1
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Fang Z, Fu J, Chen X. A combined immune and exosome-related risk signature as prognostic biomakers in acute myeloid leukemia. Hematology 2024; 29:2300855. [PMID: 38186215 DOI: 10.1080/16078454.2023.2300855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
OBJECTIVES Acute myeloid leukemia (AML) is one of the common hematological diseases with low survival rates. Studies have highlighted the dysregulated expression of immune-related and exosome-related genes (ERGs) in cancers. Nevertheless, it remains to be determined whether combining these genes have a prognostic significance in AML. METHODS Immune-ERG profiles for 151 AML patients from TCGA were analyzed. A risk model was constructed and optimized through the combination of univariate Cox regression and LASSO regression analysis. GEO datasets were utilized as the external validation for the robustness of the risk model. In addition, we performed KEGG and GO enrichment analyses to investigate the role played by these genes in AML. The variations in immune cell infiltrations among risk groups were assessed through four algorithms. Expression of hub gene in specific cell was analyzed by single-cell RNA seq. RESULTS A total of 85 immune-ERGs associated with prognosis were identified, enabling the construction of a risk model for AML. The risk model based on five immune-ERGs (CD37, NUCB2, LSP1, MGST1, and PLXNB1) demonstrated a correlation with the clinical outcomes. Additionally, age, FAB classification, cytogenetics risk, and risk score were identified as independent prognostic factors. The five immune-ERGs exhibited correlations with cytokine-cytokine receptor interaction, and antigen processing and presentation. Notably, the risk model demonstrated significant associations with immune responses and the expression of immune checkpoints. CONCLUSIONS An immune-ERG-based risk model was developed to effectively predict prognostic outcomes for AML patients. There is potential for immune therapy in AML targeting the five hub genes.
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Affiliation(s)
- Zenghui Fang
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People's Republic of China
| | - Jiali Fu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People's Republic of China
| | - Xin Chen
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People's Republic of China
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2
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Oliinyk D, Will A, Schneidmadel FR, Böhme M, Rinke J, Hochhaus A, Ernst T, Hahn N, Geis C, Lubeck M, Raether O, Humphrey SJ, Meier F. µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics. Mol Syst Biol 2024; 20:972-995. [PMID: 38907068 PMCID: PMC11297287 DOI: 10.1038/s44320-024-00050-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Mass spectrometry has revolutionized cell signaling research by vastly simplifying the analysis of many thousands of phosphorylation sites in the human proteome. Defining the cellular response to perturbations is crucial for further illuminating the functionality of the phosphoproteome. Here we describe µPhos ('microPhos'), an accessible phosphoproteomics platform that permits phosphopeptide enrichment from 96-well cell culture and small tissue amounts in <8 h total processing time. By greatly minimizing transfer steps and liquid volumes, we demonstrate increased sensitivity, >90% selectivity, and excellent quantitative reproducibility. Employing highly sensitive trapped ion mobility mass spectrometry, we quantify ~17,000 Class I phosphosites in a human cancer cell line using 20 µg starting material, and confidently localize ~6200 phosphosites from 1 µg. This depth covers key signaling pathways, rendering sample-limited applications and perturbation experiments with hundreds of samples viable. We employ µPhos to study drug- and time-dependent response signatures in a leukemia cell line, and by quantifying 30,000 Class I phosphosites in the mouse brain we reveal distinct spatial kinase activities in subregions of the hippocampal formation.
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Affiliation(s)
- Denys Oliinyk
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Andreas Will
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Felix R Schneidmadel
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Maximilian Böhme
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Jenny Rinke
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Andreas Hochhaus
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Thomas Ernst
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Nina Hahn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Markus Lubeck
- Bruker Daltonics GmbH & Co. KG, 28359, Bremen, Germany
| | | | - Sean J Humphrey
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Victoria, Australia.
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany.
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany.
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3
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Yang X, Ge G, Wang H, Liu T, Pan D, Zhao X, Chen X, Wang J, Zhang J, Zhang K, Yao D. Design, synthesis and biological evaluation of novel SIRT3 inhibitors targeting both NAD + and substrate binding sites for the treatment of acute myeloid leukemia. Eur J Med Chem 2024; 276:116689. [PMID: 39053191 DOI: 10.1016/j.ejmech.2024.116689] [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: 05/15/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
Acute myeloid leukemia (AML) represents a highly malignant subtype of leukemia with limited therapeutic options. In this study, we propose a novel therapeutic strategy for treating AML by inhibiting SIRT3 to regulate mitochondrial metabolism network involved in energy metabolism and epigenetic modifications essential for AML survival. A series of thieno [3,2-d]pyrimidine-6-carboxamide derivatives were designed and synthesized by structure-based strategy, 17f was documented to be a potent and acceptable selective SIRT3 inhibitor with IC50 value of 0.043 μM and exhibited profound anti-proliferative activity in MOLM13, MV4-11, and HL-60 cells. Through CETSA assay and the degree of deacetylation of intracellular SIRT3 substrates, we confirmed that 17f could effectively bind and inhibit SIRT3 activity in AML cells. Mechanistically, 17f suppressed mitochondrial function, triggered the accumulation of ROS, and significantly inhibited the production of ATP in AML cells. With the breakdown of mitochondrial function, 17f eventually induced apoptosis of AML cells. In addition, 17f also showed excellent anti-AML potential in nude mouse tumor models of HL-60-Luc. Collectively, these results demonstrate that 17f is a potent and acceptable selective SIRT3 inhibitor with promising potential to treat AML.
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Affiliation(s)
- Xuetao Yang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, College of Pharmacy, Shihezi University, Shihezi, 832002, China; School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China
| | - Ge Ge
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518055, China; School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China
| | - Hailing Wang
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518055, China; School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China
| | - Tianli Liu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, College of Pharmacy, Shihezi University, Shihezi, 832002, China; School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China
| | - Dabo Pan
- Department of Medical Technology, Qiandongnan Vocational & Technical College for Nationalities, Kaili, 556000, China
| | - Xi Zhao
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518055, China; School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China
| | - Xiya Chen
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518055, China; School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China
| | - Jinhui Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, College of Pharmacy, Shihezi University, Shihezi, 832002, China
| | - Jin Zhang
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518055, China.
| | - Ke Zhang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, College of Pharmacy, Shihezi University, Shihezi, 832002, China.
| | - Dahong Yao
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China.
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4
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Mangum R, Lin FY, Parsons DW. Recent Advancements and Innovations in Pediatric Precision Oncology. J Pediatr Hematol Oncol 2024; 46:262-271. [PMID: 38857189 DOI: 10.1097/mph.0000000000002871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/29/2024] [Indexed: 06/12/2024]
Abstract
Precision oncology incorporates comprehensive genomic profiling into the individualized clinical care of pediatric cancer patients. In recent years, comprehensive pan-cancer analyses have led to the successful implementation of genomics-based pediatric trials and accelerated approval of novel targeted agents. In addition, disease-specific studies have resulted in molecular subclassification of myriad cancer types with subsequent tailoring of treatment intensity based on the patient's prognostic factors. This review discusses the progress of the field and highlights developments that are leading to more personalized cancer care and improved patient outcomes. Increased understanding of the evolution of precision oncology over recent decades emphasizes the tremendous impact of improved genomic applications. New technologies and improved diagnostic modalities offer further promise for future advancements within the field.
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Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ
| | - Frank Y Lin
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
| | - D Williams Parsons
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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5
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Ma C, Hao Y, Shi B, Wu Z, Jin D, Yu X, Jin B. Unveiling mitochondrial and ribosomal gene deregulation and tumor microenvironment dynamics in acute myeloid leukemia. Cancer Gene Ther 2024; 31:1034-1048. [PMID: 38806621 DOI: 10.1038/s41417-024-00788-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024]
Abstract
Acute myeloid leukemia (AML) is a malignant clonal hematopoietic disease with a poor prognosis. Understanding the interaction between leukemic cells and the tumor microenvironment (TME) can help predict the prognosis of leukemia and guide its treatment. Re-analyzing the scRNA-seq data from the CSC and G20 cohorts, using a Python-based pipeline including machine-learning-based scVI-tools, recapitulated the distinct hierarchical structure within the samples of AML patients. Weighted correlation network analysis (WGCNA) was conducted to construct a weighted gene co-expression network and to identify gene modules primarily focusing on hematopoietic stem cells (HSCs), multipotent progenitors (MPPs), and natural killer (NK) cells. The analysis revealed significant deregulation in gene modules associated with aerobic respiration and ribosomal/cytoplasmic translation. Cell-cell communications were elucidated by the CellChat package, revealing an imbalance of activating and inhibitory immune signaling pathways. Interception of genes upregulated in leukemic HSCs & MPPs as well as in NKG2A-high NK cells was used to construct prognostic models. Normal Cox and artificial neural network models based on 10 genes were developed. The study reveals the deregulation of mitochondrial and ribosomal genes in AML patients and suggests the co-occurrence of stimulatory and inhibitory factors in the AML TME.
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Affiliation(s)
- Chao Ma
- Institute of Cancer Stem Cell, Dalian Medical University, West Section Lvshun South Road, Dalian, 116044, Liaoning, China
| | - Yuchao Hao
- Department of Hematology, The Second Hospital of Dalian Medical University, West Section Lvshun South Road, Dalian, 116027, Liaoning, China
| | - Bo Shi
- Institute of Cancer Stem Cell, Dalian Medical University, West Section Lvshun South Road, Dalian, 116044, Liaoning, China
| | - Zheng Wu
- Institute of Cancer Stem Cell, Dalian Medical University, West Section Lvshun South Road, Dalian, 116044, Liaoning, China
| | - Di Jin
- Institute of Cancer Stem Cell, Dalian Medical University, West Section Lvshun South Road, Dalian, 116044, Liaoning, China
| | - Xiao Yu
- NHC Key Laboratory of Pneumoconiosis, The First Hospital of Shanxi Medical University, South Jiefang Road, Taiyuan, 030001, Shanxi, China.
| | - Bilian Jin
- Institute of Cancer Stem Cell, Dalian Medical University, West Section Lvshun South Road, Dalian, 116044, Liaoning, China.
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6
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Ramberger E, Sapozhnikova V, Ng YLD, Dolnik A, Ziehm M, Popp O, Sträng E, Kull M, Grünschläger F, Krüger J, Benary M, Müller S, Gao X, Murgai A, Haji M, Schmidt A, Lutz R, Nogai A, Braune J, Laue D, Langer C, Khandanpour C, Bassermann F, Döhner H, Engelhardt M, Straka C, Hundemer M, Beule D, Haas S, Keller U, Einsele H, Bullinger L, Knop S, Mertins P, Krönke J. The proteogenomic landscape of multiple myeloma reveals insights into disease biology and therapeutic opportunities. NATURE CANCER 2024:10.1038/s43018-024-00784-3. [PMID: 38942927 DOI: 10.1038/s43018-024-00784-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/15/2024] [Indexed: 06/30/2024]
Abstract
Multiple myeloma (MM) is a plasma cell malignancy of the bone marrow. Despite therapeutic advances, MM remains incurable, and better risk stratification as well as new therapies are therefore highly needed. The proteome of MM has not been systematically assessed before and holds the potential to uncover insight into disease biology and improved prognostication in addition to genetic and transcriptomic studies. Here we provide a comprehensive multiomics analysis including deep tandem mass tag-based quantitative global (phospho)proteomics, RNA sequencing, and nanopore DNA sequencing of 138 primary patient-derived plasma cell malignancies encompassing treatment-naive MM, plasma cell leukemia and the premalignancy monoclonal gammopathy of undetermined significance, as well as healthy controls. We found that the (phospho)proteome of malignant plasma cells are highly deregulated as compared with healthy plasma cells and is both defined by chromosomal alterations as well as posttranscriptional regulation. A prognostic protein signature was identified that is associated with aggressive disease independent of established risk factors in MM. Integration with functional genetics and single-cell RNA sequencing revealed general and genetic subtype-specific deregulated proteins and pathways in plasma cell malignancies that include potential targets for (immuno)therapies. Our study demonstrates the potential of proteogenomics in cancer and provides an easily accessible resource for investigating protein regulation and new therapeutic approaches in MM.
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Affiliation(s)
- Evelyn Ramberger
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Valeriia Sapozhnikova
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Yuen Lam Dora Ng
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anna Dolnik
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Matthias Ziehm
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Eric Sträng
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Miriam Kull
- Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Florian Grünschläger
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Josefine Krüger
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Sina Müller
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Xiang Gao
- Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Arunima Murgai
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mohamed Haji
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Annika Schmidt
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Raphael Lutz
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Axel Nogai
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jan Braune
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dominik Laue
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Cyrus Khandanpour
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
| | - Florian Bassermann
- Department of Medicine III, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Hartmut Döhner
- Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | | | | | - Michael Hundemer
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Simon Haas
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
| | - Ulrich Keller
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Lars Bullinger
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Knop
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany.
- Nuremberg General Hospital, Nuremberg, Germany.
- Paracelsus Medical School, Nuremberg, Germany.
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.
- Berlin Institute of Health, Berlin, Germany.
| | - Jan Krönke
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany.
