The Pathophysiology of Paroxysmal
Nocturnal Haemoglobinuria
Richard John Kelly
Submitted in accordance with the requirements for the degree of Doctor of Philosophy
The University of Leeds
School of Medicine
January 2014
1
Jointly-Authored Publications
The candidate confirms that the work submitted is his own, except where work which has formed part of jointly authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly indicated below. The candidate confirms that appropriate credit has been given within the thesis where reference has been made to the work of others.
The work in Chapter 3 of the thesis has appeared in publication as follows: Kelly RJ, Hill A, Arnold LM, Brooksbank GL, Richards SJ, Cullen M, Mitchell LD, Cohen DR, Gregory WM, Hillmen P. Long-term treatment with eculizumab in paroxysmal nocturnal hemoglobinuria: sustained efficacy and improved survival. Blood 2011;117:6786-6792.
I was responsible for designing the study, collecting and analysing the data and writing the paper. Dena Cohen and Walter Gregory performed the statistical analysis. All the other authors reviewed the paper.
The work in Chapter 4 of the thesis has appeared in publication as follows: Kelly R, Arnold L, Richards S, Hill A, Bomken C, Hanley J, Loughney A, Beauchamp J, Khursigara G, Rother RP, Chalmers E, Fyfe A, Fitzsimons E, Nakamura R, Gaya A, Risitano AM, Schubert J, Norfolk D, Simpson N, Hillmen P. The management of pregnancy in paroxysmal nocturnal haemoglobinuria on long term eculizumab. Br J
Haematol 2010;149:446-450.
I was responsible for designing the study, collecting and analysing the data and writing the paper. All the other authors reviewed the paper.
This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement.
2
Abstract
Paroxysmal nocturnal haemoglobinuria (PNH) is a rare, life-threatening condition caused by an expansion of a clone of haemopoietic stem cells (HSC) harboring a somatic mutation of the PIG-A gene. PNH blood cells are deficient in glycophosphatidylinositollinked (GPI) proteins rendering PNH erythrocytes susceptible to complement attack which leads to intravascular haemolysis and an increased tendency to develop thromboses. The survival of 79 consecutive patients treated with eculizumab was compared to both age and sex matched normal controls and to 30 similar patients managed in the era immediately prior to anti-complement therapy. The survival of those treated with eculizumab was no different that of the control group and was significantly better than the group with PNH that did not receive eculizumab (p=0.3). Transfusion requirements and documented thromboses were reduced with eculizumab. Sixty-six percent of transfusion dependent patients became transfusion independent and thrombotic events reduced from 5.6 to 0.8 events per 100 years. Eleven women were monitored through 15 pregnancies whilst on eculizumab. There was 1 first trimester miscarriage and 15 healthy babies born. There were no maternal deaths observed and no thrombotic events occurred in the pregnancy or the postpartum period. Eculizumab did not appear to cross the placenta or be expressed in breast milk. Thirty-five patients were evaluated for PIG-M mutations to see if this mutation was prevalent in PNH. No PIG-M promoter mutations were identified. Two genes were evaluated to see if secondary mutations affecting them could account for clonal expansion in PNH. Thirty-six patients underwent JAK2 V617F mutation analysis with 1 patient shown to have a JAK2 mutation. Forty-two patients were evaluated for increased HMGA2 levels by 2 different PCR methods. There was an overall reduction in HMGA2 expression in PNH patients as compared to normal controls. An in vitro model of the bone marrow in PNH was developed and 18 PNH bone marrow samples were evaluated using this model. Colony forming assays (CFA) showed an increase in colony formation when T-cells were removed from the PNH bone marrow samples. This improvement was reversed when the T-cells were added back to the experiments. This work supports an immune mechanism for the expansion of the PNH clone.
3
Contents
Jointly Authored Publications Abstract
23
- Contents
- 4
List of Figures List of Tables
914 15 17 18
Publications Resulting from this Work Acknowledgements Abbreviations
- 1.
