1
|
Zhao H, Gong H, Zhu P, Sun C, Sun W, Zhou Y, Wu X, Qiu A, Wen X, Zhang J, Luo D, Liu Q, Li Y. Deciphering the cellular and molecular landscapes of Wnt/β-catenin signaling in mouse embryonic kidney development. Comput Struct Biotechnol J 2024; 23:3368-3378. [PMID: 39310276 PMCID: PMC11416353 DOI: 10.1016/j.csbj.2024.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/25/2024] Open
Abstract
Background The Wnt/β-catenin signaling pathway is critical in kidney development, yet its specific effects on gene expression in different embryonic kidney cell types are not fully understood. Methods Wnt/β-catenin signaling was activated in mouse E12.5 kidneys in vitro using CHIR99021, with RNA sequencing performed afterward, and the results were compared to DMSO controls (dataset GSE131240). Differential gene expression in ureteric buds and cap mesenchyme following pathway activation (datasets GSE20325 and GSE39583) was analyzed. Single-cell RNA-seq data from the Mouse Cell Atlas was used to link differentially expressed genes (DEGs) with kidney cell types. β-catenin ChIP-seq data (GSE39837) identified direct transcriptional targets. Results Activation of Wnt/β-catenin signaling led to 917 significant DEGs, including the upregulation of Notum and Apcdd1 and the downregulation of Crym and Six2. These DEGs were involved in kidney development and immune response. Single-cell analysis identified 787 DEGs across nineteen cell subtypes, with Macrophage_Apoe high cells showing the most pronounced enrichment of Wnt/β-catenin-activated genes. Gene expression profiles in ureteric buds and cap mesenchyme differed significantly upon β-catenin manipulation, with cap mesenchyme showing a unique set of DEGs. Analysis of β-catenin ChIP-seq data revealed 221 potential direct targets, including Dpp6 and Fgf12. Conclusion This study maps the complex gene expression driven by Wnt/β-catenin signaling in embryonic kidney cell types. The identified DEGs and β-catenin targets elucidate the molecular details of kidney development and the pathway's role in immune processes, providing a foundation for further research into Wnt/β-catenin signaling in kidney development and disease.
Collapse
Affiliation(s)
- Hui Zhao
- Guangzhou National Laboratory, Guangzhou International Bio Island, No. 9 Xing Dao Huan Bei Road, Guangzhou 510005, Guangdong Province, China
| | - Hui Gong
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Peide Zhu
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China
| | - Chang Sun
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Wuping Sun
- Department of Pain Medicine, Shenzhen Municipal Key Laboratory for Pain Medicine, The affiliated Nanshan People's Hospital, The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen 518060, China
| | - Yujin Zhou
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Xiaoxiao Wu
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Ailin Qiu
- Institute of Pharmacy and Pharmacology, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Xiaosha Wen
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Jinde Zhang
- Guangdong Medical University, Zhanjiang 524023, Guangdong China
| | - Dixian Luo
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Quan Liu
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Yifan Li
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| |
Collapse
|
2
|
Zhai F, Kong S, Song S, Guo Q, Ding L, Zhang J, Wang N, Kuo Y, Guan S, Yuan P, Yan L, Yan Z, Qiao J. Human embryos harbor complex mosaicism with broad presence of aneuploid cells during early development. Cell Discov 2024; 10:98. [PMID: 39313513 PMCID: PMC11420220 DOI: 10.1038/s41421-024-00719-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/23/2024] [Indexed: 09/25/2024] Open
Abstract
Pre-implantation genetic testing for aneuploidy (PGT-A) is used in approximately half of in vitro fertilization cycles. Given the limited understanding of the genetics of human embryos, the current use of PGT-A is based on biologically uncertain assumptions and unvalidated guidelines, leading to the possibility of disposing of embryos with pregnancy potential. We isolated and sequenced all single cells (1133) from in vitro cultured 20 human blastocysts. We found that all blastocysts exhibited mosaicism with mitotic-induced aneuploid cells and showed an ~25% aneuploidy rate per embryo. Moreover, 70% (14/20) of blastocysts contained 'chromosome-complementary' cells, suggesting genetic mosaicism is underestimated in routine PGT-A. Additionally, the analysis of 20,945 single cells from day 8-14 embryos (in vitro cultured) and embryonic/fetal organs showed that 97% of the analyzed embryos/organs were mosaic. Over 96% of their aneuploid cells harbored ≤ 2 chromosome errors. Our findings have revealed a high prevalence of mosaicism in human embryos.
Collapse
Affiliation(s)
- Fan Zhai
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China
| | - Siming Kong
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shi Song
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China
| | - Qianying Guo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China
| | - Ling Ding
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China
| | - Jiaqi Zhang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China
| | - Nan Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China
| | - Ying Kuo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China
| | - Shuo Guan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China
| | - Peng Yuan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China.
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China.
| | - Zhiqiang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China.
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Beijing Advanced Innovation Center for Genomics, Beijing, China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| |
Collapse
|
3
|
Sun Y, Sun J, Lin C, Zhang J, Yan H, Guan Z, Zhang C. Single-Cell Transcriptomics Applied in Plants. Cells 2024; 13:1561. [PMID: 39329745 PMCID: PMC11430455 DOI: 10.3390/cells13181561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 09/14/2024] [Accepted: 09/16/2024] [Indexed: 09/28/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a high-tech method for characterizing the expression patterns of heterogeneous cells in the same tissue and has changed our evaluation of biological systems by increasing the number of individual cells analyzed. However, the full potential of scRNA-seq, particularly in plant science, has not yet been elucidated. To explore the utilization of scRNA-seq technology in plants, we firstly conducted a comprehensive review of significant scRNA-seq findings in the past few years. Secondly, we introduced the research and applications of scRNA-seq technology to plant tissues in recent years, primarily focusing on model plants, crops, and wood. We then offered five databases that could facilitate the identification of distinct expression marker genes for various cell types. Finally, we analyzed the potential problems, challenges, and directions for applying scRNA-seq in plants, with the aim of providing a theoretical foundation for the better use of this technique in future plant research.
Collapse
Affiliation(s)
- Yanyan Sun
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jian Sun
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Chunjing Lin
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China
- Key Laboratory of Hybrid Soybean Breeding, Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Jingyong Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China
- Key Laboratory of Hybrid Soybean Breeding, Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Hao Yan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China
- Key Laboratory of Hybrid Soybean Breeding, Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Zheyun Guan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China
- Key Laboratory of Hybrid Soybean Breeding, Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Chunbao Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China
- Key Laboratory of Hybrid Soybean Breeding, Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| |
Collapse
|
4
|
Ali A, Manzoor S, Ali T, Asim M, Muhammad G, Ahmad A, Jamaludin MI, Devaraj S, Munawar N. Innovative aspects and applications of single cell technology for different diseases. Am J Cancer Res 2024; 14:4028-4048. [PMID: 39267684 PMCID: PMC11387862 DOI: 10.62347/vufu1836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/24/2024] [Indexed: 09/15/2024] Open
Abstract
Recent developments in single-cell technologies have provided valuable insights from cancer genomics to complex microbial communities. Single-cell technologies including the RNA-seq, next-generation sequencing (NGS), epigenomics, genomics, and transcriptomics can be used to uncover the single cell nature and molecular characterization of individual cells. These technologies also reveal the cellular transition states, evolutionary relationships between genes, the complex structure of single-cell populations, cell-to-cell interaction leading to biological discoveries and more reliable than traditional bulk technologies. These technologies are becoming the first choice for the early detection of inflammatory biomarkers affecting the proliferation and progression of tumor cells in the tumor microenvironment and improving the clinical efficacy of patients undergoing immunotherapy. These technologies also hold a central position in the detection of checkpoint inhibitors and thus determining the signaling pathways evoked by tumor invasion. This review addressed the emerging approaches of single cell-based technologies in cancer immunotherapies and different human diseases at cellular and molecular levels and the emerging role of sequencing technologies leading to drug discovery. Advancements in these technologies paved for discovering novel diagnostic markers for better understanding the pathological and biochemical mechanisms also for controlling the rate of different diseases.
Collapse
Affiliation(s)
- Ashiq Ali
- Department of Histology and Embryology, Shantou University Medical College Shantou 515041, Guangdong, China
| | - Saba Manzoor
- Department of Zoology, University of Sialkot Sialkot 51310, Pakistan
| | - Tayyab Ali
- Clinico-Molecular Biochemistry Laboratory, Department of Biochemistry, University of Agriculture Faisalabad 38000, Pakistan
| | - Muhammad Asim
- Clinico-Molecular Biochemistry Laboratory, Department of Biochemistry, University of Agriculture Faisalabad 38000, Pakistan
| | - Ghulam Muhammad
- Jinnah Burn and Reconstructive Surgery Centre, Jinnah Hospital, Allama Iqbal Medical College Lahore 54000, Pakistan
| | - Aftab Ahmad
- Biochemistry/Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad 38040, Pakistan
| | - Mohamad Ikhwan Jamaludin
- BioInspired Device and Tissue Engineering Research Group (BioInspira), Department of Biomedical Engineering and Health Sciences, Faculty of Electrical Engineering, Universiti Teknologi Malaysia Johor Bahru 81310, Johor, Malaysia
| | - Sutha Devaraj
- Graduate School of Medicine, Perdana University Wisma Chase Perdana, Changkat Semantan, Damansara Heights, Kuala Lumpur 50490, Malaysia
| | - Nayla Munawar
- Department of Chemistry, College of Science, United Arab Emirates University Al-Ain 15551, United Arab Emirates
| |
Collapse
|
5
|
Kim S, Koppitch K, Parvez RK, Guo J, Achieng M, Schnell J, Lindström NO, McMahon AP. Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development. Dev Cell 2024:S1534-5807(24)00450-7. [PMID: 39121855 DOI: 10.1016/j.devcel.2024.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 04/02/2024] [Accepted: 07/12/2024] [Indexed: 08/12/2024]
Abstract
The mammalian kidney maintains fluid homeostasis through diverse epithelial cell types generated from nephron and ureteric progenitor cells. To extend a developmental understanding of the kidney's epithelial networks, we compared chromatin organization (single-nuclear assay for transposase-accessible chromatin sequencing [ATAC-seq]; 112,864 nuclei) and gene expression (single-cell/nuclear RNA sequencing [RNA-seq]; 109,477 cells/nuclei) in the developing human (10.6-17.6 weeks; n = 10) and mouse (post-natal day [P]0; n = 10) kidney, supplementing analysis with published mouse datasets from earlier stages. Single-cell/nuclear datasets were analyzed at a species level, and then nephron and ureteric cellular lineages were extracted and integrated into a common, cross-species, multimodal dataset. Comparative computational analyses identified conserved and divergent features of chromatin organization and linked gene activity, identifying species-specific and cell-type-specific regulatory programs. In situ validation of human-enriched gene activity points to human-specific signaling interactions in kidney development. Further, human-specific enhancer regions were linked to kidney diseases through genome-wide association studies (GWASs), highlighting the potential for clinical insight from developmental modeling.
Collapse
Affiliation(s)
- Sunghyun Kim
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Kari Koppitch
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Riana K Parvez
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - MaryAnne Achieng
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Jack Schnell
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
6
|
Su J, Song Y, Zhu Z, Huang X, Fan J, Qiao J, Mao F. Cell-cell communication: new insights and clinical implications. Signal Transduct Target Ther 2024; 9:196. [PMID: 39107318 PMCID: PMC11382761 DOI: 10.1038/s41392-024-01888-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/09/2024] [Accepted: 06/02/2024] [Indexed: 09/11/2024] Open
Abstract
Multicellular organisms are composed of diverse cell types that must coordinate their behaviors through communication. Cell-cell communication (CCC) is essential for growth, development, differentiation, tissue and organ formation, maintenance, and physiological regulation. Cells communicate through direct contact or at a distance using ligand-receptor interactions. So cellular communication encompasses two essential processes: cell signal conduction for generation and intercellular transmission of signals, and cell signal transduction for reception and procession of signals. Deciphering intercellular communication networks is critical for understanding cell differentiation, development, and metabolism. First, we comprehensively review the historical milestones in CCC studies, followed by a detailed description of the mechanisms of signal molecule transmission and the importance of the main signaling pathways they mediate in maintaining biological functions. Then we systematically introduce a series of human diseases caused by abnormalities in cell communication and their progress in clinical applications. Finally, we summarize various methods for monitoring cell interactions, including cell imaging, proximity-based chemical labeling, mechanical force analysis, downstream analysis strategies, and single-cell technologies. These methods aim to illustrate how biological functions depend on these interactions and the complexity of their regulatory signaling pathways to regulate crucial physiological processes, including tissue homeostasis, cell development, and immune responses in diseases. In addition, this review enhances our understanding of the biological processes that occur after cell-cell binding, highlighting its application in discovering new therapeutic targets and biomarkers related to precision medicine. This collective understanding provides a foundation for developing new targeted drugs and personalized treatments.
