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de Camargo Magalhães ES, Hubner SE, Brown BD, Qiu Y, Kornblau SM. Proteomics for optimizing therapy in acute myeloid leukemia: venetoclax plus hypomethylating agents versus conventional chemotherapy. Leukemia 2024; 38:1046-1056. [PMID: 38531950 DOI: 10.1038/s41375-024-02208-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024]
Abstract
The use of Hypomethylating agents combined with Venetoclax (VH) for the treatment of Acute Myeloid Leukemia (AML) has greatly improved outcomes in recent years. However not all patients benefit from the VH regimen and a way to rationally select between VH and Conventional Chemotherapy (CC) for individual AML patients is needed. Here, we developed a proteomic-based triaging strategy using Reverse-phase Protein Arrays (RPPA) to optimize therapy selection. We evaluated the expression of 411 proteins in 810 newly diagnosed adult AML patients, identifying 109 prognostic proteins, that divided into five patient expression profiles, which are useful for optimizing therapy selection. Furthermore, using machine learning algorithms, we determined a set of 14 proteins, among those 109, that were able to accurately recommend therapy, making it feasible for clinical application. Next, we identified a group of patients who did not benefit from either VH or CC and proposed target-based approaches to improve outcomes. Finally, we calculated that the clinical use of our proteomic strategy would have led to a change in therapy for 30% of patients, resulting in a 43% improvement in OS, resulting in around 2600 more cures from AML per year in the United States.
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Affiliation(s)
| | - Stefan Edward Hubner
- John Sealy School of Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Brandon Douglas Brown
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030-4009, USA
| | - Yihua Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030-4009, USA
| | - Steven Mitchell Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030-4009, USA.
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2
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Alqazzaz MA, Luciani GM, Vu V, Machado RAC, Szewczyk MM, Adamson EC, Cheon S, Li F, Arrowsmith CH, Minden MD, Barsyte-Lovejoy D. Epigenetic vulnerabilities of leukemia harboring inactivating EZH2 mutations. Exp Hematol 2024; 130:104135. [PMID: 38072134 DOI: 10.1016/j.exphem.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/26/2023] [Accepted: 11/30/2023] [Indexed: 12/26/2023]
Abstract
Epigenetic regulators, such as the polycomb repressive complex 2 (PRC2), play a critical role in both normal development and carcinogenesis. Mutations and functional dysregulation of PRC2 complex components, such as EZH2, are implicated in various forms of cancer and associated with poor prognosis. This study investigated the epigenetic vulnerabilities of acute myeloid leukemia (AML) and myelodysplastic/myeloproliferative disorders (MDS/MPN) by performing a chemical probe screen in patient cells. Paradoxically, we observed increased sensitivity to EZH2 and embryonic ectoderm development (EED) inhibitors in AML and MDS/MPN patient cells harboring EZH2 mutations. Expression analysis indicated that EZH2 inhibition elicited upregulation of pathways responsible for cell death and growth arrest, specifically in patient cells with mutant EZH2. The identified EZH2 mutations had drastically reduced catalytic activity, resulting in lower cellular H3K27me3 levels, and were associated with decreased EZH2 and PRC2 component EED protein levels. Overall, this study provides an important understanding of the role of EZH2 dysregulation in blood cancers and may indicate disease etiology for these poor prognosis AML and MDS/MPN cases.
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Affiliation(s)
- Mona A Alqazzaz
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Ontario, Canada
| | - Genna M Luciani
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Ontario, Canada
| | - Victoria Vu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Ontario, Canada
| | - Raquel A C Machado
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Ella C Adamson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Ontario, Canada
| | - Sehyun Cheon
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Ontario, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Ontario, Canada
| | - Mark D Minden
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Ontario, Canada.
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3
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Sinha R, Dvorak M, Ganesan A, Kalesinskas L, Niemeyer CM, Flotho C, Sakamoto KM, Lacayo N, Patil RV, Perriman R, Cepika AM, Liu YL, Kuo A, Utz PJ, Khatri P, Bertaina A. Epigenetic Profiling of PTPN11 Mutant JMML Hematopoietic Stem and Progenitor Cells Reveals an Aberrant Histone Landscape. Cancers (Basel) 2023; 15:5204. [PMID: 37958378 PMCID: PMC10650722 DOI: 10.3390/cancers15215204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a deadly pediatric leukemia driven by RAS pathway mutations, of which >35% are gain-of-function in PTPN11. Although DNA hypermethylation portends severe clinical phenotypes, the landscape of histone modifications and chromatin profiles in JMML patient cells have not been explored. Using global mass cytometry, Epigenetic Time of Flight (EpiTOF), we analyzed hematopoietic stem and progenitor cells (HSPCs) from five JMML patients with PTPN11 mutations. These data revealed statistically significant changes in histone methylation, phosphorylation, and acetylation marks that were unique to JMML HSPCs when compared with healthy controls. Consistent with these data, assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis revealed significant alterations in chromatin profiles at loci encoding post-translational modification enzymes, strongly suggesting their mis-regulated expression. Collectively, this study reveals histone modification pathways as an additional epigenetic abnormality in JMML patient HSPCs, thereby uncovering a new family of potential druggable targets for the treatment of JMML.
