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Principal Investigator: KAPIL BHALLA
Organization: UNIVERSITY OF TX MD ANDERSON CAN CTR
Fiscal Year: 2024
Award: $452,068
Funding agency: National Cancer Institute
Myeloproliferative neoplasms with myelofibrosis (MPN-MF) exhibit constitutive activity of JAK-STAT signaling
due to mutations in JAK2, c-MPL or calreticulin genes. Additional mutations in chromatin/transcriptional
modifiers (epimutations) induce transformation to AML (sAML) in up to 20% of patients with MPN-MF. Lack of
significant activity of the JAK1 & 2 inhibitor (JAKi) ruxolitinib and of AML chemotherapy highlights the need to
develop and test novel agents and combinations that would improve clinical outcome in patients with post-
MPN sAML. Genetic alterations and dysregulated epigenome produce the dysregulated transcriptome
responsible for the transformed phenotype and therapy-refractoriness in post-MPN sAML blast progenitor
cells (BPCs). This dysregulated transcriptome is dependent on ‘chromatin-reader’ BET (bromodomain and
extra-terminal) proteins (BETPs), e.g., BRD4, and on its interactor pTEFb (positive transcription elongation
factor b), both recruited to super-enhancers and promoters of actively-transcribed oncogenes. Cyclin
dependent kinase 9 (CDK9), the catalytic subunit of pTEFb, phosphorylates RNA pol II (RNAP2), promoting
RNAP2-mediated mRNA transcript elongation of oncogenes essential for growth and survival of post-MPN
sAML BPCs. However, effects of BETP-CDK9 axis inhibition on active super-enhancers/enhancers and
promoters with resulting impact on the dysregulated transcriptome and survival have not been elucidated in
patient-derived (PD) sAML BPCs. Additionally, epigenetic mechanisms of resistance to CDK9 or BETP
inhibitor (CDK9i or BETi) treatment and their therapeutic abrogation in post-MPN sAML BPCs need
evaluation. Our preliminary studies demonstrate that CDK9i or BETP-antagonist (BETi and BETP-
PROTACs) treatment induces apoptosis of post-MPN sAML BPCs, which is associated with repression of
sAML-relevant oncogenes, e.g., c-MYC, STAT3/5, NFkB, Bcl-xL and MCL-1. We hypothesize that BETP-
antagonist and CDK9i-based combinations will repress the dysregulated transcriptome and oncogenes, and
with JAKi or BCL2/Bcl-xL inhibitor co-treatment, synergistically induce in vitro and in vivo lethality in PD, post-
MPN sAML BPCs. Specific aims of these studies are: Aim 1: To elucidate the effects of BETP-PROTAC
and CDK9i on active super-enhancers/enhancers (by ATAC-Seq and ChIP-Seq), mRNA transcriptome (by
RNA-Seq) and on protein expressions (by CyTOF), as well as determine their pre-clinical efficacy against
genetically-profiled, cultured cell lines and PD, post-MPN sAML BPCs. Aim 2: To determine lethal activity of
BETP-PROTAC and CDK9i-based combinations against JAKi-sensitive and JAKi-persister/resistant sAML
BPCs, utilizing in vitro cell cultures and in vivo xenograft models. Aim 3: To elucidate the dysregulated
epigenome and transcriptome as well as susceptibility to BETP-PROTAC-based combinations in BETi- or
CDK9i-persister/resistant post-MPN sAML BPCs.
Terms: <55-kDa High-Affinity Calcium Binding Protein><AML1><AMLCR1><ATAC sequencing><ATAC-seq><ATACseq><Acetylation><Antioncogene Protein p53><Apoptotic><Assay for Transposase-Accessible Chromatin using sequencing><Attenuated><B cell lymphoma 2><B-Cell CLL/Lymphoma 2 Gene><B-cell lymphoma-extra large><B-cell lymphoma/leukemia-2><BCL-XL><BCL2><BCL2 gene><BCL2-Like 1><BCL2-Related Gene><BCL2-Related Protein, Long Isoform><BCL2-Related Protein, Short Isoform><BCL2L1><BCL2L1 gene><BCLX><BCLXL><BCLXS><BET bromodomain inhibitor><BET inhibitor><BETi><Basal Transcription Factor><Basal transcription factor genes><Bcl-2><Binding><Binding Sites><Blood Precursor Cell><Bone Marrow Fibrosis><Bromodomain><Bromodomain and Extra-Terminal motif inhibitor><Bromodomains and extra-terminal domain inhibitor><C-terminal><CAB-63><CBFA2><CDK Inhibitor Protein><CDK9 Kinase><CDK9 Protein Kinase><CDKI Protein><Calcium-Binding Protein-3><Calregulin><Cancer Genes><Cancer-Promoting Gene><Catalytic Core><Catalytic Domain><Catalytic Region><Catalytic Site><Catalytic Subunit><Cdc2-related Kinase PITALRE><Cell Communication and Signaling><Cell Culture Techniques><Cell Line><Cell Signaling><Cell Survival><Cell Viability><CellLine><Cellular Expansion><Cellular Growth><Cellular Tumor Antigen P53><ChIP Sequencing><ChIP-seq><ChIPseq><Chromatin><Chromatin Remodeling Complex><Chromatin Remodeling Factor><Clinical><Combining Site><Cyclin Kinase Inhibitor><Cyclin-Dependent Kinase 9><Cyclin-Dependent Kinase Inhibitor><Cyclin-Dependent Kinases><Cyclin-Dependent