Myeloproliferative NeoplasmMOZARTNCT06022341
MultiOmic characteriZation of Acute Myeloid Leukemia Evolving From myelopRoliferative Neoplasm to Identify New Targeted Therapeutic Strategies
A study testing Multiomic characterization and In vitro drug screening in people with Myeloproliferative Neoplasm and Secondary Leukemia, run by University Hospital, Angers.
Trial summary
Myeloproliferative neoplasms (MPN) are chronic myeloid malignancies characterized by a risk of evolution to acute myeloid leukemia (AML). This unpredictable complication is associated with a grim outcome with median overall survival ranging between 2 to 10 months. Read more about this study
- Who is it for?
- Ages 18 years and older
- Conditions the study is for
- Myeloproliferative Neoplasm, Secondary Leukemia
- What is being tested?
- Multiomic characterization and In vitro drug screening
- Could I receive a placebo?
- No, everyone receives an active treatment
- How many people
- 120 participants
- Where
- No sites listed yet
- Study dates
- 15 Oct 2023to 31 Dec 2028
- Phase
- Interventional
- Are there results?
- Not yet: the study is under way
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages 18 years and older
- All sexes
- No healthy volunteers
- Adult, Older adult
Who may be able to join
- Patients with a prior diagnosis of MPN: polycythemia vera, essential thrombocythemia or primary myelofibrosis according to the WHO criteria
- Acute myeloid leukemia evolution defined by ≥ 20% of blasts cells
- Available material from bone marrow sampling at the time of leukemic transformation (i.e. ≥ 20% of blasts cells): DNA (1µg), RNA (500ng) +/- frozen mononuclear cells in DMSO for a subset of 60 patients (2 vials of at least 8 millions cells).
- Informed consent (or requalification procedure)
Who cannot join
- Patient not affiliated to the French health insurance
Trial locations and contacts
No sites are listed yet. Contact the study team or a site near you to ask about taking part.
About this study
Myeloproliferative neoplasms (MPN) are chronic myeloid malignancies characterized by a risk of evolution to acute myeloid leukemia (AML). This unpredictable complication is associated with a grim outcome with median overall survival ranging between 2 to 10 months. To date, even allogeneic transplantation fails to significantly improve the prognosis. Biological and molecular mechanisms driving leukemic transformation are complex, ill-defined, and heterogeneous between patients. The investigator hypothesize that deciphering the molecular heterogeneity of post-MPN AML may lead identifying efficient drugs targeting of the most relevant leukemogenic pathways.
Our main objective is to identify new targeted therapeutic approaches in post-MPN AML through in-depth characterization of the dysregulated pathways. The investigator will first characterize in an already annotated cohort of 120 post-MPN AML homogeneous patients subgroups using comprehensive multiomic analyses. Dysregulated pathways will be identified in each subgroup using the omics data and single-cell RNA-sequencing will be performed in a subset of patients in each subgroup. A customised drug-panel will be derived from the dysregulated pathway for an ex vivo drug screening, which will use a flow-cytometry read-out enabling to identity drug effect on cells survival, differentiation, and stemness. The 3 most promising drugs will be validated in a preclinical in vivo model of patient's derived xenograft (PDX) and their impact on clonal architecture will be studied in primary cell cultures using single-cell DNA-sequencing.
Overall, this proposal may provide a better understanding of MPN leukemic transformation mechanisms and provide a path for personalized therapies. Our findings may therefore pave the way to drugs development in post-MPN AML that would provide a rationale for implementation of early clinical trials in these dreadful diseases.
Read the detailed description
Patients samples and clinical data:
The investigator will study samples from 120 patients with a post-MPN acute myeloid leukemia. These samples and the corresponding clinical data are available through FIMBANK, a national network of biological resources for myeloproliferative neoplasms (grant INCa, BCB 2013, Pr Valérie Ugo) and through the prospective phase II clinical trial CPX351-TA-SMP testing CPX351 monotherapy in post-MPN AML (NCT04992949, inclusions started in 01-2022).
