Application of Single Cell Genomics to Reconstruct Stem and Progenitor Cell Hierarchies in Normal and Malignant Haematopoiesis

Lead Research Organisation: University of Oxford

Abstract

A major challenge in cancer biology is to better understand variation in the way similar cancers present and respond to treatment, in order to develop more personalised patient management. This heterogeneity partly reflects variability in the types of DNA damage or mutation carried within each cell and also the type of cell which carries the mutation. Importantly, only some cancer cells, known as cancer stem cells, are able to propagate disease relapse in patients. Our research is focused on the biology of these cancer stem cells. Our group is applying single cell analysis and state of the art genetic modelling, to better understand the cancer stem cells in certain types of blood cancer. Using patient samples, we will analyse cancer stem cells at a single cell level to understand exactly which cells might be responsible for causing relapse in patients and how they might be better detected and eradicated. Through application of these state of the art cell and molecular biology techniques in both humans and model systems, these studies will provide a substantial contribution to the understanding of blood cancer stem cells and the findings will highlight the clinical applicability of single cell technology across cancer biology.

Technical Summary

The major focus of our research programme is towards the identification and genetic modelling of leukaemic and pre-leukaemic stem cells in myeloid malignancies. Our aim is to characterise the cellular and molecular biology of these key populations of cells which are capable of propagating disease relapse in patients, in order to understand how these cells might be more effectively identified, targeted and eradicated. To achieve this, our research programme is focused on understanding the normal cellular origin of leukaemic stem cells, and to thereby identify the perturbed molecular pathways which result in the generation of preleukaemic clones, and eventually malignant transformation. There are 3 related approaches in this regard:

1. The development of genetically engineered leukaemia models to study the impact of specific mutation(s) on the establishment, evolution and propagation of leukaemic stem cells. For example, through modelling of the haematopoietic impact of leukaemia-associated Flt3 mutations during the development of acute myeloid leukaemia.
2. The study of leukaemia stem cells in patients with myeloid malignancies throughout their disease course, in order to understand the impact of novel targeted therapies and the cellular origins of clonal evolution, resistance to therapy and transformation to more aggressive forms of disease. These studies necessitate state of the art single-cell whole-transcriptome genomic analysis, a technique which has been established by our group. This technique will be applied to normal blood stem/progenitor cells in order to definitively reconstruct the haematopoietic hierarchy. This will provide the foundation for analysis of single blood cancer stem cells to better understand their origin and evolution.

3. To understand the clinical and biological consequences of germline genetic abnormalities in humans which predispose to the development of myeloid malignancies later in life.

Importantly, whilst these studies are specific to myeloid malignancies, as this is the area of clinical medicine in which AJM specialises, the findings of these studies will also be more broadly applicable across cancer biology. For example, the development of single cell genomics approaches to investigate cancer stem cells has clear potential to facilitate the translation of this pioneering technology through to patient benefit through better detection of minimal residual disease and targeting of therapy-resistant cancer stem cells.

In parallel, AJM has developed an extensive clinical research portfolio, delivering new treatments to patients with myeloproliferative neoplasms in the Thames Valley (and beyond), and also providing invaluable sample biobanks to help support the above translational research programme.

Publications

10 25 50
 
Description BCSH Myeloproliferative Disease National Guidelines for Essential Thrombocythaemia and Myelofibrosis
Geographic Reach National 
Policy Influence Type Membership of a guidance committee
Impact I am a member of the national clinical study groups for chronic myeloid leukaemia and myeloproliferative neoplasms and have helped formulate national guidelines in the research areas relevant to this grant.
 
Description Member of the NCRI clinical study group in Chronic Myeloid Leukaemia (CML)
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact The clinical study group for CML provides a national leadership for trials run in the UK.
 
Description Member of the NCRI clinical study groups in myeloproliferative neoplasms (MPNs)
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact The clinical study group for MPNs provides national leadership for trials run in the UK.
 
