xml: <clinical_study>
    <!-- This xml conforms to an XML Schema at:
      https://clinicaltrials.gov/ct2/html/images/info/public.xsd -->
    <required_header>
      <download_date>ClinicalTrials.gov processed this data on September 20, 2023</download_date>
      <link_text>Link to the current ClinicalTrials.gov record.</link_text>
      <url>https://clinicaltrials.gov/ct2/show/NCT06022341</url>
    </required_header>
    <id_info>
      <org_study_id>49RC23_0288.</org_study_id>
      <nct_id>NCT06022341</nct_id>
    </id_info>
    <brief_title>MultiOmic characteriZation of Acute Myeloid Leukemia Evolving From myelopRoliferative Neoplasm to Identify New Targeted Therapeutic Strategies</brief_title>
    <acronym>MOZART</acronym>
    <official_title>MultiOmic characteriZation of Acute Myeloid Leukemia Evolving From myelopRoliferative Neoplasm to Identify New Targeted Therapeutic Strategies</official_title>
    <sponsors>
      <lead_sponsor>
        <agency>University Hospital, Angers</agency>
        <agency_class>Other</agency_class>
      </lead_sponsor>
      <collaborator>
        <agency>University Hospital, Brest</agency>
        <agency_class>Other</agency_class>
      </collaborator>
      <collaborator>
        <agency>Institut Paoli-Calmettes</agency>
        <agency_class>Other</agency_class>
      </collaborator>
      <collaborator>
        <agency>Saint-Louis Hospital, Paris, France</agency>
        <agency_class>Other</agency_class>
      </collaborator>
      <collaborator>
        <agency>Gustave Roussy, Cancer Campus, Grand Paris</agency>
        <agency_class>Other</agency_class>
      </collaborator>
    </sponsors>
    <source>University Hospital, Angers</source>
    <oversight_info>
      <has_dmc>No</has_dmc>
      <is_fda_regulated_drug>No</is_fda_regulated_drug>
      <is_fda_regulated_device>No</is_fda_regulated_device>
    </oversight_info>
    <brief_summary>
      <textblock>
        Myeloproliferative neoplasms (MPN) are chronic myeloid malignancies characterized by a risk&#xD;
        of evolution to acute myeloid leukemia (AML). This unpredictable complication is associated&#xD;
        with a grim outcome with median overall survival ranging between 2 to 10 months. To date,&#xD;
        even allogeneic transplantation fails to significantly improve the prognosis. Biological and&#xD;
        molecular mechanisms driving leukemic transformation are complex, ill-defined, and&#xD;
        heterogeneous between patients. The investigator hypothesize that deciphering the molecular&#xD;
        heterogeneity of post-MPN AML may lead identifying efficient drugs targeting of the most&#xD;
        relevant leukemogenic pathways.&#xD;
  &#xD;
        Our main objective is to identify new targeted therapeutic approaches in post-MPN AML through&#xD;
        in-depth characterization of the dysregulated pathways. The investigator will first&#xD;
        characterize in an already annotated cohort of 120 post-MPN AML homogeneous patients&#xD;
        subgroups using comprehensive multiomic analyses. Dysregulated pathways will be identified in&#xD;
        each subgroup using the omics data and single-cell RNA-sequencing will be performed in a&#xD;
        subset of patients in each subgroup. A customised drug-panel will be derived from the&#xD;
        dysregulated pathway for an ex vivo drug screening, which will use a flow-cytometry read-out&#xD;
        enabling to identity drug effect on cells survival, differentiation, and stemness. The 3 most&#xD;
        promising drugs will be validated in a preclinical in vivo model of patient's derived&#xD;
        xenograft (PDX) and their impact on clonal architecture will be studied in primary cell&#xD;
        cultures using single-cell DNA-sequencing.&#xD;
  &#xD;
        Overall, this proposal may provide a better understanding of MPN leukemic transformation&#xD;
        mechanisms and provide a path for personalized therapies. Our findings may therefore pave the&#xD;
        way to drugs development in post-MPN AML that would provide a rationale for implementation of&#xD;
        early clinical trials in these dreadful diseases.&#xD;
      </textblock>
    </brief_summary>
    <detailed_description>
      <textblock>
        Patients samples and clinical data:&#xD;
  &#xD;
        The investigator will study samples from 120 patients with a post-MPN acute myeloid leukemia.&#xD;
        These samples and the corresponding clinical data are available through FIMBANK, a national&#xD;
