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Zhang Z, Huang J, Zhang Z, Shen H, Tang X, Wu D, Bao X, Xu G, Chen S. Application of omics in the diagnosis, prognosis, and treatment of acute myeloid leukemia. Biomark Res 2024; 12:60. [PMID: 38858750 PMCID: PMC11165883 DOI: 10.1186/s40364-024-00600-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024] Open
Abstract
Acute myeloid leukemia (AML) is the most frequent leukemia in adults with a high mortality rate. Current diagnostic criteria and selections of therapeutic strategies are generally based on gene mutations and cytogenetic abnormalities. Chemotherapy, targeted therapies, and hematopoietic stem cell transplantation (HSCT) are the major therapeutic strategies for AML. Two dilemmas in the clinical management of AML are related to its poor prognosis. One is the inaccurate risk stratification at diagnosis, leading to incorrect treatment selections. The other is the frequent resistance to chemotherapy and/or targeted therapies. Genomic features have been the focus of AML studies. However, the DNA-level aberrations do not always predict the expression levels of genes and proteins and the latter is more closely linked to disease phenotypes. With the development of high-throughput sequencing and mass spectrometry technologies, studying downstream effectors including RNA, proteins, and metabolites becomes possible. Transcriptomics can reveal gene expression and regulatory networks, proteomics can discover protein expression and signaling pathways intimately associated with the disease, and metabolomics can reflect precise changes in metabolites during disease progression. Moreover, omics profiling at the single-cell level enables studying cellular components and hierarchies of the AML microenvironment. The abundance of data from different omics layers enables the better risk stratification of AML by identifying prognosis-related biomarkers, and has the prospective application in identifying drug targets, therefore potentially discovering solutions to the two dilemmas. In this review, we summarize the existing AML studies using omics methods, both separately and combined, covering research fields of disease diagnosis, risk stratification, prognosis prediction, chemotherapy, as well as targeted therapy. Finally, we discuss the directions and challenges in the application of multi-omics in precision medicine of AML. Our review may inspire both omics researchers and clinical physicians to study AML from a different angle.
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Affiliation(s)
- Zhiyu Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, Jiangsu, China
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Jiayi Huang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhibo Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hongjie Shen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaowen Tang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiebing Bao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, Jiangsu, China.
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China.
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China.
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
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Zheng X, Wang C, Chen F, Li S, Zhang H, Dong G, Yang S, Kang X, Kang Z, Han C, Yin S, Li W. Zanubrutinib delays selinexor resistance evolution in biopsy sample-derived primary central nervous system lymphoma models. iScience 2024; 27:109799. [PMID: 38726367 PMCID: PMC11079464 DOI: 10.1016/j.isci.2024.109799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/18/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Primary central nervous system lymphoma (PCNSL) is a rare and aggressive lymphoma of the brain with poor prognosis. The scarcity of cell lines established using PCNSL makes it difficult to conduct preclinical studies on new drugs. We aimed to explore the effect of selinexor combined with zanubrutinib in PCNSL using established PCNSL cells and an orthotopic PCNSL model. Primary PCNSL cells were successfully cultured. Selinexor inhibited proliferation, induced G1 phase arrest, and promoted apoptosis, however, induced drug resistance in PCNSL. Selinexor combined with zanubrutinib had a synergistic effect on PCNSL and prevented the onset of selinexor resistance in PCNSL by inhibiting AKT signaling. Moreover, selinexor combined with zanubrutinib notably slowed tumor growth and prolonged survival compared to that of the control. Overall, the addition of zanubrutinib to selinexor monotreatment had a synergistic effect in vitro and prolonged survival in vivo.