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Affiliation(s)
- Roshani Sinha
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Mai Dvorak
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Ananthakrishnan Ganesan
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Larry Kalesinskas
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Charlotte M. Niemeyer
- Department of Pediatric Hematology and Oncology, University of Freiburg Medical Centre, 79098 Freiburg im Breisgau, Germany; (C.M.N.); (C.F.)
| | - Christian Flotho
- Department of Pediatric Hematology and Oncology, University of Freiburg Medical Centre, 79098 Freiburg im Breisgau, Germany; (C.M.N.); (C.F.)
| | - Kathleen M. Sakamoto
- Bass Center for Childhood Cancer and Blood Disorders at Lucile Packard Children’s Hospital, Palo Alto, CA 94304, USA; (K.M.S.); (N.L.)
| | - Norman Lacayo
- Bass Center for Childhood Cancer and Blood Disorders at Lucile Packard Children’s Hospital, Palo Alto, CA 94304, USA; (K.M.S.); (N.L.)
| | - Rachana Vinay Patil
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Rhonda Perriman
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Alma-Martina Cepika
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Yunying Lucy Liu
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Alex Kuo
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Paul J. Utz
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Purvesh Khatri
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Alice Bertaina
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
- Bass Center for Childhood Cancer and Blood Disorders at Lucile Packard Children’s Hospital, Palo Alto, CA 94304, USA; (K.M.S.); (N.L.)
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Khella MS, Schnee P, Weirich S, Bui T, Bröhm A, Bashtrykov P, Pleiss J, Jeltsch A. The T1150A cancer mutant of the protein lysine dimethyltransferase NSD2 can introduce H3K36 trimethylation. J Biol Chem 2023:104796. [PMID: 37150325 DOI: 10.1016/j.jbc.2023.104796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/20/2023] [Accepted: 04/29/2023] [Indexed: 05/09/2023] Open
Abstract
Protein lysine methyltransferases (PKMTs) play essential roles in gene expression regulation and cancer development. Somatic mutations in PKMTs are frequently observed in cancer cells. In biochemical experiments, we show here that the NSD1 mutations Y1971C, R2017Q and R2017L observed mostly in solid cancers are catalytically inactive suggesting that NSD1 acts as tumor suppressor gene in these tumors. In contrast, the frequently observed T1150A in NSD2 and its T2029A counterpart in NSD1, both observed in leukemia, are hyperactive and introduce up to thee methyl groups in H3K36 in biochemical and cellular assays, while wildtype NSD2 and NSD1 only introduce up to two methyl groups. In molecular dynamics simulations, we determine key mechanistic and structural features controlling the product specificity of this class of enzymes. Simulations with NSD2 revealed that H3K36me3 formation is possible due to an enlarged active site pocket of T1150A and loss of direct contacts of T1150 to critical residues which regulate the product specificity of NSD2. Bioinformatic analyses of published data suggested that the generation of H3K36me3 by NSD2 T1150A could alter gene regulation by antagonizing H3K27me3 finally leading to the upregulation of oncogenes.
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Affiliation(s)
- Mina S Khella
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany; Biochemistry Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo, 11566, Egypt
| | - Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Sara Weirich
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Tan Bui
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Alexander Bröhm
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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Salavaty A, Shehni SA, Ramialison M, Currie PD. Systematic molecular profiling of acute leukemia cancer stem cells allows identification of druggable targets. Heliyon 2022; 8:e11093. [PMID: 36281397 PMCID: PMC9586918 DOI: 10.1016/j.heliyon.2022.e11093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Acute myeloid leukemia (AML) is one of the most prevalent and acute blood cancers with a poor prognosis and low overall survival rate, especially in the elderly. Although several new AML markers and drug targets have been recently identified, the rate of long-term cancer eradication has not improved significantly due to the presence and drug resistance of AML cancer stem cells (CSCs). Here we develop a novel computational pipeline to analyze the transcriptomic profiles of AML cancer (stem) cells and identify novel candidate AML CSC markers and drug targets. In our novel pipeline we apply a top-down meta-analysis strategy to integrate The Cancer Genome Atlas data with CSC datasets to infer cell stemness features. As a result, a set of genes termed the "AML key CSC genes" along with all the available drugs/compounds that could target them were identified. Overall, our novel computational pipeline could retrieve known cancer drugs (Carfilzomib) and predicted novel drugs such as Zonisamide, Amitriptyline, and their targets amongst the top ranked drugs and drug targets for targeting AML. Additionally, the pipeline applied in this study could be used for the identification of CSC-specific markers, drivers and their respective targeting drugs in other cancer types.
