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Hu X, Cao D, Zhou Z, Wang Z, Zeng J, Hong WX. Single-cell transcriptomic profiling reveals immune cell heterogeneity in acute myeloid leukaemia peripheral blood mononuclear cells after chemotherapy. Cell Oncol (Dordr) 2024; 47:97-112. [PMID: 37615858 PMCID: PMC10899424 DOI: 10.1007/s13402-023-00853-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2023] [Indexed: 08/25/2023] Open
Abstract
PURPOSE Acute myeloid leukaemia (AML) is a heterogeneous disease characterised by the rapid clonal expansion of abnormally differentiated myeloid progenitor cells residing in a complex microenvironment. However, the immune cell types, status, and genome profile of the peripheral blood mononuclear cell (PBMC) microenvironment in AML patients after chemotherapy are poorly understood. In order to explore the immune microenvironment of AML patients after chemotherapy, we conducted this study for providing insights into precision medicine and immunotherapy of AML. METHODS In this study, we used single-cell RNA sequencing (scRNA-seq) to analyse the PBMC microenvironment from five AML patients treated with different chemotherapy regimens and six healthy donors. We compared the cell compositions in AML patients and healthy donors, and performed gene set enrichment analysis (GSEA), CellPhoneDB, and copy number variation (CNV) analysis. RESULTS Using scRNA-seq technology, 91,772 high quality cells of 44,950 PBMCs from AML patients and 46,822 PBMCs from healthy donors were classified as 14 major cell clusters. Our study revealed the sub-cluster diversity of T cells, natural killer (NK) cells, monocytes, dendritic cells (DCs), and haematopoietic stem cell progenitors (HSC-Prog) in AML patients under chemotherapy. NK cells and monocyte-DCs showed significant changes in transcription factor expression and chromosome copy number variation (CNV). We also observed significant heterogeneity in CNV and intercellular interaction networks in HSC-Prog cells. CONCLUSION Our results elucidated the PBMC single-cell landscape and provided insights into precision medicine and immunotherapy for treating AML.
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Affiliation(s)
- Xuqiao Hu
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China.
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China.
| | - Dongyan Cao
- Department of Biliary-Pancreatic Surgery, the Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhenru Zhou
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Zhaoyang Wang
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Jieying Zeng
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Wen-Xu Hong
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China.
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Han C, Zheng J, Li F, Guo W, Cai C. Novel Prognostic Signature for Acute Myeloid Leukemia: Bioinformatics Analysis of Combined CNV-Driven and Ferroptosis-Related Genes. Front Genet 2022; 13:849437. [PMID: 35559049 PMCID: PMC9086455 DOI: 10.3389/fgene.2022.849437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/22/2022] [Indexed: 12/19/2022] Open
Abstract
Background: Acute myeloid leukemia (AML), which has a difficult prognosis, is the most common hematologic malignancy. The role of copy number variations (CNVs) and ferroptosis in the tumor process is becoming increasingly prominent. We aimed to identify specific CNV-driven ferroptosis-related genes (FRGs) and establish a prognostic model for AML. Methods: The combined analysis of CNV differential data and differentially expressed genes (DEGs) data from The Cancer Genome Atlas (TCGA) database was performed to identify key CNV-driven FRGs for AML. A risk model was constructed based on univariate and multivariate Cox regression analysis. The Gene Expression Omnibus (GEO) dataset was used to validate the model. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to clarify the functional roles of DEGs and CNV-driven FRGs. Results: We identified a total of 6828 AML-related DEGs, which were shown to be significantly associated with cell cycle and immune response processes. After a comprehensive analysis of CNVs and corresponding DEGs and FRGs, six CNV-driven FRGs were identified, and functional enrichment analysis indicated that they were involved in oxidative stress, cell death, and inflammatory response processes. Finally, we screened 2 CNV-driven FRGs (DNAJB6 and HSPB1) to develop a prognostic risk model. The overall survival (OS) of patients in the high-risk group was significantly shorter in both the TCGA and GEO (all p < 0.05) datasets compared to the low-risk group. Conclusion: A novel signature based on CNV-driven FRGs was established to predict the survival of AML patients and displayed good performance. Our results may provide potential targets and new research ideas for the treatment and early detection of AML.
