1
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Tran D, Beeler JS, Liu J, Wiley B, Chan IC, Xin Z, Kramer MH, Batchi-Bouyou AL, Zong X, Walter MJ, Petrone GE, Chlamydas S, Ferraro F, Oh ST, Link DC, Busby B, Cao Y, Bolton KL. Plasma Proteomic Signature Predicts Myeloid Neoplasm Risk. Clin Cancer Res 2024; 30:3220-3228. [PMID: 38446993 PMCID: PMC11292192 DOI: 10.1158/1078-0432.ccr-23-3468] [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: 11/07/2023] [Revised: 01/10/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
PURPOSE Clonal hematopoiesis (CH) is thought to be the origin of myeloid neoplasms (MN). Yet, our understanding of the mechanisms driving CH progression to MN and clinical risk prediction of MN remains limited. The human proteome reflects complex interactions between genetic and epigenetic regulation of biological systems. We hypothesized that the plasma proteome might predict MN risk and inform our understanding of the mechanisms promoting MN development. EXPERIMENTAL DESIGN We jointly characterized CH and plasma proteomic profiles of 46,237 individuals in the UK Biobank at baseline study entry. During 500,036 person-years of follow-up, 115 individuals developed MN. Cox proportional hazard regression was used to test for an association between plasma protein levels and MN risk. RESULTS We identified 115 proteins associated with MN risk, of which 30% (N = 34) were also associated with CH. These were enriched for known regulators of the innate and adaptive immune system. Plasma proteomics improved the prediction of MN risk (AUC = 0.85; P = 5×10-9) beyond clinical factors and CH (AUC = 0.80). In an independent group (N = 381,485), we used inherited polygenic risk scores (PRS) for plasma protein levels to validate the relevance of these proteins toMNdevelopment. PRS analyses suggest that most MN-associated proteins we identified are not directly causally linked toMN risk, but rather represent downstream markers of pathways regulating the progression of CH to MN. CONCLUSIONS These data highlight the role of immune cell regulation in the progression of CH to MN and the promise of leveraging multi-omic characterization of CH to improveMN risk stratification. See related commentary by Bhalgat and Taylor, p. 3095.
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Affiliation(s)
- Duc Tran
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - J. Scott Beeler
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Jie Liu
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Brian Wiley
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Irenaeus C.C. Chan
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Zilan Xin
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Michael H. Kramer
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Armel L. Batchi-Bouyou
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Xiaoyu Zong
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.
| | - Matthew J. Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Giulia E.M. Petrone
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | | | - Francesca Ferraro
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Stephen T. Oh
- Division of Hematology, Department of Medicine, WUSM, St. Louis, Missouri.
| | - Daniel C. Link
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Ben Busby
- DNAnexus, Mountain View, California.
| | - Yin Cao
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.
| | - Kelly L. Bolton
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
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2
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Narayanan N, Marvin-Peek J, Abouelnaaj MK, Majid D, Wang B, Brown BD, Qiu Y, Kornblau SM, Abbas HA. Reverse Phase Proteomic Array Profiling of Asparagine Synthetase Expression in Newly Diagnosed Acute Myeloid Leukemia. J Proteome Res 2024; 23:2495-2504. [PMID: 38829961 PMCID: PMC11226376 DOI: 10.1021/acs.jproteome.4c00130] [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: 06/05/2024]
Abstract
Asparaginase-based therapy is a cornerstone in acute lymphoblastic leukemia (ALL) treatment, capitalizing on the methylation status of the asparagine synthetase (ASNS) gene, which renders ALL cells reliant on extracellular asparagine. Contrastingly, ASNS expression in acute myeloid leukemia (AML) has not been thoroughly investigated, despite studies suggesting that AML with chromosome 7/7q deletions might have reduced ASNS levels. Here, we leverage reverse phase protein arrays to measure ASNS expression in 810 AML patients and assess its impact on outcomes. We find that AML with inv(16) has the lowest overall ASNS expression. While AML with deletion 7/7q had ASNS levels slightly lower than those of AML without deletion 7/7q, this observation was not significant. Low ASNS expression correlated with improved overall survival (46 versus 54 weeks, respectively, p = 0.011), whereas higher ASNS levels were associated with better response to venetoclax-based therapy. Protein correlation analysis demonstrated association between ASNS and proteins involved in methylation and DNA repair. In conclusion, while ASNS expression was not lower in patients with deletion 7/7q as initially predicted, ASNS levels were highly variable across AML patients. Further studies are needed to assess whether patients with low ASNS expression are susceptible to asparaginase-based therapy due to their inability to augment compensatory ASNS expression upon asparagine depletion.
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Affiliation(s)
- Nisha Narayanan
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA, 77030
- The University of Texas MD Anderson Graduate School of Biomedical Sciences, Houston, TX, USA, 77030
| | - Jennifer Marvin-Peek
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mohamad K Abouelnaaj
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA, 77030
- University of Texas Health Science Center at Houston, McGovern Medical School, Houston TX, USA, 77030
| | - Dhabya Majid
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA, 77030
| | - Bofei Wang
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA, 77030
| | - Brandon D. Brown
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, TX, USA, 77030
| | - Yihua Qiu
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA, 77030
| | - Steven M. Kornblau
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA, 77030
| | - Hussein A Abbas
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA, 77030
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA, 77030
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3
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de Camargo Magalhães ES, Hubner SE, Brown BD, Qiu Y, Kornblau SM. Proteomics for optimizing therapy in acute myeloid leukemia: venetoclax plus hypomethylating agents versus conventional chemotherapy. Leukemia 2024; 38:1046-1056. [PMID: 38531950 DOI: 10.1038/s41375-024-02208-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024]
Abstract
The use of Hypomethylating agents combined with Venetoclax (VH) for the treatment of Acute Myeloid Leukemia (AML) has greatly improved outcomes in recent years. However not all patients benefit from the VH regimen and a way to rationally select between VH and Conventional Chemotherapy (CC) for individual AML patients is needed. Here, we developed a proteomic-based triaging strategy using Reverse-phase Protein Arrays (RPPA) to optimize therapy selection. We evaluated the expression of 411 proteins in 810 newly diagnosed adult AML patients, identifying 109 prognostic proteins, that divided into five patient expression profiles, which are useful for optimizing therapy selection. Furthermore, using machine learning algorithms, we determined a set of 14 proteins, among those 109, that were able to accurately recommend therapy, making it feasible for clinical application. Next, we identified a group of patients who did not benefit from either VH or CC and proposed target-based approaches to improve outcomes. Finally, we calculated that the clinical use of our proteomic strategy would have led to a change in therapy for 30% of patients, resulting in a 43% improvement in OS, resulting in around 2600 more cures from AML per year in the United States.
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Affiliation(s)
| | - Stefan Edward Hubner
- John Sealy School of Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Brandon Douglas Brown
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030-4009, USA
| | - Yihua Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030-4009, USA
| | - Steven Mitchell Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030-4009, USA.
