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Article ; Online: Human Stem Cell and Organoid Models to Advance Acute Kidney Injury Diagnostics and Therapeutics.

Pode-Shakked, Naomi / Devarajan, Prasad

International journal of molecular sciences

2022 Volume 23, Issue 13

Abstract: Acute kidney injury (AKI) is an increasingly common problem afflicting all ages, occurring in over 20% of non-critically ill hospitalized patients and >30% of children and >50% of adults in critical care units. AKI is associated with serious short-term ... ...

Abstract	Acute kidney injury (AKI) is an increasingly common problem afflicting all ages, occurring in over 20% of non-critically ill hospitalized patients and >30% of children and >50% of adults in critical care units. AKI is associated with serious short-term and long-term consequences, and current therapeutic options are unsatisfactory. Large gaps remain in our understanding of human AKI pathobiology, which have hindered the discovery of novel diagnostics and therapeutics. Although animal models of AKI have been extensively studied, these differ significantly from human AKI in terms of molecular and cellular responses. In addition, animal models suffer from interspecies differences, high costs and ethical considerations. Static two-dimensional cell culture models of AKI also have limited utility since they have focused almost exclusively on hypoxic or cytotoxic injury to proximal tubules alone. An optimal AKI model would encompass several of the diverse specific cell types in the kidney that could be targets of injury. Second, it would resemble the human physiological milieu as closely as possible. Third, it would yield sensitive and measurable readouts that are directly applicable to the human condition. In this regard, the past two decades have seen a dramatic shift towards newer personalized human-based models to study human AKI. In this review, we provide recent developments using human stem cells, organoids, and in silico approaches to advance personalized AKI diagnostics and therapeutics.
MeSH term(s)	Acute Kidney Injury/diagnosis ; Acute Kidney Injury/therapy ; Animals ; Critical Illness/therapy ; Humans ; Intensive Care Units ; Kidney Tubules, Proximal ; Organoids ; Stem Cells
Language	English
Publishing date	2022-06-29
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23137211
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Article ; Online: Human Stem Cell and Organoid Models to Advance Acute Kidney Injury Diagnostics and Therapeutics

Naomi Pode-Shakked / Prasad Devarajan

International Journal of Molecular Sciences, Vol 23, Iss 7211, p

2022 Volume 7211

Abstract	Acute kidney injury (AKI) is an increasingly common problem afflicting all ages, occurring in over 20% of non-critically ill hospitalized patients and >30% of children and >50% of adults in critical care units. AKI is associated with serious short-term and long-term consequences, and current therapeutic options are unsatisfactory. Large gaps remain in our understanding of human AKI pathobiology, which have hindered the discovery of novel diagnostics and therapeutics. Although animal models of AKI have been extensively studied, these differ significantly from human AKI in terms of molecular and cellular responses. In addition, animal models suffer from interspecies differences, high costs and ethical considerations. Static two-dimensional cell culture models of AKI also have limited utility since they have focused almost exclusively on hypoxic or cytotoxic injury to proximal tubules alone. An optimal AKI model would encompass several of the diverse specific cell types in the kidney that could be targets of injury. Second, it would resemble the human physiological milieu as closely as possible. Third, it would yield sensitive and measurable readouts that are directly applicable to the human condition. In this regard, the past two decades have seen a dramatic shift towards newer personalized human-based models to study human AKI. In this review, we provide recent developments using human stem cells, organoids, and in silico approaches to advance personalized AKI diagnostics and therapeutics.
Keywords	acute kidney injury ; kidney organoids ; kidney development ; tubuloids ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	616
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Increasing angiotensin-converting enzyme concentrations and absent angiotensin-converting enzyme activity are associated with adverse kidney outcomes in pediatric septic shock.

Pode-Shakked, Naomi / Ceschia, Giovanni / Rose, James E / Goldstein, Stuart L / Stanski, Natalja L

Critical care (London, England)

2023 Volume 27, Issue 1, Page(s) 230

Abstract: Background: Sepsis-induced endothelial dysfunction is proposed to cause angiotensin-converting enzyme (ACE) dysfunction and renin-angiotensin-aldosterone system (RAAS) derangement, exacerbating vasodilatory shock and acute kidney injury (AKI). Few ... ...