Collapse
Affiliation(s)
- Jimeng Su
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ying Song
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
| | - Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
| | - Xinyue Huang
- Biomedical Research Institute, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jibiao Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
- Cancer Center, Peking University Third Hospital, Beijing, China.
| |
Collapse
|
7
|
Song L, Li Q, Xia L, Sahay AE, Qiu Q, Li Y, Li H, Sasaki K, Susztak K, Wu H, Wan L. Single-cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape. Nat Commun 2024; 15:5937. [PMID: 39009564 PMCID: PMC11250843 DOI: 10.1038/s41467-024-50171-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
How disruptions to normal cell differentiation link to tumorigenesis remains incompletely understood. Wilms tumor, an embryonal tumor associated with disrupted organogenesis, often harbors mutations in epigenetic regulators, but their role in kidney development remains unexplored. Here, we show at single-cell resolution that a Wilms tumor-associated mutation in the histone acetylation reader ENL disrupts kidney differentiation in mice by rewiring the gene regulatory landscape. Mutant ENL promotes nephron progenitor commitment while restricting their differentiation by dysregulating transcription factors such as Hox clusters. It also induces abnormal progenitors that lose kidney-associated chromatin identity. Furthermore, mutant ENL alters the transcriptome and chromatin accessibility of stromal progenitors, resulting in hyperactivation of Wnt signaling. The impacts of mutant ENL on both nephron and stroma lineages lead to profound kidney developmental defects and postnatal mortality in mice. Notably, a small molecule inhibiting mutant ENL's histone acetylation binding activity largely reverses these defects. This study provides insights into how mutations in epigenetic regulators disrupt kidney development and suggests a potential therapeutic approach.
Collapse
Affiliation(s)
- Lele Song
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qinglan Li
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lingbo Xia
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of the School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Arushi Eesha Sahay
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Katalin Susztak
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Liling Wan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
8
|
Zeng Y, Ma Q, Chen J, Kong X, Chen Z, Liu H, Liu L, Qian Y, Wang X, Lu S. Single-cell sequencing: Current applications in various tuberculosis specimen types. Cell Prolif 2024:e13698. [PMID: 38956399 DOI: 10.1111/cpr.13698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/21/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Tuberculosis (TB) is a chronic disease caused by Mycobacterium tuberculosis (M.tb) and responsible for millions of deaths worldwide each year. It has a complex pathogenesis that primarily affects the lungs but can also impact systemic organs. In recent years, single-cell sequencing technology has been utilized to characterize the composition and proportion of immune cell subpopulations associated with the pathogenesis of TB disease since it has a high resolution that surpasses conventional techniques. This paper reviews the current use of single-cell sequencing technologies in TB research and their application in analysing specimens from various sources of TB, primarily peripheral blood and lung specimens. The focus is on how these technologies can reveal dynamic changes in immune cell subpopulations, genes and proteins during disease progression after M.tb infection. Based on the current findings, single-cell sequencing has significant potential clinical value in the field of TB research. Next, we will focus on the real-world applications of the potential targets identified through single-cell sequencing for diagnostics, therapeutics and the development of effective vaccines.
Collapse
Affiliation(s)
- Yuqin Zeng
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Quan Ma
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Jinyun Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xingxing Kong
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Zhanpeng Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Huazhen Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Lanlan Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Yan Qian
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xiaomin Wang
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Shuihua Lu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| |
Collapse
|
9
|
Song L, Li Q, Xia L, Sahay A, Qiu Q, Li Y, Li H, Sasaki K, Susztak K, Wu H, Wan L. Single-Cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.591709. [PMID: 38766219 PMCID: PMC11100752 DOI: 10.1101/2024.05.09.591709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Cell differentiation during organogenesis relies on precise epigenetic and transcriptional control. Disruptions to this regulation can result in developmental abnormalities and malignancies, yet the underlying mechanisms are not well understood. Wilms tumors, a type of embryonal tumor closely linked to disrupted organogenesis, harbor mutations in epigenetic regulators in 30-50% of cases. However, the role of these regulators in kidney development and pathogenesis remains unexplored. By integrating mouse modeling, histological characterizations, and single-cell transcriptomics and chromatin accessibility profiling, we show that a Wilms tumor-associated mutation in the chromatin reader protein ENL disrupts kidney development trajectory by rewiring the gene regulatory landscape. Specifically, the mutant ENL promotes the commitment of nephron progenitors while simultaneously restricting their differentiation by dysregulating key transcription factor regulons, particularly the HOX clusters. It also induces the emergence of abnormal progenitor cells that lose their chromatin identity associated with kidney specification. Furthermore, the mutant ENL might modulate stroma-nephron interactions via paracrine Wnt signaling. These multifaceted effects caused by the mutation result in severe developmental defects in the kidney and early postnatal mortality in mice. Notably, transient inhibition of the histone acetylation binding activity of mutant ENL with a small molecule displaces transcriptional condensates formed by mutant ENL from target genes, abolishes its gene activation function, and restores developmental defects in mice. This work provides new insights into how mutations in epigenetic regulators can alter the gene regulatory landscape to disrupt kidney developmental programs at single-cell resolution in vivo . It also offers a proof-of-concept for the use of epigenetics-targeted agents to rectify developmental defects.
Collapse
|
10
|
Dissanayake LV, Kravtsova O, Lowe M, McCrorey MK, Van Beusecum JP, Palygin O, Staruschenko A. The presence of xanthine dehydrogenase is crucial for the maturation of the rat kidneys. Clin Sci (Lond) 2024; 138:269-288. [PMID: 38358003 DOI: 10.1042/cs20231144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/24/2024] [Accepted: 02/14/2024] [Indexed: 02/16/2024]
Abstract
The development of the kidney involves essential cellular processes, such as cell proliferation and differentiation, which are led by interactions between multiple signaling pathways. Xanthine dehydrogenase (XDH) catalyzes the reaction producing uric acid in the purine catabolism, which plays a multifaceted role in cellular metabolism. Our previous study revealed that the genetic ablation of the Xdh gene in rats leads to smaller kidneys, kidney damage, decline of renal functions, and failure to thrive. Rats, unlike humans, continue their kidney development postnatally. Therefore, we explored whether XDH plays a critical role in kidney development using SS-/- rats during postnatal development phase. XDH expression was significantly increased from postnatal day 5 to 15 in wild-type but not homozygote rat kidneys. The transcriptomic profile of renal tissue revealed several dysregulated pathways due to the lack of Xdh expression with the remodeling in inflammasome, purinergic signaling, and redox homeostasis. Further analysis suggested that lack of Xdh affects kidney development, likely via dysregulation of epidermal growth factor and its downstream STAT3 signaling. The present study showed that Xdh is essential for kidney maturation. Our data, alongside the previous research, suggests that loss of Xdh function leads to developmental issues, rendering them vulnerable to kidney diseases in adulthood.
Collapse
Affiliation(s)
- Lashodya V Dissanayake
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida; Tampa, FL 33602, U.S.A
| | - Olha Kravtsova
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida; Tampa, FL 33602, U.S.A
| | - Melissa Lowe
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida; Tampa, FL 33602, U.S.A
| | - Marice K McCrorey
- Department of Medicine, Division of Nephrology, Medical University of South Carolina, Charleston, SC 29425, U.S.A
| | - Justin P Van Beusecum
- Department of Medicine, Division of Nephrology, Medical University of South Carolina, Charleston, SC 29425, U.S.A
- Ralph H. Johnson Veterans Affairs Healthcare System, Charleston, SC 29403, U.S.A
| | - Oleg Palygin
- Department of Medicine, Division of Nephrology, Medical University of South Carolina, Charleston, SC 29425, U.S.A
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, U.S.A
| | - Alexander Staruschenko
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida; Tampa, FL 33602, U.S.A
- Hypertension and Kidney Research Center, University of South Florida, Tampa, FL 33602, U.S.A
- James A. Haley Veterans' Hospital, Tampa, FL 33612, U.S.A
| |
Collapse
|
11
|
Cazorla-Vázquez S, Kösters P, Bertz S, Pfister F, Daniel C, Dedden M, Zundler S, Jobst-Schwan T, Amann K, Engel FB. Adhesion GPCR Gpr126 (Adgrg6) Expression Profiling in Zebrafish, Mouse, and Human Kidney. Cells 2023; 12:1988. [PMID: 37566066 PMCID: PMC10417176 DOI: 10.3390/cells12151988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/22/2023] [Accepted: 07/29/2023] [Indexed: 08/12/2023] Open
Abstract
Adhesion G protein-coupled receptors (aGPCRs) comprise the second-largest class of GPCRs, the most common target for approved pharmacological therapies. aGPCRs play an important role in development and disease and have recently been associated with the kidney. Several aGPCRs are expressed in the kidney and some aGPCRs are either required for kidney development or their expression level is altered in diseased kidneys. Yet, general aGPCR function and their physiological role in the kidney are poorly understood. Here, we characterize in detail Gpr126 (Adgrg6) expression based on RNAscope® technology in zebrafish, mice, and humans during kidney development in adults. Gpr126 expression is enriched in the epithelial linage during nephrogenesis and persists in the adult kidney in parietal epithelial cells, collecting ducts, and urothelium. Single-cell RNAseq analysis shows that gpr126 expression is detected in zebrafish in a distinct ionocyte sub-population. It is co-detected selectively with slc9a3.2, slc4a4a, and trpv6, known to be involved in apical acid secretion, buffering blood or intracellular pH, and to maintain high cytoplasmic Ca2+ concentration, respectively. Furthermore, gpr126-expressing cells were enriched in the expression of potassium transporter kcnj1a.1 and gcm2, which regulate the expression of a calcium sensor receptor. Notably, the expression patterns of Trpv6, Kcnj1a.1, and Gpr126 in mouse kidneys are highly similar. Collectively, our approach permits a detailed insight into the spatio-temporal expression of Gpr126 and provides a basis to elucidate a possible role of Gpr126 in kidney physiology.
Collapse
Affiliation(s)
- Salvador Cazorla-Vázquez
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (S.C.-V.); (P.K.)
| | - Peter Kösters
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (S.C.-V.); (P.K.)
| | - Simone Bertz
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany;
| | - Frederick Pfister
- Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (F.P.); (C.D.); (K.A.)
| | - Christoph Daniel
- Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (F.P.); (C.D.); (K.A.)
| | - Mark Dedden
- Department of Medicine 1, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.D.); (S.Z.)
| | - Sebastian Zundler
- Department of Medicine 1, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.D.); (S.Z.)
| | - Tilman Jobst-Schwan
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany;
- Research Center On Rare Kidney Diseases (RECORD), University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Kerstin Amann
- Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (F.P.); (C.D.); (K.A.)
| | - Felix B. Engel
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (S.C.-V.); (P.K.)
| |
Collapse
|
12
|
Shan D, Wang YY, Chang Y, Cui H, Tao M, Sheng Y, Kang H, Jia P, Song J. Dynamic cellular changes in acute kidney injury caused by different ischemia time. iScience 2023; 26:106646. [PMID: 37168554 PMCID: PMC10165188 DOI: 10.1016/j.isci.2023.106646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
Ischemia reperfusion injury (IRI), often related to surgical procedures, is one of the important causes of acute kidney injury (AKI). To decipher the dynamic process of AKI caused by IRI (with prolonged ischemia phase), we performed single-cell RNA sequencing (scRNA-seq) of clinically relevant IRI murine model with different ischemic intervals. We discovered that Slc5a2hi proximal tubular cells were susceptible to AKI and highly expressed neutral amino acid transporter gene Slc6a19, which was dramatically decreased over the time course. With the usage of mass spectrometry-based metabolomic analysis, we detected that the level of neutral amino acid isoleucine dropped off in AKI mouse plasma metabolites. And the reduction of plasma isoleucine was also verified in patients with cardiac surgery-associated acute kidney injury (CSA-AKI). The findings advanced the understanding of dynamic process of AKI and introduced reduction of isoleucine as a potential biomarker for CSA-AKI.
