Dysfunctional plasmacytoid dendritic cells but not NK cells in the peripheral blood of stage IV melanoma patients [Elektronische Ressource] / presented by Geok Choo, Sim

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INAUGURAL-DISSERTATION submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences Presented by Master of Science: Geok Choo, Sim born in Johor, Malaysia Dysfunctional Plasmacytoid Dendritic Cells but not NK cells in the Peripheral Blood of Stage IV Melanoma Patients Referees: Prof. Dr. Rainer Zawatzky PD. Dr. Annette Paschen The present work was performed in the research group led by PD. Dr.Annette Paschen, clinical cooperation unit for Dermato-Oncology, German Cancer Research Center (DKFZ) and University Hospital Mannheim. Publications during PhD work: 1. Annette Paschen, Antje Sucker, Bettina Hill, Iris Moll, Marc Zapatka, Xuan Duc Nguyen, Geok Choo Sim, Isabelle Gutmann, Jessica Hassel, Jürgen C. Becker, Alexander Steinle, Dirk Schadendorf and Selma Ugurel. Differential clinical significance of individual NKG2D ligands in melanoma: soluble ULBP2 as an indicator of poor prognosis superior to S100B. Clin Cancer Res 2009;15(16):5208–15 2. Geok Choo Sim, Xuan Duc Nguyen, Christine Falk, Drik Boorken, Dirk Schadendorf and Annette Paschen. Regulation of TLR9 responses in plasmacytoid dendritic cells of melanoma patients. 2010 (Maunuscript in preparation).

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INAUGURAL-DISSERTATION









submitted to the
Combined Faculties for the Natural Sciences and for Mathematics
of the Ruperto-Carola University of Heidelberg, Germany
for the degree of
Doctor of Natural Sciences














Presented by
Master of Science: Geok Choo, Sim
born in Johor, Malaysia









Dysfunctional Plasmacytoid Dendritic Cells but not NK cells in
the Peripheral Blood of Stage IV Melanoma Patients

























Referees: Prof. Dr. Rainer Zawatzky
PD. Dr. Annette Paschen





The present work was performed in the research group led by PD. Dr.Annette Paschen,
clinical cooperation unit for Dermato-Oncology, German Cancer Research Center
(DKFZ) and University Hospital Mannheim.

Publications during PhD work:

1. Annette Paschen, Antje Sucker, Bettina Hill, Iris Moll, Marc Zapatka, Xuan Duc
Nguyen, Geok Choo Sim, Isabelle Gutmann, Jessica Hassel, Jürgen C. Becker,
Alexander Steinle, Dirk Schadendorf and Selma Ugurel. Differential clinical
significance of individual NKG2D ligands in melanoma: soluble ULBP2 as an
indicator of poor prognosis superior to S100B. Clin Cancer Res 2009;15(16):5208–
15

2. Geok Choo Sim, Xuan Duc Nguyen, Christine Falk, Drik Boorken, Dirk
Schadendorf and Annette Paschen. Regulation of TLR9 responses in plasmacytoid
dendritic cells of melanoma patients. 2010 (Maunuscript in preparation).

Work presented in conferences:

3. G.C. Sim, D. Schadendorf, A. Paschen. The influence of tumour cells on the
crosstalk between activated or resting natural killer and dendritic cell. Abstract in
the proceedings of DC2007; P080, 2007.

4. Geok Choo Sim, Dirk Schadendorf and Annette Paschen. Differential Influence of
Tumor Cells and IFN- α on the Crosstalk between Activated or Resting Natural Killer
Cells and Dendritic Cells. Abstract in the proceedings of Natural Killer cells
symposium 2008; C23, 2008.

5. Geok Choo Sim, Dirk Schadendorf, Christine Falk, Annette Paschen. Serum
Cytokine, Chemokine and Growth Factor Profiles of Stage IV Melanoma Patient:
Defining Combinatorial Patterns. Abstract in the Keystone symposia: Mobilizing
Cellular Immunity for Cancer therapy, Utah; Jan 2009.

