Biology subjects

Achieng, M.

Publications and source records attributed to Achieng, M..

4 recordsLinked to original sources

bioRxiv2024

Defining and Controlling Axial Nephron Patterning in Human Kidney Organoids with Synthetic Wnt-Secreting Organizers

Current human pluripotent stem cell-derived kidney organoids contain nephron-like structures that lack organotypic patterning. It is thought that during human development, nephrons form their proximal-distal axial polarity in response to collecting duct-derived signals that are absent in kidney organoids. To delineate how nephron polarities establish, we profiled human kidney development by spatial transcriptomic approaches. Our analyses describe a new axial polarity in the nephron and demonstrate that the nephron proximal-distal polarity develops adjacent to a transcriptional boundary in the collecting duct where non-canonical WNT11 is downregulated and canonical WNT9B ligand is upregulated. The nephron region closest to this boundary in turn activates a series of canonical WNT target genes inferring positional nephron identities. To establish whether a canonical WNT source can improve organoid patterning to an in vivo-like state, we bioengineered self-organizing WNT-secreting synthetic organizers. Organizer-coupled kidney organoids respond to WNT ligands by forming expression gradients and developing distal cell identities. Tuning the WNT dose produced nephrons with continuous patterning along the proximal-distal axis. Strikingly, polarized iPSC-derived nephrons directed their distal tubules towards the WNT-source, indicating axial patterning and morphogenetic programs are tuned by WNTs from the synthetic organizers. Our data present a strategy to control organ patterning, build an artificial kidney, and highlights the power of synthetic organizer systems for advancing organoid models.

synthetic biology↗

bioRxiv2024

Stepwise developmental mimicry generates proximal-biased kidney organoids

The kidney maintains body fluid homeostasis by reabsorbing essential compounds and excreting waste. Proximal tubule cells, crucial for renal reabsorption of a range of sugars, ions, and amino acids, are highly susceptible to damage, leading to pathologies necessitating dialysis and kidney transplants. While human pluripotent stem cell-derived kidney organoids are used for modeling renal development, disease, and injury, the formation of proximal nephron cells in these 3D structures is incomplete. Here, we describe how to drive the development of proximal tubule precursors in kidney organoids by following a blueprint of in vivo human nephrogenesis. Transient manipulation of the PI3K signaling pathway activates Notch signaling in the early nephron and drives nephrons toward a proximal precursor state. These "proximal-biased" (PB) organoid nephrons proceed to generate proximal nephron precursor cells. Single-cell transcriptional analyses across the organoid nephron differentiation, comparing control and PB types, confirm the requirement of transient Notch signaling for proximal development. Indicative of functional maturity, PB organoids demonstrate dextran and albumin uptake, akin to in vivo proximal tubules. Moreover, PB organoids are highly sensitive to nephrotoxic agents, display an injury response, and drive expression of HAVCR1/KIM1, an early proximal-specific marker of kidney injury. Injured PB organoids show evidence of collapsed tubules, DNA damage, and upregulate the injury-response marker SOX9. The PB organoid model therefore has functional relevance and potential for modeling mechanisms underpinning nephron injury. These advances improve the use of iPSC-derived kidney organoids as tools to understand developmental nephrology, model disease, test novel therapeutics, and for understanding human renal physiology.

developmental biology↗

bioRxiv2023

Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development

Mammalian kidneys maintain fluid homeostasis through the cellular activity of nephrons and the conjoined collecting system. Each epithelial network originates from distinct progenitor cell populations that reciprocally interact during development. To extend our understanding of human and mouse kidney development, we profiled chromatin organization (ATAC-seq) and gene expression (RNA-seq) in developing human and mouse kidneys. Data were analyzed at a species level and then integrated into a common, cross-species multimodal data set. Comparative analysis of cell types and developmental trajectories identified conserved and divergent features of chromatin organization and linked gene activity, revealing species- and cell-type specific regulatory programs. Identification of human-specific enhancer regions linked through GWAS studies to kidney disease highlights the potential of developmental modeling to provide clinical insight.

developmental biology↗

bioRxiv2022

A comparative study of cellular diversity between the Xenopus pronephric and mouse metanephric nephron

The kidney is an essential organ that ensures bodily fluid homeostasis and removes soluble waste products from the organism. The functional units within the kidneys are epithelial tubules called nephrons. These tubules take in filtrate from the blood or coelom and selectively reabsorb nutrients through evolutionarily conserved nephron segments, leaving waste product to be eliminated in the urine. Genes coding for functional transporters are segmentally expressed, enabling nephrons to function as selective filters. The developmental patterning program that generates these segments is of great interest. The Xenopus embryonic kidney, the pronephros, has served as a valuable model to identify genes involved in nephron formation and patterning. Prior work has defined the gene expression profiles of Xenopus epithelial nephron segments via in situ hybridization strategies, but our understanding of the cellular makeup of the Xenopus pronephric kidney remains incomplete. Here, we scrutinize the cellular composition of the Xenopus pronephric nephron through comparative analyses with previous Xenopus studies and single-cell mRNA sequencing of the adult mouse kidney, this study reconstructs the cellular makeup of the pronephric kidney and identifies conserved cells, segments, and expression profiles. The data highlight significant conservation in podocytes, proximal and distal tubule cells and divergence in cellular composition underlying the evolution of the corticomedullary axis, while emphasizing the Xenopus pronephros as a model for physiology and disease. Summary StatementAssessment of the conservation of gene expression between functional Xenopus laevis pronephric and mouse metanephric nephrons through single-cell RNA sequencing.

evolutionary biology↗