Collapse
Affiliation(s)
- Dan Shan
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Yin-Ying Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yuan Chang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Hao Cui
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Menghao Tao
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Yixuan Sheng
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- Department of Cardiovascular Surgery, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou 510000, China
| | - Hongen Kang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding author
| | - Jiangping Song
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- Corresponding author
| |
Collapse
|
13
|
Kim S, Koppitch K, Parvez RK, Guo J, Achieng M, Schnell J, Lindström NO, McMahon AP. Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.540880. [PMID: 37293066 PMCID: PMC10245679 DOI: 10.1101/2023.05.16.540880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
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.
Collapse
|
14
|
A Kaleidoscope of Keratin Gene Expression and the Mosaic of Its Regulatory Mechanisms. Int J Mol Sci 2023; 24:ijms24065603. [PMID: 36982676 PMCID: PMC10052683 DOI: 10.3390/ijms24065603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Keratins are a family of intermediate filament-forming proteins highly specific to epithelial cells. A combination of expressed keratin genes is a defining property of the epithelium belonging to a certain type, organ/tissue, cell differentiation potential, and at normal or pathological conditions. In a variety of processes such as differentiation and maturation, as well as during acute or chronic injury and malignant transformation, keratin expression undergoes switching: an initial keratin profile changes accordingly to changed cell functions and location within a tissue as well as other parameters of cellular phenotype and physiology. Tight control of keratin expression implies the presence of complex regulatory landscapes within the keratin gene loci. Here, we highlight patterns of keratin expression in different biological conditions and summarize disparate data on mechanisms controlling keratin expression at the level of genomic regulatory elements, transcription factors (TFs), and chromatin spatial structure.
Collapse
|
15
|
Zhang L, Chen Z, Gao Q, Liu G, Zheng J, Ding F. Preterm birth leads to a decreased number of differentiated podocytes and accelerated podocyte differentiation. Front Cell Dev Biol 2023; 11:1142929. [PMID: 36936687 PMCID: PMC10018169 DOI: 10.3389/fcell.2023.1142929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Preterm birth was previously identified as a high-risk factor for the long-term development of chronic kidney disease. However, the detailed pattern of podocyte (PD) changes caused by preterm birth and the potential mechanism underlying this process have not been well clarified. In present study, a rat model of preterm birth was established by delivery of pups 2 days early and podometric methods were applied to identify the changes in PDs number caused by preterm birth. In addition, single-cell RNA sequencing (scRNA-seq) and subsequent bioinformatic analysis were performed in the preterm rat kidney to explore the possible mechanism caused by preterm birth. As results, when the kidney completely finished nephrogenesis at the age of 3 weeks, a reduction in the total number of differentiated PDs in kidney sections was detected. In addition, 20 distinct clusters and 12 different cell types were identified after scRNA-seq in preterm rats (postnatal day 2) and full-term rats (postnatal day 0). The numbers of PDs and most types of inherent kidney cells were decreased in the preterm birth model. In addition, 177 genes were upregulated while 82 genes were downregulated in the PDs of full-term rats compared with those of preterm rats. Further functional GO analysis revealed that ribosome-related genes were enriched in PDs from full-term rats, and kidney development-related genes were enriched in PDs from preterm rats. Moreover, known PD-specific and PD precursor genes were highly expressed in PDs from preterm rats, and pseudotemporal analysis showed that PDs were present earlier in preterm rats than in full-term rats. In conclusion, the present study showed that preterm birth could cause a reduction in the number of differentiated PDs and accelerate the differentiation of PDs.
Collapse
Affiliation(s)
- Lulu Zhang
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
| | - Zhihui Chen
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
| | - Qi Gao
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
| | - Ge Liu
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
| | - Jun Zheng
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
| | - Fangrui Ding
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
| |
Collapse
|
16
|
Treacy NJ, Clerkin S, Davis JL, Kennedy C, Miller AF, Saiani A, Wychowaniec JK, Brougham DF, Crean J. Growth and differentiation of human induced pluripotent stem cell (hiPSC)-derived kidney organoids using fully synthetic peptide hydrogels. Bioact Mater 2023; 21:142-156. [PMID: 36093324 PMCID: PMC9420433 DOI: 10.1016/j.bioactmat.2022.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/27/2022] [Accepted: 08/01/2022] [Indexed: 11/15/2022] Open
Abstract
Human induced pluripotent stem cell (hiPSC)-derived kidney organoids have prospective applications ranging from basic disease modelling to personalised medicine. However, there remains a necessity to refine the biophysical and biochemical parameters that govern kidney organoid formation. Differentiation within fully-controllable and physiologically relevant 3D growth environments will be critical to improving organoid reproducibility and maturation. Here, we matured hiPSC-derived kidney organoids within fully synthetic self-assembling peptide hydrogels (SAPHs) of variable stiffness (storage modulus, G'). The resulting organoids contained complex structures comparable to those differentiated within the animal-derived matrix, Matrigel. Single-cell RNA sequencing (scRNA-seq) was then used to compare organoids matured within SAPHs to those grown within Matrigel or at the air-liquid interface. A total of 13,179 cells were analysed, revealing 14 distinct clusters. Organoid compositional analysis revealed a larger proportion of nephron cell types within Transwell-derived organoids, while SAPH-derived organoids were enriched for stromal-associated cell populations. Notably, differentiation within a higher G' SAPH generated podocytes with more mature gene expression profiles. Additionally, maturation within a 3D microenvironment significantly reduced the derivation of off-target cell types, which are a known limitation of current kidney organoid protocols. This work demonstrates the utility of synthetic peptide-based hydrogels with a defined stiffness, as a minimally complex microenvironment for the selected differentiation of kidney organoids.
Collapse
Affiliation(s)
- Niall J Treacy
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Shane Clerkin
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Jessica L Davis
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Ciarán Kennedy
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Aline F Miller
- Department of Materials & Manchester Institute of Biotechnology (MIB), School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Alberto Saiani
- Department of Materials & Manchester Institute of Biotechnology (MIB), School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Jacek K Wychowaniec
- UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dermot F Brougham
- UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - John Crean
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| |
Collapse
|
17
|
Klämbt V, Buerger F, Wang C, Naert T, Richter K, Nauth T, Weiss AC, Sieckmann T, Lai E, Connaughton DM, Seltzsam S, Mann N, Majmundar AJ, Wu CHW, Onuchic-Whitford AC, Shril S, Schneider S, Schierbaum L, Dai R, Bekheirnia MR, Joosten M, Shlomovitz O, Vivante A, Banne E, Mane S, Lifton RP, Kirschner KM, Kispert A, Rosenberger G, Fischer KD, Lienkamp SS, Zegers MM, Hildebrandt F. Genetic Variants in ARHGEF6 Cause Congenital Anomalies of the Kidneys and Urinary Tract in Humans, Mice, and Frogs. J Am Soc Nephrol 2023; 34:273-290. [PMID: 36414417 PMCID: PMC10103091 DOI: 10.1681/asn.2022010050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 09/30/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND About 40 disease genes have been described to date for isolated CAKUT, the most common cause of childhood CKD. However, these genes account for only 20% of cases. ARHGEF6, a guanine nucleotide exchange factor that is implicated in biologic processes such as cell migration and focal adhesion, acts downstream of integrin-linked kinase (ILK) and parvin proteins. A genetic variant of ILK that causes murine renal agenesis abrogates the interaction of ILK with a murine focal adhesion protein encoded by Parva , leading to CAKUT in mice with this variant. METHODS To identify novel genes that, when mutated, result in CAKUT, we performed exome sequencing in an international cohort of 1265 families with CAKUT. We also assessed the effects in vitro of wild-type and mutant ARHGEF6 proteins, and the effects of Arhgef6 deficiency in mouse and frog models. RESULTS We detected six different hemizygous variants in the gene ARHGEF6 (which is located on the X chromosome in humans) in eight individuals from six families with CAKUT. In kidney cells, overexpression of wild-type ARHGEF6 -but not proband-derived mutant ARHGEF6 -increased active levels of CDC42/RAC1, induced lamellipodia formation, and stimulated PARVA-dependent cell spreading. ARHGEF6-mutant proteins showed loss of interaction with PARVA. Three-dimensional Madin-Darby canine kidney cell cultures expressing ARHGEF6-mutant proteins exhibited reduced lumen formation and polarity defects. Arhgef6 deficiency in mouse and frog models recapitulated features of human CAKUT. CONCLUSIONS Deleterious variants in ARHGEF6 may cause dysregulation of integrin-parvin-RAC1/CDC42 signaling, thereby leading to X-linked CAKUT.
Collapse
Affiliation(s)
- Verena Klämbt
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
| | - Florian Buerger
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Chunyan Wang
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Thomas Naert
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Karin Richter
- Institute for Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Theresa Nauth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna-Carina Weiss
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Tobias Sieckmann
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Translatationale Physiologie, Berlin, Germany
| | - Ethan Lai
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dervla M. Connaughton
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Steve Seltzsam
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nina Mann
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amar J. Majmundar
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Chen-Han W. Wu
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Departments of Genetics and Urology, Case Western Reserve University School of Medicine and University Hospitals, Cleveland, Ohio
| | - Ana C. Onuchic-Whitford
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shirlee Shril
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sophia Schneider
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Luca Schierbaum
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rufeng Dai
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mir Reza Bekheirnia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Omer Shlomovitz
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Asaf Vivante
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ehud Banne
- The Genetics Institute, Kaplan Medical Center—Rehovot, Hebrew University and Hadassah Medical School, Jerusalem, Israel
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut
| | - Richard P. Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | - Karin M. Kirschner
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Translatationale Physiologie, Berlin, Germany
| | - Andreas Kispert
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Georg Rosenberger
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus-Dieter Fischer
- Institute for Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Soeren S. Lienkamp
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Mirjam M.P. Zegers
- Department of Cell Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
18
|
Royer-Pokora B, Wruck W, Adjaye J, Beier M. Gene expression studies of WT1 mutant Wilms tumor cell lines in the frame work of published kidney development data reveals their early kidney stem cell origin. PLoS One 2023; 18:e0270380. [PMID: 36689432 PMCID: PMC9870146 DOI: 10.1371/journal.pone.0270380] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/21/2022] [Indexed: 01/24/2023] Open
Abstract
In order to get a better insight into the timing of WT1 mutant Wilms tumor development, we compared the gene expression profiles of nine established WT1 mutant Wilms tumor cell lines with published data from different kidney cell types during development. Publications describing genes expressed in nephrogenic precursor cells, ureteric bud cells, more mature nephrogenic epithelial cells and interstitial cell types were used. These studies uncovered that the WT1 mutant Wilms tumor cells lines express genes from the earliest nephrogenic progenitor cells, as well as from more differentiated nephron cells with the highest expression from the stromal/interstitial compartment. The expression of genes from all cell compartments points to an early developmental origin of the tumor in a common stem cell. Although variability of the expression of specific genes was evident between the cell lines the overall expression pattern was very similar. This is likely dependent on their different genetic backgrounds with distinct WT1 mutations and the absence/presence of mutant CTNNB1.
Collapse
Affiliation(s)
- Brigitte Royer-Pokora
- Institute of Human Genetics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wasco Wruck
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Manfred Beier
- Institute of Human Genetics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
19
|
Ryosaka M, Mae SI, Osafune K. Protocol for the generation and expansion of human iPS cell-derived ureteric bud organoids. STAR Protoc 2022; 3:101484. [PMID: 35769929 PMCID: PMC9234152 DOI: 10.1016/j.xpro.2022.101484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The ureteric bud (UB) is a kidney precursor tissue that repeats branching morphogenesis and gives rise to the collecting ducts (CDs) and lower urinary tract. Here, we describe protocols to generate iUB organoids from human iPSCs; iUB organoids repeat branching morphogenesis. We describe how to expand iUB-organoid-derived tip colonies and how to induce CD progenitors from iUB organoids. These organoids can be used to study CD development and potentially as a model of kidney and urinary tract diseases. For complete details on the use and execution of this protocol, please refer to Mae et al. (2020). Protocol for ureteric bud (UB) organoids with repeated branching potential An expansion culture approach for UB tip colonies using hydrogel Differentiation of UB organoids into 2D and 3D collecting duct progenitors
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
Collapse
|
20
|
Wu J, Ding Y, Wang J, Lyu F, Tang Q, Song J, Luo Z, Wan Q, Lan X, Xu Z, Chen L. Single‐cell RNA
sequencing in oral science: Current awareness and perspectives. Cell Prolif 2022; 55:e13287. [PMID: 35842899 PMCID: PMC9528768 DOI: 10.1111/cpr.13287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/10/2022] [Accepted: 05/29/2022] [Indexed: 11/30/2022] Open
Abstract
The emergence of single‐cell RNA sequencing enables simultaneous sequencing of thousands of cells, making the analysis of cell population heterogeneity more efficient. In recent years, single‐cell RNA sequencing has been used in the investigation of heterogeneous cell populations, cellular developmental trajectories, stochastic gene transcriptional kinetics, and gene regulatory networks, providing strong support in life science research. However, the application of single‐cell RNA sequencing in the field of oral science has not been reviewed comprehensively yet. Therefore, this paper reviews the development and application of single‐cell RNA sequencing in oral science, including fields of tissue development, teeth and jaws diseases, maxillofacial tumors, infections, etc., providing reference and prospects for using single‐cell RNA sequencing in studying the oral diseases, tissue development, and regeneration.
