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Tao W, Sinha A, Raddassi K, Pandit A. Parameter optimization for stable clustering using FlowSOM: a case study from CyTOF. Front Immunol 2024; 15:1414400. [PMID: 39445014 PMCID: PMC11497637 DOI: 10.3389/fimmu.2024.1414400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 09/20/2024] [Indexed: 10/25/2024] Open
Abstract
High-dimensional cell phenotyping is a powerful tool to study molecular and cellular changes in health and diseases. CyTOF enables high-dimensional cell phenotyping using tens of surface and intra-cellular markers. To utilize the full potential of CyTOF, we need advanced clustering and machine learning methodologies to enable automated gating of the complex data. Here we show that critical modifications to a machine learning based FlowSOM package and precise parameter optimization can enable us to reliably analyze the complex CyTOF data. We show the impact of key parameters on clustering outcomes while addressing bugs within the publicly available package. We modified the FlowSOM pipeline to fix the bugs, enable scalability to handle large datasets and perform parameter optimization. We further validated this modified pipeline on a substantial external immunological dataset demonstrating the need of data-specific tailored parameter optimization to ensure reliable definition and interrogation of immune cell populations associated with immune disorders.
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Zhou J, Chng WJ. Unveiling novel insights in acute myeloid leukemia through single-cell RNA sequencing. Front Oncol 2024; 14:1365330. [PMID: 38711849 PMCID: PMC11070491 DOI: 10.3389/fonc.2024.1365330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Acute myeloid leukemia (AML) is a complex and heterogeneous group of aggressive hematopoietic stem cell disease. The presence of diverse and functionally distinct populations of leukemia cells within the same patient's bone marrow or blood poses a significant challenge in diagnosing and treating AML. A substantial proportion of AML patients demonstrate resistance to induction chemotherapy and a grim prognosis upon relapse. The rapid advance in next generation sequencing technologies, such as single-cell RNA-sequencing (scRNA-seq), has revolutionized our understanding of AML pathogenesis by enabling high-resolution interrogation of the cellular heterogeneity in the AML ecosystem, and their transcriptional signatures at a single-cell level. New studies have successfully characterized the inextricably intertwined interactions among AML cells, immune cells and bone marrow microenvironment and their contributions to the AML development, therapeutic resistance and relapse. These findings have deepened and broadened our understanding the complexity and heterogeneity of AML, which are difficult to detect with bulk RNA-seq. This review encapsulates the burgeoning body of knowledge generated through scRNA-seq, providing the novel insights and discoveries it has unveiled in AML biology. Furthermore, we discuss the potential implications of scRNA-seq in therapeutic opportunities, focusing on immunotherapy. Finally, we highlight the current limitations and future direction of scRNA-seq in the field.
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Affiliation(s)
- Jianbiao Zhou
- Cancer Science Institute of Singapore, Center for Translational Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Center for Translational Medicine, Singapore, Singapore
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, Center for Translational Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Center for Translational Medicine, Singapore, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), Singapore, Singapore
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Kok CH, Saunders VA, Dang P, Shanmuganathan N, White D, Branford S, Yeung D, Hughes TP. Adverse outcomes for chronic myeloid leukemia patients with splenomegaly and low in vivo kinase inhibition on imatinib. Blood Cancer J 2023; 13:143. [PMID: 37696829 PMCID: PMC10495334 DOI: 10.1038/s41408-023-00917-4] [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: 07/06/2023] [Revised: 08/18/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Variability in the molecular response to frontline tyrosine kinase inhibitor (TKI) therapy in chronic myeloid leukemia may be partially driven by differences in the level of kinase inhibition induced. We measured in vivo BCR::ABL1 kinase inhibition (IVKI) in circulating mononuclear cells after 7 days of therapy. In 173 patients on imatinib 600 mg/day, 23% had low IVKI (<11% reduction in kinase activity from baseline); this was associated with higher rates of early molecular response (EMR) failure; lower rates of major molecular response (MMR), and MR4.5 by 36 months, compared to high IVKI patients. Low IVKI was more common (39%) in patients with large spleens (≥10 cm by palpation). Notably 55% of patients with large spleens and low IVKI experienced EMR failure whereas the EMR failure rate in patients with large spleens and high IVKI was only 12% (p = 0.014). Furthermore, patients with large spleen and low IVKI had a higher incidence of blast crisis, inferior MMR, MR4.5, and event-free survival compared to patients with large spleen and high IVKI and remaining patients. In nilotinib-treated patients (n = 73), only 4% had low IVKI. The combination of low IVKI and large spleen is associated with markedly inferior outcomes and interventions in this setting warrant further studies.
