1
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Dembitz V, Lawson H, Burt R, Natani S, Philippe C, James SC, Atkinson S, Durko J, Wang LM, Campos J, Magee AMS, Woodley K, Austin MJ, Rio-Machin A, Casado P, Bewicke-Copley F, Rodriguez Blanco G, Pereira-Martins D, Oudejans L, Boet E, von Kriegsheim A, Schwaller J, Finch AJ, Patel B, Sarry JE, Tamburini J, Schuringa JJ, Hazlehurst L, Copland Iii JA, Yuneva M, Peck B, Cutillas P, Fitzgibbon J, Rouault-Pierre K, Kranc K, Gallipoli P. Stearoyl-CoA desaturase inhibition is toxic to acute myeloid leukemia displaying high levels of the de novo fatty acid biosynthesis and desaturation. Leukemia 2024:10.1038/s41375-024-02390-9. [PMID: 39187579 DOI: 10.1038/s41375-024-02390-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 08/06/2024] [Accepted: 08/15/2024] [Indexed: 08/28/2024]
Abstract
Identification of specific and therapeutically actionable vulnerabilities, ideally present across multiple mutational backgrounds, is needed to improve acute myeloid leukemia (AML) patients' outcomes. We identify stearoyl-CoA desaturase (SCD), the key enzyme in fatty acid (FA) desaturation, as prognostic of patients' outcomes and, using the clinical-grade inhibitor SSI-4, show that SCD inhibition (SCDi) is a therapeutic vulnerability across multiple AML models in vitro and in vivo. Multiomic analysis demonstrates that SCDi causes lipotoxicity, which induces AML cell death via pleiotropic effects. Sensitivity to SCDi correlates with AML dependency on FA desaturation regardless of mutational profile and is modulated by FA biosynthesis activity. Finally, we show that lipotoxicity increases chemotherapy-induced DNA damage and standard chemotherapy further sensitizes AML cells to SCDi. Our work supports developing FA desaturase inhibitors in AML while stressing the importance of identifying predictive biomarkers of response and biologically validated combination therapies to realize their full therapeutic potential.
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Affiliation(s)
- Vilma Dembitz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Physiology and Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Hannah Lawson
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- The Institute of Cancer Research, London, UK
| | - Richard Burt
- Division of Cell and Molecular Biology, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Sirisha Natani
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Céline Philippe
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- INSERM U1242, University of Rennes, Rennes, France
| | - Sophie C James
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Samantha Atkinson
- Division of Cell and Molecular Biology, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Jozef Durko
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lydia M Wang
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- The Institute of Cancer Research, London, UK
| | - Joana Campos
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- The Institute of Cancer Research, London, UK
| | - Aoife M S Magee
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Keith Woodley
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Michael J Austin
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ana Rio-Machin
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Experimental Hematology Lab, IIS-Fundación Jimenez Díaz, UAM, Madrid, Spain
| | - Pedro Casado
- Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Findlay Bewicke-Copley
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Giovanny Rodriguez Blanco
- The University of Edinburgh MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Diego Pereira-Martins
- Department of Experimental Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lieve Oudejans
- Department of Experimental Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Emeline Boet
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, LabEx Toucan, Toulouse, France
- Équipe labellisée Ligue Nationale Contre le Cancer 2023, Toulouse, France
| | - Alex von Kriegsheim
- The University of Edinburgh MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Juerg Schwaller
- University Children's Hospital and Department of Biomedicine (DBM), University of Basel, Basel, Switzerland
| | - Andrew J Finch
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Bela Patel
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Jean-Emmanuel Sarry
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, LabEx Toucan, Toulouse, France
- Équipe labellisée Ligue Nationale Contre le Cancer 2023, Toulouse, France
| | - Jerome Tamburini
- Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva and Swiss Cancer Center Leman, Geneva, Switzerland
| | - Jan Jacob Schuringa
- Department of Experimental Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | | | - Barrie Peck
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Pedro Cutillas
- Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Jude Fitzgibbon
- Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Kevin Rouault-Pierre
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Kamil Kranc
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- The Institute of Cancer Research, London, UK
| | - Paolo Gallipoli
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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2
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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; 18:2020-2041. [PMID: 38650175 PMCID: PMC11306541 DOI: 10.1002/1878-0261.13625] [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: 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 CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
- Cancer BiologyCancer Center AmsterdamThe Netherlands
- Pharmacology LaboratoryCancer Center AmsterdamThe Netherlands
| | - Richard R. de Goeij‐de Haas
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Alex A. Henneman
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Jaco C. Knol
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Joanne Verheij
- Department of PathologyAmsterdam University Medical CenterThe Netherlands
| | - Frederike Dijk
- Department of PathologyAmsterdam University Medical CenterThe Netherlands
| | - Hans Halfwerk
- Department of PathologyAmsterdam University Medical CenterThe Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- Pharmacology LaboratoryCancer Center AmsterdamThe Netherlands
