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Methods in
Molecular Biology 1344
Xin-Hua Feng
Pinglong Xu
Xia Lin Editors
TGF-β
Signaling
Methods and Protocols
METHODS IN MOLECULAR BIOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
Edited by
Xin-Hua Feng
Life Sciences Institute and Innovation Center for Cell Signaling Network,
Zhejiang University, Hangzhou, Zhejiang Province, China; Departments of Surgery,
and Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
Pinglong Xu
Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Proviince, China
Xia Lin
Department of Surgery, Baylor College of Medicine, Houston, USA
Editors
Xin-Hua Feng Pinglong Xu
Life Sciences Institute and Innovation Life Sciences Institute
Center for Cell Signaling Network Zhejiang University
Zhejiang University, Hangzhou Hangzhou, Zhejiang Proviince, China
Zhejiang Province, China
Xia Lin
Departments of Surgery Department of Surgery
and Molecular & Cellular Biology Baylor College of Medicine
Baylor College of Medicine Houston, USA
Houston, Texas, USA
Cells that respond to environmental cues through the complex and dynamic network of
signaling pathways maintain a critical balance between cellular proliferation, differentiation,
and death. Since the original discovery of TGF-β about more than 30 years ago, the mole-
cule only represents a prototype of a large family that consists of at least 33 members encoded
by the human genome. The TGF-β superfamily members are secreted proteins, including
TGF-β, activins, bone morphogenetic proteins, growth/differentiation factors, and
Müllerian inhibiting substance, and can regulate many developmental processes in a range of
organisms from worms to humans. At cellular level, they control a wide range of cellular
functions such as proliferation, death, differentiation, and other functions in many cell types.
Dysfunctions of the TGF-β family members often result in the pathogenesis of cancer, auto-
immune diseases, diabetes, heart disease, hereditary hemorrhagic telangiectasia, Marfan syn-
drome, Vascular Ehlers-Danlos syndrome, Loeys–Dietz syndrome, and neurodegenerative
diseases. The characterization of the TGF-β family underscores its importance in physiologi-
cal and pathophysiological functions.
The research on TGF-β biology, including its regulation, signaling, and physiological
functions, has developed rapidly into a large field with thousands of publications per year.
In the last 20 years, the components of the canonical signaling pathways—the TGF-β recep-
tors and downstream intracellular effectors Smad proteins—have been identified, and the
concept for context-dependent TGF-β actions has been well established. Many conven-
tional methodologies or state-of-the-art technologies have been employed to elucidate how
the TGF-β pathways are regulated and what functions they have in the context from single
cells to complexed tissues to the whole organism. The rapidly evolving nature of TGF-β
signaling research also necessitates a continuous updating of methods used. TGF-β
Signaling: Methods and Protocols brings together a comprehensive collection of methods
and techniques in TGF-β signaling research that are scientifically grounded within the can-
cer and development fields. Thus, this volume grows out of the necessity that a comprehen-
sive method book covering biochemical, molecular, and biological description of TGF-β
ligands, receptors, and intracellular events is needed for researchers who are already in the
TGF-β field and for those who wish to enter the field.
This volume provides the reader with up-to-date information in this continuing evolv-
ing field and attempts to take the reader into the exciting realm of TGF-β from the basic
principles to the practical applications. All the chapters are provided by leading researchers
in the TGF-β field. The first chapter by Budi and Derynck gives a basic introduction of
TGF-β receptor signaling at the cell surface. Subsequent chapters are generally concerned
with methods and techniques for the investigation of TGF-β signaling mechanism includ-
ing receptors, intracellular kinases, microRNA, epigenetic regulation, post-translational
regulations, non-Smad pathway; the physiological implications including those in
epithelial-mesenchymal transition, endothelial cells, adipogenesis, Th differentiation, stem
v
vi Preface
cell, bone remodeling, ovary, zebrafish development, and frog animal capping; and the
methodologies including metastasis imaging, 3D morphogenesis, membrane receptor
quantification, conditional knockout, bone remodeling, kinase and phosphatase assays,
BiFC interaction assays, and genome-wide siRNA screen.
