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Article ; Online: Molecular anatomy of the kidney: what have we learned from gene expression and functional genomics?

Rumballe, Bree / Georgas, Kylie / Wilkinson, Lorine / Little, Melissa

2010 Volume 25, Issue 6, Page(s) 1005–1016

Abstract: The discipline of paediatric nephrology encompasses the congenital nephritic syndromes, renal dysplasias, neonatal renal tumours, early onset cystic disease, tubulopathies and vesicoureteric reflux, all of which arise due to defects in normal kidney ... ...

Abstract	The discipline of paediatric nephrology encompasses the congenital nephritic syndromes, renal dysplasias, neonatal renal tumours, early onset cystic disease, tubulopathies and vesicoureteric reflux, all of which arise due to defects in normal kidney development. Indeed, congenital anomalies of the kidney and urinary tract (CAKUT) represent 20-30% of prenatal anomalies, occurring in 1 in 500 births. Developmental biologists have studied the anatomical and morphogenetic processes involved in kidney development for the last five decades. However, with the advent of transgenic mice, the sequencing of the genome, improvements in mutation detection and the advent of functional genomics, our understanding of the molecular basis of kidney development has grown significantly. Here we discuss how the advent of new genetic and genomics approaches has added to our understanding of kidney development and paediatric renal disease, as well as identifying areas in which we are still lacking knowledge.
MeSH term(s)	Animals ; Child ; Gene Expression ; Gene Expression Regulation, Developmental ; Genomics ; Humans ; Kidney/abnormalities ; Kidney/embryology ; Kidney Diseases/genetics ; Morphogenesis/genetics ; Nephrology/trends ; Pediatrics/trends
Language	English
Publishing date	2010-01-05
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	631932-4
ISSN	1432-198X ; 0931-041X
ISSN (online)	1432-198X
ISSN	0931-041X
DOI	10.1007/s00467-009-1392-6
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Article ; Online: Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system.

Rumballe, Bree A / Chiu, Han Sheng / Georgas, Kylie M / Little, Melissa H

Methods in molecular biology (Clifton, N.J.)

2012 Volume 886, Page(s) 223–239

Abstract: Studies into the molecular basis of morphogenesis frequently begin with investigations into gene expression across time and cell type in that organ. One of the most anatomically informative approaches to such studies is the use of in situ hybridization, ... ...

Abstract	Studies into the molecular basis of morphogenesis frequently begin with investigations into gene expression across time and cell type in that organ. One of the most anatomically informative approaches to such studies is the use of in situ hybridization, either of intact or histologically sectioned tissues. Here, we describe the optimization of this approach for use in the temporal and spatial analysis of gene expression in the urogenital system, from embryonic development to the postnatal period. The methods described are applicable for high throughput analysis of large gene sets. As such, ISH has become a powerful technique for gene expression profiling and is valuable for the validation of profiling analyses performed using other approaches such as microarrays.
MeSH term(s)	Animals ; Gene Expression Profiling/methods ; Gene Expression Regulation, Developmental ; In Situ Hybridization/methods ; Kidney/embryology ; Kidney/growth & development ; Kidney/metabolism ; Mice ; RNA, Messenger/genetics ; RNA, Messenger/isolation & purification ; Urogenital System/embryology ; Urogenital System/growth & development ; Urogenital System/metabolism
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2012
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-61779-851-1_20
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Article ; Online: The role of p75NTR in cholinergic basal forebrain structure and function.

Boskovic, Zoran / Alfonsi, Fabienne / Rumballe, Bree A / Fonseka, Sachini / Windels, Francois / Coulson, Elizabeth J

The Journal of neuroscience : the official journal of the Society for Neuroscience

2014 Volume 34, Issue 39, Page(s) 13033–13038

Abstract: The role of the p75 neurotrophin receptor (p75(NTR)) in adult cholinergic basal forebrain (cBF) neurons is unclear due to conflicting results from previous studies and to limitations of existing p75(NTR)-knock-out mouse models. In the present study we ... ...