Description NICE technology appraisal for ruxolitinib in myelofibrosis and polycythaemia vera
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Helped advise on NICE technology appraisal
 
Description Clinical Research Training Fellowship (Nicholas Fordham): The Role of EZH2 mutation in paediatric myelodysplasia
Amount £276,500 (GBP)
Organisation The Kay Kendall Leukaemia Fund 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2017 
End 03/2020
 
Description Clinical Research Training Fellowship (Nicholas Fordham): The Role of EZH2 mutation in paediatric myelodysplasia
Amount £276,509 (GBP)
Organisation The Kay Kendall Leukaemia Fund 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2017 
End 03/2020
 
Description Combinatorial targeting of Chemokines using EVASINs in Myelofibrosis
Amount £50,000 (GBP)
Organisation University of Oxford 
Department Radcliffe Department of Medicine
Sector Academic/University
Country United Kingdom
Start 07/2015 
End 06/2016
 
Description Genome and Transcriptome analysis of patients with rare stem and Myeloid disorders
Amount £65,000 (GBP)
Organisation University of Oxford 
Department John Fell Fund
Sector Academic/University
Country United Kingdom
Start 07/2017 
End 06/2019
 
Description Impact of Leukaemia-Associated Loss of Function of Epigenetic Regulators on Distinct Haematopoietic Stem Cells (Co-applicant with Sten Eirik Jacobsen)
Amount £266 (GBP)
Organisation The Kay Kendall Leukaemia Fund 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2017 
End 12/2019
 
Description Kay Kendall Leukaemia Fund Project Grant
Amount £232,919 (GBP)
Organisation The Kay Kendall Leukaemia Fund 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2014 
End 04/2017
 
Description Late Phase Haematology Research Team
Amount £85,242 (GBP)
Organisation National Institute for Health Research 
Sector Public
Country United Kingdom
Start 04/2015 
End 03/2016
 
Description MRC CRI: The Oxford Single Cell Biology Consortium (co-investigator)
Amount £4,975,434 (GBP)
Funding ID MR/M00919X/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 04/2015 
End 04/2016
 
Description MRC Confidence in Concept Scheme
Amount £50,000 (GBP)
Organisation Medical Research Council (MRC) 
Department MRC Confidence in Concept Scheme
Sector Academic/University
Country United Kingdom
Start 05/2014 
End 11/2015
 
Description MRC Discovery Award (co-investigator)
Amount £1,000,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 04/2016 
End 04/2019
 
Description MRC Discovery Award - Identification and characterisation of cellular targets for genome editing of foetal haematopoietic stem/progenitor cells
Amount £56,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 09/2016 
End 08/2017
 
Description MRC Proximity to discovery Industry Engagement Fund
Amount £10,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 02/2016 
End 07/2016
 
Description Measuring DNA damage in Single Cells Using a Novel High Throughput Genomic Assay
Amount £15,000 (GBP)
Organisation University of Oxford 
Department John Fell Fund
Sector Academic/University
Country United Kingdom
Start 04/2017 
End 03/2018
 
Description NIHR Rare Disease TRC Fellowship Scheme PhD Studentship (Co-lead supervisor with Irene Roberts)
Amount £221,439 (GBP)
Organisation National Institute for Health Research 
Sector Public
Country United Kingdom
Start 10/2014 
End 10/2017
 
Description Wellcome Trust ISSF
Amount £150,135 (GBP)
Organisation Wellcome Trust 
Department Wellcome Trust Institutional Strategic Support Fund
Sector Charity/Non Profit
Country United Kingdom
Start 11/2014 
End 11/2017
 
Description Wellcome Trust Postdoctoral Research Training Fellowship for Clinician
Amount £248,107 (GBP)
Organisation Wellcome Trust 
Department Wellcome Trust Research Training Fellowship
Sector Charity/Non Profit
Country United Kingdom
Start 08/2016 
End 07/2019
 
Title Single Cell Biology Techniques and Infrastructure 
Description I have established the infrastructure and techniques for state of the art single cell genomics in the WIMM in Oxford. This has proven to be instrumental in obtaining a large infrastructure grant from the MRC to support single cell research in Oxford. 
Type Of Material Improvements to research infrastructure 
Year Produced 2014 
Provided To Others? Yes  
Impact Multiple publications and grants. 
 