This book would not be possible were it not for all the contributors who devoted their
precious time and considerable energy to bring this volume into reality and provide such
clear and detailed accounts of their experimental protocols and useful hints. We are greatly
indebted to them for their excellent contributions and for their patience in dealing with the
editors. I also wish to thank Dr. P.J. Higgins and their overall help and patience in keeping
the book on track. We hope this volume will prove valuable to all researchers, rookie or
veteran, in the TGF-β signaling field and serve as a useful reference for many years to come.
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
vii
viii Contents
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391
Contributors
HIROYUKI ABURATANI • Genome Science Division, Research Center for Advanced Science
and Technology (RCAST), The University of Tokyo, Tokyo, Japan
LINDSAY ALCARAZ • Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France;
CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France;
Université de Lyon, Lyon, France; Université Lyon 1, Lyon, France; Centre Léon Bérard,
Lyon, France
LAURENT BARTHOLIN • Inserm U1052, Centre de Recherche en Cancérologie de Lyon,
Lyon, France; CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, Lyon,
France; Université de Lyon, Lyon, France; Université Lyon 1, Lyon, France;
Centre Léon Bérard, Lyon, France
JUAN C. BOURNAT • Department of Pediatrics, Baylor College of Medicine,
Houston, TX, USA
CHESTER W. BROWN • Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine,
Houston, TX, USA; Texas Children’s Hospital, Houston, TX, USA
ERINE H. BUDI • Department of Cell and Tissue Biology, Broad Center, University
of California, San Francisco, CA, USA
XU CAO • Department of Orthopaedic Surgery, Johns Hopkins University School
of Medicine, Baltimore, MD, USA
JONATHON CARTHY • Ludwig Institute for Cancer Research, Science for Life Laboratory,
Uppsala University, Uppsala, Sweden
CHENBEI CHANG • Department of Cell, Developmental and Integrative Biology, University
of Alabama at Birmingham, Birmingham, AL, USA
XIAOCHU CHEN • Program in Molecular Medicine, University of Massachusetts Medical
School, Worcester, MA, USA
YAN CHEN • Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences,
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
YE-GUANG CHEN • State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing, China
JANET L. CRANE • Department of Orthopaedic Surgery, Johns Hopkins University School
of Medicine, Baltimore, MD, USA; Department of Pediatrics, Johns Hopkins University
School of Medicine, Baltimore, MD, USA
RIK DERYNCK • Department of Cell and Tissue Biology, Eli and Edythe Broad Center
of Regeneration Medicine and Stem Cell Research, Programs in Cell Biology,
and Developmental and Stem Cell Biology, University of California,
San Francisco, CA, USA
PETER TEN DIJKE • Department of Molecular Cell Biology, Cancer Genomics Centre
Netherlands, Centre for Biomedical Genetics, Leiden University Medical Center, Leiden,
The Netherlands
SHENG DING • Department of Pharmaceutical Chemistry, Gladstone Institute
of Cardiovascular Disease, University of California, San Francisco, CA, USA
ix
x Contributors
MAARTEN VAN DINTHER • Department of Molecular Cell Biology, Leiden University Medical
Center, Leiden, The Netherlands
HENG-YU FAN • Life Sciences Institute and Innovation Center for Cell Signaling Network,
Zhejiang University, Hangzhou, China
ZIPEI FENG • Department of Chemistry and Biochemistry, University of Colorado Boulder,
Boulder, CO, USA; Otto-Warburg Laboratory, Max Planck Institute for Molecular Genetics,
Berlin, Germany
MAI FUJIMOTO • Genome Science Division, Research Center for Advanced Science
and Technology (RCAST), The University of Tokyo, Tokyo, Japan; Department of
Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
TAKANORI FUJITA • Genome Science Division, Research Center for Advanced Science
and Technology (RCAST), The University of Tokyo, Tokyo, Japan
M.J. GOUMANS • Department of Molecular Cell Biology, Cancer Genomics Centre
Netherlands, Centre for Biomedical Genetics, Leiden University Medical Center, Leiden,
The Netherlands
SHYAM KUMAR GUDEY • Department of Medical Biosciences, Umeå University, Umeå, Sweden
XING GUO • Department of Pharmacology and Cancer Biology, Duke University Medical
Center, Durham, NC, USA
AKIKO HATA • Cardiovascular Research Institute, University of California, San Francisco,
CA, USA
ANDREW P. HINCK • Department of Structural Biology, University of Pittsburgh, Pittsburgh,
PA, USA
TAO HUANG • Protein Chemistry, Novo Nordisk Research Center China, Beijing, China
