Single-cell RNA-seq with spatial transcriptomics to create an atlas of human diabetic kidney disease

Unraveling diabetic kidney disease: insights from single-cell RNA sequencing

The incidence of diabetic kidney disease (DKD) is rising annually. Diabetes leads to structural damage and dysfunction in the kidneys, clinically manifesting as progressive proteinuria and declining renal function, ultimately resulting in end-stage renal disease (ESRD). Recent findings have identified a subset of DKD known as normoalbuminuric diabetic kidney disease (NADKD), characterized by normal urine albumin levels but reduced renal function. These complex clinical presentations and underlying pathophysiology challenge traditional diagnostic and treatment approaches. Single-cell RNA sequencing (scRNA-seq), a novel experimental technique, is employed to analyze gene expression in renal tissue, blood, and urine from DKD patients, enhancing our understanding of tissue function, cellular interactions, and disease progression. This approach facilitates early screening and personalized management of DKD.

A review of deoxyribonucleic acid-based single-nucleotide polymorphisms in diabetic kidney disease among Asian populations: Challenges and future directions

Diabetic kidney disease (DKD) is a persistent disorder that occurs as a result of long-term diabetes mellitus with genetic and environmental risk factors. The identification of DKD associated single-nucleotide polymorphisms (SNPs) is pivotal for patient screening. This manuscript briefly outlines the pathophysiology and the role of genetic factors in DKD expansion. The utility of bioinformatic tools and laboratory techniques in the identification of DKD-specific SNPs along with integrated data analysis pipelines valuable to enhance the accuracy of genetic interpretation is also presented. A comparative analysis of various SNPs across diverse Asian populations in conjunction with environmental and lifestyle factors was performed. The clinical relevance of SNPs in predicting DKD progression and stratifying patient risk is highlighted, with focus on gene-specific pathways and associated functional outcomes. The advances in genetic screening, gene-specific therapies, and microbiome-based therapy can facilitate the utility of SNPs-based identification of DKD in clinical settings. A structured clinical decision-making framework is proposed to support customized treatment based on SNP profiles. However, this domain is yet to gain widespread recognition with regard to variability in the effects of SNPs across diverse demographies, challenges in clinical translation, and ethical considerations in genetic testing.

Spatial genomics: Mapping the landscape of fibrosis

Organ fibrosis causes major morbidity and mortality worldwide. Treatments for fibrosis are limited, with organ transplantation being the only cure. Here, we review how various state-of-the-art spatial genomics approaches are being deployed to interrogate fibrosis across multiple organs, providing exciting insights into fibrotic disease pathogenesis. These include the detailed topographical annotation of pathogenic cell populations and states, detection of transcriptomic perturbations in morphologically normal tissue, characterization of fibrotic and homeostatic niches and their cellular constituents, and in situ interrogation of ligand-receptor interactions within these microenvironments. Together, these powerful readouts enable detailed analysis of fibrosis evolution across time and space.

Cellular crosstalk in organotypic vasculature: mechanisms of diabetic cardiorenal complications and SGLT2i responses

BACKGROUND

Diabetic panvascular disease (DPD) is the leading clinical complication of diabetes mellitus (DM), characterized by atherosclerosis across multiple organ vessels. It is a major cause of high disability and mortality rates in DM. However, the pathological mechanisms and key mediators of DPD remain unclear.

METHODS

This study constructed a single-cell organotypic atlas of the vasculature containing 321,358 cells by integrating 14 single-cell datasets from 8 major mouse organs and tissues. A total of 63 cell types were identified, including 9 vascular cell subtypes, whereas the cell-to-cell interaction (CCI) patterns of the organotypic vasculature were systematically analyzed.

RESULTS

Endothelial cells (ECs) were identified as the major cell type involved in CCI within the vasculature, with their ligands interacting with receptors of various cell types, which contribute to multiple biological processes such as stem cell differentiation and immune regulation. Notably, the study examined the cellular communication characteristics of different EC subtypes. Additionally, the inter-organ communication between the heart and kidney-key tissues in DPD-was analyzed. The BMP signaling pathway emerged as a critical communication pathway leading to cardiorenal complications in DM, with SGLT2i having a regulatory role in BMP6 modulation.

