51
|
Abstract
There are now many reports of human kidney organoids generated via the directed differentiation of human pluripotent stem cells (PSCs) based on an existing understanding of mammalian kidney organogenesis. Such kidney organoids potentially represent tractable tools for the study of normal human development and disease with improvements in scale, structure, and functional maturation potentially providing future options for renal regeneration. The utility of such organotypic models, however, will ultimately be determined by their developmental accuracy. While initially inferred from mouse models, recent transcriptional analyses of human fetal kidney have provided greater insight into nephrogenesis. In this review, we discuss how well human kidney organoids model the human fetal kidney and how the remaining differences challenge their utility.
Collapse
Affiliation(s)
- Melissa H Little
- Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia
- Department of Anatomy and Neuroscience, The University of Melbourne, Victoria 3052, Australia
- Department of Paediatrics, The University of Melbourne, Victoria 3052, Australia
| | - Alexander N Combes
- Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia
- Department of Anatomy and Neuroscience, The University of Melbourne, Victoria 3052, Australia
| |
Collapse
|
52
|
Wegert J, Zauter L, Appenzeller S, Otto C, Bausenwein S, Vokuhl C, Ernestus K, Furtwängler R, Graf N, Gessler M. High-risk blastemal Wilms tumor can be modeled by 3D spheroid cultures in vitro. Oncogene 2019; 39:849-861. [PMID: 31562394 PMCID: PMC6976522 DOI: 10.1038/s41388-019-1027-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/06/2019] [Accepted: 09/13/2019] [Indexed: 01/10/2023]
Abstract
In vitro models represent a critical tool in cancer research to study tumor biology and to evaluate new treatment options. Unfortunately, there are no effective preclinical models available that represent Wilms tumor (WT) — the most common pediatric renal tumor. Especially the high-risk blastemal WT subtype is not represented by the few primary cell lines established until now. Here, we describe a new 3D approach for in vitro cultivation of blastemal WT cells, where primary cultures grown in suspension as spheroids could be propagated long-term. Besides blastemal cultures, we could generate spheroids representing epithelial and stromal WT. Spheroid cultures were analyzed by immunohistochemistry in comparison to corresponding tumor sections and were further characterized by RNA sequencing. Histological appearance of spheroids resembled the original tumor and they expressed marker genes characteristic of early renal development and blastemal WT elements. The cultures were amenable to genetic manipulation and they formed xenograft tumors, which resemble the primary human tumor. This collection of WT spheroids that carry different genetic drivers forms a long-sought tool for drug testing and in vitro modeling.
Collapse
Affiliation(s)
- Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, University of Wuerzburg, Wuerzburg, Germany
| | - Lisa Zauter
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, University of Wuerzburg, Wuerzburg, Germany
| | - Silke Appenzeller
- Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg, Germany
| | - Christoph Otto
- Experimental Surgery, Department of General, Visceral, Vascular, and Pediatric Surgery, University Hospital of Wuerzburg, Wuerzburg, Germany
| | - Sabrina Bausenwein
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, University of Wuerzburg, Wuerzburg, Germany
| | - Christian Vokuhl
- Kiel Pediatric Tumor Registry, Section of Pediatric Pathology, Department of Pathology, University Hospital of Kiel, Kiel, Germany
| | - Karen Ernestus
- Institute for Pathology, University of Wuerzburg, Wuerzburg, Germany
| | - Rhoikos Furtwängler
- Pediatric Oncology and Hematology, Children's Hospital, Saarland University and Saarland University Medical Centre, Homburg, Germany
| | - Norbert Graf
- Pediatric Oncology and Hematology, Children's Hospital, Saarland University and Saarland University Medical Centre, Homburg, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, University of Wuerzburg, Wuerzburg, Germany. .,Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg, Germany.
| |
Collapse
|
53
|
Potter SS. Single-cell RNA sequencing for the study of development, physiology and disease. Nat Rev Nephrol 2019; 14:479-492. [PMID: 29789704 DOI: 10.1038/s41581-018-0021-7] [Citation(s) in RCA: 313] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An ongoing technological revolution is continually improving our ability to carry out very high-resolution studies of gene expression patterns. Current technology enables the global gene expression profiles of single cells to be defined, facilitating dissection of heterogeneity in cell populations that was previously hidden. In contrast to gene expression studies that use bulk RNA samples and provide only a virtual average of the diverse constituent cells, single-cell studies enable the molecular distinction of all cell types within a complex population mix, such as a tumour or developing organ. For instance, single-cell gene expression profiling has contributed to improved understanding of how histologically identical, adjacent cells make different differentiation decisions during development. Beyond development, single-cell gene expression studies have enabled the characteristics of previously known cell types to be more fully defined and facilitated the identification of novel categories of cells, contributing to improvements in our understanding of both normal and disease-related physiological processes and leading to the identification of new treatment approaches. Although limitations remain to be overcome, technology for the analysis of single-cell gene expression patterns is improving rapidly and beginning to provide a detailed atlas of the gene expression patterns of all cell types in the human body.