ATSUSHI KANEDA • Genome Science Division, Research Center for Advanced Science
and Technology (RCAST), The University of Tokyo, Tokyo, Japan; Department of
Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan;
CREST, Japan Science and Technology Agency, Saitama, Japan
YIBIN KANG • Lewis Thomas Laboratory 255, Department of Molecular Biology, Princeton
University, Princeton, NJ, USA
HARA KANG • Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon
National University, Incheon, Republic of Korea; Cardiovascular Research Institute,
University of California, San Francisco, CA, USA
MITSUYASU KATO • Department of Experimental Pathology, Graduate School
of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
MARENE LANDSTRÖM • Department of Medical Biosciences, Umeå University, Umeå, Sweden
WENLIN LI • Department of Cell Biology, Second Military Medical University, Shanghai,
China
XIA LIN • Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston,
TX, USA
XUEDONG LIU • Department of Chemistry and Biochemistry, University of Colorado Boulder,
Boulder, CO, USA
FANG LIU • Center for Advanced Biotechnology and Medicine, Rutgers, The State University of
New Jersey, Piscataway, NJ, USA; Susan Lehman Cullman Laboratory for Cancer Research,
Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State
University of New Jersey, Piscataway, NJ, USA; Rutgers Cancer Institute of New Jersey,
Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
Contributors xi
SYLVIE THUAULT • Faculty of Pharmacy, INSERM UMR 911 CRO2, Marseille, France
ULRICH VALCOURT • Inserm U1052, Centre de Recherche en Cancérologie de Lyon,
Lyon, France; ; CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon,
France; Université de Lyon, Lyon, France; Université Lyon 1, Lyon, France;
Centre Léon Bérard, Lyon, France
QIANG WANG • Institute of Zoology, Chinese Academy of Sciences, Beijing, China
XIAO-FAN WANG • Department of Pharmacology and Cancer Biology, Duke University
Medical Center, Durham, NC, USA
WANGUO WEI • Stem Cell and Regenerative Medicine Center, Chinese Academy of Science,
Shanghai Advanced Research Institute, Shanghai, China
LINGLING XIAN • Department of Orthopaedic Surgery, Johns Hopkins University School
of Medicine, Baltimore, MD, USA
JIAN XU • Center for Craniofacial Molecular Biology, Ostrow School of Dentistry of USC,
University of Southern California, Los Angeles, CA, USA
LAN XU • Blueprint Medicines, Cambridge, MA, USA
PINGLONG XU • Life Sciences Institute and Innovation Center for Cell Signaling Network,
Zhejiang University, Hangzhou, China
RYOTA YAMANAKA • Genome Science Division, Research Center for Advanced Science
and Technology (RCAST), The University of Tokyo, Tokyo, Japan
XIAOHUA YAN • State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing, China
PENGYUAN YANG • CAS Key Laboratory of Infection and Immunity, Institute of Biophysics,
Chinese Academy of Sciences, Beijing, China
AKIHIKO YOSHIMURA • Department of Microbiology and Immunology, Keio University
School of Medicine, Tokyo, Japan
CHAO YU • Life Sciences Institute and Innovation Center for Cell Signaling Network,
Zhejiang University, Hangzhou, China
LONG ZHANG • Life Sciences Institute and Innovation Center for Cell Signaling Network,
Zhejiang University, Hangzhou, China
YUN ZHANG • Department of Pharmacology and Cancer Biology, Duke University Medical
Center, Durham, NC, USA
FANGFANG ZHOU • Institutes of Biology and Medical Sciences, Soochow University,
Suzhou, China
JIAN-JIE ZHOU • Life Sciences Institute and Innovation Center for Cell Signaling Network,
Zhejiang University, Hangzhou, China
ZHIKE ZI • Otto-Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin,
Germany
Chapter 1
Abstract
In cells responding to extracellular polypeptide ligands, regulatory mechanisms at the level of cell surface
receptors are increasingly seen to define the nature of the ligand-induced signaling responses. Processes
that govern the levels of receptors at the plasma membrane, including posttranslational modifications, are
crucial to ensure receptor function and specify the downstream signals. Indeed, extracellular post-
translational modifications of the receptors help define stability and ligand binding, while intracellular
modifications mediate interactions with signaling mediators and accessory proteins that help define the
nature of the signaling response. The use of various molecular biology and biochemistry techniques, based
on chemical crosslinking, e.g., biotin or radioactive labeling, immunofluorescence to label membrane
receptors and flow cytometry, allows for quantification of changes of cell surface receptor presentation.