Abstract	Background: Sepsis-induced endothelial dysfunction is proposed to cause angiotensin-converting enzyme (ACE) dysfunction and renin-angiotensin-aldosterone system (RAAS) derangement, exacerbating vasodilatory shock and acute kidney injury (AKI). Few studies test this hypothesis directly, including none in children. We measured serum ACE concentrations and activity, and assessed their association with adverse kidney outcomes in pediatric septic shock. Methods: A pilot study of 72 subjects aged 1 week-18 years from an existing multicenter, observational study. Serum ACE concentrations and activity were measured on Day 1; renin + prorenin concentrations were available from a previous study. The associations between individual RAAS components and a composite outcome (Day 1-7 severe persistent AKI, kidney replacement therapy use, or mortality) were assessed. Results: 50/72 subjects (69%) had undetectable ACE activity (< 2.41 U/L) on Day 1 and 27/72 (38%) developed the composite outcome. Subjects with undetectable ACE activity had higher Day 1 renin + prorenin compared to those with activity (4533 vs. 2227 pg/ml, p = 0.017); ACE concentrations were no different between groups. Children with the composite outcome more commonly had undetectable ACE activity (85% vs. 65%, p = 0.025), and had higher Day 1 renin + prorenin (16,774 pg/ml vs. 3037 pg/ml, p < 0.001) and ACE concentrations (149 vs. 96 pg/ml, p = 0.019). On multivariable regression, increasing ACE concentrations (aOR 1.01, 95%CI 1.002-1.03, p = 0.015) and undetectable ACE activity (aOR 6.6, 95%CI 1.2-36.1, p = 0.031) retained associations with the composite outcome. Conclusions: ACE activity is diminished in pediatric septic shock, appears uncoupled from ACE concentrations, and is associated with adverse kidney outcomes. Further study is needed to validate these findings in larger cohorts.
MeSH term(s)	Child ; Humans ; Shock, Septic ; Renin ; Pilot Projects ; Kidney ; Acute Kidney Injury ; Angiotensins
Chemical Substances	Renin (EC 3.4.23.15) ; Angiotensins
Language	English
Publishing date	2023-06-12
Publishing country	England
Document type	Observational Study ; Multicenter Study ; Journal Article
ZDB-ID	2041406-7
ISSN	1466-609X ; 1364-8535
ISSN (online)	1466-609X
ISSN	1364-8535
DOI	10.1186/s13054-023-04518-2
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Article ; Online: RAAS-deficient organoids indicate delayed angiogenesis as a possible cause for autosomal recessive renal tubular dysgenesis.

Pode-Shakked, Naomi / Slack, Megan / Sundaram, Nambirajan / Schreiber, Ruth / McCracken, Kyle W / Dekel, Benjamin / Helmrath, Michael / Kopan, Raphael

Nature communications

2023 Volume 14, Issue 1, Page(s) 8159

Abstract: Autosomal Recessive Renal Tubular Dysgenesis (AR-RTD) is a fatal genetic disorder characterized by complete absence or severe depletion of proximal tubules (PT) in patients harboring pathogenic variants in genes involved in the Renin-Angiotensin- ... ...

Abstract	Autosomal Recessive Renal Tubular Dysgenesis (AR-RTD) is a fatal genetic disorder characterized by complete absence or severe depletion of proximal tubules (PT) in patients harboring pathogenic variants in genes involved in the Renin-Angiotensin-Aldosterone System. To uncover the pathomechanism of AR-RTD, differentiation of ACE-/- and AGTR1-/- induced pluripotent stem cells (iPSCs) and AR-RTD patient-derived iPSCs into kidney organoids is leveraged. Comprehensive marker analyses show that both mutant and control organoids generate indistinguishable PT in vitro under normoxic (21% O2) or hypoxic (2% O2) conditions. Fully differentiated (d24) AGTR1-/- and control organoids transplanted under the kidney capsule of immunodeficient mice engraft and mature well, as do renal vesicle stage (d14) control organoids. By contrast, d14 AGTR1-/- organoids fail to engraft due to insufficient pro-angiogenic VEGF-A expression. Notably, growth under hypoxic conditions induces VEGF-A expression and rescues engraftment of AGTR1-/- organoids at d14, as does ectopic expression of VEGF-A. We propose that PT dysgenesis in AR-RTD is primarily a non-autonomous consequence of delayed angiogenesis, starving PT at a critical time in their development.
MeSH term(s)	Humans ; Animals ; Mice ; Renin-Angiotensin System/genetics ; Angiogenesis ; Vascular Endothelial Growth Factor A ; Kidney Tubules, Proximal/pathology ; Organoids
Chemical Substances	Vascular Endothelial Growth Factor A
Language	English
Publishing date	2023-12-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-43795-x
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Article ; Online: RAAS-deficient organoids indicate delayed angiogenesis as a possible cause for autosomal recessive renal tubular dysgenesis