        network of biological resources for myeloproliferative neoplasms (grant INCa, BCB 2013, Pr&#xD;
        Valérie Ugo) and through the prospective phase II clinical trial CPX351-TA-SMP testing CPX351&#xD;
        monotherapy in post-MPN AML (NCT04992949, inclusions started in 01-2022).&#xD;
  &#xD;
        WP1: Deciphering the heterogeneity of post-MPN AML (primary objective) To answer these&#xD;
        objectives, the investigator will conduct a multi-omics approach including targeted-NGS with&#xD;
        a 400-genes panel, RNA-seq and methylome in a total of 120 post-MPN AML samples. All the&#xD;
        genomic libraries will be constructed at the genomic facility of Angers University Hospital&#xD;
        and the sequencing will be performed on a NovaSeq6000 in the GenoBIRD Platform in Nantes.&#xD;
        Bioinformatic analysis will be performed by teams #1 and #3 and will derive for each sample:&#xD;
        SNV/Indel and CNV from DNA sequencing, expression of mRNA and lncRNA, genes fusion and&#xD;
        splicing events from RNA-seq, and methylation beta-values from methylome.&#xD;
  &#xD;
        In order to identify homogeneous subgroups from the genomic data, the investigator will&#xD;
        perform unsupervised clustering analyses of each layer of genomic data. Then, all layers will&#xD;
        be combined for integration of clusters using the Cluster Of Clusters Analysis (COCA) method&#xD;
        (Wilkerson and Hayes, 2010).&#xD;
  &#xD;
        WP2: Identify the mechanisms of transformation and putative targets for therapy For this&#xD;
        purpose, the investigator will analyze omics data generated in WP1 to identify the main&#xD;
        molecular mechanisms driving the leukemic transformation of MPN. The investigator will&#xD;
        perform a 2-step procedure: first by analyzing each genomic dataset separately and then, by&#xD;
        analyzing all datasets together in an integrated multiblock analysis using the MOGSA method&#xD;
        (Integrative Single Sample Gene-set).&#xD;
  &#xD;
        A total of 60 samples originating from a subset of patients classified in WP1 will be tested&#xD;
        for ex vivo drug screening. The investigator will design a custom-made drug panel including&#xD;
        standards of care, several drugs in clinical development in AML and, more importantly, a&#xD;
        selection of drugs specifically targeting potential leukemic vulnerabilities identified.&#xD;
  &#xD;
        WP3: Confirm the efficacy of selected best drugs and their impact on clonal architecture To&#xD;
        further validate the translational relevance of post-MPN AML deregulated pathways, the three&#xD;
        most promising drug candidates will then be evaluated in a set of five post-MPN PDX models&#xD;
        including at least 2 TP53-mutated post-MPN AML. The investigator will also evaluate how the&#xD;
        drugs identified in WP2 may impact clonal evolution of the disease which is a key step&#xD;
        towards understanding and improving the treatment of post-MPN AML. The 3 best candidate drugs&#xD;
        or combinations identified in WP2 will be studied in cells from 5 selected patients with a&#xD;
        complex molecular profile to evaluate the response of various subclones.&#xD;
      </textblock>
    </detailed_description>
    <overall_status>Not yet recruiting</overall_status>
    <start_date type="Anticipated">October 15, 2023</start_date>
    <completion_date type="Anticipated">December 31, 2028</completion_date>
    <primary_completion_date type="Anticipated">December 31, 2027</primary_completion_date>
    <phase>N/A</phase>
    <study_type>Interventional</study_type>
    <has_expanded_access>No</has_expanded_access>
    <study_design_info>
      <allocation>N/A</allocation>
      <intervention_model>Single Group Assignment</intervention_model>
      <primary_purpose>Basic Science</primary_purpose>
      <masking>None (Open Label)</masking>
      <masking_description>Patients will be recruited in the French biobank of MPN (BCB INCa FIMBANK) and the FILO's national biobank of acute leukemias (FILOthèque). All clinical and biological data are anonymized.</masking_description>
    </study_design_info>
    <primary_outcome>
      <measure>Ward's minimum variance criterion to minimize the intra-cluster variance</measure>
      <time_frame>24 months</time_frame>
      <description>Decipher the heterogeneity of post-MPN AML to identify homogeneous subgroups</description>
