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

Crosstalk between macrophages and adjacent cells in AKI to CKD transition

Acute kidney injury (AKI), triggered by ischemia, sepsis, toxicity, or obstruction, is marked by a rapid impairment of renal function and could lead to the initiation and advancement of chronic kidney disease (CKD). The concept of AKI to CKD transition has gained much interest. Despite a series of studies highlighting the diverse roles of renal macrophages in the immune response following AKI, the intricate mechanisms of macrophage-driven cell-cell communication in AKI to CKD transition remains incompletely understood. In this review, we introduce the dynamic phenotype change of macrophages under the different stages of kidney injury. Importantly, we present novel perspectives on the extensive interaction of renal macrophages with adjacent cells, including tubular epithelial cells, vascular endothelial cells, fibroblasts, and other immune cells via soluble factors, extracellular vesicles, and direct contact, to facilitate the transition from AKI to CKD. Additionally, we summarize the potential therapeutic strategies based on the adverse macrophage-neighboring cell crosstalk.

Gas Bubbles from Biodegradable Magnesium Implants Convey Mechanical Cues and Promote Immune Cell Stimulation

In ever-increasing numbers, patients are treated with biodegradable magnesium implants. While gas bubbles frequently arise in soft tissue overlying magnesium implants, their biological implications remain uncertain. This study investigates how bubble accumulation and evolution across various biological lengths and time scales influence adjacent tissue and cell behavior in rats. Bubbles accumulate in tissues around magnesium during initial postimplantation days, then fully resorb. Alterations in tissue and cell geometry around bubbles coincide with accumulation of cells, many with macrophage phenotypes, and increased expression of the mechanosensitive ion-channel Piezo1. Using spatially resolved transcriptomics, strong proinflammatory pathway activation is revealed near bubbles with marked expression of the proliferative macrophage marker secreted phosphoprotein 1 (Spp1). Spatial transcriptomics also reveals strong enrichment of cytoskeletal rearrangement genes, demonstrating that cells respond to mechanical cues from bubbles. Notably, both time and bubble-implant distance strongly influence the cellular response. Over time, as bubbles are located farther from the implant, regenerative processes decline, and inflammation predominates. These findings suggest that bubbles from magnesium implant degradation create an intricate local response influencing tissue healing through inflammatory and mechanical pathways. This study underscores the need for magnesium implants with controlled gas release and meticulous monitoring of bubble evolution in patients.

Spatial Omics in Clinical Research: A Comprehensive Review of Technologies and Guidelines for Applications

Spatial omics integrates molecular profiling with spatial tissue context, enabling high-resolution analysis of gene expression, protein interactions, and epigenetic modifications. This approach provides critical insights into disease mechanisms and therapeutic responses, with applications in cancer, neurology, and immunology. Spatial omics technologies, including spatial transcriptomics, proteomics, and epigenomics, facilitate the study of cellular heterogeneity, tissue organization, and cell-cell interactions within their native environments. Despite challenges in data complexity and integration, advancements in multi-omics pipelines and computational tools are enhancing data accuracy and biological interpretation. This review provides a comprehensive overview of key spatial omics technologies, their analytical methods, validation strategies, and clinical applications. By integrating spatially resolved molecular data with traditional omics, spatial omics is transforming precision medicine, biomarker discovery, and personalized therapy. Future research should focus on improving standardization, reproducibility, and multimodal data integration to fully realize the potential of spatial omics in clinical and translational research.

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.

From morphology to single-cell molecules: high-resolution 3D histology in biomedicine

High-resolution three-dimensional (3D) tissue analysis has emerged as a transformative innovation in the life sciences, providing detailed insights into the spatial organization and molecular composition of biological tissues. This review begins by tracing the historical milestones that have shaped the development of high-resolution 3D histology, highlighting key breakthroughs that have facilitated the advancement of current technologies. We then systematically categorize the various families of high-resolution 3D histology techniques, discussing their core principles, capabilities, and inherent limitations. These 3D histology techniques include microscopy imaging, tomographic approaches, single-cell and spatial omics, computational methods and 3D tissue reconstruction (e.g. 3D cultures and spheroids). Additionally, we explore a wide range of applications for single-cell 3D histology, demonstrating how single-cell and spatial technologies are being utilized in the fields such as oncology, cardiology, neuroscience, immunology, developmental biology and regenerative medicine. Despite the remarkable progress made in recent years, the field still faces significant challenges, including high barriers to entry, issues with data robustness, ambiguous best practices for experimental design, and a lack of standardization across methodologies. This review offers a thorough analysis of these challenges and presents recommendations to surmount them, with the overarching goal of nurturing ongoing innovation and broader integration of cellular 3D tissue analysis in both biology research and clinical practice.