Here, we discuss recent progress in our understanding of the regulation of TGF-β receptors, i.e., the type
I (TβRI) and type II (TβRII) TGF-β receptors, and describe basic methods to identify and quantify TGF-β
cell surface receptors.
Key words TβRI, TβRII, Posttranslational modifications, Cell surface receptor, Clathrin, Caveolin,
Biotin labeling, Affinity labeling, Immunoprecipitation, Neutravidin precipitation, Cell sorting,
Chemical crosslinking, Immunofluorescence
1 Introduction
Xin-Hua Feng et al. (eds.), TGF-β Signaling: Methods and Protocols, Methods in Molecular Biology, vol. 1344,
DOI 10.1007/978-1-4939-2966-5_1, © Springer Science+Business Media New York 2016
1
2 Erine H. Budi et al.
1.1 Posttranslational Similarly to other cell surface receptors, TGF-β receptors are tar-
Modifications gets of posttranslational modifications in both their extracellular
of the TGF-β and cytoplasmic domains (Fig. 1). These modifications involve
Receptors actions of various enzymes and interacting proteins, and provide
mechanisms that define the functions of the receptors as initiators
of signaling.
1.1.1 TGF-β Receptor TGF-β binding to the receptor complex leads to Smad activation
Phosphorylation and non-Smad signaling pathways. Accordingly, cytoplasmic
Fig. 1 Posttranslational modifications of TβRI and TβRII receptors. The underlying enzymatic reactions of
receptor phosphorylation, ubiquitylation, sumoylation, and N-glycosylation are shown
4 Erine H. Budi et al.
1.1.3 TGF-β Receptor The TβRI receptor is also targeted for sumoylation, a process that
Sumoylation results in covalent attachment of a single SUMO polypeptide to a
and Neddylation targeted lysine of a substrate. The process of sumoylation shows
similarities with ubiquitylation. Not only does SUMO structurally
resemble ubiquitin, but sumoylation also requires three-step enzy-
matic actions of an E1, E2, and E3 SUMO ligase [41, 42]. Most
known targets for sumoylation are transcription factors, perinu-
clear and nuclear proteins [43]. Similar to ubiquitylation, only a
small fraction of the targeted proteins are sumoylated at any given time,
consistent with the reversible nature of sumoylation [42, 44, 45].
In response to TGF-β binding, TβRI is sumoylated at a single
lysine residue [46]. TβRI sumoylation depends on the kinase activ-
ities of both TβRI and TβRII, strongly suggesting that TβRI
sumoylation requires TβRI phosphorylation, and effectively illus-
trating functional cross talk between two types of posttranslational
modifications [46]. Sumoylation of the TβRI cytoplasmic domain
enhances the efficiency of Smad2/3 recruitment to TβRI, thus
increasing the level of Smad2/3 activation and Smad-mediated
signaling in response to TGF-β [46].
