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Article ; Online: Protocol to analyze bioenergetics in single human induced-pluripotent-stem-cell-derived kidney organoids using Seahorse XF96.

Miguel, Verónica / Reimer, Katharina Charlotte / Galyga, Anna Katharina / Jansen, Jitske / Möllmann, Julia / Meyer, Luisa / Schneider, Rebekka K / Kramann, Rafael

STAR protocols

2023 Volume 4, Issue 1, Page(s) 101999

Abstract: Metabolic derangement is a key culprit in kidney pathophysiology. Organoids have emerged as a promising in vitro tool for kidney research. Here, we present a fine-tuned protocol to analyze bioenergetics in single human induced-pluripotent-stem-cell (iPSC) ...

Abstract	Metabolic derangement is a key culprit in kidney pathophysiology. Organoids have emerged as a promising in vitro tool for kidney research. Here, we present a fine-tuned protocol to analyze bioenergetics in single human induced-pluripotent-stem-cell (iPSC)-derived kidney organoids using Seahorse XF96. We describe the generation of self-organized three-dimensional kidney organoids, followed by preparation of organoids for Seahorse XF96 analysis. We then detail how to carry out stress tests to determine mitochondrial and glycolytic rates in single kidney organoids.
MeSH term(s)	Humans ; Induced Pluripotent Stem Cells ; Solitary Kidney/metabolism ; Cell Differentiation ; Kidney ; Organoids ; Energy Metabolism
Language	English
Publishing date	2023-01-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2022.101999
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Article ; Online: Regulating Chemokine-Receptor Interactions through the Site-Specific Bioorthogonal Conjugation of Photoresponsive DNA Strands.

van Stevendaal, Marleen H M E / Hazegh Nikroo, Arjan / Mason, Alexander F / Jansen, Jitske / Yewdall, N Amy / van Hest, Jan C M

Bioconjugate chemistry

2023 Volume 34, Issue 11, Page(s) 2089–2095

Abstract: Oligonucleotide conjugation has emerged as a versatile molecular tool for regulating protein activity. A state-of-the-art labeling strategy includes the site-specific conjugation of DNA, by employing bioorthogonal groups genetically incorporated in ... ...

Abstract	Oligonucleotide conjugation has emerged as a versatile molecular tool for regulating protein activity. A state-of-the-art labeling strategy includes the site-specific conjugation of DNA, by employing bioorthogonal groups genetically incorporated in proteins through unnatural amino acids (UAAs). The incorporation of UAAs in chemokines has to date, however, remained underexplored, probably due to their sometimes poor stability following recombinant expression. In this work, we designed a fluorescent stromal-derived factor-1β (SDF-1β) chemokine fusion protein with a bioorthogonal functionality amenable for click reactions. Using amber stop codon suppression, p-azido-
MeSH term(s)	Amino Acids/chemistry ; Phenylalanine/chemistry ; Green Fluorescent Proteins/chemistry ; DNA ; Chemokines
Chemical Substances	Amino Acids ; Phenylalanine (47E5O17Y3R) ; Green Fluorescent Proteins (147336-22-9) ; DNA (9007-49-2) ; Chemokines
Language	English
Publishing date	2023-10-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1024041-x
ISSN	1520-4812 ; 1043-1802
ISSN (online)	1520-4812
ISSN	1043-1802
DOI	10.1021/acs.bioconjchem.3c00390
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Article ; Online: The podocyte as a direct target of glucocorticoids in nephrotic syndrome.

Broek, Martijn van den / Smeets, Bart / Schreuder, Michiel F / Jansen, Jitske

Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association

2021 Volume 37, Issue 10, Page(s) 1808–1815

Abstract: Nephrotic syndrome (NS) is characterized by massive proteinuria; podocyte loss or altered function is a central event in its pathophysiology. Treatment with glucocorticoids is the mainstay of therapy, however, many patients experience one or multiple ... ...