6. Geok Choo Sim, Dirk Schadendorf, Christine Falk, Annette Paschen. Defining
combinatorial patterns of chemokines, cytokines and growth factors in sera from
stage IV melanoma patients. Abstract in the proceedings of Cancer Imunotherapy
CIMT, P75; 2009.




Table of contents

Table of contents

Acknowledgement…………………………………………………… IX
Abstract………………………………………………………………. X
Zusammenfassung.................................................................................XII
List of abbreviations…………………………………………………. XIV
1.0 INTRODUCTION
1.1 Cancer…………………………………………………………………….. 1
1.1.1 Melanoma…………………………………………………………. 1
1.1.2 Melanoma therapies……………………………………………….. 2
1.2 The immune system………………………………………………………. 4
1.2.1 Innate immunity……………………………………………………. 5
1.2.2 Adaptive immunity……………………………………… 6
1.3 Dendritic Cells (DCs)…………………………………………………….. 7
1.3.1 DC development…………………………………………………… 8
1.3.2 Antigen uptake and processing by DC…………………………….. 9
1.3.3 DC as Antigen Presenting Cell……………………………………. 9
1.3.4 Human DCs……………………………………………………….. 10
1.3.5 mDC and NK interaction…………………………………………. 12
1.3.6 Plasmacytoid dendritic cells (pDCs)……………………………… 12
1.3.7 DCs in cancer……………………………………………………… 16
1.4 Natural Killer (NK) cells and their subsets…………………………….. 17
1.4.1 NK cell receptors…………………………………………………. 18
1.4.2 NK cells killing…………………………………………………….. 21
1.4.3 NK cells in cancer…………………………………………………. 21
1.5 TLR family and signalling………………………………………………. 22
1.5.1 TLR family………………………………………………………… 22
1.5.2 TLR signalling………………………………………………………24
1.5.3 TLRs expression on DC subsets…………………………………… 24
1.5.4 TLR9 ligands………………………………………………………. 25
1.6 Regulation of type I IFN production……………………………………. 26
1.6.1 Interferons…………………………………………………………. 26
1.6.2 The regulation of IFN-α/β production……………………………... 27
1.6.3 The role of transcription factors IRF3 and IRF7………………….. 29
1.6.4 ISGF3 signalling pathway…………………………………………. 31
1.7 Chemokines……………………………………………………………….. 31
1.7.1 Chemokine classification………………………………………….. 31
1.7.2 Chemokines in leucocytes recruitment…………………………….. 31
1.8 Aims of study ………………………………………………………………32


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2.0 MATERIALS
2.1 Lab Equipments…………………………………………………………. 35
2.2 Chemicals…………………………………………………………………. 35
2.3 Consumables……………………………………………………………… 36
2.4 Enzyme/Reagents……………………………………………………….. 37
2.5 Antibodies for flow ctyometry and immunofluorescence staining…… 37
2.5.1 Primary Antibody and Fc fusion proteins…………………………. 37
2.5.2 Secondary antibodies………………………………………………. 38
2.6 Cell culture media and supplements…………………………………….. 38
2.6.1 Media………………………………………………………………. 38
2.6.2 Media supplements………………………………………………….38
2.7 Cells ……………………………………………………………………….. 38
2.7.1 Primary cells……………………………………………………….. 38
2.7.2 Human cell lines…………………………………………………… 38
2.8 Oligonucleotides…………………………………………………………. 39
2.8.1 Oligonucleotides used for standard PCR……………………………39
2.8.2 Labelled oligonucleotides used for quantitative real-time PCR…… 39
2.8.3 Oligonucleotides used for cell stimulation………………………… 39
2.9 Kits and standards………………………………………………………. 39
2.10 Multiple protein bead array (Luminex) cytokine assay ………………39
2.11 Buffers…………………………………………………………………… 39
2.12 Software………………………………………………………………….. 40

