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Davis SN, Grindel SH, Viola JM, Liu GY, Liu J, Qian G, Porter CM, Hughes AJ. Nephron progenitors rhythmically alternate between renewal and differentiation phases that synchronize with kidney branching morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568157. [PMID: 38045273 PMCID: PMC10690271 DOI: 10.1101/2023.11.21.568157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The mammalian kidney achieves massive parallelization of function by exponentially duplicating nephron-forming niches during development. Each niche caps a tip of the ureteric bud epithelium (the future urinary collecting duct tree) as it undergoes branching morphogenesis, while nephron progenitors within niches balance self-renewal and differentiation to early nephron cells. Nephron formation rate approximately matches branching rate over a large fraction of mouse gestation, yet the nature of this apparent pace-maker is unknown. Here we correlate spatial transcriptomics data with branching 'life-cycle' to discover rhythmically alternating signatures of nephron progenitor differentiation and renewal across Wnt, Hippo-Yap, retinoic acid (RA), and other pathways. We then find in human stem-cell derived nephron progenitor organoids that Wnt/β-catenin-induced differentiation is converted to a renewal signal when it temporally overlaps with YAP activation. Similar experiments using RA activation indicate a role in setting nephron progenitor exit from the naive state, the spatial extent of differentiation, and nephron segment bias. Together the data suggest that nephron progenitor interpretation of consistent Wnt/β-catenin differentiation signaling in the niche may be modified by rhythmic activity in ancillary pathways to set the pace of nephron formation. This would synchronize nephron formation with ureteric bud branching, which creates new sites for nephron condensation. Our data bring temporal resolution to the renewal vs. differentiation balance in the nephrogenic niche and inform new strategies to achieve self-sustaining nephron formation in synthetic human kidney tissues.
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Affiliation(s)
- Sachin N Davis
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Samuel H Grindel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - John M Viola
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Grace Y Liu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Jiageng Liu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Grace Qian
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Catherine M Porter
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Alex J Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, 19104, PA, USA
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Li Z, Chen Y, Zhang B, Xie L, Shi B. Global trends and hotspots in Cyclin-dependent Kinase Subunit 2 research from 1999 to 2022: A bibliometric and visualized analysis. Medicine (Baltimore) 2023; 102:e36319. [PMID: 38050288 PMCID: PMC10695487 DOI: 10.1097/md.0000000000036319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/18/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Cyclin-dependent Kinase Subunit 2 is a protein closely related to the regulation of the cell cycle. In recent years, there has been an increasing number of research articles on this topic. However, there is a lack of comprehensive synthesis and evaluation in the field of CKS2 research. This study aims to summarize and visualize the literature distribution, research hotspots, and development trends of CKS2 based on bibliometric methods. METHODS Publications from 1999 to 2022 were extracted from the Web of Science. Citespace was used to analyze the relevant information of each article. RESULTS A total of 138 publications focused on CKS2 showed a positive growth trend from 1999 to 2022 and were published by 27 countries. The most prolific countries are China and the USA. The most prolific institution is Scripps Research Institute. The most prolific author is Steven I. Reed from Scripps Research Institute. The most cited article is published by Todd R Golub. The most cited author is Hanna-Stina Martinsson-Ahlzen. The journal with the most published articles is International Journal of Oncology. The high frequency keywords suggest that expression and function of CKS2 in cancer are dominated topics. The clusters and burst words suggest that expression and function of CKS2 still active in the future. CONCLUSION SUBSECTIONS The results of this bibliometric analysis provide information on the state and trends in CKS2 from 1999 to 2022. It is helpful for scholars to pinpoint hot issues and discover new areas of study.
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Affiliation(s)
- Ziteng Li
- School of Acupuncture-Tuina, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yuanzhen Chen
- Neck-Shoulder and Lumbocrural Pain Hospital of Shandong First Medical University, Jinan, China
| | - Bo Zhang
- Neck-Shoulder and Lumbocrural Pain Hospital of Shandong First Medical University, Jinan, China
| | - Liangyu Xie
- Neck-Shoulder and Lumbocrural Pain Hospital of Shandong First Medical University, Jinan, China
| | - Bin Shi
- Neck-Shoulder and Lumbocrural Pain Hospital of Shandong First Medical University, Jinan, China
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Abstract
Vascular endothelial cells form the inner layer of blood vessels where they have a key role in the development and maintenance of the functional circulatory system and provide paracrine support to surrounding non-vascular cells. Technical advances in the past 5 years in single-cell genomics and in in vivo genetic labelling have facilitated greater insights into endothelial cell development, plasticity and heterogeneity. These advances have also contributed to a new understanding of the timing of endothelial cell subtype differentiation and its relationship to the cell cycle. Identification of novel tissue-specific gene expression patterns in endothelial cells has led to the discovery of crucial signalling pathways and new interactions with other cell types that have key roles in both tissue maintenance and disease pathology. In this Review, we describe the latest findings in vascular endothelial cell development and diversity, which are often supported by large-scale, single-cell studies, and discuss the implications of these findings for vascular medicine. In addition, we highlight how techniques such as single-cell multimodal omics, which have become increasingly sophisticated over the past 2 years, are being utilized to study normal vascular physiology as well as functional perturbations in disease.
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Affiliation(s)
- Emily Trimm
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Kristy Red-Horse
- Department of Biology, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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Clugston A, Bodnar A, Cerqueira DM, Phua YL, Lawler A, Boggs K, Pfenning A, Ho J, Kostka D. Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development. Genomics 2022; 114:278-291. [PMID: 34942352 PMCID: PMC8792369 DOI: 10.1016/j.ygeno.2021.12.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 01/03/2023]
Abstract
Mammalian nephrons originate from a population of nephron progenitor cells, and changes in these cells' transcriptomes contribute to the cessation of nephrogenesis, an important determinant of nephron number. To characterize microRNA (miRNA) expression and identify putative cis-regulatory regions, we collected nephron progenitor cells from mouse kidneys at embryonic day 14.5 and postnatal day zero and assayed small RNA expression and transposase-accessible chromatin. We detect expression of 1104 miRNA (114 with expression changes), and 46,374 chromatin accessible regions (2103 with changes in accessibility). Genome-wide, our data highlight processes like cellular differentiation, cell migration, extracellular matrix interactions, and developmental signaling pathways. Furthermore, they identify new candidate cis-regulatory elements for Eya1 and Pax8, both genes with a role in nephron progenitor cell differentiation. Finally, we associate expression-changing miRNAs, including let-7-5p, miR-125b-5p, miR-181a-2-3p, and miR-9-3p, with candidate cis-regulatory elements and target genes. These analyses highlight new putative cis-regulatory loci for miRNA in nephron progenitors.
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Affiliation(s)
- Andrew Clugston
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| | - Andrew Bodnar
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| | - Débora Malta Cerqueira
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| | - Yu Leng Phua
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Alyssa Lawler
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA,Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kristy Boggs
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Andreas Pfenning
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jacqueline Ho
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA,Co-Corresponding authors:Dr. Dennis Kostka, Rangos Research Center 8117, Department of Developmental Biology, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-9905, ; Dr. Jacqueline Ho, Rangos Research Center 5127, Department of Pediatrics, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-5303,
| | - Dennis Kostka
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Department of Computational & Systems Biology and Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Co-Corresponding authors:Dr. Dennis Kostka, Rangos Research Center 8117, Department of Developmental Biology, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-9905, ; Dr. Jacqueline Ho, Rangos Research Center 5127, Department of Pediatrics, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-5303,
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