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Bantounas I, Rooney KM, Lopes FM, Tengku F, Woods S, Zeef LAH, Lin IH, Kuba SY, Bates N, Hummelgaard S, Hillman KA, Cereghini S, Woolf AS, Kimber SJ. Human pluripotent stem cell-derived kidney organoids reveal tubular epithelial pathobiology of heterozygous HNF1B-associated dysplastic kidney malformations. Stem Cell Reports 2024; 19:859-876. [PMID: 38788724 DOI: 10.1016/j.stemcr.2024.04.011] [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: 02/14/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Hepatocyte nuclear factor 1B (HNF1B) encodes a transcription factor expressed in developing human kidney epithelia. Heterozygous HNF1B mutations are the commonest monogenic cause of dysplastic kidney malformations (DKMs). To understand their pathobiology, we generated heterozygous HNF1B mutant kidney organoids from CRISPR-Cas9 gene-edited human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) reprogrammed from a family with HNF1B-associated DKMs. Mutant organoids contained enlarged malformed tubules displaying deregulated cell turnover. Numerous genes implicated in Mendelian kidney tubulopathies were downregulated, and mutant tubules resisted the cyclic AMP (cAMP)-mediated dilatation seen in controls. Bulk and single-cell RNA sequencing (scRNA-seq) analyses indicated abnormal Wingless/Integrated (WNT), calcium, and glutamatergic pathways, the latter hitherto unstudied in developing kidneys. Glutamate ionotropic receptor kainate type subunit 3 (GRIK3) was upregulated in malformed mutant nephron tubules and prominent in HNF1B mutant fetal human dysplastic kidney epithelia. These results reveal morphological, molecular, and physiological roles for HNF1B in human kidney tubule differentiation and morphogenesis illuminating the developmental origin of mutant-HNF1B-causing kidney disease.
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Affiliation(s)
- Ioannis Bantounas
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
| | - Kirsty M Rooney
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
| | - Filipa M Lopes
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
| | - Faris Tengku
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
| | - Steven Woods
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
| | - Leo A H Zeef
- Bioinformatics Core Facility, University of Manchester, Manchester, UK
| | - I-Hsuan Lin
- Bioinformatics Core Facility, University of Manchester, Manchester, UK
| | - Shweta Y Kuba
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
| | - Nicola Bates
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
| | - Sandra Hummelgaard
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK; Department of Biomedicine, Aarhus University, Denmark
| | - Katherine A Hillman
- Manchester Institute of Nephrology and Transplantation, Manchester University NHS Foundation Trust, Manchester, UK
| | - Silvia Cereghini
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratorial de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK; Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK.
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Abstract
MicroRNAs (miRNAs) belong to a class of endogenous small noncoding RNAs that regulate gene expression at the posttranscriptional level, through both translational repression and mRNA destabilization. They are key regulators of kidney morphogenesis, modulating diverse biological processes in different renal cell lineages. Dysregulation of miRNA expression disrupts early kidney development and has been implicated in the pathogenesis of developmental kidney diseases. In this Review, we summarize current knowledge of miRNA biogenesis and function and discuss in detail the role of miRNAs in kidney morphogenesis and developmental kidney diseases, including congenital anomalies of the kidney and urinary tract and Wilms tumor. We conclude by discussing the utility of miRNAs as potentially novel biomarkers and therapeutic agents.
