proliferation. We performed spatial-specific transcriptomic profiling on kidney biopsy tissues using the GeoMx Digital Spatial Profiler. Twelve cases with three glomeruli for each case were profiled using direct pathologic classification (4 M1-IgAN, 4 M0-IgAN, and 4 donor controls). The results of enriched glom-specific genes demonstrated that M1-IgAN could be distinguished from controls (77 upregulated and 55 downregulated DEGs), while some DEGs were identified between M1-IgAN and M0-IgAN cases (24 upregulated and 8 downregulated DEGs) or between M0 and controls (1 upregulated and 16 downregulated DEGs). TCF21, an early podocyte damage marker, was the only differentially expressed gene (DEG) consistently upregulated in both M1-IgAN and M0-IgAN patients, whereas ATF3, EGR1, DUSP1, FOS, JUNB, KLF2, NR4A1, RHOB, and ZFP36 were consistently downregulated in IgAN cases. Glomeruli from M1-IgAN cases were significantly enriched for cell surface/adhesion molecules and gene expressions associated with vascular development or the extracellular matrix. Spatial transcriptomic analysis may contribute to dissecting structure-specific pathophysiology and molecular changes in IgAN.

Kidney and urine cell transcriptomics in IgA nephropathy and lupus nephritis: a narrative review

This narrative review sheds light on the use of transcriptomics in the analysis of kidney biopsies and urinary cell samples from patients with immunoglobulin A nephropathy or lupus nephritis. The conventional methods of examining kidney biopsy through light microscopy, immunofluorescence and electron microscopy provide valuable clinical information for diagnosis and prognosis but have some limitations that transcriptomics can address. Some recent studies have reported that kidney transcriptomics has uncovered new molecular biomarkers implicated in the inflammatory process induced by the deposition of circulating immune complexes in the investigated kidney diseases. In addition, transcriptomics applied to urinary cells mirrors the inflammatory process that occurs in the kidney. This means that we can study urinary cell transcriptomics in clinical practice to diagnose the stage of the inflammatory process. Furthermore, the transcriptomics of urinary cells can be used to make therapy decisions during patient follow-up to avoid the stress of a second kidney biopsy. The studies analyzed in this review have a significant limitation. Biomarkers have been identified in small cohorts of patients but none of them has been validated in independent external cohorts. Further prospective studies in large cohorts of patients are necessary for accurate and complete validation. Only after that can these biomarkers be widely used in clinical practice.

Should we enlarge the indication for kidney biopsy in patients with diabetes? The pro part

Diabetic nephropathy (DN) and non-diabetic renal diseases (NDRD) represent intricate challenges in diagnosis and treatment within the context of the global diabetes epidemic. As the prevalence of diabetes continues to escalate, effective management of renal complications becomes paramount. Recent advancements in comprehending the multifaceted nature of renal damage, fueled by insights from histopathological investigations, offer unprecedented prospects for refining diagnostic strategies and customizing therapeutic interventions. Renal biopsies have emerged as indispensable tools for unraveling the diverse phenotypes of renal damage in diabetes. The pioneering study by Mazzucco identified three classes of renal damage in type 2 diabetes patients: classical diabetic glomerulosclerosis (DN), vascular and ischemic glomerular changes (NDRD), and other glomerulonephritides in the presence (DN + NDRD, mixed forms) or absence of DN (NDRD). The prevalence of these classes varies widely in published studies, influenced by factors such as ethnicity, geography and selection criteria for renal biopsy. Moreover, the international Renal Pathology Society consensus classification system has stratified the classical diabetic nephropathy into progressive categories of renal impairment, a breakthrough that aids in prognostication. Histopathological scrutiny, particularly the intricate correlation between glomerular and tubulointerstitial lesions, contributes profoundly to enhancing our grasp of the phenotype's heterogeneity. This amplified comprehension holds the potential to steer personalized treatment strategies. Cutting-edge interventions, encompassing sodium-glucose cotransporter 2 inhibitors, mineralocorticoid receptor antagonists and anti-endothelin receptor agents, are broadening the arsenal against renal injury in diabetes. When combined with the profound insights garnered from histopathological, omics, imaging and clinical data, these therapeutic avenues promise a transformative shift towards precision-driven care paradigms. Collaborative efforts uniting researchers, clinicians and patients are indispensable for propelling our knowledge of diabetic renal damage and ameliorating patient outcomes. The fusion of histopathological, omics and imaging findings into clinical decision-making harbors the potential to customize interventions and optimize care for individuals grappling with diabetes-associated renal complications. Furthermore, groundbreaking initiatives like the iBeat Study within the BEAt-DKD (Biomarker Enterprise to Attack Diabetic Kidney Disease) project (https://www.beat-dkd.eu/), elucidating distinct phenotypes of renal damage within diabetes, underscore the imperative necessity of integrating histopathological data into the broader framework of diabetic renal management.

Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease

Kidney injury disrupts the intricate renal architecture and triggers limited regeneration, and injury-invoked inflammation and fibrosis. Deciphering molecular pathways and cellular interactions driving these processes is challenging due to the complex renal architecture. Here, we applied single cell spatial transcriptomics to examine ischemia-reperfusion injury in the mouse kidney. Spatial transcriptomics revealed injury-specific and spatially-dependent gene expression patterns in distinct cellular microenvironments within the kidney and predicted Clcf1-Crfl1 in a molecular interplay between persistently injured proximal tubule cells and neighboring fibroblasts. Immune cell types play a critical role in organ repair. Spatial analysis revealed cellular microenvironments resembling early tertiary lymphoid structures and identified associated molecular pathways. Collectively, this study supports a focus on molecular interactions in cellular microenvironments to enhance understanding of injury, repair and disease.

Long-term viable chimeric nephrons generated from progenitor cells are a reliable model in cisplatin-induced toxicity

Kidney organoids have shown promise as evaluation tools, but their in vitro maturity remains limited. Transplantation into adult mice has aided in maturation; however, their lack of urinary tract connection limits long-term viability. Thus, long-term viable generated nephrons have not been demonstrated. In this study, we present an approachable method in which mouse and rat renal progenitor cells are injected into the developing kidneys of neonatal mice, resulting in the generation of chimeric nephrons integrated with the host urinary tracts. These chimeric nephrons exhibit similar maturation to the host nephrons, long-term viability with excretion and reabsorption functions, and cisplatin-induced renal injury in both acute and chronic phases, as confirmed by single-cell RNA-sequencing. Additionally, induced human nephron progenitor cells differentiate into nephrons within the neonatal kidneys. Collectively, neonatal injection represents a promising approach for in vivo nephron generation, with potential applications in kidney regeneration, drug screening, and pathological analysis.

Metabolic reprogramming heterogeneity in chronic kidney disease

Fibrosis driven by excessive accumulation of extracellular matrix (ECM) is the hallmark of chronic kidney disease (CKD). Myofibroblasts, which are the cells responsible for ECM production, are activated by cross talk with injured proximal tubule and immune cells. Emerging evidence suggests that alterations in metabolism are not only a feature of but also play an influential role in the pathogenesis of renal fibrosis. The application of omics technologies to cell-tracing animal models and follow-up functional data suggest that cell-type-specific metabolic shifts have particular roles in the fibrogenic response. In this review, we cover the main metabolic reprogramming outcomes in renal fibrosis and provide a future perspective on the field of renal fibrometabolism.

Immune cell heterogeneity in a mouse model of diabetic kidney disease

Typical kidney single-cell RNA-sequencing contains relatively few leukocytes, complicating efforts to understand how immune cells impact kidney disease progression. In this issue, Fu et al. use a flow sorting strategy to generate a very large immune cell single-cell RNA-sequencing atlas in a mouse model of diabetic kidney disease. These findings highlight the importance of leukocyte cell subtypes in diabetic kidney disease.

Where Are They Now: Spatial and Molecular Diversity of Tissue-Resident Macrophages in the Kidney

Kidney resident macrophages (KRMs) are involved in homeostasis, phagocytosis, defense against infectious agents, response to insults, inflammation, and tissue repair. They also play critical roles in the pathogenesis and recovery from many kidney diseases such as acute kidney injury. KRMs historically have been studied as one homogenous population, but the wide-ranging roles and phenotypes observed suggest that there is greater heterogeneity than previously understood. Advancements in RNA sequencing technologies (single-cell RNA sequencing and spatial transcriptomics) have identified specific subsets of KRMs that are molecularly, functionally, and spatially distinct with dynamic changes after kidney injury. Multiple studies have identified unique markers that represent these subpopulations, permitting further characterization of the function and roles they play in the kidney. Understanding the diversity of KRM subpopulations will be key in the development of novel therapies used in treating kidney diseases and promoting kidney health.