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7
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Bordeleau ME, Audemard É, Métois A, Theret L, Lisi V, Farah A, Spinella JF, Chagraoui J, Moujaber O, Aubert L, Khakipoor B, Mallinger L, Boivin I, Mayotte N, Hajmirza A, Bonneil É, Béliveau F, Pfammatter S, Feghaly A, Boucher G, Gendron P, Thibault P, Barabé F, Lemieux S, Richard-Carpentier G, Hébert J, Lavallée VP, Roux PP, Sauvageau G. Immunotherapeutic targeting of surfaceome heterogeneity in AML. Cell Rep 2024; 43:114260. [PMID: 38838225 DOI: 10.1016/j.celrep.2024.114260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/29/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
Immunotherapy remains underexploited in acute myeloid leukemia (AML) compared to other hematological malignancies. Currently, gemtuzumab ozogamicin is the only therapeutic antibody approved for this disease. Here, to identify potential targets for immunotherapeutic intervention, we analyze the surface proteome of 100 genetically diverse primary human AML specimens for the identification of cell surface proteins and conduct single-cell transcriptome analyses on a subset of these specimens to assess antigen expression at the sub-population level. Through this comprehensive effort, we successfully identify numerous antigens and markers preferentially expressed by primitive AML cells. Many identified antigens are targeted by therapeutic antibodies currently under clinical evaluation for various cancer types, highlighting the potential therapeutic value of the approach. Importantly, this initiative uncovers AML heterogeneity at the surfaceome level, identifies several antigens and potential primitive cell markers characterizing AML subgroups, and positions immunotherapy as a promising approach to target AML subgroup specificities.
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Affiliation(s)
- Marie-Eve Bordeleau
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada.
| | - Éric Audemard
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Arnaud Métois
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Louis Theret
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Véronique Lisi
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada
| | - Azer Farah
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada
| | - Jean-François Spinella
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Jalila Chagraoui
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Ossama Moujaber
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Léo Aubert
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Banafsheh Khakipoor
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada
| | - Laure Mallinger
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Isabel Boivin
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Nadine Mayotte
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Azadeh Hajmirza
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Éric Bonneil
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - François Béliveau
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada
| | - Sybille Pfammatter
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Albert Feghaly
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Geneviève Boucher
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Patrick Gendron
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Pierre Thibault
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Department of Chemistry, Faculty of Arts and Science, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Frédéric Barabé
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Centre de Recherche du Centre Hospitalier Universitaire de Québec, Université Laval, Québec, QC G1V 4G2, Canada
| | - Sébastien Lemieux
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada.
| | - Guillaume Richard-Carpentier
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Medicine, Division of Medical Oncology and Hematology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Josée Hébert
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada; Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada.
| | - Vincent-Philippe Lavallée
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Hematology and Oncology Division, Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC H3T 1C5, Canada.
| | - Philippe P Roux
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada.
| | - Guy Sauvageau
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada; Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada.
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8
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Zhang Z, Huang J, Zhang Z, Shen H, Tang X, Wu D, Bao X, Xu G, Chen S. Application of omics in the diagnosis, prognosis, and treatment of acute myeloid leukemia. Biomark Res 2024; 12:60. [PMID: 38858750 PMCID: PMC11165883 DOI: 10.1186/s40364-024-00600-1] [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: 03/20/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024] Open
Abstract
Acute myeloid leukemia (AML) is the most frequent leukemia in adults with a high mortality rate. Current diagnostic criteria and selections of therapeutic strategies are generally based on gene mutations and cytogenetic abnormalities. Chemotherapy, targeted therapies, and hematopoietic stem cell transplantation (HSCT) are the major therapeutic strategies for AML. Two dilemmas in the clinical management of AML are related to its poor prognosis. One is the inaccurate risk stratification at diagnosis, leading to incorrect treatment selections. The other is the frequent resistance to chemotherapy and/or targeted therapies. Genomic features have been the focus of AML studies. However, the DNA-level aberrations do not always predict the expression levels of genes and proteins and the latter is more closely linked to disease phenotypes. With the development of high-throughput sequencing and mass spectrometry technologies, studying downstream effectors including RNA, proteins, and metabolites becomes possible. Transcriptomics can reveal gene expression and regulatory networks, proteomics can discover protein expression and signaling pathways intimately associated with the disease, and metabolomics can reflect precise changes in metabolites during disease progression. Moreover, omics profiling at the single-cell level enables studying cellular components and hierarchies of the AML microenvironment. The abundance of data from different omics layers enables the better risk stratification of AML by identifying prognosis-related biomarkers, and has the prospective application in identifying drug targets, therefore potentially discovering solutions to the two dilemmas. In this review, we summarize the existing AML studies using omics methods, both separately and combined, covering research fields of disease diagnosis, risk stratification, prognosis prediction, chemotherapy, as well as targeted therapy. Finally, we discuss the directions and challenges in the application of multi-omics in precision medicine of AML. Our review may inspire both omics researchers and clinical physicians to study AML from a different angle.
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Affiliation(s)
- Zhiyu Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, Jiangsu, China
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Jiayi Huang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhibo Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hongjie Shen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaowen Tang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiebing Bao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, Jiangsu, China.
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China.
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China.
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
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9
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Yang L, Zhang Z, Jiang P, Kong D, Yu Z, Shi D, Han Y, Chen E, Zheng W, Sun J, Zhao Y, Luo Y, Shi J, Yao H, Huang H, Qian P. Phase separation-competent FBL promotes early pre-rRNA processing and translation in acute myeloid leukaemia. Nat Cell Biol 2024; 26:946-961. [PMID: 38745030 DOI: 10.1038/s41556-024-01420-z] [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: 02/17/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
RNA-binding proteins (RBPs) are pivotal in acute myeloid leukaemia (AML), a lethal disease. Although specific phase separation-competent RBPs are recognized in AML, the effect of their condensate formation on AML leukaemogenesis, and the therapeutic potential of inhibition of phase separation are underexplored. In our in vivo CRISPR RBP screen, fibrillarin (FBL) emerges as a crucial nucleolar protein that regulates AML cell survival, primarily through its phase separation domains rather than methyltransferase or acetylation domains. These phase separation domains, with specific features, coordinately drive nucleoli formation and early processing of pre-rRNA (including efflux, cleavage and methylation), eventually enhancing the translation of oncogenes such as MYC. Targeting the phase separation capability of FBL with CGX-635 leads to elimination of AML cells, suggesting an additional mechanism of action for CGX-635 that complements its established therapeutic effects. We highlight the potential of PS modulation of critical proteins as a possible therapeutic strategy for AML.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- RNA Precursors/metabolism
- RNA Precursors/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- RNA Processing, Post-Transcriptional
- Animals
- Cell Line, Tumor
- Protein Biosynthesis
- Cell Nucleolus/metabolism
- Cell Nucleolus/genetics
- Mice
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/genetics
- Gene Expression Regulation, Leukemic
- Phase Separation
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Affiliation(s)
- Lin Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Zhaoru Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Penglei Jiang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Delin Kong
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Zebin Yu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Danrong Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yingli Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Ertuo Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Weiyan Zheng
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Sun
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanmin Zhao
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Luo
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jimin Shi
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - He Huang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China.
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Pengxu Qian
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China.
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10
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Felipe Fumero E, Walter C, Frenz JM, Seifert F, Alla V, Hennig T, Angenendt L, Hartmann W, Wolf S, Serve H, Oellerich T, Lenz G, Müller-Tidow C, Schliemann C, Huber O, Dugas M, Mann M, Jayavelu AK, Mikesch JH, Arteaga MF. Epigenetic control over the cell-intrinsic immune response antagonizes self-renewal in acute myeloid leukemia. Blood 2024; 143:2284-2299. [PMID: 38457355 PMCID: PMC11181352 DOI: 10.1182/blood.2023021640] [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: 06/29/2023] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 03/10/2024] Open
Abstract
ABSTRACT Epigenetic modulation of the cell-intrinsic immune response holds promise as a therapeutic approach for leukemia. However, current strategies designed for transcriptional activation of endogenous transposons and subsequent interferon type-I (IFN-I) response, show limited clinical efficacy. Histone lysine methylation is an epigenetic signature in IFN-I response associated with suppression of IFN-I and IFN-stimulated genes, suggesting histone demethylation as key mechanism of reactivation. In this study, we unveil the histone demethylase PHF8 as a direct initiator and regulator of cell-intrinsic immune response in acute myeloid leukemia (AML). Site-specific phosphorylation of PHF8 orchestrates epigenetic changes that upregulate cytosolic RNA sensors, particularly the TRIM25-RIG-I-IFIT5 axis, thereby triggering the cellular IFN-I response-differentiation-apoptosis network. This signaling cascade largely counteracts differentiation block and growth of human AML cells across various disease subtypes in vitro and in vivo. Through proteome analysis of over 200 primary AML bone marrow samples, we identify a distinct PHF8/IFN-I signature in half of the patient population, without significant associations with known clinically or genetically defined AML subgroups. This profile was absent in healthy CD34+ hematopoietic progenitor cells, suggesting therapeutic applicability in a large fraction of patients with AML. Pharmacological support of PHF8 phosphorylation significantly impairs the growth in samples from patients with primary AML. These findings provide novel opportunities for harnessing the cell-intrinsic immune response in the development of immunotherapeutic strategies against AML.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Epigenesis, Genetic
- Animals
- Histone Demethylases/genetics
- Histone Demethylases/metabolism
- Mice
- Interferon Type I/metabolism
- Cell Self Renewal
- Gene Expression Regulation, Leukemic
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Affiliation(s)
| | - Carolin Walter
- Institute of Medical Informatics, Gerhard-Domagk-Institute for Pathology, University Hospital Muenster, Muenster, Germany
| | - Joris Maximillian Frenz
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children’s Cancer Center, University of Heidelberg, Heidelberg, Germany
| | - Franca Seifert
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
| | - Vijay Alla
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
| | - Thorben Hennig
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children’s Cancer Center, University of Heidelberg, Heidelberg, Germany
| | - Linus Angenendt
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk-Institute for Pathology, University Hospital Muenster, Muenster, Germany
| | - Sebastian Wolf
- Department of Hematology/Oncology, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Hubert Serve
- Department of Hematology/Oncology, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Thomas Oellerich
- Department of Hematology/Oncology, Johann Wolfgang Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Georg Lenz
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
| | | | | | - Otmar Huber
- Department of Biochemistry II, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ashok Kumar Jayavelu
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children’s Cancer Center, University of Heidelberg, Heidelberg, Germany
| | - Jan-Henrik Mikesch
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
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11
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Yu PC, Hou D, Chang B, Liu N, Xu CH, Chen X, Hu CL, Liu T, Wang X, Zhang Q, Liu P, Jiang Y, Fei MY, Zong LJ, Zhang JY, Liu H, Chen BY, Chen SB, Wang Y, Li ZJ, Li X, Deng CH, Ren YY, Zhao M, Jiang S, Wang R, Jin J, Yang S, Xue K, Shi J, Chang CK, Shen S, Wang Z, He PC, Chen Z, Chen SJ, Sun XJ, Wang L. SMARCA5 reprograms AKR1B1-mediated fructose metabolism to control leukemogenesis. Dev Cell 2024:S1534-5807(24)00296-X. [PMID: 38776924 DOI: 10.1016/j.devcel.2024.04.023] [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: 11/14/2023] [Revised: 03/13/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
A significant variation in chromatin accessibility is an epigenetic feature of leukemia. The cause of this variation in leukemia, however, remains elusive. Here, we identify SMARCA5, a core ATPase of the imitation switch (ISWI) chromatin remodeling complex, as being responsible for aberrant chromatin accessibility in leukemia cells. We find that SMARCA5 is required to maintain aberrant chromatin accessibility for leukemogenesis and then promotes transcriptional activation of AKR1B1, an aldo/keto reductase, by recruiting transcription co-activator DDX5 and transcription factor SP1. Higher levels of AKR1B1 are associated with a poor prognosis in leukemia patients and promote leukemogenesis by reprogramming fructose metabolism. Moreover, pharmacological inhibition of AKR1B1 has been shown to have significant therapeutic effects in leukemia mice and leukemia patient cells. Thus, our findings link the aberrant chromatin state mediated by SMARCA5 to AKR1B1-mediated endogenous fructose metabolism reprogramming and shed light on the essential role of AKR1B1 in leukemogenesis, which may provide therapeutic strategies for leukemia.
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Affiliation(s)
- Peng-Cheng Yu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Dan Hou
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Binhe Chang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Na Liu
- Department of Hematology, Institute of Hematology, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Chun-Hui Xu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinchi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng-Long Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ting Liu
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiaoning Wang
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Qunling Zhang
- Department of Medical Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ping Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yilun Jiang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming-Yue Fei
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li-Juan Zong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Ying Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Liu
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Bing-Yi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shu-Bei Chen
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zi-Juan Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiya Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chu-Han Deng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi-Yi Ren
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Muying Zhao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shiyu Jiang
- Department of Medical Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Roujia Wang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Jiacheng Jin
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Shaoxin Yang
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Kai Xue
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jun Shi
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Chun-Kang Chang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhikai Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei 230027, China
| | - Peng-Cheng He
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao-Jian Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lan Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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12
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Shi X, Feng M, Nakada D. Metabolic dependencies of acute myeloid leukemia stem cells. Int J Hematol 2024:10.1007/s12185-024-03789-x. [PMID: 38750343 DOI: 10.1007/s12185-024-03789-x] [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: 02/19/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy primarily driven by an immature population of AML cells termed leukemia stem cells (LSCs) that are implicated in AML development, chemoresistance, and relapse. An emerging area of research in AML focuses on identifying and targeting the aberrant metabolism in LSCs. Dysregulated metabolism is involved in sustaining functional properties of LSCs, impeding myeloid differentiation, and evading programmed cell death, both in the process of leukemogenesis and in response to chemotherapy. This review discusses recent discoveries regarding the aberrant metabolic processes of AML LSCs that have begun to change the therapeutic landscape of AML.
