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Methods in
Molecular Biology 1397
Tim D. Hewitson
Edward R. Smith
Stephen G. Holt Editors
Kidney
Research
Experimental Protocols
Second Edition
METHODS IN MOLECULAR BIOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
Second Edition
Edited by
Tim D. Hewitson
Department of Nephrology, Royal Melbourne Hospital, Melbourne, VIC, Australia
Edward R. Smith
Department of Nephrology, Royal Melbourne Hospital, Melbourne, VIC, Australia
Stephen G. Holt
Department of Nephrology, Royal Melbourne Hospital, Melbourne, VIC, Australia
Editors
Tim D. Hewitson Edward R. Smith
Department of Nephrology Department of Nephrology
Royal Melbourne Hospital Royal Melbourne Hospital
Melbourne, VIC, Australia Melbourne, VIC, Australia
Stephen G. Holt
Department of Nephrology
Royal Melbourne Hospital
Melbourne, VIC, Australia
Acute and chronic forms of kidney disease are major causes of morbidity and mortality
worldwide. In compiling this volume, we have attempted to collate both established and
novel experimental methods that can be used to study this debilitating condition.
The first edition of this book gathered together a collection of techniques that focused
on solving the inherent problems that exist in renal research, most notably the complexity
of renal anatomy and physiology and the associated plethora of different cell types found in
the kidney. It is hoped that the new volume complements the first edition by emphasizing
recent innovations that are relevant to the questions currently being asked in basic renal
research. In addition the present volume takes a more holistic approach by considering
associated disorders such as complications seen with peritoneal dialysis, the cardiorenal
syndrome, and vascular calcification.
Part I of the second edition provides a number of in vitro, in vivo, and ex vivo models
of kidney disease and associated complications. The first two chapters describe the isolation
and propagation of podocytes (Chapter 1) and fibroblasts (Chapter 2), while Chapters 3
and 4 address the pathology of peritoneal dialysis complications. An important technique
for studying the poorly understood sympathetic nervous system link between renal and
cardiac disease is provided in Chapter 5. In a number of organs, decellularized extracellular
matrix is being used to provide both a scaffold for organ regeneration studies and a more
accurate ex vivo representation of the in vivo microenvironment. Jin et al. provide a proto-
col for the kidney in Chapter 6.
Part II looks at recent advances in imaging techniques. Estimation of glomerular num-
ber has long been a tedious and time-consuming process, poorly suited to comparative stud-
ies with even small numbers of animals. The exciting developments described in Chapter 7
provide a means of measuring glomerular endowment through magnetic resonance imag-
ing. Likewise in Chapter 8 Ashraf et al. offer us the tantalizing opportunity to image living
tissue in a time-critical manner that yields novel insights into intact cell functions.
The next two parts provide protocols to study two important clinical complications
experimentally. Part III covers recent advances in studying metabolism in renal ischemia
and reperfusion via telemetry (Chapter 9), magnetic resonance imaging (Chapters 10 and
11), and multiphoton microscopy (Chapter 12). Part IV addresses the study and measure-
ment of vascular calcification, an important manifestation of uremia-induced disturbances
in bone metabolism and mineral handling. This includes a state-of-the-art review on the
topic (Chapter 13), in addition to protocols of an in vitro model of mineralization (Chapter
14), the isolation and quantitation of novel mediators of extraosseous mineral stress
(Chapter 15), and fluorescent imaging of vascular calcification (Chapter 16).
Finally, the last three chapters (Part V) provide analytical techniques that are both topi-
cal and of widespread relevance to the study of experimental renal disease. These are
improved methodologies for studying protein phosphorylation in signal transduction
(Chapter 17), laser capture microdissection (Chapter 18), and in situ insights into the epig-
enome (Chapter 19).
v
vi Preface
Nephrology is a discipline that combines both basic and clinical sciences. In editing this
book, we have attempted to provide a collection of protocols useful to those with some
laboratory experience in Nnephrology and those new to the field. Protocols are written in
the standard Methods in Molecular Biology format which includes a general introduction, an
extensive list of materials required, and stepwise instructions to follow. As is characteristic
of this series, a complementary notes section with key tips for troubleshooting accompanies
each protocol. In many cases, the authors provide case studies as well as detailed protocols
to illustrate their application.