Abstract	The role of the p75 neurotrophin receptor (p75(NTR)) in adult cholinergic basal forebrain (cBF) neurons is unclear due to conflicting results from previous studies and to limitations of existing p75(NTR)-knock-out mouse models. In the present study we used a novel conditional knock-out line (ChAT-cre p75(in/in)) to assess the role of p75(NTR) in the cBF by eliminating p75(NTR) in choline acetyl-transferase-expressing cells. We show that the absence of p75(NTR) results in a lasting increase in cBF cell number, cell size, and cholinergic innervation to the cortex. Analysis of adult ChAT-cre p75(in/in) mice revealed that mutant animals show a similar loss of cBF neurons with age to that observed in wild-type animals, indicating that p75(NTR) does not play a significant role in mediating this age-related decline in cBF neuronal number. However, the increased cholinergic axonal innervation of the cortex, but not the hippocampus, corresponded to alterations in idiothetic but not allothetic navigation. These findings support a role for p75(NTR)-mediated regulation of cholinergic-dependent cognitive function, and suggest that the variability in previous reports of cBF neuron number may stem from limited spatial and temporal control of p75(NTR) expression in existing knock-out models.
MeSH term(s)	Animals ; Cholinergic Neurons/metabolism ; Cholinergic Neurons/physiology ; Cognition ; Female ; Male ; Maze Learning ; Mice ; Mice, Inbred C57BL ; Prosencephalon/cytology ; Prosencephalon/growth & development ; Prosencephalon/metabolism ; Prosencephalon/physiology ; Receptors, Nerve Growth Factor/genetics ; Receptors, Nerve Growth Factor/metabolism ; Synaptic Transmission
Chemical Substances	Receptors, Nerve Growth Factor ; Ngfr protein, mouse
Language	English
Publishing date	2014-09-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	604637-x
ISSN	1529-2401 ; 0270-6474
ISSN (online)	1529-2401
ISSN	0270-6474
DOI	10.1523/JNEUROSCI.2364-14.2014
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Article: High-throughput paraffin section in situ hybridization and dual immunohistochemistry on mouse tissues.

Rumballe, Bree / Georgas, Kylie / Little, Melissa H

CSH protocols

2008 Volume 2008, Page(s) pdb.prot5030

Abstract: INTRODUCTIONSection in situ hybridization (SISH) is a high-resolution tool used to analyze gene expression patterns. This protocol utilizes the Tecan Freedom EVO150 platform to perform high-throughput SISH on paraffin sections to detect mRNA with a ... ...

Abstract	INTRODUCTIONSection in situ hybridization (SISH) is a high-resolution tool used to analyze gene expression patterns. This protocol utilizes the Tecan Freedom EVO150 platform to perform high-throughput SISH on paraffin sections to detect mRNA with a digoxigenin (DIG)-labeled probe. The slide is mounted and imaged before performing immunohistochemistry (IHC) on the same section. The dual reaction enables a marker of protein expression to be localized on the same section as the mRNA and facilitates more accurate annotation of the gene expression.
Language	English
Publishing date	2008-07-01
Publishing country	United States
Document type	Journal Article
DOI	10.1101/pdb.prot5030
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Article ; Online: Defining and redefining the nephron progenitor population.

Hendry, Caroline / Rumballe, Bree / Moritz, Karen / Little, Melissa H

Pediatric nephrology (Berlin, Germany)

2011 Volume 26, Issue 9, Page(s) 1395–1406

Abstract: It has long been appreciated that the mammalian kidney arises via reciprocal interactions between an epithelial ureteric epithelium and the surrounding metanephric mesenchyme. More recently, lineage tracing has confirmed that the portion of the ... ...