Collapse
Affiliation(s)
- S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA.
| |
Collapse
|
54
|
A bigenic mouse model of FSGS reveals perturbed pathways in podocytes, mesangial cells and endothelial cells. PLoS One 2019; 14:e0216261. [PMID: 31461442 PMCID: PMC6713350 DOI: 10.1371/journal.pone.0216261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/12/2019] [Indexed: 11/24/2022] Open
Abstract
Focal segmental glomerulosclerosis is a major cause of end stage renal disease. Many patients prove unresponsive to available therapies. An improved understanding of the molecular basis of the disease process could provide insights leading to novel therapeutic approaches. In this study we carried out an RNA-seq analysis of the altered gene expression patterns of podocytes, mesangial cells and glomerular endothelial cells of the bigenic Cd2ap+/-, Fyn-/- mutant mouse model of FSGS. In the podocytes we observed upregulation of many genes related to the Tgfβ family/pathway, including Gdnf, Tgfβ1, Tgfβ2, Snai2, Vegfb, Bmp4, and Tnc. The mutant podocytes also showed upregulation of Acta2, a marker of smooth muscle and associated with myofibroblasts, which are implicated in driving fibrosis. GO analysis of the podocyte upregulated genes identified elevated protein kinase activity, increased expression of growth factors, and negative regulation of cell adhesion, perhaps related to the observed podocyte loss. Both podocytes and mesangial cells showed strong upregulation of aldehyde dehydrogenase genes involved in the synthesis of retinoic acid. Similarly, the Cd2ap+/-, Fyn-/- mesangial cells, as well as podocytes in other genetic models, and the glomeruli of human FSGS patients, all show upregulation of the serine protease Prss23, with the common thread suggesting important functionality. Another gene with strong upregulation in the Cd2ap+/-, Fyn-/- mutant mesangial cells as well as multiple other mutant mouse models of FSGS was thrombospondin, which activates the secreted inactive form of Tgfβ. The Cd2ap+/-, Fyn-/- mutant endothelial cells showed elevated expression of genes involved in cell proliferation, angioblast migration, angiogenesis, and neovasculature, all consistent with the formation of new blood vessels in the diseased glomerulus. The resulting global definition of the perturbed molecular pathways in the three major cell types of the mutant glomerulus provide deeper understanding of the molecular pathogenic pathways.
Collapse
|
55
|
Abstract
Kidney organoids are regarded as important tools with which to study the development of the normal and diseased human kidney. Since the first reports of human pluripotent stem cell-derived kidney organoids 5 years ago, kidney organoids have been successfully used to model glomerular and tubular diseases. In parallel, advances in single-cell RNA sequencing have led to identification of a variety of cell types in the organoids, and have shown these to be similar to, but more immature than, human kidney cells in vivo. Protocols for the in vitro expansion of stem cell-derived nephron progenitor cells (NPCs), as well as those for the selective induction of specific lineages, especially glomerular podocytes, have also been reported. Although most current organoids are based on the induction of NPCs, an induction protocol for ureteric buds (collecting duct precursors) has also been developed, and approaches to generate more complex kidney structures may soon be possible. Maturation of organoids is a major challenge, and more detailed analysis of the developing kidney at a single cell level is needed. Eventually, organotypic kidney structures equipped with nephrons, collecting ducts, ureters, stroma and vascular flow are required to generate transplantable kidneys; such attempts are in progress.
Collapse
|
56
|
Combes AN, Phipson B, Lawlor KT, Dorison A, Patrick R, Zappia L, Harvey RP, Oshlack A, Little MH. Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk. Development 2019; 146:dev.178673. [PMID: 31118232 DOI: 10.1242/dev.178673] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022]
Abstract
Recent advances in the generation of kidney organoids and the culture of primary nephron progenitors from mouse and human have been based on knowledge of the molecular basis of kidney development in mice. Although gene expression during kidney development has been intensely investigated, single cell profiling provides new opportunities to further subsect component cell types and the signalling networks at play. Here, we describe the generation and analysis of 6732 single cell transcriptomes from the fetal mouse kidney [embryonic day (E)18.5] and 7853 sorted nephron progenitor cells (E14.5). These datasets provide improved resolution of cell types and specific markers, including subdivision of the renal stroma and heterogeneity within the nephron progenitor population. Ligand-receptor interaction and pathway analysis reveals novel crosstalk between cellular compartments and associates new pathways with differentiation of nephron and ureteric epithelium cell types. We identify transcriptional congruence between the distal nephron and ureteric epithelium, showing that most markers previously used to identify ureteric epithelium are not specific. Together, this work improves our understanding of metanephric kidney development and provides a template to guide the regeneration of renal tissue.