CONCLUSIONS

The study provides, for the first time, a single-cell analysis of the CCI patterns of the organotypic vasculature and highlights the central role of ECs. Moreover, the key role of BMP6 in diabetic cardiorenal complications is elucidated. These findings offer new insights into the mechanisms underlying DPD co-morbidities and provide a novel scientific basis for clinical prevention, treatment strategies for DPD, and the understanding of the action mechanism of SGLT2i.

Integrative transcriptome analysis reveals Serpine2 promotes glomerular mesangial cell proliferation and extracellular matrix accumulation via activating ERK1/2 signalling pathway in diabetic nephropathy

BACKGROUND

Diabetic nephropathy (DN) is one of the main causes of end-stage renal disease (ESRD), but its mechanism has not been clearly studied. We utilized integrative transcriptome analysis to explore the pathogenesis of DN.

METHODS

We conducted an analysis by combining bulk dataset and single-cell transcriptome dataset. Through this approach, we identified that Serpine2 may regulate the 'collagen-containing extracellular matrix' pathway involved in DN. Subsequently, we established DN animal and cell models using db/db mice and mesangial cells (MCs) to validate the role of Serpine2 in DN. In the animal model, we detected the expression level of Serpine2 in DN using western blotting (WB) and immunofluorescence (IF) assays. To further clarify the molecular mechanism of Serpine2 in DN, we knocked down Serpine2 and observed its effects on MCs proliferation and extracellular matrix (ECM) accumulation.

RESULTS

Our single-cell analysis of DN models highlighted a pivotal role for MCs in the disease's initiation. Next, through Cytoscape analysis of differentially expressed genes (DEGs) in MCs, we identified the following 10 hub genes: Acta2, Angpt2, Ccn1, Col4a1, Col4a2, Col8a1, Kdr, Thbs1, Tpm4 and Serpine2. Subsequently, we identified that Serpine2 and Kdr were also significantly DEGs in the bulk analysis of glomeruli. Additionally, our integrated gene set enrichment analysis of bulk dataset and single-cell RNA dataset revealed that the 'collagen-containing extracellular matrix' was a key pathway in DN progression. Serpine2 was one of the crucial genes involved in regulating this pathway. Therefore, we speculated that the regulation of the 'collagen-containing extracellular matrix' pathway by Serpine2 was an important mechanism. Importantly, WB and IF staining confirmed that Serpine2 expression was upregulated in the MCs of diabetic mice. Knockdown of Serpine2 in cultured MCs alleviated high-glucose-induced excessive MCs proliferation and ECM accumulation. Finally, we found that ERK agonist Ro 67-7476 eliminated the effect of Serpine2 siRNA.

CONCLUSIONS

In summary, Serpine2 regulates MCs proliferation and ECM synthesis through activation of the ERK1/2 pathway, which is an important pathogenesis mechanism of DN. These findings offer fresh perspectives on the mechanisms of glomerulosclerosis in DN pathogenesis and may provide new targets for treating DN.

Integrated multiomic analyses: An approach to improve understanding of diabetic kidney disease

AIM

Diabetes is increasing in prevalence worldwide, with a 20% rise in prevalence predicted between 2021 and 2030, bringing an increased burden of complications, such as diabetic kidney disease (DKD). DKD is a leading cause of end-stage kidney disease, with significant impacts on patients, families and healthcare providers. DKD often goes undetected until later stages, due to asymptomatic disease, non-standard presentation or progression, and sub-optimal screening tools and/or provision. Deeper insights are needed to improve DKD diagnosis, facilitating the identification of higher-risk patients. Improved tools to stratify patients based on disease prognosis would facilitate the optimisation of resources and the individualisation of care. This review aimed to identify how multiomic approaches provide an opportunity to understand the complex underlying biology of DKD.

METHODS

This review explores how multiomic analyses of DKD are improving our understanding of DKD pathology, and aiding in the identification of novel biomarkers to detect disease earlier or predict trajectories.