Protein Kinases><DNA Alteration><DNA Polymerase II><DNA Polymerase epsilon><DNA Sequence Alteration><DNA mutation><DNA-Dependent DNA Polymerase II><DNMT3a><Dependence><Disease Progression><ENX-1><ERp60><EZH1><EZH2><EZH2 gene><Elements><Enhancer of Zeste 2 Polycomb Repressive Complex 2 Subunit><Enhancers><Enzyme Gene><Enzymes><Epigenetic><Epigenetic Change><Epigenetic Mechanism><Epigenetic Process><Evaluation><Exhibits><Family member><Gene Transcription><General Transcription Factor Gene><General Transcription Factors><Generalized Growth><Genes><Genetic Alteration><Genetic Change><Genetic Transcription><Genetic defect><Genetic mutation><Growth><HACBP><Hematopoietic Progenitor Cells><Hematopoietic stem cells><Histones><Immunoglobulin Enhancer-Binding Protein><In Vitro><Induction of Apoptosis><Intracellular Communication and Signaling><JAK kinase><JAK-2><JAK1><JAK1 gene><JAK1 protein><JAK1A><JAK2><JAK2 gene><JAK2 protein><Jak1 kinase><Janus kinase><Janus kinase 1><Janus kinase 2><KMT6><KMT6A><L-Lysine><L-Serine><Lysine><MCL-1><MCL1><MCL1 gene><Mediating><Mediator><Messenger RNA><Metastasis><Metastasize><Metastatic Lesion><Metastatic Mass><Metastatic Neoplasm><Metastatic Tumor><Molecular Interaction><Mutation><Myelofibrosis><Myeloid Disease><Myeloid Malignancy><Myeloid Neoplasm><Myeloid Tumor><Myeloproliferative Disorders><Myeloproliferative Tumors><Myeloproliferative disease><Myelosclerosis><NELF><NF-kB><NF-kappa B><NF-kappaB><NFKB><NFKB3><Neoplasm Metastasis><Non-Polyadenylated RNA><Nuclear Factor kappa B><Nuclear Transcription Factor NF-kB><Oncogenes><Oncoprotein p53><Outcome><P-TEFb><P53><PEBP2A2><PEBP2aB><PIM1><PIM1 gene><PITALRE Kinase><Patients><Phenotype><Phosphoprotein P53><Phosphoprotein pp53><Phosphorylation><Pol II><Positive Transcription Elongation Factor B><Positive Transcriptional Elongation Factor B><Predisposition><Productivity><Progenitor Cells><Protac><Protein Family><Protein Phosphorylation><Protein TP53><Proteins><Proteolysis targeting chimeric><Provirus Insertion Site Gene-1><RELA><RELA gene><RNA><RNA Expression><RNA Gene Products><RNA Seq><RNA sequencing><RNAseq><RUNX1><RUNX1 gene><Reactive Site><Reader><Refractory><Repression><Resistance><Ribonucleic Acid><SC35><SRSF2><SRSF2 gene><STAT3><STAT3 gene><Secondary Neoplasm><Secondary Tumor><Secondary acute myeloid leukemia><Sequence Alteration><Serine><Serine/Arginine-Rich Splicing Factor 2><Signal Transduction><Signal Transduction Systems><Signaling><Strains Cell Lines><Susceptibility><TP53><TP53 gene><TRP53><Techniques><Testing><Therapeutic><Time><Tissue Growth><Transcript><Transcription><Transcription Factor NF-kB><Transcription Factor Proto-Oncogene><Transcription factor genes><Transforming Genes><Tumor Protein p53><Tumor Protein p53 Gene><Tyrosine-Protein Kinase JAK1><Tyrosine-Protein Kinase JAK2><Xenograft Model><antagonism><antagonist><assay for transposase accessible chromatin followed by sequencing><assay for transposase accessible chromatin seq><assay for transposase accessible chromatin sequencing><assay for transposase-accessible chromatin with sequencing><attenuate><attenuates><bcl-2 Genes><biological signal transduction><blood cell progenitor><blood progenitor><blood stem cell><blood-forming stem cell><bromodomain extra-terminal inhibitor><c myc><c-myc Genes><cC1qR Protein><calreticulin><cancer metastasis><cdk Proteins><ced9 homolog><cell culture><cell cultures><cell growth><chemotherapy><chromatin immunoprecipitation-sequencing><chromatin modifier><cmyc><cultured cell line><cyclin T><cyclin T1><epigenetic regulation><epigenetically><epigenome><genome mutation><genomic alteration><genomic profiles><global gene expression><global transcription profile><hDNA methyltransferase 3a><hematopoietic progenitor><hematopoietic stem progenitor cell><hemopoietic progenitor><hemopoietic stem cell><improved><in vivo><inhibitor><kappa B Enhancer Binding Protein><mRNA><mimetics><myeloid cell leukemia 1><myeloid cell leukemia sequence 1><myeloid leukemia cell differentiation protein><myeloproliferative neoplasm><negative elongation factor><novel><nuclear factor kappa beta><ontogeny><p53 Antigen><p53 Genes><p53 Tumor Suppressor><pre-clinical><pre-clinical efficacy><preclinical><preclinical efficacy><promoter><promotor><protein expression><protein p53><proteolysis targeting chimera><recruit><resistance mechanism><resistant><resistant mechanism><sAML><secondary AML><stem cells><tat-Associated Kinase><transcription factor><transcriptome><transcriptome sequencing><transcriptomic sequencing><tumor cell metastasis><v-myc Avian Myelocytomatosis Viral Oncogene Cellular Homolog><xenograft transplant model><xenotransplant model>