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Zhu Z, Li L, Ye Y, Zhong Q. Integrating bulk and single-cell transcriptomics to elucidate the role and potential mechanisms of autophagy in aging tissue. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00996-w. [PMID: 39414741 DOI: 10.1007/s13402-024-00996-w] [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] [Accepted: 09/20/2024] [Indexed: 10/18/2024] Open
Abstract
PURPOSE Autophagy is frequently observed in tissues during the aging process, yet the tissues most strongly correlated with autophagy during aging and the underlying regulatory mechanisms remain inadequately understood. The purpose of this study is to identify the tissues with the highest correlation between autophagy and aging, and to explore the functions and mechanisms of autophagy in the aging tissue microenvironment. METHODS Integrated bulk RNA-seq from over 7000 normal tissue samples, single-cell sequencing data from blood samples of different ages, more than 2000 acute myeloid leukemia (AML) bulk RNA-seq, and multiple sets of AML single-cell data. The datasets were analysed using various bioinformatic approaches. RESULTS Blood tissue exhibited the highest positive correlation between autophagy and aging among healthy tissues. Single-cell resolution analysis revealed that in aged blood, classical monocytes (C. monocytes) are most closely associated with elevated autophagy levels. Increased autophagy in these monocytes correlated with a higher proportion of C. monocytes, with hypoxia identified as a crucial contributing factor. In AML, a representative myeloid blood disease, enhanced autophagy was accompanied by an increased proportionof C. monocytes. High autophagy levels in monocytes are associated with pro-inflammatory gene upregulation and Reactive Oxygen Species (ROS) accumulation, contributing to tissue aging. CONCLUSION This study revealed that autophagy is most strongly correlated with aging in blood tissue. Enhanced autophagy levels in C. monocytes demonstrate a positive correlation with increased secretion of pro-inflammatory factors and elevated production of ROS, which may contribute to a more rapid aging process. This discovery underscores the critical role of autophagy in blood aging and suggests potential therapeutic targets to mitigate aging-related health issues.
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Affiliation(s)
- Zhenhua Zhu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Linsen Li
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Youqiong Ye
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Qing Zhong
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Wei QJ, Liang HQ, Liang YW, Huang ZX. TET3 is expressed in prostate cancer tumor-associated macrophages and is associated with anti-androgen resistance. Clin Transl Oncol 2024:10.1007/s12094-024-03708-w. [PMID: 39240303 DOI: 10.1007/s12094-024-03708-w] [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: 07/13/2024] [Accepted: 08/28/2024] [Indexed: 09/07/2024]
Abstract
PURPOSE The aim of this study is to investigate the expression of TET3 in prostate cancer and its effect on the efficacy of anti-androgen therapy (ADT). METHODS The expression of TET3 in 1965 cases of prostate cancer and 493 cases of normal prostate tissues were analyzed. The CIBERSORT algorithm evaluated the abundance of 22 tumor-infiltrating immune cells in 497 prostate cancers. Subsequently, the expression of TET3 in prostate cancer TAMs was analyzed using 21,292 cells from single-cell RNA sequencing (scRNAseq). In addition, the trajectory of the differentiation process was reconstructed based on pseudotime analysis. Sensitivity prediction of prostate cancers to ADT was evaluated based on GDSC2 and CTRP databases. Another dataset GSE111177 was employed for further analysis. RESULTS TET3 was over-expressed in prostate cancer, and the expression of TET3 in metastatic prostate cancer was higher than that in non-metastatic prostate cancer. The scRNAseq analysis of prostate cancer showed that TET3 was mainly expressed in TAM. TET3 expressed in early and active TAMs, with the activation of signaling pathways such as energy metabolism, cell communication, and cytokine production. Prostate cancer in TET3 high expression group was more sensitive to ADT drugs such as Bicalutamide and AZD3514, and was also more sensitive to chemotherapy drugs such as Cyclophosphamide, Paclitaxel, and Vincristine, and MAPK pathway inhibitors of Docetaxel and Dabrafenib. CONCLUSIONS The efficacy of ADT in prostate cancer is related to the expression of TET3 in TAMs, and TET3 may be a potential therapeutic target for coordinating ADT.
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Affiliation(s)
- Qiu-Ju Wei
- Guangxi Medical University, 22 Shuang-Yong Road, Nanning, 530021, Guangxi, China
| | - Hai-Qi Liang
- Guangxi Medical University, 22 Shuang-Yong Road, Nanning, 530021, Guangxi, China.
| | - Yao-Wen Liang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zu-Xin Huang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Ben-Crentsil NA, Padron E. If You Build It, Patients with Rare Cancers Will Come: A Successful Clinical Trial in Relapsed and Refractory JMML. Cancer Discov 2024; 14:1574-1576. [PMID: 39228296 DOI: 10.1158/2159-8290.cd-24-0752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 09/05/2024]
Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare pediatric hematologic malignancy with a high relapse rate and a poor prognosis hallmarked by RAS pathway mutations. Stieglitz and colleagues conducted a phase II clinical trial using the MEK inhibitor trametinib to treat patients with relapsed and refractory juvenile myelomonocytic leukemia and observed an objective response rate of 50% and an overall survival of 80% after 4 years. See related article by Stieglitz et al., p. 1590 (4) .
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Affiliation(s)
| | - Eric Padron
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, Florida
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Jiang T, Sun H, Xue S, Xu T, Xia W, Wang Y, Guo L, Lin H. Prognostic significance of hemoglobin, albumin, lymphocyte, and platelet (HALP) score in breast cancer: a propensity score-matching study. Cancer Cell Int 2024; 24:230. [PMID: 38956686 PMCID: PMC11218366 DOI: 10.1186/s12935-024-03419-w] [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: 09/25/2023] [Accepted: 06/22/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND The hemoglobin-albumin-lymphocyte-platelet (HALP) score functions as a comprehensive index that assesses the systemic inflammatory response, nutritional, and immune status. This study aimed to explore the relationship between preoperative HALP score and the prognosis of BC patients and to develop predictive nomograms. METHODS Clinicopathological data were collected for BC patients who underwent mastectomy between December 2010 and April 2014 from Sun Yat-sen University Cancer Center. The optimal cutoff value for HALP was determined by maximally selected rank statistics for overall survival data. Propensity score matching (PSM) was applied to develop comparable cohorts of high-HALP group and low-HALP group. Kaplan-Meier curves and Cox regression analyses were performed to determine the impact of HALP on BC patients. Prognostic nomograms were developed based on the multivariate Cox regression method. Then, the concordance index (C-index), calibration plots, and decision curves analysis (DCA) were applied to evaluate the prognostic performance of the nomograms. RESULTS A total of 1,856 patients were included as the primary cohort, and 1,470 patients were matched and considered as the PSM cohort. In the primary cohort, the 5-year overall survival (OS) and progression-free survival (PFS) rates for high-HALP group (≥ 47.89) and low-HALP group (< 47.89) were 94.4% vs. 91.0% (P = 0.005) and 87.8% vs. 82.1% (P = 0.005), respectively. Similar results were observed in PSM cohort (5-year OS, 94.3% vs. 90.8%, P = 0.015; 5-year PFS, 87.5% vs. 83.2%, P = 0.036). Notably, multivariate Cox regression analysis in the PSM cohort showed that HALP could independently predict BC patient prognosis in both OS (HR: 0.596, 95%CI [0.405-0.875], P = 0.008) and PFS (HR: 0.707, 95%CI [0.538-0.930], P = 0.013). OS and PFS nomograms showed excellent predictive performance with the C-indexes of 0.783 and 0.720, respectively. The calibration plots and DCA also indicated the good predictability of the nomograms. Finally, subgroup analysis further demonstrated a favorable impact of HALP on both OS and PFS. CONCLUSION Preoperative HALP score can be used as a reliable independent predictor of OS and PFS in BC patients, and the nomograms may provide a personalized treatment strategy.