RESULTS

Effective multiomic data integration allows novel interactions to be uncovered and empathises the need for harmonised studies and the incorporation of additional data types, such as co-morbidity, environmental and demographic data to understand DKD complexity. This will facilitate a better understanding of kidney health inequalities, such as social-, ethnicity- and sex-related differences in DKD risk, onset and progression.

CONCLUSION

Multiomics provides opportunities to uncover how lifetime exposures become molecularly embodied to impact kidney health. Such insights would advance DKD diagnosis and treatment, inform preventative strategies and reduce the global impact of this disease.

Cellular cross-talk drives mesenchymal transdifferentiation in diabetic kidney disease

While changes in glomerular function and structure may herald diabetic kidney disease (DKD), many studies have underscored the significance of tubule-interstitial changes in the progression of DKD. Indeed, tubule-interstitial fibrosis may be the most important determinant of progression of DKD as in many forms of chronic glomerulopathies. The mechanisms underlying the effects of tubular changes on glomerular function in DKD have intrigued many investigators, and therefore, the signaling mechanisms underlying the cross-talk between tubular cells and glomerular cells have been the focus of investigation in many recent studies. Additionally, the observations of slowing of glomerular filtration rate (GFR) decline and reduction of proteinuria by recent drugs such as SGLT-2 blockers, whose primary mechanism of action is on proximal tubules, further strengthen the concept of cross-talk between the tubular and glomerular cells. Recently, the focus of research on the pathogenesis of DKD has primarily centered around exploring the cross-talk between various signaling pathways in the diabetic kidney as well as cross-talk between tubular and glomerular endothelial cells and podocytes with special relevance to epithelial-to-mesenchymal transition (EMT) and endothelial-to-mesenchymal transition (EndoMT). The focus of this review is to provide a general description of cell-to-cell cross-talk in the diabetic kidney and to highlight these concepts with evidence in relation to the physiology and pathophysiology of DKD.

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.

The advance of single cell transcriptome to study kidney immune cells in diabetic kidney disease

Diabetic kidney disease (DKD) is a prevalent microvascular complication of diabetes mellitus and a primary cause of end-stage renal disease (ESRD). Increasing studies suggest that immune cells are involved in regulating renal inflammation, which contributes to the progression of DKD. Compared with conventional methods, single-cell sequencing technology is more developed technique that has advantages in resolving cellular heterogeneity, parallel multi-omics studies, and discovering new cell types. ScRNA-seq helps researchers to analyze specifically gene expressions, signaling pathways, intercellular communication as well as their regulations in various immune cells of kidney biopsy and urine samples. It is still challenging to investigate the function of each cell type in the pathophysiology of kidney due to its complex and heterogeneous structure and function. Here, we discuss the application of single-cell transcriptomics in the field of DKD and highlight several recent studies that explore the important role of immune cells including macrophage, T cells, B cells etc. in DKD through scRNA-seq analyses. Through combing the researches of scRNA-seq on immune cells in DKD, this review provides novel perspectives on the pathogenesis and immune therapeutic strategy for DKD.

Spatial transcriptomics in health and disease

The ability to localize hundreds of macromolecules to discrete locations, structures and cell types in a tissue is a powerful approach to understand the cellular and spatial organization of an organ. Spatially resolved transcriptomic technologies enable mapping of transcripts at single-cell or near single-cell resolution in a multiplex manner. The rapid development of spatial transcriptomic technologies has accelerated the pace of discovery in several fields, including nephrology. Its application to preclinical models and human samples has provided spatial information about new cell types discovered by single-cell sequencing and new insights into the cell-cell interactions within neighbourhoods, and has improved our understanding of the changes that occur in response to injury. Integration of spatial transcriptomic technologies with other omics methods, such as proteomics and spatial epigenetics, will further facilitate the generation of comprehensive molecular atlases, and provide insights into the dynamic relationships of molecular components in homeostasis and disease. This Review provides an overview of current and emerging spatial transcriptomic methods, their applications and remaining challenges for the field.