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Affiliation(s)
- Xiangguo Shi
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Mengdie Feng
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daisuke Nakada
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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13
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Akiyama H, Zhao R, Ostermann LB, Li Z, Tcheng M, Yazdani SJ, Moayed A, Pryor ML, Slngh S, Baran N, Ayoub E, Nishida Y, Mak PY, Ruvolo VR, Carter BZ, Schimmer AD, Andreeff M, Ishizawa J. Mitochondrial regulation of GPX4 inhibition-mediated ferroptosis in acute myeloid leukemia. Leukemia 2024; 38:729-740. [PMID: 38148395 PMCID: PMC11082873 DOI: 10.1038/s41375-023-02117-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 12/28/2023]
Abstract
Resistance to apoptosis in acute myeloid leukemia (AML) cells causes refractory or relapsed disease, associated with dismal clinical outcomes. Ferroptosis, a mode of non-apoptotic cell death triggered by iron-dependent lipid peroxidation, has been investigated as potential therapeutic modality against therapy-resistant cancers, but our knowledge of its role in AML is limited. We investigated ferroptosis in AML cells and identified its mitochondrial regulation as a therapeutic vulnerability. GPX4 knockdown induced ferroptosis in AML cells, accompanied with characteristic mitochondrial lipid peroxidation, exerting anti-AML effects in vitro and in vivo. Electron transport chains (ETC) are primary sources of coenzyme Q10 (CoQ) recycling for its function of anti-lipid peroxidation in mitochondria. We found that the mitochondria-specific CoQ potently inhibited GPX4 inhibition-mediated ferroptosis, suggesting that mitochondrial lipid redox regulates ferroptosis in AML cells. Consistently, Rho0 cells, which lack functional ETC, were more sensitive to GPX4 inhibition-mediated mitochondrial lipid peroxidation and ferroptosis than control cells. Furthermore, degradation of ETC through hyperactivation of a mitochondrial protease, caseinolytic protease P (ClpP), synergistically enhanced the anti-AML effects of GPX4 inhibition. Collectively, our findings indicate that in AML cells, GPX4 inhibition induces ferroptosis, which is regulated by mitochondrial lipid redox and ETC.
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Affiliation(s)
- Hiroki Akiyama
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ran Zhao
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren B Ostermann
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew Tcheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Samar J Yazdani
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Arman Moayed
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Malcolm L Pryor
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sandeep Slngh
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Natalia Baran
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edward Ayoub
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuki Nishida
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Po Yee Mak
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivian R Ruvolo
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bing Z Carter
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jo Ishizawa
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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14
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Paudel BB, Tan SF, Fox TE, Ung J, Golla U, Shaw JJP, Dunton W, Lee I, Fares WA, Patel S, Sharma A, Viny AD, Barth BM, Tallman MS, Cabot M, Garrett-Bakelman FE, Levine RL, Kester M, Feith DJ, Claxton D, Janes KA, Loughran TP. Acute myeloid leukemia stratifies as 2 clinically relevant sphingolipidomic subtypes. Blood Adv 2024; 8:1137-1142. [PMID: 38170742 PMCID: PMC10909712 DOI: 10.1182/bloodadvances.2023010535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/06/2023] [Accepted: 10/27/2023] [Indexed: 01/05/2024] Open
Affiliation(s)
- B. Bishal Paudel
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
| | - Su-Fern Tan
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Todd E. Fox
- Department of Pharmacology, University of Virginia, Charlottesville, VA
| | - Johnson Ung
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Microbiology/Immunology/Cancer Biology, University of Virginia, Charlottesville, VA
| | - Upendarrao Golla
- Department of Medicine, Division of Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA
| | - Jeremy J. P. Shaw
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Wendy Dunton
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Irene Lee
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Internal Medicine, Baylor College of Medicine, Houston, TX
| | - Wisam A. Fares
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
| | - Satyam Patel
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA
| | - Arati Sharma
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA
- Penn State Cancer Institute, Hershey, PA
| | - Aaron D. Viny
- Department of Medicine, Division of Hematology & Oncology, and of Genetics & Development, Herbert Irving Comprehensive Cancer Center, New York, NY
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY
| | - Brian M. Barth
- Department of Chemistry, Biology, and Health Sciences, South Dakota School of Mines and Technology, Rapid City, SD
- Department of Natural Sciences, University of Alaska Southeast, Juneau, AK
| | - Martin S. Tallman
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Myles Cabot
- Department of Biochemistry & Molecular Biology, East Carolina University, Greenville, NC
- East Carolina Diabetes and Obesity Institute, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Francine E. Garrett-Bakelman
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Kester
- Department of Pharmacology, University of Virginia, Charlottesville, VA
| | - David J. Feith
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - David Claxton
- Department of Medicine, Division of Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA
- Penn State Cancer Institute, Hershey, PA
| | - Kevin A. Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - Thomas P. Loughran
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
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15
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Jin J, Hou S, Yao Y, Liu M, Mao L, Yang M, Tong H, Zeng T, Huang J, Zhu Y, Wang H. Phosphoproteomic Characterization and Kinase Signature Predict Response to Venetoclax Plus 3+7 Chemotherapy in Acute Myeloid Leukemia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305885. [PMID: 38161214 PMCID: PMC10953567 DOI: 10.1002/advs.202305885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Resistance to chemotherapy remains a formidable obstacle in acute myeloid leukemia (AML) therapeutic management, necessitating the exploration of optimal strategies to maximize therapeutic benefits. Venetoclax with 3+7 daunorubicin and cytarabine (DAV regimen) in young adult de novo AML patients is evaluated. 90% of treated patients achieved complete remission, underscoring the potential of this regimen as a compelling therapeutic intervention. To elucidate underlying mechanisms governing response to DAV in AML, quantitative phosphoproteomics to discern distinct molecular signatures characterizing a subset of DAV-sensitive patients is used. Cluster analysis reveals an enrichment of phosphoproteins implicated in chromatin organization and RNA processing within DAV-susceptible and DA-resistant AML patients. Furthermore, kinase activity profiling identifies AURKB as a candidate indicator of DAV regimen efficacy in DA-resistant AML due to AURKB activation. Intriguingly, AML cells overexpressing AURKB exhibit attenuated MCL-1 expression, rendering them receptive to DAV treatment and maintaining them resistant to DA treatment. Moreover, the dataset delineates a shared kinase, AKT1, associated with DAV response. Notably, AKT1 inhibition augments the antileukemic efficacy of DAV treatment in AML. Overall, this phosphoproteomic study identifies the role of AURKB as a predictive biomarker for DA, but not DAV, resistance and proposes a promising strategy to counteract therapy resistance in AML.
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Affiliation(s)
- Jie Jin
- Department of Hematologythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- Zhejiang Provincial Key Lab of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangP. R. China
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouChina
- Zhejiang University Cancer CenterHangzhouZhejiangP. R. China
- Jinan Microecological Biomedicine Shandong LaboratoryJinanP. R. China
| | - Shangyu Hou
- Research Center for Translational MedicineShanghai East HospitalSchool of Life Sciences and TechnologyTongji UniversityShanghai200092P.R. China
| | - Yiyi Yao
- Department of Hematologythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- Zhejiang Provincial Key Lab of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangP. R. China
| | - Miaomiao Liu
- Research Center for Translational MedicineShanghai East HospitalSchool of Life Sciences and TechnologyTongji UniversityShanghai200092P.R. China
| | - Liping Mao
- Department of Hematologythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- Zhejiang Provincial Key Lab of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangP. R. China
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouChina
| | - Min Yang
- Department of Hematologythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- Zhejiang Provincial Key Lab of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangP. R. China
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouChina
| | - Hongyan Tong
- Department of Hematologythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- Zhejiang Provincial Key Lab of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangP. R. China
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouChina
- Zhejiang University Cancer CenterHangzhouZhejiangP. R. China
| | - Tao Zeng
- Biomedical big data centerthe First Affiliated HospitalZhejiang University School of MedicineHangzhou, Zhejiang310003P.R. China
| | - Jinyan Huang
- Biomedical big data centerthe First Affiliated HospitalZhejiang University School of MedicineHangzhou, Zhejiang310003P.R. China
| | - Yinghui Zhu
- Research Center for Translational MedicineShanghai East HospitalSchool of Life Sciences and TechnologyTongji UniversityShanghai200092P.R. China
- Frontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchTongji UniversityShanghai200092P.R. China
| | - Huafeng Wang
- Department of Hematologythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- Zhejiang Provincial Key Lab of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangP. R. China
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouChina
- Zhejiang University Cancer CenterHangzhouZhejiangP. R. China
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16
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Ding Y, Bajpai AK, Wu F, Lu W, Xu L, Mao J, Li Q, Pan Q, Lu L, Wang X. 5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia. Aging (Albany NY) 2024; 16:2340-2361. [PMID: 38277218 PMCID: PMC10911375 DOI: 10.18632/aging.205484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024]
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous malignant disease of the blood cell. The current therapies for AML are unsatisfactory and the molecular mechanisms underlying AML are unclear. 5-methylcytosine (m5C) is an important posttranscriptional modification of mRNA, and is involved in the regulation of mRNA stability, translation, and other aspects of RNA metabolism. However, based on our knowledge of published literature, the role of the m5C regulators has not been explored in AML till date. In this study, we clarified the expression and gene variants of m5C regulators in AML and found that most m5C regulators were differentially expressed and correlated with disease prognosis. We also found that the methylation status of certain m5C regulators (e.g., DNMT3A, DNMT3B) affects the survival of AML patients. Two m5C modification subtypes, and high- and low-risk subgroups identified based on the expression of m5C regulators showed significant differences in the prognosis as well as immune cell infiltration. In addition, most of the m5C regulators were found to be correlated with miRNA expression in AML, as well as IC50 values of many drugs. The miRNA and GSVA analysis were used to identify the different miRNAs and KEGG or hallmark pathways between high- and low-risk subgroups. We also built a prognostic model based on m5C regulators, which was validated by two GSE databases. To verify the reliability of our analysis and conclusions, qPCR was used to identify the expressions of m5C regulators between normal and AML. In summary, we comprehensively explored the molecular characteristics of m5C regulators and built a prognostic model in AML. We proposed new mechanistic insights into the role of m5C in multiple databases and clinical data, which may pave novel ways for the development of therapeutic strategies.
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Affiliation(s)
- Yuhong Ding
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Akhilesh K. Bajpai
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Cente, Memphis, TN 38163, USA
| | - Fengxia Wu
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Weihua Lu
- Department of Hematology and Oncology, The Branch Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Lin Xu
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Jiawei Mao
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Qiang Li
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Qi Pan
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Lu Lu
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Cente, Memphis, TN 38163, USA
| | - Xinfeng Wang
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
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17
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Joshi SK, Piehowski P, Liu T, Gosline SJC, McDermott JE, Druker BJ, Traer E, Tyner JW, Agarwal A, Tognon CE, Rodland KD. Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine. Annu Rev Pharmacol Toxicol 2024; 64:455-479. [PMID: 37738504 PMCID: PMC10950354 DOI: 10.1146/annurev-pharmtox-022723-113921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools.
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Paul Piehowski
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sara J C Gosline
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jason E McDermott
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Karin D Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Pacific Northwest National Laboratory, Richland, Washington, USA
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18
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Pino JC, Posso C, Joshi SK, Nestor M, Moon J, Hansen JR, Hutchinson-Bunch C, Gritsenko MA, Weitz KK, Watanabe-Smith K, Long N, McDermott JE, Druker BJ, Liu T, Tyner JW, Agarwal A, Traer E, Piehowski PD, Tognon CE, Rodland KD, Gosline SJC. Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia. Cell Rep Med 2024; 5:101359. [PMID: 38232702 PMCID: PMC10829797 DOI: 10.1016/j.xcrm.2023.101359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/20/2023] [Accepted: 12/10/2023] [Indexed: 01/19/2024]
Abstract
Acute myeloid leukemia is a poor-prognosis cancer commonly stratified by genetic aberrations, but these mutations are often heterogeneous and fail to consistently predict therapeutic response. Here, we combine transcriptomic, proteomic, and phosphoproteomic datasets with ex vivo drug sensitivity data to help understand the underlying pathophysiology of AML beyond mutations. We measure the proteome and phosphoproteome of 210 patients and combine them with genomic and transcriptomic measurements to identify four proteogenomic subtypes that complement existing genetic subtypes. We build a predictor to classify samples into subtypes and map them to a "landscape" that identifies specific drug response patterns. We then build a drug response prediction model to identify drugs that target distinct subtypes and validate our findings on cell lines representing various stages of quizartinib resistance. Our results show how multiomics data together with drug sensitivity data can inform therapy stratification and drug combinations in AML.