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Affiliation(s)
- Adrian Salavaty
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- Systems Biology Institute Australia, Monash University, Clayton, VIC 3800, Australia
| | - Sara Alaei Shehni
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- Systems Biology Institute Australia, Monash University, Clayton, VIC 3800, Australia
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
- Department of Pediatrics, The Royal Children's Hospital, University of Melbourne Parkville, VIC, 3052, Australia
| | - Peter D. Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC 3800, Australia
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van Gils N, Verhagen HJ, Broux M, Martiáñez T, Denkers F, Vermue E, Rutten A, Csikós T, Demeyer S, Çil M, Al M, Cools J, Janssen JJ, Ossenkoppele GJ, Menezes RX, Smit L. Targeting histone methylation to reprogram the transcriptional state that drives survival of drug-tolerant myeloid leukemia persisters. iScience 2022; 25:105013. [PMID: 36097617 PMCID: PMC9463578 DOI: 10.1016/j.isci.2022.105013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Although chemotherapy induces complete remission in the majority of acute myeloid leukemia (AML) patients, many face a relapse. This relapse is caused by survival of chemotherapy-resistant leukemia (stem) cells (measurable residual disease; MRD). Here, we demonstrate that the anthracycline doxorubicin epigenetically reprograms leukemia cells by inducing histone 3 lysine 27 (H3K27) and H3K4 tri-methylation. Within a doxorubicin-sensitive leukemia cell population, we identified a subpopulation of reversible anthracycline-tolerant cells (ATCs) with leukemic stem cell (LSC) features lacking doxorubicin-induced H3K27me3 or H3K4me3 upregulation. These ATCs have a distinct transcriptional landscape than the leukemia bulk and could be eradicated by KDM6 inhibition. In primary AML, reprogramming the transcriptional state by targeting KDM6 reduced MRD load and survival of LSCs residing within MRD, and enhanced chemotherapy response in vivo. Our results reveal plasticity of anthracycline resistance in AML cells and highlight the potential of transcriptional reprogramming by epigenetic-based therapeutics to target chemotherapy-resistant AML cells. Reversible anthracycline-tolerant leukemia cells (ATCs) have low H3K27me3 or H3K4me3 ATCs exhibit stem cell features similar to leukemic stem cells Reprogramming the transcriptional state by inhibition of KDM6 depletes ATCs Inhibiting KDM6 adds to doxorubicin treatment and eradicates AML MRD (stem) cells
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Liang Y, Turcan S. Epigenetic Drugs and Their Immune Modulating Potential in Cancers. Biomedicines 2022; 10:biomedicines10020211. [PMID: 35203421 PMCID: PMC8868629 DOI: 10.3390/biomedicines10020211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 11/19/2022] Open
Abstract
Epigenetic drugs are used for the clinical treatment of hematologic malignancies; however, their therapeutic potential in solid tumors is still under investigation. Current evidence suggests that epigenetic drugs may lead to antitumor immunity by increasing antigen presentation and may enhance the therapeutic effect of immune checkpoint inhibitors. Here, we highlight their impact on the tumor epigenome and discuss the recent evidence that epigenetic agents may optimize the immune microenvironment and promote antiviral response.
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RPPA-based proteomics recognizes distinct epigenetic signatures in chronic lymphocytic leukemia with clinical consequences. Leukemia 2021; 36:712-722. [PMID: 34625713 DOI: 10.1038/s41375-021-01438-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/11/2021] [Accepted: 09/21/2021] [Indexed: 11/08/2022]
Abstract
The chronic lymphocytic leukemia (CLL) armamentarium has evolved significantly, with novel therapies that inhibit Bruton Tyrosine Kinase, PI3K delta and/or the BCL2 protein improving outcomes. Still, the clinical course of CLL patients is highly variable and most previously recognized prognostic features lack the capacity to predict response to modern treatments indicating the need for new prognostic markers. In this study, we identified four epigenetically distinct proteomic signatures of a large cohort of CLL and related diseases derived samples (n = 871) using reverse phase protein array technology. These signatures are associated with clinical features including age, cytogenetic abnormalities [trisomy 12, del(13q) and del(17p)], immunoglobulin heavy-chain locus (IGHV) mutational load, ZAP-70 status, Binet and Rai staging as well as with the outcome measures of time to treatment and overall survival. Protein signature membership was identified as predictive marker for overall survival regardless of other clinical features. Among the analyzed epigenetic proteins, EZH2, HDAC6, and loss of H3K27me3 levels were the most independently associated with poor survival. These findings demonstrate that proteomic based epigenetic biomarkers can be used to better classify CLL patients and provide therapeutic guidance.
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