Description Investigating the impact of Nilotinib on Imatinib-Resistant Chronic Myeloid Leukaemia Stem Cells 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution This is an educational award from Novartis UK (approx £250K) for a research project focused on leukaemia stem cells in patients with chronic myeloid leukaemia and how these might be better eradicated. Details of the research proposal are below: Chronic myeloid leukaemia (CML) is a stem-cell driven chronic leukaemia propagated by a population of therapy-resistant cancer stem cells (CSCs) that, over time, are capable of causing disease relapse and progression, making this an ideal disease for the study of the cellular and molecular biology of CSCs. Current evidence supports that imatinib does not effectively eradicate CML-CSCs. The high proportion of patients in cytogenetic remission on imatinib therapy allows for ready availability of biological material for the study of these therapy-resistant CML-CSCs. It is perhaps surprising, therefore, that the phenotype and, in particular, the biology of CML-CSCs remains poorly characterized. Whilst second generation tyrosine kinase inhibitors such as nilotinib have shown considerable efficacy in CML, with a higher frequency of deeper molecular remissions than seen with imatinib, the optimal indication and timing of a change in therapy to second generation tyrosine kinase inhibitors such as nilotinib also remains unclear. Furthermore, whether patients in complete molecular remission can safely discontinue nilotinib is largely dependent on the presence or absence of residual CML-CSCs. Thus, understanding the response of the CML-CSC population to first or second line nilotinib therapy in pre-clinical studies is a key hurdle to help inform strategies towards the "path to cure" of patients with CML.
Collaborator Contribution The aims of this research, which is still underway, were: 1. Establish the cell population(s) with CSC properties in patients with CML at diagnosis using state of the art FACS, molecular biology and xenograft techniques. 2. To determine the CML-CSC burden in patients with suboptimal response to imatinib and in patients on 1st or 2nd line nilotinib therapy 3. To further characterise the biology of these residual CML-CSCs functionally and at the molecular level throughout the course of the disease in a series of patients on imatinib and nilotinib to: a. Compare and contrast mechanisms mediating resistance of CML-CSCs to imatinib and 1st or 2nd line nilotinib b. To understand whether 2nd line nilotinib can effectively eradicate residual CML-CSCs in imatinib suboptimal responders c. Most importantly, to directly compare the biology of normal stem cells with CML-CSCs in patients on imatinib and 1st or 2nd line nilotinib to understand how these cells might be selectively targeted with novel agents.
Impact This work has been presented at an international meeting (American Society of Hematology) as an oral presentation and is currently under review at Nature Medicine. Cost of tyrosine kinase inhibitor (TKI) treatment is the UK over the next few years will be £billions with tens of thousands of patients living with CML; so any treatments that might allow patients to discontinue TKI will have a major economic and societal impact.
Start Year 2015
 
Description Stem Cell Biology Research with Professor Sten Eirik Jacobsen 
Organisation University of Oxford
Department Weatherall Institute of Molecular Medicine (WIMM)
Country United Kingdom 
Sector Public 
PI Contribution Longstanding research collaboration
Collaborator Contribution Multiple publications and joint grant applications
Impact See publications
Start Year 2008
 