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4
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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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5
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Hubner SE, de Camargo Magalhães ES, Hoff FW, Brown BD, Qiu Y, Horton TM, Kornblau SM. DNA Damage Response-Related Proteins Are Prognostic for Outcome in Both Adult and Pediatric Acute Myelogenous Leukemia Patients: Samples from Adults and from Children Enrolled in a Children's Oncology Group Study. Int J Mol Sci 2023; 24:5898. [PMID: 36982970 PMCID: PMC10058043 DOI: 10.3390/ijms24065898] [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: 02/08/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The survival of malignant leukemic cells is dependent on DNA damage repair (DDR) signaling. Reverse Phase Protein Array (RPPA) data sets were assembled using diagnostic samples from 810 adult and 500 pediatric acute myelogenous leukemia (AML) patients and were probed with 412 and 296 strictly validated antibodies, respectively, including those detecting the expression of proteins directly involved in DDR. Unbiased hierarchical clustering identified strong recurrent DDR protein expression patterns in both adult and pediatric AML. Globally, DDR expression was associated with gene mutational statuses and was prognostic for outcomes including overall survival (OS), relapse rate, and remission duration (RD). In adult patients, seven DDR proteins were individually prognostic for either RD or OS. When DDR proteins were analyzed together with DDR-related proteins operating in diverse cellular signaling pathways, these expanded groupings were also highly prognostic for OS. Analysis of patients treated with either conventional chemotherapy or venetoclax combined with a hypomethylating agent revealed protein clusters that differentially predicted favorable from unfavorable prognoses within each therapy cohort. Collectively, this investigation provides insight into variable DDR pathway activation in AML and may help direct future individualized DDR-targeted therapies in AML patients.
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Affiliation(s)
- Stefan E. Hubner
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Fieke W. Hoff
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brandon D. Brown
- Division of Pediatrics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Yihua Qiu
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Terzah M. Horton
- Department of Pediatrics, Dan Duncan Cancer Center, Texas Children’s Hospital, Houston, TX 77584, USA
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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6
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Aitken MJL, Malaney P, Zhang X, Herbrich SM, Chan L, Benitez O, Rodriguez A, Ma H, Jacamo R, Duan R, Link T, Kornblau S, Kanagal-Shamanna R, Bueso-Ramos C, Post S. Heterogeneous nuclear ribonucleoprotein K is overexpressed in acute myeloid leukemia and causes myeloproliferation in mice via altered Runx1 splicing. NAR Cancer 2022; 4:zcac039. [PMID: 36518526 PMCID: PMC9732523 DOI: 10.1093/narcan/zcac039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/07/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Acute myeloid leukemia (AML) is driven by numerous molecular events that contribute to disease progression. Herein, we identify hnRNP K overexpression as a recurrent abnormality in AML that negatively correlates with patient survival. Overexpression of hnRNP K in murine fetal liver cells results in altered self-renewal and differentiation potential. Further, murine transplantation models reveal that hnRNP K overexpression results in myeloproliferation in vivo. Mechanistic studies expose a direct functional relationship between hnRNP K and RUNX1-a master transcriptional regulator of hematopoiesis often dysregulated in leukemia. Molecular analyses show that overexpression of hnRNP K results in an enrichment of an alternatively spliced isoform of RUNX1 lacking exon 4. Our work establishes hnRNP K's oncogenic potential in influencing myelogenesis through its regulation of RUNX1 splicing and subsequent transcriptional activity.
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Affiliation(s)
- Marisa J L Aitken
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Prerna Malaney
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Xiaorui Zhang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shelley M Herbrich
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren Chan
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Oscar Benitez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashley G Rodriguez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huaxian Ma
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rodrigo Jacamo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruizhi Duan
- School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - Todd M Link
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carlos E Bueso-Ramos
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sean M Post
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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7
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Proteomic and phosphoproteomic landscapes of acute myeloid leukemia. Blood 2022; 140:1533-1548. [PMID: 35895896 PMCID: PMC9523374 DOI: 10.1182/blood.2022016033] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/14/2022] [Indexed: 01/21/2023] Open
Abstract
We have developed a deep-scale proteome and phosphoproteome database from 44 representative acute myeloid leukemia (AML) patients from the LAML TCGA dataset and 6 healthy bone marrow-derived controls. After confirming data quality, we orthogonally validated several previously undescribed features of AML revealed by the proteomic data. We identified examples of posttranscriptionally regulated proteins both globally (ie, in all AML samples) and also in patients with recurrent AML driver mutations. For example, samples with IDH1/2 mutations displayed elevated levels of the 2-oxoglutarate-dependent histone demethylases KDM4A/B/C, despite no changes in messenger RNA levels for these genes; we confirmed this finding in vitro. In samples with NPMc mutations, we identified several nuclear importins with posttranscriptionally increased protein abundance and showed that they interact with NPMc but not wild-type NPM1. We identified 2 cell surface proteins (CD180 and MRC1/CD206) expressed on AML blasts of many patients (but not healthy CD34+ stem/progenitor cells) that could represent novel targets for immunologic therapies and confirmed these targets via flow cytometry. Finally, we detected nearly 30 000 phosphosites in these samples; globally, AML samples were associated with the abnormal phosphorylation of specific residues in PTPN11, STAT3, AKT1, and PRKCD. FLT3-TKD samples were associated with increased phosphorylation of activating tyrosines on the cytoplasmic Src-family tyrosine kinases FGR and HCK and related signaling proteins. PML-RARA-initiated AML samples displayed a unique phosphorylation signature, and TP53-mutant samples showed abundant phosphorylation of serine-183 on TP53 itself. This publicly available database will serve as a foundation for further investigations of protein dysregulation in AML pathogenesis.
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8
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Li B, Liu H, He Y, Zhao M, Ge C, Younis MR, Huang P, Chen X, Lin J. A "Self-Checking" pH/Viscosity-Activatable NIR-II Molecule for Real-Time Evaluation of Photothermal Therapy Efficacy. Angew Chem Int Ed Engl 2022; 61:e202200025. [PMID: 35170174 DOI: 10.1002/anie.202200025] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Indexed: 02/06/2023]
Abstract
We present a second near-infrared (NIR-II) self-checking molecule, LET-1052, for acidic tumor microenvironment (TME) turn-on photothermal therapy (PTT), followed by viscosity based therapeutic efficacy evaluation by itself in two independent channels, denoted as "self-checking" strategy. In acidic TME, LET-1052 was protonated and turned on NIR-II absorption for PTT under 1064 nm laser irradiation. Subsequently, PTT-induced cellular death increases intracellular viscosity, which inhibited the intramolecular rotation of LET-1052, resulting in the enhancement of NIR-I fluorescence for real-time evaluation of PTT efficacy. After PTT of tumor-bearing mice for different periods of NIR-II laser irradiation, NIR-I fluorescence in the tumor region showed positive correlation with tumor growth inhibition rate, demonstrating reliable and prompt prediction of PTT efficacy. The strategy may be expanded for instant evaluation of other therapeutic modalities for personalized medicine.