WP1: Deciphering the heterogeneity of post-MPN AML (primary objective) To answer these objectives, the investigator will conduct a multi-omics approach including targeted-NGS with a 400-genes panel, RNA-seq and methylome in a total of 120 post-MPN AML samples. All the genomic libraries will be constructed at the genomic facility of Angers University Hospital and the sequencing will be performed on a NovaSeq6000 in the GenoBIRD Platform in Nantes. Bioinformatic analysis will be performed by teams #1 and #3 and will derive for each sample: SNV/Indel and CNV from DNA sequencing, expression of mRNA and lncRNA, genes fusion and splicing events from RNA-seq, and methylation beta-values from methylome.
In order to identify homogeneous subgroups from the genomic data, the investigator will perform unsupervised clustering analyses of each layer of genomic data. Then, all layers will be combined for integration of clusters using the Cluster Of Clusters Analysis (COCA) method (Wilkerson and Hayes, 2010).
WP2: Identify the mechanisms of transformation and putative targets for therapy For this purpose, the investigator will analyze omics data generated in WP1 to identify the main molecular mechanisms driving the leukemic transformation of MPN. The investigator will perform a 2-step procedure: first by analyzing each genomic dataset separately and then, by analyzing all datasets together in an integrated multiblock analysis using the MOGSA method (Integrative Single Sample Gene-set).
A total of 60 samples originating from a subset of patients classified in WP1 will be tested for ex vivo drug screening. The investigator will design a custom-made drug panel including standards of care, several drugs in clinical development in AML and, more importantly, a selection of drugs specifically targeting potential leukemic vulnerabilities identified.
WP3: Confirm the efficacy of selected best drugs and their impact on clonal architecture To further validate the translational relevance of post-MPN AML deregulated pathways, the three most promising drug candidates will then be evaluated in a set of five post-MPN PDX models including at least 2 TP53-mutated post-MPN AML. The investigator will also evaluate how the drugs identified in WP2 may impact clonal evolution of the disease which is a key step towards understanding and improving the treatment of post-MPN AML. The 3 best candidate drugs or combinations identified in WP2 will be studied in cells from 5 selected patients with a complex molecular profile to evaluate the response of various subclones.
- Conditions
- Myeloproliferative Neoplasm, Secondary Leukemia
- Being tested
- Multiomic characterization, In vitro drug screening
- Keywords
- multiomics, in vitro drug screening
- Medical subject headings
- Myeloproliferative Disorders
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
Multiomic characterizationOther
Multiomics analysis include targeted-NGS with a 400-genes panel, RNA-seq and methylome. All the genomic libraries will be constructed at the genomic facility of Angers University Hospital and the sequencing will be performed on a NovaSeq6000 in the GenoBIRD Platform in Nantes. Bioinformatic analysis will be performed and will derive for each sample: SNV/Indel and CNV from DNA sequencing, expression of mRNA and lncRNA, genes fusion and splicing events from RNA-seq, and methylation beta-values from methylome.
In vitro drug screeningOther
The drug screening will be performed on the 'NEXT-AML' platform at St-Louis Hospital, Paris. This platform uses a multiparametric screening strategy based on flow cytometry measurements of cell viability, cell differentiation and stem cell compartment. Primary patient cells will be cultured in a specific niche-like medium with amino-acids, cytokines and stromal cells (Dal Bello et al. 2022). Twenty-five drugs at 6 concentrations covering a 1000-fold concentration range will be studied for each sample.
| Study group | Role | What they receive |
|---|---|---|
| Leukemic transformation of myeloproliferative neoplasms | Other | 120 patients will be studied for :
* Multiomic characterization
* In vitro drug screening Receives: Other: Multiomic characterization; Other: In vitro drug screening |
What is being measured
The primary outcome is the main question the study is designed to answer.