3.0 METHODS
3.1 Cell biology methods ………………………………………………………40
3.1.1 Sample collection…………………………………………………... 40
3.1.2 Cell culture method………………………………………………… 40
3.1.3 Preparation of human PBMC from buffy coats……………………. 41
3.1.4 Cryopreservation and thawing of cells……………………………...41
3.1.5 Dead cells removal………………………………………………… 42
+ + mDCs and BDCA4 pDCs 3.1.6 Isolation of BDCA1
from cryopreserved PBMCs using MACS eparation ………………42
+ +3.1.7 Co-culture of BDCA1 mDCs with BDCA4 pDCs………………. 42
3.1.8 PBMC stimulation for cytokines, chemokines and
growth factor analysis……………………………………………… 43
3.1.9 Immunofluorescence Staining………………………………………43
3.1.10 Confocal microscopy analysis and quantification of nuclear
translocation……………………………………………………….. 43
3.1.11 Analysis on NK and DC interactions……………………………… 44
3.1.11.1 Generation of monocyte-derived DC…………………… 44
3.1.11.2 Interaction of IL-2 activated NK cells with moDCs…….. 44
3.1.11.3 Interaction of IL-2 activated NK cells with mDC1……... 45
3.2 Immunological methods………………………………………………….. 45
3.2.1 Determination of cell surface antigen expression using flow
cytometry ………………………………………………………….. 45
3.2.2 Whole blood enumeration of mDCs and pDCs……………………. 46
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3.2.3 Whole blood enumeration of NK cells…………………………….46
3.2.4 Cell sorting using flow cytometry…………………………………. 47
3.2.5 Detection of intracellular TLR9, MyD88, p4E-BP1 and IRF7
by flow cytometry analysis………………………………………… 47
3.2.6 Enzyme-link immunosorbent sandwich assay (ELISA)
for cytokine detection in cell culture supernatants………………… 48
3.2.7 ELISA for soluble NKG2DL detection in sera from
melanoma patients…………………………………………………..49
3.2.8 Degranulation assay………………………………………………... 49
3.2.9 Detection of intracellular IFN-γ and perforin by flow cytometry….. 49
3.2.10 Multiplex protein bead array assays for cytokines, chemokines and
growth factors detection……………………………………………. 50
3.3 Molecular biological method……………………………………………...50
3.3.1 RNA isolation from PBMCs……………………………………… 50
3.3.2 Quantitation of nucleic acids concentration using the 51
spectrophotometer…………………………………………………. 51
3.3.3 cDNA synthesis from total RNA………………………………….. 51
3.3.4 Polymerase chain reaction (PCR)………………………………….. 51
3.3.5 Quantitative real-time RT-PCR…………………………………… 52
3.4 Protein chemical methods……………………………………………….. 52
3.4.1 Generation of cell lysates………………………………………….. 52
3.4.2 Bradford protein assay…………………………………………….. 53
3.4.3 SDS poly-acrylamide gel electrophoresis and Western Blot……… 53
3.5 Statistical analysis 54

4.0 RESULTS
4.1 Absolute number and balance of circulating DC subsets in
advanced melanoma patients
4.1.1 Reduction of pDC and mDC2 but not mDC1 numbers in
melanoma patients………………………………………………… 55
4.1.2 Imbalance in blood DC compartments of melanoma patients……. 56

4.2 mDC1/pDC interaction upon TLR9 engagement in stage IV
melanoma patients
4.2.1 TLR9 triggering on pDCs leads to an up-regulation of CD40 on
co-cultured mDC1 from healthy donors but not from melanoma
patients……………………………………………………………... 57
4.2.2 Aberrant IFN-α production by pDCs from melanoma patients……. 59
4.2.3 TLR4 engagement up-regulates CD40 and CD80 on mDC1 from
patients and healthy donors ……………………………………….. 61
4.2.4 TLR4 activation by LPS triggers IL-10 production by blood
mDC1………………………………………………………………. 62