Although TβRII is not known to be ubiquitylated or
sumoylated, it is modified by neddylation, i.e., addition of the
ubiquitin-like protein Nedd8. The ubiquitin E3 ligase encoded
by the proto-oncogene c-Cbl was shown to mediate covalent
linkage of Nedd8 to TβRII at two lysine positions, thus promoting
enhanced stability of TβRII [47]. Targeted inactivation of c-Cbl
decreases the TβRII levels and desensitizes hematopoietic stem/
progenitor cells to TGF-β signaling [47]. Inactivating c-Cbl
Regulation of TGF-β Receptors 7
1.1.4 TGF-β Receptor Both TβRII and TβRI are N-glycosylated [48–50]. N-glycosylation
N-glycosylation of the extracellular domains of transmembrane proteins and
secreted proteins is thought to contribute to protein stability and
solubility and may facilitate intracellular transport through the
Golgi to the plasma membrane [49, 51–53]. In TβRII, N-linked
glycosylation occurs on two asparagine residues in the extracellular
domain [53]. Mutation of these two sites, which prevents
N-glycosylation, blocks transport of the TβRII receptor to the
plasma membrane and leads to receptor accumulation in the ER,
while mutants with a single residue mutation are still able to local-
ize TβRII at the cell surface [53]. The defect in N-glycosylation
results in impaired TGF-β signaling [53]. The role of glycosylation
in the type I receptor in cell surface transport and signaling is
unknown. Whether N-linked glycosylation affects TβRI-TβRII
complex formation is similarly unknown.
MED12, a component of transcription Mediator complex, is
found to interact with a partially and unglycosylated form of
TβRII [54]. MED12 overexpression causes a decrease in cell sur-
face TβRII by interfering with proper glycosylation of TβRII,
hence blocking the appearance of TβRII at the cell surface.
Conversely, attenuation of MED12 expression confers resistance
to a range of chemotherapy drugs that are used in treating colon
cancer, melanoma, and liver cancer, through activation of TGF-β
signaling [54].