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Affiliation(s)
- Tongchao Jiang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
- Department of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510060, Guangdong Province, China
| | - Haishuang Sun
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
| | - Shuyu Xue
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
| | - Tiankai Xu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
| | - Wen Xia
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
| | - Ying Wang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.
| | - Ling Guo
- Department of Nasopharyngeal Carcinoma, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.
| | - Huanxin Lin
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.
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Vadakekolathu J, Rutella S. Escape from T-cell-targeting immunotherapies in acute myeloid leukemia. Blood 2024; 143:2689-2700. [PMID: 37467496 PMCID: PMC11251208 DOI: 10.1182/blood.2023019961] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023] Open
Abstract
ABSTRACT Single-cell and spatial multimodal technologies have propelled discoveries of the solid tumor microenvironment (TME) molecular features and their correlation with clinical response and resistance to immunotherapy. Computational tools are incessantly being developed to characterize tumor-infiltrating immune cells and to model tumor immune escape. These advances have led to substantial research into T-cell hypofunctional states in the TME and their reinvigoration with T-cell-targeting approaches, including checkpoint inhibitors (CPIs). Until recently, we lacked a high-dimensional picture of the acute myeloid leukemia (AML) TME, including compositional and functional differences in immune cells between disease onset and postchemotherapy or posttransplantation relapse, and the dynamic interplay between immune cells and AML blasts at various maturation stages. AML subgroups with heightened interferon gamma (IFN-γ) signaling were shown to derive clinical benefit from CD123×CD3-bispecific dual-affinity retargeting molecules and CPIs, while being less likely to respond to standard-of-care cytotoxic chemotherapy. In this review, we first highlight recent progress into deciphering immune effector states in AML (including T-cell exhaustion and senescence), oncogenic signaling mechanisms that could reduce the susceptibility of AML cells to T-cell-mediated killing, and the dichotomous roles of type I and II IFN in antitumor immunity. In the second part, we discuss how this knowledge could be translated into opportunities to manipulate the AML TME with the aim to overcome resistance to CPIs and other T-cell immunotherapies, building on recent success stories in the solid tumor field, and we provide an outlook for the future.
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Affiliation(s)
- Jayakumar Vadakekolathu
- John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, United Kingdom
| | - Sergio Rutella
- John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, United Kingdom
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Jiang T, Sun H, Xu T, Xue S, Xia W, Xiao X, Wang Y, Guo L, Lin H. Significance of Pre-Treatment CALLY Score Combined with EBV-DNA Levels for Prognostication in Non-Metastatic Nasopharyngeal Cancer Patients: A Clinical Perspective. J Inflamm Res 2024; 17:3353-3369. [PMID: 38803689 PMCID: PMC11129745 DOI: 10.2147/jir.s460109] [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: 01/17/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Background The C-reactive protein-albumin-lymphocyte (CALLY) score is a novel indicator associated with inflammation, immunity, and nutrition, utilized for cancer prognostic stratification. This study aimed to evaluate the integrated prognostic significance of the pre-treatment CALLY score and Epstein-Barr virus (EBV) DNA levels in nasopharyngeal carcinoma (NPC) patients and to develop prognostic models. Patients and Methods A total of 1707 NPC patients from September 2015 to December 2017 were retrospectively enrolled. The cut-off point for the CALLY score, determined by maximum selected rank statistics, integrates with the published cut-off point for pre-EBV DNA to develop a comprehensive index. Subsequently, patients were randomly allocated in a 1:1 ratio into training and validation cohorts. Survival analysis was conducted using the Kaplan-Meier method with Log rank tests, and the Cox proportional hazards model was applied to identify independent prognostic factors for constructing predictive nomograms. The predictive ability of the nomograms were assessed through the concordance index (C-index), calibration curves, and decision curve analysis. Results By integrating CALLY scores and EBV-DNA levels, patients were categorized into three risk clusters. Kaplan-Meier curves reveal significant differences in overall survival (OS), distant metastasis-free survival (DMFS), and locoregional relapse-free survival (LRRFS) outcomes among different risk groups (all P values < 0.05). Multivariate analysis revealed that CALLY-EBV DNA index serves as an independent prognostic factor for the OS, DMFS, and LRRFS. The prognostic nomograms based on the CALLY-EBV DNA index provided accurate predictions for 1-year, 3-year, and 5-year OS, DMFS, and LRRFS. Additionally, compared to the traditional TNM staging system, the nomograms exhibited enhanced discriminatory power, calibration capability, and clinical applicability. All results were in agreement with the validation cohort. Conclusion The CALLY-EBV DNA index is an independent prognostic biomarker. The nomogram prediction models, constructed based on the CALLY-EBV DNA index, demonstrates superior predictive performance compared to the traditional TNM staging.
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Affiliation(s)
- Tongchao Jiang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People’s Republic of China
| | - Haishuang Sun
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People’s Republic of China
| | - Tiankai Xu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People’s Republic of China
| | - Shuyu Xue
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People’s Republic of China
| | - Wen Xia
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People’s Republic of China
| | - Xiang Xiao
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People’s Republic of China
| | - Ying Wang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People’s Republic of China
| | - Ling Guo
- Department of Nasopharyngeal Carcinoma, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People’s Republic of China
| | - Huanxin Lin
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People’s Republic of China
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7
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Quin C, DeJong EN, Cook EK, Luo YZ, Vlasschaert C, Sadh S, McNaughton AJ, Buttigieg MM, Breznik JA, Kennedy AE, Zhao K, Mewburn J, Dunham-Snary KJ, Hindmarch CC, Bick AG, Archer SL, Rauh MJ, Bowdish DM. Neutrophil-mediated innate immune resistance to bacterial pneumonia is dependent on Tet2 function. J Clin Invest 2024; 134:e171002. [PMID: 38573824 PMCID: PMC11142737 DOI: 10.1172/jci171002] [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: 03/30/2023] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
Individuals with clonal hematopoiesis of indeterminate potential (CHIP) are at increased risk of aging related health conditions and all-cause mortality, but whether CHIP affects risk of infection is much less clear. Using UK Biobank data, we revealed a positive association between CHIP and incident pneumonia in 438,421 individuals. We show that inflammation enhanced pneumonia risk, as CHIP carriers with a hypomorphic IL6 receptor polymorphism were protected. To better characterize the pathways of susceptibility, we challenged hematopoietic Tet Methylcytosine Dioxygenase 2-knockout (Tet2-/-) and floxed control mice (Tet2fl/fl) with Streptococcus pneumoniae. As with human CHIP carriers, Tet2-/- mice had hematopoietic abnormalities resulting in the expansion of inflammatory monocytes and neutrophils in peripheral blood. Yet, these cells were insufficient in defending against S. pneumoniae and resulted in increased pathology, impaired bacterial clearance, and higher mortality in Tet2-/- mice. We delineated the transcriptional landscape of Tet2-/- neutrophils and found that, while inflammation-related pathways were upregulated in Tet2-/- neutrophils, migration and motility pathways were compromised. Using live-imaging techniques, we demonstrated impairments in motility, pathogen uptake, and neutrophil extracellular trap (NET) formation by Tet2-/- neutrophils. Collectively, we show that CHIP is a risk factor for bacterial pneumonia related to innate immune impairments.