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Affiliation(s)
- Débora Malta Cerqueira
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- John G. Rangos Sr. Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Maliha Tayeb
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- John G. Rangos Sr. Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jacqueline Ho
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- John G. Rangos Sr. Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Liu W, Zheng L, Zhang R, Hou P, Wang J, Wu L, Li J. Circ-ZEB1 promotes PIK3CA expression by silencing miR-199a-3p and affects the proliferation and apoptosis of hepatocellular carcinoma. Mol Cancer 2022; 21:72. [PMID: 35277182 PMCID: PMC8915544 DOI: 10.1186/s12943-022-01529-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/01/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Although the prognostic outcomes of liver cancer (LC) cases have improved with the advancement in diagnostic technology and treatment methods, the transferability and recurrence of HCC and the 5-year and 10-year survival rates of patients have remained unsatisfactory. As a result, there is a need for more accurate diagnostic indicators that can detect liver cancer early, effectively improving the prognosis of patients. Whole-genome sequencing (WGS) revealed that circ-ZEB1 and PIK3CA are highly expressed in HCC tissues, whereas miR-199a-3p is significantly downregulated in HCC. Multiple databases search and biological analysis revealed that elevated expression of circ-ZEB1 and PIK3CA was related to poor prognosis of HCC. In vitro and in vivo studies revealed that upregulated levels of PIK3CA and circ-ZEB1 were closely associated with HCC proliferation and apoptosis. Based on these results, we believe that circ-ZEB1 and PIK3CA could be used as biomarkers to diagnose and treat patients with HCC. More importantly, circ-ZEB1 can promotes the expression of PIK3CA by silencing miR-199a-3p and affecting the progression of HCC. METHODS AND RESULTS Postoperative specimens from 56 patients with HCC who had not undergone chemotherapy from 2015 to 2018 were collected from the Department of Hepatobiliary Surgery, Second Affiliated Hospital of Nanchang University. WGS revealed differential expression of genes in HCC. Furthermore, RT-qPCR detected the expression of circ-ZEB1, miR-199a-3p, and PIK3CA in HCC tissues. MTT, EdU, and plate cloning experiments were conducted to detect cell proliferation, whereas flow cytometry analysis was used to detect apoptosis. FISH was used to co-localize circ-ZEB1 and miR-199a-3p, and biotin-coupled probe pull-down assay was used to detect the specific binding of circ-ZEB1 and miR-199a-3p. The dual-luciferase report assay detected the association of miR-199a-3p with PIK3CA. Western blotting was used to study the expression of PIK3CA protein. Circ-ZEB1 and PIK3CA were upregulated in HCC and predicted a poor prognosis. MiR-199a-3p showed low expression in HCC, whereas downregulation of circ-ZEB1 reduced HCC cell proliferation and promoted cell apoptosis. MiR-199a-3p blocked the effect of circ-ZEB1 on HCC. Circ-ZEB1 served as a biomarker of HCC. Circ-ZEB1 promoted the expression of PIK3CA by silencing miR-199a-3p to affect the progress of HCC. CONCLUSIONS Circ-ZEB1 promoted the expression of PIK3CA by depleting miR-199a-3p, thereby affecting HCC proliferation and apoptosis.
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Affiliation(s)
- Weiwei Liu
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang University, 1 Mindle Road, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Lu Zheng
- Department of Hepatobiliary Surgery, Xinqiao Hospital, Third Military Medical University, 83 Xinqiao Main Street, Chongqing, 400000, People's Republic of China
| | - Rongguiyi Zhang
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang University, 1 Mindle Road, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Ping Hou
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang University, 1 Mindle Road, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Jiakun Wang
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang University, 1 Mindle Road, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Linquan Wu
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang University, 1 Mindle Road, Nanchang, Jiangxi, 330006, People's Republic of China.
| | - Jing Li
- Department of Hepatobiliary Surgery, Xinqiao Hospital, Third Military Medical University, 83 Xinqiao Main Street, Chongqing, 400000, People's Republic of China.
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Kandettu A, Adiga D, Devi V, Suresh PS, Chakrabarty S, Radhakrishnan R, Kabekkodu SP. Deregulated miRNA clusters in ovarian cancer: Imperative implications in personalized medicine. Genes Dis 2022; 9:1443-1465. [PMID: 36157483 PMCID: PMC9485269 DOI: 10.1016/j.gendis.2021.12.026] [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: 07/02/2021] [Revised: 12/04/2021] [Accepted: 12/31/2021] [Indexed: 11/25/2022] Open
Abstract
Ovarian cancer (OC) is one of the most common and fatal types of gynecological cancer. OC is usually detected at the advanced stages of the disease, making it highly lethal. miRNAs are single-stranded, small non-coding RNAs with an approximate size ranging around 22 nt. Interestingly, a considerable proportion of miRNAs are organized in clusters with miRNA genes placed adjacent to one another, getting transcribed together to result in miRNA clusters (MCs). MCs comprise two or more miRNAs that follow the same orientation during transcription. Abnormal expression of the miRNA cluster has been identified as one of the key drivers in OC. MC exists both as tumor-suppressive and oncogenic clusters and has a significant role in OC pathogenesis by facilitating cancer cells to acquire various hallmarks. The present review summarizes the regulation and biological function of MCs in OC. The review also highlights the utility of abnormally expressed MCs in the clinical management of OC.