1.1.5 Ectodomain The levels of functional TGF-β receptor at the cell surface are also
Shedding of TGF-β regulated by ectodomain shedding, i.e., proteolytic release of
Receptors ectodomains by cell surface metalloproteases [55]. The transmem-
brane metalloprotease TACE, also known as ADAM17, cleaves
and thus removes the extracellular domain of TβRI, but not TβRII,
resulting in TβRI inactivation without affecting TGF-β binding to
TβRII. TACE-mediated ectodomain shedding is activated by the
Erk MAPK pathway, e.g., in response to growth factors that act
through receptor tyrosine kinases, and by p38 MAPK signaling in
response to inflammatory stimuli, thus decreasing functional recep-
tor availability under these conditions, and attenuating TGFβ-
induced Smad responses [56, 57]. Ectodomain cleavage of TβRI
not only leads to the release of its extracellular domain, but also
leads to the release of the intracellular domain of TβRI into the
cytosol. This domain can then translocate into the nucleus and act
as a transcription regulator [36]. Another metalloprotease,
ADAM12, also known as meltrin-α, was found to interact with the
extracellular domain of TβRII [58]. ADAM12 does not impair
TGF-β signaling, as one would expect from its protease activity,
8 Erine H. Budi et al.
Table 1
Proteins interacting with TGF-ß receptors
Interacting
proteins Regulatory mechanism References
Axin Facilitates Smad3 activation by TβRI and interacts with Smad7 [103–105]
and Arkadia to promote Smad7 degradation
BAT3 Interacts with TβRI and TβRII and enhances TGF-β-induced [106]
transcription
c-Ski Associates with activated TβRI and stabilizes a non-functional [107]
TβRI/R-Smad/Smad4 complex
CD109 Enhances TGF-β binding to its receptors, promotes caveolae- [70, 71]
mediated receptor internalization and Smad7-Smurf
mediated receptor degradation
CD44 Associates with TβRI to promote Smad2/3 activation and [108]
PTH-RP expression
cPML Stabilizes R-Smad/SARA complex and enriches TGF-β and [109]
SARA in early endosomes
Dab2 Associates with TGF-β receptors and R-Smads to facilitate [94, 95]
R-Smad activation and promotes clathrin-mediated
recycling of TβRII to decrease degradation
Dpr2 Binds to TβRI receptor and promote lysosomal degradation [97, 98]
of the receptor
ETV6- Binds directly to TβRII and prevents TβRII from interacting [68]
NTRK3 with TβRI
FKBP12 Binds to the GS domain of TβRI and prevents leaky TGF-β [72, 110,
signaling, interacts with Smad7, Smurf1, and TβRI to target 111]
TβRI for degradation
Hgs/Hrs Cooperates with SARA to stabilize TGF-β receptor/R-Smad complexes [77, 112]
HSP90 Binds to TβRI and TβRII and protects receptors from [78, 113]
Smurf2-mediated ubiquitylation and degradation
Integrin αvβ3 Interacts with TβRII to enhance TGF-β1 activation [63]
Itch/AIP4 Enhances Smad2 or Smad7 association with TβRI and modulates [114, 115]
R-Smad activation
Km23–1 Associates with TGF-β receptors and Smad2 in early endosomes [116]
to enhance Smad activation
MED12 Interacts with TβRII and inhibits Smad2 and Erk MAPK activation [54]
Mgat5 Modifies TGF-β receptor N-glycosylation and delays internalization [117]
Occludin Regulates TβRI localization and facilitates TGF-β-dependent tight [118]
junction dissolution
PDK1 Facilitates STRAP-induced stabilization of Smad7-receptor complexes [119]
Rock2 Binds to TβRI receptor and promotes lysosomal degradation of the [120]
receptor
(continued)
Regulation of TGF-β Receptors 11
Table 1
(continued)
Interacting
proteins Regulatory mechanism References
SARA Stabilizes the association of TGF-β receptors and R-Smads, [76, 89,
and directs activated receptors towards clathrin-mediated endocytic 121]
pathways
Shc Interacts with and is phosphorylated by TβRI, activates [6]
ERK-MAPK signaling
SIK Associates with Smad7, TβRI, and Smurf2 and promotes [122, 123]
proteasomal degradation of the receptor
Smad7 Competes with R-Smads for TβRI receptor binding to prevent [18, 27,
R-Smad activation, recruits ubiquitin E3 ligases to TβRI 30,
receptor for receptor degradation, and GADD34-PP1c 33, 122]
to TβRI for receptor dephosphorylation
STRAP Interacts with TβRI and TβRII receptors and stabilizes [75]
Smad7-receptor complexes
Tctex2β Interacts with TβRII and inhibits TGF-β signaling when [74]
overexpressed
TLP Associates with TβRI and TβRII to regulate the balance [124]
between Smad2 and Smad3 signaling
TMEPAI Competes with TβRI receptor for R-Smad binding [125]
Tollip Interacts with ubiquitylated TβRI and promotes receptor degradation [126]
TRAF6 Associates with activated TGF-β receptors, inhibits TGF-β-induced [35, 80]
R-Smad activation and IL-2 blockage in T cells, and mediates
p38 and JNK activation in response to TGF-β
TrkC Binds to TβRII, suppresses TβRII interaction with TβRI, [67]
and TGF-β signaling
VE-cadherin Promotes active TGF-β receptor complex formation and enhances [65]
R-Smad phosphorylation
xIAP Associates with TβRI and ubiquitylates TAK1 to activate NF-κB [81]
YAP-65 Enhances Smad7 association to activated TβRI and inhibits R-Smad [127]
activation
1.3.2 Caveolin- and Lipid TGF-β receptors are also found in lipid raft microdomains and
Raft-Mediated Endocytosis caveolin-positive endocytic compartments, i.e., caveolae [85, 90, 91].
TβRI interacts with caveolin-1, a key integral membrane protein in
caveolae [90]. This interaction promotes TGF-β receptor turnover
via Smad7-mediated recruitment of Smurf1 or Smurf2 [85, 90].
Interfering with caveolin-1 expression using antisense RNA results
in an enhanced TGF-β-induced Smad activation [90]. Similar
results are seen with suppression of caveolae-mediated internaliza-
tion by nystatin [85]. In contrast, expression of caveolin-1 in cave-
olin-1-deficient cells increases the turnover of TGF-β receptors
[85]. The GPI-anchored cell surface protein CD109 may play a
role in partitioning the receptor complexes between clathrin- and
caveolin-mediated endocytosis. CD109 associates with caveolin
and TβRI, and colocalizes with activated-TGF-β receptors com-
plex in caveolae [69, 70]. CD109 enhances the association of
ligand-activated TβRI with Smad7-Smurf2-complex and thus
inhibits TGF-β signaling and responses [70, 71].