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Affiliation(s)
- Candice Quin
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Firestone Institute for Respiratory Health, St. Joseph’s Healthcare, Hamilton, Ontario, Canada
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Erica N. DeJong
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Firestone Institute for Respiratory Health, St. Joseph’s Healthcare, Hamilton, Ontario, Canada
| | - Elina K. Cook
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences
| | - Yi Zhen Luo
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences
| | | | - Sanathan Sadh
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences
| | | | - Marco M. Buttigieg
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences
| | - Jessica A. Breznik
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Firestone Institute for Respiratory Health, St. Joseph’s Healthcare, Hamilton, Ontario, Canada
| | - Allison E. Kennedy
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Firestone Institute for Respiratory Health, St. Joseph’s Healthcare, Hamilton, Ontario, Canada
| | - Kevin Zhao
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Firestone Institute for Respiratory Health, St. Joseph’s Healthcare, Hamilton, Ontario, Canada
| | | | | | - Charles C.T. Hindmarch
- Department of Medicine
- Queen’s CardioPulmonary Unit, Queen’s University, Kingston, Ontario, Canada
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Stephen L. Archer
- Department of Medicine
- Queen’s CardioPulmonary Unit, Queen’s University, Kingston, Ontario, Canada
| | - Michael J. Rauh
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences
| | - Dawn M.E. Bowdish
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Firestone Institute for Respiratory Health, St. Joseph’s Healthcare, Hamilton, Ontario, Canada
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8
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de Jong MME, Chen L, Raaijmakers MHGP, Cupedo T. Bone marrow inflammation in haematological malignancies. Nat Rev Immunol 2024:10.1038/s41577-024-01003-x. [PMID: 38491073 DOI: 10.1038/s41577-024-01003-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2024] [Indexed: 03/18/2024]
Abstract
Tissue inflammation is a hallmark of tumour microenvironments. In the bone marrow, tumour-associated inflammation impacts normal niches for haematopoietic progenitor cells and mature immune cells and supports the outgrowth and survival of malignant cells residing in these niche compartments. This Review provides an overview of our current understanding of inflammatory changes in the bone marrow microenvironment of myeloid and lymphoid malignancies, using acute myeloid leukaemia and multiple myeloma as examples and highlights unique and shared features of inflammation in niches for progenitor cells and plasma cells. Importantly, inflammation exerts profoundly different effects on normal bone marrow niches in these malignancies, and we provide context for possible drivers of these divergent effects. We explore the role of tumour cells in inflammatory changes, as well as the role of cellular constituents of normal bone marrow niches, including myeloid cells and stromal cells. Integrating knowledge of disease-specific dynamics of malignancy-associated bone marrow inflammation will provide a necessary framework for future targeting of these processes to improve patient outcome.
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Affiliation(s)
- Madelon M E de Jong
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Lanpeng Chen
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Tom Cupedo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
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9
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Guarnera L, Jha BK. TET2 mutation as prototypic clonal hematopoiesis lesion. Semin Hematol 2024; 61:51-60. [PMID: 38431463 PMCID: PMC10978279 DOI: 10.1053/j.seminhematol.2024.01.013] [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: 10/30/2023] [Revised: 01/12/2024] [Accepted: 01/28/2024] [Indexed: 03/05/2024]
Abstract
Loss of function TET2 mutation (TET2MT) is one of the most frequently observed lesions in clonal hematopoiesis (CH). TET2 a member TET-dioxygenase family of enzymes that along with TET1 and TET3, progressively oxidize 5-methyl cytosine (mC) resulting in regulated demethylation of promoter, enhancer and silencer elements of the genome. This process is critical for efficient transcription that determine cell lineage fate, proliferation and survival and the maintenance of the genomic fidelity with aging of the organism. Partial or complete loss-of-function TET2 mutations create regional and contextual DNA hypermethylation leading to gene silencing or activation that result in skewed myeloid differentiation and clonal expansion. In addition to myeloid skewing, loss of TET2 creates differentiation block and provides proliferative advantage to hematopoietic stem and progenitor cells (HSPCs). TET2MT is a prototypical lesion in CH, since the mutant clones dominate during stress hematopoiesis and often associates with evolution of myeloid malignancies. TET2MT clones has unique privilege to create and persist in pro-inflammatory milieu. Despite extensive knowledge regarding biochemical mechanisms underlying distorted myeloid differentiation, and enhanced self-replication of TET2MT HSPC, the mechanistic link of various pathogenesis associated with TET2 loss in CHIP is less understood. Here we review the recent development in TET2 biology and its probable mechanistic link in CH with aging and inflammation. We also explored the therapeutic strategies of targeting TET2MT associated CHIP and the utility of targeting TET2 in normal hematopoiesis and somatic cell reprograming. We explore the biochemical mechanisms and candidate therapies that emerged in last decade of research.
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Affiliation(s)
- Luca Guarnera
- Department of Biomedicine and Prevention, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy; Department of Translational Haematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Babal K Jha
- Department of Translational Haematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH; Center for Immunotherapy and Precision Immuno-Oncology (CITI), Lerner Research Institute (LRI) Cleveland Clinic, Cleveland, OH.
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10
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Kwon R, Yeung CCS. Advances in next-generation sequencing and emerging technologies for hematologic malignancies. Haematologica 2024; 109:379-387. [PMID: 37584286 PMCID: PMC10828783 DOI: 10.3324/haematol.2022.282442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/17/2023] [Indexed: 08/17/2023] Open
Abstract
Innovations in molecular diagnostics have often evolved through the study of hematologic malignancies. Examples include the pioneering characterization of the Philadelphia chromosome by cytogenetics in the 1970s, the implementation of polymerase chain reaction for high-sensitivity detection and monitoring of mutations and, most recently, targeted next- generation sequencing to drive the prognostic and therapeutic assessment of leukemia. Hematologists and hematopath- ologists have continued to advance in the past decade with new innovations improving the type, amount, and quality of data generated for each molecule of nucleic acid. In this review article, we touch on these new developments and discuss their implications for diagnostics in hematopoietic malignancies. We review advances in sequencing platforms and library preparation chemistry that can lead to faster turnaround times, novel sequencing techniques, the development of mobile laboratories with implications for worldwide benefits, the current status of sample types, improvements to quality and reference materials, bioinformatic pipelines, and the integration of machine learning and artificial intelligence into mol- ecular diagnostic tools for hematologic malignancies.
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Affiliation(s)
- Regina Kwon
- Department of Laboratory Medicine and Pathology, University of Washington
| | - Cecilia C. S. Yeung
- Department of Laboratory Medicine and Pathology, University of Washington
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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11
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Eisfeld AK, Mardis ER. Acute Myeloid Leukemia Genomics: Impact on Care and Remaining Challenges. Clin Chem 2024; 70:4-12. [PMID: 38175584 DOI: 10.1093/clinchem/hvad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/03/2023] [Indexed: 01/05/2024]
Affiliation(s)
- Ann-Kathrin Eisfeld
- Division of Hematology, The Ohio State University College of Medicine, Columbus, OH, United States
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Elaine R Mardis
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
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12
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Calderon A, Han C, Karma S, Wang E. Non-genetic mechanisms of drug resistance in acute leukemias. Trends Cancer 2024; 10:38-51. [PMID: 37839973 DOI: 10.1016/j.trecan.2023.09.003] [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] [Received: 06/20/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
Acute leukemia is characterized by clonal heterogeneity that contributes to poor drug responses in patients. Despite treatment advances, the occurrence of relapse remains a major barrier to achieving cures as current therapeutic approaches are inadequate to effectively prevent or overcome resistance. Given that only a few genetic mutations are associated with relapse in acute leukemia patients, there is a growing focus on 'non-genetic' mechanisms that affect the hallmarks of cancer to allow leukemic cells to survive post therapy. In this review, we provide an overview of the therapeutic landscape in acute leukemias. Importantly, we discuss non-genetic mechanisms exploited by leukemic cells to promote their survival after treatment. Last, we present current strategies to prevent or overcome drug resistance in this disease.