Table of contents

4.3 Cytokine and chemokine levels in PBMCs and in seraof stageIV
melanoma patients
4.3.1 Aberrant IFN-α secretion by PBMCs from melanoma patients…… 63
4.3.2 Reduced cytokine and chemokine production by PBMCs from
stage IV melanoma patients………………………………………... 64
4.3.2.1 TLR-9 engagement by CpG A results in TNF-α, IL-1β
and IL-6 production in PBMCs……………………………. 65
4.3.2.2 Reduced CCL3 and CCL5 secretion by CpG A treated
PBMCs…………………………………………………….. 66
4.3.2.3 Production of CXCL10 and CCL2 by PBMCs after
TLR9 activation …………………………………………… 68
4.3.3 Dysregulated cytokine and chemokine profiles in the sera of
melanoma patients…………………………………………………. 69

4.4 The role of TLR9 signalling in the aberrant immune function of
pDCs in stage IV melanoma patients
4.4.1 BDCA2 expression by pDCs from melanoma patients…………... . 70
4.4.2 Conserved intracellular TLR9 expression in pDCs from
melanoma patients…………………………………………………. 71
4.4.3 Impaired MyD88 up-regulation in pDCs from melanoma
patients upon CpG A ligand stimulation…………………… ………72
4.4.4 Regulation of IRF7 expression at the mRNA level ……………….. 74
4.4.5 Hyporesponsiveness of pDCs to TLR-9-CpG A activation
leads to impaired IRF7 up-regulation……………………………… 76
4.4.6 Low levels of 4E-BP1 phosphorylation in PBMCs from melanoma
patients after CpG A stimulation…………………………………... 77
4.4.7 Hyporesponsiveness of pDCs to TLR-9-CpG A activation is
associated with an impaired IRF7 nucleus translocation…………. 79

4.5 Absolute number and phenotype analysis of NK cells in melanoma
patients
4.5.1 Altered absolute numbers of NK cells in peripheral blood of
melanoma patients………………………………………………….. 82
4.5.2 Melanoma cell line expresses ligands for NK cell-activating
Receptors and sheds sMICA and sULBP2 were detected in
the sera of melanoma patients ………………………………………83
4.5.3 Circulating NK cells from melanoma patients displayed increased
NCR expression but no aberrant expression of NKG2D…………... 85

4.6 Functional properties of NK cells from stage IV melanoma
patients
4.6.1 Conserved NK cell degranulation, perforin content and IFN-γ
secretion in melanoma patients…………………………………….. 86
4.6.2 IL-2 activated NK cells induced up-regulation of CD40 and
CD80 expression on moDCs……………………………………….. 87
4.6.3 IL-2 activated NK cells induced up-regulation of CD40
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expression on mDC1 in both healthy and melanoma patients………88
5.0 Discussion………………………………………………………………… 90
5.1 Reduced DC numbers in peripheral blood of melanoma patients…. 90
5.2 Altered balance of the peripheral blood DC compartment in
melanoma patients…………………………………………………. 93
5.3 Impaired interaction between mDCs and pDCs from melanoma
patients………………………………………………………………94
5.4 Altered cytokine and chemokine profile released by PBMC
after CpG A stimulation and in sera of melanoma patients………... 97
5.5 Reduced NK cell numbers but conserved NK function
in melanoma patients………………………………………………. 99
5.6 Involvement of MyD88, IRF7 and p4E-BP1 in aberrant
IFN-α production by pDCs from melanoma patients ……………... 101
6.0 Conclusion………………………………………………………………… 105
7.0 References…………………………………………………………………106
8.0 Appendix…………………………………………………………………...131
8.1 Buffers………………………………………………………………131
8.2 MyD88 and IRF7 expression by pDCs from melanoma patients
upon NDV stimulation…………………...133