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Affiliation(s)
- Xiaohong Zheng
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Can Wang
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Feng Chen
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shenglan Li
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hua Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shoubo Yang
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xun Kang
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhuang Kang
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chunlei Han
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shuo Yin
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenbin Li
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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3
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Lai C, Xu L, Dai S. The nuclear export protein exportin-1 in solid malignant tumours: From biology to clinical trials. Clin Transl Med 2024; 14:e1684. [PMID: 38783482 PMCID: PMC11116501 DOI: 10.1002/ctm2.1684] [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: 12/07/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Exportin-1 (XPO1), a crucial protein regulating nuclear-cytoplasmic transport, is frequently overexpressed in various cancers, driving tumor progression and drug resistance. This makes XPO1 an attractive therapeutic target. Over the past few decades, the number of available nuclear export-selective inhibitors has been increasing. Only KPT-330 (selinexor) has been successfully used for treating haematological malignancies, and KPT-8602 (eltanexor) has been used for treating haematologic tumours in clinical trials. However, the use of nuclear export-selective inhibitors for the inhibition of XPO1 expression has yet to be thoroughly investigated in clinical studies and therapeutic outcomes for solid tumours. METHODS We collected numerous literatures to explain the efficacy of XPO1 Inhibitors in preclinical and clinical studies of a wide range of solid tumours. RESULTS In this review, we focus on the nuclear export function of XPO1 and results from clinical trials of its inhibitors in solid malignant tumours. We summarized the mechanism of action and therapeutic potential of XPO1 inhibitors, as well as adverse effects and response biomarkers. CONCLUSION XPO1 inhibition has emerged as a promising therapeutic strategy in the fight against cancer, offering a novel approach to targeting tumorigenic processes and overcoming drug resistance. SINE compounds have demonstrated efficacy in a wide range of solid tumours, and ongoing research is focused on optimizing their use, identifying response biomarkers, and developing effective combination therapies. KEY POINTS Exportin-1 (XPO1) plays a critical role in mediating nucleocytoplasmic transport and cell cycle. XPO1 dysfunction promotes tumourigenesis and drug resistance within solid tumours. The therapeutic potential and ongoing researches on XPO1 inhibitors in the treatment of solid tumours. Additional researches are essential to address safety concerns and identify biomarkers for predicting patient response to XPO1 inhibitors.
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Affiliation(s)
- Chuanxi Lai
- Department of Colorectal SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Biotherapy of Zhejiang ProvinceHangzhouChina
| | - Lingna Xu
- Department of Colorectal SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Biotherapy of Zhejiang ProvinceHangzhouChina
| | - Sheng Dai
- Department of Colorectal SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Biotherapy of Zhejiang ProvinceHangzhouChina
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4
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Bortel P, Piga I, Koenig C, Gerner C, Martinez-Val A, Olsen JV. Systematic Optimization of Automated Phosphopeptide Enrichment for High-Sensitivity Phosphoproteomics. Mol Cell Proteomics 2024; 23:100754. [PMID: 38548019 PMCID: PMC11087715 DOI: 10.1016/j.mcpro.2024.100754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/08/2024] [Accepted: 03/22/2024] [Indexed: 05/05/2024] Open
Abstract
Improving coverage, robustness, and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography-tandem mass spectrometry (LC-MS/MS) from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-bead phosphoproteomics sample preparation with a focus on low-input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores, and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample, and loading buffer volumes allowed us to confidently identify >16,000 phosphopeptides in half-an-hour LC-MS/MS on an Orbitrap Exploris 480 using 30 μg of peptides as starting material. Furthermore, we evaluated how sequential enrichment can boost phosphoproteome coverage and showed that pooling fractions into a single LC-MS/MS analysis increased the depth. We also present an alternative phosphopeptide enrichment strategy based on stepwise addition of beads thereby boosting phosphoproteome coverage by 20%. Finally, we applied our optimized strategy to evaluate phosphoproteome depth with the Orbitrap Astral MS using a cell dilution series and were able to identify >32,000 phosphopeptides from 0.5 million HeLa cells in half-an-hour LC-MS/MS using narrow-window data-independent acquisition (nDIA).