We are indebted to all the authors for their generosity in sharing their expertise and
experience for this book and for the ongoing support of the editor-in-chief, Professor John
Walker. We trust that those using this new edition will find it a valuable aid in studying the
mechanisms of kidney disease.
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
vii
viii Contents
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291
Contributors
ix
x Contributors
Abstract
Genetic studies on hereditary kidney diseases and in vivo experimental model studies have revealed a critical
role for the podocyte in glomerular function and disease. Primary podocyte cultures as well as immortal-
ized podocyte cell lines have been used extensively to study podocyte function. Although, primary cells
often more closely resemble the in vivo cells, they may have only a finite replicative life span before they
reach senescence. Therefore, the success of studies using primary cell cultures depends on standardized
isolation and culture protocols that allow reproducible generation of stable primary cultures.
This chapter describes the isolation of primary podocytes with a proven origin using the novel tech-
nology of cell-specific genetic tagging. Podocytes are isolated from glomeruli from a podocyte-specific
transgenic reporter mouse. The podocyte-specific reporter gene beta-galactosidase is used to identify and
specifically isolate the labeled podocytes from other glomerular cells by FACS.
Key words Podocytes, Cell culture, Glomerulus, Primary cell culture, Cell-specific tagging,
Pod-rtTA/LC1/R26R mice
1 Introduction
Tim D. Hewitson et al. (eds.), Kidney Research: Experimental Protocols, Methods in Molecular Biology, vol. 1397,
DOI 10.1007/978-1-4939-3353-2_1, © Springer Science+Business Media New York 2016
3
4 Bart Smeets et al.
Pod-rtTA
NPHS2 promoter
rtTA
+ Dox
LC1
TRE
luciferase Cre
R26R STOP
ROSA26 lox
neo lox
LacZ
Cre excision
ROSA26 lox
LacZ
Fig. 2 Flow scheme for the isolation of genetically tagged podocytes. Podocytes are specifically and irrevers-
ibly labeled by administration of doxycycline in transgenic Pod-rtTA/LC1/R26R mice. Inset in mouse illustrates
X-Gal staining of labeled podocytes (blue staining). The mice are perfused with magnetic iron oxide which
accumulates in the capillaries of the glomeruli (white arrow). Glomeruli are isolated and cultured. Single-cell
suspensions of the glomerular outgrowths are treated with FDG, which is hydrolyzed by β-gal into an insoluble
fluorescent product, and are subjected to FACS. After FACS, X-Gal staining can be performed to assess the
purity of the podocyte culture (blue staining, black arrowhead). The primary podocytes form large arborized cell
bodies with several intracytoplasmic extensions, i.e., thickenings
6 Bart Smeets et al.
2 Materials
1. Pod-rtTA/LC1/R26R mice.
2. Doxycycline solution: 5 % sucrose (w/v) and 1 mg/mL doxy-
cycline hydrochloride (Fargon GmbH&Co, Barsbüttel,
Germany), in normal tap water.
3. Anesthetic: mixture of 2 % xylazine (20 mg/mL) and 10 %
ketamine (100 mg/mL).
4. Iron oxide solution: normal saline (0.9 % NaCl) containing
0.9 % w/v iron (II,III) oxide (Fe3O4, 98 % purity, 20–30 nm
particle powder; Alfa Aesar GmbH, Karlsruhe, Germany).