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Affiliation(s)
- Benhao Li
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, China.,Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore.,Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.,Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Hengke Liu
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Yaling He
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Mengyao Zhao
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore.,Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.,Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Chen Ge
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Muhammad Rizwan Younis
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Peng Huang
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore.,Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.,Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jing Lin
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, China
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9
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Proteomic profiling based classification of CLL provides prognostication for modern therapy and identifies novel therapeutic targets. Blood Cancer J 2022; 12:43. [PMID: 35301276 PMCID: PMC8931092 DOI: 10.1038/s41408-022-00623-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/06/2022] [Accepted: 01/14/2022] [Indexed: 01/04/2023] Open
Abstract
Protein expression for 384 total and post-translationally modified proteins was assessed in 871 CLL and MSBL patients and was integrated with clinical data to identify strategies for improving diagnostics and therapy, making this the largest CLL proteomics study to date. Proteomics identified six recurrent signatures that were highly prognostic of survival and time to first or second treatment at three levels: individual proteins, when grouped into 40 functionally related groups (PFGs), and systemically in signatures (SGs). A novel SG characterized by hairy cell leukemia like proteomics but poor therapy response was discovered. SG membership superseded other prognostic factors (Rai Staging, IGHV Status) and were prognostic for response to modern (BTK inhibition) and older CLL therapies. SGs and PFGs membership provided novel drug targets and defined optimal candidates for Watch and Wait vs. early intervention. Collectively proteomics demonstrates promise for improving classification, therapeutic strategy selection, and identifying novel therapeutic targets.
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10
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van Dijk AD, Hoff FW, Qiu Y, Gerbing RB, Gamis AS, Aplenc R, Kolb EA, Alonzo TA, Meshinchi S, Jenkins G, de Bont ESJM, Kornblau SM, Horton TM. Bortezomib is significantly beneficial for de novo pediatric AML patients with low phosphorylation of the NF-κB subunit RelA. Proteomics Clin Appl 2022; 16:e2100072. [PMID: 34719869 PMCID: PMC9041833 DOI: 10.1002/prca.202100072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/30/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022]
Abstract
PURPOSE The addition of the proteasome inhibitor (PI) bortezomib to standard chemotherapy (ADE: cytarabine [Ara-C], daunorubicin, and etoposide) did not improve overall outcome of pediatric AML patients in the Children's Oncology Group AAML1031 phase 3 randomized clinical trial (AAML1031) . Bortezomib prevents protein degradation, including RelA via the intracellular NF-kB pathway. In this study, we hypothesized that subgroups of pediatric AML patients benefitting from standard therapy plus bortezomib (ADEB) could be identified based on pre-treatment RelA expression and phosphorylation status. EXPERIMENTAL DESIGN RelA-total and phosphorylation at serine 536 (RelA-pSer536 ) were measured in 483 patient samples using reverse phase protein array technology. RESULTS In ADEB-treated patients, low-RelA-pSer536 was favorably prognostic when compared to high-RelA-pSer536 (3-yr overall survival (OS): 81% vs. 68%, p = 0.032; relapse risk (RR): 30% vs. 49%, p = 0.004). Among low-RelA-pSer536 patients, RR significantly decreased with ADEB compared to ADE (RR: 30% vs. 44%, p = 0.035). Correlation between RelA-pSer536 and 295 other assayed proteins identified a strong correlation with HSF1-pSer326 , another protein previously identified as modifying ADEB response. The combination of low-RelA-pSer536 and low-HSF1-pSer326 was a significant predictor of ADEB response (3-yr OS: 86% vs. 67%, p = 0.013). CONCLUSION AND CLINICAL RELEVANCE Bortezomib may improve clinical outcome in a subgroup of AML patients identified by low-RelA-pSer536 and low-HSF1-pSer326 .
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Affiliation(s)
- Anneke D. van Dijk
- Divison of Pediatric Oncology/Hematology, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Fieke W. Hoff
- Divison of Pediatric Oncology/Hematology, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands,Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yihua Qiu
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | | | - Alan S. Gamis
- Department of Hematology-Oncology, Children’s Mercy Hospitals and Clinics, Kansas City, MO
| | - Richard Aplenc
- Division of Pediatric Oncology/Stem Cell Transplant, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - E. Anders Kolb
- Nemours Center for Cancer and Blood Disorders, Alfred I. DuPont Hospital for Children, Wilmington, DE
| | - Todd A. Alonzo
- Keck School of Medicine, University of Southern California, CA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Gaye Jenkins
- Department of Pediatrics, Baylor College of Medicine/Dan L. Duncan Cancer Center and Texas Children’s Cancer Center, Houston, Texas
| | - Eveline S. J. M. de Bont
- Divison of Pediatric Oncology/Hematology, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Terzah M. Horton
- Department of Pediatrics, Baylor College of Medicine/Dan L. Duncan Cancer Center and Texas Children’s Cancer Center, Houston, Texas
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11
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Li B, Liu H, He Y, Zhao M, Ge C, Younis MR, Huang P, Chen X, Lin J. A “Self‐Checking” pH/Viscosity‐Activatable NIR‐II Molecule for Real‐Time Evaluation of Photothermal Therapy Efficacy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Benhao Li
- Marshall Laboratory of Biomedical Engineering International Cancer Center Laboratory of Evolutionary Theranostics (LET) School of Biomedical Engineering Shenzhen University Health Science Center Shenzhen 518060 China
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering Yong Loo Lin School of Medicine and Faculty of Engineering National University of Singapore Singapore 119074 Singapore
- Clinical Imaging Research Centre Centre for Translational Medicine Yong Loo Lin School of Medicine National University of Singapore Singapore 117599 Singapore
- Nanomedicine Translational Research Program NUS Center for Nanomedicine Yong Loo Lin School of Medicine National University of Singapore Singapore 117597 Singapore
| | - Hengke Liu
- Marshall Laboratory of Biomedical Engineering International Cancer Center Laboratory of Evolutionary Theranostics (LET) School of Biomedical Engineering Shenzhen University Health Science Center Shenzhen 518060 China
| | - Yaling He
- Marshall Laboratory of Biomedical Engineering International Cancer Center Laboratory of Evolutionary Theranostics (LET) School of Biomedical Engineering Shenzhen University Health Science Center Shenzhen 518060 China
| | - Mengyao Zhao
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering Yong Loo Lin School of Medicine and Faculty of Engineering National University of Singapore Singapore 119074 Singapore
- Clinical Imaging Research Centre Centre for Translational Medicine Yong Loo Lin School of Medicine National University of Singapore Singapore 117599 Singapore
- Nanomedicine Translational Research Program NUS Center for Nanomedicine Yong Loo Lin School of Medicine National University of Singapore Singapore 117597 Singapore
| | - Chen Ge
- Marshall Laboratory of Biomedical Engineering International Cancer Center Laboratory of Evolutionary Theranostics (LET) School of Biomedical Engineering Shenzhen University Health Science Center Shenzhen 518060 China