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Affiliation(s)
- Patricia Bortel
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria; Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
| | - Ilaria Piga
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Claire Koenig
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Christopher Gerner
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria; Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Ana Martinez-Val
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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5
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Vallés-Martí A, de Goeij-de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Verheij J, Dijk F, Halfwerk H, Giovannetti E, Jiménez CR, Bijlsma MF. Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues. Mol Oncol 2024. [PMID: 38650175 DOI: 10.1002/1878-0261.13625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/12/2023] [Accepted: 02/21/2024] [Indexed: 04/25/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a limited number of known driver mutations but considerable cancer cell heterogeneity. Phosphoproteomics provides a direct read-out of aberrant signaling and the resultant clinically relevant phenotype. Mass spectrometry (MS)-based proteomics and phosphoproteomics were applied to 42 PDAC tumors. Data encompassed over 19 936 phosphoserine or phosphothreonine (pS/T; in 5412 phosphoproteins) and 1208 phosphotyrosine (pY; in 501 phosphoproteins) sites and a total of 3756 proteins. Proteome data identified three distinct subtypes with tumor intrinsic and stromal features. Subsequently, three phospho-subtypes were apparent: two tumor intrinsic (Phos1/2) and one stromal (Phos3), resembling known PDAC molecular subtypes. Kinase activity was analyzed by the Integrative iNferred Kinase Activity (INKA) scoring. Phospho-subtypes displayed differential phosphorylation signals and kinase activity, such as FGR and GSK3 activation in Phos1, SRC kinase family and EPHA2 in Phos2, and EGFR, INSR, MET, ABL1, HIPK1, JAK, and PRKCD in Phos3. Kinase activity analysis of an external PDAC cohort supported our findings and underscored the importance of PI3K/AKT and ERK pathways, among others. Interestingly, unfavorable patient prognosis correlated with higher RTK, PAK2, STK10, and CDK7 activity and high proliferation, whereas long survival was associated with MYLK and PTK6 activity, which was previously unknown. Subtype-associated activity profiles can guide therapeutic combination approaches in tumor and stroma-enriched tissues, and emphasize the critical role of parallel signaling pathways. In addition, kinase activity profiling identifies potential disease markers with prognostic significance.
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Affiliation(s)
- Andrea Vallés-Martí
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
- Cancer Biology, Cancer Center Amsterdam, The Netherlands
- Pharmacology Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Richard R de Goeij-de Haas
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Alex A Henneman
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Joanne Verheij
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Frederike Dijk
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Hans Halfwerk
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- Pharmacology Laboratory, Cancer Center Amsterdam, The Netherlands
- Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, San Giuliano Terme, Italy
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Maarten F Bijlsma
- Cancer Biology, Cancer Center Amsterdam, The Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam University Medical Center, University of Amsterdam, The Netherlands
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6
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Bhardwaj S, Bulluss M, D'Aubeterre A, Derakhshani A, Penner R, Mahajan M, Mahajan VB, Dufour A. Integrating the analysis of human biopsies using post-translational modifications proteomics. Protein Sci 2024; 33:e4979. [PMID: 38533548 DOI: 10.1002/pro.4979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/07/2024] [Accepted: 03/16/2024] [Indexed: 03/28/2024]
Abstract
Proteome diversities and their biological functions are significantly amplified by post-translational modifications (PTMs) of proteins. Shotgun proteomics, which does not typically survey PTMs, provides an incomplete picture of the complexity of human biopsies in health and disease. Recent advances in mass spectrometry-based proteomic techniques that enrich and study PTMs are helping to uncover molecular detail from the cellular level to system-wide functions, including how the microbiome impacts human diseases. Protein heterogeneity and disease complexity are challenging factors that make it difficult to characterize and treat disease. The search for clinical biomarkers to characterize disease mechanisms and complexity related to patient diagnoses and treatment has proven challenging. Knowledge of PTMs is fundamentally lacking. Characterization of complex human samples that clarify the role of PTMs and the microbiome in human diseases will result in new discoveries. This review highlights the key role of proteomic techniques used to characterize unknown biological functions of PTMs derived from complex human biopsies. Through the integration of diverse methods used to profile PTMs, this review explores the genetic regulation of proteoforms, cells of origin expressing specific proteins, and several bioactive PTMs and their subsequent analyses by liquid chromatography and tandem mass spectrometry.