5. Collagenase Type 4 (Worthington, Lakewood, NJ, USA).
6. EGM medium: Endothelial Growth Media (EGM™) Bullet
Kit (Lonza, Walkersville, MD USA). To formulate EGM
medium, basal medium EBM™ is supplemented with the
Bullet Kit components (i.e., human epidermal growth factor
[hEGF], hydrocortisone, bovine brain extract [BBE], ascorbic
acid, fetal bovine serum [FBS], and gentamicin/amphotericin-
B [GA]), according to manufacturer’s protocol. Final concen-
tration of FBS is 20 % v/v.
7. RPMI medium: RPMI 1640 supplemented with 10 % v/v FBS.
8. HBSS-Tween: 0.05 % v/v Tween®20 in Hank’s balanced salt
solution (HBSS).
9. Fluorescein di-β-galactopyranoside (FDG) (Molecular Probes,
Leiden, the Netherlands).
10. Cell culture antibiotics: penicillin‐streptomycin solution
(10,000 U/mL).
11. Trypsin‐EDTA cell culture formulation to remove cells from
cell culture vessel.
12. 50 mL centrifuge tubes.
13. Six-well cell culture plates.
14. 75 cm2 cell culture flask.
15. Automatic FACS cell sorter (e.g., BD FACSAria cell sorter,
BD Biosciences, San Jose, CA, USA).
Isolation and Primary Culture of Murine Podocytes with Proven Origin 7
3 Methods
3.1 Isolation All transgenic animals used to establish these methods were housed
of Podocytes under SPF-free conditions, and the procedures were approved by
the local state government authorities of LANUV Cologne. All
procedures are performed using aseptic techniques.
1. To induce the genetic labeling of the podocytes, the podocyte
reporter mice (Pod-rtTA/LC1/R26R) receive the doxycycline
solution via drinking water for a total of 10 days. The solution
needs to be protected from light and exchanged every 2 days.
2. Mice are anesthetized with ketamine (80 mg/kg bodyweight)
and xylazine (4 mg/kg bodyweight) and perfused via the left
heart ventricle with 20–40 mL iron oxide solution (see Note 1).
3. Kidneys are transferred into 50 mL RPMI medium containing
1 % (v/v) penicillin-streptomycin solution and cut into small
fragments.
4. The kidney fragments are incubated for 30 min at 37 °C with
1 mg/mL collagenase Type 4.
5. The small kidney fragments are gently pressed and sieved
through a 70 μm nylon mesh cell strainer/sieve. During this
process the strainer is repeatedly rinsed with cold HBSS-
Tween. The filtrate is collected in 50 mL centrifuge tubes.
6. HBSS-Tween is added to the filtrate to a final volume of 40 mL
per 50 mL falcon tube and incubated on ice for 20 min. During
this period the relatively large glomeruli form a sediment,
whereas cell debris and smaller structures will remain largely in
the supernatant. The supernatant is discarded and the sedi-
ment is resuspended in 40 mL of HBSS-Tween and incubated
on ice for another 20 min.
7. The sediment is resuspended in 1 mL of HBSS-Tween and
placed in a magnetic particle concentrator. The “magnetic”
glomeruli containing the iron oxide particles will be attracted
to the magnet. Other cells/structures will stay in the solution
and can be discarded carefully.
8 Bart Smeets et al.
8. The glomeruli still bound to the magnet are washed twice with
1 mL HBSS-Tween.
9. The washed glomeruli are resuspended in EGM medium with
1 % penicillin‐streptomycin solution and incubated for 7 to 14
days at 37 °C in a humidified atmosphere containing 95 % air
5 % CO2. During this culture period, the glomeruli will adhere
to the culture dish and glomerular cell outgrowths are formed
(see Note 2).
10. The cellular outgrowths are trypsinized, and the cells are resus-
pended in RPMI medium containing 1 % penicillin-
streptomycin solution and cultured in a 75 cm2 flask in a
humidified atmosphere containing 95 % air 5 % CO2.
11. When the cells have grown to 80 % confluence, the cells are
trypsinized and resuspended in RPMI medium, centrifuged at
600 × g, and resuspended in 1 mL RPMI medium containing
1 % penicillin-streptomycin solution.