- Introduction
- 20
22 22 25 28 28 29 31 31 32 33 33 35
- 1.1.
- Identifying the Genetic Defect
1.1.1 Disruption of the Glycophosphatidylinositol Anchor 1.1.2 Haemolysis in PNH
- 1.2
- Diagnosis
1.2.1 Historical Background 1.2.2 Current Techniques for Diagnosis
- A Classification of PNH
- 1.3
1.4 1.5
The Relative Incidence of Molecular and Symptomatic PNH Clinical Features of PNH 1.5.1 The Consequences of Haemolysis 1.5.2 Thrombosis 1.5.3 Renal Dysfunction
4
1.5.4 Pulmonary Hypertension 1.5.5 Quality of Life
35 36 36 37 37 37 38 39 40 42 42 43 45 48 48
1.5.6 Pregnancy
1.6
1.7
Mortality and Treatment Prior to Anti-complement Therapy 1.6.1 General Measures 1.6.2 Anticoagulation 1.6.3 Allogeneic Bone Marrow Transplantation The Complement System 1.7.1 Targeting Complement 1.7.2 Anti-Complement Strategies in PNH 1.7.3 CD59 Replacement 1.7.4 Eculizumab 1.7.5 Eculizumab Clinical Studies in PNH
- Pathogenesis
- 1.8
1.9
1.8.1 Bone Marrow Failure 1.8.2 Mutations in Normal Individuals, Other Conditions and in the Context of
- Antibody Therapy
- 49
51 51 51 52 53
Clonal Expansion 1.9.1 Multiple Clones and Clonal Dominance 1.9.2 Hypotheses of Clonal Expansion 1.9.3 Animal Models of PNH 1.9.4 Potential Mechanisms Mediating HSC Destruction 1.9.5 Humoral Antibody Dependent Cell Mediated Cytotoxicity (ADCC) and
- Complement
- 54
54 56 57 58
1.9.6 Cell Mediated Immunity and Natural Killer (NK) cells 1.9.7 The Wilms Tumour Gene 1.9.8 Secondary Genetic Mutations – HMGA2 1.9.9 Apoptosis
1.10 Haematopoietic Stem Cell Immunophenotype and Long Term Bone Marrow
- Culture (LTBMC) Studies
- 59
59 59
1.10.1 Early Progenitor Cells 1.10.2 Long Term Bone Marrow Cultures in PNH and AA
5
- 2
- Materials and Methods
- 61
63 63 63 64 64 64 65 65 66 66 69 69 69 70 70 70 71 72 73 73 75 75 76 76 77 78 78
- 2.1
- Patients
2.1.1 Patients Treated with Eculizumab 2.1.2 Patients Treated during Pregnancy Evaluation of HMGA2 in PNH Patients and Normal Subjects 2.2.1 Patient and Control Groups
2.2
2.2.2 Red Cell Lysis 2.2.3 RNA Extraction 2.2.4 DNase Treatment 2.2.5 cDNA Synthesis 2.2.6 Quantitative PCR 2.2.7 Conventional PCR Reactions 2.2.8 Agarose Gel Electrophoresis 2.2.9 CD15 Positive Selection
2.3
2.4
Evaluation of Prevalence of PIG-M Promoter Site and JAK2 Mutations 2.3.1 Patient Cohort 2.3.2 Genomic DNA Extraction 2.3.3 Val617Phe JAK2 Point Mutation Analysis 2.3.4 PIG-M Promoter Mutation Analysis Long Term Bone Marrow Cultures 2.4.1 Flow Cytometry Analysis of Bone Marrow 2.4.2 Isolation of Bone Marrow Mononuclear Cells 2.4.3 Isolation of Bone Marrow CD34+ Cells 2.4.4 T-cell Depletion of CD15+ Bone Marrow Mononuclear Cells 2.4.5 Isolation of T-cells from Bone Marrow Mononuclear Cells 2.4.6 Maintaining Long Term Cultures 2.4.7 Colony Forming Assays 2.4.8 Colony Analysis
- 3
- Long-Term Follow Up of Patients with PNH
Introduction
79
81 81
3.1
- 3.2
- Additional Patient Information
6
3.3 3.4 3.5 3.6
- Eculizumab Therapy
- 82
- Statistical Analysis
- 83
- Individual Patient Data
- 84
Patient Data at Diagnosis and Prior to Starting Eculizumab 3.6.1 Sex
109 109 110 111 111 112 112 113 113 117 117 117 117 117 122 123 124 124 124 124 127
3.6.2 Age 3.6.3 Symptoms at Diagnosis 3.6.4 Cytopenias in PNH 3.6.5 Haemolysis as a Complication of PNH 3.6.6 Thrombosis as a Complication of PNH Patient Data at the Start of Eculizumab Treatment 3.7.1 Laboratory Findings 3.7.2 Clone Evaluation