Collapse
Affiliation(s)
- Alexander N Combes
- Department of Anatomy & Neuroscience, University of Melbourne, Parkville, Victoria 3010, Australia .,Cell Biology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria 3052, Australia
| | - Belinda Phipson
- Cell Biology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria 3052, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kynan T Lawlor
- Cell Biology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria 3052, Australia
| | - Aude Dorison
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Ralph Patrick
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Kensington, New South Wales 2033, Australia
| | - Luke Zappia
- Cell Biology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria 3052, Australia.,School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Richard P Harvey
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Kensington, New South Wales 2033, Australia.,School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, New South Wales 2010, Australia
| | - Alicia Oshlack
- Department of Anatomy & Neuroscience, University of Melbourne, Parkville, Victoria 3010, Australia.,School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Melissa H Little
- Department of Anatomy & Neuroscience, University of Melbourne, Parkville, Victoria 3010, Australia .,Cell Biology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria 3052, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
57
|
Kong Y, Rastogi D, Seoighe C, Greally JM, Suzuki M. Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data. PLoS One 2019; 14:e0215987. [PMID: 31022271 PMCID: PMC6483354 DOI: 10.1371/journal.pone.0215987] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Cell subtype proportion variability between samples contributes significantly to the variation of functional genomic properties such as gene expression or DNA methylation. Although the impact of the variation of cell subtype composition on measured genomic quantities is recognized, and some innovative tools have been developed for the analysis of heterogeneous samples, most functional genomics studies using samples with mixed cell types still ignore the influence of cell subtype proportion variation, or just deal with it as a nuisance variable to be eliminated. Here we demonstrate how harvesting information about cell subtype proportions from functional genomics data can provide insights into cellular changes associated with phenotypes. We focused on two types of mixed cell populations, human blood and mouse kidney. Cell type prediction is well developed in the former, but not currently in the latter. Estimating the cellular repertoire is easier when a reference dataset from purified samples of all cell types in the tissue is available, as is the case for blood. However, reference datasets are not available for most other tissues, such as the kidney. In this study, we showed that the proportion of alterations attributable to changes in the cellular composition varies strikingly in the two disorders (asthma and systemic lupus erythematosus), suggesting that the contribution of cell subtype proportion changes to functional genomic properties can be disease-specific. We also showed that a reference dataset from a single-cell RNA-seq study successfully estimated the cell subtype proportions in mouse kidney and allowed us to distinguish altered cell subtype differences between two different knock-out mouse models, both of which had reported a reduced number of glomeruli compared to their wild-type counterparts. These findings demonstrate that testing for changes in cell subtype proportions between conditions can yield important insights in functional genomics studies.
Collapse
Affiliation(s)
- Yu Kong
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Deepa Rastogi
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, University Road, Galway, Ireland
| | - John M. Greally
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Masako Suzuki
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
| |
Collapse
|
58
|
Mucenski ML, Mahoney R, Adam M, Potter AS, Potter SS. Single cell RNA-seq study of wild type and Hox9,10,11 mutant developing uterus. Sci Rep 2019; 9:4557. [PMID: 30872674 PMCID: PMC6418183 DOI: 10.1038/s41598-019-40923-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/25/2019] [Indexed: 12/17/2022] Open
Abstract
The uterus is a remarkable organ that must guard against infections while maintaining the ability to support growth of a fetus without rejection. The Hoxa10 and Hoxa11 genes have previously been shown to play essential roles in uterus development and function. In this report we show that the Hoxa9,10,11, Hoxc9,10,11, Hoxd9,10,11 genes play a redundant role in the formation of uterine glands. In addition, we use single cell RNA-seq to create a high resolution gene expression atlas of the developing wild type mouse uterus. Cell types and subtypes are defined, for example dividing endothelial cells into arterial, venous, capillary, and lymphatic, while epithelial cells separate into luminal and glandular subtypes. Further, a surprising heterogeneity of stromal and myocyte cell types are identified. Transcription factor codes and ligand/receptor interactions are characterized. We also used single cell RNA-seq to globally define the altered gene expression patterns in all developing uterus cell types for two Hox mutants, with 8 or 9 mutant Hox genes. The mutants show a striking disruption of Wnt signaling as well as the Cxcl12/Cxcr4 ligand/receptor axis.
Collapse
Affiliation(s)
- Michael L Mucenski
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Robert Mahoney
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Andrew S Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
| |
Collapse
|
59
|
Hulin A, Hortells L, Gomez-Stallons MV, O'Donnell A, Chetal K, Adam M, Lancellotti P, Oury C, Potter SS, Salomonis N, Yutzey KE. Maturation of heart valve cell populations during postnatal remodeling. Development 2019; 146:dev.173047. [PMID: 30796046 DOI: 10.1242/dev.173047] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/07/2019] [Indexed: 01/23/2023]
Abstract
Heart valve cells mediate extracellular matrix (ECM) remodeling during postnatal valve leaflet stratification, but phenotypic and transcriptional diversity of valve cells in development is largely unknown. Single cell analysis of mouse heart valve cells was used to evaluate cell heterogeneity during postnatal ECM remodeling and leaflet morphogenesis. The transcriptomic analysis of single cells from postnatal day (P)7 and P30 murine aortic (AoV) and mitral (MV) heart valves uncovered distinct subsets of melanocytes, immune and endothelial cells present at P7 and P30. By contrast, interstitial cell populations are different from P7 to P30. P7 valve leaflets exhibit two distinct collagen- and glycosaminoglycan-expressing interstitial cell clusters, and prevalent ECM gene expression. At P30, four interstitial cell clusters are apparent with leaflet specificity and differential expression of complement factors, ECM proteins and osteogenic genes. This initial transcriptomic analysis of postnatal heart valves at single cell resolution demonstrates that subpopulations of endothelial and immune cells are relatively constant throughout postnatal development, but interstitial cell subpopulations undergo changes in gene expression and cellular functions in primordial and mature valves.