The role of intercellular communication in diabetic nephropathy

Diabetic nephropathy, a common and severe complication of diabetes, is the leading cause of end-stage renal disease, ultimately leading to renal failure and significantly affecting the prognosis and lives of diabetics worldwide. However, the complexity of its developmental mechanisms makes treating diabetic nephropathy a challenging task, necessitating the search for improved therapeutic targets. Intercellular communication underlies the direct and indirect influence and interaction among various cells within a tissue. Recently, studies have shown that beyond traditional communication methods, tunnel nanotubes, exosomes, filopodial tip vesicles, and the fibrogenic niche can influence pathophysiological changes in diabetic nephropathy by disrupting intercellular communication. Therefore, this paper aims to review the varied roles of intercellular communication in diabetic nephropathy, focusing on recent advances in this area.

New tools to study renal fibrogenesis

PURPOSE OF REVIEW

Kidney fibrosis is a key pathological aspect and outcome of chronic kidney disease (CKD). The advent of multiomic analyses using human kidney tissue, enabled by technological advances, marks a new chapter of discovery in fibrosis research of the kidney. This review highlights the rapid advancements of single-cell and spatial multiomic techniques that offer new avenues for exploring research questions related to human kidney fibrosis development.

RECENT FINDINGS

We recently focused on understanding the origin and transition of myofibroblasts in kidney fibrosis using single-cell RNA sequencing (scRNA-seq) [1] . We analysed cells from healthy human kidneys and compared them to patient samples with CKD. We identified PDGFRα+/PDGFRβ+ mesenchymal cells as the primary cellular source of extracellular matrix (ECM) in human kidney fibrosis. We found several commonly shared cell states of fibroblasts and myofibroblasts and provided insights into molecular regulators. Novel single-cell and spatial multiomics tools are now available to shed light on cell lineages, the plasticity of kidney cells and cell-cell communication in fibrosis.

SUMMARY

As further single-cell and spatial multiomic approaches are being developed, opportunities to apply these methods to human kidney tissues expand similarly. Careful design and optimisation of the multiomic experiments are needed to answer questions related to cell lineages, plasticity and cell-cell communication in kidney fibrosis.

Identification of ligand and receptor interactions in CKD and MASH through the integration of single cell and spatial transcriptomics

BACKGROUND

Chronic Kidney Disease (CKD) and Metabolic dysfunction-associated steatohepatitis (MASH) are metabolic fibroinflammatory diseases. Combining single-cell (scRNAseq) and spatial transcriptomics (ST) could give unprecedented molecular disease understanding at single-cell resolution. A more comprehensive analysis of the cell-specific ligand-receptor (L-R) interactions could provide pivotal information about signaling pathways in CKD and MASH. To achieve this, we created an integrative analysis framework in CKD and MASH from two available human cohorts.

RESULTS

The analytical framework identified L-R pairs involved in cellular crosstalk in CKD and MASH. Interactions between cell types identified using scRNAseq data were validated by checking the spatial co-presence using the ST data and the co-expression of the communicating targets. Multiple L-R protein pairs identified are known key players in CKD and MASH, while others are novel potential targets previously observed only in animal models.

CONCLUSION

Our study highlights the importance of integrating different modalities of transcriptomic data for a better understanding of the molecular mechanisms. The combination of single-cell resolution from scRNAseq data, combined with tissue slide investigations and visualization of cell-cell interactions obtained through ST, paves the way for the identification of future potential therapeutic targets and developing effective therapies.