Collapse
Affiliation(s)
- Jie Wu
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology Sun Yat‐sen University Guangzhou China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yumei Ding
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Jinyu Wang
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Fengyuan Lyu
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
- Center of Stomatology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Qingming Tang
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Jiangyuan Song
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Zhiqiang Luo
- National Engineering Research Center for Nanomedicine College of Life Science and Technolog Huazhong University of Science and Technology Wuhan China
| | - Qian Wan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy Huazhong University of Science and Technology Wuhan China
- Institute of Brain Research Huazhong University of Science and Technology Wuhan China
| | - Xiaoli Lan
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Key Laboratory of Molecular Imaging Wuhan China
| | - Zhi Xu
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Lili Chen
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| |
Collapse
|
21
|
Dai Y, Hu R, Liu A, Cho KS, Manuel AM, Li X, Dong X, Jia P, Zhao Z. WebCSEA: web-based cell-type-specific enrichment analysis of genes. Nucleic Acids Res 2022; 50:W782-W790. [PMID: 35610053 DOI: 10.1093/nar/gkac392] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/19/2022] [Accepted: 05/04/2022] [Indexed: 02/02/2023] Open
Abstract
Human complex traits and common diseases show tissue- and cell-type- specificity. Recently, single-cell RNA sequencing (scRNA-seq) technology has successfully depicted cellular heterogeneity in human tissue, providing an unprecedented opportunity to understand the context-specific expression of complex trait-associated genes in human tissue-cell types (TCs). Here, we present the first web-based application to quickly assess the cell-type-specificity of genes, named Web-based Cell-type Specific Enrichment Analysis of Genes (WebCSEA, available at https://bioinfo.uth.edu/webcsea/). Specifically, we curated a total of 111 scRNA-seq panels of human tissues and 1,355 TCs from 61 different general tissues across 11 human organ systems. We adapted our previous decoding tissue-specificity (deTS) algorithm to measure the enrichment for each tissue-cell type (TC). To overcome the potential bias from the number of signature genes between different TCs, we further developed a permutation-based method that accurately estimates the TC-specificity of a given inquiry gene list. WebCSEA also provides an interactive heatmap that displays the cell-type specificity across 1355 human TCs, and other interactive and static visualizations of cell-type specificity by human organ system, developmental stage, and top-ranked tissues and cell types. In short, WebCSEA is a one-click application that provides a comprehensive exploration of the TC-specificity of genes among human major TC map.
Collapse
Affiliation(s)
- Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ruifeng Hu
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,Center for Advanced Parkinson Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Genomics and Bioinformatics Hub, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andi Liu
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Kyung Serk Cho
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Astrid Marilyn Manuel
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaoyang Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xianjun Dong
- Center for Advanced Parkinson Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Genomics and Bioinformatics Hub, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| |
Collapse
|
22
|
Generation of the organotypic kidney structure by integrating pluripotent stem cell-derived renal stroma. Nat Commun 2022; 13:611. [PMID: 35105870 PMCID: PMC8807595 DOI: 10.1038/s41467-022-28226-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/03/2022] [Indexed: 01/12/2023] Open
Abstract
Organs consist of the parenchyma and stroma, the latter of which coordinates the generation of organotypic structures. Despite recent advances in organoid technology, induction of organ-specific stroma and recapitulation of complex organ configurations from pluripotent stem cells (PSCs) have remained challenging. By elucidating the in vivo molecular features of the renal stromal lineage at a single-cell resolution level, we herein establish an in vitro induction protocol for stromal progenitors (SPs) from mouse PSCs. When the induced SPs are assembled with two differentially induced parenchymal progenitors (nephron progenitors and ureteric buds), the completely PSC-derived organoids reproduce the complex kidney structure, with multiple types of stromal cells distributed along differentiating nephrons and branching ureteric buds. Thus, integration of PSC-derived lineage-specific stroma into parenchymal organoids will pave the way toward recapitulation of the organotypic architecture and functions.
Collapse
|
23
|
Mircea M, Hochane M, Fan X, Chuva de Sousa Lopes SM, Garlaschelli D, Semrau S. Phiclust: a clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations. Genome Biol 2022; 23:18. [PMID: 35012604 PMCID: PMC8751334 DOI: 10.1186/s13059-021-02590-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/23/2021] [Indexed: 12/25/2022] Open
Abstract
The ability to discover new cell phenotypes by unsupervised clustering of single-cell transcriptomes has revolutionized biology. Currently, there is no principled way to decide whether a cluster of cells contains meaningful subpopulations that should be further resolved. Here, we present phiclust (ϕclust), a clusterability measure derived from random matrix theory that can be used to identify cell clusters with non-random substructure, testably leading to the discovery of previously overlooked phenotypes.
Collapse
Affiliation(s)
- Maria Mircea
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Mazène Hochane
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Xueying Fan
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Diego Garlaschelli
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
- Networks Unit, IMT School for Advanced Studies, Lucca, Italy
| | - Stefan Semrau
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands.
| |
Collapse
|
24
|
Miao R, Dong X, Gong J, Li Y, Guo X, Wang J, Huang Q, Wang Y, Li J, Yang S, Kuang T, Liu M, Wan J, Zhai Z, Zhong J, Yang Y. Examining the Development of Chronic Thromboembolic Pulmonary Hypertension at the Single-Cell Level. Hypertension 2021; 79:562-574. [PMID: 34965740 DOI: 10.1161/hypertensionaha.121.18105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The mechanism of chronic thromboembolic pulmonary hypertension (CTEPH) is known to be multifactorial but remains incompletely understood. METHODS In this study, single-cell RNA sequencing, which facilitates the identification of molecular profiles of samples on an individual cell level, was applied to investigate individual cell types in pulmonary endarterectomized tissues from 5 patients with CTEPH. The order of single-cell types was then traced along the developmental trajectory of CTEPH by trajectory inference analysis, and intercellular communication was characterized by analysis of ligand-receptor pairs between cell types. Finally, comprehensive bioinformatics tools were used to analyze possible functions of branch-specific cell types and the underlying mechanisms. RESULTS Eleven cell types were identified, with immune-related cell types (T cells, natural killer cells, macrophages, and mast cells) distributed in the left (early) branch of the pseudotime tree, cancer stem cells, and CRISPLD2+ cells as intermediate cell types, and classic disease-related cell types (fibroblasts, smooth muscle cells, myofibroblasts, and endothelial cells) in the right (later) branch. Ligand-receptor interactions revealed close communication between macrophages and disease-related cell types as well as between smooth muscle cells and fibroblasts or endothelial cells. Moreover, the ligands and receptors were significantly enriched in key pathways such as the PI3K/Akt signaling pathway. Furthermore, highly expressed genes specific to the undefined cell type were significantly enriched in important functions associated with regulation of endoplasmic reticulum stress. CONCLUSIONS This single-cell RNA sequencing analysis revealed the order of single cells along a developmental trajectory in CTEPH as well as close communication between different cell types in CTEPH pathogenesis.
Collapse
Affiliation(s)
- Ran Miao
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, China. (R.M.).,Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, China. (R.M., J.G., J.L., S.Y., T.K., Y.Y.).,Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Institute of Respiratory Medicine, Beijing, China (R.M., J.G., J.L., S.Y., T.K., Y.Y.)
| | - Xingbei Dong
- Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China (X.D.)
| | - Juanni Gong
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, China. (R.M., J.G., J.L., S.Y., T.K., Y.Y.).,Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Institute of Respiratory Medicine, Beijing, China (R.M., J.G., J.L., S.Y., T.K., Y.Y.)
| | - Yidan Li
- Department of Echocardiography, Beijing Chao-Yang Hospital, Capital Medical University, China. (Y.L.)
| | - Xiaojuan Guo
- Department of Radiology, Beijing Chao-Yang Hospital, Capital Medical University, China. (X.G.)
| | - Jianfeng Wang
- Department of Interventional Radiology, Beijing Chao-Yang Hospital, Capital Medical University, China. (J. Wang, Q.H.)
| | - Qiang Huang
- Department of Interventional Radiology, Beijing Chao-Yang Hospital, Capital Medical University, China. (J. Wang, Q.H.)
| | - Ying Wang
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, China. (Y.W.)
| | - Jifeng Li
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, China. (R.M., J.G., J.L., S.Y., T.K., Y.Y.).,Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Institute of Respiratory Medicine, Beijing, China (R.M., J.G., J.L., S.Y., T.K., Y.Y.)
| | - Suqiao Yang
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, China. (R.M., J.G., J.L., S.Y., T.K., Y.Y.).,Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Institute of Respiratory Medicine, Beijing, China (R.M., J.G., J.L., S.Y., T.K., Y.Y.)
| | - Tuguang Kuang
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, China. (R.M., J.G., J.L., S.Y., T.K., Y.Y.).,Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Institute of Respiratory Medicine, Beijing, China (R.M., J.G., J.L., S.Y., T.K., Y.Y.)
| | - Min Liu
- Department of Radiology, China-Japan Friendship Hospital, Beijing, China. (M.L.)
| | - Jun Wan
- Department of Pulmonary and Critical Care Medicine Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China. (J. Wan, Z.Z.).,National Clinical Research Center for Respiratory Diseases, Beijing, China (J. Wan, Z.Z.)
| | - Zhenguo Zhai
- Department of Pulmonary and Critical Care Medicine Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China. (J. Wan, Z.Z.).,National Clinical Research Center for Respiratory Diseases, Beijing, China (J. Wan, Z.Z.)
| | - Jiuchang Zhong
- Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chao-Yang Hospital, Capital Medical University, China.(J.Z.)
| | - Yuanhua Yang
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, China. (R.M., J.G., J.L., S.Y., T.K., Y.Y.).,Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Institute of Respiratory Medicine, Beijing, China (R.M., J.G., J.L., S.Y., T.K., Y.Y.)
| |
Collapse
|
25
|
Chen D, Sun J, Zhu J, Ding X, Lan T, Wang X, Wu W, Ou Z, Zhu L, Ding P, Wang H, Luo L, Xiang R, Wang X, Qiu J, Wang S, Li H, Chai C, Liang L, An F, Zhang L, Han L, Zhu Y, Wang F, Yuan Y, Wu W, Sun C, Lu H, Wu J, Sun X, Zhang S, Sahu SK, Liu P, Xia J, Zhang L, Chen H, Fang D, Zeng Y, Wu Y, Cui Z, He Q, Jiang S, Ma X, Feng W, Xu Y, Li F, Liu Z, Chen L, Chen F, Jin X, Qiu W, Wang T, Li Y, Xing X, Yang H, Xu Y, Hua Y, Liu Y, Liu H, Xu X. Single cell atlas for 11 non-model mammals, reptiles and birds. Nat Commun 2021; 12:7083. [PMID: 34873160 PMCID: PMC8648889 DOI: 10.1038/s41467-021-27162-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 09/18/2021] [Indexed: 01/08/2023] Open
Abstract
The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening of animal cells could reveal the expression patterns of viral entry genes in different hosts. However, such exploration for SARS-CoV-2 remains limited. Here, we perform single-nucleus RNA sequencing for 11 non-model species, including pets (cat, dog, hamster, and lizard), livestock (goat and rabbit), poultry (duck and pigeon), and wildlife (pangolin, tiger, and deer), and investigated the co-expression of ACE2 and TMPRSS2. Furthermore, cross-species analysis of the lung cell atlas of the studied mammals, reptiles, and birds reveals core developmental programs, critical connectomes, and conserved regulatory circuits among these evolutionarily distant species. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and putative zoonotic reservoirs.