Description The Genetic Landscape in Transfusion Dependent Myelofibrosis 
Organisation Celgene
Country United States 
Sector Private 
PI Contribution This is a research collaboration with Celgene. Detail of the original research proposal are below. This research is currently underway and still active. Myelofibrosis is a clinically and genetically heterogeneous BCR-ABL-negative myeloproliferative neoplasm (MPN) with reported mutations in a number of genes primarily affecting signalling pathways, epigenetic regulators and splicing machinery e.g. JAK2, CALR, MPL, TET2, ASXL1, EZH2, DNMT3A, IDH1/2, CBL, IKZF1, U2AF1, CHEK2, TP53, SF3B1, SRSF2 and LNK.1-3 The most frequent reported genetic event is a gain of function recurrent mutation in JAK2 (V617F) causing constitutive activation of the kinase with consequent activation of downstream signalling. Furthermore, many patients show activation of the JAK2 signalling pathway in the absence of the JAK2 mutation, likely caused by mutations indirectly activating the JAK2 pathway e.g. MPL. Recently, somatic mutation of CALR has been reported in MPN patients without the JAK2V617F mutation.4,5 These mutations are mutually exclusive of JAK2V617F and MPL mutations, suggesting that they might activate similar pathways. Severe anaemia with RBC-transfusion-dependence is common in patients with advanced MPN-associated myelofibrosis. The above signalling pathway mutations are associated with high as well as low blood counts and rather mutations affecting splicing (SRSF2) and epigenetic regulation (ASXL1) are associated with development of anaemia in myelofibrosis. Pomalidomide, an immune-modulating drug with pleiotrophic bone marrow effects, resulted in improvements in the level of anaemia in several phase 2 studies, however, preliminary results in a phase 3 study are disappointing. Nevertheless, in this phase 3 study, 16% of patients showed an anaemia response (16% also in placebo arm) and 22% a platelet response suggesting that some response does occur in a subgroup of patients. There also were some possible differences in clinical parameters between patients achieving transfusion independence on placebo versus pomalidomide. Together, these findings suggest that a there might be a subgroup of transfusion-dependent or thrombocytopenic patients who would benefit from pomalidomide therapy, although this subgroup is relatively small and lost within the context of heterogeneous patients included in this large phase 3 trial. With the advent of next generation sequencing and personalised medicine it is possible that molecular features might better define a subgroup of patients predicted to respond to pomalidomide.
Collaborator Contribution Samples are available from 250 patients with high/intermediate risk myelofibrosis enrolled on a phase III trial of pomalidomide (2:1 randomisation pomalidomide:placebo). All samples will be analysed by targeted resequencing using a gene panel developed in our institution (TruSeq™ target enrichment kit) followed by sequencing using MiSeq. This assay will require minimum of 1µg gDNA using PicoGreen quantification. The panel will include all the genes listed above. For this project it is important that deep coverage is obtained to gain insights into clonal architecture and evolution in myelofibrosis patients during response to pomalidomide therapy, during prolonged follow-up, and at the point of any disease progression events. Thus, we will aim to achieve 100x coverage for each of the above gene targets. Any patients not carrying any of the above mutations (likely to be a small minority (<5%) will be subject to exome sequencing. Using algorithms well established in Oxford by the computational biology research group housed at the WIMM (http://www.molbiol.ox.ac.uk/CBRG_home.shtml) we will carry out state of the art bioinformatics analysis to identify likely somatic driver mutations in this large cohort. Through the interaction with Celgene, these data will be correlated with the robust clinical information collected as part of the trial to understand the relationship between somatic mutations, clinical characteristics and response to pomalidomide. For such a large and well annotated cohort of patients with carefully defined transfusion dependent myelofibrosis, this will also provide unique insights into genetic heterogeneity in this disorder and the relationship to clinical phenotype and disease course. Recurrent, previously undescribed mutations predicted to be functionally relevant will all be validated using sanger sequencing and tracked through serial samples. Importantly, we are also well placed in the HSCB laboratory to follow-up findings from the sequencing with biological studies to understand how any novel candidate genes/pathways might modulate response to pomalidomide. In addition to state of the art cell culture and molecular platforms, we also have a number of highly relevant mouse models available (JAK2 V617F conditional knock-in, EZH2 conditional knockout) providing powerful platforms for understanding the in vivo consequence of different mutations for development of anaemia and response to pomalidomide. Any candidate genes will initially be studied in cell lines by lentiviral transduction of the relevant mutation or shRNA mediated knockdown if genes are inactivated/deleted to understand if the candidate gene(s) affects the response to pomalidomide in vitro. Once validated in cell lines, candidate genes will be further studied using the above in vivo models, including in vivo treatment of mice with pomalidomide, to understand how different mutations may interact to modulate response to this treatment. Finally, using our extensive cell bank of samples from patients with myelofibrosis, we will then validate possible candidate genes using human myelofibrosis patient samples using either lentiviral transduction as above or by using targeted agents if available, both with and without pomalidomide treatment.
Impact AJM is a newly established group leader and MRC Senior Clinical Fellow in the WIMM working in the field of myeloid malignancies. The intention for initiating this collaboration is to generate substantial information with regards to the genomic architecture in myelofibrosis that will result in a strong publication. Thus, it would be expected that AJM would "own" the genomic data arising from this research and will have the right to publish these data following an appropriate review period by Celgene.
Start Year 2015
 