Ward's minimum variance criterion to minimize the intra-cluster variance
Decipher the heterogeneity of post-MPN AML to identify homogeneous subgroups
Measured: 24 months
Secondary outcomes (5)
GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways identified among the different subgroups by integration of omics data, cell type and trajectories inferred using scRNA-Seq
Identify the oncogenic molecular mechanisms among each subgroup of post-MPN AML
Measured: 36 months
Median effective concentration (EC50) of each evaluated drug
Identify efficient in vitro therapies targeting the dysregulated pathways of post-MPN AML
Measured: 36 months
Mice survival
Confirm the efficacy of the most promising newly identified candidate drugs or therapeutic combinations in vivo in PDX models
Measured: 48 months
Leukemic disease burden modification
Confirm the efficacy of the most promising newly identified candidate drugs or therapeutic combinations in vivo in PDX models
Measured: 48 months
Identify the effect of the best candidate drugs/therapeutic combinations at the single-cell level and assess how clonal architecture evolves after treatment
Absolute change of the proportion of each leukemic clone in single-cell DNA-sequencing of in vitro culture
Measured: 48 months
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted1 Sep 2023
- Study start15 Oct 2023 (estimated)
- Primary completion31 Dec 2027 (estimated)
- Study completion31 Dec 2028 (estimated)
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Other trials for Myeloproliferative NeoplasmStudies of the same condition, open and under way.
- More trials run by University Hospital, AngersThe sponsor's other registered studies.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Interventional
- Phase
- Phase N/A
- Primary purpose
- Basic science
- Allocation
- Not applicable
- Intervention model
- Single group
- Masking
- None (open label)
- Enrolment
- 120 participants (estimated)
Sponsor and investigators
- Lead sponsor
- University Hospital, Angers
- Sponsor type
- Other government
- Collaborators
- University Hospital, Brest, Institut Paoli-Calmettes, Saint-Louis Hospital, Paris, France, Gustave Roussy, Cancer Campus, Grand Paris
- Responsible party
- Sponsor
- Investigators
- Damien LUQUE PAZ, PharmD. PhD., Principal investigator, University Hospital of Angers
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT06022341
- Sponsor's protocol ID
- 49RC23_0288.
- Acronym
- MOZART
- Status last verified
- Aug 2023
- First submitted
- 22 Aug 2023
- Last updated
- 1 Sep 2023
- Results posted
- No
- Data monitoring committee
- No
- FDA-regulated drug
- No
- FDA-regulated device
- No
- Individual data sharing
- No
Study at a glance
From the registry record, last updated by the sponsor on 1 Sep 2023. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- MultiOmic characteriZation of Acute Myeloid Leukemia Evolving From myelopRoliferative Neoplasm to Identify New Targeted Therapeutic Strategies
- ClinicalTrials.gov ID
- NCT06022341
- Acronym / sponsor ID
- MOZART / 49RC23_0288.
- Conditions
- Myeloproliferative Neoplasm, Secondary Leukemia
- Keywords
- multiomics, in vitro drug screening
- Study type
- Interventional
- Recruitment status
- Not yet recruiting
- Enrolment
- 120 participants (estimated)
- Lead sponsor
- University Hospital, AngersOther government
- Collaborators
- University Hospital, Brest, Institut Paoli-Calmettes, Saint-Louis Hospital, Paris, France, Gustave Roussy, Cancer Campus, Grand Paris
- Study start
- 15 Oct 2023 (estimated)
- Primary completion
- 31 Dec 2027 (estimated)
- Study completion
- 31 Dec 2028 (estimated)
- First posted
- 1 Sep 2023 (actual)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
Myeloproliferative neoplasms (MPN) are chronic myeloid malignancies characterized by a risk of evolution to acute myeloid leukemia (AML). This unpredictable complication is associated with a grim outcome with median overall survival ranging between 2 to 10 months. To date, even allogeneic transplantation fails to significantly improve the prognosis. Biological and molecular mechanisms driving leukemic transformation are complex, ill-defined, and heterogeneous between patients. The investigator hypothesize that deciphering the molecular heterogeneity of post-MPN AML may lead identifying efficient drugs targeting of the most relevant leukemogenic pathways.