New insights into the role of immunity and inflammation in diabetic kidney disease in the omics era

Diabetic kidney disease (DKD) is becoming the leading cause of chronic kidney disease, especially in the industrialized world. Despite mounting evidence has demonstrated that immunity and inflammation are highly involved in the pathogenesis and progression of DKD, the underlying mechanisms remain incompletely understood. Substantial molecules, signaling pathways, and cell types participate in DKD inflammation, by integrating into a complex regulatory network. Most of the studies have focused on individual components, without presenting their importance in the global or system-based processes, which largely hinders clinical translation. Besides, conventional technologies failed to monitor the different behaviors of resident renal cells and immune cells, making it difficult to understand their contributions to inflammation in DKD. Recently, the advancement of omics technologies including genomics, epigenomics, transcriptomics, proteomics, and metabolomics has revolutionized biomedical research, which allows an unbiased global analysis of changes in DNA, RNA, proteins, and metabolites in disease settings, even at single-cell and spatial resolutions. They help us to identify critical regulators of inflammation processes and provide an overview of cell heterogeneity in DKD. This review aims to summarize the application of multiple omics in the field of DKD and emphasize the latest evidence on the interplay of inflammation and DKD revealed by these technologies, which will provide new insights into the role of inflammation in the pathogenesis of DKD and lead to the development of novel therapeutic approaches and diagnostic biomarkers.

Crosstalk among podocytes, glomerular endothelial cells and mesangial cells in diabetic kidney disease: an updated review

Diabetic kidney disease (DKD) is a long-term and serious complication of diabetes that affects millions of people worldwide. It is characterized by proteinuria, glomerular damage, and renal fibrosis, leading to end-stage renal disease, and the pathogenesis is complex and involves multiple cellular and molecular mechanisms. Among three kinds of intraglomerular cells including podocytes, glomerular endothelial cells (GECs) and mesangial cells (MCs), the alterations in one cell type can produce changes in the others. The cell-to-cell crosstalk plays a crucial role in maintaining the glomerular filtration barrier (GFB) and homeostasis. In this review, we summarized the recent advances in understanding the pathological changes and interactions of these three types of cells in DKD and then focused on the signaling pathways and factors that mediate the crosstalk, such as angiopoietins, vascular endothelial growth factors, transforming growth factor-β, Krüppel-like factors, retinoic acid receptor response protein 1 and exosomes, etc. Furthermore, we also simply introduce the application of the latest technologies in studying cell interactions within glomerular cells and new promising mediators for cell crosstalk in DKD. In conclusion, this review provides a comprehensive and updated overview of the glomerular crosstalk in DKD and highlights its importance for the development of novel intervention approaches.

Spatial omics: An innovative frontier in aging research

Disentangling the impact of aging on health and disease has become critical as population aging progresses rapidly. Studying aging at the molecular level is complicated by the diverse aging profiles and dynamics. However, the examination of cellular states within aging tissues in situ is hampered by the lack of high-resolution spatial data. Emerging spatial omics technologies facilitate molecular and spatial analysis of tissues, providing direct access to precise information on various functional regions and serving as a favorable tool for unraveling the heterogeneity of aging. In this review, we summarize the recent advances in spatial omics application in multi-organ aging research, which has enhanced the understanding of aging mechanisms from multiple standpoints. We also discuss the main challenges in spatial omics research to date, the opportunities for further developing the technology, and the potential applications of spatial omics in aging and aging-related diseases.

Enhanced Levels of Glycosphingolipid GM3 Delay the Progression of Diabetic Nephropathy

We recently found that albuminuria levels in patients with minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS) inversely correlate with glycosphingolipid GM3 expression levels in glomerular podocytes. Moreover, we showed enhanced expression of GM3 via activation of the GM3 synthase gene upon administration of valproic acid (VPA) is effective in suppressing albuminuria and podocyte injury in mice with anti-nephrin antibody-induced podocytopathy. However, the therapeutic effect of GM3 on diabetic nephropathy, which is the most common underlying disease in patients undergoing dialysis and with podocyte injury, remains unclear. Here, we investigated the therapeutic effect of enhanced GM3 expression via VPA on podocyte injury using streptozotocin-induced diabetic nephropathy model mice. Administration of VPA clearly decreased levels of albuminuria and glomerular lesions and inhibited the loss of podocytes and expansion in the mesangial area. Furthermore, we found that albuminuria levels in patients with diabetic nephropathy inversely correlate with the expression of GM3 in podocytes. These results indicate that maintaining GM3 expression in podocytes by administration of VPA may be effective in treating not only podocyte injury, such as MCD and FSGS, but also the late stage of diabetic nephropathy.