Description The Oxford SIngle Cell Consortium 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Abstract of the grant application: Limitations in our ability to study the biology of individual cells has historically been a major obstacle, inhibiting our understanding of some fundamental problems in biomedical research such as the onset of cancer, the immunological determination of 'self', and the ability to purify tissue-specific stem cells. Recent developments in the field of single cell genomics is now opening up unprecedented opportunities to uncover individual cell differences within such complex tissues. The objective of the proposed research is to establish a Centre of Single Cell Biology (CSCB) in Oxford that will take advantage of this pioneering technology in order to improve the diagnosis, stratification and treatment of a wide variety of human diseases. The CSCB will be coordinated by the Weatherall Institute of Molecular Medicine (WIMM) which has a long-standing technical and strategic expertise in single cell research. The capital development will be used to enhance single-cell research capabilities across the campus in a number of key areas: Data analysis: Single cell genomics studies generate an enormous amount of data, with consequent challenges for the analysis and correct interpretation of these complex data sets. We propose to establish an entirely new research group devoted to the development of novel approaches for the statistical and computational analysis of single cell biology data and its application to medicine. This group will be located in new space to be developed at the WIMM, but jointly led by leading scientists across the campus. This new initiative will provide a clear pathway to integrate multidisciplinary, scientific and technical innovation in single cell biology research across the Oxford University Campus and to provide ground-breaking applications of this approach to medicine in the UK. State of the art facilities: We will develop single cell biology research laboratories to allow practical access for research groups conducting these studies across the campus. These facilities will house cutting edge technology platforms and, importantly, will create "ultra clean" environments to carry out single cell experiments. This is necessary as very low levels of background "contamination" make the interpretation of single cell experiments challenging. Projects: As a specific example of how this technology will be applied to address fundamental problems in human disease, the lead programme of research in the CSCB will be focused on inherited disorders of red blood cells. These disorders are amongst the most common of all human genetic diseases worldwide with an estimated 300,000 affected babies born each year and a total number of affected UK patients of ~16,000. Currently, severely affected individuals are treated with supportive care, including lifelong blood transfusion and treatment to prevent accumulation of iron in the body, which is costly, burdensome, and gives rise to serious, long-term clinical complications. Here we propose to "genetically repair" the damaged genes in the patient's own blood stem cells. Single cell biology will be central to this project: First, single cell genomic approaches will be used to identify the blood stem cells which are the best target for this therapy. Second, single-cell analysis will be used to assess the safety and efficiency of this approach. This programme, focussed on developing an entirely new approach to treating the haemoglobinopathies, has the potential to transform the treatment of all human genetic diseases that can be cured by stem cell transplantation. This is one example of many projects in development across the campus which will be greatly facilitated by the development of improved single cell research capabilities. Oxford is in a very strong position to take a world-leading role in the up-and-coming area of Single Cell Biology and application of these technologies to important clinical and basic biology questions across the University and beyond.
Collaborator Contribution Abstract of the grant application: Limitations in our ability to study the biology of individual cells has historically been a major obstacle, inhibiting our understanding of some fundamental problems in biomedical research such as the onset of cancer, the immunological determination of 'self', and the ability to purify tissue-specific stem cells. Recent developments in the field of single cell genomics is now opening up unprecedented opportunities to uncover individual cell differences within such complex tissues. The objective of the proposed research is to establish a Centre of Single Cell Biology (CSCB) in Oxford that will take advantage of this pioneering technology in order to improve the diagnosis, stratification and treatment of a wide variety of human diseases. The CSCB will be coordinated by the Weatherall Institute of Molecular Medicine (WIMM) which has a long-standing technical and strategic expertise in single cell research. The capital development will be used to enhance single-cell research capabilities across the campus in a number of key areas: Data analysis: Single cell genomics studies generate an enormous amount of data, with consequent challenges for the analysis and correct interpretation of these complex data sets. We propose to establish an entirely new research group devoted to the development of novel approaches for the statistical and computational analysis of single cell biology data and its application to medicine. This group will be located in new space to be developed at the WIMM, but jointly led by leading scientists across the campus. This new initiative will provide a clear pathway to integrate multidisciplinary, scientific and technical innovation in single cell biology research across the Oxford University Campus and to provide ground-breaking applications of this approach to medicine in the UK. State of the art facilities: We will develop single cell biology research laboratories to allow practical access for research groups conducting these studies across the campus. These facilities will house cutting edge technology platforms and, importantly, will create "ultra clean" environments to carry out single cell experiments. This is necessary as very low levels of background "contamination" make the interpretation of single cell experiments challenging. Projects: As a specific example of how this technology will be applied to address fundamental problems in human disease, the lead programme of research in the CSCB will be focused on inherited disorders of red blood cells. These disorders are amongst the most common of all human genetic diseases worldwide with an estimated 300,000 affected babies born each year and a total number of affected UK patients of ~16,000. Currently, severely affected individuals are treated with supportive care, including lifelong blood transfusion and treatment to prevent accumulation of iron in the body, which is costly, burdensome, and gives rise to serious, long-term clinical complications. Here we propose to "genetically repair" the damaged genes in the patient's own blood stem cells. Single cell biology will be central to this project: First, single cell genomic approaches will be used to identify the blood stem cells which are the best target for this therapy. Second, single-cell analysis will be used to assess the safety and efficiency of this approach. This programme, focussed on developing an entirely new approach to treating the haemoglobinopathies, has the potential to transform the treatment of all human genetic diseases that can be cured by stem cell transplantation. This is one example of many projects in development across the campus which will be greatly facilitated by the development of improved single cell research capabilities. Oxford is in a very strong position to take a world-leading role in the up-and-coming area of Single Cell Biology and application of these technologies to important clinical and basic biology questions across the University and beyond.
Impact The Oxford Single Cell Consortium was established in 2014 followed by successful application for MRC CRI funding (£5 million) led by Professors Doug Higgs and Kay Davies, I am a coauthor on this grant application. The consortium has established 2 single cell facilities across the Oxford campus and I have led the development of protocols and infrastructure required for single cell experiments. We held the official consortium launch in October 2014, supported by a press release and webinars from international experts.
Start Year 2014
 