Naomi Pode-Shakked / Megan Slack / Nambirajan Sundaram / Ruth Schreiber / Kyle W. McCracken / Benjamin Dekel / Michael Helmrath / Raphael Kopan

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 18

Abstract: Abstract Autosomal Recessive Renal Tubular Dysgenesis (AR-RTD) is a fatal genetic disorder characterized by complete absence or severe depletion of proximal tubules (PT) in patients harboring pathogenic variants in genes involved in the Renin–Angiotensin– ...

Abstract	Abstract Autosomal Recessive Renal Tubular Dysgenesis (AR-RTD) is a fatal genetic disorder characterized by complete absence or severe depletion of proximal tubules (PT) in patients harboring pathogenic variants in genes involved in the Renin–Angiotensin–Aldosterone System. To uncover the pathomechanism of AR-RTD, differentiation of ACE-/- and AGTR1-/- induced pluripotent stem cells (iPSCs) and AR-RTD patient-derived iPSCs into kidney organoids is leveraged. Comprehensive marker analyses show that both mutant and control organoids generate indistinguishable PT in vitro under normoxic (21% O2) or hypoxic (2% O2) conditions. Fully differentiated (d24) AGTR1-/- and control organoids transplanted under the kidney capsule of immunodeficient mice engraft and mature well, as do renal vesicle stage (d14) control organoids. By contrast, d14 AGTR1-/- organoids fail to engraft due to insufficient pro-angiogenic VEGF-A expression. Notably, growth under hypoxic conditions induces VEGF-A expression and rescues engraftment of AGTR1-/- organoids at d14, as does ectopic expression of VEGF-A. We propose that PT dysgenesis in AR-RTD is primarily a non-autonomous consequence of delayed angiogenesis, starving PT at a critical time in their development.
Keywords	Science ; Q
Subject code	616
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Severe fetal hydronephrosis: the added value of associated congenital anomalies of the kidneys and urinary tract (CAKUT) in the prediction of postnatal outcome.

Perlman, Sharon / Roitman, Lucia / Lotan, Danny / Kivilevitch, Zvi / Pode-Shakked, Naomi / Pode-Shakked, Ben / Achiron, Reuven / Dekel, Benjamin / Gilboa, Yinon

Prenatal diagnosis

2018 Volume 38, Issue 3, Page(s) 179–183

Abstract: Objective: The aim of this study was to focus on fetuses diagnosed with severe hydronephrosis and correlate prenatal sonographic characteristics with postnatal outcome.: Methods: Cases presenting prenatally with severe hydronephrosis (anterior- ... ...

Abstract	Objective: The aim of this study was to focus on fetuses diagnosed with severe hydronephrosis and correlate prenatal sonographic characteristics with postnatal outcome. Methods: Cases presenting prenatally with severe hydronephrosis (anterior-posterior renal pelvic diameter >15 mm) were collected retrospectively over a period of 11 years and divided into 2 groups: (1) isolated hydronephrosis and (2) those associated with congenital anomalies of the kidney and urinary tract (CAKUT). Results: A total of 83 fetuses comprised the study group: 35 fetuses had isolated severe hydronephrosis and 48 had associated CAKUT. The mean anterior-posterior renal pelvic diameter was 22.6 ± 8.5 mm (range 15.0-66.0 mm). The CAKUT group was associated with a significantly increased incidence of postnatal need for surgery (17.6% vs 44.2%, P = .014), dysplastic kidney (0% vs 14%, P = .023), and total abnormal outcome (52.9% vs 86%, P = .001) in comparison with isolated severe prenatal hydronephrosis. Conclusions: Severe fetal hydronephrosis has a wide postnatal clinical spectrum, which is mainly influenced by the presence of associated sonographic CAKUT findings. These clinical data have biological relevance: a genetic or environmental defect that influences multiple renal developmental processes leads to hydronephrosis but also to concomitant malformations (CAKUT) and critically influences renal prognosis. A more selective abnormal developmental process that results in isolated enlarged pelvis even to a severe extent has less influence on renal prognosis.
MeSH term(s)	Child, Preschool ; Female ; Humans ; Hydronephrosis/diagnostic imaging ; Hydronephrosis/epidemiology ; Hydronephrosis/etiology ; Israel/epidemiology ; Male ; Pregnancy ; Retrospective Studies ; Urinary Tract Infections/epidemiology ; Urogenital Abnormalities/complications ; Urogenital Abnormalities/diagnostic imaging ; Urogenital Abnormalities/epidemiology
Language	English
Publishing date	2018-02-07
Publishing country	England
Document type	Journal Article
ZDB-ID	82031-3
ISSN	1097-0223 ; 0197-3851
ISSN (online)	1097-0223
ISSN	0197-3851
DOI	10.1002/pd.5206
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Article ; Online: Revisiting the role of Notch in nephron segmentation confirms a role for proximal fate selection during mouse and human nephrogenesis.