Collapse
Affiliation(s)
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jiacheng Zhu
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangning Ding
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tianming Lan
- BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Xiran Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | | | - Zhihua Ou
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Peiwen Ding
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haoyu Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lihua Luo
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rong Xiang
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoling Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiaying Qiu
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiyou Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haimeng Li
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaochao Chai
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Langchao Liang
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fuyu An
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Le Zhang
- College of Wildlife Resources Northeast Forestry University, Harbin, 150040, China
| | - Lei Han
- College of Wildlife Resources Northeast Forestry University, Harbin, 150040, China
| | - Yixin Zhu
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | | | - Wendi Wu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Chengcheng Sun
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haorong Lu
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jihong Wu
- Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, China
| | - Xinghuai Sun
- Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, China
| | - Shenghai Zhang
- Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, China
| | | | - Ping Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jun Xia
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Lijing Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haixia Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Yuying Zeng
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiquan Wu
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892-1868, USA
| | - Zehua Cui
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qian He
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | | | - Xiaoyan Ma
- Department of Biochemistry, University of Cambridge, Cambridge, CB21QW, UK
| | | | - Yan Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Fang Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China
| | - Zhongmin Liu
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China
| | - Lei Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Wei Qiu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, China
| | - Tianjiao Wang
- Institute of Special Animal and Plant Sciences (ISAPS) of Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yang Li
- Institute of Special Animal and Plant Sciences (ISAPS) of Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xiumei Xing
- Institute of Special Animal and Plant Sciences (ISAPS) of Chinese Academy of Agricultural Sciences, Changchun, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yanchun Xu
- College of Wildlife Resources Northeast Forestry University, Harbin, 150040, China
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Yan Hua
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China.
| | - Yahong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, 518083, Shenzhen, China.
| |
Collapse
|
26
|
Zhang S, Afanassiev A, Greenstreet L, Matsumoto T, Schiebinger G. Optimal transport analysis reveals trajectories in steady-state systems. PLoS Comput Biol 2021; 17:e1009466. [PMID: 34860824 PMCID: PMC8691649 DOI: 10.1371/journal.pcbi.1009466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 12/21/2021] [Accepted: 09/20/2021] [Indexed: 01/25/2023] Open
Abstract
Understanding how cells change their identity and behaviour in living systems is an important question in many fields of biology. The problem of inferring cell trajectories from single-cell measurements has been a major topic in the single-cell analysis community, with different methods developed for equilibrium and non-equilibrium systems (e.g. haematopoeisis vs. embryonic development). We show that optimal transport analysis, a technique originally designed for analysing time-courses, may also be applied to infer cellular trajectories from a single snapshot of a population in equilibrium. Therefore, optimal transport provides a unified approach to inferring trajectories that is applicable to both stationary and non-stationary systems. Our method, StationaryOT, is mathematically motivated in a natural way from the hypothesis of a Waddington's epigenetic landscape. We implement StationaryOT as a software package and demonstrate its efficacy in applications to simulated data as well as single-cell data from Arabidopsis thaliana root development.
Collapse
Affiliation(s)
- Stephen Zhang
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Anton Afanassiev
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Laura Greenstreet
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Tetsuya Matsumoto
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | | |
Collapse
|
27
|
Bais AS, Cerqueira DM, Clugston A, Bodnar AJ, Ho J, Kostka D. Single-cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis. Sci Rep 2021; 11:22434. [PMID: 34789782 PMCID: PMC8599654 DOI: 10.1038/s41598-021-01790-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 10/27/2021] [Indexed: 02/08/2023] Open
Abstract
The kidney is a complex organ composed of more than 30 terminally differentiated cell types that all are required to perform its numerous homeostatic functions. Defects in kidney development are a significant cause of chronic kidney disease in children, which can lead to kidney failure that can only be treated by transplant or dialysis. A better understanding of molecular mechanisms that drive kidney development is important for designing strategies to enhance renal repair and regeneration. In this study, we profiled gene expression in the developing mouse kidney at embryonic day 14.5 at single-cell resolution. Consistent with previous studies, clusters with distinct transcriptional signatures clearly identify major compartments and cell types of the developing kidney. Cell cycle activity distinguishes between the "primed" and "self-renewing" sub-populations of nephron progenitors, with increased expression of the cell cycle-related genes Birc5, Cdca3, Smc2 and Smc4 in "primed" nephron progenitors. In addition, augmented expression of cell cycle related genes Birc5, Cks2, Ccnb1, Ccnd1 and Tuba1a/b was detected in immature distal tubules, suggesting cell cycle regulation may be required for early events of nephron patterning and tubular fusion between the distal nephron and collecting duct epithelia.
Collapse
Affiliation(s)
- Abha S Bais
- Department of Developmental Biology, Rangos Research Center 8117, University of Pittsburgh School of Medicine, 530 45th St, Pittsburgh, PA, 15224, USA
| | - Débora M Cerqueira
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
- Division of Nephrology, Department of Pediatrics, Rangos Research Center 5127, University of Pittsburgh School of Medicine, 530 45th St, Pittsburgh, PA, 15224, USA
| | - Andrew Clugston
- Department of Developmental Biology, Rangos Research Center 8117, University of Pittsburgh School of Medicine, 530 45th St, Pittsburgh, PA, 15224, USA
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
- Division of Nephrology, Department of Pediatrics, Rangos Research Center 5127, University of Pittsburgh School of Medicine, 530 45th St, Pittsburgh, PA, 15224, USA
| | - Andrew J Bodnar
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
- Division of Nephrology, Department of Pediatrics, Rangos Research Center 5127, University of Pittsburgh School of Medicine, 530 45th St, Pittsburgh, PA, 15224, USA
| | - Jacqueline Ho
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
- Division of Nephrology, Department of Pediatrics, Rangos Research Center 5127, University of Pittsburgh School of Medicine, 530 45th St, Pittsburgh, PA, 15224, USA.
| | - Dennis Kostka
- Department of Developmental Biology, Rangos Research Center 8117, University of Pittsburgh School of Medicine, 530 45th St, Pittsburgh, PA, 15224, USA.
- Department of Computational and Systems Biology and Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| |
Collapse
|
28
|
Jarmas AE, Brunskill EW, Chaturvedi P, Salomonis N, Kopan R. Progenitor translatome changes coordinated by Tsc1 increase perception of Wnt signals to end nephrogenesis. Nat Commun 2021; 12:6332. [PMID: 34732708 PMCID: PMC8566581 DOI: 10.1038/s41467-021-26626-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/17/2021] [Indexed: 11/29/2022] Open
Abstract
Mammalian nephron endowment is determined by the coordinated cessation of nephrogenesis in independent niches. Here we report that translatome analysis in Tsc1+/- nephron progenitor cells from mice with elevated nephron numbers reveals how differential translation of Wnt antagonists over agonists tips the balance between self-renewal and differentiation. Wnt agonists are poorly translated in young niches, resulting in an environment with low R-spondin and high Fgf20 promoting self-renewal. In older niches we find increased translation of Wnt agonists, including R-spondin and the signalosome-promoting Tmem59, and low Fgf20, promoting differentiation. This suggests that the tipping point for nephron progenitor exit from the niche is controlled by the gradual increase in stability and possibly clustering of Wnt/Fzd complexes in individual cells, enhancing the response to ureteric bud-derived Wnt9b inputs and driving synchronized differentiation. As predicted by these findings, removing one Rspo3 allele in nephron progenitors delays cessation and increases nephron numbers in vivo.
Collapse
Affiliation(s)
- Alison E Jarmas
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Eric W Brunskill
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Praneet Chaturvedi
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Raphael Kopan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| |
Collapse
|
29
|
Sarkany B, Kovacs G. Connecting tubules develop from the tip of the ureteric bud in the human kidney. Histochem Cell Biol 2021; 156:555-560. [PMID: 34554322 DOI: 10.1007/s00418-021-02033-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2021] [Indexed: 01/14/2023]
Abstract
The connecting tubule (CNT) is a unique segment of the nephron connecting the metanephric mesenchyme (MM)-derived distal convoluted tubule (DCT) and ureteric bud (UB)-derived collecting duct (CD). Views on the cellular origin of the CNT in the human kidney are controversial. It was suggested that in mice, the connecting segment arises from the distal compartment of the renal vesicle (RV). However, there are several differences in embryonic development between the mouse and human kidney. The aim of our study was to establish the possible origin of the CNT in the human kidney. We analysed the expression of markers defining distinct cells of the CNT CD in foetal and adult human kidneys by immunohistochemistry. Based on microscopic observation, we suggest that CNT differentiates from the outgrowth of cells of the UB tip, and therefore the CNT is an integral part of the CD system. In the adult kidney, the CNT and CD consist of functionally and morphologically similar cells expressing α- and β-intercalated cell (IC) and principal cell (PC) markers, indicating their common origin.
Collapse
Affiliation(s)
- Beatrix Sarkany
- Department of Urology, Medical School, University of Pecs, Pecs, 7621, Hungary
| | - Gyula Kovacs
- Department of Urology, Medical School, University of Pecs, Pecs, 7621, Hungary.
- Medical Faculty, Ruprecht-Karls-University, 69120, Heidelberg, Germany.
| |
Collapse
|
30
|
Xu L. The Role of Myeloid Cells in Acute Kidney Injury and Kidney Repair. KIDNEY360 2021; 2:1852-1864. [PMID: 35372990 PMCID: PMC8785849 DOI: 10.34067/kid.0000672021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 09/17/2021] [Indexed: 02/04/2023]
Abstract
AKI remains highly prevalent, yet no optimal therapy is available to prevent it or promote recovery after initial insult. Experimental studies have demonstrated that both innate and adaptive immune responses play a central role during AKI. In response to injury, myeloid cells are first recruited and activated on the basis of specific signals from the damaged microenvironment. The subsequent recruitment and activation state of the immune cells depends on the stage of injury and recovery, reflecting a dynamic and diverse spectrum of immunophenotypes. In this review, we highlight our current understanding of the mechanisms by which myeloid cells contribute to injury, repair, and fibrosis after AKI.
Collapse
Affiliation(s)
- Leyuan Xu
- Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut
| |
Collapse
|
31
|
Dong J, Zhou P, Wu Y, Chen Y, Xie H, Gao Y, Lu J, Yang J, Zhang X, Wen L, Li T, Tang F. Integrating single-cell datasets with ambiguous batch information by incorporating molecular network features. Brief Bioinform 2021; 23:6373559. [PMID: 34553223 DOI: 10.1093/bib/bbab366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 01/30/2023] Open
Abstract
With the rapid development of single-cell sequencing techniques, several large-scale cell atlas projects have been launched across the world. However, it is still challenging to integrate single-cell RNA-seq (scRNA-seq) datasets with diverse tissue sources, developmental stages and/or few overlaps, due to the ambiguity in determining the batch information, which is particularly important for current batch-effect correction methods. Here, we present SCORE, a simple network-based integration methodology, which incorporates curated molecular network features to infer cellular states and generate a unified workflow for integrating scRNA-seq datasets. Validating on real single-cell datasets, we showed that regardless of batch information, SCORE outperforms existing methods in accuracy, robustness, scalability and data integration.