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Affiliation(s)
| | - Cuijuan Han
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Sadik Karma
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA
| | - Eric Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
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13
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McClatchy J, Strogantsev R, Wolfe E, Lin HY, Mohammadhosseini M, Davis BA, Eden C, Goldman D, Fleming WH, Conley P, Wu G, Cimmino L, Mohammed H, Agarwal A. Clonal hematopoiesis related TET2 loss-of-function impedes IL1β-mediated epigenetic reprogramming in hematopoietic stem and progenitor cells. Nat Commun 2023; 14:8102. [PMID: 38062031 PMCID: PMC10703894 DOI: 10.1038/s41467-023-43697-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Clonal hematopoiesis (CH) is defined as a single hematopoietic stem/progenitor cell (HSPC) gaining selective advantage over a broader range of HSPCs. When linked to somatic mutations in myeloid malignancy-associated genes, such as TET2-mediated clonal hematopoiesis of indeterminate potential or CHIP, it represents increased risk for hematological malignancies and cardiovascular disease. IL1β is elevated in patients with CHIP, however, its effect is not well understood. Here we show that IL1β promotes expansion of pro-inflammatory monocytes/macrophages, coinciding with a failure in the demethylation of lymphoid and erythroid lineage associated enhancers and transcription factor binding sites, in a mouse model of CHIP with hematopoietic-cell-specific deletion of Tet2. DNA-methylation is significantly lost in wild type HSPCs upon IL1β administration, which is resisted by Tet2-deficient HSPCs, and thus IL1β enhances the self-renewing ability of Tet2-deficient HSPCs by upregulating genes associated with self-renewal and by resisting demethylation of transcription factor binding sites related to terminal differentiation. Using aged mouse models and human progenitors, we demonstrate that targeting IL1 signaling could represent an early intervention strategy in preleukemic disorders. In summary, our results show that Tet2 is an important mediator of an IL1β-promoted epigenetic program to maintain the fine balance between self-renewal and lineage differentiation during hematopoiesis.
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Affiliation(s)
- J McClatchy
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - R Strogantsev
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - E Wolfe
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - H Y Lin
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - M Mohammadhosseini
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - B A Davis
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - C Eden
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - D Goldman
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA
- Division of Pediatric Hematology and Oncology, Oregon Health & Science University, Portland, OR, USA
| | - W H Fleming
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA
- Division of Pediatric Hematology and Oncology, Oregon Health & Science University, Portland, OR, USA
| | - P Conley
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - G Wu
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - L Cimmino
- University of Miami, Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miami, USA
| | - H Mohammed
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - A Agarwal
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA.
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA.
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA.
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14
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Stelmach P, Richter S, Sauer S, Fabre MA, Gu M, Rohde C, Janssen M, Liebers N, Proynova R, Weinhold N, Raab MS, Goldschmidt H, Besenbeck B, Pavel P, Laier S, Trumpp A, Dietrich S, Vassiliou GS, Müller-Tidow C. Clonal hematopoiesis with DNMT3A and PPM1D mutations impairs regeneration in autologous stem cell transplant recipients. Haematologica 2023; 108:3308-3320. [PMID: 37381752 PMCID: PMC10690900 DOI: 10.3324/haematol.2023.282992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
Clonal hematopoiesis (CH) is an age-related condition driven by stem and progenitor cells harboring recurrent mutations linked to myeloid neoplasms. Currently, potential effects on hematopoiesis, stem cell function and regenerative potential under stress conditions are unknown. We performed targeted DNA sequencing of 457 hematopoietic stem cell grafts collected for autologous stem cell transplantation (ASCT) in myeloma patients and correlated our findings with high-dimensional longitudinal clinical and laboratory data (26,510 data points for blood cell counts/serum values in 25 days around transplantation). We detected CHrelated mutations in 152 patients (33.3%). Since many patients (n=54) harbored multiple CH mutations in one or more genes, we applied a non-negative matrix factorization (NMF) clustering algorithm to identify genes that are commonly co-mutated in an unbiased approach. Patients with CH were assigned to one of three clusters (C1-C3) and compared to patients without CH (C0) in a gene specific manner. To study the dynamics of blood cell regeneration following ASCT, we developed a time-dependent linear mixed effect model to validate differences in blood cell count trajectories amongst different clusters. The results demonstrated that C2, composed of patients with DNMT3A and PPM1D single and co-mutated CH, correlated with reduced stem cell yields and delayed platelet count recovery following ASCT. Also, the benefit of maintenance therapy was particularly strong in C2 patients. Taken together, these data indicate an impaired regenerative potential of hematopoietic stem cell grafts harboring CH with DNMT3A and PPM1D mutations.
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Affiliation(s)
- Patrick Stelmach
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany; Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM, gGmbH), Heidelberg
| | - Sarah Richter
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Sandra Sauer
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Margarete A Fabre
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R/D, AstraZeneca, Cambridge
| | - Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge
| | - Christian Rohde
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Maike Janssen
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Nora Liebers
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany; National Center for Tumor Diseases (NCT), Heidelberg
| | - Rumyana Proynova
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Niels Weinhold
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Marc S Raab
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | | | - Birgit Besenbeck
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Petra Pavel
- Stem Cell Laboratory, Institute of Clinical Transfusion Medicine and Cell Therapy Heidelberg GmbH, Heidelberg
| | - Sascha Laier
- Stem Cell Laboratory, Institute of Clinical Transfusion Medicine and Cell Therapy Heidelberg GmbH, Heidelberg
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM, gGmbH), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg
| | - Sascha Dietrich
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), Heidelberg
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge
| | - Carsten Müller-Tidow
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany; National Center for Tumor Diseases (NCT), Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), Heidelberg.
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15
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Nazaret A, Fan JL, Lavallée VP, Cornish AE, Kiseliovas V, Masilionis I, Chun J, Bowman RL, Eisman SE, Wang J, Shi L, Levine RL, Mazutis L, Blei D, Pe'er D, Azizi E. Deep generative model deciphers derailed trajectories in acute myeloid leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566719. [PMID: 38014231 PMCID: PMC10680623 DOI: 10.1101/2023.11.11.566719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Single-cell genomics has the potential to map cell states and their dynamics in an unbiased way in response to perturbations like disease. However, elucidating the cell-state transitions from healthy to disease requires analyzing data from perturbed samples jointly with unperturbed reference samples. Existing methods for integrating and jointly visualizing single-cell datasets from distinct contexts tend to remove key biological differences or do not correctly harmonize shared mechanisms. We present Decipher, a model that combines variational autoencoders with deep exponential families to reconstruct derailed trajectories ( https://github.com/azizilab/decipher ). Decipher jointly represents normal and perturbed single-cell RNA-seq datasets, revealing shared and disrupted dynamics. It further introduces a novel approach to visualize data, without the need for methods such as UMAP or TSNE. We demonstrate Decipher on data from acute myeloid leukemia patient bone marrow specimens, showing that it successfully characterizes the divergence from normal hematopoiesis and identifies transcriptional programs that become disrupted in each patient when they acquire NPM1 driver mutations.
