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Zhong L, Luo J, Dong J, Yang X, Wang X. Identifying acute myeloid leukemia subtypes based on pathway enrichment. Front Pharmacol 2025; 16:1557112. [PMID: 40191420 PMCID: PMC11968745 DOI: 10.3389/fphar.2025.1557112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2025] [Accepted: 03/14/2025] [Indexed: 04/09/2025] Open
Abstract
Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults and the second most common in children. Despite the introduction of targeted therapies, AML survival rates have shown limited improvement, particularly among older patients. This study explored personalized treatment strategies for AML by proposing a novel subtyping method. Through unsupervised clustering based on the enrichment scores of 14 pathways related to metabolism, immunity, DNA repair, and oncogenic signaling, we identified three AML subtypes: DNA repair (DR), immune-enriched (ImE), and immune-deprived (ImD), consistent in four independent datasets. DR is marked by high expression of DNA repair and metabolic pathways, high stemness and proliferation potential, as well as high sensitivity to chemotherapy. ImD is characterized by low expression of immune and oncogenic pathways, favorable survival prognosis, low mutation rates of RUNX1 and TP53, high homeostasis, and low migration potential. ImE exhibits high enrichment of immune and oncogenic pathways, low stemness and proliferation capacity, low homeostasis, high migration potential, and low sensitivity to chemotherapy. Our pathway enrichment-based subtyping approach would offer a promising framework for understanding the molecular heterogeneity of AML and guiding personalized treatment of this disease.
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Affiliation(s)
- Ling Zhong
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Intelligent Pharmacy Interdisciplinary Research Center, China Pharmaceutical University, Nanjing, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, China
| | - Jiangti Luo
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Intelligent Pharmacy Interdisciplinary Research Center, China Pharmaceutical University, Nanjing, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, China
| | - Junze Dong
- Nanjing Foreign Language School, Nanjing, China
| | - Xiang Yang
- Department of Oncology, JunXie Hospital, Nanjing, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Intelligent Pharmacy Interdisciplinary Research Center, China Pharmaceutical University, Nanjing, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, China
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Ide AD, Carpenter KA, Elaswad M, Opria K, Marcellin K, Gilliland C, Grainger S. Secreted Frizzled-Related Protein 1a regulates hematopoietic development in a dose-dependent manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.10.632371. [PMID: 39829913 PMCID: PMC11741364 DOI: 10.1101/2025.01.10.632371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) arise only during embryonic development, and their identity specification, emergence from the floor of the dorsal aorta, and proliferation are all tightly regulated by molecular mechanisms such as signaling cues. Among these, Wnt signaling plays an important role in HSPC specification, differentiation, and self-renewal, requiring precise modulation for proper development and homeostasis. Wnt signaling is initiated when a Wnt ligand binds to cell surface receptors such as those encoded by the frizzled gene family, activating intracellular signaling pathways that regulate gene expression. Secreted frizzled-related proteins (Sfrps) are known modulators of Wnt signaling, acting as both agonists and antagonists of this pathway. Yet, in vivo functions of Sfrps in HSPC development remain incompletely understood. Here, we demonstrate that Sfrp1a regulates zebrafish HSPC development and differentiation in a dose-dependent manner. In Sfrp1a loss of function animals, we observe an increase in HSPCs, an upregulation of canonical Wnt signaling, and a decrease in differentiation into both lymphoid and myeloid lineages. Conversely, at low-dose sfrp1a overexpression, there is a decrease in HSPCs and an increase in lymphoid differentiation. High-dose sfrp1a overexpression phenocopies the loss of function animals, with an increase in HSPCs, increased canonical Wnt signaling, and decreased lymphoid and myeloid differentiation. These findings highlight the importance of dose-dependent modulation of Sfrps, paralleling what is observed in hematopoietic cancers where SFRP1 loss-of-function and gain-of-function variants can drive tumorigenesis.