Duvall, Kathryn / Crist, Lauren / Perl, Alison J / Pode Shakked, Naomi / Chaturvedi, Praneet / Kopan, Raphael

Development (Cambridge, England)

2022 Volume 149, Issue 10

Abstract: Notch signaling promotes maturation of nephron epithelia, but its proposed contribution to nephron segmentation into proximal and distal domains has been called into doubt. We leveraged single cell and bulk RNA-seq, quantitative immunofluorescent lineage/ ...

Abstract	Notch signaling promotes maturation of nephron epithelia, but its proposed contribution to nephron segmentation into proximal and distal domains has been called into doubt. We leveraged single cell and bulk RNA-seq, quantitative immunofluorescent lineage/fate tracing, and genetically modified human induced pluripotent stem cells (iPSCs) to revisit this question in developing mouse kidneys and human kidney organoids. We confirmed that Notch signaling is needed for maturation of all nephron lineages, and thus mature lineage markers fail to detect a fate bias. By contrast, early markers identified a distal fate bias in cells lacking Notch2, and a concomitant increase in early proximal and podocyte fates in cells expressing hyperactive Notch1 was observed. Orthogonal support for a conserved role for Notch signaling in the distal/proximal axis segmentation is provided by the demonstration that nicastrin (NCSTN)-deficient human iPSC-derived organoids differentiate into TFA2B+ distal tubule and CDH1+ connecting segment progenitors, but not into HNF4A+ or LTL+ proximal progenitors.
MeSH term(s)	Animals ; Cell Differentiation ; Gene Expression Regulation, Developmental ; Humans ; Induced Pluripotent Stem Cells/metabolism ; Kidney/metabolism ; Mice ; Nephrons/metabolism ; Organogenesis/genetics ; Receptors, Notch/genetics ; Receptors, Notch/metabolism
Chemical Substances	Receptors, Notch
Language	English
Publishing date	2022-05-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.200446
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Article: Refining the Phenotypic Spectrum of

Eliyahu, Aviva / Barel, Ortal / Greenbaum, Lior / Zaks Hoffer, Gal / Goldberg, Yael / Raas-Rothschild, Annick / Singer, Amihood / Bar-Joseph, Ifat / Kunik, Vered / Javasky, Elisheva / Staretz-Chacham, Orna / Pode-Shakked, Naomi / Bazak, Lily / Ruhrman-Shahar, Noa / Pras, Elon / Frydman, Moshe / Shohat, Mordechai / Pode-Shakked, Ben

Frontiers in pediatrics

2022 Volume 10, Page(s) 844845

Abstract: The role of lysine methyltransferases (KMTs) and demethylases (KDMs) in the regulation of chromatin modification is well-established. Recently, deleterious heterozygous variants ... ...

Abstract	The role of lysine methyltransferases (KMTs) and demethylases (KDMs) in the regulation of chromatin modification is well-established. Recently, deleterious heterozygous variants in
Language	English
Publishing date	2022-03-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711999-3
ISSN	2296-2360
ISSN	2296-2360
DOI	10.3389/fped.2022.844845
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Article ; Online: Geometry of Gene Expression Space of Wilms' Tumors From Human Patients.