    </primary_outcome>
    <secondary_outcome>
      <measure>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</measure>
      <time_frame>36 months</time_frame>
      <description>Identify the oncogenic molecular mechanisms among each subgroup of post-MPN AML</description>
    </secondary_outcome>
    <secondary_outcome>
      <measure>Median effective concentration (EC50) of each evaluated drug</measure>
      <time_frame>36 months</time_frame>
      <description>Identify efficient in vitro therapies targeting the dysregulated pathways of post-MPN AML</description>
    </secondary_outcome>
    <secondary_outcome>
      <measure>Mice survival</measure>
      <time_frame>48 months</time_frame>
      <description>Confirm the efficacy of the most promising newly identified candidate drugs or therapeutic combinations in vivo in PDX models</description>
    </secondary_outcome>
    <secondary_outcome>
      <measure>Leukemic disease burden modification</measure>
      <time_frame>48 months</time_frame>
      <description>Confirm the efficacy of the most promising newly identified candidate drugs or therapeutic combinations in vivo in PDX models</description>
    </secondary_outcome>
    <secondary_outcome>
      <measure>Identify the effect of the best candidate drugs/therapeutic combinations at the single-cell level and assess how clonal architecture evolves after treatment</measure>
      <time_frame>48 months</time_frame>
      <description>Absolute change of the proportion of each leukemic clone in single-cell DNA-sequencing of in vitro culture</description>
    </secondary_outcome>
    <number_of_arms>1</number_of_arms>
    <enrollment type="Anticipated">120</enrollment>
    <condition>Myeloproliferative Neoplasm</condition>
    <condition>Secondary Leukemia</condition>
    <arm_group>
      <arm_group_label>Leukemic transformation of myeloproliferative neoplasms</arm_group_label>
      <arm_group_type>Other</arm_group_type>
      <description>120 patients will be studied for :&#xD;
  Multiomic characterization&#xD;
  In vitro drug screening</description>
    </arm_group>
    <intervention>
      <intervention_type>Other</intervention_type>
      <intervention_name>Multiomic characterization</intervention_name>
      <description>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.</description>
      <arm_group_label>Leukemic transformation of myeloproliferative neoplasms</arm_group_label>
    </intervention>
    <intervention>
      <intervention_type>Other</intervention_type>
      <intervention_name>In vitro drug screening</intervention_name>
      <description>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.</description>
      <arm_group_label>Leukemic transformation of myeloproliferative neoplasms</arm_group_label>
    </intervention>
    <eligibility>
      <criteria>
        <textblock>
          Inclusion Criteria:&#xD;
  &#xD;
            -  Patients with a prior diagnosis of MPN: polycythemia vera, essential thrombocythemia&#xD;
               or primary myelofibrosis according to the WHO criteria&#xD;
  &#xD;
            -  Acute myeloid leukemia evolution defined by ≥ 20% of blasts cells&#xD;
  &#xD;
            -  Available material from bone marrow sampling at the time of leukemic transformation&#xD;
               (i.e. ≥ 20% of blasts cells): DNA (1µg), RNA (500ng) +/- frozen mononuclear cells in&#xD;
               DMSO for a subset of 60 patients (2 vials of at least 8 millions cells).&#xD;
  &#xD;
            -  Informed consent (or requalification procedure)&#xD;
  &#xD;
          Exclusion Criteria:&#xD;
  &#xD;
          - Patient not affiliated to the French health insurance&#xD;
        </textblock>
      </criteria>
      <gender>All</gender>
      <minimum_age>18 Years</minimum_age>
      <maximum_age>N/A</maximum_age>
      <healthy_volunteers>No</healthy_volunteers>
    </eligibility>
    <overall_official>
      <last_name>Damien LUQUE PAZ, PharmD. PhD.</last_name>
      <role>Principal Investigator</role>
      <affiliation>University Hospital of Angers</affiliation>
    </overall_official>
    <overall_contact>
      <last_name>Damien LUQUE PAZ, PharmD. PhD.</last_name>
      <phone>241355353</phone>
      <phone_ext>0033</phone_ext>
      <email>damien.luquepaz@chu-angers.fr</email>
    </overall_contact>
    <overall_contact_backup>
      <last_name>Béatrice GABLE</last_name>
      <phone>241356825</phone>
      <phone_ext>0033</phone_ext>
      <email>begable@chu-angers.fr</email>