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Affiliation(s)
- Amber D. Ide
- Department of Cell Biology, Van Andel Institute, Grand Rapids, Michigan, 49503, USA RRID: SCR_021956
| | - Kelsey A. Carpenter
- Department of Cell Biology, Van Andel Institute, Grand Rapids, Michigan, 49503, USA RRID: SCR_021956
| | - Mohamed Elaswad
- Department of Cell Biology, Van Andel Institute, Grand Rapids, Michigan, 49503, USA RRID: SCR_021956
| | - Katherine Opria
- Department of Cell Biology, Van Andel Institute, Grand Rapids, Michigan, 49503, USA RRID: SCR_021956
| | - Kendersley Marcellin
- Department of Cell Biology, Van Andel Institute, Grand Rapids, Michigan, 49503, USA RRID: SCR_021956
| | - Carla Gilliland
- Department of Cell Biology, Van Andel Institute, Grand Rapids, Michigan, 49503, USA RRID: SCR_021956
| | - Stephanie Grainger
- Department of Cell Biology, Van Andel Institute, Grand Rapids, Michigan, 49503, USA RRID: SCR_021956
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Gajos-Michniewicz A, Czyz M. Therapeutic Potential of Natural Compounds to Modulate WNT/β-Catenin Signaling in Cancer: Current State of Art and Challenges. Int J Mol Sci 2024; 25:12804. [PMID: 39684513 DOI: 10.3390/ijms252312804] [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: 10/22/2024] [Revised: 11/22/2024] [Accepted: 11/26/2024] [Indexed: 12/18/2024] Open
Abstract
Targeted therapies and immunotherapies have improved the clinical outcome of cancer patients; however, the efficacy of treatment remains frequently limited due to low predictability of response and development of drug resistance. Therefore, novel therapeutic strategies for various cancer types are needed. Current research emphasizes the potential therapeutic value of targeting WNT/β-catenin dependent signaling that is deregulated in various cancer types. Targeting the WNT/β-catenin signaling pathway with diverse synthetic and natural agents is the subject of a number of preclinical studies and clinical trials for cancer patients. The usage of nature-derived agents is attributed to their health benefits, reduced toxicity and side effects compared to synthetic agents. The review summarizes preclinical studies and ongoing clinical trials that aim to target components of the WNT/β-catenin pathway across a diverse spectrum of cancer types, highlighting their potential to improve cancer treatment.
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Affiliation(s)
- Anna Gajos-Michniewicz
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215 Lodz, Poland
| | - Malgorzata Czyz
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215 Lodz, Poland
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Chen X, Yuan Y, Zhou F, Li L, Pu J, Jiang X. RNA modification in normal hematopoiesis and hematologic malignancies. MedComm (Beijing) 2024; 5:e787. [PMID: 39445003 PMCID: PMC11496571 DOI: 10.1002/mco2.787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 09/26/2024] [Accepted: 09/26/2024] [Indexed: 10/25/2024] Open
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification in eukaryotic cells. Previous studies have shown that m6A plays a critical role under both normal physiological and pathological conditions. Hematopoiesis and differentiation are highly regulated processes, and recent studies on m6A mRNA methylation have revealed how this modification controls cell fate in both normal and malignant hematopoietic states. However, despite these insights, a comprehensive understanding of its complex roles between normal hematopoietic development and malignant hematopoietic diseases remains elusive. This review first provides an overview of the components and biological functions of m6A modification regulators. Additionally, it highlights the origin, differentiation process, biological characteristics, and regulatory mechanisms of hematopoietic stem cells, as well as the features, immune properties, and self-renewal pathways of leukemia stem cells. Last, the article systematically reviews the latest research advancements on the roles and mechanisms of m6A regulatory factors in normal hematopoiesis and related malignant diseases. More importantly, this review explores how targeting m6A regulators and various signaling pathways could effectively intervene in the development of leukemia, providing new insights and potential therapeutic targets. Targeting m6A modification may hold promise for achieving more precise and effective leukemia treatments.