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Affiliation(s)
- James C Pino
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Camilo Posso
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Michael Nestor
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jamie Moon
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Joshua R Hansen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chelsea Hutchinson-Bunch
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marina A Gritsenko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl K Weitz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kevin Watanabe-Smith
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Nicola Long
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Jason E McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Tao Liu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Paul D Piehowski
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Karin D Rodland
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
| | - Sara J C Gosline
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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19
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Park J, Lee SH, Shin D, Kim Y, Kim YS, Seong MY, Lee JJ, Seo HG, Cho WS, Ro YS, Kim Y, Oh BM. Multiplexed Quantitative Proteomics Reveals Proteomic Alterations in Two Rodent Traumatic Brain Injury Models. J Proteome Res 2024; 23:249-263. [PMID: 38064581 DOI: 10.1021/acs.jproteome.3c00544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
In many cases of traumatic brain injury (TBI), conspicuous abnormalities, such as scalp wounds and intracranial hemorrhages, abate over time. However, many unnoticeable symptoms, including cognitive, emotional, and behavioral dysfunction, often last from several weeks to years after trauma, even for mild injuries. Moreover, the cause of such persistence of symptoms has not been examined extensively. Recent studies have implicated the dysregulation of the molecular system in the injured brain, necessitating an in-depth analysis of the proteome and signaling pathways that mediate the consequences of TBI. Thus, in this study, the brain proteomes of two TBI models were examined by quantitative proteomics during the recovery period to determine the molecular mechanisms of TBI. Our results show that the proteomes in both TBI models undergo distinct changes. A bioinformatics analysis demonstrated robust activation and inhibition of signaling pathways and core proteins that mediate biological processes after brain injury. These findings can help determine the molecular mechanisms that underlie the persistent effects of TBI and identify novel targets for drug interventions.
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Affiliation(s)
- Junho Park
- Department of Pharmacology, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Research Institute for Basic Medical Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Seung Hak Lee
- Department of Rehabilitation Medicine, Asan Medical Center, 88 Olympic-Ro 43-Gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Dongyoon Shin
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Yeongshin Kim
- Department of Life Science, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Young Sik Kim
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Min Yong Seong
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Jin Joo Lee
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Han Gil Seo
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Won-Sang Cho
- Department of Neurosurgery, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Young Sun Ro
- Department of Emergency Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Youngsoo Kim
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Department of Life Science, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Byung-Mo Oh
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
- Institute of Aging, Seoul National University College of Medicine, 71 Ihwajang-gil, Jongno-gu, Seoul 03080, Republic of Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
- National Traffic Injury Rehabilitation Hospital, 260 Jungang-ro, Yangpyeong-gun 12564, Gyeonggi-do, Republic of Korea
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20
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Lv D, Li D, Cai Y, Guo J, Chu S, Yu J, Liu K, Jiang T, Ding N, Jin X, Li Y, Xu J. CancerProteome: a resource to functionally decipher the proteome landscape in cancer. Nucleic Acids Res 2024; 52:D1155-D1162. [PMID: 37823596 PMCID: PMC10767844 DOI: 10.1093/nar/gkad824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/07/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
Advancements in mass spectrometry (MS)-based proteomics have greatly facilitated the large-scale quantification of proteins and microproteins, thereby revealing altered signalling pathways across many different cancer types. However, specialized and comprehensive resources are lacking for cancer proteomics. Here, we describe CancerProteome (http://bio-bigdata.hrbmu.edu.cn/CancerProteome), which functionally deciphers and visualizes the proteome landscape in cancer. We manually curated and re-analyzed publicly available MS-based quantification and post-translational modification (PTM) proteomes, including 7406 samples from 21 different cancer types, and also examined protein abundances and PTM levels in 31 120 proteins and 4111 microproteins. Six major analytical modules were developed with a view to describe protein contributions to carcinogenesis using proteome analysis, including conventional analyses of quantitative and the PTM proteome, functional enrichment, protein-protein associations by integrating known interactions with co-expression signatures, drug sensitivity and clinical relevance analyses. Moreover, protein abundances, which correlated with corresponding transcript or PTM levels, were evaluated. CancerProteome is convenient as it allows users to access specific proteins/microproteins of interest using quick searches or query options to generate multiple visualization results. In summary, CancerProteome is an important resource, which functionally deciphers the cancer proteome landscape and provides a novel insight for the identification of tumor protein markers in cancer.
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Affiliation(s)
- Dezhong Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
| | - Donghao Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
| | - Yangyang Cai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
| | - Jiyu Guo
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
| | - Sen Chu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
| | - Jiaxin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
| | - Kefan Liu
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
| | - Tiantongfei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
| | - Xiyun Jin
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang Province 150000, China
| | - Yongsheng Li
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
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21
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Frank D, Patnana PK, Vorwerk J, Mao L, Gopal LM, Jung N, Hennig T, Ruhnke L, Frenz JM, Kuppusamy M, Autry R, Wei L, Sun K, Mohammed Ahmed HM, Künstner A, Busch H, Müller H, Hutter S, Hoermann G, Liu L, Xie X, Al-Matary Y, Nimmagadda SC, Cano FC, Heuser M, Thol F, Göhring G, Steinemann D, Thomale J, Leitner T, Fischer A, Rad R, Röllig C, Altmann H, Kunadt D, Berdel WE, Hüve J, Neumann F, Klingauf J, Calderon V, Opalka B, Dührsen U, Rosenbauer F, Dugas M, Varghese J, Reinhardt HC, von Bubnoff N, Möröy T, Lenz G, Batcha AMN, Giorgi M, Selvam M, Wang E, McWeeney SK, Tyner JW, Stölzel F, Mann M, Jayavelu AK, Khandanpour C. Germ line variant GFI1-36N affects DNA repair and sensitizes AML cells to DNA damage and repair therapy. Blood 2023; 142:2175-2191. [PMID: 37756525 PMCID: PMC10733838 DOI: 10.1182/blood.2022015752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 09/29/2023] Open
Abstract
ABSTRACT Growth factor independence 1 (GFI1) is a DNA-binding transcription factor and a key regulator of hematopoiesis. GFI1-36N is a germ line variant, causing a change of serine (S) to asparagine (N) at position 36. We previously reported that the GFI1-36N allele has a prevalence of 10% to 15% among patients with acute myeloid leukemia (AML) and 5% to 7% among healthy Caucasians and promotes the development of this disease. Using a multiomics approach, we show here that GFI1-36N expression is associated with increased frequencies of chromosomal aberrations, mutational burden, and mutational signatures in both murine and human AML and impedes homologous recombination (HR)-directed DNA repair in leukemic cells. GFI1-36N exhibits impaired binding to N-Myc downstream-regulated gene 1 (Ndrg1) regulatory elements, causing decreased NDRG1 levels, which leads to a reduction of O6-methylguanine-DNA-methyltransferase (MGMT) expression levels, as illustrated by both transcriptome and proteome analyses. Targeting MGMT via temozolomide, a DNA alkylating drug, and HR via olaparib, a poly-ADP ribose polymerase 1 inhibitor, caused synthetic lethality in human and murine AML samples expressing GFI1-36N, whereas the effects were insignificant in nonmalignant GFI1-36S or GFI1-36N cells. In addition, mice that received transplantation with GFI1-36N leukemic cells treated with a combination of temozolomide and olaparib had significantly longer AML-free survival than mice that received transplantation with GFI1-36S leukemic cells. This suggests that reduced MGMT expression leaves GFI1-36N leukemic cells particularly vulnerable to DNA damage initiating chemotherapeutics. Our data provide critical insights into novel options to treat patients with AML carrying the GFI1-36N variant.
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Affiliation(s)
- Daria Frank
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
| | - Pradeep Kumar Patnana
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Jan Vorwerk
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Lianghao Mao
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Lavanya Mokada Gopal
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Noelle Jung
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Thorben Hennig
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Leo Ruhnke
- Department of Internal Medicine I, University Hospital Dresden, Technical University Dresden, Dresden, Germany
| | - Joris Maximillian Frenz
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Maithreyan Kuppusamy
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Robert Autry
- Hopp Children’s Cancer Center, Heidelberg, Germany
| | - Lanying Wei
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Kaiyan Sun
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Helal Mohammed Mohammed Ahmed
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Axel Künstner
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | | | | | | | - Longlong Liu
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoqing Xie
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Yahya Al-Matary
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Subbaiah Chary Nimmagadda
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Fiorella Charles Cano
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Jürgen Thomale
- Institute of Cell Biology, University Hospital Essen, Essen, Germany
| | - Theo Leitner
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research, School of Medicine, Technische Universität München, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research, School of Medicine, Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum Rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
| | | | | | | | - Wolfgang E. Berdel
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Jana Hüve
- Fluorescence Microscopy Facility Münster, Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Felix Neumann
- Fluorescence Microscopy Facility Münster, Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
- Refined Laser Systems GmbH, Münster, Germany
| | - Jürgen Klingauf
- Fluorescence Microscopy Facility Münster, Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Virginie Calderon
- Bioinformatic Core Facility, Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
| | - Bertram Opalka
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
| | - Ulrich Dührsen
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
| | - Nikolas von Bubnoff
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Georg Lenz
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Aarif M. N. Batcha
- Institute of Medical Data Processing, Biometrics and Epidemiology, Faculty of Medicine, Ludwig Maximilians University Munich, Munich, Germany
- Data Integration for Future Medicine, Ludwig Maximilian University Munich, Munich, Germany
| | - Marianna Giorgi
- Roswell Park Comprehensive Cancer Center, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY
| | - Murugan Selvam
- Roswell Park Comprehensive Cancer Center, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY
| | - Eunice Wang
- Roswell Park Comprehensive Cancer Center, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY
| | - Shannon K. McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR
| | - Jeffrey W. Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR
| | - Friedrich Stölzel
- Department of Internal Medicine I, University Hospital Dresden, Technical University Dresden, Dresden, Germany
- Department of Medicine II, Division for Stem Cell Transplantation and Cellular Immunotherapy, University Cancer Center Schleswig-Holstein, University Hospital Schleswig-Holstein Kiel, Christian Albrecht University Kiel, Kiel, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Munich, Germany
| | - Ashok Kumar Jayavelu
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
- Hopp Children’s Cancer Center, Heidelberg, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Munich, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Cyrus Khandanpour
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
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22
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Selheim F, Aasebø E, Bruserud Ø, Hernandez-Valladares M. High Mitochondrial Protein Expression as a Potential Predictor of Relapse Risk in Acute Myeloid Leukemia Patients with the Monocytic FAB Subtypes M4 and M5. Cancers (Basel) 2023; 16:8. [PMID: 38201437 PMCID: PMC10778527 DOI: 10.3390/cancers16010008] [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: 10/24/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
AML is a highly aggressive and heterogeneous form of hematological cancer. Proteomics-based stratification of patients into more refined subgroups may contribute to a more precise characterization of the patient-derived AML cells. Here, we reanalyzed liquid chromatography-tandem mass spectrometry (LC-MS/MS) generated proteomic and phosphoproteomic data from 26 FAB-M4/M5 patients. The patients achieved complete hematological remission after induction therapy. Twelve of them later developed chemoresistant relapse (RELAPSE), and 14 patients were relapse-free (REL_FREE) long-term survivors. We considered not only the RELAPSE and REL_FREE characteristics but also integrated the French-American-British (FAB) classification, along with considering the presence of nucleophosmin 1 (NPM1) mutation and cytogenetically normal AML. We found a significant number of differentially enriched proteins (911) and phosphoproteins (257) between the various FAB subtypes in RELAPSE patients. Patients with the myeloblastic M1/M2 subtype showed higher levels of RNA processing-related routes and lower levels of signaling related to terms like translation and degranulation when compared with the M4/M5 subtype. Moreover, we found that a high abundance of proteins associated with mitochondrial translation and oxidative phosphorylation, particularly observed in the RELAPSE M4/M5 NPM1 mutated subgroup, distinguishes relapsing from non-relapsing AML patient cells with the FAB subtype M4/M5. Thus, the discovery of subtype-specific biomarkers through proteomic profiling may complement the existing classification system for AML and potentially aid in selecting personalized treatment strategies for individual patients.
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Affiliation(s)
- Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Elise Aasebø
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (Ø.B.)
| | - Øystein Bruserud
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (Ø.B.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, Institute of Biotechnology, Excellence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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23
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Isobe T, Kucinski I, Barile M, Wang X, Hannah R, Bastos HP, Chabra S, Vijayabaskar M, Sturgess KH, Williams MJ, Giotopoulos G, Marando L, Li J, Rak J, Gozdecka M, Prins D, Shepherd MS, Watcham S, Green AR, Kent DG, Vassiliou GS, Huntly BJ, Wilson NK, Göttgens B. Preleukemic single-cell landscapes reveal mutation-specific mechanisms and gene programs predictive of AML patient outcomes. CELL GENOMICS 2023; 3:100426. [PMID: 38116120 PMCID: PMC10726426 DOI: 10.1016/j.xgen.2023.100426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/13/2023] [Accepted: 09/29/2023] [Indexed: 12/21/2023]
Abstract
Acute myeloid leukemia (AML) and myeloid neoplasms develop through acquisition of somatic mutations that confer mutation-specific fitness advantages to hematopoietic stem and progenitor cells. However, our understanding of mutational effects remains limited to the resolution attainable within immunophenotypically and clinically accessible bulk cell populations. To decipher heterogeneous cellular fitness to preleukemic mutational perturbations, we performed single-cell RNA sequencing of eight different mouse models with driver mutations of myeloid malignancies, generating 269,048 single-cell profiles. Our analysis infers mutation-driven perturbations in cell abundance, cellular lineage fate, cellular metabolism, and gene expression at the continuous resolution, pinpointing cell populations with transcriptional alterations associated with differentiation bias. We further develop an 11-gene scoring system (Stem11) on the basis of preleukemic transcriptional signatures that predicts AML patient outcomes. Our results demonstrate that a single-cell-resolution deep characterization of preleukemic biology has the potential to enhance our understanding of AML heterogeneity and inform more effective risk stratification strategies.