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16
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Vallelonga V, Gandolfi F, Ficara F, Della Porta MG, Ghisletti S. Emerging Insights into Molecular Mechanisms of Inflammation in Myelodysplastic Syndromes. Biomedicines 2023; 11:2613. [PMID: 37892987 PMCID: PMC10603842 DOI: 10.3390/biomedicines11102613] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Inflammation impacts human hematopoiesis across physiologic and pathologic conditions, as signals derived from the bone marrow microenvironment, such as pro-inflammatory cytokines and chemokines, have been shown to alter hematopoietic stem cell (HSCs) homeostasis. Dysregulated inflammation can skew HSC fate-related decisions, leading to aberrant hematopoiesis and potentially contributing to the pathogenesis of hematological disorders such as myelodysplastic syndromes (MDS). Recently, emerging studies have used single-cell sequencing and muti-omic approaches to investigate HSC cellular heterogeneity and gene expression in normal hematopoiesis as well as in myeloid malignancies. This review summarizes recent reports mechanistically dissecting the role of inflammatory signaling and innate immune response activation due to MDS progression. Furthermore, we highlight the growing importance of using multi-omic techniques, such as single-cell profiling and deconvolution methods, to unravel MDSs' heterogeneity. These approaches have provided valuable insights into the patterns of clonal evolution that drive MDS progression and have elucidated the impact of inflammation on the composition of the bone marrow immune microenvironment in MDS.
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Affiliation(s)
- Veronica Vallelonga
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20139 Milan, Italy
| | - Francesco Gandolfi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20139 Milan, Italy
| | - Francesca Ficara
- Milan Unit, CNR-IRGB, 20090 Milan, Italy
- IRCCS Humanitas Research Hospital, 20089 Milan, Italy
| | - Matteo Giovanni Della Porta
- IRCCS Humanitas Research Hospital, 20089 Milan, Italy
- Department of Biomedical Sciences, Humanitas University, 20072 Milan, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20139 Milan, Italy
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17
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Neelamraju Y, Gjini E, Chhangawala S, Fan H, He S, Jing CB, Nguyen AT, Prajapati S, Sheridan C, Houvras Y, Melnick A, Look AT, Garrett-Bakelman FE. Depletion of tet2 results in age-dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome. FRONTIERS IN HEMATOLOGY 2023; 2:1235170. [PMID: 37937078 PMCID: PMC10629367 DOI: 10.3389/frhem.2023.1235170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Introduction Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis, cytopenias, and dysplasia. The gene encoding ten-eleven translocation 2 (tet2), a dioxygenase enzyme that catalyzes the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine, is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously, we reported a stable zebrafish line with a loss-of-function mutation in the tet2 gene. The tet2m/m-mutant zebrafish developed a pre-MDS state with kidney marrow dysplasia, but normal circulating blood counts by 11 months of age and accompanying anemia, signifying the onset of MDS, by 24 months of age. Methods In the current study, we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 and 15 months of age and conducted enhanced reduced representation of bisulfite sequencing (ERRBS) and bulk RNA-seq to measure changes in DNA methylation and gene expression of hematopoietic stem and progenitor cells (HSPCs). Results and discussion A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 months of age when compared with the wild type. Furthermore, hypermethylated genes were significantly enriched for targets of SUZ12 and the metal-response-element-binding transcription factor 2 (MTF2)-involved in the polycomb repressive complex 2 (PRC2). However, between 4 and 15 months of age, we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analyses identified upregulation of genes associated with mTORC1 signaling and interferon gamma and alpha responses in tet2m/m HSPCs at 4 months of age when compared with the wild type. Downregulated genes in HSPCs of tet2-mutant fish at 4 months of age were enriched for cell cycle regulation, heme metabolism, and interleukin 2 (IL2)/signal transducer and activator of transcription 5 (STAT5) signaling, possibly related to increased self-renewal and clonal advantage in HSPCs with tet2 loss of function. Finally, there was an overall inverse correlation between overall increased promoter methylation and gene expression.
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Affiliation(s)
- Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Evisa Gjini
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | | | - Hao Fan
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | | | - Ashley T. Nguyen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Subhash Prajapati
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Caroline Sheridan
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | | | - Ari Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Francine E. Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
- Department of Medicine, University of Virginia, Charlottesville, VA, United States
- University of Virginia Cancer Center, Charlottesville, VA, United States
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18
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Marongiu F, Cheri S, Laconi E. Clones of aging: When better fitness can be dangerous. Eur J Cell Biol 2023; 102:151340. [PMID: 37423036 DOI: 10.1016/j.ejcb.2023.151340] [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] [Received: 02/28/2023] [Revised: 05/29/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023] Open
Abstract
The biological and clinical significance of aberrant clonal expansions in aged tissues is being intensely discussed. Evidence is accruing that these clones often result from the normal dynamics of cell turnover in our tissues. The aged tissue microenvironment is prone to favour the emergence of specific clones with higher fitness partly because of an overall decline in cell intrinsic regenerative potential of surrounding counterparts. Thus, expanding clones in aged tissues need not to be mechanistically associated with the development of cancer, albeit this is a possibility. We suggest that growth pattern is a critical phenotypic attribute that impacts on the fate of such clonal proliferations. The acquisition of a better proliferative fitness, coupled with a defect in tissue pattern formation, could represent a dangerous mix setting the stage for their evolution towards neoplasia.
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Affiliation(s)
- Fabio Marongiu
- Department of Biomedical Sciences, University of Cagliari, Italy
| | - Samuele Cheri
- Department of Biomedical Sciences, University of Cagliari, Italy
| | - Ezio Laconi
- Department of Biomedical Sciences, University of Cagliari, Italy.
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19
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Avagyan S, Zon LI. Clonal hematopoiesis and inflammation - the perpetual cycle. Trends Cell Biol 2023; 33:695-707. [PMID: 36593155 PMCID: PMC10310890 DOI: 10.1016/j.tcb.2022.12.001] [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: 10/03/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 01/01/2023]
Abstract
Acquired genetic or cytogenetic alterations in a blood stem cell that confer clonal fitness promote its relative expansion leading to clonal hematopoiesis (CH). Despite a largely intact hematopoietic output, CH is associated with a heightened risk of progression to hematologic malignancies and with non-hematologic health manifestations, including cardiovascular disease and overall mortality. We focus on the evidence for the role of inflammation in establishing, maintaining and reciprocally being affected by CH. We describe the known pro-inflammatory signals associated with CH and preclinical studies that elucidated the cellular mechanisms involved. We review the evolving literature on early-onset CH in germline predisposition conditions and the possible role of immune dysregulation in this context.
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Affiliation(s)
- Serine Avagyan
- Dana-Farber/Boston Children's Hospital Cancer and Blood Disorders Center, Boston, MA, USA.
| | - Leonard I Zon
- Boston Children's Hospital, Boston, MA 02215, USA; Howard Hughes Medical Institute, USA
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20
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Balandrán JC, Lasry A, Aifantis I. The Role of Inflammation in the Initiation and Progression of Myeloid Neoplasms. Blood Cancer Discov 2023; 4:254-266. [PMID: 37052531 PMCID: PMC10320626 DOI: 10.1158/2643-3230.bcd-22-0176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 04/14/2023] Open
Abstract
Myeloid malignancies are devastating hematologic cancers with limited therapeutic options. Inflammation is emerging as a novel driver of myeloid malignancy, with important implications for tumor composition, immune response, therapeutic options, and patient survival. Here, we discuss the role of inflammation in normal and malignant hematopoiesis, from clonal hematopoiesis to full-blown myeloid leukemia. We discuss how inflammation shapes clonal output from hematopoietic stem cells, how inflammation alters the immune microenvironment in the bone marrow, and novel therapies aimed at targeting inflammation in myeloid disease. SIGNIFICANCE Inflammation is emerging as an important factor in myeloid malignancies. Understanding the role of inflammation in myeloid transformation, and the interplay between inflammation and other drivers of leukemogenesis, may yield novel avenues for therapy.