| | - Muhammad Rizwan Younis
- Marshall Laboratory of Biomedical Engineering International Cancer Center Laboratory of Evolutionary Theranostics (LET) School of Biomedical Engineering Shenzhen University Health Science Center Shenzhen 518060 China
| | - Peng Huang
- Marshall Laboratory of Biomedical Engineering International Cancer Center Laboratory of Evolutionary Theranostics (LET) School of Biomedical Engineering Shenzhen University Health Science Center Shenzhen 518060 China
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering Yong Loo Lin School of Medicine and Faculty of Engineering National University of Singapore Singapore 119074 Singapore
- Clinical Imaging Research Centre Centre for Translational Medicine Yong Loo Lin School of Medicine National University of Singapore Singapore 117599 Singapore
- Nanomedicine Translational Research Program NUS Center for Nanomedicine Yong Loo Lin School of Medicine National University of Singapore Singapore 117597 Singapore
| | - Jing Lin
- Marshall Laboratory of Biomedical Engineering International Cancer Center Laboratory of Evolutionary Theranostics (LET) School of Biomedical Engineering Shenzhen University Health Science Center Shenzhen 518060 China
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12
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Hoff FW, Horton TM, Kornblau SM. Reverse phase protein arrays in acute leukemia: investigative and methodological challenges. Expert Rev Proteomics 2021; 18:1087-1097. [PMID: 34965151 PMCID: PMC9148717 DOI: 10.1080/14789450.2021.2020655] [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: 09/15/2021] [Accepted: 12/16/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Acute leukemia results from a series of mutational events that alter cell growth and proliferation. Mutations result in protein changes that orchestrate growth alterations characteristic of leukemia. Proteomics is a methodology appropriate for study of protein changes found in leukemia. The high-throughput reverse phase protein array (RPPA) technology is particularly well-suited for the assessment of protein changes in samples derived from clinical trials. AREAS COVERED This review discusses the technical, methodological, and analytical issues related to the successful development of acute leukemia RPPAs. EXPERT COMMENTARY To obtain representative protein sample lysates, samples should be prepared from freshly collected blood or bone marrow material. Variables such as sample shipment, transit time, and holding temperature only have minimal effects on protein expression. CellSave preservation tubes are preferred for cells collected after exposure to chemotherapy, and incorporation of standardized guidelines for antibody validation is recommended. A more systematic biological approach to analyze protein expression is desired, searching for recurrent patterns of protein expression that allow classification of patients into risk groups, or groups of patients that may be treated similarly. Comparing RPPA protein analysis between cell lines and primary samples shows that cell lines are not representative of patient proteomic patterns.
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Affiliation(s)
- Fieke W. Hoff
- Department of Internal Medicine, UT Southwestern Medical Center, TX, USA
| | - Terzah M. Horton
- Department of Pediatrics, Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
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13
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Guzman NA, Guzman DE. Immunoaffinity Capillary Electrophoresis in the Era of Proteoforms, Liquid Biopsy and Preventive Medicine: A Potential Impact in the Diagnosis and Monitoring of Disease Progression. Biomolecules 2021; 11:1443. [PMID: 34680076 PMCID: PMC8533156 DOI: 10.3390/biom11101443] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 01/08/2023] Open
Abstract
Over the years, multiple biomarkers have been used to aid in disease screening, diagnosis, prognosis, and response to therapy. As of late, protein biomarkers are gaining strength in their role for early disease diagnosis and prognosis in part due to the advancements in identification and characterization of a distinct functional pool of proteins known as proteoforms. Proteoforms are defined as all of the different molecular forms of a protein derived from a single gene caused by genetic variations, alternative spliced RNA transcripts and post-translational modifications. Monitoring the structural changes of each proteoform of a particular protein is essential to elucidate the complex molecular mechanisms that guide the course of disease. Clinical proteomics therefore holds the potential to offer further insight into disease pathology, progression, and prevention. Nevertheless, more technologically advanced diagnostic methods are needed to improve the reliability and clinical applicability of proteomics in preventive medicine. In this manuscript, we review the use of immunoaffinity capillary electrophoresis (IACE) as an emerging powerful diagnostic tool to isolate, separate, detect and characterize proteoform biomarkers obtained from liquid biopsy. IACE is an affinity capture-separation technology capable of isolating, concentrating and analyzing a wide range of biomarkers present in biological fluids. Isolation and concentration of target analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. IACE has the potential to generate rapid results with significant accuracy, leading to reliability and reproducibility in diagnosing and monitoring disease. Additionally, IACE has the capability of monitoring the efficacy of therapeutic agents by quantifying companion and complementary protein biomarkers. With advancements in telemedicine and artificial intelligence, the implementation of proteoform biomarker detection and analysis may significantly improve our capacity to identify medical conditions early and intervene in ways that improve health outcomes for individuals and populations.
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Affiliation(s)
| | - Daniel E. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08543, USA;
- Division of Hospital Medicine, Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
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14
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Abbas HA, Mohanty V, Wang R, Huang Y, Liang S, Wang F, Zhang J, Qiu Y, Hu CW, Qutub AA, Dail M, Bolen CR, Daver N, Konopleva M, Futreal A, Chen K, Wang L, Kornblau SM. Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated With Outcomes. Front Oncol 2021; 11:705627. [PMID: 34422660 PMCID: PMC8372368 DOI: 10.3389/fonc.2021.705627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease with variable responses to therapy. Cytogenetic and genomic features are used to classify AML patients into prognostic and treatment groups. However, these molecular characteristics harbor significant patient-to-patient variability and do not fully account for AML heterogeneity. RNA-based classifications have also been applied in AML as an alternative approach, but transcriptomic grouping is strongly associated with AML morphologic lineages. We used a training cohort of newly diagnosed AML patients and conducted unsupervised RNA-based classification after excluding lineage-associated genes. We identified three AML patient groups that have distinct biological pathways associated with outcomes. Enrichment of inflammatory pathways and downregulation of HOX pathways were associated with improved outcomes, and this was validated in 2 independent cohorts. We also identified a group of AML patients who harbored high metabolic and mTOR pathway activity, and this was associated with worse clinical outcomes. Using a comprehensive reverse phase protein array, we identified higher mTOR protein expression in the highly metabolic group. We also identified a positive correlation between degree of resistance to venetoclax and mTOR activation in myeloid and lymphoid cell lines. Our approach of integrating RNA, protein, and genomic data uncovered lineage-independent AML patient groups that share biologic mechanisms and can inform outcomes independent of commonly used clinical and demographic variables; these groups could be used to guide therapeutic strategies.