Abstract	Nephrotic syndrome (NS) is characterized by massive proteinuria; podocyte loss or altered function is a central event in its pathophysiology. Treatment with glucocorticoids is the mainstay of therapy, however, many patients experience one or multiple relapses and prolonged use may be associated with severe adverse effects. Recently the beneficial effects of glucocorticoids have been attributed to a direct effect on podocytes in addition to the well-known immunosuppressive effects. The molecular effects of glucocorticoid action have been studied using animal and cell models of NS. This review provides a comprehensive overview of different molecular mediators regulated by glucocorticoids, including an overview of the model systems that were used to study them. Glucocorticoids are described to stimulate podocyte recovery by restoring pro-survival signalling of slit diaphragm-related proteins and limiting inflammatory responses. Of special interest is the effect of glucocorticoids on stabilizing the cytoskeleton of podocytes, since these effects are also described for other therapeutic agents used in NS, such as cyclosporin. Current models provide much insight but do not fully recapitulate the human condition since the pathophysiology underlying NS is poorly understood. New and promising models include the glomerulus-on-a-chip and kidney organoids, which have the potential to be further developed into functional NS models in the future.
MeSH term(s)	Animals ; Cyclosporins/metabolism ; Cyclosporins/pharmacology ; Cyclosporins/therapeutic use ; Glucocorticoids/pharmacology ; Glucocorticoids/therapeutic use ; Humans ; Kidney Glomerulus/metabolism ; Nephrotic Syndrome/drug therapy ; Nephrotic Syndrome/metabolism ; Podocytes/metabolism
Chemical Substances	Cyclosporins ; Glucocorticoids
Language	English
Publishing date	2021-01-29
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	90594-x
ISSN	1460-2385 ; 0931-0509
ISSN (online)	1460-2385
ISSN	0931-0509
DOI	10.1093/ndt/gfab016
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Zs.A 2198: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 329: Show issues

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Article ; Online: Tubuloid culture enables long-term expansion of functional human kidney tubule epithelium from iPSC-derived organoids.

Yousef Yengej, Fjodor A / Jansen, Jitske / Ammerlaan, Carola M E / Dilmen, Emre / Pou Casellas, Carla / Masereeuw, Rosalinde / Hoenderop, Joost G / Smeets, Bart / Rookmaaker, Maarten B / Verhaar, Marianne C / Clevers, Hans

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 6, Page(s) e2216836120

Abstract: Kidney organoids generated from induced pluripotent stem cells (iPSC) have proven valuable for studies of kidney development, disease, and therapeutic screening. However, specific applications have been hampered by limited expansion capacity, immaturity, ...

Abstract	Kidney organoids generated from induced pluripotent stem cells (iPSC) have proven valuable for studies of kidney development, disease, and therapeutic screening. However, specific applications have been hampered by limited expansion capacity, immaturity, off-target cells, and inability to access the apical side. Here, we apply recently developed tubuloid protocols to purify and propagate kidney epithelium from d7+18 (post nephrogenesis) iPSC-derived organoids. The resulting 'iPSC organoid-derived (iPSCod)' tubuloids can be exponentially expanded for at least 2.5 mo, while retaining expression of important tubular transporters and segment-specific markers. This approach allows for selective propagation of the mature tubular epithelium, as immature cells, stroma, and undesirable off-target cells rapidly disappeared. iPSCod tubuloids provide easy apical access, which enabled functional evaluation and demonstration of essential secretion and electrolyte reabsorption processes. In conclusion, iPSCod tubuloids provide a different, complementary human kidney model that unlocks opportunities for functional characterization, disease modeling, and regenerative nephrology.
MeSH term(s)	Humans ; Induced Pluripotent Stem Cells/metabolism ; Kidney/metabolism ; Epithelium ; Organoids/metabolism ; Kidney Tubules ; Cell Differentiation
Language	English
Publishing date	2023-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2216836120
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Article: Topographic Guidance in Melt-Electrowritten Tubular Scaffolds Enhances Engineered Kidney Tubule Performance.

van Genderen, Anne Metje / Jansen, Katja / Kristen, Marleen / van Duijn, Joost / Li, Yang / Schuurmans, Carl C L / Malda, Jos / Vermonden, Tina / Jansen, Jitske / Masereeuw, Rosalinde / Castilho, Miguel

Frontiers in bioengineering and biotechnology

2021 Volume 8, Page(s) 617364

Abstract: Introduction: ...

Abstract	Introduction:
Language	English
Publishing date	2021-01-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2020.617364
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Article ; Online: Kidney Organoids and Tubuloids.

Yousef Yengej, Fjodor A / Jansen, Jitske / Rookmaaker, Maarten B / Verhaar, Marianne C / Clevers, Hans

Cells

2020 Volume 9, Issue 6

Abstract: In the past five years, pluripotent stem cell (PSC)-derived kidney organoids and adult stem or progenitor cell (ASC)-based kidney tubuloids have emerged as advanced in vitro models of kidney development, physiology, and disease. PSC-derived organoids ... ...