Trink, Ariel / Kanter, Itamar / Pode-Shakked, Naomi / Urbach, Achia / Dekel, Benjamin / Kalisky, Tomer

Neoplasia (New York, N.Y.)

2018 Volume 20, Issue 8, Page(s) 871–881

Abstract: Wilms' tumor is a pediatric malignancy that is thought to originate from faulty kidney development during the embryonic stage. However, there is a large variation between tumors from different patients in both histology and gene expression that is not ... ...

Abstract	Wilms' tumor is a pediatric malignancy that is thought to originate from faulty kidney development during the embryonic stage. However, there is a large variation between tumors from different patients in both histology and gene expression that is not well characterized. Here we use a meta-analysis of published microarray datasets to show that Favorable Histology Wilms' Tumors (FHWT's) fill a triangle-shaped continuum in gene expression space of which the vertices represent three idealized "archetypes". We show that these archetypes have predominantly renal blastemal, stromal, and epithelial characteristics and that they correlate well with the three major lineages of the developing embryonic kidney. Moreover, we show that advanced stage tumors shift towards the renal blastemal archetype. These results illustrate the potential of this methodology for characterizing the cellular composition of Wilms' tumors and for assessing disease progression.
MeSH term(s)	Disease Progression ; Gene Expression/genetics ; Gene Expression Regulation, Neoplastic/genetics ; Genes, Wilms Tumor ; Humans ; Kidney/metabolism ; Kidney/pathology ; Kidney Neoplasms/genetics ; Kidney Neoplasms/pathology ; Wilms Tumor/genetics ; Wilms Tumor/pathology
Language	English
Publishing date	2018-07-18
Publishing country	United States
Document type	Journal Article ; Meta-Analysis
ZDB-ID	1483840-0
ISSN	1476-5586 ; 1522-8002
ISSN (online)	1476-5586
ISSN	1522-8002
DOI	10.1016/j.neo.2018.06.006
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Zs.A 5203: Show issues

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Article ; Online: Wilms tumor--a renal stem cell malignancy?

Pode-Shakked, Naomi / Dekel, Benjamin

Pediatric nephrology (Berlin, Germany)

2011 Volume 26, Issue 9, Page(s) 1535–1543

Abstract: Wilms' tumor (WT; nephroblastoma) is the most common pediatric renal malignancy and rated fourth in overall incidence among childhood cancers. It is viewed as a prototype of differentiation failure in human neoplasia as it recapitulates the histology of ... ...

Abstract	Wilms' tumor (WT; nephroblastoma) is the most common pediatric renal malignancy and rated fourth in overall incidence among childhood cancers. It is viewed as a prototype of differentiation failure in human neoplasia as it recapitulates the histology of the nephrogenic zone of the growing fetal kidney. The cellular origin of WT is unclear. However, recent genomic, genetic and epigenetic studies point to an early renal stem/progenitor cell that undergoes malignant transformation as the source for WT. In this context, classical WT shares genes and pathways activated in progenitors committed to the renal lineage. However, direct proof and characterization of the WT initiating cell have remained elusive. Novel methodologies recently adopted from the cancer stem cell scientific field, including the analysis of sorted single human tumor cells, have been applied to WT. These have enabled the identification of cell sub-populations that show similarities-in terms of molecular marker expression-to human fetal kidney progenitors and are, therefore, likely to be derivatives of the same lineage. Further elucidation of the WT cancer stem cell or the cell of origin in human tumors and in transgenic mouse models that generate murine tumors may not only provide novel therapeutic targets but also shed light on the normal kidney stem cell.
MeSH term(s)	Animals ; Cell Lineage ; Epigenesis, Genetic ; Gene Expression Profiling/methods ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Neoplastic ; Humans ; Kidney Neoplasms/genetics ; Kidney Neoplasms/metabolism ; Kidney Neoplasms/pathology ; Neoplastic Stem Cells/metabolism ; Neoplastic Stem Cells/pathology ; Oligonucleotide Array Sequence Analysis ; Signal Transduction ; Wilms Tumor/genetics ; Wilms Tumor/metabolism ; Wilms Tumor/pathology
Language	English
Publishing date	2011-04-16
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	631932-4
ISSN	1432-198X ; 0931-041X
ISSN (online)	1432-198X
ISSN	0931-041X
DOI	10.1007/s00467-011-1858-1
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