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Affiliation(s)
- Sonali Bhardwaj
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mitchell Bulluss
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ana D'Aubeterre
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Afshin Derakhshani
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Regan Penner
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - MaryAnn Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA
| | - Antoine Dufour
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Joshi SK, Piehowski P, Liu T, Gosline SJC, McDermott JE, Druker BJ, Traer E, Tyner JW, Agarwal A, Tognon CE, Rodland KD. Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine. Annu Rev Pharmacol Toxicol 2024; 64:455-479. [PMID: 37738504 PMCID: PMC10950354 DOI: 10.1146/annurev-pharmtox-022723-113921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools.
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Paul Piehowski
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sara J C Gosline
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jason E McDermott
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Karin D Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Pacific Northwest National Laboratory, Richland, Washington, USA
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8
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Newell S, van der Watt PJ, Leaner VD. Therapeutic targeting of nuclear export and import receptors in cancer and their potential in combination chemotherapy. IUBMB Life 2024; 76:4-25. [PMID: 37623925 PMCID: PMC10952567 DOI: 10.1002/iub.2773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/03/2023] [Indexed: 08/26/2023]
Abstract
Systemic modalities are crucial in the management of disseminated malignancies and liquid tumours. However, patient responses and tolerability to treatment are generally poor and those that enter remission often return with refractory disease. Combination therapies provide a methodology to overcome chemoresistance mechanisms and address dose-limiting toxicities. A deeper understanding of tumorigenic processes at the molecular level has brought a targeted therapy approach to the forefront of cancer research, and novel cancer biomarkers are being identified at a rapid rate, with some showing potential therapeutic benefits. The Karyopherin superfamily of proteins is soluble receptors that mediate nucleocytoplasmic shuttling of proteins and RNAs, and recently, nuclear transport receptors have been recognized as novel anticancer targets. Inhibitors against nuclear export have been approved for clinical use against certain cancer types, whereas inhibitors against nuclear import are in preclinical stages of investigation. Mechanistically, targeting nucleocytoplasmic shuttling has shown to abrogate oncogenic signalling and restore tumour suppressor functions through nuclear sequestration of relevant proteins and mRNAs. Hence, nuclear transport inhibitors display broad spectrum anticancer activity and harbour potential to engage in synergistic interactions with a wide array of cytotoxic agents and other targeted agents. This review is focussed on the most researched nuclear transport receptors in the context of cancer, XPO1 and KPNB1, and highlights how inhibitors targeting these receptors can enhance the therapeutic efficacy of standard of care therapies and novel targeted agents in a combination therapy approach. Furthermore, an updated review on the therapeutic targeting of lesser characterized karyopherin proteins is provided and resistance to clinically approved nuclear export inhibitors is discussed.