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Affiliation(s)
- Tomoya Isobe
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Melania Barile
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Xiaonan Wang
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Rebecca Hannah
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Hugo P. Bastos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Shirom Chabra
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - M.S. Vijayabaskar
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Katherine H.M. Sturgess
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Matthew J. Williams
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Juan Li
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Justyna Rak
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Malgorzata Gozdecka
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Daniel Prins
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Mairi S. Shepherd
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Sam Watcham
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Anthony R. Green
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - David G. Kent
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Brian J.P. Huntly
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Nicola K. Wilson
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
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24
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Zhang YW, Schönberger K, Cabezas‐Wallscheid N. Bidirectional interplay between metabolism and epigenetics in hematopoietic stem cells and leukemia. EMBO J 2023; 42:e112348. [PMID: 38010205 PMCID: PMC10711668 DOI: 10.15252/embj.2022112348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 11/29/2023] Open
Abstract
During the last decades, remarkable progress has been made in further understanding the complex molecular regulatory networks that maintain hematopoietic stem cell (HSC) function. Cellular and organismal metabolisms have been shown to directly instruct epigenetic alterations, and thereby dictate stem cell fate, in the bone marrow. Epigenetic regulatory enzymes are dependent on the availability of metabolites to facilitate DNA- and histone-modifying reactions. The metabolic and epigenetic features of HSCs and their downstream progenitors can be significantly altered by environmental perturbations, dietary habits, and hematological diseases. Therefore, understanding metabolic and epigenetic mechanisms that regulate healthy HSCs can contribute to the discovery of novel metabolic therapeutic targets that specifically eliminate leukemia stem cells while sparing healthy HSCs. Here, we provide an in-depth review of the metabolic and epigenetic interplay regulating hematopoietic stem cell fate. We discuss the influence of metabolic stress stimuli, as well as alterations occurring during leukemic development. Additionally, we highlight recent therapeutic advancements toward eradicating acute myeloid leukemia cells by intervening in metabolic and epigenetic pathways.
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Affiliation(s)
- Yu Wei Zhang
- Max Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
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25
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Wang H, Lim KP, Kong W, Gao H, Wong BJH, Phua SX, Guo T, Goh WWB. MultiPro: DDA-PASEF and diaPASEF acquired cell line proteomic datasets with deliberate batch effects. Sci Data 2023; 10:858. [PMID: 38042886 PMCID: PMC10693559 DOI: 10.1038/s41597-023-02779-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/23/2023] [Indexed: 12/04/2023] Open
Abstract
Mass spectrometry-based proteomics plays a critical role in current biological and clinical research. Technical issues like data integration, missing value imputation, batch effect correction and the exploration of inter-connections amongst these technical issues, can produce errors but are not well studied. Although proteomic technologies have improved significantly in recent years, this alone cannot resolve these issues. What is needed are better algorithms and data processing knowledge. But to obtain these, we need appropriate proteomics datasets for exploration, investigation, and benchmarking. To meet this need, we developed MultiPro (Multi-purpose Proteome Resource), a resource comprising four comprehensive large-scale proteomics datasets with deliberate batch effects using the latest parallel accumulation-serial fragmentation in both Data-Dependent Acquisition (DDA) and Data Independent Acquisition (DIA) modes. Each dataset contains a balanced two-class design based on well-characterized and widely studied cell lines (A549 vs K562 or HCC1806 vs HS578T) with 48 or 36 biological and technical replicates altogether, allowing for investigation of a multitude of technical issues. These datasets allow for investigation of inter-connections between class and batch factors, or to develop approaches to compare and integrate data from DDA and DIA platforms.
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Affiliation(s)
- He Wang
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Kai Peng Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Weijia Kong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Huanhuan Gao
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, 310030, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, 310030, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310030, China
| | - Bertrand Jern Han Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Ser Xian Phua
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, 310030, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, 310030, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310030, China
| | - Wilson Wen Bin Goh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- Center for Biomedical Informatics, Nanyang Technological University, Singapore, 636921, Singapore.
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Alshamleh I, Kurrle N, Makowka P, Bhayadia R, Kumar R, Süsser S, Seibert M, Ludig D, Wolf S, Koschade SE, Stoschek K, Kreitz J, Fuhrmann DC, Toenges R, Notaro M, Comoglio F, Schuringa JJ, Berg T, Brüne B, Krause DS, Klusmann JH, Oellerich T, Schnütgen F, Schwalbe H, Serve H. PDP1 is a key metabolic gatekeeper and modulator of drug resistance in FLT3-ITD-positive acute myeloid leukemia. Leukemia 2023; 37:2367-2382. [PMID: 37935978 PMCID: PMC10681906 DOI: 10.1038/s41375-023-02041-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/18/2023] [Accepted: 09/14/2023] [Indexed: 11/09/2023]
Abstract
High metabolic flexibility is pivotal for the persistence and therapy resistance of acute myeloid leukemia (AML). In 20-30% of AML patients, activating mutations of FLT3, specifically FLT3-ITD, are key therapeutic targets. Here, we investigated the influence of FLT3-ITD on AML metabolism. Nuclear Magnetic Resonance (NMR) profiling showed enhanced reshuffling of pyruvate towards the tricarboxylic acid (TCA) cycle, suggesting an increased activity of the pyruvate dehydrogenase complex (PDC). Consistently, FLT3-ITD-positive cells expressed high levels of PDP1, an activator of the PDC. Combining endogenous tagging of PDP1 with genome-wide CRISPR screens revealed that FLT3-ITD induces PDP1 expression through the RAS signaling axis. PDP1 knockdown resulted in reduced cellular respiration thereby impairing the proliferation of only FLT3-ITD cells. These cells continued to depend on PDP1, even in hypoxic conditions, and unlike FLT3-ITD-negative cells, they exhibited a rapid, PDP1-dependent revival of their respiratory capacity during reoxygenation. Moreover, we show that PDP1 modifies the response to FLT3 inhibition. Upon incubation with the FLT3 tyrosine kinase inhibitor quizartinib (AC220), PDP1 persisted or was upregulated, resulting in a further shift of glucose/pyruvate metabolism towards the TCA cycle. Overexpression of PDP1 enhanced, while PDP1 depletion diminished AC220 resistance in cell lines and peripheral blasts from an AC220-resistant AML patient in vivo. In conclusion, FLT3-ITD assures the expression of PDP1, a pivotal metabolic regulator that enhances oxidative glucose metabolism and drug resistance. Hence, PDP1 emerges as a potentially targetable vulnerability in the management of AML.
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Affiliation(s)
- Islam Alshamleh
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany
| | - Nina Kurrle
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany
| | - Philipp Makowka
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
| | - Raj Bhayadia
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany
- Department of Pediatrics, Goethe University Frankfurt, 60590, Frankfurt, Germany
| | - Rahul Kumar
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596, Frankfurt am Main, Germany
| | - Sebastian Süsser
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
| | - Marcel Seibert
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany
| | - Damian Ludig
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Sebastian Wolf
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany
| | - Sebastian E Koschade
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
| | - Karoline Stoschek
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
| | - Johanna Kreitz
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany
| | - Dominik C Fuhrmann
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590, Frankfurt am Main, Germany
| | - Rosa Toenges
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
| | | | | | - Jan Jacob Schuringa
- Department of Experimental Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Tobias Berg
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
- Centre for Discovery in Cancer Research and Department of Oncology, McMaster University, Hamilton, ON, Canada
| | - Bernhard Brüne
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590, Frankfurt am Main, Germany
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology, 60596, Frankfurt am Main, Germany
| | - Daniela S Krause
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596, Frankfurt am Main, Germany
- Georg-Speyer-Haus; German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan-Henning Klusmann
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany
- Department of Pediatrics, Goethe University Frankfurt, 60590, Frankfurt, Germany
| | - Thomas Oellerich
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany
| | - Frank Schnütgen
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany.
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany.
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany.
| | - Hubert Serve
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, 60590, Frankfurt, Germany.
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596, Frankfurt, Germany.
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27
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Xiong G, Zhang K, Ma Y, Song Y, Zhang W, Qi T, Qiu H, Shi J, Kan C, Zhang J, Sun X. BAM15 as a mitochondrial uncoupler: a promising therapeutic agent for diverse diseases. Front Endocrinol (Lausanne) 2023; 14:1252141. [PMID: 37900126 PMCID: PMC10600450 DOI: 10.3389/fendo.2023.1252141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023] Open
Abstract
Subcellular organelles dysfunction is implicated in various diseases, including metabolic diseases, neurodegenerative diseases, cancer, and cardiovascular diseases. BAM15, a selective mitochondrial uncoupler, has emerged as a promising therapeutic agent due to its ability to enhance mitochondrial respiration and metabolic flexibility. By disrupting the coupling between electron transport and ATP synthesis, BAM15 dissipates the proton gradient, leading to increased mitochondrial respiration and energy expenditure. This review provides a comprehensive overview of BAM15, including its mechanism of action and potential therapeutic applications in diverse disease contexts. BAM15 has shown promise in obesity by increasing energy expenditure and reducing fat accumulation. In diabetes, it improves glycemic control and reverses insulin resistance. Additionally, BAM15 has potential in non-alcoholic fatty liver disease, sepsis, and cardiovascular diseases by mitigating oxidative stress, modulating inflammatory responses, and promoting cardioprotection. The safety profile of BAM15 is encouraging, with minimal adverse effects and remarkable tolerability. However, challenges such as its high lipophilicity and the need for alternative delivery methods need to be addressed. Further research is necessary to fully understand the therapeutic potential of BAM15 and optimize its application in clinical settings.
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Affiliation(s)
- Guoji Xiong
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Kexin Zhang
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Yujie Ma
- Department of Pathophysiology, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Yixin Song
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Wenqiang Zhang
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
- Department of Pathology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Tongbing Qi
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Hongyan Qiu
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Junfeng Shi
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Chengxia Kan
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jingwen Zhang
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Xiaodong Sun
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
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28
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Pourcelot E, El Samra G, Mossuz P, Moulis JM. Molecular Insight into Iron Homeostasis of Acute Myeloid Leukemia Blasts. Int J Mol Sci 2023; 24:14307. [PMID: 37762610 PMCID: PMC10531764 DOI: 10.3390/ijms241814307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Acute myeloid leukemia (AML) remains a disease of gloomy prognosis despite intense efforts to understand its molecular foundations and to find efficient treatments. In search of new characteristic features of AML blasts, we first examined experimental conditions supporting the amplification of hematological CD34+ progenitors ex vivo. Both AML blasts and healthy progenitors heavily depended on iron availability. However, even if known features, such as easier engagement in the cell cycle and amplification factor by healthy progenitors, were observed, multiplying progenitors in a fully defined medium is not readily obtained without modifying their cellular characteristics. As such, we measured selected molecular data including mRNA, proteins, and activities right after isolation. Leukemic blasts showed clear signs of metabolic and signaling shifts as already known, and we provide unprecedented data emphasizing disturbed cellular iron homeostasis in these blasts. The combined quantitative data relative to the latter pathway allowed us to stratify the studied patients in two sets with different iron status. This categorization is likely to impact the efficiency of several therapeutic strategies targeting cellular iron handling that may be applied to eradicate AML blasts.
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Affiliation(s)
- Emmanuel Pourcelot
- Laboratory of Fundamental and Applied Bioenergetics (LBFA), University Grenoble Alpes, INSERM U1055, 38000 Grenoble, France; (E.P.); (G.E.S.)
- Department of Biological Hematology, Institute of Biology and Pathology, Hospital of Grenoble Alpes (CHUGA), CS 20217, 38043 Grenoble, CEDEX a9, France;
| | - Ghina El Samra
- Laboratory of Fundamental and Applied Bioenergetics (LBFA), University Grenoble Alpes, INSERM U1055, 38000 Grenoble, France; (E.P.); (G.E.S.)
| | - Pascal Mossuz
- Department of Biological Hematology, Institute of Biology and Pathology, Hospital of Grenoble Alpes (CHUGA), CS 20217, 38043 Grenoble, CEDEX a9, France;
- Team “Epigenetic and Cellular Signaling”, Institute for Advanced Biosciences, University Grenoble Alpes (UGA), INSERM U1209/CNRS 5309, 38700 Grenoble, France
| | - Jean-Marc Moulis
- Laboratory of Fundamental and Applied Bioenergetics (LBFA), University Grenoble Alpes, INSERM U1055, 38000 Grenoble, France; (E.P.); (G.E.S.)
- University Grenoble Alpes, CEA, IRIG, 38000 Grenoble, France
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29
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Feng L, Zhang PY, Gao W, Yu J, Robson SC. Targeting chemoresistance and mitochondria-dependent metabolic reprogramming in acute myeloid leukemia. Front Oncol 2023; 13:1244280. [PMID: 37746249 PMCID: PMC10513429 DOI: 10.3389/fonc.2023.1244280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Chemoresistance often complicates the management of cancer, as noted in the instance of acute myeloid leukemia (AML). Mitochondrial function is considered important for the viability of AML blasts and appears to also modulate chemoresistance. As mitochondrial metabolism is aberrant in AML, any distinct pathways could be directly targeted to impact both cell viability and chemoresistance. Therefore, identifying and targeting those precise rogue elements of mitochondrial metabolism could be a valid therapeutic strategy in leukemia. Here, we review the evidence for abnormalities in mitochondria metabolic processes in AML cells, that likely impact chemoresistance. We further address several therapeutic approaches targeting isocitrate dehydrogenase 2 (IDH2), CD39, nicotinamide phosphoribosyl transferase (NAMPT), electron transport chain (ETC) complex in AML and also consider the roles of mesenchymal stromal cells. We propose the term "mitotherapy" to collectively refer to such regimens that attempt to override mitochondria-mediated metabolic reprogramming, as used by cancer cells. Mounting evidence suggests that mitotherapy could provide a complementary strategy to overcome chemoresistance in liquid cancers, as well as in solid tumors.