Collapse
Affiliation(s)
- Alexia Hulin
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA.,Laboratory of Cardiology, GIGA Cardiovascular Sciences, University of Liège, CHU Sart Tilman, Liège 4000, Belgium
| | - Luis Hortells
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA
| | - M Victoria Gomez-Stallons
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA
| | - Anna O'Donnell
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA
| | - Patrizio Lancellotti
- Laboratory of Cardiology, GIGA Cardiovascular Sciences, University of Liège, CHU Sart Tilman, Liège 4000, Belgium.,University of Liège Hospital, GIGA Cardiovascular Sciences, Department of Cardiology, Heart Valve Clinic, CHU Sart Tilman, Liège 4000, Belgium.,Gruppo Villa Maria Care and Research, Anthea Hospital, Bari 70124, Italy
| | - Cecile Oury
- Laboratory of Cardiology, GIGA Cardiovascular Sciences, University of Liège, CHU Sart Tilman, Liège 4000, Belgium
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH45229, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH45229, USA
| | - Katherine E Yutzey
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH45229, USA
| |
Collapse
|
60
|
Revolutionizing immunology with single-cell RNA sequencing. Cell Mol Immunol 2019; 16:242-249. [PMID: 30796351 DOI: 10.1038/s41423-019-0214-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/30/2019] [Indexed: 12/30/2022] Open
Abstract
The immune system is composed of a complex hierarchy of cell types that protect the organism against disease and maintain homeostasis. Identifying heterogeneity of immune cells is the key to understanding the immune system. Advanced single-cell RNA sequencing (scRNA-seq) technologies are revolutionizing our ability to study immunology. By measuring transcriptomes at the single-cell level, scRNA-seq enables identification of cellular heterogeneity in far greater detail than conventional methods. In this review, we introduce the existing scRNA-seq technologies and present their strengths and weaknesses. We also discuss potential applications and future innovations of scRNA-seq in immunology.
Collapse
|
61
|
Combes AN, Zappia L, Er PX, Oshlack A, Little MH. Single-cell analysis reveals congruence between kidney organoids and human fetal kidney. Genome Med 2019; 11:3. [PMID: 30674341 DOI: 10.0.4.162/s13073-019-0615-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/14/2019] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Human kidney organoids hold promise for studying development, disease modelling and drug screening. However, the utility of stem cell-derived kidney tissues will depend on how faithfully these replicate normal fetal development at the level of cellular identity and complexity. METHODS Here, we present an integrated analysis of single cell datasets from human kidney organoids and human fetal kidney to assess similarities and differences between the component cell types. RESULTS Clusters in the combined dataset contained cells from both organoid and fetal kidney with transcriptional congruence for key stromal, endothelial and nephron cell type-specific markers. Organoid enriched neural, glial and muscle progenitor populations were also evident. Major transcriptional differences between organoid and human tissue were likely related to technical artefacts. Cell type-specific comparisons revealed differences in stromal, endothelial and nephron progenitor cell types including expression of WNT2B in the human fetal kidney stroma. CONCLUSIONS This study supports the fidelity of kidney organoids as models of the developing kidney and affirms their potential in disease modelling and drug screening.
Collapse
Affiliation(s)
- Alexander N Combes
- Department of Anatomy & Neuroscience, University of Melbourne, Melbourne, VIC, Australia.
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
| | - Luke Zappia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Pei Xuan Er
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Alicia Oshlack
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Melissa H Little
- Department of Anatomy & Neuroscience, University of Melbourne, Melbourne, VIC, Australia.
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia.
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia.
| |
Collapse
|
62
|
Combes AN, Zappia L, Er PX, Oshlack A, Little MH. Single-cell analysis reveals congruence between kidney organoids and human fetal kidney. Genome Med 2019; 11:3. [PMID: 30674341 PMCID: PMC6345028 DOI: 10.1186/s13073-019-0615-0] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/14/2019] [Indexed: 01/12/2023] Open
Abstract
Background Human kidney organoids hold promise for studying development, disease modelling and drug screening. However, the utility of stem cell-derived kidney tissues will depend on how faithfully these replicate normal fetal development at the level of cellular identity and complexity. Methods Here, we present an integrated analysis of single cell datasets from human kidney organoids and human fetal kidney to assess similarities and differences between the component cell types. Results Clusters in the combined dataset contained cells from both organoid and fetal kidney with transcriptional congruence for key stromal, endothelial and nephron cell type-specific markers. Organoid enriched neural, glial and muscle progenitor populations were also evident. Major transcriptional differences between organoid and human tissue were likely related to technical artefacts. Cell type-specific comparisons revealed differences in stromal, endothelial and nephron progenitor cell types including expression of WNT2B in the human fetal kidney stroma. Conclusions This study supports the fidelity of kidney organoids as models of the developing kidney and affirms their potential in disease modelling and drug screening. Electronic supplementary material The online version of this article (10.1186/s13073-019-0615-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alexander N Combes
- Department of Anatomy & Neuroscience, University of Melbourne, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Melbourne, VIC, Australia.
| | - Luke Zappia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Pei Xuan Er
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Alicia Oshlack
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Melissa H Little
- Department of Anatomy & Neuroscience, University of Melbourne, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Melbourne, VIC, Australia. .,School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia. .,Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia.