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Affiliation(s)
- Stella Newell
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Pauline J. van der Watt
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
- Institute of Infectious Diseases and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Virna D. Leaner
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
- UCT/SAMRC Gynaecological Cancer Research CentreUniversity of Cape TownCape TownSouth Africa
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9
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Selheim F, Aasebø E, Bruserud Ø, Hernandez-Valladares M. High Mitochondrial Protein Expression as a Potential Predictor of Relapse Risk in Acute Myeloid Leukemia Patients with the Monocytic FAB Subtypes M4 and M5. Cancers (Basel) 2023; 16:8. [PMID: 38201437 PMCID: PMC10778527 DOI: 10.3390/cancers16010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
AML is a highly aggressive and heterogeneous form of hematological cancer. Proteomics-based stratification of patients into more refined subgroups may contribute to a more precise characterization of the patient-derived AML cells. Here, we reanalyzed liquid chromatography-tandem mass spectrometry (LC-MS/MS) generated proteomic and phosphoproteomic data from 26 FAB-M4/M5 patients. The patients achieved complete hematological remission after induction therapy. Twelve of them later developed chemoresistant relapse (RELAPSE), and 14 patients were relapse-free (REL_FREE) long-term survivors. We considered not only the RELAPSE and REL_FREE characteristics but also integrated the French-American-British (FAB) classification, along with considering the presence of nucleophosmin 1 (NPM1) mutation and cytogenetically normal AML. We found a significant number of differentially enriched proteins (911) and phosphoproteins (257) between the various FAB subtypes in RELAPSE patients. Patients with the myeloblastic M1/M2 subtype showed higher levels of RNA processing-related routes and lower levels of signaling related to terms like translation and degranulation when compared with the M4/M5 subtype. Moreover, we found that a high abundance of proteins associated with mitochondrial translation and oxidative phosphorylation, particularly observed in the RELAPSE M4/M5 NPM1 mutated subgroup, distinguishes relapsing from non-relapsing AML patient cells with the FAB subtype M4/M5. Thus, the discovery of subtype-specific biomarkers through proteomic profiling may complement the existing classification system for AML and potentially aid in selecting personalized treatment strategies for individual patients.
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Affiliation(s)
- Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Elise Aasebø
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (Ø.B.)
| | - Øystein Bruserud
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (Ø.B.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, Institute of Biotechnology, Excellence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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10
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Ung J, Tan SF, Fox TE, Shaw JJP, Taori M, Horton BJ, Golla U, Sharma A, Szulc ZM, Wang HG, Chalfant CE, Cabot MC, Claxton DF, Loughran TP, Feith DJ. Acid Ceramidase Inhibitor LCL-805 Antagonizes Akt Signaling and Promotes Iron-Dependent Cell Death in Acute Myeloid Leukemia. Cancers (Basel) 2023; 15:5866. [PMID: 38136410 PMCID: PMC10742122 DOI: 10.3390/cancers15245866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive hematologic malignancy requiring urgent treatment advancements. Ceramide is a cell-death-promoting signaling lipid that plays a central role in therapy-induced cell death. We previously determined that acid ceramidase (AC), a ceramide-depleting enzyme, is overexpressed in AML and promotes leukemic survival and drug resistance. The ceramidase inhibitor B-13 and next-generation lysosomal-localizing derivatives termed dimethylglycine (DMG)-B-13 prodrugs have been developed but remain untested in AML. Here, we report the in vitro anti-leukemic efficacy and mechanism of DMG-B-13 prodrug LCL-805 across AML cell lines and primary patient samples. LCL-805 inhibited AC enzymatic activity, increased total ceramides, and reduced sphingosine levels. A median EC50 value of 11.7 μM was achieved for LCL-805 in cell viability assays across 32 human AML cell lines. As a single agent tested across a panel of 71 primary AML patient samples, a median EC50 value of 15.8 μM was achieved. Exogenous ceramide supplementation with C6-ceramide nanoliposomes, which is entering phase I/II clinical trial for relapsed/refractory AML, significantly enhanced LCL-805 killing. Mechanistically, LCL-805 antagonized Akt signaling and led to iron-dependent cell death distinct from canonical ferroptosis. These findings elucidated key factors involved in LCL-805 cytotoxicity and demonstrated the potency of combining AC inhibition with exogenous ceramide.
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Affiliation(s)
- Johnson Ung
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Su-Fern Tan
- Department of Medicine, Division of Hematology & Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; (S.-F.T.); (T.E.F.); (J.J.P.S.); (M.T.); (C.E.C.)
- University of Virginia Cancer Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Todd E. Fox
- Department of Medicine, Division of Hematology & Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; (S.-F.T.); (T.E.F.); (J.J.P.S.); (M.T.); (C.E.C.)