12. The cell suspension is placed in a magnetic particle concentra-
tor. Free iron oxide particles and remaining glomerular struc-
tures containing iron oxide will be attracted to the magnet.
The oxide-free cell suspension can be transferred to a clean
1.5 mL test tube.
13. Fluorescein di-β-galactopyranoside (FDG) is added to the cell
suspension to a final concentration of 2 mM and incubated for
1 min at 37 °C (see Note 3).
14. Subsequently, the samples are diluted tenfold with RPMI
medium and incubated on ice for 60 min. The fluorescent-
labeled podocytes are sorted from non-labeled cells at 514 nm
using FACS (BD FACSAria II cell sorter).
15. Primary podocytes are cultured in RPMI medium containing
1 % penicillin-streptomycin solution at 37 °C in a humidified
atmosphere containing 95 % air 5 % CO2 (see Note 4).
3.2 Characterization Primary podocytes have a distinct phenotype. When the culture is
of Isolated Podocytes below 80 % confluence, the cells show a large cell body with several
arborized intracytoplasmic extensions (Fig. 2) (see Note 4).
The podocyte origin and purity of the culture can be verified
by enzymatic X-Gal staining. The enzymatic X-Gal staining is used
to detect the constitutive beta-galactosidase expression in the
labeled podocytes. For the enzymatic X-Gal staining:
1. Cells are washed with HBSS and fixed with 2 % glutaraldehyde
for 5 min.
2. Cells are washed with HBSS and treated with 1 % Triton®
X-100 for 5 min.
3. The cells are washed again with HBSS and incubated over-
night at 37 °C in a humidified atmosphere in X-Gal staining
solution.
Isolation and Primary Culture of Murine Podocytes with Proven Origin 9
4 Notes
Acknowledgments
References
1. Wiggins RC (2007) The spectrum of podocyto- 3. Kreisberg JI, Hoover RL, Karnovsky MJ (1978)
pathies: a unifying view of glomerular diseases. Isolation and characterization of rat glomerular
Kidney Int 71:1205–1214 epithelial cells in vitro. Kidney Int 14:21–30
2. Shankland SJ, Pippin JW, Reiser J, Mundel P 4. Striker GE, Killen PD, Farin FM (1980) Human
(2007) Podocytes in culture: past, present, and glomerular cells in vitro: isolation and character-
future. Kidney Int 72:26–36 ization. Transplant Proc 12:88–99
10 Bart Smeets et al.
5. Kabgani N, Grigoleit T, Schulte K et al (2012) 7. Moeller MJ, Sanden SK, Soofi A, Wiggins RC,
Primary cultures of glomerular parietal epithelial Holzman LB (2003) Podocyte-specific expres-
cells or podocytes with proven origin. PLoS One sion of cre recombinase in transgenic mice.
7:e34907 Genesis 35:39–42
6. Shigehara T, Zaragoza C, Kitiyakara C et al (2003) 8. Soriano P (1999) Generalized lacZ expression
Inducible podocyte-specific gene expression in with the ROSA26 Cre reporter strain. Nat Genet
transgenic mice. J Am Soc Nephrol 14:1998–2003 21:70–71
Chapter 2
Abstract
The renal fibroblast and phenotypically related myofibroblast are universally present in all forms of pro-
gressive kidney disease. The in vitro study of the fibroblast, its behavior, and factors affecting its activity is
therefore key to understanding both its role and significance. In this protocol, we describe a reproducible
method for selective propagation and culture of primary human renal fibroblasts from the human kidney
cortex. Techniques for their isolation, subculture, characterization, and cryogenic storage and retrieval are
described in detail.