| |
Collapse
|
63
|
Image-based modeling of kidney branching morphogenesis reveals GDNF-RET based Turing-type mechanism and pattern-modulating WNT11 feedback. Nat Commun 2019; 10:239. [PMID: 30651543 PMCID: PMC6484223 DOI: 10.1038/s41467-018-08212-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 12/22/2018] [Indexed: 11/08/2022] Open
Abstract
Branching patterns and regulatory networks differ between branched organs. It has remained unclear whether a common regulatory mechanism exists and how organ-specific patterns can emerge. Of all previously proposed signalling-based mechanisms, only a ligand-receptor-based Turing mechanism based on FGF10 and SHH quantitatively recapitulates the lung branching patterns. We now show that a GDNF-dependent ligand-receptor-based Turing mechanism quantitatively recapitulates branching of cultured wildtype and mutant ureteric buds, and achieves similar branching patterns when directing domain outgrowth in silico. We further predict and confirm experimentally that the kidney-specific positive feedback between WNT11 and GDNF permits the dense packing of ureteric tips. We conclude that the ligand-receptor based Turing mechanism presents a common regulatory mechanism for lungs and kidneys, despite the differences in the molecular implementation. Given its flexibility and robustness, we expect that the ligand-receptor-based Turing mechanism constitutes a likely general mechanism to guide branching morphogenesis and other symmetry breaks during organogenesis. Many organs develop through branching morphogenesis, but whether the underlying mechanisms are shared is unknown. Here, the authors show that a ligand-receptor based Turing mechanisms, similar to that observed in lung development, likely underlies branching morphogenesis of the kidney.
Collapse
|
64
|
Abstract
Advances in single-cell transcriptome profiling have contributed to new insights into the cellular states and underlying regulatory networks that govern lineage commitment. Such cell states include multipotent progenitors that can manifest as mixed-lineage patterns of gene expression at a single-cell level. Multipotent and other self-renewing progenitors are often difficult to isolate and characterized by subtle transcriptional differences that are challenging to define. This chapter examines the application of newly developed analytical tools to define heterogeneity in diverse stem cell and multipotent progenitor populations from single-cell RNA-Seq data. In addition to the methodology and output of these approaches, we explore their application to diverse single-cell technologies (e.g., Fluidigm, Drop-Seq, 10× Genomics Chromium) and their usability by computational and non-computational biologists. We focus specifically on the use of one tool, called Iterative Clustering and Guide-gene Selection (ICGS), which has been shown to uncover novel committed, transitional, and metastable progenitor cell states. As a component of the AltAnalyze toolkit, ICGS provides advanced methods to evaluate cellular heterogeneity in combination with regulatory prediction, pathway, and alternative splicing analyses. We walk through the individual steps required to perform these analyses in hematopoietic and embryonic kidney progenitor datasets in both graphical user and command-line interfaces. By the end of this chapter, users should be able to analyze their own single-cell RNA-Seq data and obtain deeper insights into the regulatory biology of the discovered cell states.
Collapse
Affiliation(s)
- Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA.
| |
Collapse
|
65
|
Huang XT, Li X, Qin PZ, Zhu Y, Xu SN, Chen JP. Technical Advances in Single-Cell RNA Sequencing and Applications in Normal and Malignant Hematopoiesis. Front Oncol 2018; 8:582. [PMID: 30581771 PMCID: PMC6292934 DOI: 10.3389/fonc.2018.00582] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/19/2018] [Indexed: 12/20/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has been tremendously developed in the past decade owing to overcoming challenges associated with isolation of massive quantities of single cells. Previously, cell heterogeneity and low quantities of available biological material posed significant difficulties to scRNA-seq. Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of normal and malignant hematopoietic cells; this heterogeneity has often been ignored in omics studies. The application of scRNA-seq has profoundly changed our comprehension of many biological phenomena, including organ development and carcinogenesis. Hematopoiesis, is actually a maturation process for more than ten distinct blood and immune cells, and is thought to be critically involved in hematological homeostasis and in sustaining the physiological functions. However, aberrant hematopoiesis directly leads to hematological malignancy, and a deeper understanding of malignant hematopoiesis will provide deeper insights into diagnosis and prognosis for patients with hematological malignancies. Here, we aim to review the recent technical progress and future prospects for scRNA-seq, as applied in physiological and malignant hematopoiesis, in efforts to further understand the hematopoietic hierarchy and to illuminate personalized therapy and precision medicine approaches used in the clinical treatment of hematological malignancies.
Collapse
Affiliation(s)
- Xiang-Tao Huang
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xi Li
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Pei-Zhong Qin
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yao Zhu
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Shuang-Nian Xu
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jie-Ping Chen
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| |
Collapse
|
66
|
O'Brien LL, Combes AN, Short KM, Lindström NO, Whitney PH, Cullen-McEwen LA, Ju A, Abdelhalim A, Michos O, Bertram JF, Smyth IM, Little MH, McMahon AP. Wnt11 directs nephron progenitor polarity and motile behavior ultimately determining nephron endowment. eLife 2018; 7:e40392. [PMID: 30516471 PMCID: PMC6281319 DOI: 10.7554/elife.40392] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/16/2018] [Indexed: 01/09/2023] Open
Abstract
A normal endowment of nephrons in the mammalian kidney requires a balance of nephron progenitor self-renewal and differentiation throughout development. Here, we provide evidence for a novel action of ureteric branch tip-derived Wnt11 in progenitor cell organization and interactions within the nephrogenic niche, ultimately determining nephron endowment. In Wnt11 mutants, nephron progenitors dispersed from their restricted niche, intermixing with interstitial progenitors. Nephron progenitor differentiation was accelerated, kidneys were significantly smaller, and the nephron progenitor pool was prematurely exhausted, halving the final nephron count. Interestingly, RNA-seq revealed no significant differences in gene expression. Live imaging of nephron progenitors showed that in the absence of Wnt11 they lose stable attachments to the ureteric branch tips, continuously detaching and reattaching. Further, the polarized distribution of several markers within nephron progenitors is disrupted. Together these data highlight the importance of Wnt11 signaling in directing nephron progenitor behavior which determines a normal nephrogenic program.