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Affiliation(s)
- Xi Chen
- Department of NeurosurgeryThe Second Affiliated Hospital of Kunming Medical UniversityKunmingChina
- NHC Key Laboratory of Drug Addiction MedicineKunming Medical UniversityKunmingYunnanChina
| | - Yixiao Yuan
- Department of MedicineUF Health Cancer CenterUniversity of FloridaGainesvilleFloridaUSA
- Department of Medicine and Department of Biochemistry and Molecular BiologyUniversity of FloridaGainesvilleFloridaUSA
| | - Fan Zhou
- Department of NeurosurgeryThe Second Affiliated Hospital of Kunming Medical UniversityKunmingChina
- NHC Key Laboratory of Drug Addiction MedicineKunming Medical UniversityKunmingYunnanChina
| | - Lihua Li
- NHC Key Laboratory of Drug Addiction MedicineKunming Medical UniversityKunmingYunnanChina
| | - Jun Pu
- Department of NeurosurgeryThe Second Affiliated Hospital of Kunming Medical UniversityKunmingChina
- NHC Key Laboratory of Drug Addiction MedicineKunming Medical UniversityKunmingYunnanChina
| | - Xiulin Jiang
- Department of MedicineUF Health Cancer CenterUniversity of FloridaGainesvilleFloridaUSA
- Department of Medicine and Department of Biochemistry and Molecular BiologyUniversity of FloridaGainesvilleFloridaUSA
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Liu S, Han B, Wang R, Fang J. Elucidating the role of FOS in modulating the immune microenvironment through fibroblast and myeloid cell regulation in locoregional recurrent HNSCC. ENVIRONMENTAL TOXICOLOGY 2024; 39:4531-4546. [PMID: 38567514 DOI: 10.1002/tox.24262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/10/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) presents a significant clinical challenge, particularly due to its high propensity for locoregional recurrence. Current research underscores the need to unravel the complex interactions within the tumor microenvironment. This study addresses the critical gap in understanding how FOS modulates the immune landscape in HNSCC, with a focus on its influence on fibroblast and myeloid cell dynamics. METHODS Employing a comprehensive approach, we analyzed tissue samples from HNSCC patients and adjacent non-cancerous tissues using bulk RNA sequencing complemented by in-depth bioinformatics analyses, including gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis, and immune infiltration assessment. A pivotal aspect of our research involved dissecting single-cell RNA-seq data from GSE234933 to elucidate the cell-type-specific expression of FOS. RESULTS We found that FOS expression varies significantly in different cell populations in the HNSCC tumor microenvironment, especially in fibroblasts and myeloid cells. This expression difference may reflect the different roles of these cells in tumor progression and their impact on the tumor microenvironment. CONCLUSION Our results uncover a significant correlation between FOS expression and key immune and hypoxia-related pathways, suggesting its integral role in the tumor microenvironment. These findings not only enhance our understanding of HNSCC pathogenesis but also highlight FOS as a potential therapeutic target. This study marks a significant step towards addressing the urgent need for targeted interventions in HNSCC, particularly in the context of locoregional recurrence.
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Affiliation(s)
- Shaokun Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Boxuan Han
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ru Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jugao Fang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Bruserud Ø, Reikvam H. Casein Kinase 2 (CK2): A Possible Therapeutic Target in Acute Myeloid Leukemia. Cancers (Basel) 2023; 15:3711. [PMID: 37509370 PMCID: PMC10378128 DOI: 10.3390/cancers15143711] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
The protein kinase CK2 (also known as casein kinase 2) is one of the main contributors to the human phosphoproteome. It is regarded as a possible therapeutic strategy in several malignant diseases, including acute myeloid leukemia (AML), which is an aggressive bone marrow malignancy. CK2 is an important regulator of intracellular signaling in AML cells, especially PI3K-Akt, Jak-Stat, NFκB, Wnt, and DNA repair signaling. High CK2 levels in AML cells at the first time of diagnosis are associated with decreased survival (i.e., increased risk of chemoresistant leukemia relapse) for patients receiving intensive and potentially curative antileukemic therapy. However, it is not known whether these high CK2 levels can be used as an independent prognostic biomarker because this has not been investigated in multivariate analyses. Several CK2 inhibitors have been developed, but CX-4945/silmitasertib is best characterized. This drug has antiproliferative and proapoptotic effects in primary human AML cells. The preliminary results from studies of silmitasertib in the treatment of other malignancies suggest that gastrointestinal and bone marrow toxicities are relatively common. However, clinical AML studies are not available. Taken together, the available experimental and clinical evidence suggests that the possible use of CK2 inhibition in the treatment of AML should be further investigated.
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Affiliation(s)
- Øystein Bruserud
- Institute for Clinical Science, Faculty of Medicine, University of Bergen, 5021 Bergen, Norway
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Håkon Reikvam
- Institute for Clinical Science, Faculty of Medicine, University of Bergen, 5021 Bergen, Norway
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
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