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Affiliation(s)
- Hussein A Abbas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yuefan Huang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Biostatistics & Data Science, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Computer Science, Rice University, Houston, TX, United States
| | - Feng Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yihua Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Chenyue W Hu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Amina A Qutub
- Department of Bioengineering, Rice University, Houston, TX, United States
| | - Monique Dail
- Oncology Biomarker Development, Genentech Inc, South San Francisco, CA, United States
| | - Christopher R Bolen
- Oncology Bioinformatics, Genentech Inc, South San Francisco, CA, United States
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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15
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Docking TR, Parker JDK, Jädersten M, Duns G, Chang L, Jiang J, Pilsworth JA, Swanson LA, Chan SK, Chiu R, Nip KM, Mar S, Mo A, Wang X, Martinez-Høyer S, Stubbins RJ, Mungall KL, Mungall AJ, Moore RA, Jones SJM, Birol İ, Marra MA, Hogge D, Karsan A. A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia. Nat Commun 2021; 12:2474. [PMID: 33931648 PMCID: PMC8087683 DOI: 10.1038/s41467-021-22625-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/17/2021] [Indexed: 02/08/2023] Open
Abstract
As more clinically-relevant genomic features of myeloid malignancies are revealed, it has become clear that targeted clinical genetic testing is inadequate for risk stratification. Here, we develop and validate a clinical transcriptome-based assay for stratification of acute myeloid leukemia (AML). Comparison of ribonucleic acid sequencing (RNA-Seq) to whole genome and exome sequencing reveals that a standalone RNA-Seq assay offers the greatest diagnostic return, enabling identification of expressed gene fusions, single nucleotide and short insertion/deletion variants, and whole-transcriptome expression information. Expression data from 154 AML patients are used to develop a novel AML prognostic score, which is strongly associated with patient outcomes across 620 patients from three independent cohorts, and 42 patients from a prospective cohort. When combined with molecular risk guidelines, the risk score allows for the re-stratification of 22.1 to 25.3% of AML patients from three independent cohorts into correct risk groups. Within the adverse-risk subgroup, we identify a subset of patients characterized by dysregulated integrin signaling and RUNX1 or TP53 mutation. We show that these patients may benefit from therapy with inhibitors of focal adhesion kinase, encoded by PTK2, demonstrating additional utility of transcriptome-based testing for therapy selection in myeloid malignancy.
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Affiliation(s)
- T Roderick Docking
- Experimental Medicine Program, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jeremy D K Parker
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Martin Jädersten
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Gerben Duns
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Linda Chang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jihong Jiang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jessica A Pilsworth
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Lucas A Swanson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Simon K Chan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Samantha Mar
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Angela Mo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Xuan Wang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Ryan J Stubbins
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - İnanç Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Donna Hogge
- Leukemia Bone Marrow Transplant Program of BC, Vancouver General Hospital, Vancouver, BC, Canada
| | - Aly Karsan
- Experimental Medicine Program, Department of Medicine, University of British Columbia, Vancouver, BC, Canada. .,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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16
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Shi C, Zhou Z, Lin H, Gao J. Imaging Beyond Seeing: Early Prognosis of Cancer Treatment. SMALL METHODS 2021; 5:e2001025. [PMID: 34927817 DOI: 10.1002/smtd.202001025] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/24/2020] [Indexed: 06/14/2023]
Abstract
Assessing cancer response to therapeutic interventions has been realized as an important course to early predict curative efficacy and treatment outcomes due to tumor heterogeneity. Compared to the traditional invasive tissue biopsy method, molecular imaging techniques have fundamentally revolutionized the ability to evaluate cancer response in a spatiotemporal manner. The past few years has witnessed a paradigm shift on the efforts from manufacturing functional molecular imaging probes for seeing a tumor to a vantage stage of interpreting the tumor response during different treatments. This review is to stand by the current development of advanced imaging technologies aiming to predict the treatment response in cancer therapy. Special interest is placed on the systems that are able to provide rapid and noninvasive assessment of pharmacokinetic drug fates (e.g., drug distribution, release, and activation) and tumor microenvironment heterogeneity (e.g., tumor cells, macrophages, dendritic cells (DCs), T cells, and inflammatory cells). The current status, practical significance, and future challenges of the emerging artificial intelligence (AI) technology and machine learning in the applications of medical imaging fields is overviewed. Ultimately, the authors hope that this review is timely to spur research interest in molecular imaging and precision medicine.
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Affiliation(s)
- Changrong Shi
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics and Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Zijian Zhou
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics and Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Hongyu Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The Key Laboratory for Chemical Biology of Fujian Province and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jinhao Gao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The Key Laboratory for Chemical Biology of Fujian Province and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
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17
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Hoff FW, van Dijk AD, Qiu Y, Ruvolo PP, Gerbing RB, Leonti AR, Jenkins GN, Gamis AS, Aplenc R, Kolb EA, Alonzo TA, Meshinchi S, de Bont ESJM, Bruggeman SWM, Kornblau SM, Horton TM. Heat shock factor 1 (HSF1-pSer326) predicts response to bortezomib-containing chemotherapy in pediatric AML: a COG report. Blood 2021; 137:1050-1060. [PMID: 32959058 PMCID: PMC7907722 DOI: 10.1182/blood.2020005208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/25/2020] [Indexed: 11/20/2022] Open
Abstract
Bortezomib (BTZ) was recently evaluated in a randomized phase 3 clinical trial by the Children's Oncology Group (COG) that compared standard chemotherapy (cytarabine, daunorubicin, and etoposide [ADE]) vs standard therapy with BTZ (ADEB) for de novo pediatric acute myeloid leukemia (AML). Although the study concluded that BTZ did not improve outcome overall, we examined patient subgroups benefiting from BTZ-containing chemotherapy using proteomic analyses. The proteasome inhibitor BTZ disrupts protein homeostasis and activates cytoprotective heat shock responses. Total heat shock factor 1 (HSF1) and phosphorylated HSF1 (HSF1-pSer326) were measured in leukemic cells from 483 pediatric patients using reverse phase protein arrays. HSF1-pSer326 phosphorylation was significantly lower in pediatric AML compared with CD34+ nonmalignant cells. We identified a strong correlation between HSF1-pSer326 expression and BTZ sensitivity. BTZ significantly improved outcome of patients with low-HSF1-pSer326 with a 5-year event-free survival of 44% (ADE) vs 67% for low-HSF1-pSer326 treated with ADEB (P = .019). To determine the effect of HSF1 expression on BTZ potency in vitro, cell viability with HSF1 gene variants that mimicked phosphorylated (S326A) and nonphosphorylated (S326E) HSF1-pSer326 were examined. Those with increased HSF1 phosphorylation showed clear resistance to BTZ vs those with wild-type or reduced HSF1-phosphorylation. We hypothesize that HSF1-pSer326 expression could identify patients who benefit from BTZ-containing chemotherapy.