Profiling signaling mediators for cell-cell interactions and communications with microfluidics-based single-cell analysis tools

Cell-cell interactions and communication represent the fundamental cornerstone of cells' collaborative efforts in executing diverse biological processes. A profound understanding of how cells interface through various mediators is pivotal across a spectrum of biological systems. Recent strides in microfluidic technologies have significantly bolstered the precision and prowess in capturing and manipulating cells with exceptional spatial and temporal resolution. These advanced methodologies converge with multi-signal mediator detection systems, furnishing potent, high-throughput platforms for dissecting cell-cell interactions at the single-cell level. This approach empowers researchers to delve into intricate cellular dynamics with unprecedented accuracy and efficiency. Here, we present a critical evaluation of the latest advancements in microfluidics-driven techniques for detecting signal mediators involved in cell-cell interactions and communication at the single-cell level. We underscore notable biological applications that have benefited from these technologies and identify pressing challenges that must be addressed in future endeavors leveraging microfluidic tools for single-cell interaction studies.

SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues

Deciphering the link between tissue architecture and function requires methods to identify and interpret patterns in spatial arrangement of cells. We present SMORE, an approach to detect patterns in sequential arrangements of cells and examine their associated gene expression specializations. Applied to retina, brain, and embryonic tissue maps, SMORE identifies novel spatial motifs, including one that offers a new mechanism of action for type 1b bipolar cells. Structural signatures detected by SMORE also form a basis for classifying tissues. Together, our method provides a new framework for uncovering spatial complexity in tissue organization and offers novel insights into tissue function.

T cell metabolism in kidney immune homeostasis

Kidney immune homeostasis is intricately linked to T cells. Inappropriate differentiation, activation, and effector functions of T cells lead to a spectrum of kidney disease. While executing immune functions, T cells undergo a series of metabolic rewiring to meet the rapid energy demand. The key enzymes and metabolites involved in T cell metabolism metabolically and epigenetically modulate T cells' differentiation, activation, and effector functions, thereby being capable of modulating kidney immune homeostasis. In this review, we first summarize the latest advancements in T cell immunometabolism. Second, we outline the alterations in the renal microenvironment under certain kidney disease conditions. Ultimately, we highlight the metabolic modulation of T cells within kidney immune homeostasis, which may shed light on new strategies for treating kidney disease.

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 Reveals the Temporal Architecture of the Seminiferous Epithelial Cycle and Precise Sertoli-Germ Synchronization

Spermatogenesis is characterized by the seminiferous epithelial cycle, a periodic pattern of germ cell differentiation with a wave-like progression along the length of seminiferous tubules. While key signaling and metabolic components of the cycle are known, the transcriptional changes across the cycle and the correlations between germ cell and somatic lineages remain undefined. Here, we use spatial transcriptomics via RNA SeqFISH+ to profile 2,638 genes in 216,090 cells in mouse testis and identify a periodic transcriptional pattern across tubules that precisely recapitulates the seminiferous epithelial cycle, enabling us to map cells to specific timepoints along the developmental cycle. Analyzing gene expression in somatic cells reveals that Sertoli cells exhibit a cyclic transcriptional profile closely synchronized with germ cell development while other somatic cells do not demonstrate such synchronization. Remarkably, in mouse testis with drug-induced ablation of germ cells, Sertoli cells independently maintain their cyclic transcriptional dynamics. By analyzing expression data, we identify an innate retinoic acid cycle, a network of transcription factors with cyclic activation, and signaling from germ cells that could interact with this network. Together, this work leverages spatial geometries for mapping the temporal dynamics and reveals a regulatory mechanism in spermatogenesis where Sertoli cells oscillate and coordinate with the cyclical progression of germ cell development.

Pathology of Chronic Kidney Disease and Spatial Metabolomics

Chronic kidney disease (CKD) has diverse etiologies but exhibits common features in presentation and progression. These include glomerular sclerosis, tubular atrophy, and interstitial fibrosis, often with inflammation and vascular rarefaction. Although these pathologic features have been described in CKD for decades, the molecular drivers of the disease process remain poorly understood. In the era of multiomics and spatial biology, the spatial metabolomics platform could well be a critical technology to guide characterization of the shared cellular programs, capturing the important protective and destructive pathways that ultimately culminate in each of these pathologic features. In this review, we discuss the specific approaches and challenges to developing spatial metabolomics signatures for pathologic features in CKD.