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Affiliation(s)
- Chunjiao Han
- Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China
| | - Jiafeng Zheng
- Department of Pulmonology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Fangfang Li
- Department of Rheumatology and Immunology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Wei Guo
- Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China.,Department of Pulmonology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Chunquan Cai
- Department of Institute of Pediatrics, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
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A perceptually optimised bivariate visualisation scheme for high-dimensional fold-change data. ADV DATA ANAL CLASSI 2020. [DOI: 10.1007/s11634-020-00416-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractVisualising data as diagrams using visual attributes such as colour, shape, size, and orientation is challenging. In particular, large data sets demand graphical display as an essential step in the analysis. In order to achieve comprehension often different attributes need to be displayed simultaneously. In this work a comprehensible bivariate, perceptually optimised visualisation scheme for high-dimensional data is proposed and evaluated. It can be used to show fold changes together with confidence values within a single diagram. The visualisation scheme consists of two parts: a uniform, symmetric, two-sided colour scale and a patch grid representation. Evaluation of uniformity and symmetry of the two-sided colour scale was performed in comparison to a standard RGB scale by twenty-five observers. Furthermore, the readability of the generated map was validated and compared to a bivariate heat map scheme.
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Almeida-Paulo GN, Dapía García I, Lubomirov R, Borobia AM, Alonso-Sánchez NL, Espinosa L, Carcas-Sansuán AJ. Weight of ABCB1 and POR genes on oral tacrolimus exposure in CYP3A5 nonexpressor pediatric patients with stable kidney transplant. THE PHARMACOGENOMICS JOURNAL 2017; 18:180-186. [DOI: 10.1038/tpj.2016.93] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/08/2016] [Indexed: 02/02/2023]
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Madian AG, Panigrahi A, Perera MA, Pinto N. Case report: Inability to achieve a therapeutic dose of tacrolimus in a pediatric allogeneic stem cell transplant patient after generic substitution. BMC Pharmacol Toxicol 2014; 15:69. [PMID: 25472557 PMCID: PMC4287354 DOI: 10.1186/2050-6511-15-69] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 11/18/2014] [Indexed: 11/24/2022] Open
Abstract
Background Tacrolimus is an immunosuppressive drug that is used to lower the activity of the patient’s immune system to prevent organ rejection. Unfortunately, there is limited data regarding the therapeutic equivalency of generic tacrolimus formulations especially in children. We report the case of a pediatric patient having an inability to achieve a therapeutic trough level for tacrolimus after conversion from brand name to the generic formulation. Case presentation A 17-month-old male patient diagnosed with T-cell acute lymphoblastic leukemia underwent allogeneic stem cell transplantation. The patient initially received intravenous (IV) tacrolimus for graft-versus-host disease (GVHD) prophylaxis and achieved therapeutic levels. The patient was then switched to an oral brand formulation of tacrolimus, and was able to maintain trough levels within the therapeutic range. After being discharged, the patient received the generic formulation of tacrolimus from an outside pharmacy and the care team was unable to reach therapeutic levels despite multiple dose escalations. Returning to brand name tacrolimus resulted in prompt achievement of therapeutic levels. Conclusions A likely etiology for the inability to achieve therapeutic trough levels in this patient is the change in formulation from brand formulation to generic version. Other factors including drug-drug interaction, preparation of the medication by a different pharmacy, drug-food interaction and genetic factors were also considered. Physicians and pharmacists must be aware of the inability to achieve targeted therapeutic concentrations of tacrolimus resulting from the conversion of brand name to the generic formulation until these generic formulations are tested in clinical trials in a pediatric population.
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Affiliation(s)
| | | | | | - Navin Pinto
- Committee of Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, IL, USA.
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Ordóñez R, Gallo-Oller G, Martínez-Soto S, Legarra S, Pata-Merci N, Guegan J, Danglot G, Bernheim A, Meléndez B, Rey JA, Castresana JS. Genome-wide microarray expression and genomic alterations by array-CGH analysis in neuroblastoma stem-like cells. PLoS One 2014; 9:e113105. [PMID: 25392930 PMCID: PMC4231109 DOI: 10.1371/journal.pone.0113105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/14/2014] [Indexed: 01/08/2023] Open
Abstract
Neuroblastoma has a very diverse clinical behaviour: from spontaneous regression to a very aggressive malignant progression and resistance to chemotherapy. This heterogeneous clinical behaviour might be due to the existence of Cancer Stem Cells (CSC), a subpopulation within the tumor with stem-like cell properties: a significant proliferation capacity, a unique self-renewal capacity, and therefore, a higher ability to form new tumors. We enriched the CSC-like cell population content of two commercial neuroblastoma cell lines by the use of conditioned cell culture media for neurospheres, and compared genomic gains and losses and genome expression by array-CGH and microarray analysis, respectively (in CSC-like versus standard tumor cells culture). Despite the array-CGH did not show significant differences between standard and CSC-like in both analyzed cell lines, the microarray expression analysis highlighted some of the most relevant biological processes and molecular functions that might be responsible for the CSC-like phenotype. Some signalling pathways detected seem to be involved in self-renewal of normal tissues (Wnt, Notch, Hh and TGF-β) and contribute to CSC phenotype. We focused on the aberrant activation of TGF-β and Hh signalling pathways, confirming the inhibition of repressors of TGF-β pathway, as SMAD6 and SMAD7 by RT-qPCR. The analysis of the Sonic Hedgehog pathway showed overexpression of PTCH1, GLI1 and SMO. We found overexpression of CD133 and CD15 in SIMA neurospheres, confirming that this cell line was particularly enriched in stem-like cells. This work shows a cross-talk among different pathways in neuroblastoma and its importance in CSC-like cells.