Abstract	It has long been appreciated that the mammalian kidney arises via reciprocal interactions between an epithelial ureteric epithelium and the surrounding metanephric mesenchyme. More recently, lineage tracing has confirmed that the portion of the metanephric mesenchyme closest to the advancing ureteric tips, the cap mesenchyme, represents the progenitor population for the nephron epithelia. This Six2(+)Cited1(+) population undergoes self-renewal throughout nephrogenesis while retaining the potential to epithelialize. In contrast, the Foxd1(+) portion of the metanephric mesenchyme shows no epithelial potential, developing instead into the interstitial, perivascular, and possibly endothelial elements of the kidney. The cap mesenchyme rests within a nephrogenic niche, surrounded by the stroma and the ureteric tip. While the role of Wnt signaling in nephron induction is known, there remains a lack of clarity over the intrinsic and extrinsic regulation of cap mesenchyme specification, self-renewal, and nephron potential. It is also not known what regulates cessation of nephrogenesis, but there is no nephron generation in response to injury during the postnatal period. In this review, we will examine what is and is not known about this nephron progenitor population and discuss how an increased understanding of the regulation of this population may better explain the observed variation in final nephron number and potentially facilitate the reinitiation or prolongation of nephron formation.
MeSH term(s)	Animals ; Cell Differentiation ; Cell Lineage ; Cell Proliferation ; Epithelial-Mesenchymal Transition ; Humans ; Mesenchymal Stem Cells/physiology ; Nephrons/embryology ; Organogenesis ; Stem Cell Niche
Language	English
Publishing date	2011-01-14
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; 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/s00467-010-1750-4
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Article ; Online: Defining the molecular character of the developing and adult kidney podocyte.

Brunskill, Eric W / Georgas, Kylie / Rumballe, Bree / Little, Melissa H / Potter, S Steven

PloS one

2011 Volume 6, Issue 9, Page(s) e24640

Abstract: Background: The podocyte is a remarkable cell type, which encases the capillaries of the kidney glomerulus. Although mesodermal in origin it sends out axonal like projections that wrap around the capillaries. These extend yet finer projections, the foot ...

Abstract	Background: The podocyte is a remarkable cell type, which encases the capillaries of the kidney glomerulus. Although mesodermal in origin it sends out axonal like projections that wrap around the capillaries. These extend yet finer projections, the foot processes, which interdigitate, leaving between them the slit diaphragms, through which the glomerular filtrate must pass. The podocytes are a subject of keen interest because of their key roles in kidney development and disease. Methodology/principal findings: In this report we identified and characterized a novel transgenic mouse line, MafB-GFP, which specifically marked the kidney podocytes from a very early stage of development. These mice were then used to facilitate the fluorescent activated cell sorting based purification of podocytes from embryos at E13.5 and E15.5, as well as adults. Microarrays were then used to globally define the gene expression states of podocytes at these different developmental stages. A remarkable picture emerged, identifying the multiple sets of genes that establish the neuronal, muscle, and phagocytic properties of podocytes. The complete combinatorial code of transcription factors that create the podocyte was characterized, and the global lists of growth factors and receptors they express were defined. Conclusions/significance: The complete molecular character of the in vivo podocyte is established for the first time. The active molecular functions and biological processes further define their unique combination of features. The results provide a resource atlas of gene expression patterns of developing and adult podocytes that will help to guide further research of these incredible cells.
MeSH term(s)	Animals ; Cells, Cultured ; Flow Cytometry ; Gene Expression Regulation, Developmental ; In Situ Hybridization ; Mice ; Mice, Transgenic ; Oligonucleotide Array Sequence Analysis ; Podocytes/metabolism
Language	English
Publishing date	2011-09-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0024640
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Article ; Online: Defining the molecular character of the developing and adult kidney podocyte.

Eric W Brunskill / Kylie Georgas / Bree Rumballe / Melissa H Little / S Steven Potter

PLoS ONE, Vol 6, Iss 9, p e

2011 Volume 24640

Abstract: The podocyte is a remarkable cell type, which encases the capillaries of the kidney glomerulus. Although mesodermal in origin it sends out axonal like projections that wrap around the capillaries. These extend yet finer projections, the foot processes, ... ...