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Affiliation(s)
- Lili Feng
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Center for Inflammation Research, Department of Anesthesia, Critical Care & Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Philip Y. Zhang
- Center for Inflammation Research, Department of Anesthesia, Critical Care & Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Wenda Gao
- Antagen Institute for Biomedical Research, Canton, MA, United States
| | - Jinming Yu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Simon C. Robson
- Center for Inflammation Research, Department of Anesthesia, Critical Care & Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
- Department of Medicine, Division of Gastroenterology/Hepatology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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30
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Rulten SL, Grose RP, Gatz SA, Jones JL, Cameron AJM. The Future of Precision Oncology. Int J Mol Sci 2023; 24:12613. [PMID: 37628794 PMCID: PMC10454858 DOI: 10.3390/ijms241612613] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Our understanding of the molecular mechanisms underlying cancer development and evolution have evolved rapidly over recent years, and the variation from one patient to another is now widely recognized. Consequently, one-size-fits-all approaches to the treatment of cancer have been superseded by precision medicines that target specific disease characteristics, promising maximum clinical efficacy, minimal safety concerns, and reduced economic burden. While precision oncology has been very successful in the treatment of some tumors with specific characteristics, a large number of patients do not yet have access to precision medicines for their disease. The success of next-generation precision oncology depends on the discovery of new actionable disease characteristics, rapid, accurate, and comprehensive diagnosis of complex phenotypes within each patient, novel clinical trial designs with improved response rates, and worldwide access to novel targeted anticancer therapies for all patients. This review outlines some of the current technological trends, and highlights some of the complex multidisciplinary efforts that are underway to ensure that many more patients with cancer will be able to benefit from precision oncology in the near future.
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Affiliation(s)
| | - Richard P. Grose
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
| | - Susanne A. Gatz
- Cancer Research UK Clinical Trials Unit (CRCTU), Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - J. Louise Jones
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
| | - Angus J. M. Cameron
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
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31
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Arévalo CM, Cruz-Rodriguez N, Quijano S, Fiorentino S. Plant-derived extracts and metabolic modulation in leukemia: a promising approach to overcome treatment resistance. Front Mol Biosci 2023; 10:1229760. [PMID: 37520325 PMCID: PMC10382028 DOI: 10.3389/fmolb.2023.1229760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023] Open
Abstract
Leukemic cells acquire complex and often multifactorial mechanisms of resistance to treatment, including various metabolic alterations. Although the use of metabolic modulators has been proposed for several decades, their use in clinical practice has not been established. Natural products, the so-called botanical drugs, are capable of regulating tumor metabolism, particularly in hematopoietic tumors, which could partly explain the biological activity attributed to them for a long time. This review addresses the most recent findings relating to metabolic reprogramming-Mainly in the glycolytic pathway and mitochondrial activity-Of leukemic cells and its role in the generation of resistance to conventional treatments, the modulation of the tumor microenvironment, and the evasion of immune response. In turn, it describes how the modulation of metabolism by plant-derived extracts can counteract resistance to chemotherapy in this tumor model and contribute to the activation of the antitumor immune system.
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Affiliation(s)
- Cindy Mayerli Arévalo
- Grupo de Inmunobiología y Biología Celular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | - Sandra Quijano
- Grupo de Inmunobiología y Biología Celular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Susana Fiorentino
- Grupo de Inmunobiología y Biología Celular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
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32
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Bahrami E, Schmid JP, Jurinovic V, Becker M, Wirth AK, Ludwig R, Kreissig S, Duque Angel TV, Amend D, Hunt K, Öllinger R, Rad R, Frenz JM, Solovey M, Ziemann F, Mann M, Vick B, Wichmann C, Herold T, Jayavelu AK, Jeremias I. Combined proteomics and CRISPR‒Cas9 screens in PDX identify ADAM10 as essential for leukemia in vivo. Mol Cancer 2023; 22:107. [PMID: 37422628 PMCID: PMC10329331 DOI: 10.1186/s12943-023-01803-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 06/08/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Acute leukemias represent deadly malignancies that require better treatment. As a challenge, treatment is counteracted by a microenvironment protecting dormant leukemia stem cells. METHODS To identify responsible surface proteins, we performed deep proteome profiling on minute numbers of dormant patient-derived xenograft (PDX) leukemia stem cells isolated from mice. Candidates were functionally screened by establishing a comprehensive CRISPR‒Cas9 pipeline in PDX models in vivo. RESULTS A disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) was identified as an essential vulnerability required for the survival and growth of different types of acute leukemias in vivo, and reconstitution assays in PDX models confirmed the relevance of its sheddase activity. Of translational importance, molecular or pharmacological targeting of ADAM10 reduced PDX leukemia burden, cell homing to the murine bone marrow and stem cell frequency, and increased leukemia response to conventional chemotherapy in vivo. CONCLUSIONS These findings identify ADAM10 as an attractive therapeutic target for the future treatment of acute leukemias.
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Affiliation(s)
- Ehsan Bahrami
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Jan Philipp Schmid
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
| | - Vindi Jurinovic
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany
| | - Martin Becker
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Anna-Katharina Wirth
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Romina Ludwig
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
| | - Sophie Kreissig
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Tania Vanessa Duque Angel
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Diana Amend
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Katharina Hunt
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Rupert Öllinger
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, and Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, Technische Universität München, Munich, Germany
| | - Roland Rad
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, and Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, Technische Universität München, Munich, Germany
| | - Joris Maximilian Frenz
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
| | - Maria Solovey
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Chair of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Munich, Germany
| | - Frank Ziemann
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
| | - Christian Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Tobias Herold
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany
| | - Ashok Kumar Jayavelu
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
- Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital, LMU Munich, Munich, Germany
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Boscaro E, Urbino I, Catania FM, Arrigo G, Secreto C, Olivi M, D'Ardia S, Frairia C, Giai V, Freilone R, Ferrero D, Audisio E, Cerrano M. Modern Risk Stratification of Acute Myeloid Leukemia in 2023: Integrating Established and Emerging Prognostic Factors. Cancers (Basel) 2023; 15:3512. [PMID: 37444622 DOI: 10.3390/cancers15133512] [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: 06/06/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
An accurate estimation of AML prognosis is complex since it depends on patient-related factors, AML manifestations at diagnosis, and disease genetics. Furthermore, the depth of response, evaluated using the level of MRD, has been established as a strong prognostic factor in several AML subgroups. In recent years, this rapidly evolving field has made the prognostic evaluation of AML more challenging. Traditional prognostic factors, established in cohorts of patients treated with standard intensive chemotherapy, are becoming less accurate as new effective therapies are emerging. The widespread availability of next-generation sequencing platforms has improved our knowledge of AML biology and, consequently, the recent ELN 2022 recommendations significantly expanded the role of new gene mutations. However, the impact of rare co-mutational patterns remains to be fully disclosed, and large international consortia such as the HARMONY project will hopefully be instrumental to this aim. Moreover, accumulating evidence suggests that clonal architecture plays a significant prognostic role. The integration of clinical, cytogenetic, and molecular factors is essential, but hierarchical methods are reaching their limit. Thus, innovative approaches are being extensively explored, including those based on "knowledge banks". Indeed, more robust prognostic estimations can be obtained by matching each patient's genomic and clinical data with the ones derived from very large cohorts, but further improvements are needed.
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Affiliation(s)
- Eleonora Boscaro
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Irene Urbino
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Federica Maria Catania
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Giulia Arrigo
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Carolina Secreto
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Matteo Olivi
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Stefano D'Ardia
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Chiara Frairia
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Valentina Giai
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Roberto Freilone
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Dario Ferrero
- Division of Hematology, Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Turin, Italy
| | - Ernesta Audisio
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Marco Cerrano
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
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Tomasoni C, Pievani A, Rambaldi B, Biondi A, Serafini M. A Question of Frame: The Role of the Bone Marrow Stromal Niche in Myeloid Malignancies. Hemasphere 2023; 7:e896. [PMID: 37234820 PMCID: PMC10208717 DOI: 10.1097/hs9.0000000000000896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 04/18/2023] [Indexed: 05/28/2023] Open
Abstract
Until a few years ago, the onset of acute myeloid leukemia (AML) was entirely ascribed to genetic lesions in hematopoietic stem cells. These mutations generate leukemic stem cells, which are known to be the main ones responsible for chemoresistance and relapse. However, in the last years, increasing evidence demonstrated that dynamic interplay between leukemic cells and bone marrow (BM) niche is of paramount relevance in the pathogenesis of myeloid malignancies, including AML. Specifically, BM stromal niche components, such as mesenchymal stromal cells (MSCs) and their osteoblastic cell derivatives, play a key role not only in supporting normal hematopoiesis but also in the manifestation and progression of myeloid malignancies. Here, we reviewed recent clinical and experimental findings about how genetic and functional alterations in MSCs and osteolineage progeny can contribute to leukemogenesis and how leukemic cells in turn generate a corrupted niche able to support myeloid neoplasms. Moreover, we discussed how the newest single-cell technologies may help dissect the interactions between BM stromal cells and malignant hematopoiesis. The deep comprehension of the tangled relationship between stroma and AML blasts and their modulation during disease progression may have a valuable impact on the development of new microenvironment-directed therapeutic strategies, potentially useful for a wide cohort of patients.
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Affiliation(s)
- Chiara Tomasoni
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Alice Pievani
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Benedetta Rambaldi
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Andrea Biondi
- Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Marta Serafini
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
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Guinn BA, Schuler PJ, Schrezenmeier H, Hofmann S, Weiss J, Bulach C, Götz M, Greiner J. A Combination of the Immunotherapeutic Drug Anti-Programmed Death 1 with Lenalidomide Enhances Specific T Cell Immune Responses against Acute Myeloid Leukemia Cells. Int J Mol Sci 2023; 24:ijms24119285. [PMID: 37298237 DOI: 10.3390/ijms24119285] [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: 03/08/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Immune checkpoint inhibitors can block inhibitory molecules on the surface of T cells, switching them from an exhausted to an active state. One of these inhibitory immune checkpoints, programmed cell death protein 1 (PD-1) is expressed on T cell subpopulations in acute myeloid leukemia (AML). PD-1 expression has been shown to increase with AML progression following allo-haematopoeitic stem cell transplantation, and therapy with hypomethylating agents. We have previously shown that anti-PD-1 can enhance the response of leukemia-associated antigen (LAA)-specific T cells against AML cells as well as leukemic stem and leukemic progenitor cells (LSC/LPCs) ex vivo. In concurrence, blocking of PD-1 with antibodies such as nivolumab has been shown to enhance response rates post-chemotherapy and stem cell transplant. The immune modulating drug lenalidomide has been shown to promote anti-tumour immunity including anti-inflammatory, anti-proliferative, pro-apoptotic and anti-angiogenicity. The effects of lenalidomide are distinct from chemotherapy, hypomethylating agents or kinase inhibitors, making lenalidomide an attractive agent for use in AML and in combination with existing active agents. To determine whether anti-PD-1 (nivolumab) and lenalidomide alone or in combination could enhance LAA-specific T cell immune responses, we used colony-forming immune and ELISpot assays. Combinations of immunotherapeutic approaches are believed to increase antigen-specific immune responses against leukemic cells including LPC/LSCs. In this study we used a combination of LAA-peptides with the immune checkpoint inhibitor anti-PD-1 and lenalidomide to enhance the killing of LSC/LPCs ex vivo. Our data offer a novel insight into how we could improve AML patient responses to treatment in future clinical studies.
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Affiliation(s)
- Barbara-Ann Guinn
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
| | - Patrick J Schuler
- Department of Otorhinolaryngology, University Hospital Ulm, 89081 Ulm, Germany
| | - Hubert Schrezenmeier
- Institute of Transfusion Medicine, University of Ulm and German Red Cross, 89073 Ulm, Germany
| | - Susanne Hofmann
- Department of Internal Medicine V, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Johanna Weiss
- Department of Internal Medicine III, University Hospital Ulm, 89081 Ulm, Germany
| | - Christiane Bulach
- Department of Internal Medicine III, University Hospital Ulm, 89081 Ulm, Germany
| | - Marlies Götz
- Department of Internal Medicine III, University Hospital Ulm, 89081 Ulm, Germany
| | - Jochen Greiner
- Department of Internal Medicine III, University Hospital Ulm, 89081 Ulm, Germany
- Department of Internal Medicine, Diakonie Hospital Stuttgart, 70176 Stuttgart, Germany
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36
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Paudel BB, Tan SF, Fox TE, Ung J, Shaw J, Dunton W, Lee I, Sharma A, Viny AD, Barth BM, Tallman MS, Cabot M, Garrett-Bakelman FE, Levine RL, Kester M, Claxton D, Feith DJ, Janes KA, Loughran TP. Acute myeloid leukemia stratifies as two clinically relevant sphingolipidomic subtypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.13.536805. [PMID: 37131653 PMCID: PMC10153188 DOI: 10.1101/2023.04.13.536805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Acute myeloid leukemia (AML) is an aggressive disease with complex and heterogeneous biology. Although several genomic classifications have been proposed, there is a growing interest in going beyond genomics to stratify AML. In this study, we profile the sphingolipid family of bioactive molecules in 213 primary AML samples and 30 common human AML cell lines. Using an integrative approach, we identify two distinct sphingolipid subtypes in AML characterized by a reciprocal abundance of hexosylceramide (Hex) and sphingomyelin (SM) species. The two Hex-SM clusters organize diverse samples more robustly than known AML driver mutations and are coupled to latent transcriptional states. Using transcriptomic data, we develop a machine-learning classifier to infer the Hex-SM status of AML cases in TCGA and BeatAML clinical repositories. The analyses show that the sphingolipid subtype with deficient Hex and abundant SM is enriched for leukemic stemness transcriptional programs and comprises an unappreciated high-risk subgroup with poor clinical outcomes. Our sphingolipid-focused examination of AML identifies patients least likely to benefit from standard of care and raises the possibility that sphingolipidomic interventions could switch the subtype of AML patients who otherwise lack targetable alternatives.