Collapse
Affiliation(s)
- Lori L O'Brien
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell ResearchKeck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Alexander N Combes
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneAustralia
- Department of Anatomy and NeuroscienceThe University of MelbourneMelbourneAustralia
- Murdoch Children’s Research InstituteRoyal Children's HospitalMelbourneAustralia
| | - Kieran M Short
- Department of Anatomy and Neuroscience, Monash Biomedicine Discovery InstituteMonash UniversityMelbourneAustralia
- Development and Stem Cells Program, Monash Biomedicine Discovery InstituteMonash UniversityMelbourneAustralia
| | - Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell ResearchKeck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Peter H Whitney
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell ResearchKeck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Luise A Cullen-McEwen
- Department of Anatomy and Neuroscience, Monash Biomedicine Discovery InstituteMonash UniversityMelbourneAustralia
| | - Adler Ju
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneAustralia
| | - Ahmed Abdelhalim
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell ResearchKeck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Odyssé Michos
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell ResearchKeck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - John F Bertram
- Department of Anatomy and Neuroscience, Monash Biomedicine Discovery InstituteMonash UniversityMelbourneAustralia
| | - Ian M Smyth
- Department of Anatomy and Neuroscience, Monash Biomedicine Discovery InstituteMonash UniversityMelbourneAustralia
- Development and Stem Cells Program, Monash Biomedicine Discovery InstituteMonash UniversityMelbourneAustralia
| | - Melissa H Little
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneAustralia
- Department of Anatomy and NeuroscienceThe University of MelbourneMelbourneAustralia
- Murdoch Children’s Research InstituteRoyal Children's HospitalMelbourneAustralia
- Department of PediatricsUniversity of MelbourneParkvilleAustralia
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell ResearchKeck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| |
Collapse
|
67
|
Muench DE, Ferchen K, Velu CS, Pradhan K, Chetal K, Chen X, Weirauch MT, Colmenares C, Verma A, Salomonis N, Grimes HL. SKI controls MDS-associated chronic TGF-β signaling, aberrant splicing, and stem cell fitness. Blood 2018; 132:e24-e34. [PMID: 30249787 PMCID: PMC6251005 DOI: 10.1182/blood-2018-06-860890] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/18/2018] [Indexed: 01/19/2023] Open
Abstract
The transforming growth factor beta (TGF-β) signaling pathway controls hematopoietic stem cell (HSC) behavior in the marrow niche; however, TGF-β signaling becomes chronic in early-stage myelodysplastic syndrome (MDS). Although TGF-β signaling normally induces negative feedback, in early-stage MDS, high levels of microRNA-21 (miR-21) contribute to chronic TGF-β signaling. We found that a TGF-β signal-correlated gene signature is sufficient to identify an MDS patient population with abnormal RNA splicing (eg, CSF3R) independent of splicing factor mutations and coincident with low HNRNPK activity. Levels of SKI messenger RNA (mRNA) encoding a TGF-β antagonist are sufficient to identify these patients. However, MDS patients with high SKI mRNA and chronic TGF-β signaling lack SKI protein because of miR-21 activity. To determine the impact of SKI loss, we examined murine Ski -/- HSC function. First, competitive HSC transplants revealed a profound defect in stem cell fitness (competitive disadvantage) but not specification, homing, or multilineage production. Aged recipients of Ski -/- HSCs exhibited mild phenotypes similar to phenotypes in those with macrocytic anemia. Second, blastocyst complementation revealed a dramatic block in Ski -/- hematopoiesis in the absence of transplantation. Similar to SKI-high MDS patient samples, Ski -/- HSCs strikingly upregulated TGF-β signaling and deregulated expression of spliceosome genes (including Hnrnpk). Moreover, novel single-cell splicing analyses demonstrated that Ski -/- HSCs and high levels of SKI expression in MDS patient samples share abnormal alternative splicing of common genes (including those that encode splicing factors). We conclude that miR-21-mediated loss of SKI activates TGF-β signaling and alternative splicing to impair the competitive advantage of normal HSCs (fitness), which could contribute to selection of early-stage MDS-genic clones.
Collapse
Affiliation(s)
- David E Muench
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Kyle Ferchen
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Chinavenmeni S Velu
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Kith Pradhan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Matthew T Weirauch
- Division of Biomedical Informatics
- Center for Autoimmune Genomics and Etiology, and
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Clemencia Colmenares
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
| | - Amit Verma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY; and
| | | | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| |
Collapse
|
68
|
Wu H, Uchimura K, Donnelly EL, Kirita Y, Morris SA, Humphreys BD. Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics. Cell Stem Cell 2018; 23:869-881.e8. [PMID: 30449713 DOI: 10.1016/j.stem.2018.10.010] [Citation(s) in RCA: 358] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 08/09/2018] [Accepted: 10/06/2018] [Indexed: 12/18/2022]
Abstract
Kidney organoids derived from human pluripotent stem cells have great utility for investigating organogenesis and disease mechanisms and, potentially, as a replacement tissue source, but how closely organoids derived from current protocols replicate adult human kidney is undefined. We compared two directed differentiation protocols by single-cell transcriptomics of 83,130 cells from 65 organoids with single-cell transcriptomes of fetal and adult kidney cells. Both protocols generate a diverse range of kidney cells with differing ratios, but organoid-derived cell types are immature, and 10%-20% of cells are non-renal. Reconstructing lineage relationships by pseudotemporal ordering identified ligands, receptors, and transcription factor networks associated with fate decisions. Brain-derived neurotrophic factor (BDNF) and its cognate receptor NTRK2 were expressed in the neuronal lineage during organoid differentiation. Inhibiting this pathway improved organoid formation by reducing neurons by 90% without affecting kidney differentiation, highlighting the power of single-cell technologies to characterize and improve organoid differentiation.