Abstract	In the past five years, pluripotent stem cell (PSC)-derived kidney organoids and adult stem or progenitor cell (ASC)-based kidney tubuloids have emerged as advanced in vitro models of kidney development, physiology, and disease. PSC-derived organoids mimic nephrogenesis. After differentiation towards the kidney precursor tissues ureteric bud and metanephric mesenchyme, their reciprocal interaction causes self-organization and patterning in vitro to generate nephron structures that resemble the fetal kidney. ASC tubuloids on the other hand recapitulate renewal and repair in the adult kidney tubule and give rise to long-term expandable and genetically stable cultures that consist of adult proximal tubule, loop of Henle, distal tubule, and collecting duct epithelium. Both organoid types hold great potential for: (1) studies of kidney physiology, (2) disease modeling, (3) high-throughput screening for drug efficacy and toxicity, and (4) regenerative medicine. Currently, organoids and tubuloids are successfully used to model hereditary, infectious, toxic, metabolic, and malignant kidney diseases and to screen for effective therapies. Furthermore, a tumor tubuloid biobank was established, which allows studies of pathogenic mutations and novel drug targets in a large group of patients. In this review, we discuss the nature of kidney organoids and tubuloids and their current and future applications in science and medicine.
MeSH term(s)	Adult Stem Cells/cytology ; Animals ; Humans ; Kidney Tubules/physiology ; Organogenesis ; Organoids/physiology ; Pluripotent Stem Cells/cytology ; Regeneration/physiology
Language	English
Publishing date	2020-05-26
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells9061326
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Article ; Online: Using human iPSC-derived kidney organoids to decipher SARS-CoV-2 pathology on single cell level.

Reimer, Katharina C / Jansen, Jitske / Overheul, Gijs J / Miesen, Pascal / van Rij, Ronald P / Triana, Sergio H / Smeets, Bart / Schneider, Rebekka K / Kramann, Rafael

STAR protocols

2022 Volume 3, Issue 3, Page(s) 101612

Abstract: ... For complete details on the use and execution of this protocol, please refer to Jansen et al. (2022). ...

Abstract	We describe a protocol for single-cell RNA sequencing of SARS-CoV-2-infected human induced pluripotent stem cell (iPSC)-derived kidney organoids. After inoculation of kidney organoids with virus, we use mechanical and enzymatic disruption to obtain single cell suspensions. Next, we process the organoid-derived cells into sequencing-ready SARS-CoV-2-targeted libraries. Subsequent sequencing analysis reveals changes in kidney cells after virus infection. The protocol was designed for kidney organoids cultured in a 6-well transwell format but can be adapted to organoids with different organ backgrounds. For complete details on the use and execution of this protocol, please refer to Jansen et al. (2022).
MeSH term(s)	COVID-19 ; Humans ; Induced Pluripotent Stem Cells ; Kidney ; Organoids ; SARS-CoV-2
Language	English
Publishing date	2022-07-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2022.101612
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Article ; Online: Using human iPSC-derived kidney organoids to decipher SARS-CoV-2 pathology on single cell level

Katharina C. Reimer / Jitske Jansen / Gijs J. Overheul / Pascal Miesen / Ronald P. van Rij / Sergio H. Triana / Bart Smeets / Rebekka K. Schneider / Rafael Kramann

STAR Protocols, Vol 3, Iss 3, Pp 101612- (2022)

2022

Abstract: ... For complete details on the use and execution of this protocol, please refer to Jansen et al. (2022 ...

Abstract	Summary: We describe a protocol for single-cell RNA sequencing of SARS-CoV-2-infected human induced pluripotent stem cell (iPSC)-derived kidney organoids. After inoculation of kidney organoids with virus, we use mechanical and enzymatic disruption to obtain single cell suspensions. Next, we process the organoid-derived cells into sequencing-ready SARS-CoV-2-targeted libraries. Subsequent sequencing analysis reveals changes in kidney cells after virus infection. The protocol was designed for kidney organoids cultured in a 6-well transwell format but can be adapted to organoids with different organ backgrounds.For complete details on the use and execution of this protocol, please refer to Jansen et al. (2022). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
Keywords	Cell biology ; Single cell ; Microbiology ; Stem cells ; Organoids ; Science (General) ; Q1-390
Language	English
Publishing date	2022-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Advances in predictive in vitro models of drug-induced nephrotoxicity.