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Affiliation(s)
- Fieke W Hoff
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke D van Dijk
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Peter P Ruvolo
- Department of Leukemia and
- Section of Molecular Hematology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Amanda R Leonti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Gaye N Jenkins
- Department of Pediatrics, Baylor College of Medicine/Dan L. Duncan Cancer Center and Texas Children's Cancer and Hematology Centers, Houston, TX
| | - Alan S Gamis
- Department of Hematology-Oncology, Children's Mercy Hospitals and Clinics, Kansas City, MO
| | - Richard Aplenc
- Division of Pediatric Oncology/Stem Cell Transplant, Children's Hospital of Philadelphia, Philadelphia, PA
| | - E Anders Kolb
- Nemours/Alfred I. duPont Hospital for Children, Atlanta, GA
| | - Todd A Alonzo
- COG Statistics and Data Center, Monrovia, CA
- Keck School of Medicine, University of Southern California, Los Angeles, CA; and
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Eveline S J M de Bont
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Sophia W M Bruggeman
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Terzah M Horton
- Department of Pediatrics, Baylor College of Medicine/Dan L. Duncan Cancer Center and Texas Children's Cancer and Hematology Centers, Houston, TX
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18
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van Dijk AD, Hoff FW, Qiu YH, Chandra J, Jabbour E, de Bont ESJM, Horton TM, Kornblau SM. Loss of H3K27 methylation identifies poor outcomes in adult-onset acute leukemia. Clin Epigenetics 2021; 13:21. [PMID: 33509276 PMCID: PMC7841917 DOI: 10.1186/s13148-021-01011-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/11/2021] [Indexed: 12/23/2022] Open
Abstract
Background Acute leukemia is an epigenetically heterogeneous disease. The intensity of treatment is currently guided by cytogenetic and molecular genetic risk classifications; however these incompletely predict outcomes, requiring additional information for more accurate outcome predictions. We aimed to identify potential prognostic implications of epigenetic modification of histone proteins, with a focus on H3K4 and H3K27 methylation marks in relation to mutations in chromatin, splicing and transcriptional regulators in adult-onset acute lymphoblastic and myeloid leukemia. Results Histone 3 lysine 4 di- and trimethylation (H3K4me2, H3K4me3) and lysine 27 trimethylation (H3K27me3) mark expression was evaluated in 241 acute myeloid leukemia (AML), 114 B-cell acute lymphoblastic leukemia (B-ALL) and 14T-cell ALL (T-ALL) patient samples at time of diagnosis using reverse phase protein array. Expression levels of the marks were significantly lower in AML than in B and T-ALL in both bone marrow and peripheral blood, as well as compared to normal CD34+ cells. In AML, greater loss of H3K27me3 was associated with increased proliferative potential and shorter overall survival in the whole patient population, as well as in subsets with DNA methylation mutations. To study the prognostic impact of H3K27me3 in the context of cytogenetic aberrations and mutations, multivariate analysis was performed and identified lower H3K27me3 level as an independent unfavorable prognostic factor in all, as well as in TP53 mutated patients. AML with decreased H3K27me3 demonstrated an upregulated anti-apoptotic phenotype. In ALL, the relative quantity of histone methylation expression correlated with response to tyrosine kinase inhibitor in patients who carried the Philadelphia cytogenetic aberration and prior smoking behavior. Conclusion This study shows that proteomic profiling of epigenetic modifications has clinical implications in acute leukemia and supports the idea that epigenetic patterns contribute to a more accurate picture of the leukemic state that complements cytogenetic and molecular genetic subgrouping. A combination of these variables may offer more accurate outcome prediction and we suggest that histone methylation mark measurement at time of diagnosis might be a suitable method to improve patient outcome prediction and subsequent treatment intensity stratification in selected subgroups.
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Affiliation(s)
- A D van Dijk
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, Groningen, The Netherlands.
| | - F W Hoff
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, Groningen, The Netherlands
| | - Y H Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Chandra
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - E Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - E S J M de Bont
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, Groningen, The Netherlands
| | - T M Horton
- Department of Pediatrics, Division of Hematology/Oncology, Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX, USA
| | - S M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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19
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Chae HD, Dutta R, Tiu B, Hoff FW, Accordi B, Serafin V, Youn M, Huang M, Sumarsono N, Davis KL, Lacayo NJ, Pigazzi M, Horton TM, Kornblau SM, Sakamoto KM. RSK inhibitor BI-D1870 inhibits acute myeloid leukemia cell proliferation by targeting mitotic exit. Oncotarget 2020; 11:2387-2403. [PMID: 32637030 PMCID: PMC7321696 DOI: 10.18632/oncotarget.27630] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/20/2020] [Indexed: 01/04/2023] Open
Abstract
The 90 kDa Ribosomal S6 Kinase (RSK) drives cell proliferation and survival in cancers, although its oncogenic mechanism has not been well characterized. Phosphorylated level of RSK (T573) was increased in acute myeloid leukemia (AML) patients and associated with poor survival. To examine the role of RSK in AML, we analyzed apoptosis and the cell cycle profile following treatment with BI-D1870, a potent inhibitor of RSK. BI-D1870 treatment increased the G2/M population and induced apoptosis in AML cell lines and patient AML cells. Characterization of mitotic phases showed that the metaphase/anaphase transition was significantly inhibited by BI-D1870. BI-D1870 treatment impeded the association of activator CDC20 with APC/C, but increased binding of inhibitor MAD2 to CDC20, preventing mitotic exit. Moreover, the inactivation of spindle assembly checkpoint or MAD2 knockdown released cells from BI-D1870-induced metaphase arrest. Therefore, we investigated whether BI-D1870 potentiates the anti-leukemic activity of vincristine by targeting mitotic exit. Combination treatment of BI-D1870 and vincristine synergistically increased mitotic arrest and apoptosis in acute leukemia cells. These data show that BI-D1870 induces apoptosis of AML cells alone and in combination with vincristine through blocking mitotic exit, providing a novel approach to overcoming vincristine resistance in AML cells.
