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Ravindran A, Holappa L, Niskanen H, Skovorodkin I, Kaisto S, Beter M, Kiema M, Selvarajan I, Nurminen V, Aavik E, Aherrahrou R, Pasonen-Seppänen S, Fortino V, Laakkonen JP, Ylä-Herttuala S, Vainio S, Örd T, Kaikkonen MU. Translatome profiling reveals Itih4 as a novel smooth muscle cell-specific gene in atherosclerosis. Cardiovasc Res 2024:cvae028. [PMID: 38289873 DOI: 10.1093/cvr/cvae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 12/01/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024] Open
Abstract
AIMS Vascular smooth muscle cells (SMCs) and their derivatives are key contributors to the development of atherosclerosis. However, studying changes in SMC gene expression in heterogeneous vascular tissues is challenging due to the technical limitations and high cost associated with current approaches. In this paper, we apply Translating Ribosome Affinity Purification sequencing (TRAP-Seq) to profile SMC-specific gene expression directly from tissue. METHODS AND RESULTS To facilitate SMC-specific translatome analysis, we generated SMCTRAP mice, a transgenic mouse line expressing EGFP-tagged ribosomal protein L10a (EGFP-L10a) under the control of the SMC-specific αSMA promoter. These mice were further crossed with the atherosclerosis model Ldlr-/-, ApoB100/100 to generate SMCTRAP-AS mice and used to profile atherosclerosis-associated SMCs in thoracic aorta samples of 15-month-old SMCTRAP and SMCTRAP-AS mice. Our analysis of SMCTRAP-AS mice showed that EGFP-L10a expression was localized to SMCs in various tissues, including the aortic wall and plaque. The TRAP fraction demonstrated high enrichment of known SMC-specific genes, confirming the specificity of our approach. We identified several genes, including Cemip, Lum, Mfge8, Spp1, and Serpina3, that are known to be involved in atherosclerosis-induced gene expression. Moreover, we identified several novel genes not previously linked to SMCs in atherosclerosis, such as Anxa4, Cd276, Itih4, Myof, Pcdh11x, Rab31, Serpinb6b, Slc35e4, Slc8a3, and Spink5. Among them, we confirmed the SMC-specific expression of Itih4 in atherosclerotic lesions using immunofluorescence staining of mouse aortic roots and spatial transcriptomics of human carotid arteries. Furthermore, our more detailed analysis of Itih4 showed its link to coronary artery disease (CAD) through the colocalization of GWAS, splice-QTL, and protein-QTL signals. CONCLUSIONS We generated a SMC-specific TRAP mouse line to study atherosclerosis and identified Itih4 as a novel SMC-expressed gene in atherosclerotic plaques, warranting further investigation of its putative function in extracellular matrix stability and genetic evidence of causality.
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Affiliation(s)
- Aarthi Ravindran
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Lari Holappa
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Henri Niskanen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Ilya Skovorodkin
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Susanna Kaisto
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Mustafa Beter
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Miika Kiema
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Ilakya Selvarajan
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Valtteri Nurminen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Einari Aavik
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Rédouane Aherrahrou
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
- Institute for Cardiogenetics, Universität zu Lübeck; DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Germany; University Heart Centre Lübeck, 23562 Lübeck, Germany
| | - Sanna Pasonen-Seppänen
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Johanna P Laakkonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Seppo Ylä-Herttuala
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Seppo Vainio
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Tiit Örd
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Minna U Kaikkonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
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Kaisto S, Saarela U, Dönges L, Raykhel I, Skovorodkin I, Vainio SJ. Optimization of Renal Organoid and Organotypic Culture for Vascularization, Extended Development, and Improved Microscopy Imaging. J Vis Exp 2020. [PMID: 32281976 DOI: 10.3791/60995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Embryonic kidney organotypic cultures, and especially pluripotent stem cell-derived kidney organoids, are excellent tools for following developmental processes and modelling kidney disease. However, the models are limited by a lack of vascularization and functionality. To address this, an improved protocol for the method of xenografting cells and tissues to the chorioallantoic membrane (CAM) of an avian embryo to gain vascularization and restoration of blood flow was developed. The grafts are overlaid with custom-made minireservoirs that fix the samples to the CAM and supply them with culture medium that protects the grafts from drying. The improved culture method allows xenografts to grow for up to 9 days. The manuscript also describes how to provide optimal conditions for long-term confocal imaging of renal organoids and organotypic cultures using the previously published Fixed Z-Direction (FiZD) method. This method gently compresses an embryonic organ or organoid between a glass coverslip and membrane in a large amount of medium and provides excellent conditions for imaging for up to 12 days. Together, these methods allow vascularization and blood flow to renal organoids and organotypic kidney cultures with improved confocal imaging. The methods described here are highly beneficial for studying fundamental and applied functions of kidneys ex vivo. Both methods are applicable to various types of tissues and organoids.