1 Introduction
Tim D. Hewitson et al. (eds.), Kidney Research: Experimental Protocols, Methods in Molecular Biology, vol. 1397,
DOI 10.1007/978-1-4939-3353-2_2, © Springer Science+Business Media New York 2016
11
12 Sven-Jean Tan and Tim D. Hewitson
2 Materials
2.1 General Sterile 1. Glass media bottles: 100, 200, and 500 mL.
Cell Culture Materials 2. 60 mm2 cell culture petri dishes.
3. 50 mL centrifuge tubes.
4. Tissue culture flasks: 25 and 75 cm2.
5. Six-well cell culture plates.
6. Graduated 5 and 10 mL pipettes.
7. Cell scrapers.
8. Disposable 50 mL syringes.
9. Disposable 0.2 μm pore syringe filters.
10. 0.2 μm 500 mL bottle-top vacuum filter unit.
11. Sterile containers for tissue collection.
12. Disposable basic sterile dressing pack for dissection.
13. N° 22 scalpel blades.
14. Pasteur transfer pipettes.
15. Waste bottle.
16. Laboratory grade double deionized water (ddH2O).
Table 1
Immunocytochemical antiserum specifications
Raised
Antibody Clone in Dilution Specificity Manufacturer
α-SMA 1A4 Mouse 1:50 Smooth muscle Dako, Glostrup, Denmark
isoform of actin
Collagen I – Rabbit 1:1000 Collagen type I Southern Biotech,
Birmingham, AL, USA
Cytokeratin MNF116 Mouse 1:100 Pan-keratin Dako
Desmin D33 Mouse 1:100 Desmin Dako
E-cadherin 36/E-cadherin Mouse 1:100 E-cadherin BD Biosciences, San
Jose, CA, USA
Vimentin V9 Mouse 1:50 Vimentin Dako
3 Methods
3.1 Gelatin Coating Petri dishes are coated with 1 % gelatin solution prior to explanting
of Petri Dishes of kidney tissue. This will enable minced tissue to secure to the
petri dish and provide a substrate for the initial cultivation of cell
populations.
1. Dilute 2 % gelatin solution with 0.01 M PBS (1:1 dilution) and
filter sterilize into a centrifuge tube using a disposable syringe
and a 0.2 μm pore syringe filter.
2. Coat entire surface of the petri dish with 1 mL of 1 % gelatin
solution and incubate for ≥30 min at 37 °C.
3. Remove excess gelatin solution and rinse the petri dish with
0.01 M PBS prior to explanting.
3.2 Propagation Collection of and conducting research with any human tissue
of Human Renal should be performed in strict accordance with the Human Research
Interstitial Cultures Ethics guidelines and the Declaration of Helsinki. Collection of
from Kidney Explants human tissue is subject to approval by the appropriate Human
Research Ethics Committee and requires individual human/
patient consent.
1. Retrieve the human kidney cortical tissue in tissue collection
buffer as soon as possible after removal of tissue. Keep this on
ice until required for explanting (see Note 1).
2. Set out a sterile field in the biohazard hood using a basic dress-
ing pack.
3. Pour out the kidney tissue and tissue collection buffer onto
one small section of a sterile tray (e.g., dressing pack tray) and
use the sterile disposable forceps to gently transfer the kidney
into another clean section of the tray.
4. Cover the kidney tissue with warm enriched medium to keep
moist.
5. Dissect this piece of tissue with surgical forceps into ~0.25 cm2
pieces.
6. Transfer one piece of ~0.25 cm2 kidney tissue to a gelatin-
coated petri dish (which has been rinsed).
7. Dice this piece of tissue until a minced consistency is achieved.
8. Make crosswise scratches across the surface of the petri dish
using the surgical blade in order to adhere the minced tissue to
the gelatin surface. Continue until 75 % of this dish is
covered.
9. Cover explanted tissue with ~2 mL of enriched medium using
a plastic Pasteur pipette, then label, and date.
10. Incubate overnight at 37 °C with 95 % O2/5 % CO2.
11. Supplement with an additional 1 mL of enriched medium 24 h
after the explanting procedure.
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