Abstract	The podocyte is a remarkable cell type, which encases the capillaries of the kidney glomerulus. Although mesodermal in origin it sends out axonal like projections that wrap around the capillaries. These extend yet finer projections, the foot processes, which interdigitate, leaving between them the slit diaphragms, through which the glomerular filtrate must pass. The podocytes are a subject of keen interest because of their key roles in kidney development and disease.In this report we identified and characterized a novel transgenic mouse line, MafB-GFP, which specifically marked the kidney podocytes from a very early stage of development. These mice were then used to facilitate the fluorescent activated cell sorting based purification of podocytes from embryos at E13.5 and E15.5, as well as adults. Microarrays were then used to globally define the gene expression states of podocytes at these different developmental stages. A remarkable picture emerged, identifying the multiple sets of genes that establish the neuronal, muscle, and phagocytic properties of podocytes. The complete combinatorial code of transcription factors that create the podocyte was characterized, and the global lists of growth factors and receptors they express were defined.The complete molecular character of the in vivo podocyte is established for the first time. The active molecular functions and biological processes further define their unique combination of features. The results provide a resource atlas of gene expression patterns of developing and adult podocytes that will help to guide further research of these incredible cells.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2011-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Targeting mesothelin receptors with drug-loaded bacterial nanocells suppresses human mesothelioma tumour growth in mouse xenograft models.

Alfaleh, Mohamed A / Howard, Christopher B / Sedliarou, Ilya / Jones, Martina L / Gudhka, Reema / Vanegas, Natasha / Weiss, Jocelyn / Suurbach, Julia H / de Bakker, Christopher J / Milne, Michael R / Rumballe, Bree A / MacDiarmid, Jennifer A / Brahmbhatt, Himanshu / Mahler, Stephen M

PloS one

2017 Volume 12, Issue 10, Page(s) e0186137

Abstract: Human malignant mesothelioma is a chemoresistant tumour that develops from mesothelial cells, commonly associated with asbestos exposure. Malignant mesothelioma incidence rates in European countries are still rising and Australia has one of the highest ... ...

Abstract	Human malignant mesothelioma is a chemoresistant tumour that develops from mesothelial cells, commonly associated with asbestos exposure. Malignant mesothelioma incidence rates in European countries are still rising and Australia has one of the highest burdens of malignant mesothelioma on a population basis in the world. Therapy using systemic delivery of free cytotoxic agents is associated with many undesirable side effects due to non-selectivity, and is thus dose-limited which limits its therapeutic potential. Therefore, increasing the selectivity of anti-cancer agents has the potential to dramatically enhance drug efficacy and reduce toxicity. EnGeneIC Dream Vectors (EDV) are antibody-targeted nanocells which can be loaded with cytotoxic drugs and delivered to specific cancer cells via bispecific antibodies (BsAbs) which target the EDV and a cancer cell-specific receptor, simultaneously. BsAbs were designed to target doxorubicin-loaded EDVs to cancer cells via cell surface mesothelin (MSLN). Flow cytometry was used to investigate cell binding and induction of apoptosis, and confocal microscopy to visualize internalization. Mouse xenograft models were used to assess anti-tumour effects in vivo, followed by immunohistochemistry for ex vivo evaluation of proliferation and necrosis. BsAb-targeted, doxorubicin-loaded EDVs were able to bind to and internalize within mesothelioma cells in vitro via MSLN receptors and induce apoptosis. In mice xenografts, the BsAb-targeted, doxorubicin-loaded EDVs suppressed the tumour growth and also decreased cell proliferation. Thus, the use of MSLN-specific antibodies to deliver encapsulated doxorubicin can provide a novel and alternative modality for treatment of mesothelioma.
MeSH term(s)	Animals ; Cell Proliferation ; Humans ; Mesothelioma/pathology ; Mice ; Receptors, Cell Surface/metabolism ; Xenograft Model Antitumor Assays
Chemical Substances	Receptors, Cell Surface
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0186137
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Article ; Online: Nephron formation adopts a novel spatial topology at cessation of nephrogenesis.

Rumballe, Bree A / Georgas, Kylie M / Combes, Alexander N / Ju, Adler L / Gilbert, Thierry / Little, Melissa H

Developmental biology

2011 Volume 360, Issue 1, Page(s) 110–122

Abstract: Nephron number in the mammalian kidney is known to vary dramatically, with postnatal renal function directly influenced by nephron complement. What determines final nephron number is poorly understood but nephron formation in the mouse kidney ceases ... ...