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Affiliation(s)
- Susanna Kaisto
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Ulla Saarela
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Laura Dönges
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Irina Raykhel
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Ilya Skovorodkin
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Seppo J Vainio
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu; InfoTech Oulu, University of Oulu; Biobank Borealis of Northern Finland, Oulu University Hospital;
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Pietilä I, Prunskaite-Hyyryläinen R, Kaisto S, Tika E, van Eerde AM, Salo AM, Garma L, Miinalainen I, Feitz WF, Bongers EMHF, Juffer A, Knoers NVAM, Renkema KY, Myllyharju J, Vainio SJ. Wnt5a Deficiency Leads to Anomalies in Ureteric Tree Development, Tubular Epithelial Cell Organization and Basement Membrane Integrity Pointing to a Role in Kidney Collecting Duct Patterning. PLoS One 2016; 11:e0147171. [PMID: 26794322 PMCID: PMC4721645 DOI: 10.1371/journal.pone.0147171] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/30/2015] [Indexed: 11/26/2022] Open
Abstract
The Wnts can be considered as candidates for the Congenital Anomaly of Kidney and Urinary Tract, CAKUT diseases since they take part in the control of kidney organogenesis. Of them Wnt5a is expressed in ureteric bud (UB) and its deficiency leads to duplex collecting system (13/90) uni- or bilateral kidney agenesis (10/90), hypoplasia with altered pattern of ureteric tree organization (42/90) and lobularization defects with partly fused ureter trunks (25/90) unlike in controls. The UB had also notably less tips due to Wnt5a deficiency being at E15.5 306 and at E16.5 765 corresponding to 428 and 1022 in control (p<0.02; p<0.03) respectively. These changes due to Wnt5a knock out associated with anomalies in the ultrastructure of the UB daughter epithelial cells. The basement membrane (BM) was malformed so that the BM thickness increased from 46.3 nm to 71.2 nm (p<0.01) at E16.5 in the Wnt5a knock out when compared to control. Expression of a panel of BM components such as laminin and of type IV collagen was also reduced due to the Wnt5a knock out. The P4ha1 gene that encodes a catalytic subunit of collagen prolyl 4-hydroxylase I (C-P4H-I) in collagen synthesis expression and the overall C-P4H enzyme activity were elevated by around 26% due to impairment in Wnt5a function from control. The compound Wnt5a+/-;P4ha1+/- embryos demonstrated Wnt5a-/- related defects, for example local hyperplasia in the UB tree. A R260H WNT5A variant was identified from renal human disease cohort. Functional studies of the consequence of the corresponding mouse variant in comparison to normal ligand reduced Wnt5a-signalling in vitro. Together Wnt5a has a novel function in kidney organogenesis by contributing to patterning of UB derived collecting duct development contributing putatively to congenital disease.
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Affiliation(s)
- Ilkka Pietilä
- Laboratory of Developmental Biology, Oulu Centre for Cell-Matrix Research, Biocenter Oulu and Infotech Oulu, and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Renata Prunskaite-Hyyryläinen
- Laboratory of Developmental Biology, Oulu Centre for Cell-Matrix Research, Biocenter Oulu and Infotech Oulu, and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Susanna Kaisto
- Laboratory of Developmental Biology, Oulu Centre for Cell-Matrix Research, Biocenter Oulu and Infotech Oulu, and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Elisavet Tika
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Albertien M. van Eerde
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Antti M. Salo
- Oulu Centre for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Leonardo Garma
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Wout F. Feitz
- Department of Urology, Radboudumc Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ernie M. H. F. Bongers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - André Juffer
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Nine V. A. M. Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kirsten Y. Renkema
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johanna Myllyharju
- Oulu Centre for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Seppo J. Vainio
- Laboratory of Developmental Biology, Oulu Centre for Cell-Matrix Research, Biocenter Oulu and Infotech Oulu, and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- * E-mail:
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