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Woolf AS. Building human renal tracts. J Pediatr Surg 2022; 57:172-177. [PMID: 34838308 PMCID: PMC8837266 DOI: 10.1016/j.jpedsurg.2021.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022]
Abstract
Severe kidney failure affects several million people worldwide. Among these are children born with abnormal renal tracts, and some carry mutations of genes active in renal tract development. Kidney transplants are in short supply, and long term dialysis does not obviate uraemia and its associated harmful effects. It has been envisaged that a combination of stem cell technology, developmental biology, and genetics will revolutionise our understanding of kidney disease and provide novel therapies for kidney failure. Here, we review progress towards making functional kidney tissues from human pluripotent stem cells. Organoids rich in immature glomeruli and tubules can be created in culture from pluripotent stem cells. Moreover, differentiation can be increased by implanting these cells into immunodeficient mice. Challenges remain to be overcome, however, before these tissues can be used for regenerative medicine therapies. Current limitations include the small size of an organoid, the lack of large blood vessels feeding it, and the lack of a urinary tract to plumb the kidney organoid. Pluripotent stem cell technology is also being used to create 'diseases in a dish' to understand the pathobiology underlying human renal tract malformations.
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Affiliation(s)
- Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Michael Smith Building, Faculty of Biology Medicine and Health, University of Manchester, Oxford Road, Manchester, Northern Ireland M13 9PT, United Kingdom; Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Center, Manchester, Northern Ireland, United Kingdom.
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Lopes FM, Kimber SJ, Bantounas I. In situ Hybridization of miRNAs in Human Embryonic Kidney and Human Pluripotent Stem Cell-derived Kidney Organoids. Bio Protoc 2021; 11:e4150. [PMID: 34604455 PMCID: PMC8443451 DOI: 10.21769/bioprotoc.4150] [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: 03/26/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 11/02/2022] Open
Abstract
MicroRNAs are small RNAs that negatively regulate gene expression and play an important role in fine-tuning molecular pathways during development. There is increasing interest in studying their function in the kidney, but the majority of studies to date use kidney cell lines and assess the total amounts of miRNAs of interest either by qPCR or by high-throughput methods such as next generation sequencing. However, this provides little information as to the distribution of the miRNAs in the developing kidney, which is crucial in deciphering their role, especially as there are multiple kidney cell types, each with its own specific transcriptome. Thus, we present a protocol for obtaining spatial information for miRNA expression during kidney development by in situ hybridization (ISH) of anti-miRNA, digoxigenin-labelled (DIG), Locked Nucleic Acid (LNA®) probes on (i) native human embryonic tissue and (ii) human pluripotent stem cell (hPSC)-derived 3D kidney organoids that model kidney development. We found that the method reveals the precise localization of miRNA in specific anatomical structures and/or cell types and confirms their absence from others, thus informing as to their specific role during development.
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Affiliation(s)
- Filipa M. Lopes
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
| | - Susan J. Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
| | - Ioannis Bantounas
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
- *For correspondence:
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Rooney KM, Woolf AS, Kimber SJ. Towards Modelling Genetic Kidney Diseases with Human Pluripotent Stem Cells. Nephron Clin Pract 2021; 145:285-296. [PMID: 33774632 DOI: 10.1159/000514018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 12/19/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Kidney disease causes major suffering and premature mortality worldwide. With no cure for kidney failure currently available, and with limited options for treatment, there is an urgent need to develop effective pharmaceutical interventions to slow or prevent kidney disease progression. SUMMARY In this review, we consider the feasibility of using human pluripotent stem cell-derived kidney tissues, or organoids, to model genetic kidney disease. Notable successes have been made in modelling genetic tubular diseases (e.g., cystinosis), polycystic kidney disease, and medullary cystic kidney disease. Organoid models have also been used to test novel therapies that ameliorate aberrant cell biology. Some progress has been made in modelling congenital glomerular disease, even though glomeruli within organoids are developmentally immature. Less progress has been made in modelling structural kidney malformations, perhaps because sufficiently mature metanephric mesenchyme-derived nephrons, ureteric bud-derived branching collecting ducts, and a prominent stromal cell population are not generated together within a single protocol. Key Messages: We predict that the field will advance significantly if organoids can be generated with a full complement of cell lineages and with kidney components displaying key physiological functions, such as glomerular filtration. The future economic upscaling of reproducible organoid generation will facilitate more widespread research applications, including the potential therapeutic application of these stem cell-based technologies.
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Affiliation(s)
- Kirsty M Rooney
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, United Kingdom
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, United Kingdom
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