3.7 3.8
3.7.3 Other Laboratory Tests Patient Data on Eculizumab Treatment 3.8.1 Complications of PNH
3.8.1.1 Intravascular Haemolysis 3.8.1.2 Thrombosis 3.8.1.3 Clone Evolution
3.8.2 Effects of Eculizumab
3.8.2.1 Platelets 3.8.2.2 Meningococcal Infection 3.8.2.3 Survival
- 3.9
- Discussion
- 4
- Management of Patients During Pregnancy
Introduction
132
133 133 133 138 141 142
4.1 4.2 4.3 4.4 4.5 4.6
Additional Patient Information Individual Patient Data Complications during Pregnancy Delivery and the Postpartum Period Discussion
7
- 5
- PIG-M Mutations and Secondary Genetic Events
Rationale
143
144 145 145 146 150 152 156 157
5.1
- 5.2
- PIG-M Promoter Mutations
5.2.1 PCR Amplification of the SP1 Binding Site 5.2.2 SAPEX Purification and Sequencing
- JAK2 Mutation Analysis
- 5.3
5.4 5.5 5.6
HMGA2 Expression
Further Assessment of HMGA2 Expression using TaqMan Assay Discussion
- 6
- In Vitro Culture Experiments Involving PNH Stem Cells
Rationale
160
161 161 169 174 175 179 179 187 188 193
6.1 6.2 6.3 6.4 6.5 6.6
Normal Control Samples Initial LTBMC Findings with PNH Samples Difficulties with Stromal Layer Minimisation Experiments Extraction of T-cells from Bone Marrow MNCs 6.61 T-Cell Removal before MNCs Are Added to the Culture Model 6.62 T-Cell Removal Immediately Prior to the CFAs
- Add-Back Experiments
- 6.7
- 6.8
- Discussion
- 7
- General Discussion
- 197
198 199 201 203
7.1 7.2 7.3 7.4
Clinical Overview of PNH Complement and Future Therapies Disease Pathogenesis - Secondary Genetic Events Disease Pathogenesis – Escape of the Immune Attack
- References
- 205
8
List of Figures
Figure 1.1 GPI biosynthesis in the endoplasmic reticulum Figure 1.2 Terminal complement activation causing cell lysis
25 27
Figure 1.3 FACS plot of erythrocytes in a PNH patient. Type I express CD59 normally, Type II have a reduced expression and Type III have no CD59 expression 28 Figure 1.4 FACS plot depicting a large granulocyte PNH clone of 98.2% (Q3) identified using FLAER and CD16 (GPI linked protein) and using these markers the population of PNH and normal granulocytes can easily be identified Figure 1.5 The complement cascade adapted from Kelly et al, 2007 Figure 1.6 Structure of the monoclonal antibody eculizumab Figure 1.7 Action of eculizumab
30 39 44 45
Figure 1.8 A representation of the two hit hypothesis leading to expansion of PNH stem
- cells
- 53
- Figure 3.1 The age at diagnosis of 79 patients
- 110
Figure 3.2 Symptoms experienced by 79 PNH patients at the time the disease was
- diagnosed
- 111
- 113
- Figure 3.3 Sites of thrombosis experienced
Figure 3.4 LDH levels taken both at the start of eculizumab treatment and at the most recent clinical review 121 Figure 3.5 Blood transfusion requirements in the 12 months before eculizumab therapy and the most recent 12 months on eculizumab treatment in 61 patients 122 Figure 3.6 Overall survival of the 79 patients from initiation of eculizumab treatment compared to age- and sex-matched controls 125 Figure 3.7 Overall survival of the 79 patients from initiation of eculizumab treatment
- according to age
- 126
- 127
- Figure 3.8 Overall survival of patients before and after eculizumab
Figure 5.1 Diagrammatic representation showing the positions of the forward and reverse