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Affiliation(s)
- B. Bishal Paudel
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
| | - Su-Fern Tan
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Todd E. Fox
- Department of Pharmacology, University of Virginia, Charlottesville, VA
| | - Johnson Ung
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Microbiology, Immunology & Cancer Biology, University of Virginia, Charlottesville, VA
| | - Jeremy Shaw
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Wendy Dunton
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Irene Lee
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Arati Sharma
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA
- Penn State Cancer Institute, Hershey, PA
| | - Aaron D. Viny
- Departments of Medicine, Division of Hematology & Oncology, and of Genetics & Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
| | - Brian M. Barth
- Department of Chemistry, Biology, and Health Sciences, South Dakota School of Mines and Technology, Rapid City, SD
| | - Martin S. Tallman
- Northwestern University Feinberg School of Medicine Robert H. Lurie Comprehensive Cancer Center Chicago, IL
| | - Myles Cabot
- Department of Biochemistry & Molecular Biology, Brody School of Medicine, and the East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Francine E. Garrett-Bakelman
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Kester
- Department of Pharmacology, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - David Claxton
- Penn State Cancer Institute, Hershey, PA
- Department of Medicine, Division of Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA
| | - David J. Feith
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - Kevin A. Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - Thomas P. Loughran
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
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Messner CB, Demichev V, Wang Z, Hartl J, Kustatscher G, Mülleder M, Ralser M. Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology. Proteomics 2023; 23:e2200013. [PMID: 36349817 DOI: 10.1002/pmic.202200013] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022]
Abstract
There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a consequence, many conditions need to be considered to reach generalizable conclusions. Moreover, human population and clinical studies only reach sufficient statistical power if conducted at scale and with precise measurement methods. Finally, many proteins remain without sufficient functional annotations, because they have not been systematically studied under a broad range of conditions. In this review, we discuss the latest technical developments in mass spectrometry (MS)-based proteomics that facilitate large-scale studies by fast and efficient chromatography, fast scanning mass spectrometers, data-independent acquisition (DIA), and new software. We further highlight recent studies which demonstrate how high-throughput (HT) proteomics can be applied to capture biological diversity, to annotate gene functions or to generate predictive and prognostic models for human diseases.
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Affiliation(s)
- Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Vadim Demichev
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ziyue Wang
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes Hartl
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh, Scotland, UK
| | - Michael Mülleder
- Core Facility High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Ralser
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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38
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Casado P, Cutillas PR. Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine. Mol Cell Proteomics 2023; 22:100517. [PMID: 36805445 PMCID: PMC10152134 DOI: 10.1016/j.mcpro.2023.100517] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous cancer of the hematopoietic system with no cure for most patients. In addition to chemotherapy, treatment options for AML include recently approved therapies that target proteins with roles in AML pathobiology, such as FLT3, BLC2, and IDH1/2. However, due to disease complexity, these therapies produce very diverse responses, and survival rates are still low. Thus, despite considerable advances, there remains a need for therapies that target different aspects of leukemic biology and for associated biomarkers that define patient populations likely to respond to each available therapy. To meet this need, drugs that target different AML vulnerabilities are currently in advanced stages of clinical development. Here, we review proteomics and phosphoproteomics studies that aimed to provide insights into AML biology and clinical disease heterogeneity not attainable with genomic approaches. To place the discussion in context, we first provide an overview of genetic and clinical aspects of the disease, followed by a summary of proteins targeted by compounds that have been approved or are under clinical trials for AML treatment and, if available, the biomarkers that predict responses. We then discuss proteomics and phosphoproteomics studies that provided insights into AML pathogenesis, from which potential biomarkers and drug targets were identified, and studies that aimed to rationalize the use of synergistic drug combinations. When considered as a whole, the evidence summarized here suggests that proteomics and phosphoproteomics approaches can play a crucial role in the development and implementation of precision medicine for AML patients.
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Affiliation(s)
- Pedro Casado
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Pedro R Cutillas
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom; The Alan Turing Institute, The British Library, London, United Kingdom; Digital Environment Research Institute (DERI), Queen Mary University of London, London, United Kingdom.
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39
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Zhan D, Zheng N, Zhao B, Cheng F, Tang Q, Liu X, Wang J, Wang Y, Liua H, Li X, Su J, Zhong X, Bu Q, Cheng Y, Wang Y, Qin J. Expanding individualized therapeutic options via genoproteomics. Cancer Lett 2023; 560:216123. [PMID: 36907503 DOI: 10.1016/j.canlet.2023.216123] [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: 01/04/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/13/2023]
Abstract
Clinical next-generation sequencing (NGS)2 tests have enabled treatment recommendations for cancer patients with driver gene mutations. Targeted therapy options for patients without driver gene mutations are currently unavailable. Herein, we performed NGS and proteomics tests on 169 formalin-fixed paraffin-embedded (FFPE)3 samples of non-small cell lung cancers (NSCLC, 65),4 colorectal cancers (CRC, 61),5 thyroid carcinomas (THCA, 14),6 gastric cancers (GC, 2),7 gastrointestinal stromal tumors (GIST, 11),8 and malignant melanomas (MM, 6).9 Of the 169 samples, NGS detected 14 actionable mutated genes in 73 samples, providing treatment options for 43% of the patients. Proteomics identified 61 actionable clinical drug targets approved by the FDA or undergoing clinical trials in 122 samples, providing treatment options for 72% of the patients. In vivo experiments demonstrated that the Mitogen-Activated Protein Kinase (MEK)10 inhibitor induced the overexpression of MEK1 (Map2k1) to block lung tumor growth in mice. Therefore, protein overexpression is a potentially feasible indicator for guiding targeted therapies. Collectively, our analysis suggests that combining NGS and proteomics (genoproteomics) could expand the targeted treatment options to 85% of cancer patients.
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Affiliation(s)
- Dongdong Zhan
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China
| | - Nairen Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Beibei Zhao
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Fang Cheng
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China
| | - Qi Tang
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Xiangqian Liu
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Juanfei Wang
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Yushen Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Haibo Liua
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China
| | - Xinliang Li
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China
| | - Juming Su
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Xuejun Zhong
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Qing Bu
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Yating Cheng
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China.
| | - Yi Wang
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Jun Qin
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China; State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
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40
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Proteogenomic analysis of acute myeloid leukemia associates relapsed disease with reprogrammed energy metabolism both in adults and children. Leukemia 2023; 37:550-559. [PMID: 36572751 PMCID: PMC9991901 DOI: 10.1038/s41375-022-01796-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/27/2022]
Abstract
Despite improvement of current treatment strategies and novel targeted drugs, relapse and treatment resistance largely determine the outcome for acute myeloid leukemia (AML) patients. To identify the underlying molecular characteristics, numerous studies have been aimed to decipher the genomic- and transcriptomic landscape of AML. Nevertheless, further molecular changes allowing malignant cells to escape treatment remain to be elucidated. Mass spectrometry is a powerful tool enabling detailed insights into proteomic changes that could explain AML relapse and resistance. Here, we investigated AML samples from 47 adult and 22 pediatric patients at serial time-points during disease progression using mass spectrometry-based in-depth proteomics. We show that the proteomic profile at relapse is enriched for mitochondrial ribosomal proteins and subunits of the respiratory chain complex, indicative of reprogrammed energy metabolism from diagnosis to relapse. Further, higher levels of granzymes and lower levels of the anti-inflammatory protein CR1/CD35 suggest an inflammatory signature promoting disease progression. Finally, through a proteogenomic approach, we detected novel peptides, which present a promising repertoire in the search for biomarkers and tumor-specific druggable targets. Altogether, this study highlights the importance of proteomic studies in holistic approaches to improve treatment and survival of AML patients.
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Special Issue "Personal Therapy for Blood Disorders". J Pers Med 2023; 13:jpm13020339. [PMID: 36836573 PMCID: PMC9963067 DOI: 10.3390/jpm13020339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/18/2023] Open
Abstract
This editorial of the Special Issue "Personal Therapy for Blood disorders" aims to draw more attention to blood cancer heterogeneity and personalized strategies for diagnosis, prognosis and therapeutic treatment [...].
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Chaudhary S, Ganguly S, Palanichamy JK, Singh A, Pradhan D, Bakhshi R, Chopra A, Bakhshi S. Mitochondrial gene expression signature predicts prognosis of pediatric acute myeloid leukemia patients. Front Oncol 2023; 13:1109518. [PMID: 36845715 PMCID: PMC9947241 DOI: 10.3389/fonc.2023.1109518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/11/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction Gene expression profile of mitochondrial-related genes is not well deciphered in pediatric acute myeloid leukaemia (AML). We aimed to identify mitochondria-related differentially expressed genes (DEGs) in pediatric AML with their prognostic significance. Methods Children with de novo AML were included prospectively between July 2016-December 2019. Transcriptomic profiling was done for a subset of samples, stratified by mtDNA copy number. Top mitochondria-related DEGs were identified and validated by real-time PCR. A prognostic gene signature risk score was formulated using DEGs independently predictive of overall survival (OS) in multivariable analysis. Predictive ability of the risk score was estimated along with external validation in The Tumor Genome Atlas (TCGA) AML dataset. Results In 143 children with AML, twenty mitochondria-related DEGs were selected for validation, of which 16 were found to be significantly dysregulated. Upregulation of SDHC (p<0.001), CLIC1 (p=0.013) and downregulation of SLC25A29 (p<0.001) were independently predictive of inferior OS, and included for developing prognostic risk score. The risk score model was independently predictive of survival over and above ELN risk categorization (Harrell's c-index: 0.675). High-risk patients (risk score above median) had significantly inferior OS (p<0.001) and event free survival (p<0.001); they were associated with poor-risk cytogenetics (p=0.021), ELN intermediate/poor risk group (p=0.016), absence of RUNX1-RUNX1T1 (p=0.027), and not attaining remission (p=0.016). On external validation, the risk score also predicted OS (p=0.019) in TCGA dataset. Discussion We identified and validated mitochondria-related DEGs with prognostic impact in pediatric AML and also developed a novel 3-gene based externally validated gene signature predictive of survival.
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Affiliation(s)
- Shilpi Chaudhary
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Shuvadeep Ganguly
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | | | - Archna Singh
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Dibyabhaba Pradhan
- Computational Genomics Centre, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Radhika Bakhshi
- Shaheed Rajguru College of Applied Sciences for Women, University of Delhi, Delhi, India
| | - Anita Chopra
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Sameer Bakhshi
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India,*Correspondence: Sameer Bakhshi,
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Mitochondrial fusion is a therapeutic vulnerability of acute myeloid leukemia. Leukemia 2023; 37:765-775. [PMID: 36739349 PMCID: PMC10079528 DOI: 10.1038/s41375-023-01835-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
Mitochondrial metabolism recently emerged as a critical dependency in acute myeloid leukemia (AML). The shape of mitochondria is tightly regulated by dynamin GTPase proteins, which drive opposing fusion and fission forces to consistently adapt bioenergetics to the cellular context. Here, we showed that targeting mitochondrial fusion was a new vulnerability of AML cells, when assayed in patient-derived xenograft (PDX) models. Genetic depletion of mitofusin 2 (MFN2) or optic atrophy 1 (OPA1) or pharmacological inhibition of OPA1 (MYLS22) blocked mitochondrial fusion and had significant anti-leukemic activity, while having limited impact on normal hematopoietic cells ex vivo and in vivo. Mechanistically, inhibition of mitochondrial fusion disrupted mitochondrial respiration and reactive oxygen species production, leading to cell cycle arrest at the G0/G1 transition. These results nominate the inhibition of mitochondrial fusion as a promising therapeutic approach for AML.