Collapse
Affiliation(s)
- Ji Dong
- Guangzhou Laboratory, Guangzhou, China
| | - Peijie Zhou
- Department of Mathematics, University of California at Irvine, Irvine, CA, USA
| | - Yichong Wu
- School of Mathematical Sciences, Peking University, Beijing, China
| | - Yidong Chen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Haoling Xie
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Peking University, Beijing, China
| | - Yuan Gao
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Peking University, Beijing, China
| | - Jiansen Lu
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Peking University, Beijing, China
| | - Jingwei Yang
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Peking University, Beijing, China
| | - Xiannian Zhang
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Lu Wen
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Peking University, Beijing, China
| | - Tiejun Li
- School of Mathematical Sciences, Peking University, Beijing, China
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Peking University, Beijing, China
| |
Collapse
|
32
|
Wen-Jin C, Xiu-Wu P, Jian C, Da X, Jia-Xin C, Wei-Jie C, Lin-Hui W, Xin-Gang C. Study of cellular heterogeneity and differential dynamics of autophagy in human embryonic kidney development by single-cell RNA sequencing. Cancer Cell Int 2021; 21:460. [PMID: 34461918 PMCID: PMC8404318 DOI: 10.1186/s12935-021-02154-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/16/2021] [Indexed: 11/17/2022] Open
Abstract
Background Autophagy is believed to participate in embryonic development, but whether the expression of autophagy-associated genes undergoes changes during the development of human embryonic kidneys remains unknown. Methods In this work, we identified 36,151 human renal cells from embryonic kidneys of 9–18 gestational weeks in 16 major clusters by single-cell RNA sequencing (scRNA-seq), and detected 1350 autophagy-related genes in all fetal renal cells. The abundance of each cell cluster in Wilms tumor samples from scRNA-seq and GDC TARGET WT datasets was detected by CIBERSORTx. R package Monocle 3 was used to determine differentiation trajectories. Cyclone tool of R package scran was applied to calculate the cell cycle scores. R package SCENIC was used to investigate the transcriptional regulons. The FindMarkers tool from Seurat was used to calculate DEGs. GSVA was used to perform gene set enrichment analyses. CellphoneDB was utilized to analyze intercellular communication. Results It was found that cells in the 13th gestational week showed the lowest transcriptional level in each cluster in all stages. Nephron progenitors could be divided into four subgroups with diverse levels of autophagy corresponding to different SIX2 expressions. SSBpod (podocyte precursors) could differentiate into four types of podocytes (Pod), and autophagy-related regulation was involved in this process. Pseudotime analysis showed that interstitial progenitor cells (IPCs) potentially possessed two primitive directions of differentiation to interstitial cells with different expressions of autophagy. It was found that NPCs, pretubular aggregates and interstitial cell clusters had high abundance in Wilms tumor as compared with para-tumor samples with active intercellular communication. Conclusions All these findings suggest that autophagy may be involved in the development and cellular heterogeneity of early human fetal kidneys. In addition, part of Wilms tumor cancer cells possess the characteristics of some fetal renal cell clusters. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02154-w.
Collapse
Affiliation(s)
- Chen Wen-Jin
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Pan Xiu-Wu
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China.,Department of Urology, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Chu Jian
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China.,Department of Urology, Gongli Hospital of Second Military Medical University, 219 Miaopu Road, Shanghai, 200135, China
| | - Xu Da
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Chen Jia-Xin
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Chen Wei-Jie
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Wang Lin-Hui
- Department of Urology, Changzheng Hospital of Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China.
| | - Cui Xin-Gang
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China. .,Department of Urology, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China.
| |
Collapse
|
33
|
Chan K, Li X. Current Epigenetic Insights in Kidney Development. Genes (Basel) 2021; 12:genes12081281. [PMID: 34440455 PMCID: PMC8391601 DOI: 10.3390/genes12081281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/07/2021] [Accepted: 08/19/2021] [Indexed: 12/31/2022] Open
Abstract
The kidney is among the best characterized developing tissues, with the genes and signaling pathways that regulate embryonic and adult kidney patterning and development having been extensively identified. It is now widely understood that DNA methylation and histone modification patterns are imprinted during embryonic development and must be maintained in adult cells for appropriate gene transcription and phenotypic stability. A compelling question then is how these epigenetic mechanisms play a role in kidney development. In this review, we describe the major genes and pathways that have been linked to epigenetic mechanisms in kidney development. We also discuss recent applications of single-cell RNA sequencing (scRNA-seq) techniques in the study of kidney development. Additionally, we summarize the techniques of single-cell epigenomics, which can potentially be used to characterize epigenomes at single-cell resolution in embryonic and adult kidneys. The combination of scRNA-seq and single-cell epigenomics will help facilitate the further understanding of early cell lineage specification at the level of epigenetic modifications in embryonic and adult kidney development, which may also be used to investigate epigenetic mechanisms in kidney diseases.
Collapse
Affiliation(s)
- Katrina Chan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA;
| | - Xiaogang Li
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-507-266-0110
| |
Collapse
|
34
|
Schumacher A, Rookmaaker MB, Joles JA, Kramann R, Nguyen TQ, van Griensven M, LaPointe VLS. Defining the variety of cell types in developing and adult human kidneys by single-cell RNA sequencing. NPJ Regen Med 2021; 6:45. [PMID: 34381054 PMCID: PMC8357940 DOI: 10.1038/s41536-021-00156-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/22/2021] [Indexed: 01/14/2023] Open
Abstract
The kidney is among the most complex organs in terms of the variety of cell types. The cellular complexity of human kidneys is not fully unraveled and this challenge is further complicated by the existence of multiple progenitor pools and differentiation pathways. Researchers disagree on the variety of renal cell types due to a lack of research providing a comprehensive picture and the challenge to translate findings between species. To find an answer to the number of human renal cell types, we discuss research that used single-cell RNA sequencing on developing and adult human kidney tissue and compares these findings to the literature of the pre-single-cell RNA sequencing era. We find that these publications show major steps towards the discovery of novel cell types and intermediate cell stages as well as complex molecular signatures and lineage pathways throughout development. The variety of cell types remains variable in the single-cell literature, which is due to the limitations of the technique. Nevertheless, our analysis approaches an accumulated number of 41 identified cell populations of renal lineage and 32 of non-renal lineage in the adult kidney, and there is certainly much more to discover. There is still a need for a consensus on a variety of definitions and standards in single-cell RNA sequencing research, such as the definition of what is a cell type. Nevertheless, this early-stage research already proves to be of significant impact for both clinical and regenerative medicine, and shows potential to enhance the generation of sophisticated in vitro kidney tissue.
Collapse
Affiliation(s)
- A Schumacher
- MERLN Institute for Technology-Inspired Regenerative Medicine, Department of Cell Biology-Inspired Tissue Engineering, Maastricht University, Maastricht, The Netherlands
| | - M B Rookmaaker
- Department of Nephrology, University Medical Center, Utrecht, The Netherlands
| | - J A Joles
- Department of Nephrology, University Medical Center, Utrecht, The Netherlands
| | - R Kramann
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands
| | - T Q Nguyen
- Department of Pathology, University Medical Center, Utrecht, The Netherlands
| | - M van Griensven
- MERLN Institute for Technology-Inspired Regenerative Medicine, Department of Cell Biology-Inspired Tissue Engineering, Maastricht University, Maastricht, The Netherlands
| | - V L S LaPointe
- MERLN Institute for Technology-Inspired Regenerative Medicine, Department of Cell Biology-Inspired Tissue Engineering, Maastricht University, Maastricht, The Netherlands.
| |
Collapse
|
35
|
Hyman LB, Christopher CR, Romero PA. Single-cell nucleic acid profiling in droplets (SNAPD) enables high-throughput analysis of heterogeneous cell populations. Nucleic Acids Res 2021; 49:e103. [PMID: 34233007 PMCID: PMC8501953 DOI: 10.1093/nar/gkab577] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/03/2022] Open
Abstract
Experimental methods that capture the individual properties of single cells are revealing the key role of cell-to-cell variability in countless biological processes. These single-cell methods are becoming increasingly important across the life sciences in fields such as immunology, regenerative medicine and cancer biology. In addition to high-dimensional transcriptomic techniques such as single-cell RNA sequencing, there is a need for fast, simple and high-throughput assays to enumerate cell samples based on RNA biomarkers. In this work, we present single-cell nucleic acid profiling in droplets (SNAPD) to analyze sets of transcriptional markers in tens of thousands of single mammalian cells. Individual cells are encapsulated in aqueous droplets on a microfluidic chip and the RNA markers in each cell are amplified. Molecular logic circuits then integrate these amplicons to categorize cells based on the transcriptional markers and produce a detectable fluorescence output. SNAPD is capable of analyzing over 100,000 cells per hour and can be used to quantify distinct cell types within heterogeneous populations, detect rare cells at frequencies down to 0.1% and enrich specific cell types using microfluidic sorting. SNAPD provides a simple, rapid, low cost and scalable approach to study complex phenotypes in heterogeneous cell populations.
Collapse
Affiliation(s)
- Leland B Hyman
- Graduate Program in Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Clare R Christopher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Philip A Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.,The University of Wisconsin Carbone Cancer Center, Madison, WI 53706, USA
| |
Collapse
|
36
|
Li Y, Zeng W, Li T, Guo Y, Zheng G, He X, Bai L, Ding G, Jin L, Liu X. Integrative Single-Cell Transcriptomic Analysis of Human Fetal Thymocyte Development. Front Genet 2021; 12:679616. [PMID: 34276782 PMCID: PMC8284395 DOI: 10.3389/fgene.2021.679616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/03/2021] [Indexed: 11/23/2022] Open
Abstract
Intrathymic differentiation of T lymphocytes begins as early as intrauterine stage, yet the T cell lineage decisions of human fetal thymocytes at different gestational ages are not currently understood. Here, we performed integrative single-cell analyses of thymocytes across gestational ages. We identified conserved candidates underlying the selection of T cell receptor (TCR) lineages in different human fetal stages. The trajectory of early thymocyte commitment during fetal growth was also characterized. Comparisons with mouse data revealed conserved and species-specific transcriptional dynamics of thymocyte proliferation, apoptosis and selection. Genome-wide association study (GWAS) data associated with multiple autoimmune disorders were analyzed to characterize susceptibility genes that are highly expressed at specific stages during fetal thymocyte development. In summary, our integrative map describes previously underappreciated aspects of human thymocyte development, and provides a comprehensive reference for understanding T cell lymphopoiesis in a self-tolerant and functional adaptive immune system.
Collapse
Affiliation(s)
- Yuchen Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Weihong Zeng
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Tong Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yanyan Guo
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Guangyong Zheng
- Bio-Med Big Data Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoying He
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Lilian Bai
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Guolian Ding
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Li Jin
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Xinmei Liu
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| |
Collapse
|
37
|
Determination of the dynamic cellular transcriptional profiles during kidney development from birth to maturity in rats by single-cell RNA sequencing. Cell Death Discov 2021; 7:162. [PMID: 34226524 PMCID: PMC8257621 DOI: 10.1038/s41420-021-00542-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/27/2021] [Accepted: 06/03/2021] [Indexed: 01/02/2023] Open
Abstract
Recent single-cell RNA sequencing (scRNA-seq) analyses have offered much insight into the gene expression profiles in early-stage kidney development. However, comprehensive gene expression profiles from mid- and late-stage kidney development are lacking. In the present study, by using the scRNA-seq technique, we analyzed 54,704 rat kidney cells from just after birth to adulthood (six time points: postnatal days 0, 2, 5, 10, 20, and 56) including the mid and late stages of kidney development. Twenty-five original clusters and 13 different cell types were identified during these stages. Gene expression in these 13 cell types was mapped, and single cell atlas of the rat kidney from birth to maturity ( http://youngbearlab.com ) was built to enable users to search for a gene of interest and to evaluate its expression in different cells. The variation trend of six major types of kidney cells-intercalated cells of the collecting duct (CD-ICs), principal cells of the collecting duct (CD-PCs), cells of the distal convoluted tubules (DCTs), cells of the loop of Henle (LOH), podocytes (PDs), and cells of the proximal tubules (PTs)-during six postnatal time points was demonstrated. The trajectory of rat kidney development and the order of induction of the six major types of kidney cells from just after birth to maturity were determined. In addition, features of the dynamically changing genes as well as transcription factors during postnatal rat kidney development were identified. The present study provides a resource for achieving a deep understanding of the molecular basis of and regulatory events in the mid and late stages of kidney development.
Collapse
|
38
|
Young MD, Mitchell TJ, Custers L, Margaritis T, Morales-Rodriguez F, Kwakwa K, Khabirova E, Kildisiute G, Oliver TRW, de Krijger RR, van den Heuvel-Eibrink MM, Comitani F, Piapi A, Bugallo-Blanco E, Thevanesan C, Burke C, Prigmore E, Ambridge K, Roberts K, Braga FAV, Coorens THH, Del Valle I, Wilbrey-Clark A, Mamanova L, Stewart GD, Gnanapragasam VJ, Rampling D, Sebire N, Coleman N, Hook L, Warren A, Haniffa M, Kool M, Pfister SM, Achermann JC, He X, Barker RA, Shlien A, Bayraktar OA, Teichmann SA, Holstege FC, Meyer KB, Drost J, Straathof K, Behjati S. Single cell derived mRNA signals across human kidney tumors. Nat Commun 2021; 12:3896. [PMID: 34162837 PMCID: PMC8222373 DOI: 10.1038/s41467-021-23949-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/25/2021] [Indexed: 01/16/2023] Open
Abstract
Tumor cells may share some patterns of gene expression with their cell of origin, providing clues into the differentiation state and origin of cancer. Here, we study the differentiation state and cellular origin of 1300 childhood and adult kidney tumors. Using single cell mRNA reference maps of normal tissues, we quantify reference "cellular signals" in each tumor. Quantifying global differentiation, we find that childhood tumors exhibit fetal cellular signals, replacing the presumption of "fetalness" with a quantitative measure of immaturity. By contrast, in adult cancers our assessment refutes the suggestion of dedifferentiation towards a fetal state in most cases. We find an intimate connection between developmental mesenchymal populations and childhood renal tumors. We demonstrate the diagnostic potential of our approach with a case study of a cryptic renal tumor. Our findings provide a cellular definition of human renal tumors through an approach that is broadly applicable to human cancer.