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Affiliation(s)
- Chung H Kok
- Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
- Clinical Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Verity A Saunders
- Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Phuong Dang
- Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Naranie Shanmuganathan
- Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
- Clinical Health Sciences, University of South Australia, Adelaide, SA, Australia
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
- Australasian Leukaemia and Lymphoma Group (ALLG), Richmond, VIC, Australia
| | - Deborah White
- Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Australasian Leukaemia and Lymphoma Group (ALLG), Richmond, VIC, Australia
| | - Susan Branford
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
- Clinical Health Sciences, University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - David Yeung
- Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia
- Australasian Leukaemia and Lymphoma Group (ALLG), Richmond, VIC, Australia
| | - Timothy P Hughes
- Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia.
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia.
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia.
- Australasian Leukaemia and Lymphoma Group (ALLG), Richmond, VIC, Australia.
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Danzi F, Pacchiana R, Mafficini A, Scupoli MT, Scarpa A, Donadelli M, Fiore A. To metabolomics and beyond: a technological portfolio to investigate cancer metabolism. Signal Transduct Target Ther 2023; 8:137. [PMID: 36949046 PMCID: PMC10033890 DOI: 10.1038/s41392-023-01380-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 03/24/2023] Open
Abstract
Tumour cells have exquisite flexibility in reprogramming their metabolism in order to support tumour initiation, progression, metastasis and resistance to therapies. These reprogrammed activities include a complete rewiring of the bioenergetic, biosynthetic and redox status to sustain the increased energetic demand of the cells. Over the last decades, the cancer metabolism field has seen an explosion of new biochemical technologies giving more tools than ever before to navigate this complexity. Within a cell or a tissue, the metabolites constitute the direct signature of the molecular phenotype and thus their profiling has concrete clinical applications in oncology. Metabolomics and fluxomics, are key technological approaches that mainly revolutionized the field enabling researchers to have both a qualitative and mechanistic model of the biochemical activities in cancer. Furthermore, the upgrade from bulk to single-cell analysis technologies provided unprecedented opportunity to investigate cancer biology at cellular resolution allowing an in depth quantitative analysis of complex and heterogenous diseases. More recently, the advent of functional genomic screening allowed the identification of molecular pathways, cellular processes, biomarkers and novel therapeutic targets that in concert with other technologies allow patient stratification and identification of new treatment regimens. This review is intended to be a guide for researchers to cancer metabolism, highlighting current and emerging technologies, emphasizing advantages, disadvantages and applications with the potential of leading the development of innovative anti-cancer therapies.
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Affiliation(s)
- Federica Danzi
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Raffaella Pacchiana
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maria T Scupoli
- Department of Neurosciences, Biomedicine and Movement Sciences, Biology and Genetics Section, University of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy.
| | - Alessandra Fiore
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
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Caprioli C, Nazari I, Milovanovic S, Pelicci PG. Single-Cell Technologies to Decipher the Immune Microenvironment in Myeloid Neoplasms: Perspectives and Opportunities. Front Oncol 2022; 11:796477. [PMID: 35186713 PMCID: PMC8847379 DOI: 10.3389/fonc.2021.796477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/31/2021] [Indexed: 11/26/2022] Open
Abstract
Myeloid neoplasms (MN) are heterogeneous clonal disorders arising from the expansion of hematopoietic stem and progenitor cells. In parallel with genetic and epigenetic dynamics, the immune system plays a critical role in modulating tumorigenesis, evolution and therapeutic resistance at the various stages of disease progression. Single-cell technologies represent powerful tools to assess the cellular composition of the complex tumor ecosystem and its immune environment, to dissect interactions between neoplastic and non-neoplastic components, and to decipher their functional heterogeneity and plasticity. In addition, recent progress in multi-omics approaches provide an unprecedented opportunity to study multiple molecular layers (DNA, RNA, proteins) at the level of single-cell or single cellular clones during disease evolution or in response to therapy. Applying single-cell technologies to MN holds the promise to uncover novel cell subsets or phenotypic states and highlight the connections between clonal evolution and immune escape, which is crucial to fully understand disease progression and therapeutic resistance. This review provides a perspective on the various opportunities and challenges in the field, focusing on key questions in MN research and discussing their translational value, particularly for the development of more efficient immunotherapies.
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Affiliation(s)
- Chiara Caprioli
- Department of Experimental Oncology, IRCCS Istituto Europeo di Oncologia, Milan, Italy
- Scuola Europea di Medicina Molecolare (SEMM) European School of Molecular Medicine, Milan, Italy
- Hematology and Bone Marrow Transplant Unit, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Iman Nazari
- Department of Experimental Oncology, IRCCS Istituto Europeo di Oncologia, Milan, Italy
- Scuola Europea di Medicina Molecolare (SEMM) European School of Molecular Medicine, Milan, Italy
| | - Sara Milovanovic
- Department of Experimental Oncology, IRCCS Istituto Europeo di Oncologia, Milan, Italy
- Scuola Europea di Medicina Molecolare (SEMM) European School of Molecular Medicine, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IRCCS Istituto Europeo di Oncologia, Milan, Italy
- Scuola Europea di Medicina Molecolare (SEMM) European School of Molecular Medicine, Milan, Italy
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