    </overall_contact_backup>
    <verification_date>August 2023</verification_date>
    <study_first_submitted>August 22, 2023</study_first_submitted>
    <study_first_submitted_qc>August 28, 2023</study_first_submitted_qc>
    <study_first_posted type="Actual">September 1, 2023</study_first_posted>
    <last_update_submitted>August 28, 2023</last_update_submitted>
    <last_update_submitted_qc>August 28, 2023</last_update_submitted_qc>
    <last_update_posted type="Actual">September 1, 2023</last_update_posted>
    <responsible_party>
      <responsible_party_type>Sponsor</responsible_party_type>
    </responsible_party>
    <keyword>multiomics</keyword>
    <keyword>in vitro drug screening</keyword>
    <condition_browse>
      <!-- CAUTION:  The following MeSH terms are assigned with an imperfect algorithm            -->
      <mesh_term>Leukemia</mesh_term>
      <mesh_term>Neoplasms</mesh_term>
      <mesh_term>Leukemia, Myeloid, Acute</mesh_term>
      <mesh_term>Myeloproliferative Disorders</mesh_term>
    </condition_browse>
    <patient_data>
      <sharing_ipd>No</sharing_ipd>
    </patient_data>
    <!-- Results have not yet been posted for this study                                          -->
  </clinical_study>
  
  
text: download date: ClinicalTrials.gov processed this data on September 20, 2023
  link text: Link to the current ClinicalTrials.gov record.
  url: https://clinicaltrials.gov/ct2/show/NCT06022341
  org study id: 49RC23_0288.
  nct id: NCT06022341
  lead sponsor: 
  collaborator: 
  collaborator: 
  collaborator: 
  collaborator: 
  has dmc: No
  is fda regulated drug: No
  is fda regulated device: No
  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.
  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.
  allocation: N/A
  intervention model: Single Group Assignment
  primary purpose: Basic Science
  masking: None (Open Label)
  masking description: Patients will be recruited in the French biobank of MPN (BCB INCa FIMBANK) and the FILO's national biobank of acute leukemias (FILOthèque). All clinical and biological data are anonymized.
  measure: Ward's minimum variance criterion to minimize the intra-cluster variance
  time frame: 24 months
  description: Decipher the heterogeneity of post-MPN AML to identify homogeneous subgroups
  measure: 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
  description: Identify the oncogenic molecular mechanisms among each subgroup of post-MPN AML
  measure: Median effective concentration (EC50) of each evaluated drug
  time frame: 36 months
  description: Identify efficient in vitro therapies targeting the dysregulated pathways of post-MPN AML
  measure: Mice survival
  time frame: 48 months
  description: Confirm the efficacy of the most promising newly identified candidate drugs or therapeutic combinations in vivo in PDX models
  measure: Leukemic disease burden modification
  time frame: 48 months
  description: Confirm the efficacy of the most promising newly identified candidate drugs or therapeutic combinations in vivo in PDX models
  measure: 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
  description: Absolute change of the proportion of each leukemic clone in single-cell DNA-sequencing of in vitro culture
  arm group label: Leukemic transformation of myeloproliferative neoplasms
  arm group type: Other
  description: 120 patients will be studied for :
  Multiomic characterization
  In vitro drug screening
  intervention type: Other
  intervention name: Multiomic characterization
  description: 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.
  arm group label: Leukemic transformation of myeloproliferative neoplasms
  intervention type: Other
  intervention name: In vitro drug screening
  description: 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.
  arm group label: Leukemic transformation of myeloproliferative neoplasms
  criteria: 
  gender: All
  minimum age: 18 Years
  maximum age: N/A
  healthy volunteers: No
  last name: Damien LUQUE PAZ, PharmD. PhD.
  role: Principal Investigator
  affiliation: University Hospital of Angers
  last name: Damien LUQUE PAZ, PharmD. PhD.
  phone: 241355353
  phone ext: 0033
  email: damien.luquepaz@chu-angers.fr
  last name: Béatrice GABLE
  phone: 241356825
  phone ext: 0033
  email: begable@chu-angers.fr
  responsible party type: Sponsor
  mesh term: Leukemia
  mesh term: Neoplasms
  mesh term: Leukemia, Myeloid, Acute
  mesh term: Myeloproliferative Disorders
  sharing ipd: No