Title A Randomized, Single Blind, Multicenter, Phase 2 Study to Evaluate the Activity of 2 Dose Levels of Imetelstat (GRN163L) in Subjects with Intermediate-2 or High-Risk Myelofibrosis (MF)Relapsed / Refractory to Janus Kinase Inhibitor 
Description A Randomized, Single Blind, Multicenter, Phase 2 Study to Evaluate the Activity of 2 Dose Levels of Imetelstat (GRN163L) in Subjects with Intermediate-2 or High-Risk Myelofibrosis (MF)Relapsed / Refractory to Janus Kinase Inhibitor 
Type Therapeutic Intervention - Drug
Current Stage Of Development Early clinical assessment
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact N/A - trial still in recruitment 
 
Title BFORE. A Multicenter Phase 3 Randomized, Open-Label Study of Bosutinib versus Imatinib 
Description Principal Investigator - BFORE. A Multicenter Phase 3 Randomized, Open-Label Study of Bosutinib versus Imatinib in Adult Patients with Newly Diagnosed Chronic Phase Chronic Myelogenous Leukemia. Open to recruitment 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Currently in follow up. 
 
Title DESTINY. A trial of de-escalation and stopping treatment 
Description Principal Investigator - DESTINY. A trial of de-escalation and stopping treatment in chronic myeloid leukaemia patients with excellent responses to tyrosine kinase inhibitor therapy. In follow-up. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Currently in follow up. Preliminary results to be presented at the European Haematology Association meeting in 2016. 
 
Title ENEST1st; A phase IIIb, multicentre, open-label study 
Description Local Principal investigator - ENEST1st; A phase IIIb, multicentre, open-label study of nilotinib in adult patients with newly diagnosed Philadelphia chromosome and/ or bcr-abl positive CML in chronic phase, ENEST1st, CAMN107EIC01. Closed to recruitment. Lead UK recruiter. Closed. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2014
Development Status Under active development/distribution
Clinical Trial? Yes
Impact This was a phase 3b study using nilotinib as first line therapy in CML. Oxford was the lead recruiter with AJM as the principal investigator. Nilotinib is now NICE approved for first line use in the UK. Results have been presented at international meetings. 
 
Title ENESTfreedom. A single-arm, multicenter, nilotinib treatment-free remission study 
Description 12. Chief Investigator - ENESTfreedom. A single-arm, multicenter, nilotinib treatment-free remission study in patients with BCR-ABL1 positive Chronic Myelogenous Leukemia in chronic phase who have achieved durable minimal residual disease (MRD) status on first line nilotinib treatment. In follow up. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Currently in follow up. Results will be reported in 2016. 
 
Title ENESToberve. An observational, open-label, multi-center, prospective follow-up study 
Description UK Chief Investigator - ENESToberve. An observational, open-label, multi-center, prospective follow-up study of patients with chronic phase CML treated with Nilotinib in the ENEST1st (CAMN107EIC01) study. In follow up. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Currently in follow up. 
 
Title EPIC - A Phase 3 Randomized, OpenLabel Study of Ponatinib versus Imatinib 
Description Principal investigator - EPIC - A Phase 3 Randomized, OpenLabel Study of Ponatinib versus Imatinib in Adult Patients with Newly Diagnosed Chronic Myeloid Leukemia in Chronic Phase. Closed. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2015
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Results presented in abstract form. 
 
Title INForMeD Study 
Description INvestigating the genetic and cellular basis of sporadic & Familial Myeloid Disorders 
Type Therapeutic Intervention - Drug
Current Stage Of Development Initial development
Year Development Stage Completed 2016
Development Status Under active development/distribution
Impact This study provides the ethical framework for all the translational research in my research group. 
 
Title JAKARTA; A Phase 3, RandomiSed, Double-Blinded, Placebo Controlled 3 arm Study 
Description Principal investigator - JAKARTA; A Phase 3, RandomiSed, Double-Blinded, Placebo Controlled 3 arm Study of SAR302503 in Patients with Intermediate-2 or High Risk Primary (PMF), Post-Polycythemia Vera (PPVM), or Post-Essential Thrombocythemia Myelofibrosis (PTM) with Splenomegaly. Closed. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2014
Development Status Closed
Clinical Trial? Yes
Impact The clinical development of fedratinib was put on hold due to an excess of encephalopathy (adverse events). 
 