Soo, Joanne Y-C / Jansen, Jitske / Masereeuw, Rosalinde / Little, Melissa H

Nature reviews. Nephrology

2018 Volume 14, Issue 6, Page(s) 378–393

Abstract: In vitro screens for nephrotoxicity are currently poorly predictive of toxicity in humans. Although the functional proteins that are expressed by nephron tubules and mediate drug susceptibility are well known, current in vitro cellular models poorly ... ...

Abstract	In vitro screens for nephrotoxicity are currently poorly predictive of toxicity in humans. Although the functional proteins that are expressed by nephron tubules and mediate drug susceptibility are well known, current in vitro cellular models poorly replicate both the morphology and the function of kidney tubules and therefore fail to demonstrate injury responses to drugs that would be nephrotoxic in vivo. Advances in protocols to enable the directed differentiation of pluripotent stem cells into multiple renal cell types and the development of microfluidic and 3D culture systems have opened a range of potential new platforms for evaluating drug nephrotoxicity. Many of the new in vitro culture systems have been characterized by the expression and function of transporters, enzymes, and other functional proteins that are expressed by the kidney and have been implicated in drug-induced renal injury. In vitro platforms that express these proteins and exhibit molecular biomarkers that have been used as readouts of injury demonstrate improved functional maturity compared with static 2D cultures and represent an opportunity to model injury to renal cell types that have hitherto received little attention. As nephrotoxicity screening platforms become more physiologically relevant, they will facilitate the development of safer drugs and improved clinical management of nephrotoxicants.
MeSH term(s)	Acute Kidney Injury/chemically induced ; Acute Kidney Injury/metabolism ; Animals ; Biological Assay ; Biomarkers/metabolism ; Cell Differentiation ; Cells, Cultured ; In Vitro Techniques/trends ; Kidney/drug effects ; Kidney/metabolism ; Predictive Value of Tests ; Stem Cells/metabolism ; Toxicity Tests/methods
Chemical Substances	Biomarkers
Language	English
Publishing date	2018-04-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2490366-8
ISSN	1759-507X ; 1759-5061
ISSN (online)	1759-507X
ISSN	1759-5061
DOI	10.1038/s41581-018-0003-9
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Zs.A 6334: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
Zs.MG 107: Show issues

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Article: Motile Cilia on Kidney Proximal Tubular Epithelial Cells Are Associated With Tubular Injury and Interstitial Fibrosis.

Eymael, Jennifer / Willemsen, Brigith / Xu, Joyce / Mooren, Fieke / Steenbergen, Eric / Wetzels, Jack F / Dijkman, Henry / Jansen, Jitske / Van der Vlag, Johan / Smeets, Bart

Frontiers in cell and developmental biology

2022 Volume 10, Page(s) 765887

Abstract: It is well established that mammalian kidney epithelial cells contain a single non-motile primary cilium (9 + 0 pattern). However, we noted the presence of multiple motile cilia with a central microtubular pair (9 + 2 pattern) in kidney biopsies of 11 ... ...

Abstract	It is well established that mammalian kidney epithelial cells contain a single non-motile primary cilium (9 + 0 pattern). However, we noted the presence of multiple motile cilia with a central microtubular pair (9 + 2 pattern) in kidney biopsies of 11 patients with various kidney diseases, using transmission electron microscopy. Immunofluorescence staining revealed the expression of the motile cilia-specific markers Radial Spoke Head Protein 4 homolog A, Forkhead-box-protein J1 and Regulatory factor X3. Multiciliated cells were exclusively observed in proximal tubuli and a relative frequent observation in human kidney tissue: in 16.7% of biopsies with tubular injury and atrophy (3 of 18 tissues), in 17.6% of biopsies from patients with membranous nephropathy (3 of 17 tissues) and in 10% of the human kidney tissues derived from the unaffected pole after tumour nephrectomy (3 of 30 tissues). However, these particular tissues showed marked tubular injury and fibrosis. Further analysis showed a significant relation between the presence of multiciliated cells and an increased expression of alpha-smooth-muscle-actin (
Language	English
Publishing date	2022-03-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2022.765887
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