- Cancer Pharmacology Lab, AIRC Start‐Up UnitFondazione Pisana per la ScienzaSan Giuliano TermeItaly
| | - Connie R. Jiménez
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Maarten F. Bijlsma
- Cancer BiologyCancer Center AmsterdamThe Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam University Medical CenterUniversity of AmsterdamThe Netherlands
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3
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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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4
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Di Mambro A, Arroyo-Berdugo Y, Fioretti T, Randles M, Cozzuto L, Rajeeve V, Cevenini A, Austin MJ, Esposito G, Ponomarenko J, Lucas CM, Cutillas P, Gribben J, Williams O, Calle Y, Patel B, Esposito MT. SET-PP2A complex as a new therapeutic target in KMT2A (MLL) rearranged AML. Oncogene 2023; 42:3670-3683. [PMID: 37891368 PMCID: PMC10709139 DOI: 10.1038/s41388-023-02840-1] [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: 02/21/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 10/29/2023]
Abstract
KMT2A-rearranged (KMT2A-R) is an aggressive and chemo-refractory acute leukemia which mostly affects children. Transcriptomics-based characterization and chemical interrogation identified kinases as key drivers of survival and drug resistance in KMT2A-R leukemia. In contrast, the contribution and regulation of phosphatases is unknown. In this study we uncover the essential role and underlying mechanisms of SET, the endogenous inhibitor of Ser/Thr phosphatase PP2A, in KMT2A-R-leukemia. Investigation of SET expression in acute myeloid leukemia (AML) samples demonstrated that SET is overexpressed, and elevated expression of SET is correlated with poor prognosis and with the expression of MEIS and HOXA genes in AML patients. Silencing SET specifically abolished the clonogenic ability of KMT2A-R leukemic cells and the transcription of KMT2A targets genes HOXA9 and HOXA10. Subsequent mechanistic investigations showed that SET interacts with both KMT2A wild type and fusion proteins, and it is recruited to the HOXA10 promoter. Pharmacological inhibition of SET by FTY720 disrupted SET-PP2A interaction leading to cell cycle arrest and increased sensitivity to chemotherapy in KMT2A-R-leukemic models. Phospho-proteomic analyses revealed that FTY720 reduced the activity of kinases regulated by PP2A, including ERK1, GSK3β, AURB and PLK1 and led to suppression of MYC, supporting the hypothesis of a feedback loop among PP2A, AURB, PLK1, MYC, and SET. Our findings illustrate that SET is a novel player in KMT2A-R leukemia and they provide evidence that SET antagonism could serve as a novel strategy to treat this aggressive leukemia.
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Affiliation(s)
| | | | - Tiziana Fioretti
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, Napoli, Italy
| | - Michael Randles
- Chester Centre for Leukaemia Research, Chester Medical School, University of Chester, Chester, UK
| | - Luca Cozzuto
- Centre Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Armando Cevenini
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, Napoli, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131, Naples, Italy
| | - Michael J Austin
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Gabriella Esposito
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, Napoli, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131, Naples, Italy
| | - Julia Ponomarenko
- Centre Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- University Pompeu Fabra (UPF), Barcelona, Spain
| | - Claire M Lucas
- Chester Centre for Leukaemia Research, Chester Medical School, University of Chester, Chester, UK
| | - Pedro Cutillas
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - John Gribben
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Owen Williams
- Great Ormond Street Institute of Child Health London, UCL, London, UK
| | - Yolanda Calle
- School of Life and Health Sciences, University of Roehampton, London, UK
| | - Bela Patel
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Maria Teresa Esposito
- School of Life and Health Sciences, University of Roehampton, London, UK.
- School of Biosciences, University of Surrey, Guildford, UK.
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5
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Rulten SL, Grose RP, Gatz SA, Jones JL, Cameron AJM. The Future of Precision Oncology. Int J Mol Sci 2023; 24:12613. [PMID: 37628794 PMCID: PMC10454858 DOI: 10.3390/ijms241612613] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Our understanding of the molecular mechanisms underlying cancer development and evolution have evolved rapidly over recent years, and the variation from one patient to another is now widely recognized. Consequently, one-size-fits-all approaches to the treatment of cancer have been superseded by precision medicines that target specific disease characteristics, promising maximum clinical efficacy, minimal safety concerns, and reduced economic burden. While precision oncology has been very successful in the treatment of some tumors with specific characteristics, a large number of patients do not yet have access to precision medicines for their disease. The success of next-generation precision oncology depends on the discovery of new actionable disease characteristics, rapid, accurate, and comprehensive diagnosis of complex phenotypes within each patient, novel clinical trial designs with improved response rates, and worldwide access to novel targeted anticancer therapies for all patients. This review outlines some of the current technological trends, and highlights some of the complex multidisciplinary efforts that are underway to ensure that many more patients with cancer will be able to benefit from precision oncology in the near future.
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Affiliation(s)
| | - Richard P. Grose
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
| | - Susanne A. Gatz
- Cancer Research UK Clinical Trials Unit (CRCTU), Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - J. Louise Jones
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
| | - Angus J. M. Cameron
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
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6
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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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