Acknowledgements

ACKNOWLEDGEMENTS
First and foremost, the author would like to take this opportunity to express her profound
gratitude to the supervising committee members, PD. Dr. Annette Paschen from clinical
cooperation unit for Dermato-Oncology of the German Cancer Research Center (DKFZ)
and University Medicine Mannheim (UMM) for her patience and encouragement
throughout the completion of the research. I thank very much also Prof. Dirk
Schadendorf, Dr. Dirk Booken, Dr. Lisa Zimmer, Dr. Wolfram Fink and Dr. Xuan Duc
Nguyen who have supported the work by providing valuable healthy donor and patient
materials. Without their assistance and valuable contribution, this work would have been
impossible. I am especially grateful to DKFZ for the financial support of this research.
My special appreciations to Prof. Dr. Rainer Zawatzky (DKFZ), Prof. Dr. Victor
Umansky (DKFZ) and Prof. Dr. Gernot Geginat (UMM), who generously provided their
insightful scientific expertise and suggestions during the course of this project. In
addition, I would like to thank Prof. Dr. Rainer Zawatzky for supplying me with cytokine
and UV-inactivated Newcastle virus (NDV) for my work.

My appreciations to Dr. Steffen Schmidt from the core facility of flow cytometry (DKFZ)
and Melanie Ficht (UMM core facility of flow cytometry) for their technical assistance in
flow cytometry and in cell sorting during the course of my study. I also would like to
thank Dr. Christine Falk for her assistance in multiplex cytokine and chemokine assay. I
thank also Dr. Felix Bestvater and Manuela Brom from the light microscopy facility
(DKFZ) for their great assistance in the confocal microscopy analysis. Thanks also to Dr.
Jessica Hassel and Silvia Pustal for their assistance in my study, my research group, and
everybody in the clinical cooperation unit for Dermato-Oncology (DKFZ) and
department of dermatology (UMM). My appreciation also extends to my friends
especially Cleopatra Gkianatsuo, Kevin Richler, Marta Galach, Francis Peyre, Lydia
Tome and Astrid Schmieder for bringing good memorial time during my course of study.
Last but not least, I would like to express my heartiest appreciation and thanks to my
family member and Vladimir Riabov. Thanks for all your understanding and support
throughout my studies.
IX Abstract

Abstract

Dendritic cells (DCs) and Natural Killer (NK) cells are two key innate immune effectors
that are of importance in the initiation and linkage of both innate and adaptive immune
responses for preventing growth and spreading of malignant tumours. Immune
dysfunction of DCs and NK cells in cancer patients apparently has a critical role in
promoting tumour progression and limiting the efficacy of various immunotherapies.
Therefore, identification of the mechanisms underlying this impairment and the
molecules involved could facilitate the design of effective cancer therapies.

In the current work, the integrity of the number and functions of peripheral blood DC
subsets, mDC1, mDC2 and pDCs from stage IV melanoma patients were analysed. We
found a significant decrease in the absolute numbers of circulating pDCs and mDC2 in
melanoma patients compared to aged-matched healthy controls. This change led to
alterations of the mDC1/pDC and mDC2/mDC1 balance. Co-incubation experiments
revealed an impairment of the mDC/pDC interaction upon CpG A stimulation, with little
or no enhancement of surface CD40 expression on mDC1 from melanoma patients. This
was in contrast to an up-regulation of CD40 expression on mDC1 from healthy donors
under similar condition.

The activation of TLR9 signalling in pDCs by CpG A typically induces the production of
various pro-inflammatory cytokines and chemokines. Interestingly, purified pDCs and
PBMCs from melanoma patients when stimulated with CpG A produced lesser amounts
of IFN-α than healthy controls. Furthermore, PBMCs from melanoma patients showed
lower CCL5, CCL3 and CCL4 fold change compared to healthy controls, suggesting an
impairment of TLR9 signalling in pDCs in response to CpG A stimulation. Interestingly,
a dysregulated profile of cytokines and chemokines including IL-6, IL-8, CXCL10,
CCL2, CCL4, CCL5 and IL-10 was also observed in the sera of patients.

Further analysis revealed a significantly stronger up-regulation of MyD88 and both IRF7
mRNA and protein expression in pDCs from healthy controls compared to patients upon
TLR9 activation. Using flow cytometry and immunoblot analysis, it was demonstrated
X