Abstract	Nephron number in the mammalian kidney is known to vary dramatically, with postnatal renal function directly influenced by nephron complement. What determines final nephron number is poorly understood but nephron formation in the mouse kidney ceases within the first few days after birth, presumably due to the loss of all remaining nephron progenitors via epithelial differentiation. What initiates this event is not known. Indeed, whether nephron formation occurs in the same way at this time as during embryonic development has also not been examined. In this study, we investigate the key cellular compartments involved in nephron formation; the ureteric tip, cap mesenchyme and early nephrons; from postnatal day (P) 0 to 6 in the mouse. High resolution analyses of gene and protein expression indicate that loss of nephron progenitors precedes loss of ureteric tip identity, but show spatial shifts in the expression of cap mesenchyme genes during this time. In addition, cap mesenchymal volume and rate of proliferation decline prior to birth. Section-based 3D modeling and Optical Projection Tomography revealed a burst of ectopic nephron induction, with the formation of multiple (up to 5) nephrons per ureteric tip evident from P2. While the distal-proximal patterning of these nephrons occurred normally, their spatial relationship with the ureteric compartment was altered. We propose that this phase of nephron formation represents an acceleration of differentiation within the cap mesenchyme due to a displacement of signals within the nephrogenic niche.
MeSH term(s)	Animals ; Animals, Newborn ; Cyclin D1/genetics ; Cyclin D1/metabolism ; Female ; Gene Expression Regulation, Developmental ; Homeodomain Proteins/genetics ; Homeodomain Proteins/metabolism ; Imaging, Three-Dimensional ; Kidney/embryology ; Kidney/growth & development ; Kidney/physiology ; Mice ; Models, Anatomic ; Models, Biological ; Nephrons/embryology ; Nephrons/growth & development ; Nephrons/physiology ; Organogenesis/genetics ; Organogenesis/physiology ; Pregnancy ; Tomography, Optical ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Ureter/embryology ; Ureter/growth & development
Chemical Substances	Ccnd1 protein, mouse ; Homeodomain Proteins ; Six2 protein, mouse ; Transcription Factors ; Cyclin D1 (136601-57-5)
Language	English
Publishing date	2011-09-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1114-9
ISSN	1095-564X ; 0012-1606
ISSN (online)	1095-564X
ISSN	0012-1606
DOI	10.1016/j.ydbio.2011.09.011
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Article ; Online: Global quantification of tissue dynamics in the developing mouse kidney.

Short, Kieran M / Combes, Alexander N / Lefevre, James / Ju, Adler L / Georgas, Kylie M / Lamberton, Timothy / Cairncross, Oliver / Rumballe, Bree A / McMahon, Andrew P / Hamilton, Nicholas A / Smyth, Ian M / Little, Melissa H

Developmental cell

2014 Volume 29, Issue 2, Page(s) 188–202

Abstract: Although kidneys of equal size can vary 10-fold in nephron number at birth, discovering what regulates such variation has been hampered by a lack of quantitative parameters defining kidney development. Here we report a comprehensive, quantitative, ... ...

Abstract	Although kidneys of equal size can vary 10-fold in nephron number at birth, discovering what regulates such variation has been hampered by a lack of quantitative parameters defining kidney development. Here we report a comprehensive, quantitative, multiscale analysis of mammalian kidney development in which we measure changes in cell number, compartment volumes, and cellular dynamics across the entirety of organogenesis, focusing on two key nephrogenic progenitor populations: the ureteric epithelium and the cap mesenchyme. In doing so, we describe a discontinuous developmental program governed by dynamic changes in interactions between these key cellular populations occurring within a previously unappreciated structurally stereotypic organ architecture. We also illustrate the application of this approach to the detection of a subtle mutant phenotype. This baseline program of kidney morphogenesis provides a framework for assessing genetic and environmental developmental perturbation and will serve as a gold standard for the analysis of other organs.
MeSH term(s)	Animals ; Cell Count ; Embryonic Stem Cells/physiology ; Female ; Gene Expression Regulation, Developmental ; Kidney/cytology ; Kidney/embryology ; Kidney/physiology ; Male ; Mice ; Mice, Inbred C57BL ; Mutation ; Nephrons/cytology ; Nephrons/embryology ; Nephrons/physiology ; Phenotype ; Pregnancy ; Ureter/cytology ; Ureter/embryology ; Ureter/physiology ; Urothelium/cytology ; Urothelium/embryology ; Urothelium/physiology
Language	English
Publishing date	2014-04-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2014.02.017
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