- primers used to sequence the SP1 site in the PIG-M promoter
- 145
9
Figure 5.2 Agarose gel electrophoresis showing an example of PCR products obtained prior to sequencing. Lane 1 is a negative control, 2-6 are patient samples (U.P.N. 6,7,10,11,16) and lane 7 is a 100 base pair ladder (New England Biolabs) Figure 5.3 Sequencing read out showing an example of the nucleotides of the PIG-M promoter region 148 Figure 5.4 Closer view of the sequencing read out of each nucleotide around -270 in the PIG-M promoter region 148 Figure 5.5 Sequence readout of the PIG-M promoter region with the forward and reverse
146
- sequences from a patient alongside
- 149
- 151
- Figure 5.6 V617F JAK2 mutation analysis of PNH patients
Figure 5.7 HMGA2 expression in PNH patients compared to the median of the normal control group 154 Figure 5.8 Level of HMGA2 expression in those with and without CD15 positive selection 155 Figure 6.1 Variations in M210B4 stromal cell concentrations and their effect on the quantity of progenitor cells 163 Figure 6.2 Flow cytometry of MNCs from a normal bone marrow sample. (A) Cells evaluated using forward and side scatter. (B) CD34+ cells selected in gate P2 and shown in green. (C) Further gating (P3, blue) of CD34+ selected cells using CD45 and side
- scatter. (D) Expression of FLAER on CD34+ cells
- 164
Figure 6.3 Flow cytometry of CD34+ selected cells from a normal bone marrow sample. (A) Cells evaluated using forward and side scatter. (B) CD34+ cells selected in gate P2 and shown in green. (C) Further gating (P3, blue) of CD34+ selected cells using CD45
- and side scatter. (D) Expression of FLAER on CD34+ cells
- 165
Figure 6.4 Light microscopy (magnification x 40) of stromal layer showing haemopoietic
- cells clustered under the stromal layer
- 166
- 167
- Figure 6.5 Light microscopy (magnification x 40) view of a CFU-GM colony
Figure 6.6 Mean number of cells from the supernant of the control group using MNCs and CD34+ selected cells 167 Figure 6.7 Mean number of colonies formed in the CFAs from the cells in the supernant
- of the LTBMCs of the control group using MNCs and CD34+ selected cells
- 168
10
Figure 6.8 Flow cytometry of MNCs from a PNH bone marrow sample (U.P.N. 24). (A) Cells evaluated using forward and side scatter. (B) CD34+ cells selected in gate P2 (green). (C and D) Further gating (P3, blue and P4, red) of CD34+ selected cells using CD45 (red), forward and side scatter (blue). (E) Expression of FLAER on CD34+ cells
- (97.8% GPI deficient)
- 170
Figure 6.9 Flow cytometry of CD34+ selected cells from a PNH bone marrow sample (U.P.N. 24). (A) Cells evaluated using forward and side scatter. (B) CD34+ cells selected in gate P2 (green). (C) Further gating (P3, blue and P4, red) of CD34+ selected cells using CD45 (red, not shown), forward and side scatter (blue). (E) Expression of FLAER on CD34+ cells (97.8% GPI deficient) Figure 6.10 Mean number of cells from the supernant of both the control and PNH samples using MNCs and CD34+ selected cells 172
171
Figure 6.11 Number of colonies formed in the CFAs from the cells in the supernant of the LTBMCs of the initial PNH samples using MNCs compared to the mean number of colonies from the PNH CD34+ selected samples and the MNCs from the control group