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jeremy J. P. Shaw
- Department of Medicine, Division of Hematology & Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; (S.-F.T.); (T.E.F.); (J.J.P.S.); (M.T.); (C.E.C.)
| | - Maansi Taori
- Department of Medicine, Division of Hematology & Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; (S.-F.T.); (T.E.F.); (J.J.P.S.); (M.T.); (C.E.C.)
| | - Bethany J. Horton
- Department of Public Health Sciences, Division of Translational Research and Applied Statistics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA;
| | - Upendarrao Golla
- Department of Medicine, Division of Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (U.G.); (D.F.C.)
| | - Arati Sharma
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA;
- Penn State Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA;
| | - Zdzislaw M. Szulc
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina College of Medicine, Charleston, SC 29425, USA;
| | - Hong-Gang Wang
- Penn State Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA;
| | - Charles E. Chalfant
- Department of Medicine, Division of Hematology & Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; (S.-F.T.); (T.E.F.); (J.J.P.S.); (M.T.); (C.E.C.)
- University of Virginia Cancer Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Research Service, Richmond Veterans Administration Medical Center, Richmond, VA 23249, USA
| | - Myles C. Cabot
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC 27858, USA;
- Department of Biochemistry & Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - David F. Claxton
- Department of Medicine, Division of Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (U.G.); (D.F.C.)
- Penn State Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA;
| | - Thomas P. Loughran
- Department of Medicine, Division of Hematology & Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; (S.-F.T.); (T.E.F.); (J.J.P.S.); (M.T.); (C.E.C.)
- University of Virginia Cancer Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - David J. Feith
- Department of Medicine, Division of Hematology & Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; (S.-F.T.); (T.E.F.); (J.J.P.S.); (M.T.); (C.E.C.)
- University of Virginia Cancer Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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11
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Xiao D, Lin M, Liu C, Geddes TA, Burchfield J, Parker B, Humphrey SJ, Yang P. SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data. NAR Genom Bioinform 2023; 5:lqad099. [PMID: 37954574 PMCID: PMC10632189 DOI: 10.1093/nargab/lqad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/18/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
A major challenge in mass spectrometry-based phosphoproteomics lies in identifying the substrates of kinases, as currently only a small fraction of substrates identified can be confidently linked with a known kinase. Machine learning techniques are promising approaches for leveraging large-scale phosphoproteomics data to computationally predict substrates of kinases. However, the small number of experimentally validated kinase substrates (true positive) and the high data noise in many phosphoproteomics datasets together limit their applicability and utility. Here, we aim to develop advanced kinase-substrate prediction methods to address these challenges. Using a collection of seven large phosphoproteomics datasets, and both traditional and deep learning models, we first demonstrate that a 'pseudo-positive' learning strategy for alleviating small sample size is effective at improving model predictive performance. We next show that a data resampling-based ensemble learning strategy is useful for improving model stability while further enhancing prediction. Lastly, we introduce an ensemble deep learning model ('SnapKin') by incorporating the above two learning strategies into a 'snapshot' ensemble learning algorithm. We propose SnapKin, an ensemble deep learning method, for predicting substrates of kinases from large-scale phosphoproteomics data. We demonstrate that SnapKin consistently outperforms existing methods in kinase-substrate prediction. SnapKin is freely available at https://github.com/PYangLab/SnapKin.