Collapse
Affiliation(s)
- Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kohei Uchimura
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Erinn L Donnelly
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yuhei Kirita
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
69
|
Kurtzeborn K, Cebrian C, Kuure S. Regulation of Renal Differentiation by Trophic Factors. Front Physiol 2018; 9:1588. [PMID: 30483151 PMCID: PMC6240607 DOI: 10.3389/fphys.2018.01588] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/23/2018] [Indexed: 12/11/2022] Open
Abstract
Classically, trophic factors are considered as proteins which support neurons in their growth, survival, and differentiation. However, most neurotrophic factors also have important functions outside of the nervous system. Especially essential renal growth and differentiation regulators are glial cell line-derived neurotrophic factor (GDNF), bone morphogenetic proteins (BMPs), and fibroblast growth factors (FGFs). Here we discuss how trophic factor-induced signaling contributes to the control of ureteric bud (UB) branching morphogenesis and to maintenance and differentiation of nephrogenic mesenchyme in embryonic kidney. The review includes recent advances in trophic factor functions during the guidance of branching morphogenesis and self-renewal versus differentiation decisions, both of which dictate the control of kidney size and nephron number. Creative utilization of current information may help better recapitulate renal differentiation in vitro, but it is obvious that significantly more basic knowledge is needed for development of regeneration-based renal therapies.
Collapse
Affiliation(s)
- Kristen Kurtzeborn
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Medicum, University of Helsinki, Helsinki, Finland
| | - Cristina Cebrian
- Developmental Biology Division, Cincinnati Children’s Hospital, Cincinnati, OH, United States
| | - Satu Kuure
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Medicum, University of Helsinki, Helsinki, Finland
- GM-Unit, Laboratory Animal Centre, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| |
Collapse
|
70
|
Key features of the nephrogenic zone in the fetal human kidney—hardly known but relevant for the detection of first traces impairing nephrogenesis. Cell Tissue Res 2018; 375:589-603. [DOI: 10.1007/s00441-018-2937-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/21/2018] [Indexed: 01/09/2023]
|
71
|
Hay SB, Ferchen K, Chetal K, Grimes HL, Salomonis N. The Human Cell Atlas bone marrow single-cell interactive web portal. Exp Hematol 2018; 68:51-61. [PMID: 30243574 PMCID: PMC6296228 DOI: 10.1016/j.exphem.2018.09.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/11/2018] [Accepted: 09/14/2018] [Indexed: 01/17/2023]
Abstract
The Human Cell Atlas (HCA) is expected to facilitate the creation of reference cell profiles, marker genes, and gene regulatory networks that will provide a deeper understanding of healthy and disease cell types from clinical biospecimens. The hematopoietic system includes dozens of distinct, transcriptionally coherent cell types, including intermediate transitional populations that have not been previously described at a molecular level. Using the first data release from the HCA bone marrow tissue project, we resolved common, rare, and potentially transitional cell populations from over 100,000 hematopoietic cells spanning 35 transcriptionally coherent groups across eight healthy donors using emerging new computational approaches. These data highlight novel mixed-lineage progenitor populations and putative trajectories governing granulocytic, monocytic, lymphoid, erythroid, megakaryocytic, and eosinophil specification. Our analyses suggest significant variation in cell-type composition and gene expression among donors, including biological processes affected by donor age. To enable broad exploration of these findings, we provide an interactive website to probe intra-cell and extra-cell population differences within and between donors and reference markers for cellular classification and cellular trajectories through associated progenitor states.
Collapse
Affiliation(s)
- Stuart B Hay
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kyle Ferchen
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - H Leighton Grimes
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA; Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Division of Experimental Hematology and Cancer 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; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA.
| |
Collapse
|
72
|
Lindström NO, De Sena Brandine G, Ransick A, McMahon AP. Single-Cell RNA Sequencing of the Adult Mouse Kidney: From Molecular Cataloging of Cell Types to Disease-Associated Predictions. Am J Kidney Dis 2018; 73:140-142. [PMID: 30241960 DOI: 10.1053/j.ajkd.2018.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/22/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Guilherme De Sena Brandine
- Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Andrew Ransick
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA.