Title JakaviPASS. A Non-Interventional Long-term Safety Study of Ruxolitinib in Myelofibrosis. 
Description Principal investigator - JakaviPASS. A Non-Interventional Long-term Safety Study of Ruxolitinib in Myelofibrosis. In follow up. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Currently in follow up. 
 
Title MAJIC; A RandoMised study of best Available therapy versus JAK Inhibition in patients with high risk Polycythaemia Vera or Essential Thrombocythaemia 
Description Co-invesigator - MAJIC; A RandoMised study of best Available therapy versus JAK Inhibition in patients with high risk Polycythaemia Vera or Essential Thrombocythaemia who are resistant or intolerant to HydroxyCarbamide. Planned to open Spring 2012. First study to be run through the LLR Trial Acceleration Program. Open to recruitment. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact I am co-investigator of this trial which is the first investigator led study assessing JAK2 inhibitor treatments in the world and also the first Bloodwise Trial Acceleration Programme trial. Preliminary results will be presented in 2016 and I expect multiple publications to folow. 
 
Title Myeloproliferative Disorders-Research Consortium (MPD-RC) MPD-RC Protocol 114. 
Description 18. Co-Chair: Myeloproliferative Disorders-Research Consortium (MPD-RC) MPD-RC Protocol 114. Exploring the Potential of Dual Kinase JAK 1/2 Inhibitor Ruxolitinib (INC424) with Reduced Intensity Allogeneic Hematopoietic Cell Transplantation in Patients with Myelofibrosis. 
Type Management of Diseases and Conditions
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2015
Development Status Under active development/distribution
Impact I am the chief Investigator of this NIH-funded investigator-led, international, multicentre phase 2 clinical study testing JAK2 inhibitor therapy before allogeneic transplantation in myelofibrosis. Preliminary results will be presented at the American Society of Hematology meeting in 2016 
 
Title NCRN-3257 - A Phase 3, Randomized Study To Evaluate the Efficacy of Momelotinib 
Description Principal Investigator: NCRN-3257 - A Phase 3, Randomized Study To Evaluate the Efficacy of Momelotinib Versus Best Available Therapy in Anemic or Thrombocytopenic Subjects with Primary Myelofibrosis, Postpolycythemia Vera Myelofibrosis, or Post-essential Thrombocythemia Myelofibrosis who were Treated with Ruxolitinib (protocol ID: GS-US-352-1214). Due to open Q3 2015. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2015
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Trial currently in follow up, no outputs as yet. 
 
Title PERSIST-1 - A Randomized Controlled Phase 3 Study of Oral Pacritinib versus 
Description UK Chief investigator - PERSIST-1 - A Randomized Controlled Phase 3 Study of Oral Pacritinib versus Best Available Therapy in Patients with Primary Myelofibrosis, Post-Polycythemia Vera Myelofibrosis, or Post-Essential Thrombocythemia Myelofibrosis. In follow up. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact A number of abstracts have been presented at ASCO, ASH and EHA, including the late breaking abstract which I presented in 2015 at EHA. 
 
Title PERSIST-2 - A Randomized Controlled Phase 3 Study of Oral Pacritinib versus Best Available Therapy 
Description Chief investigator - PERSIST-2 - A Randomized Controlled Phase 3 Study of Oral Pacritinib versus Best Available Therapy in Patients with Thrombocytopenia and Primary Myelofibrosis, Post-Polycythemia Vera Myelofibrosis, or Post-Essential Thrombocythemia Myelofibrosis (PAC326). Open to recruitment. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Currently in follow up. 
 
Title PT1; A randomised trial to compare aspirin vs hydroxyurea/aspirin 
Description Local Principal investigator - PT1; A randomised trial to compare aspirin vs hydroxyurea/aspirin in intermediate risk primary thrombocythaemia and aspirin only with observation in low risk primary thrombocythaemia. Phase 3 trial. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Multiple high profile publications. 
 