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Affiliation(s)
- Hee-Don Chae
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ritika Dutta
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Bruce Tiu
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Fieke W Hoff
- Department of Pediatric Oncology/Hematology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Benedetta Accordi
- Department of Women's and Children's Health, Onco-Hematology Clinic, University of Padova, Padova, Italy
| | - Valentina Serafin
- Department of Women's and Children's Health, Onco-Hematology Clinic, University of Padova, Padova, Italy
| | - Minyoung Youn
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Min Huang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathan Sumarsono
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kara L Davis
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Norman J Lacayo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Martina Pigazzi
- Department of Women's and Children's Health, Onco-Hematology Clinic, University of Padova, Padova, Italy
| | - Terzah M Horton
- Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathleen M Sakamoto
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
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20
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Zhou Z, Deng H, Yang W, Wang Z, Lin L, Munasinghe J, Jacobson O, Liu Y, Tang L, Ni Q, Kang F, Liu Y, Niu G, Bai R, Qian C, Song J, Chen X. Early stratification of radiotherapy response by activatable inflammation magnetic resonance imaging. Nat Commun 2020; 11:3032. [PMID: 32541769 PMCID: PMC7295999 DOI: 10.1038/s41467-020-16771-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
Tumor heterogeneity is one major reason for unpredictable therapeutic outcomes, while stratifying therapeutic responses at an early time may greatly benefit the better control of cancer. Here, we developed a hybrid nanovesicle to stratify radiotherapy response by activatable inflammation magnetic resonance imaging (aiMRI) approach. The high Pearson's correlation coefficient R values are obtained from the correlations between the T1 relaxation time changes at 24-48 h and the ensuing adaptive immunity (R = 0.9831) at day 5 and the tumor inhibition ratios (R = 0.9308) at day 18 after different treatments, respectively. These results underscore the role of acute inflammatory oxidative response in bridging the innate and adaptive immunity in tumor radiotherapy. Furthermore, the aiMRI approach provides a non-invasive imaging strategy for early prediction of the therapeutic outcomes in cancer radiotherapy, which may contribute to the future of precision medicine in terms of prognostic stratification and therapeutic planning.
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Affiliation(s)
- Zijian Zhou
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hongzhang Deng
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, 350116, Fujian, China
| | - Weijing Yang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zhantong Wang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lisen Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, 350116, Fujian, China
| | - Jeeva Munasinghe
- Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Orit Jacobson
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yijing Liu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Longguang Tang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Qianqian Ni
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Fei Kang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yuan Liu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gang Niu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ruiliang Bai
- Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Zhejiang University, Hangzhou, 310029, China
| | - Chunqi Qian
- Department of Radiology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jibin Song
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, 350116, Fujian, China.
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA.
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21
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Aasebø E, Berven FS, Bartaula-Brevik S, Stokowy T, Hovland R, Vaudel M, Døskeland SO, McCormack E, Batth TS, Olsen JV, Bruserud Ø, Selheim F, Hernandez-Valladares M. Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia. Cancers (Basel) 2020; 12:cancers12030709. [PMID: 32192169 PMCID: PMC7140113 DOI: 10.3390/cancers12030709] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/05/2020] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly two-thirds relapse within a short interval. Understanding biological factors that determine relapse has become of major clinical interest in AML. We utilized liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify the protein changes and protein phosphorylation events associated with AML relapse in primary cells from 41 AML patients at time of diagnosis. Patients were defined as relapse-free if they had not relapsed within a five-year clinical follow-up after AML diagnosis. Relapse was associated with increased expression of RNA processing proteins and decreased expression of V-ATPase proteins. We also observed an increase in phosphorylation events catalyzed by cyclin-dependent kinases (CDKs) and casein kinase 2 (CSK2). The biological relevance of the proteome findings was supported by cell proliferation assays using inhibitors of V-ATPase (bafilomycin), CSK2 (CX-4945), CDK4/6 (abemaciclib) and CDK2/7/9 (SNS-032). While bafilomycin preferentially inhibited the cells from relapse patients, the kinase inhibitors were less efficient in these cells. This suggests that therapy against the upregulated kinases could also target the factors inducing their upregulation rather than their activity. This study, therefore, presents markers that could help predict AML relapse and direct therapeutic strategies.
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Affiliation(s)
- Elise Aasebø
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
| | - Frode S. Berven
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Sushma Bartaula-Brevik
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
| | - Randi Hovland
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway
| | - Marc Vaudel
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | | | - Emmet McCormack
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
| | - Tanveer S. Batth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Maria Hernandez-Valladares
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- Correspondence: ; Tel.: +47-5558-6368
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22
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Alanazi B, Munje CR, Rastogi N, Williamson AJK, Taylor S, Hole PS, Hodges M, Doyle M, Baker S, Gilkes AF, Knapper S, Pierce A, Whetton AD, Darley RL, Tonks A. Integrated nuclear proteomics and transcriptomics identifies S100A4 as a therapeutic target in acute myeloid leukemia. Leukemia 2020; 34:427-440. [PMID: 31611628 PMCID: PMC6995695 DOI: 10.1038/s41375-019-0596-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/18/2019] [Accepted: 09/30/2019] [Indexed: 12/20/2022]
Abstract
Inappropriate localization of proteins can interfere with normal cellular function and drive tumor development. To understand how this contributes to the development of acute myeloid leukemia (AML), we compared the nuclear proteome and transcriptome of AML blasts with normal human CD34+ cells. Analysis of the proteome identified networks and processes that significantly affected transcription regulation including misexpression of 11 transcription factors with seven proteins not previously implicated in AML. Transcriptome analysis identified changes in 40 transcription factors but none of these were predictive of changes at the protein level. The highest differentially expressed protein in AML nuclei compared with normal CD34+ nuclei (not previously implicated in AML) was S100A4. In an extended cohort, we found that over-expression of nuclear S100A4 was highly prevalent in AML (83%; 20/24 AML patients). Knock down of S100A4 in AML cell lines strongly impacted their survival whilst normal hemopoietic stem progenitor cells were unaffected. These data are the first analysis of the nuclear proteome in AML and have identified changes in transcription factor expression or regulation of transcription that would not have been seen at the mRNA level. These data also suggest that S100A4 is essential for AML survival and could be a therapeutic target in AML.
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Affiliation(s)
- Bader Alanazi
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Chinmay R Munje
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Paul O'Gorman Leukaemia Research Centre, University of Glasgow, Glasgow, G12 0ZD, UK
| | - Namrata Rastogi
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Andrew J K Williamson
- Stoller Biomarker Discovery Centre, The University of Manchester, Manchester, M20 3LJ, UK
| | - Samuel Taylor
- Stoller Biomarker Discovery Centre, The University of Manchester, Manchester, M20 3LJ, UK
| | - Paul S Hole
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Marie Hodges
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Michelle Doyle
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Sarah Baker
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Amanda F Gilkes
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Steven Knapper
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Andrew Pierce
- Stoller Biomarker Discovery Centre, The University of Manchester, Manchester, M20 3LJ, UK
| | - Anthony D Whetton
- Stoller Biomarker Discovery Centre, The University of Manchester, Manchester, M20 3LJ, UK
| | - Richard L Darley
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Alex Tonks
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK.
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23
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van Dijk AD, de Bont ESJM, Kornblau SM. Targeted therapy in acute myeloid leukemia: current status and new insights from a proteomic perspective. Expert Rev Proteomics 2020; 17:1-10. [PMID: 31945303 DOI: 10.1080/14789450.2020.1717951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: The biological heterogeneity of acute myeloid leukemia (AML) complicates personalized medicine. Individual prognosis is typically based on the presence of chromosomal and genetic lesions. Nevertheless, these classifications often lack a priori information about response to therapy. Since the protein expression landscape reflects the functional activity state of cells, we hypothesize that analyzing this can be used for the identification of protein activity markers to provide better risk stratification as well as may provide targeted therapeutic guidance in AML.Areas covered: Herein, we review recently new adopted drugs in the treatment for AML and discuss how quantitative proteomic techniques may contribute to better therapeutic selection in AML.Expert commentary: The net functional state of the cell is defined by the activity of protein within all the pathways that are active in the cell. Recognition of the proteomic profile of the leukemic blast could, therefore, complement current classification systems by providing a better a priori description of what pathways are important within a cell as a guide to the selection of therapy for the patient.