Our main objective is to identify new targeted therapeutic approaches in post-MPN AML through in-depth characterization of the dysregulated pathways. The investigator will first characterize in an already annotated cohort of 120 post-MPN AML homogeneous patients subgroups using comprehensive multiomic analyses. Dysregulated pathways will be identified in each subgroup using the omics data and single-cell RNA-sequencing will be performed in a subset of patients in each subgroup. A customised drug-panel will be derived from the dysregulated pathway for an ex vivo drug screening, which will use a flow-cytometry read-out enabling to identity drug effect on cells survival, differentiation, and stemness. The 3 most promising drugs will be validated in a preclinical in vivo model of patient's derived xenograft (PDX) and their impact on clonal architecture will be studied in primary cell cultures using single-cell DNA-sequencing.
Overall, this proposal may provide a better understanding of MPN leukemic transformation mechanisms and provide a path for personalized therapies. Our findings may therefore pave the way to drugs development in post-MPN AML that would provide a rationale for implementation of early clinical trials in these dreadful diseases.
Detailed description
Patients samples and clinical data:
The investigator will study samples from 120 patients with a post-MPN acute myeloid leukemia. These samples and the corresponding clinical data are available through FIMBANK, a national network of biological resources for myeloproliferative neoplasms (grant INCa, BCB 2013, Pr Valérie Ugo) and through the prospective phase II clinical trial CPX351-TA-SMP testing CPX351 monotherapy in post-MPN AML (NCT04992949, inclusions started in 01-2022).
WP1: Deciphering the heterogeneity of post-MPN AML (primary objective) To answer these objectives, the investigator will conduct a multi-omics approach including targeted-NGS with a 400-genes panel, RNA-seq and methylome in a total of 120 post-MPN AML samples. All the genomic libraries will be constructed at the genomic facility of Angers University Hospital and the sequencing will be performed on a NovaSeq6000 in the GenoBIRD Platform in Nantes. Bioinformatic analysis will be performed by teams #1 and #3 and will derive for each sample: SNV/Indel and CNV from DNA sequencing, expression of mRNA and lncRNA, genes fusion and splicing events from RNA-seq, and methylation beta-values from methylome.
In order to identify homogeneous subgroups from the genomic data, the investigator will perform unsupervised clustering analyses of each layer of genomic data. Then, all layers will be combined for integration of clusters using the Cluster Of Clusters Analysis (COCA) method (Wilkerson and Hayes, 2010).
WP2: Identify the mechanisms of transformation and putative targets for therapy For this purpose, the investigator will analyze omics data generated in WP1 to identify the main molecular mechanisms driving the leukemic transformation of MPN. The investigator will perform a 2-step procedure: first by analyzing each genomic dataset separately and then, by analyzing all datasets together in an integrated multiblock analysis using the MOGSA method (Integrative Single Sample Gene-set).
A total of 60 samples originating from a subset of patients classified in WP1 will be tested for ex vivo drug screening. The investigator will design a custom-made drug panel including standards of care, several drugs in clinical development in AML and, more importantly, a selection of drugs specifically targeting potential leukemic vulnerabilities identified.
WP3: Confirm the efficacy of selected best drugs and their impact on clonal architecture To further validate the translational relevance of post-MPN AML deregulated pathways, the three most promising drug candidates will then be evaluated in a set of five post-MPN PDX models including at least 2 TP53-mutated post-MPN AML. The investigator will also evaluate how the drugs identified in WP2 may impact clonal evolution of the disease which is a key step towards understanding and improving the treatment of post-MPN AML. The 3 best candidate drugs or combinations identified in WP2 will be studied in cells from 5 selected patients with a complex molecular profile to evaluate the response of various subclones.