Collapse
Affiliation(s)
- Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | | | - Francisco Morales-Rodriguez
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Kwasi Kwakwa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Eleonora Khabirova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gerda Kildisiute
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Alice Piapi
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | | | | | - Christina Burke
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kirsty Ambridge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Tim H H Coorens
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ignacio Del Valle
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Vincent J Gnanapragasam
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Urology Translational Research and Clinical Trials office, Cambridge Biomedical Campus Cambridge CB2 0QQ University of Cambridge, Cambridge, UK
| | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Neil Sebire
- NIHR Great Ormond Street Hospital BRC and Institute of Child Health, London, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Anne Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Intitute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hopp Children´s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Division of Pediatric Neurooncology, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children´s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Division of Pediatric Neurooncology, Heidelberg, Germany
- Heidelberg University Hospital, Department of Pediatric Hematology and Oncology, Heidelberg, Germany
| | - John C Achermann
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Xiaoling He
- MRC-WT Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Roger A Barker
- MRC-WT Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Omer A Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Frank C Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Karin Straathof
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK.
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
| |
Collapse
|
39
|
Teixeira SA, Marques DBD, Costa TC, Oliveira HC, Costa KA, Carrara ER, da Silva W, Guimarães JD, Neves MM, Ibelli AMG, Cantão ME, Ledur MC, Peixoto JO, Guimarães SEF. Transcription Landscape of the Early Developmental Biology in Pigs. Animals (Basel) 2021; 11:ani11051443. [PMID: 34069910 PMCID: PMC8157595 DOI: 10.3390/ani11051443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Since pre- and postnatal development are programmed during early prenatal life, studies addressing the complete transcriptional landscape during organogenesis are needed. Therefore, we aimed to disentangle differentially expressed (DE) genes between fetuses (at 35 days old) and embryos (at 25 days old) through RNA-sequencing analysis using the pig as model. In total, 1705 genes were DE, including the top DE IBSP, COL6A6, HBE1, HBZ, HBB, and NEUROD6 genes, which are associated with developmental transition from embryos to fetuses, such as ossification, skeletal muscle development, extracellular matrix organization, cardiovascular system, erythrocyte differentiation, and neuronal system. In pathway analysis, embryonic development highlighted those mainly related to morphogenic signaling and cell interactions, which are crucial for transcriptional control during the establishment of the main organs in early prenatal development, while pathways related to myogenesis, neuronal development, and cardiac and striated muscle contraction were enriched for fetal development, according to the greater complexity of organs and body structures at this developmental stage. Our findings provide an exploratory and informative transcriptional landscape of pig organogenesis, which might contribute to further studies addressing specific developmental events in pigs and in other mammals.
Collapse
Affiliation(s)
- Susana A. Teixeira
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Daniele B. D. Marques
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Thaís C. Costa
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Haniel C. Oliveira
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Karine A. Costa
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Eula R. Carrara
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Walmir da Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - José D. Guimarães
- Department of Veterinary Medicine, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil;
| | - Mariana M. Neves
- Department of General Biology, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil;
| | - Adriana M. G. Ibelli
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil; (A.M.G.I.); (M.E.C.); (M.C.L.); (J.O.P.)
| | - Maurício E. Cantão
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil; (A.M.G.I.); (M.E.C.); (M.C.L.); (J.O.P.)
| | - Mônica C. Ledur
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil; (A.M.G.I.); (M.E.C.); (M.C.L.); (J.O.P.)
| | - Jane O. Peixoto
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil; (A.M.G.I.); (M.E.C.); (M.C.L.); (J.O.P.)
| | - Simone E. F. Guimarães
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
- Correspondence: ; Tel.: +55-31-36124671
| |
Collapse
|
40
|
Schuh MP, Alkhudairy L, Potter A, Potter SS, Chetal K, Thakkar K, Salomonis N, Kopan R. The Rhesus Macaque Serves As a Model for Human Lateral Branch Nephrogenesis. J Am Soc Nephrol 2021; 32:1097-1112. [PMID: 33789950 PMCID: PMC8259676 DOI: 10.1681/asn.2020101459] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/18/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Most nephrons are added in late gestation. Truncated extrauterine nephrogenesis in premature infants results in fewer nephrons and significantly increased risk for CKD in adulthood. To overcome the ethical and technical difficulties associated with studies of late-gestation human fetal kidney development, third-trimester rhesus macaques served as a model to understand lateral branch nephrogenesis (LBN) at the molecular level. METHODS Immunostaining and 3D rendering assessed morphology. Single-cell (sc) and single-nucleus (sn) RNA-Seq were performed on four cortically enriched fetal rhesus kidneys of 129-131 days gestational age (GA). An integrative bioinformatics strategy was applied across single-cell modalities, species, and time. RNAScope validation studies were performed on human archival tissue. RESULTS Third-trimester rhesus kidney undergoes human-like LBN. scRNA-Seq of 23,608 cells revealed 37 transcriptionally distinct cell populations, including naïve nephron progenitor cells (NPCs), with the prior noted marker genes CITED1, MEOX1, and EYA1 (c25). These same populations and markers were reflected in snRNA-Seq of 5972 nuclei. Late-gestation rhesus NPC markers resembled late-gestation murine NPC, whereas early second-trimester human NPC markers aligned to midgestation murine NPCs. New, age-specific rhesus NPCs (SHISA8) and ureteric buds (POU3F4 and TWIST) predicted markers were verified in late-gestation human archival samples. CONCLUSIONS Rhesus macaque is the first model of bona fide LBN, enabling molecular studies of late gestation, human-like nephrogenesis. These molecular findings support the hypothesis that aging nephron progenitors have a distinct molecular signature and align to their earlier human counterparts, with unique markers highlighting LBN-specific progenitor maturation.
Collapse
Affiliation(s)
- Meredith P. Schuh
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Nephrology and Hypertension, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Lyan Alkhudairy
- Division of Nephrology and Hypertension, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Andrew Potter
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - S. Steven Potter
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kairavee Thakkar
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, Ohio
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Raphael Kopan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| |
Collapse
|
41
|
Kim J, Park J. Single-cell transcriptomics: a novel precision medicine technique in nephrology. Korean J Intern Med 2021; 36:479-490. [PMID: 33076636 PMCID: PMC8137400 DOI: 10.3904/kjim.2020.415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
Due to the complex structure and function of the kidneys, the mechanism of kidney disease is unclear. In particular, transcriptomics approaches at the bulk level are unable to differentiate primary autonomous responses, which lead to disease development, from secondary cell non-autonomous responses. Single-cell analysis techniques can overcome the limitations inherent in the measurement of heterogeneous cell populations and clarify the central issues in kidney biology and disease pathogenesis. Single-cell sequencing helps in identifying disease-related biomarkers and pathways, stratifying patients, and deciding on appropriate treatment methods. Here we review a variety of single-cell analysis techniques and single-cell transcriptomics studies performed in the field of nephrology. Moreover, we discuss the future prospects of single-cell analysis-based precision medicine in nephrology.
Collapse
Affiliation(s)
- Jisoo Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Korea
| |
Collapse
|
42
|
Tsujimoto H, Kasahara T, Sueta SI, Araoka T, Sakamoto S, Okada C, Mae SI, Nakajima T, Okamoto N, Taura D, Nasu M, Shimizu T, Ryosaka M, Li Z, Sone M, Ikeya M, Watanabe A, Osafune K. A Modular Differentiation System Maps Multiple Human Kidney Lineages from Pluripotent Stem Cells. Cell Rep 2021; 31:107476. [PMID: 32268094 DOI: 10.1016/j.celrep.2020.03.040] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 01/17/2020] [Accepted: 03/13/2020] [Indexed: 02/08/2023] Open
Abstract
Recent studies using human pluripotent stem cells (hPSCs) have developed protocols to induce kidney-lineage cells and reconstruct kidney organoids. However, the separate generation of metanephric nephron progenitors (NPs), mesonephric NPs, and ureteric bud (UB) cells, which constitute embryonic kidneys, in in vitro differentiation culture systems has not been fully investigated. Here, we create a culture system in which these mesoderm-like cell types and paraxial and lateral plate mesoderm-like cells are separately generated from hPSCs. We recapitulate nephrogenic niches from separately induced metanephric NP-like and UB-like cells, which are subsequently differentiated into glomeruli, renal tubules, and collecting ducts in vitro and further vascularized in vivo. Our selective differentiation protocols should contribute to understanding the mechanisms underlying human kidney development and disease and also supply cell sources for regenerative therapies.
Collapse
Affiliation(s)
- Hiraku Tsujimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tomoko Kasahara
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shin-Ichi Sueta
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Toshikazu Araoka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Satoko Sakamoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Chihiro Okada
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Mitsubishi Space Software, 5-4-36 Tsukaguchi-honmachi, Amagasaki, Hyogo 661-0001, Japan
| | - Shin-Ichi Mae
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Taiki Nakajima
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Natsumi Okamoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Daisuke Taura
- Department of Medicine and Clinical Science, Kyoto University Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Makoto Nasu
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tatsuya Shimizu
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Makoto Ryosaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Zhongwei Li
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, 1333 San Pablo Street, MMR 618, Los Angeles, CA 90033, USA
| | - Masakatsu Sone
- Department of Medicine and Clinical Science, Kyoto University Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Makoto Ikeya
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Akira Watanabe
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kenji Osafune
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
| |
Collapse
|
43
|
Shimizu T, Yamagata K, Osafune K. Kidney organoids: Research in developmental biology and emerging applications. Dev Growth Differ 2021; 63:166-177. [PMID: 33569792 DOI: 10.1111/dgd.12714] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/11/2022]
Abstract
Kidney organoids generated from human pluripotent stem cells (hPSCs) have drastically changed the field of stem cell research on human kidneys within a few years. They are self-organizing multicellular structures that contain nephron components such as glomeruli and renal tubules in most cases, but hPSC-derived ureteric buds, the progenitors of collecting ducts and ureters, can also form three-dimensional organoids. Today's challenges facing human kidney organoids are further maturation and anatomical integrity in order to achieve a complete model of the developing kidneys and ultimately a complete adult organ. Since chronic kidney disease (CKD) and impaired kidney function are an increasing burden on public health worldwide, there is an urgent need to develop effective treatments for various renal conditions. In this regard, hPSC-derived kidney organoids may impact medicine by providing new translational approaches. The unique ability of kidney organoids derived from disease-specific hPSCs to reproduce human diseases caused by genetic alterations may help provide the next generation of kidney disease models. Recent advances in the field of kidney organoid research have been generally accompanied by progress in developmental biology and other technological breakthroughs. In this review, we consider the current trends in kidney organoid technology, especially focusing on the relationship to the study of human kidney development, and discuss the remaining hurdles and prospects in regenerating human kidney structures beyond organoids.