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Affiliation(s)
- Di Xiao
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Michael Lin
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chunlei Liu
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Thomas A Geddes
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Environmental and Life Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - James G Burchfield
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Environmental and Life Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin L Parker
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, Melbourne, VIC 3010, Australia
| | - Sean J Humphrey
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Environmental and Life Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Melbourne, VIC, 3052, Australia
| | - Pengyi Yang
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
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12
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Gunji D, Narumi R, Muraoka S, Isoyama J, Ikemoto N, Ishida M, Tomonaga T, Sakai Y, Obama K, Adachi J. Integrative analysis of cancer dependency data and comprehensive phosphoproteomics data revealed the EPHA2-PARD3 axis as a cancer vulnerability in KRAS-mutant colorectal cancer. Mol Omics 2023; 19:624-639. [PMID: 37232035 DOI: 10.1039/d3mo00042g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Colorectal cancer (CRC), a common malignant tumour of the gastrointestinal tract, is a life-threatening cancer worldwide. Mutations in KRAS and BRAF, the major driver mutation subtypes in CRC, activate the RAS pathway, contribute to tumorigenesis in CRC and are being investigated as potential therapeutic targets. Despite recent advances in clinical trials targeting KRASG12C or RAS downstream signalling molecules for KRAS-mutant CRC, there is a lack of effective therapeutic interventions. Therefore, understanding the unique molecular characteristics of KRAS-mutant CRC is essential for identifying molecular targets and developing novel therapeutic interventions. We obtained in-depth proteomics and phosphoproteomics quantitative data for over 7900 proteins and 38 700 phosphorylation sites in cells from 35 CRC cell lines and performed informatic analyses, including proteomics-based coexpression analysis and correlation analysis between phosphoproteomics data and cancer dependency scores of the corresponding phosphoproteins. Our results revealed novel dysregulated protein-protein associations enriched specifically in KRAS-mutant cells. Our phosphoproteomics analysis revealed activation of EPHA2 kinase and downstream tight junction signalling in KRAS-mutant cells. Furthermore, the results implicate the phosphorylation site Y378 in the tight junction protein PARD3 as a cancer vulnerability in KRAS-mutant cells. Together, our large-scale phosphoproteomics and proteomics data across 35 steady-state CRC cell lines represent a valuable resource for understanding the molecular characteristics of oncogenic mutations. Our approach to predicting cancer dependency from phosphoproteomics data identified the EPHA2-PARD3 axis as a cancer vulnerability in KRAS-mutant CRC.
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Affiliation(s)
- Daigo Gunji
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
- Department of Surgery, Kyoto University Graduate School of Medicine Faculty of Medicine, Kyoto, 606-8507, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Satoshi Muraoka
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
- Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Junko Isoyama
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Narumi Ikemoto
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Mimiko Ishida
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Yoshiharu Sakai
- Department of Surgery, Kyoto University Graduate School of Medicine Faculty of Medicine, Kyoto, 606-8507, Japan
| | - Kazutaka Obama
- Department of Surgery, Kyoto University Graduate School of Medicine Faculty of Medicine, Kyoto, 606-8507, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
- Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
- Laboratory of Proteomics and Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
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13
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Tong X, Zhang Y, Chen J, Wu DP. [The development of selective XPO1 inhibitors in the treatment of acute myeloid leukemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2023; 44:788-792. [PMID: 38049328 PMCID: PMC10630573 DOI: 10.3760/cma.j.issn.0253-2727.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Indexed: 12/06/2023]
Affiliation(s)
- X Tong
- Department of Pathology, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Y Zhang
- Department of Hematology, the First Affiliated Hospital of Soochow Universityy, Suzhou 215006, China
| | - J Chen
- Department of Hematology, the First Affiliated Hospital of Soochow Universityy, Suzhou 215006, China
| | - D P Wu
- Department of Hematology, the First Affiliated Hospital of Soochow Universityy, Suzhou 215006, China
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14
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Casado P, Cutillas PR. Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine. Mol Cell Proteomics 2023; 22:100517. [PMID: 36805445 PMCID: PMC10152134 DOI: 10.1016/j.mcpro.2023.100517] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous cancer of the hematopoietic system with no cure for most patients. In addition to chemotherapy, treatment options for AML include recently approved therapies that target proteins with roles in AML pathobiology, such as FLT3, BLC2, and IDH1/2. However, due to disease complexity, these therapies produce very diverse responses, and survival rates are still low. Thus, despite considerable advances, there remains a need for therapies that target different aspects of leukemic biology and for associated biomarkers that define patient populations likely to respond to each available therapy. To meet this need, drugs that target different AML vulnerabilities are currently in advanced stages of clinical development. Here, we review proteomics and phosphoproteomics studies that aimed to provide insights into AML biology and clinical disease heterogeneity not attainable with genomic approaches. To place the discussion in context, we first provide an overview of genetic and clinical aspects of the disease, followed by a summary of proteins targeted by compounds that have been approved or are under clinical trials for AML treatment and, if available, the biomarkers that predict responses. We then discuss proteomics and phosphoproteomics studies that provided insights into AML pathogenesis, from which potential biomarkers and drug targets were identified, and studies that aimed to rationalize the use of synergistic drug combinations. When considered as a whole, the evidence summarized here suggests that proteomics and phosphoproteomics approaches can play a crucial role in the development and implementation of precision medicine for AML patients.