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Affiliation(s)
- Anneke D van Dijk
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, University Medical Center Groningen, Groningen, the Netherlands
| | - Eveline S J M de Bont
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, University Medical Center Groningen, Groningen, the Netherlands
| | - Steven M Kornblau
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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24
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Prognostic hallmarks in AML. Nat Biomed Eng 2019; 3:847-849. [PMID: 31705121 DOI: 10.1038/s41551-019-0474-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Ruvolo PP, Hu CW, Qiu Y, Ruvolo VR, Go RL, Hubner SE, Coombes KR, Andreeff M, Qutub AA, Kornblau SM. LGALS3 is connected to CD74 in a previously unknown protein network that is associated with poor survival in patients with AML. EBioMedicine 2019; 44:126-137. [PMID: 31105032 PMCID: PMC6604360 DOI: 10.1016/j.ebiom.2019.05.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 02/06/2023] Open
Abstract
Background Galectin 3 (LGALS3) gene expression is associated with poor survival in acute myeloid leukemia (AML) but the prognostic impact of LGALS3 protein expression in AML is unknown. LGALS3 supports diverse survival pathways including RAS mediated cascades, protein expression and stability of anti-apoptotic BCL2 family members, and activation of proliferative pathways including those mediated by beta Catenin. CD74 is a positive regulator of CD44 and CXCR4 signaling and this molecule may be critical for AML stem cell function. At present, the role of LGALS3 and CD74 in AML is unclear. In this study, we examine protein expression of LGALS3 and CD74 by reverse phase protein analysis (RPPA) and identify new protein networks associated with these molecules. In addition, we determine prognostic potential of LGALS3, CD74, and their protein networks for clinical correlates in AML patients. Methods RPPA was used to determine relative expression of LGALS3, CD74, and 229 other proteins in 231 fresh AML patient samples and 205 samples were from patients who were treated and evaluable for outcome. Pearson correlation analysis was performed to identify proteins associated with LGALS3 and CD74. Progeny clustering was performed to generate protein networks. String analysis was performed to determine protein:protein interactions in networks and to perform gene ontology analysis. Kaplan-Meir method was used to generate survival curves. Findings LGALS3 is highest in monocytic AML patients and those with elevated LGALS3 had significantly shorter remission duration compared to patients with lower LGALS3 levels (median 21.9 vs 51.3 weeks, p = 0.016). Pearson correlation of LGALS3 with 230 other proteins identifies a distinct set of 37 proteins positively correlated with LGALS3 expression levels with a high representation of proteins involved in AKT and ERK signaling pathways. Thirty-one proteins were negatively correlated with LGALS3 including an AKT phosphatase. Pearson correlation of proteins associated with CD74 identified 12 proteins negatively correlated with CD74 and 16 proteins that are positively correlated with CD74. CD74 network revealed strong association with CD44 signaling and a high representation of apoptosis regulators. Progeny clustering was used to build protein networks based on LGALS3 and CD74 associated proteins. A strong relationship of the LGALS3 network with the CD74 network was identified. For AML patients with both the LGALS3 and CD74 protein cluster active, median overall survival was only 24.3 weeks, median remission duration was 17.8 weeks, and no patient survived beyond one year. Interpretation The findings from this study identify for the first time protein networks associated with LGALS3 and CD74 in AML. Each network features unique pathway characteristics. The data also suggest that the LGALS3 network and the CD74 network each support AML cell survival and the two networks may cooperate in a novel high risk AML population. Fund Leukemia Lymphoma Society provided funds to SMK for RPPA study of AML patient population. Texas Leukemia provided funds to PPR and SMK to study CD74 and LGALS3 expression in AML patients using RPPA. No payment was involved in the production of this manuscript.
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Affiliation(s)
- Peter P Ruvolo
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Division of Molecular Hematology and Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Chenyue W Hu
- Department of Biomechanical Engineering, University Texas San Antonio, San Antonio, TX, USA
| | - Yihua Qiu
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Division of Molecular Hematology and Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivian R Ruvolo
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Division of Molecular Hematology and Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robin L Go
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Division of Molecular Hematology and Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stefan E Hubner
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Division of Molecular Hematology and Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kevin R Coombes
- Departments of Biomedical Informatics, The Ohio State University, USA
| | - Michael Andreeff
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Division of Molecular Hematology and Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amina A Qutub
- Department of Biomechanical Engineering, University Texas San Antonio, San Antonio, TX, USA
| | - Steven M Kornblau
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Division of Molecular Hematology and Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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26
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Hu CW, Qiu Y, Ligeralde A, Raybon AY, Yoo SY, Coombes KR, Qutub AA, Kornblau SM. A quantitative analysis of heterogeneities and hallmarks in acute myelogenous leukaemia. Nat Biomed Eng 2019; 3:889-901. [PMID: 30988472 PMCID: PMC7051028 DOI: 10.1038/s41551-019-0387-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 03/08/2019] [Indexed: 01/18/2023]
Abstract
Acute myelogenous leukaemia (AML) is associated with risk factors that are largely unknown and with a heterogeneous response to treatment. Here, we provide a comprehensive quantitative understanding of AML proteomic heterogeneities and hallmarks by using the AML proteome atlas, a proteomics database that we have newly derived from MetaGalaxy analyses, for the proteomic profiling of 205 AML patients and 111 leukaemia cell lines. The analysis of the dataset revealed 154 functional patterns based on common molecular pathways, 11 constellations of correlated functional patterns, and 13 signatures that stratify the patients’ outcomes. We find limited overlap between proteomics data and both cytogenetics and genetic mutations, and also that leukaemia cell lines show limited proteomic similarities with cells from AML patients, suggesting that a deeper focus on patient-derived samples is needed to gain disease-relevant insights. The AML proteome atlas provides a knowledge base for proteomic patterns in AML, a guide to leukaemia cell-line selection, and a broadly applicable computational approach for quantifying the heterogeneities of protein expression and proteomic hallmarks in AML.
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Affiliation(s)
- C W Hu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Y Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - A Ligeralde
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - A Y Raybon
- Department of Biomedical Engineering, The University of Texas at San Antonio, San Antonio, TX, USA
| | - S Y Yoo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - K R Coombes
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - A A Qutub
- Department of Bioengineering, Rice University, Houston, TX, USA. .,Department of Biomedical Engineering, The University of Texas at San Antonio, San Antonio, TX, USA.
| | - S M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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