173
- Figure 6.12 Light microscopy (magnification x 5) images of the stromal layer
- 174
Figure 6.13 Flow cytometry from a control bone marrow sample used in the minimisation experiments. (A) Unmanipulated bone marrow (CD34+ proportion 0.9% in red). (B)
- MNCs (CD34+ proportion 2.2% in red)
- 175
Figure 6.14 Mean number of cells from the supernant of the control group using MNCs
176
Figure 6.15 Mean number of colonies formed in the CFAs from the cells in the supernant
- of the LTBMCs of the control group using MNCs
- 176
Figure 6.16 The number of cells from the supernant of a control group sample using different amounts of input MNCs and different volumes of MyelocultTM H5100 media
177
Figure 6.17 The number of colonies formed in the CFAs from the cells in the supernant of a control group sample using different amounts of input MNCs and different volumes
- of MyelocultTM H5100 media
- 178
Figure 6.18 Flow cytometry of MNCs from a PNH bone marrow sample (U.P.N. 74). (A) P1 gating (red) of the CD34+ cells (1.5% of MNCs). (B) Further gating (P2, blue) of cells
11
using forward and side scatter. (C) Gating of CD3+ cells (P3, green, 60.3% of MNCs). (D) Expression of FLAER on CD34+ CD38+ cells (80.6% GPI deficient) 179 Figure 6.19 Flow cytometry of MNCs from a PNH bone marrow sample (U.P.N. 74) with T-cells removed using anti-CD3 MicroBeads. (A) P1 gating (red) of the CD34+ cells (2.9% of MNCs). (B) Further gating (P2, blue) of cells using forward and side scatter. (C) Gating of CD3+ cells (P3, green, 5.4% of MNCs). (D) Expression of FLAER on CD34+
- CD38+ cells (97.3% GPI deficient)
- 180
Figure 6.20 Flow cytometry of MNCs from a PNH bone marrow sample prior to T-cell removal (U.P.N. 19). (A) P1 gating (red) of the CD34+ cells (1.4% of MNCs). (B) Further gating (P2, blue) of cells using forward and side scatter. (C) Gating of CD3+ cells (P3, green, 35% of MNCs). (D) Expression of FLAER on CD34+ CD38+ cells (77.1%
- GPI deficient)
- 181
Figure 6.21 Flow cytometry of MNCs from a PNH bone marrow sample (U.P.N. 19) with T-cells removed using CD15 selection followed by CD3 depletion. (A) P1 gating (red) of the CD34+ cells (1.6% of MNCs). (B) Further gating (P2, blue) of cells using forward and side scatter. (C) Gating of CD3+ cells (P3, green, 0.1% of MNCs). (D) Expression of
- FLAER on CD34+ CD38+ cells (73.4% GPI deficient)
- 182
Figure 6.22 Mean number of cells from the supernant of MNCs from the control group, MNCs, T-cell depleted MNCs and T-cell depleted MNCs with the T-cells added back to
- them from PNH samples
- 183
Figure 6.23 Number of colonies formed in the CFAs from the control group, MNCs, T- cell depleted MNCs and T-cell depleted MNCs with the T-cells added back to them from
- PNH samples
- 184
Figure 6.24 Flow cytometry of colonies formed from a PNH sample (U.P.N. 32). (A and B) PNH MNCs at week 1 and 2, respectively. (C, D, E and F) T-cell depleted PNH
- MNCs at weeks 1-4, respectively
- 185
Figure 6.25 Flow cytometry of colonies formed from a PNH sample (U.P.N. 55). (A and B) PNH MNCs at week 1 and 2, respectively. (C, D and E) T-cell depleted PNH MNCs
- at weeks 1-3, respectively
- 186
Figure 6.26 T-cell removal in a normal bone marrow MNC sample prior to the CFA, showing the proportion of CD45+ and CD3+ input cells after 1 week (A and B) and 2