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Affiliation(s)
- Pedro Casado
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Pedro R Cutillas
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom; The Alan Turing Institute, The British Library, London, United Kingdom; Digital Environment Research Institute (DERI), Queen Mary University of London, London, United Kingdom.
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15
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Franciosa G, Locard-Paulet M, Jensen LJ, Olsen JV. Recent advances in kinase signaling network profiling by mass spectrometry. Curr Opin Chem Biol 2023; 73:102260. [PMID: 36657259 DOI: 10.1016/j.cbpa.2022.102260] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 01/19/2023]
Abstract
Mass spectrometry-based phosphoproteomics is currently the leading methodology for the study of global kinase signaling. The scientific community is continuously releasing technological improvements for sensitive and fast identification of phosphopeptides, and their accurate quantification. To interpret large-scale phosphoproteomics data, numerous bioinformatic resources are available that help understanding kinase network functional role in biological systems upon perturbation. Some of these resources are databases of phosphorylation sites, protein kinases and phosphatases; others are bioinformatic algorithms to infer kinase activity, predict phosphosite functional relevance and visualize kinase signaling networks. In this review, we present the latest experimental and bioinformatic tools to profile protein kinase signaling networks and provide examples of their application in biomedicine.
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Affiliation(s)
- Giulia Franciosa
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie Locard-Paulet
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars J Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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16
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Higgins L, Gerdes H, Cutillas PR. Principles of phosphoproteomics and applications in cancer research. Biochem J 2023; 480:403-420. [PMID: 36961757 PMCID: PMC10212522 DOI: 10.1042/bcj20220220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/25/2023]
Abstract
Phosphorylation constitutes the most common and best-studied regulatory post-translational modification in biological systems and archetypal signalling pathways driven by protein and lipid kinases are disrupted in essentially all cancer types. Thus, the study of the phosphoproteome stands to provide unique biological information on signalling pathway activity and on kinase network circuitry that is not captured by genetic or transcriptomic technologies. Here, we discuss the methods and tools used in phosphoproteomics and highlight how this technique has been used, and can be used in the future, for cancer research. Challenges still exist in mass spectrometry phosphoproteomics and in the software required to provide biological information from these datasets. Nevertheless, improvements in mass spectrometers with enhanced scan rates, separation capabilities and sensitivity, in biochemical methods for sample preparation and in computational pipelines are enabling an increasingly deep analysis of the phosphoproteome, where previous bottlenecks in data acquisition, processing and interpretation are being relieved. These powerful hardware and algorithmic innovations are not only providing exciting new mechanistic insights into tumour biology, from where new drug targets may be derived, but are also leading to the discovery of phosphoproteins as mediators of drug sensitivity and resistance and as classifiers of disease subtypes. These studies are, therefore, uncovering phosphoproteins as a new generation of disruptive biomarkers to improve personalised anti-cancer therapies.
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Affiliation(s)
- Luke Higgins
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Henry Gerdes
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Pedro R. Cutillas
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
- Alan Turing Institute, The British Library, London, U.K
- Digital Environment Research Institute, Queen Mary University of London, London, U.K
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17
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Joshi SK, Tognon CE, Druker BJ, Rodland KD. Oncoproteomic profiling of AML: moving beyond genomics. Expert Rev Proteomics 2022; 19:283-287. [PMID: 36734985 PMCID: PMC10505090 DOI: 10.1080/14789450.2023.2176757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023]
Affiliation(s)
- Sunil K. Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Cristina E. Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Karin D. Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
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