Title Phase II study of INC424 for patients with primary myelofibrosis (PMF) or post polycythaemia myelofibrosis (PPV MF) 
Description Chief investigator - A UK open-label, multicentre, exploratory Phase II study of INC424 for patients with primary myelofibrosis (PMF) or post polycythaemia myelofibrosis (PPV MF) or post-essential thrombocythaemia myelofibrosis (PET-MF). Closed and published in The British Journal of Haematology. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2015
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Mead, A.J., Milojkovic, M., Knapper, S., Garg, M., Chacko, J., Farquharson, M., Yin, J., Ali, S., Clark, R.E., Andrews, C., Ktiouet-Dawson, M., Harrison, C. Response to ruxolitinib in patients with intermediate-1-, intermediate-2-, and high-risk myelofibrosis: results of the UK ROBUST Trial. British Journal of Haematology, 2015;170(1):29-39. 
 
Title RESUME; A phase-3, multi-center, randomized, doubleblind, placebo-controlled, parallel-group study to compare efficacy and safety of pomalidomide in subjects with myeloproliferative neoplasm -associated myelofibrosis and red blood cell-transfusiondependence. 
Description Local Principal investigator - RESUME; A phase-3, multi-center, randomized, doubleblind, placebo-controlled, parallel-group study to compare efficacy and safety of pomalidomide in subjects with myeloproliferative neoplasm -associated myelofibrosis and red blood cell-transfusiondependence. Closed to recruitment. In follow-up. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Currently in follow up. Results presented at international meetings. I also have a research collaboration with Celgene using samples collected as part of this trial. 
 
Title Randomized Trial of Pegylated Interferon Alfa-2a versus Hydroxyurea Therapy 
Description Local Principal Investigator - Myeloproliferative Disorders-Research Consortium (MPD-RC) MPD-RC 112. Randomized Trial of Pegylated Interferon Alfa-2a versus Hydroxyurea Therapy in the Treatment of High Risk Polycythemia Vera and High Risk Essential Thrombocythemia. Mandatory Companion Protocol MPD-RC 107. EudraCT #2010-019501-41. Open to recruitment. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2014
Development Status Under active development/distribution
Clinical Trial? Yes
Impact The trial is actively recruiting. 
 
Title SPIRIT2; STI571 Prospective International Randomised Trial 2. 
Description Local Principal investigator - SPIRIT2; STI571 Prospective International Randomised Trial 2. Closed to recruitment, in follow-up. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2016
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Results presented as at international meetings. 
 
Title UK TARGET - CML Study : Real World UK use of Tyrosine Kinase Inhibitors (TKIs) 
Description Chief Investigator: Real World UK use of Tyrosine Kinase Inhibitors (TKIs): A Retrospective description of management pathways, clinical responses and compliance with 2013 European LeukemiaNeT (ELN) recommendations for Chronic Myeloid Leukaemia (CML) - the UK TARGET-CML study. Due to open Q4 2015. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Late clinical evaluation
Year Development Stage Completed 2015
Development Status Under active development/distribution
Impact Trial currently recruiting. No impact yet. 
 
Description MPN Advances 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Patients, carers and/or patient groups
Results and Impact I regularly talk at the national myeloproliferative neoplasms patients and carers day, updating patients about scientific advances in the field. Usually about 200 patients/carers attend this annual meeting.
Year(s) Of Engagement Activity 2014,2015
 
Description Museum of Natural History - Lucy Field 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Hands on activities about blood (The Blood Factory).
Year(s) Of Engagement Activity 2017
 
Description National CML patient and carers day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Patients, carers and/or patient groups
Results and Impact Very liverly discussions.

Very positive feedback formally collected from participants
Year(s) Of Engagement Activity 2013
 
Description Nguyen Tran - Science Roadshow 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact As part of the MRC Festival for Medical Research 2016, three MRC Units within Oxford collaborated to pool funds and resources to develop the 'Science in the Supermarket' roadshow. The team travelled to supermarkets and shopping centres all over Oxfordshire over the course of the Festival week, describing to the general public how the immune system fights cancer using three activities representing research currently ongoing in each of the three units.
Year(s) Of Engagement Activity 2016
 
Description Patient forum for chronic myeloid malignancies 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact We have established a regular patient forum in Oxford led by our advanced nurse practitioner and involving patients with chronic myeloid malignancies.

Positive feedback from participants
Year(s) Of Engagement Activity 2014
 
Description Public lecture at the Oxford BRC open day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The BRC regularly holds open days and I gave the lecture focused on Blood diseases.
Year(s) Of Engagement Activity 2013
 
Description Royal Society Summer Science Exhibition - Lucy Field 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Hands-on activities, including virtual reality tour of DNA.Huge amount of positive feedback at the time from visitors, engagement with social media posts, collaborative working across department and WIMM
Year(s) Of Engagement Activity 2017