| |
Collapse
|
73
|
Ye Y, Song H, Zhang J, Shi S. Understanding the Biology and Pathogenesis of the Kidney by Single-Cell Transcriptomic Analysis. KIDNEY DISEASES 2018; 4:214-225. [PMID: 30574498 DOI: 10.1159/000492470] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/26/2018] [Indexed: 12/20/2022]
Abstract
Background Single-cell RNA-seq (scRNA-seq) has recently emerged as a revolutionary and powerful tool for biomedical research. However, there have been relatively few studies using scRNA-seq in the field of kidney study. Summary scRNA-seq achieves gene expression profiling at single-cell resolution in contrast with the conventional methods of gene expression profiling, which are based on cell population and give averaged values of gene expression of the cells. Single-cell transcriptomic analysis is crucial because individual cells of the same type are highly heterogeneous in gene expression, which reflects the existence of subpopulations, different cellular states, or molecular dynamics, of the cells, and should be resolved for further insights. In addition, gene expression analysis of tissues or organs that usually comprise multiple cell types or subtypes results in data that are not fully applicable to any given cell type. scRNA-seq is capable of identifying all cell types and subtypes in a tissue, including those that are new or present in small quantity. With these unique capabilities, scRNA-seq has been used to dissect molecular processes in cell differentiation and to trace cell lineages in development. It is also used to analyze the cells in a lesion of disease to identify the cell types and molecular dynamics implicated in the injury. With continuous technical improvement, scRNA-seq has become extremely high throughput and cost effective, making it accessible to all laboratories. In the present review article, we provide an overall review of scRNA-seq concerning its history, improvements, and applications. In addition, we describe the available studies in which scRNA-seq was employed in the field of kidney research. Lastly, we discuss other potential uses of scRNA-seq for kidney research. Key Message This review article provides general information on scRNA-seq and its various uses. Particularly, we summarize the studies in the field of kidney diseases in which scRNA-seq was used and discuss potential additional uses of scRNA-seq for kidney research.
Collapse
Affiliation(s)
- Yuting Ye
- National Clinical Research Center for Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Hui Song
- National Clinical Research Center for Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Jiong Zhang
- National Clinical Research Center for Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Shaolin Shi
- National Clinical Research Center for Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| |
Collapse
|
74
|
Magella B, Mahoney R, Adam M, Potter SS. Reduced Abd-B Hox function during kidney development results in lineage infidelity. Dev Biol 2018; 438:84-93. [PMID: 29596840 DOI: 10.1016/j.ydbio.2018.03.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 02/28/2018] [Accepted: 03/21/2018] [Indexed: 02/05/2023]
Abstract
Hox genes can function as key drivers of segment identity, with Hox mutations in Drosophila often resulting in dramatic homeotic transformations. In addition, however, they can serve other essential functions. In mammals, the study of Hox gene roles in development is complicated by the presence of four Hox clusters with a total of 39 genes showing extensive functional overlap. In this study, in order to better understand shared core Hox functions, we examined kidney development in mice with frameshift mutations of multiple Abd-B type Hox genes. The resulting phenotypes included dramatically reduced branching morphogenesis of the ureteric bud, premature depletion of nephron progenitors and abnormal development of the stromal compartment. Most unexpected, however, we also observed a cellular level lineage infidelity in nephron segments. Scattered cells within the proximal tubules, for example, expressed genes normally expressed only in collecting ducts. Multiple combinations of inappropriate nephron segment specific marker expression were found. In some cases, cells within a tubule showed incorrect identity, while in other cases cells showed ambiguous character, with simultaneous expression of genes associated with more than one nephron segment. These results give evidence that Hox genes have an overlapping core function at the cellular level in driving and/or maintaining correct differentiation decisions.
Collapse
Affiliation(s)
- Bliss Magella
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, United States
| | - Robert Mahoney
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, United States
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, United States
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, United States.
| |
Collapse
|
75
|
Muthukrishnan SD, Ryzhov S, Karolak M, Oxburgh L. Nephron progenitor cell death elicits a limited compensatory response associated with interstitial expansion in the neonatal kidney. Dis Model Mech 2018; 11:dmm.030544. [PMID: 29196442 PMCID: PMC5818074 DOI: 10.1242/dmm.030544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 11/23/2017] [Indexed: 12/11/2022] Open
Abstract
The final nephron number in an adult kidney is regulated by nephron progenitor cell availability and collecting duct branching in the fetal period. Fetal environmental perturbations that cause reductions in cell numbers in these two compartments result in low nephron endowment. Previous work has shown that maternal dietary factors influence nephron progenitor cell availability, with both caloric restriction and protein deprivation leading to reduced cell numbers through apoptosis. In this study, we evaluate the consequences of inducing nephron progenitor cell death on progenitor niche dynamics and on nephron endowment. Depletion of approximately 40% of nephron progenitor cells by expression of diphtheria toxin A at embryonic day 15 in the mouse results in 10-20% nephron reduction in the neonatal period. Analysis of cell numbers within the progenitor cell pool following induction of apoptosis reveals a compensatory response in which surviving progenitor cells increase their proliferation and replenish the niche. The proliferative response is temporally associated with infiltration of macrophages into the nephrogenic zone. Colony stimulating factor 1 (CSF1) has a mitogenic effect on nephron progenitor cells, providing a potential explanation for the compensatory proliferation. However, CSF1 also promotes interstitial cell proliferation, and the compensatory response is associated with interstitial expansion in recovering kidneys which can be pharmacologically inhibited by treatment with clodronate liposomes. Our findings suggest that the fetal kidney employs a macrophage-dependent compensatory regenerative mechanism to respond to acute injury caused by death of nephron progenitor cells, but that this regenerative response is associated with neonatal interstitial expansion. Editor's choice: Formation of the kidney relies on maintaining progenitor cells throughout development. The authors find that apoptotic loss of nephron progenitor cells provokes compensatory proliferation mediated by trophic factors released by phagocytes.
Collapse
Affiliation(s)
- Sree Deepthi Muthukrishnan
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA.,Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
| | - Sergey Ryzhov
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA
| | - Michele Karolak
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA
| | - Leif Oxburgh
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA
| |
Collapse
|