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Affiliation(s)
- Juan Carlos Balandrán
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Audrey Lasry
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
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21
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Galloway-Peña JR, Jobin C. Microbiota Influences on Hematopoiesis and Blood Cancers: New Horizons? Blood Cancer Discov 2023; 4:267-275. [PMID: 37052501 PMCID: PMC10320642 DOI: 10.1158/2643-3230.bcd-22-0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 04/14/2023] Open
Abstract
Hematopoiesis governs the generation of immune cells through the differentiation of hematopoietic stem cells (HSC) into various progenitor cells, a process controlled by intrinsic and extrinsic factors. Among extrinsic factors influencing hematopoiesis is the microbiota, or the collection of microorganisms present in various body sites. The microbiota has a profound impact on host homeostasis by virtue of its ability to release various molecules and structural components, which promote normal organ function. In this review, we will discuss the role of microbiota in influencing hematopoiesis and how disrupting the microbiota/host network could lead to hematologic malignancies, as well as highlight important knowledge gaps to move this field of research forward. SIGNIFICANCE Microbiota dysfunction is associated with many pathologic conditions, including hematologic malignancies. In this review, we discuss the role of microbiota in influencing hematopoiesis and how disrupting the microbiota/host network could lead to hematologic malignancies. Understanding how the microbiota influences hematologic malignancies could have an important therapeutic impact for patients.
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Affiliation(s)
- Jessica R. Galloway-Peña
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, Florida
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22
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Bewersdorf JP, Xie Z, Bejar R, Borate U, Boultwood J, Brunner AM, Buckstein R, Carraway HE, Churpek JE, Daver NG, Porta MGD, DeZern AE, Fenaux P, Figueroa ME, Gore SD, Griffiths EA, Halene S, Hasserjian RP, Hourigan CS, Kim TK, Komrokji R, Kuchroo VK, List AF, Loghavi S, Majeti R, Odenike O, Patnaik MM, Platzbecker U, Roboz GJ, Sallman DA, Santini V, Sanz G, Sekeres MA, Stahl M, Starczynowski DT, Steensma DP, Taylor J, Abdel-Wahab O, Xu ML, Savona MR, Wei AH, Zeidan AM. Current landscape of translational and clinical research in myelodysplastic syndromes/neoplasms (MDS): Proceedings from the 1 st International Workshop on MDS (iwMDS) Of the International Consortium for MDS (icMDS). Blood Rev 2023; 60:101072. [PMID: 36934059 DOI: 10.1016/j.blre.2023.101072] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
Biological events that contribute to the pathogenesis of myelodysplastic syndromes/neoplasms (MDS) are becoming increasingly characterized and are being translated into rationally designed therapeutic strategies. Herein, we provide updates from the first International Workshop on MDS (iwMDS) of the International Consortium for MDS (icMDS) detailing recent advances in understanding the genetic landscape of MDS, including germline predisposition, epigenetic and immune dysregulation, the complexities of clonal hematopoiesis progression to MDS, as well as novel animal models of the disease. Connected to this progress is the development of novel therapies targeting specific molecular alterations, the innate immune system, and immune checkpoint inhibitors. While some of these agents have entered clinical trials (e.g., splicing modulators, IRAK1/4 inhibitors, anti-CD47 and anti-TIM3 antibodies, and cellular therapies), none have been approved for MDS. Additional preclinical and clinical work is needed to develop a truly individualized approach to the care of MDS patients.
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Affiliation(s)
- Jan Philipp Bewersdorf
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoer Xie
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Rafael Bejar
- Division of Hematology and Oncology, Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Uma Borate
- Ohio State University Comprehensive Cancer/ James Cancer Hospital, Ohio State University, Columbus, OH, USA
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew M Brunner
- Leukemia Program, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Rena Buckstein
- Department of Medical Oncology/Hematology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Hetty E Carraway
- Leukemia Program, Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jane E Churpek
- Department of Hematology, Oncology, and Palliative Care, Carbone Cancer Center, The University of Wisconsin-Madison, Madison, WI, USA
| | - Naval G Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matteo Giovanni Della Porta
- IRCCS Humanitas Clinical and Research Center & Humanitas University, Department of Biomedical Sciences, via Manzoni 56, 20089 Rozzano - Milan, Italy
| | - Amy E DeZern
- Division of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Pierre Fenaux
- Hôpital Saint Louis, Assistance Publique Hôpitaux de Paris and Paris Cité University, Paris, France
| | - Maria E Figueroa
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Steven D Gore
- National Cancer Institute, Cancer Therapy Evaluation Program, Bethesda, MD, USA
| | | | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | | | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, and Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD, USA
| | - Tae Kon Kim
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rami Komrokji
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Alan F List
- Precision BioSciences, Inc., Durham, NC, USA
| | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Olatoyosi Odenike
- Leukemia Program, University of Chicago Medicine and University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - Mrinal M Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Gail J Roboz
- Weill Cornell Medical College, New York, NY, USA
| | - David A Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | | | - Guillermo Sanz
- Health Research Institute La Fe, Valencia, Spain; Hospital Universitario y Politécnico La Fe, Valencia, Spain; CIBERONC, IS Carlos III, Madrid, Spain
| | - Mikkael A Sekeres
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Omar Abdel-Wahab
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mina L Xu
- Departments of Pathology & Laboratory Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | - Michael R Savona
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew H Wei
- Department of Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Walter and Eliza Hall Institute of Medical Research and University of Melbourne, Victoria, Australia
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA.
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23
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Weinhäuser I, Pereira-Martins DA, Almeida LY, Hilberink JR, Silveira DRA, Quek L, Ortiz C, Araujo CL, Bianco TM, Lucena-Araujo A, Mota JM, Hogeling SM, Sternadt D, Visser N, Diepstra A, Ammatuna E, Huls G, Rego EM, Schuringa JJ. M2 macrophages drive leukemic transformation by imposing resistance to phagocytosis and improving mitochondrial metabolism. SCIENCE ADVANCES 2023; 9:eadf8522. [PMID: 37058562 DOI: 10.1126/sciadv.adf8522] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
It is increasingly becoming clear that cancers are a symbiosis of diverse cell types and tumor clones. Combined single-cell RNA sequencing, flow cytometry, and immunohistochemistry studies of the innate immune compartment in the bone marrow of patients with acute myeloid leukemia (AML) reveal a shift toward a tumor-supportive M2-polarized macrophage landscape with an altered transcriptional program, with enhanced fatty acid oxidation and NAD+ generation. Functionally, these AML-associated macrophages display decreased phagocytic activity and intra-bone marrow coinjection of M2 macrophages together with leukemic blasts strongly enhances in vivo transformation potential. A 2-day in vitro exposure to M2 macrophages results in the accumulation of CALRlow leukemic blast cells, which are now protected against phagocytosis. Moreover, M2-exposed "trained" leukemic blasts display increased mitochondrial metabolism, in part mediated via mitochondrial transfer. Our study provides insight into the mechanisms by which the immune landscape contributes to aggressive leukemia development and provides alternatives for targeting strategies aimed at the tumor microenvironment.