In addition to its role in promoting receptor degradation, lipid
raft-caveolar endocytosis has also been linked to TGF-β-induced
Erk MAPK signaling [92]. Whether activation of non-Smad signal-
ing pathways requires differential endosomal receptor routing
requires further studies.
14 Erine H. Budi et al.
1.3.3 Roles of GTPases The differential routing of the internalized receptors is regulated
and Other Proteins by different Rab GTPases that localize in specific intracellular
in TGF-β Receptor membrane structures, where they function as regulators of distinct
Trafficking steps in vesicle or membrane trafficking. Rab5 promotes internal-
ization of the activated TGF-β receptors into early EEA-1-positive
endosomes [85]. Like other GTPases, Rab5 is active in its GTP-
bound form, and the generation of the activated form is promoted
by a Rab-specific guanine nucleotide-exchange factor (GEF) such
as RIN1 that promotes exchange of GDP for GTP. Consistent
with the role of Rab5, RIN1 promotes TGF-β-induced Smad sig-
naling [93].
Another small GTPase, Rab11, is involved in recycling the
TGF-β receptors back to the plasma membrane [84]. The clathrin
adaptor Dab2 (disabled-2) has been shown to associate with the
type I and type II TGF-β receptors [94] and regulates TGF-β
receptor trafficking between EEA1-positive early endosomes and
Rab11-positive recycling endosomes [95]. Rap2, a Ras family
GTPase, has also been implicated in enhancing the TGF-β response
by promoting recycling of the receptors, preventing their degrada-
tion, and thus maintaining their levels on the cell surface [96].
Rap2 competes with Smad7 for binding to activated TβRI to pre-
vent their degradation, and therefore contributes to the upregula-
tion of Smad activation [96].
Lastly, Rab7 is known to direct the TGF-β receptors to
lysosomes for degradation via a Dapper2 (Dpr2) binding com-
plex. Dpr2, first identified as a Dishevelled (Dsh)-interacting
protein, preferentially forms a complex with activated TβRI
[97]. It negatively regulates TGF-β/nodal signaling by facilitat-
ing the transport of the activated receptors to lysosomes [97, 98].
Consistent with this notion, TGF-β-induced TβRI degradation
is enhanced by Dpr2 and inhibited by lysosomal inhibitors, e.g.,
bafilomycin A or chloroquine, but not by the proteasome inhibitor
MG132 [97].
2 Materials
2.1 Biotin Labeling TGF-β1 is from Humanzyme (Product No. HZ-1011). The
of Cell Surface TGF-β chemical crosslinkers EZ-link sulfo NHS-LC-biotin (Product No.
Receptors 21335), EZ-Link-NHS-SS-Biotin (Product No. 21441), and the
NeutrAvidin beads (Product No. 29201) are from Thermo
2.1.1 Chemicals
Scientific. See Blue Plus2 protein marker (Product No. LC5925),
4× LDS sample buffer (Product No. NP0008), and NuPAGE 10×
MOPS-SDS running buffer (Product No. NP0001) are from
Invitrogen. The Bio-Rad Protein dye assay (Product No. 500-
0006) and β-mercaptoethanol (BME) electrophoresis purity
reagent (Product No. 161-0710) are from Bio-Rad. Complete
protease inhibitor cocktail tablets (Product No. 11 836 170 001)
are from Roche. Bovine Serum Albumin (BSA) and Tween 20 are
from Sigma.
2.1.2 Antibodies Anti-TGF-β receptor type I and II are from Abcam (Product No.
ab31013 and ab61213).
Anti-phospho-Smad2 and phospho-Smad3 antibodies are
from Cell Signaling Technology (Product No. 3108 and No.
9520).