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Zhang Q, Ma R, Chen H, Guo W, Li Z, Xu K, Chen W. CD86 Is Associated with Immune Infiltration and Immunotherapy Signatures in AML and Promotes Its Progression. JOURNAL OF ONCOLOGY 2023; 2023:9988405. [PMID: 37064861 PMCID: PMC10104747 DOI: 10.1155/2023/9988405] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/21/2022] [Accepted: 07/25/2022] [Indexed: 04/18/2023]
Abstract
Background Cluster of differentiation 86 (CD86), also known as B7-2, is a molecule expressed on antigen-presenting cells that provides the costimulatory signals required for T cell activation and survival. CD86 binds to two ligands on the surface of T cells: the antigen CD28 and cytotoxic T lymphocyte-associated protein 4 (CTLA-4). By binding to CD28, CD86-together with CD80-promotes the participation of T cells in the antigen presentation process. However, the interrelationships among CD86, immunotherapy, and immune infiltration in acute myeloid leukemia (AML) are unclear. Methods The immunological effects of CD86 in various cancers (including on chemokines, immunostimulators, MHC, and receptors) were evaluated through a pan-cancer analysis using TCGA and GEO databases. The relationship between CD86 expression and mononucleotide variation, gene copy number variation, methylation, immune checkpoint blockers (ICBs), and T-cell inflammation score in AML was subsequently examined. ESTIMATE and limma packages were used to identify genes at the intersection of CD86 with StromalScore and ImmuneScore. Subsequently, GO/KEGG and PPI network analyses were performed. The immune risk score (IRS) model was constructed, and the validation set was used for verification. The predictive value was compared with the TIDE score. Results CD86 was overexpressed in many cancers, and its overexpression was associated with a poor prognosis. CD86 expression was positively correlated with the expression of CTLA4, PDCD1LG2, IDO1, HAVCR2, and other genes and negatively correlated with CD86 methylation. The expression of CD86 in AML cell lines was detected by QRT-PCR and Western blot, and the results showed that CD86 was overexpressed in AML cell lines. Immune infiltration assays showed that CD86 expression was positively correlated with CD8 T cell, Dendritic cell, macrophage, NK cell, and Th1_cell and also with immune examination site, immune regulation, immunotherapy response, and TIICs. ssGSEA showed that CD86 was enriched in immune-related pathways, and CD86 expression was correlated with mutations in the genes RB1, ERBB2, and FANCC, which are associated with responses to radiotherapy and chemotherapy. The IRS score performed better than the TIDE website score. Conclusion CD86 appears to participate in immune invasion in AML and is an important player in the tumor microenvironment in this malignancy. At the same time, the IRS score developed by us has a good effect and may provide some support for the diagnosis of AML. Thus, CD86 may serve as a potential target for AML immunotherapy.
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Affiliation(s)
- Qianqian Zhang
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ruixue Ma
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Huimin Chen
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Wentong Guo
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhenyu Li
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of Bone Marrow Stem Cells, Xuzhou, Jiangsu, China
| | - Kailin Xu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of Bone Marrow Stem Cells, Xuzhou, Jiangsu, China
| | - Wei Chen
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of Bone Marrow Stem Cells, Xuzhou, Jiangsu, China
- Department of Hematology, The First People's Hospital of Suqian, Suqian, Jiangsu, China
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Creighton CJ. Clinical proteomics towards multiomics in cancer. MASS SPECTROMETRY REVIEWS 2022:e21827. [PMID: 36495097 DOI: 10.1002/mas.21827] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recent technological advancements in mass spectrometry (MS)-based proteomics technologies have accelerated its application to study greater and greater numbers of human tumor specimens. Over the last several years, the Clinical Proteomic Tumor Analysis Consortium, the International Cancer Proteogenome Consortium, and others have generated MS-based proteomic profiling data combined with corresponding multiomics data on thousands of human tumors to date. Proteomic data sets in the public domain can be re-examined by other researchers with different questions in mind from what the original studies explored. In this review, we examine the increasing role of proteomics in studying cancer, along with the potential for previous studies and their associated data sets to contribute to improving the diagnosis and treatment of cancer in the clinical setting. We also explore publicly available proteomics and multi-omics data from cancer cell line models to show how such data may aid in identifying therapeutic strategies for cancer subsets.
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Affiliation(s)
- Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
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Zhang N, Liu X, Wu J, Li X, Wang Q, Chen G, Ma L, Wu S, Zhou F. Serum proteomics screening intercellular adhesion molecule-2 improves intermediate-risk stratification in acute myeloid leukemia. Ther Adv Hematol 2022; 13:20406207221132346. [PMID: 36324489 PMCID: PMC9619266 DOI: 10.1177/20406207221132346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/12/2022] [Indexed: 11/22/2022] Open
Abstract
Background The clinical risk classification of acute myelocytic leukemia (AML) is largely based on cytogenetic and molecular genetic detection. However, the optimal treatment for intermediate-risk AML patients remains uncertain. Further refinement and improvement of prognostic stratification are therefore necessary. Objectives The aim of this study was to identify serum protein biomarkers to refine risk stratification in AML patients. Design This study is a retrospective study. Methods Label-free proteomics was used to identify the differential abundance of serum proteins in AML patients. Transcriptomic data were combined to identify key altered markers that could indicate the risk rank of AML patients. The survival status was assessed by Kaplan-Meier and multivariate Cox regression analyses. Results We delineated serum protein expression in a population of AML patients. Many biological processes were influenced by the identified differentially expressed proteins. Association analysis of transcriptome data showed that intercellular adhesion molecule-2 (ICAM2) had a higher survival prediction value in the intermediate-risk AML group. ICAM2 was detrimental for intermediate-risk AML, regardless of whether patients received bone marrow transplantation. ICAM2 well distinguishes the intermediate group of patients, whose probability of survival is comparable to that of patients with the ELN-2017 according to the reference classification. In addition, newly established stratified clinical features were associated with leukemia stem cell scores. Conclusion The inclusion of ICAM2 expression into the AML risk classification according to ELN-2017 was a good way to transfer patients from three to two groups. Thus, providing more information for clinical decision-making to improve intermediate-risk stratification in AML patients.
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Affiliation(s)
| | | | - Jinxian Wu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinqi Li
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qian Wang
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guopeng Chen
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Linlu Ma
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Sanyun Wu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
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Xie X, Yang W, Zhang W, Qiu Y, Qiu Z, Wang H, Hu Y, Li Y, Zhou X, Li L, Chen Z, Zhao C, Lu Y, Zhang K, Lai E, Bai X. Tegaserod maleate exhibits antileukemic activity by targeting TRPM8. Biomed Pharmacother 2022; 154:113566. [PMID: 35994820 DOI: 10.1016/j.biopha.2022.113566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 12/20/2022] Open
Abstract
To identify therapeutic targets in acute myeloid leukemia (AML), we conducted growth inhibition screens of 2040 small molecules from a library of FDA-approved drugs using a panel of 12 AML cell lines. Tegaserod maleate, a 5-hydroxytryptamine 4 receptor partial agonist, elicits strong anti-AML effects in vitro and in vivo by targeting transient receptor potential melastatin subtype 8 (TRPM8), which plays critical roles in several important processes. However, the role of TRPM8 remains incompletely described in AML, whose treatment is based mostly on antimitotic chemotherapy. Here, we report an unexpected role of TRPM8 in leukemogenesis. Strikingly, TRPM8 knockout inhibits AML cell survival/proliferation by promoting apoptosis. Mechanistically, TRPM8 exerts its oncogenic effect by regulating the ERK-CREB/c-Fos signaling axis. Hyperactivation of ERK signaling can be reversed by TRPM8 inhibition. Importantly, TRPM8 is overexpressed in AML patients, indicating that it is a new prognostic factor in AML. Collectively, our work demonstrates the anti-AML effects of tegaserod maleate via targeting TRPM8 and indicates that TRPM8 is a regulator of leukemogenesis with therapeutic potential in AML.
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Affiliation(s)
- Xiaoling Xie
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China; Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Wanwen Yang
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wuju Zhang
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yingqi Qiu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Zeyou Qiu
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hao Wang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Yuxing Hu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Yuhua Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; Department of Basic Research & International Cooperation, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Xuan Zhou
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Luyao Li
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhuanzhuan Chen
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Chenbo Zhao
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Yao Lu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Keqin Zhang
- Department of Oncology, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou 510999, China.
| | - Eryong Lai
- Department of Oncology, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou 510999, China.
| | - Xiaochun Bai
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
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Targeting Ca2+ and Mitochondrial Homeostasis by Antipsychotic Thioridazine in Leukemia Cells. Life (Basel) 2022; 12:life12101477. [PMID: 36294912 PMCID: PMC9605445 DOI: 10.3390/life12101477] [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: 08/19/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Mitochondria have pivotal roles in cellular physiology including energy metabolism, reactive oxygen species production, Ca2+ homeostasis, and apoptosis. Altered mitochondrial morphology and function is a common feature of cancer cells and the regulation of mitochondrial homeostasis has been identified as a key to the response to chemotherapeutic agents in human leukemias. Here, we explore the mechanistic aspects of cytotoxicity produced by thioridazine (TR), an antipsychotic drug that has been investigated for its anticancer potential in human leukemia cellular models. TR exerts selective cytotoxicity against human leukemia cells in vitro. A PCR array provided a general view of the expression of genes involved in cell death pathways. TR immediately produced a pulse of cytosolic Ca2+, followed by mitochondrial uptake, resulting in mitochondrial permeabilization, caspase 9/3 activation, endoplasmic reticulum stress, and apoptosis. Ca2+ chelators, thiol reducer dithiothreitol, or CHOP knockdown prevented TR-induced cell death. TR also exhibited potent cytotoxicity against BCL-2/BCL-xL-overexpressing leukemia cells. Additionally, previous studies have shown that TR exhibits potent antitumor activity in vivo in different solid tumor models. These findings show that TR induces a Ca2+-mediated apoptosis with involvement of mitochondrial permeabilization and ER stress in leukemia and it emphasizes the pharmacological potential of TR as an adjuvant in antitumor chemotherapy.
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Vergez F, Largeaud L, Bertoli S, Nicolau ML, Rieu JB, Vergnolle I, Saland E, Sarry A, Tavitian S, Huguet F, Picard M, Vial JP, Lechevalier N, Bidet A, Dumas PY, Pigneux A, Luquet I, Mansat-De Mas V, Delabesse E, Carroll M, Danet-Desnoyers G, Sarry JE, Récher C. Phenotypically-defined stages of leukemia arrest predict main driver mutations subgroups, and outcome in acute myeloid leukemia. Blood Cancer J 2022; 12:117. [PMID: 35973983 PMCID: PMC9381519 DOI: 10.1038/s41408-022-00712-7] [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: 02/22/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Classifications of acute myeloid leukemia (AML) patients rely on morphologic, cytogenetic, and molecular features. Here we have established a novel flow cytometry-based immunophenotypic stratification showing that AML blasts are blocked at specific stages of differentiation where features of normal myelopoiesis are preserved. Six stages of leukemia differentiation-arrest categories based on CD34, CD117, CD13, CD33, MPO, and HLA-DR expression were identified in two independent cohorts of 2087 and 1209 AML patients. Hematopoietic stem cell/multipotent progenitor-like AMLs display low proliferation rate, inv(3) or RUNX1 mutations, and high leukemic stem cell frequency as well as poor outcome, whereas granulocyte-monocyte progenitor-like AMLs have CEBPA mutations, RUNX1-RUNX1T1 or CBFB-MYH11 translocations, lower leukemic stem cell frequency, higher chemosensitivity, and better outcome. NPM1 mutations correlate with most mature stages of leukemia arrest together with TET2 or IDH mutations in granulocyte progenitors-like AML or with DNMT3A mutations in monocyte progenitors-like AML. Overall, we demonstrate that AML is arrested at specific stages of myeloid differentiation (SLA classification) that significantly correlate with AML genetic lesions, clinical presentation, stem cell properties, chemosensitivity, response to therapy, and outcome.
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Affiliation(s)
- François Vergez
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France. .,Université Toulouse III Paul Sabatier, Toulouse, France. .,Cancer Research Center of Toulouse, UMR1037 INSERM, ERL5294 CNRS, Toulouse, France. .,Stem Cell and Xenograft Core, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
| | - Laetitia Largeaud
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Cancer Research Center of Toulouse, UMR1037 INSERM, ERL5294 CNRS, Toulouse, France
| | - Sarah Bertoli
- Cancer Research Center of Toulouse, UMR1037 INSERM, ERL5294 CNRS, Toulouse, France.,Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Marie-Laure Nicolau
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Jean-Baptiste Rieu
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Inès Vergnolle
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Estelle Saland
- Cancer Research Center of Toulouse, UMR1037 INSERM, ERL5294 CNRS, Toulouse, France
| | - Audrey Sarry
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Suzanne Tavitian
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Françoise Huguet
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Muriel Picard
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Jean-Philippe Vial
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Bordeaux, Pessac, France
| | - Nicolas Lechevalier
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Bordeaux, Pessac, France
| | - Audrey Bidet
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Bordeaux, Pessac, France
| | - Pierre-Yves Dumas
- Service d'Hématologie Clinique et de Thérapie Cellulaire, Centre Hospitalier Universitaire de Bordeaux, Pessac, France
| | - Arnaud Pigneux
- Service d'Hématologie Clinique et de Thérapie Cellulaire, Centre Hospitalier Universitaire de Bordeaux, Pessac, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Véronique Mansat-De Mas
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Eric Delabesse
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Martin Carroll
- Stem Cell and Xenograft Core, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Gwenn Danet-Desnoyers
- Stem Cell and Xenograft Core, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Jean-Emmanuel Sarry
- Cancer Research Center of Toulouse, UMR1037 INSERM, ERL5294 CNRS, Toulouse, France.,Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - Christian Récher
- Université Toulouse III Paul Sabatier, Toulouse, France. .,Cancer Research Center of Toulouse, UMR1037 INSERM, ERL5294 CNRS, Toulouse, France. .,Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France.
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Joshi SK, Tognon CE, Druker BJ, Rodland KD. Oncoproteomic profiling of AML: moving beyond genomics. Expert Rev Proteomics 2022; 19:283-287. [PMID: 36734985 PMCID: PMC10505090 DOI: 10.1080/14789450.2023.2176757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023]
Affiliation(s)
- Sunil K. Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Cristina E. Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Karin D. Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
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