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Affiliation(s)
- Isabel Weinhäuser
- Department of Experimental Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine, Medical School of Ribeirao Preto, University of São Paulo, Ribeirao Preto, Brazil
- Center for Cell Based Therapy, University of São Paulo, Ribeirao Preto, Brazil
| | - Diego A Pereira-Martins
- Department of Experimental Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine, Medical School of Ribeirao Preto, University of São Paulo, Ribeirao Preto, Brazil
- Center for Cell Based Therapy, University of São Paulo, Ribeirao Preto, Brazil
| | - Luciana Y Almeida
- Department of Internal Medicine, Medical School of Ribeirao Preto, University of São Paulo, Ribeirao Preto, Brazil
| | - Jacobien R Hilberink
- Department of Experimental Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Douglas R A Silveira
- Myeloid Leukaemia Genomics and Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, SE5 8AF, UK
| | - Lynn Quek
- Myeloid Leukaemia Genomics and Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, SE5 8AF, UK
| | - Cesar Ortiz
- Department of Internal Medicine, Medical School of Ribeirao Preto, University of São Paulo, Ribeirao Preto, Brazil
- Center for Cell Based Therapy, University of São Paulo, Ribeirao Preto, Brazil
| | - Cleide L Araujo
- Department of Internal Medicine, Medical School of Ribeirao Preto, University of São Paulo, Ribeirao Preto, Brazil
| | - Thiago M Bianco
- Department of Internal Medicine, Medical School of Ribeirao Preto, University of São Paulo, Ribeirao Preto, Brazil
| | | | - Jose Mauricio Mota
- Medical Oncology Service, Sao Paulo State Cancer Institute, University of Sao Paulo, Brazil
| | - Shanna M Hogeling
- Department of Experimental Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Dominique Sternadt
- Department of Experimental Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Nienke Visser
- Department of Experimental Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Emanuele Ammatuna
- Department of Experimental Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Gerwin Huls
- Department of Experimental Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Eduardo M Rego
- Center for Cell Based Therapy, University of São Paulo, Ribeirao Preto, Brazil
| | - Jan Jacob Schuringa
- Department of Experimental Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
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24
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Harada T, Kalfon J, Perez MW, Eagle K, Braes FD, Batley R, Heshmati Y, Ferrucio JX, Ewers J, Mehta S, Kossenkov A, Ellegast JM, Bowker A, Wickramasinghe J, Nabet B, Paralkar VR, Dharia NV, Stegmaier K, Orkin SH, Pimkin M. Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532438. [PMID: 36993171 PMCID: PMC10054969 DOI: 10.1101/2023.03.13.532438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Lineage-defining transcription factors form densely interconnected circuits in chromatin occupancy assays, but the functional significance of these networks remains underexplored. We reconstructed the functional topology of a leukemia cell transcription network from the direct gene-regulatory programs of eight core transcriptional regulators established in pre-steady state assays coupling targeted protein degradation with nascent transcriptomics. The core regulators displayed narrow, largely non-overlapping direct transcriptional programs, forming a sparsely interconnected functional hierarchy stabilized by incoherent feed-forward loops. BET bromodomain and CDK7 inhibitors disrupted the core regulators' direct programs, acting as mixed agonists/antagonists. The network is predictive of dynamic gene expression behaviors in time-resolved assays and clinically relevant pathway activity in patient populations.
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Affiliation(s)
- Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Jérémie Kalfon
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Monika W. Perez
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Kenneth Eagle
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Ken Eagle Consulting, Houston, TX, 77494, USA
| | - Flora Dievenich Braes
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Rashad Batley
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Yaser Heshmati
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Juliana Xavier Ferrucio
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Jazmin Ewers
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Stuti Mehta
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | | | - Jana M. Ellegast
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Allyson Bowker
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | | | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Vikram R. Paralkar
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Neekesh V. Dharia
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Kimberly Stegmaier
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Stuart H. Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
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25
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Mao S, Qian Y, Wei W, Lin X, Ling Q, Ye W, Li F, Pan J, Zhou Y, Zhao Y, Huang X, Huang J, Hu C, Li M, Sun J, Jin J. FLOT1 knockdown inhibits growth of AML cells through triggering apoptosis and pyroptosis. Ann Hematol 2023; 102:583-595. [PMID: 36697954 DOI: 10.1007/s00277-023-05103-x] [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: 07/14/2022] [Accepted: 01/15/2023] [Indexed: 01/27/2023]
Abstract
Acute myeloid leukemia (AML) is a group of hematological malignancies characterized by clonal proliferation of immature myeloid cells. Lipid rafts are highly organized membrane subdomains enriched in cholesterol, sphingolipids, and gangliosides and play roles in regulating apoptosis through subcellular redistribution. Flotillin1 (FLOT1) is a component and also a marker of lipid rafts and had been reported to be involved in the progression of cancers and played important roles in cell death. However, the role of FLOT1 in AML remains to be explored. In this study, we found that increased expression of FLOT1 was correlated with poor clinical outcome in AML patients. Knockdown of FLOT1 in AML cells not only promoted cell death in vitro but also inhibited malignant cells engraftment in vivo. Mechanically, FLOT1 knockdown triggered apoptosis and pyroptosis. FLOT1 overexpression promoted AML cell growth and apoptosis resistance. Our findings indicate that FLOT1 is a prognostic factor of AML and may be a potential target for AML treatment.
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Affiliation(s)
- Shihui Mao
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Yu Qian
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Wenwen Wei
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Xiangjie Lin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Qing Ling
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Wenle Ye
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Fenglin Li
- The Affiliated People's Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
| | - Jiajia Pan
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Yutong Zhou
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Yanchun Zhao
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Xin Huang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Jiansong Huang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Chao Hu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Mengjing Li
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China.,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Jie Sun
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China. .,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China. .,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China. .,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China.
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Zhejiang, People's Republic of China. .,Zhejiang Provincial Key Laboratory of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China. .,Zhejiang Provincial Clinical Research Center For Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China. .,Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China. .,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, People's Republic of China.
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26
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The Application of Single-Cell RNA Sequencing in the Inflammatory Tumor Microenvironment. Biomolecules 2023; 13:biom13020344. [PMID: 36830713 PMCID: PMC9953711 DOI: 10.3390/biom13020344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
The initiation and progression of tumors are complex. The cancer evolution-development hypothesis holds that the dysregulation of immune balance is caused by the synergistic effect of immune genetic factors and environmental factors that stimulate and maintain non-resolving inflammation. Throughout the cancer development process, this inflammation creates a microenvironment for the evolution and development of cancer. Research on the inflammatory tumor microenvironment (TME) explains the initiation and progression of cancer and guides anti-cancer immunotherapy. Single-cell RNA sequencing (scRNA-seq) can detect the transcription levels of cells at the single-cell resolution level, reveal the heterogeneity and evolutionary trajectory of infiltrated immune cells and cancer cells, and provide insight into the composition and function of each cell group in the inflammatory TME. This paper summarizes the application of scRNA-seq in inflammatory TME.