Collapse
Affiliation(s)
- Tatsuya Shimizu
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,Department of Nephrology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Kunihiro Yamagata
- Department of Nephrology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Kenji Osafune
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| |
Collapse
|
44
|
Mann N, Mzoughi S, Schneider R, Kühl SJ, Schanze D, Klämbt V, Lovric S, Mao Y, Shi S, Tan W, Kühl M, Onuchic-Whitford AC, Treimer E, Kitzler TM, Kause F, Schumann S, Nakayama M, Buerger F, Shril S, van der Ven AT, Majmundar AJ, Holton KM, Kolb A, Braun DA, Rao J, Jobst-Schwan T, Mildenberger E, Lennert T, Kuechler A, Wieczorek D, Gross O, Ermisch-Omran B, Werberger A, Skalej M, Janecke AR, Soliman NA, Mane SM, Lifton RP, Kadlec J, Guccione E, Schmeisser MJ, Zenker M, Hildebrandt F. Mutations in PRDM15 Are a Novel Cause of Galloway-Mowat Syndrome. J Am Soc Nephrol 2021; 32:580-596. [PMID: 33593823 PMCID: PMC7920168 DOI: 10.1681/asn.2020040490] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/18/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Galloway-Mowat syndrome (GAMOS) is characterized by neurodevelopmental defects and a progressive nephropathy, which typically manifests as steroid-resistant nephrotic syndrome. The prognosis of GAMOS is poor, and the majority of children progress to renal failure. The discovery of monogenic causes of GAMOS has uncovered molecular pathways involved in the pathogenesis of disease. METHODS Homozygosity mapping, whole-exome sequencing, and linkage analysis were used to identify mutations in four families with a GAMOS-like phenotype, and high-throughput PCR technology was applied to 91 individuals with GAMOS and 816 individuals with isolated nephrotic syndrome. In vitro and in vivo studies determined the functional significance of the mutations identified. RESULTS Three biallelic variants of the transcriptional regulator PRDM15 were detected in six families with proteinuric kidney disease. Four families with a variant in the protein's zinc-finger (ZNF) domain have additional GAMOS-like features, including brain anomalies, cardiac defects, and skeletal defects. All variants destabilize the PRDM15 protein, and the ZNF variant additionally interferes with transcriptional activation. Morpholino oligonucleotide-mediated knockdown of Prdm15 in Xenopus embryos disrupted pronephric development. Human wild-type PRDM15 RNA rescued the disruption, but the three PRDM15 variants did not. Finally, CRISPR-mediated knockout of PRDM15 in human podocytes led to dysregulation of several renal developmental genes. CONCLUSIONS Variants in PRDM15 can cause either isolated nephrotic syndrome or a GAMOS-type syndrome on an allelic basis. PRDM15 regulates multiple developmental kidney genes, and is likely to play an essential role in renal development in humans.
Collapse
Affiliation(s)
- Nina Mann
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Slim Mzoughi
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ronen Schneider
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Susanne J Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Verena Klämbt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Svjetlana Lovric
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Youying Mao
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shasha Shi
- Grenoble Alpes University, National Center for Scientific Research (CNRS), French Alternative Energies and Atomic Energy Commission (CEA), Institute of Structural Biology, Grenoble, France
| | - Weizhen Tan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Ana C Onuchic-Whitford
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ernestine Treimer
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Thomas M Kitzler
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Franziska Kause
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sven Schumann
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Makiko Nakayama
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Florian Buerger
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amelie T van der Ven
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amar J Majmundar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Amy Kolb
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jia Rao
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eva Mildenberger
- Division of Neonatology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Thomas Lennert
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University of Duisburg-Essen, Essen, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Faculty of Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Oliver Gross
- Clinic of Nephrology and Rheumatology, University Medical Center Goettingen, University of Goettingen, Goettingen, Germany
| | - Beate Ermisch-Omran
- Department of Pediatric Nephrology, University Children's Hospital, Münster, Germany
| | - Anja Werberger
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Martin Skalej
- Institute of Neuroradiology, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Andreas R Janecke
- Department of Pediatrics I, Medical University of Innsbruck, Innsbruck, Austria
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt
- The Egyption Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | - Jan Kadlec
- Grenoble Alpes University, National Center for Scientific Research (CNRS), French Alternative Energies and Atomic Energy Commission (CEA), Institute of Structural Biology, Grenoble, France
| | - Ernesto Guccione
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael J Schmeisser
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
- Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
45
|
Wu M, Xia M, Li W, Li H. Single-Cell Sequencing Applications in the Inner Ear. Front Cell Dev Biol 2021; 9:637779. [PMID: 33644075 PMCID: PMC7907461 DOI: 10.3389/fcell.2021.637779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/21/2021] [Indexed: 01/29/2023] Open
Abstract
Genomics studies face specific challenges in the inner ear due to the multiple types and limited amounts of inner ear cells that are arranged in a very delicate structure. However, advances in single-cell sequencing (SCS) technology have made it possible to analyze gene expression variations across different cell types as well as within specific cell groups that were previously considered to be homogeneous. In this review, we summarize recent advances in inner ear research brought about by the use of SCS that have delineated tissue heterogeneity, identified unknown cell subtypes, discovered novel cell markers, and revealed dynamic signaling pathways during development. SCS opens up new avenues for inner ear research, and the potential of the technology is only beginning to be explored.
Collapse
Affiliation(s)
- Mingxuan Wu
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Mingyu Xia
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Wenyan Li
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Huawei Li
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, China.,The Institutes of Brain Science and The Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| |
Collapse
|
46
|
Sene LDB, Scarano WR, Zapparoli A, Gontijo JAR, Boer PA. Impact of gestational low-protein intake on embryonic kidney microRNA expression and in nephron progenitor cells of the male fetus. PLoS One 2021; 16:e0246289. [PMID: 33544723 PMCID: PMC7864410 DOI: 10.1371/journal.pone.0246289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/15/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Here, we have demonstrated that gestational low-protein (LP) intake offspring present lower birth weight, reduced nephron numbers, renal salt excretion, arterial hypertension, and renal failure development compared to regular protein (NP) intake rats in adulthood. We evaluated the expression of various miRNAs and predicted target genes in the kidney in gestational 17-days LP (DG-17) fetal metanephros to identify molecular pathways involved in the proliferation and differentiation of renal embryonic or fetal cells. METHODS Pregnant Wistar rats were classified into two groups based on protein supply during pregnancy: NP (regular protein diet, 17%) or LP diet (6%). Renal miRNA sequencing (miRNA-Seq) performed on the MiSeq platform, RT-qPCR of predicted target genes, immunohistochemistry, and morphological analysis of 17-DG NP and LP offspring were performed using previously described methods. RESULTS A total of 44 miRNAs, of which 19 were up and 25 downregulated, were identified in 17-DG LP fetuses compared to age-matched NP offspring. We selected 7 miRNAs involved in proliferation, differentiation, and cellular apoptosis. Our findings revealed reduced cell number and Six-2 and c-Myc immunoreactivity in metanephros cap (CM) and ureter bud (UB) in 17-DG LP fetuses. Ki-67 immunoreactivity in CM was 48% lesser in LP compared to age-matched NP fetuses. Conversely, in LP CM and UB, β-catenin was 154%, and 85% increased, respectively. Furthermore, mTOR immunoreactivity was higher in LP CM (139%) and UB (104%) compared to that in NP offspring. TGFβ-1 positive cells in the UB increased by approximately 30% in the LP offspring. Moreover, ZEB1 metanephros-stained cells increased by 30% in the LP offspring. ZEB2 immunofluorescence, although present in the entire metanephros, was similar in both experimental groups. CONCLUSIONS Maternal protein restriction changes the expression of miRNAs, mRNAs, and proteins involved in proliferation, differentiation, and apoptosis during renal development. Renal ontogenic dysfunction, caused by maternal protein restriction, promotes reduced reciprocal interaction between CM and UB; consequently, a programmed and expressive decrease in nephron number occurs in the fetus.
Collapse
Affiliation(s)
- Letícia de Barros Sene
- Fetal Programming and Hydroelectrolyte Metabolism Laboratory, Nucleus of Medicine and Experimental Surgery, Department of Internal Medicine, Faculty of Medical Sciences at State University of Campinas, Campinas, SP, Brazil
| | - Wellerson Rodrigo Scarano
- Department of Structural and Functional Biology, Bioscience Institute, São Paulo State University, Botucatu, SP, Brazil
| | - Adriana Zapparoli
- Fetal Programming and Hydroelectrolyte Metabolism Laboratory, Nucleus of Medicine and Experimental Surgery, Department of Internal Medicine, Faculty of Medical Sciences at State University of Campinas, Campinas, SP, Brazil
| | - José Antônio Rocha Gontijo
- Fetal Programming and Hydroelectrolyte Metabolism Laboratory, Nucleus of Medicine and Experimental Surgery, Department of Internal Medicine, Faculty of Medical Sciences at State University of Campinas, Campinas, SP, Brazil
| | - Patrícia Aline Boer
- Fetal Programming and Hydroelectrolyte Metabolism Laboratory, Nucleus of Medicine and Experimental Surgery, Department of Internal Medicine, Faculty of Medical Sciences at State University of Campinas, Campinas, SP, Brazil
| |
Collapse
|
47
|
The Renal Extracellular Matrix as a Supportive Scaffold for Kidney Tissue Engineering: Progress and Future Considerations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1345:103-118. [PMID: 34582017 DOI: 10.1007/978-3-030-82735-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
During the past decades, diverse methods have been used toward renal tissue engineering in order to replace renal function. The goals of all these techniques included the recapitulation of renal filtration, re-absorptive, and secretary functions, and replacement of endocrine/metabolic activities. It is also imperative to develop a reliable, up scalable, and timely manufacturing process. Decellularization of the kidney with intact ECM is crucial for in-vivo compatibility and targeted clinical application. Contemporarily there is an increasing interest and research in the field of regenerative medicine including stem cell therapy and tissue bioengineering in search for new and reproducible sources of kidneys. In this chapter, we sought to determine the most effective method of renal decellularization and recellularization with emphasis on biologic composition and support of stem cell growth. Current barriers and limitations of bioengineered strategies will be also discussed, and strategies to overcome these are suggested.
Collapse
|
48
|
Kuppe C, Perales-Patón J, Saez-Rodriguez J, Kramann R. Experimental and computational technologies to dissect the kidney at the single-cell level. Nephrol Dial Transplant 2020; 37:628-637. [PMID: 33332571 DOI: 10.1093/ndt/gfaa233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Indexed: 02/06/2023] Open
Abstract
The field of single-cell technologies, in particular single-cell genomics with transcriptomics and epigenomics, and most recently single-cell proteomics, is rapidly growing and holds promise to advance our understanding of organ homoeostasis and disease, and facilitate the identification of novel therapeutic targets and biomarkers. This review offers an introduction to these technologies. In addition, as the size and complexity of the data require sophisticated computational methods for analysis and interpretation, we will also provide an overview of these methods and summarize the single-cell literature specifically pertaining to the kidney.
Collapse
Affiliation(s)
- Christoph Kuppe
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Javier Perales-Patón
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
| | - Rafael Kramann
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
49
|
Cao J, O'Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R, Zhang F, Spielmann M, Palis J, Doherty D, Steemers FJ, Glass IA, Trapnell C, Shendure J. A human cell atlas of fetal gene expression. Science 2020; 370:370/6518/eaba7721. [PMID: 33184181 DOI: 10.1126/science.aba7721] [Citation(s) in RCA: 351] [Impact Index Per Article: 87.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022]
Abstract
The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, ultimately profiling ~4 million single cells. We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues. Our analyses focused on organ-specific specializations of broadly distributed cell types (such as blood, endothelial, and epithelial), sites of fetal erythropoiesis (which notably included the adrenal gland), and integration with mouse developmental atlases (such as conserved specification of blood cells). These data represent a rich resource for the exploration of in vivo human gene expression in diverse tissues and cell types.
Collapse
Affiliation(s)
- Junyue Cao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Diana R O'Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Hannah A Pliner
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paul D Kingsley
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Mei Deng
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael A Zager
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kimberly A Aldinger
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ronnie Blecher-Gonen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Malte Spielmann
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Ian A Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
| |
Collapse
|
50
|
Molecular detection of maturation stages in the developing kidney. Dev Biol 2020; 470:62-73. [PMID: 33197428 DOI: 10.1016/j.ydbio.2020.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022]
Abstract
Recent advances in stem cell biology have enabled the generation of kidney organoids in vitro, and further maturation of these organoids is observed after experimental transplantation. However, the current organoids remain immature and their precise maturation stages are difficult to determine because of limited information on developmental stage-dependent gene expressions in the kidney in vivo. To establish relevant molecular coordinates, we performed single-cell RNA sequencing (scRNA-seq) on developing kidneys at different stages in the mouse. By selecting genes that exhibited upregulation at birth compared with embryonic day 15.5 as well as cell lineage-specific expression, we generated gene lists correlated with developmental stages in individual cell lineages. Application of these lists to transplanted embryonic kidneys revealed that most cell types, other than the collecting ducts, exhibited similar maturation to kidneys at the neonatal stage in vivo, revealing non-synchronous maturation across the cell lineages. Thus, our scRNA-seq data can serve as useful molecular coordinates to assess the maturation of developing kidneys and eventually of kidney organoids.
Collapse
|