2.1.3 Solutions PBS (sterile filtered-tissue culture grade): 0.1 g/L CaCl2, 0.1 g/L
MgCl2⋅6H2O, 0.2 g/L KCl, 0.2 g/L KH2PO4, 8 g/L NaCl,
2.16 g/L Na2HPO4⋅7H2O.
MLB lysis buffer: 20 mM Tris–HCl pH 8.0, 200 mM NaCl,
10 mM NaF, 1 mM Na3VO4, 1 % NP-40, and Complete Protease
inhibitor (Roche); MLB lysis buffer can be made in advance, ali-
quotted and stored at −20 °C.
MLB wash buffer: 20 mM Tris–HCl pH 8.0, 200 mM NaCl,
10 mM NaF, 1 mM Na3VO4, 1 % NP-40; MLB wash buffer can be
made in advance and stored at 4 °C.
RIPA lysis buffer: 20 mM Tris–HCl pH. 8.0, 150 mM NaCl,
10 mM NaF, 1 mM Na3VO4, 1 % NP-40, 0.1 % SDS, 0.25 %
C24H39O4Na (sodium deoxycholate), and complete Protease
inhibitor (Roche); RIPA lysis buffer can be made in advance, ali-
quotted, and stored at −20 °C.
Stop buffer: 0.1 M Glycine in PBS.
Western blot sample buffer: 4× LDS from Invitrogen.
Western blot transfer buffer (4 L): 57.8 g Glycine, 12.0 g Tris base,
750 mL Methanol, top up to 4 L.
10× TBS (1 L): 24.23 g Tris base, 80.06 g NaCl, pH to 7.6 with
HCl, top up to 1 L with ultrapure water.
1× TBS (1 L): 100 mL of 10× TBS, 900 mL of water.
1× TBST (1 L): 100 mL of 10× TBS, 900 mL of water, 1 mL of
Tween 20.
Western blot membrane wash buffer: 1× TBST.
16 Erine H. Budi et al.
2.2.2 Radioactive Na125I, consult with your EH&S office for purchasing radioactive
materials.
2.2.3 Solutions Cold binding buffer: 128 mM NaCl, 5 mM KCl, 1.2 mM CaCl2,
5 mM MgSO4, 50 mM HEPES pH 7.4.
Elution buffer: 4 mM HCl, 100 mM NaCl, 0.1 mg/mL BSA.
Detachment buffer: 0.25 M sucrose, 10 mM Tris–HCl pH 7.4, 1 mM
EDTA, 1 mM C7H7FO2S (phenylmethylsulfonyl fluoride).
2.3 Fluorescence- HA.11 Clone 16B12 is from Covance. Mouse or rabbit IgG is
Based Detection from Upstate Biotechnology. Alexa Fluor® 488 Goat Anti-Rabbit
of Cell Surface TGF-β IgG (H + L) or Alexa Fluor® 568 Goat Anti-Rabbit IgG (H + L) are
Receptors from Invitrogen-Molecular Probes (Product No. A-11034 and
A11036). Anti-Flag M2 monoclonal antibody is from Sigma.
2.3.1 Antibodies
2.3.2 Solutions PBS (sterile filtered, cell culture grade): 0.1 g/L CaCl2, 0.1 g/L
MgCl2⋅6H2O, 0.2 g/L KCl, 0.2 g/L KH2PO4, 8 g/L NaCl,
2.16 g/L Na2HPO4⋅7H2O.
PBS-IHC (sterile filtered, cell culture grade): 0.2 g/L KH2PO4,
2.16 g/L Na2HPO4⋅7H2O, 0.2 g/L KCl, 8.0 g/L NaCl; this PBS
contains no Mg and Ca and is used for immunohistochemistry.
FC (Flow Cytometry) staining buffer: PBS-IHC containing 3 %
BSA, and 0.5 % sodium azide.
IHC fixation: 3.7 % paraformaldehyde in PBS-IHC (PFA) pH 7.4.
IHC blocking: 3 % BSA in PBS-IHC, filter through a standard
0.2 μm filter before use, and store at 4 °C.
PBT: PBS-IHC with 0.2 % Triton X.