Study design
- Primary purpose
- Basic science
- Allocation
- Not applicable
- Intervention model
- Single group
- Masking
- None (open label)
- Number of arms
- 1
| Arm | Type | Receives |
|---|---|---|
| Leukemic transformation of myeloproliferative neoplasms | Other | Other: Multiomic characterization, Other: In vitro drug screening120 patients will be studied for : * Multiomic characterization * In vitro drug screening |
Who may qualify
- Ages
- 18 years and older
- Sex
- All
- Healthy volunteers
- Not accepted
- Age groups
- Adult, Older adult
Key inclusion criteria (4 listed)
- Patients with a prior diagnosis of MPN: polycythemia vera, essential thrombocythemia or primary myelofibrosis according to the WHO criteria
- Acute myeloid leukemia evolution defined by ≥ 20% of blasts cells
- Available material from bone marrow sampling at the time of leukemic transformation (i.e. ≥ 20% of blasts cells): DNA (1µg), RNA (500ng) +/- frozen mononuclear cells in DMSO for a subset of 60 patients (2 vials of at least 8 millions cells).
- Informed consent (or requalification procedure)
Key exclusion criteria (1 listed)
- Patient not affiliated to the French health insurance
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Interventions
| Intervention | Type | Arms |
|---|---|---|
| Multiomic characterizationMultiomics analysis include targeted-NGS with a 400-genes panel, RNA-seq and methylome. All the genomic libraries will be constructed at the genomic facility of Angers University Hospital and the sequencing will be performed on a NovaSeq6000 in the GenoBIRD Platform in Nantes. Bioinformatic analysis will be performed and will derive for each sample: SNV/Indel and CNV from DNA sequencing, expression of mRNA and lncRNA, genes fusion and splicing events from RNA-seq, and methylation beta-values from methylome. | Other | Leukemic transformation of myeloproliferative neoplasms |
| In vitro drug screeningThe drug screening will be performed on the 'NEXT-AML' platform at St-Louis Hospital, Paris. This platform uses a multiparametric screening strategy based on flow cytometry measurements of cell viability, cell differentiation and stem cell compartment. Primary patient cells will be cultured in a specific niche-like medium with amino-acids, cytokines and stromal cells (Dal Bello et al. 2022). Twenty-five drugs at 6 concentrations covering a 1000-fold concentration range will be studied for each sample. | Other | Leukemic transformation of myeloproliferative neoplasms |
Primary outcome
Ward's minimum variance criterion to minimize the intra-cluster variance
Time frame: 24 months
Decipher the heterogeneity of post-MPN AML to identify homogeneous subgroups
5 secondary outcomes
GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways identified among the different subgroups by integration of omics data, cell type and trajectories inferred using scRNA-Seq
Time frame: 36 months
Median effective concentration (EC50) of each evaluated drug
Time frame: 36 months
Mice survival
Time frame: 48 months
Leukemic disease burden modification
Time frame: 48 months
Identify the effect of the best candidate drugs/therapeutic combinations at the single-cell level and assess how clonal architecture evolves after treatment
Time frame: 48 months
Results and safety
This study is still under way. Results are not available in the source record yet.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 1 Sep 2023.
- Individual participant dataSharing planned: No
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Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part.
Damien LUQUE PAZ, PharmD. PhD. principal investigator
University Hospital of Angers
Questions about this trial
What is this clinical trial studying?
A study testing Multiomic characterization and In vitro drug screening in people with Myeloproliferative Neoplasm and Secondary Leukemia, run by University Hospital, Angers.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 4 inclusion and 1 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: opening soon, as of the sponsor's last update on 1 Sep 2023. Status can change between updates, so confirm with the study contact before making plans.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
This study is still under way. Results are not available in the source record yet.
How can a doctor refer a patient or contact the research team?
Contact Damien LUQUE PAZ, PharmD. PhD. (241355353 ext. 0033, damien.luquepaz@chu-angers.fr), or a site near the patient. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Ward's minimum variance criterion to minimize the intra-cluster variance (time frame: 24 months). It is what the study was designed to measure, not a finding.
Where can I read the original study information?
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 1 Sep 2023.