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27
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Stelmach P, Trumpp A. Leukemic stem cells and therapy resistance in acute myeloid leukemia. Haematologica 2023; 108:353-366. [PMID: 36722405 PMCID: PMC9890038 DOI: 10.3324/haematol.2022.280800] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Indexed: 02/02/2023] Open
Abstract
A major obstacle in the treatment of acute myeloid leukemia (AML) is refractory disease or relapse after achieving remission. The latter arises from a few therapy-resistant cells within minimal residual disease (MRD). Resistant cells with long-term self-renewal capacity that drive clonal outgrowth are referred to as leukemic stem cells (LSC). The cancer stem cell concept considers LSC as relapse-initiating cells residing at the top of each genetically defined AML subclone forming epigenetically controlled downstream hierarchies. LSC display significant phenotypic and epigenetic plasticity, particularly in response to therapy stress, which results in various mechanisms mediating treatment resistance. Given the inherent chemotherapy resistance of LSC, targeted strategies must be incorporated into first-line regimens to prevent LSC-mediated AML relapse. The combination of venetoclax and azacitidine is a promising current strategy for the treatment of AML LSC. Nevertheless, the selection of patients who would benefit either from standard chemotherapy or venetoclax + azacitidine treatment in first-line therapy has yet to be established and the mechanisms of resistance still need to be discovered and overcome. Clinical trials are currently underway that investigate LSC susceptibility to first-line therapies. The era of single-cell multi-omics has begun to uncover the complex clonal and cellular architectures and associated biological networks. This should lead to a better understanding of the highly heterogeneous AML at the inter- and intra-patient level and identify resistance mechanisms by longitudinal analysis of patients' samples. This review discusses LSC biology and associated resistance mechanisms, potential therapeutic LSC vulnerabilities and current clinical trial activities.
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Affiliation(s)
- Patrick Stelmach
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM, gGmbH),Department of Medicine V, Heidelberg University Hospital
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM, gGmbH); Faculty of Biosciences, Heidelberg University; German Cancer Consortium (DKTK), Heidelberg.
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28
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Yanir AD, Izraeli S. Inflammation meets translation in AML. NATURE CANCER 2023; 4:3-4. [PMID: 36721071 DOI: 10.1038/s43018-022-00499-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Asaf D Yanir
- Schneider Children's Medical Center, Petach Tikva, Israel
| | - Shai Izraeli
- Schneider Children's Medical Center, Petach Tikva, Israel.
- Felsentein Research Institute, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Beckman Research Institute, City of Hope, Duarte, CA, USA.
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29
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Tsagaratou A. TET Proteins in the Spotlight: Emerging Concepts of Epigenetic Regulation in T Cell Biology. Immunohorizons 2023; 7:106-115. [PMID: 36645853 PMCID: PMC10152628 DOI: 10.4049/immunohorizons.2200067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
Ten-eleven translocation (TET) proteins are dioxygenases that oxidize 5-methylcytosine to form 5-hydroxymethylcytosine and downstream oxidized modified cytosines. In the past decade, intensive research established that TET-mediated DNA demethylation is critical for immune cell development and function. In this study, we discuss major advances regarding the role of TET proteins in regulating gene expression in the context of T cell lineage specification, function, and proliferation. Then, we focus on open questions in the field. We discuss recent findings regarding the diverse roles of TET proteins in other systems, and we ask how these findings might relate to T cell biology. Finally, we ask how this tremendous progress on understanding the multifaceted roles of TET proteins in shaping T cell identity and function can be translated to improve outcomes of human disease, such as hematological malignancies and immune response to cancer.
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Affiliation(s)
- Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; and Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC
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Lasry A, Nadorp B, Fornerod M, Nicolet D, Wu H, Walker CJ, Sun Z, Witkowski MT, Tikhonova AN, Guillamot-Ruano M, Cayanan G, Yeaton A, Robbins G, Obeng EA, Tsirigos A, Stone RM, Byrd JC, Pounds S, Carroll WL, Gruber TA, Eisfeld AK, Aifantis I. An inflammatory state remodels the immune microenvironment and improves risk stratification in acute myeloid leukemia. NATURE CANCER 2023; 4:27-42. [PMID: 36581735 PMCID: PMC9986885 DOI: 10.1038/s43018-022-00480-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/04/2022] [Indexed: 12/31/2022]
Abstract
Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and limited treatment options. Here we provide a comprehensive census of the bone marrow immune microenvironment in adult and pediatric patients with AML. We characterize unique inflammation signatures in a subset of AML patients, associated with inferior outcomes. We identify atypical B cells, a dysfunctional B-cell subtype enriched in patients with high-inflammation AML, as well as an increase in CD8+GZMK+ and regulatory T cells, accompanied by a reduction in T-cell clonal expansion. We derive an inflammation-associated gene score (iScore) that associates with poor survival outcomes in patients with AML. Addition of the iScore refines current risk stratifications for patients with AML and may enable identification of patients in need of more aggressive treatment. This work provides a framework for classifying patients with AML based on their immune microenvironment and a rationale for consideration of the inflammatory state in clinical settings.
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Affiliation(s)
- Audrey Lasry
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Bettina Nadorp
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Maarten Fornerod
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher J Walker
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Zhengxi Sun
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Matthew T Witkowski
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Anastasia N Tikhonova
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Maria Guillamot-Ruano
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Geraldine Cayanan
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Anna Yeaton
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Gabriel Robbins
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Esther A Obeng
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John C Byrd
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William L Carroll
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Tanja A Gruber
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Ann-Kathrin Eisfeld
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA.
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, USA.
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY, USA.
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.
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Zhou H, Wang F, Niu T. Prediction of prognosis and immunotherapy response of amino acid metabolism genes in acute myeloid leukemia. Front Nutr 2022; 9:1056648. [PMID: 36618700 PMCID: PMC9815546 DOI: 10.3389/fnut.2022.1056648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Background Amino acid (AA) metabolism plays a crucial role in cancer. However, its role in acute myeloid leukemia (AML) is still unavailable. We screened out AA metabolic genes, which related to prognosis, and analyzed their correlation with tumor immune microenvironment in AML. Methods We evaluated 472 amino acid metabolism-related genes in 132 AML patients. The predictive risk model was developed according to differentially expressed genes, univariate Cox and LASSO analyses. We validated the risk signature by survival analysis and independence tests. Single-sample gene set enrichment analysis (ssGSEA), tumor immune microenvironment (TME), tumor mutation burden (TMB), functional enrichment, and the IC50 of drugs were assessed to explore the correlations among the risk model, immunity, and drug sensitivity of AML. Results Six amino acid metabolism-related genes were confirmed to develop the risk model, including TRH, HNMT, TFEB, SDSL, SLC43A2, and SFXN3. The high-risk subgroup had an immune "hot" phenotype and was related to a poor prognosis. The high-risk group was also associated with more activity of immune cells, such as Tregs, had higher expression of some immune checkpoints, including PD1 and CTLA4, and might be more susceptible to immunotherapy. Xenobiotic metabolism, the reactive oxygen species (ROS) pathway, fatty acid metabolism, JAK/STAT3, and the inflammatory response were active in the high-risk subgroup. Furthermore, the high-risk subgroup was sensitive to sorafenib, selumetinib, and entospletinib. ssGSEA discovered that the processes of glutamine, arginine, tryptophan, cysteine, histidine, L-serine, isoleucine, threonine, tyrosine, and L-phenylalanine metabolism were more active in the high-risk subgroup. Conclusion This study revealed that AA metabolism-related genes were correlated with the immune microenvironment of AML patients and could predict the prognosis and immunotherapy response of AML patients.
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Affiliation(s)
- Hui Zhou
- Department of Hematology and Research Laboratory of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fengjuan Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ting Niu
- Department of Hematology and Research Laboratory of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China,*Correspondence: Ting Niu,
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