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Affiliation(s)
- Raquel Ordóñez
- Department of Biochemistry and Genetics, University of Navarra School of Sciences, Pamplona, Spain
| | - Gabriel Gallo-Oller
- Department of Biochemistry and Genetics, University of Navarra School of Sciences, Pamplona, Spain
| | - Soledad Martínez-Soto
- Department of Biochemistry and Genetics, University of Navarra School of Sciences, Pamplona, Spain
| | - Sheila Legarra
- Department of Biochemistry and Genetics, University of Navarra School of Sciences, Pamplona, Spain
| | | | | | | | | | - Bárbara Meléndez
- Molecular Pathology Research Unit, Department of Pathology, Virgen de la Salud Hospital, Toledo, Spain
| | - Juan A. Rey
- IdiPaz Research Unit, La Paz University Hospital, Madrid, Spain
| | - Javier S. Castresana
- Department of Biochemistry and Genetics, University of Navarra School of Sciences, Pamplona, Spain
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Increased leukemia-associated gene expression in benzene-exposed workers. Sci Rep 2014; 4:5369. [PMID: 24993241 PMCID: PMC4081871 DOI: 10.1038/srep05369] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/29/2014] [Indexed: 01/08/2023] Open
Abstract
Long-term exposure to benzene causes several adverse health effects, including an increased risk of acute myeloid leukemia. This study was to identify genetic alternations involved in pathogenesis of leukemia in benzene-exposed workers without clinical symptoms of leukemia. This study included 33 shoe-factory workers exposed to benzene at levels from 1 ppm to 10 ppm. These workers were divided into 3 groups based on the benzene exposure time, 1- < 7, 7- < 12, and 12- < 24 years. 17 individuals without benzene exposure history were recruited as controls. Cytogenetic analysis using Affymetrix Cytogenetics Array found copy-number variations (CNVs) in several chromosomes of benzene-exposed workers. Expression of targeted genes in these altered chromosomes, NOTCH1 and BSG, which play roles in leukemia pathogenesis, was further examined using real-time PCR. The NOTCH1 mRNA level was significantly increased in all 3 groups of workers, and the NOTCH1 mRNA level in the 12- < 24 years group was significantly higher than that in 1- < 7 and 7- < 12 years groups. Compared to the controls, the BSG mRNA level was significantly increased in 7- < 12 and 12- < 24 years groups, but not in the 1- < 7 years group. These results suggest that CNVs and leukemia-related gene expression might play roles in leukemia development in benzene-exposed workers.
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Moreira MB, Quaio CRD, Zandoná-Teixeira AC, Novo-Filho GM, Zanardo EA, Kulikowski LD, Kim CA. Discrepant outcomes in two Brazilian patients with Bloom syndrome and Wilms' tumor: two case reports. J Med Case Rep 2013; 7:284. [PMID: 24377487 PMCID: PMC3897898 DOI: 10.1186/1752-1947-7-284] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 10/21/2013] [Indexed: 11/17/2022] Open
Abstract
Introduction Bloom syndrome is a rare, autosomal recessive, chromosomal instability disorder caused by mutations in the BLM gene that increase the risk of developing neoplasias, particularly lymphomas and leukemias, at an early age. Case presentation Case 1 was a 10-year-old Brazilian girl, the third child of a non-consanguineous non-Jewish family, who was born at 36 weeks of gestation and presented with severe intrauterine growth restriction. She had Bloom syndrome and was diagnosed with a unilateral Wilms’ tumor at the age of 3.5 years. She responded well to oncological treatment and has remained disease-free for the last 17 years. Case 2 was a 2-year-old Brazilian girl born to non-Jewish first-degree cousins. Her gestation was marked by intrauterine growth restriction. She had Bloom syndrome; a unilateral stage II Wilms’ tumor was diagnosed at the age of 4 years after the evaluation of a sudden onset abdominal mass. Surgical removal, neoadjuvant chemotherapy and radiotherapy were not sufficient to control the neoplasia. The tumor recurred after 8 months and she died from clinical complications. Conclusion Our study reports the importance of rapid diagnostics and clinical follow-up of these patients.
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Affiliation(s)
- Marilia Borges Moreira
- Genetics Unit, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil.
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