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Katerndahl CDS, Rogers ORS, Day RB, Xu Z, Helton NM, Ramakrishnan SM, Miller CA, Ley TJ. PML::RARA and GATA2 proteins interact via DNA templates to induce aberrant self-renewal in mouse and human hematopoietic cells. Proc Natl Acad Sci U S A 2024; 121:e2317690121. [PMID: 38648485 PMCID: PMC11067031 DOI: 10.1073/pnas.2317690121] [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: 10/17/2023] [Accepted: 03/15/2024] [Indexed: 04/25/2024] Open
Abstract
The underlying mechanism(s) by which the PML::RARA fusion protein initiates acute promyelocytic leukemia is not yet clear. We defined the genomic binding sites of PML::RARA in primary mouse and human hematopoietic progenitor cells with V5-tagged PML::RARA, using anti-V5-PML::RARA chromatin immunoprecipitation sequencing and CUT&RUN approaches. Most genomic PML::RARA binding sites were found in regions that were already chromatin-accessible (defined by ATAC-seq) in unmanipulated, wild-type promyelocytes, suggesting that these regions are "open" prior to PML::RARA expression. We found that GATA binding motifs, and the direct binding of the chromatin "pioneering factor" GATA2, were significantly enriched near PML::RARA binding sites. Proximity labeling studies revealed that PML::RARA interacts with ~250 proteins in primary mouse hematopoietic cells; GATA2 and 33 others require PML::RARA binding to DNA for the interaction to occur, suggesting that binding to their cognate DNA target motifs may stabilize their interactions. In the absence of PML::RARA, Gata2 overexpression induces many of the same epigenetic and transcriptional changes as PML::RARA. These findings suggested that PML::RARA may indirectly initiate its transcriptional program by activating Gata2 expression: Indeed, we demonstrated that inactivation of Gata2 prior to PML::RARA expression prevented its ability to induce self-renewal. These data suggested that GATA2 binding creates accessible chromatin regions enriched for both GATA and Retinoic Acid Receptor Element motifs, where GATA2 and PML::RARA can potentially bind and interact with each other. In turn, PML::RARA binding to DNA promotes a feed-forward transcriptional program by positively regulating Gata2 expression. Gata2 may therefore be required for PML::RARA to establish its transcriptional program.
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Affiliation(s)
- Casey D. S. Katerndahl
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Olivia R. S. Rogers
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Ryan B. Day
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Ziheng Xu
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Nichole M. Helton
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Sai Mukund Ramakrishnan
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Christopher A. Miller
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Timothy J. Ley
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
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Hua J, Chu M, Wang C, Zhang H, Luan J, Zhang Y, Li Q, Xiao T, Zhu C, Li X, Fu B. Digital PCR-based GRHL2 methylation testing in acute myeloid leukemia: diagnosis, prognosis and monitoring. Epigenomics 2024; 16:233-247. [PMID: 38343387 DOI: 10.2217/epi-2023-0406] [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] [Indexed: 02/17/2024] Open
Abstract
Background: Acute myeloid leukemia (AML) is a challenging disease with high rates of recurrence. The role of the cancer-related gene GRHL2 in AML has not been widely studied. Methods: Peripheral blood samples were collected from 73 AML patients and 68 healthy controls. Droplet digital PCR was used to detect GRHL2 methylation levels to explore the value of GRHL2 methylation in the diagnosis, treatment response and prognosis of AML. Result: GRHL2 methylation was significantly increased in AML patients (p < 0.01), with high diagnostic accuracy (area under the curve: 0.848; p < 0.001). GRHL2 methylation was correlated with chemotherapy response (p < 0.05) and is an independent prognostic factor for AML (p < 0.05). Conclusion: GRHL2 methylation is expected to serve as a biomarker for diagnosing AML patients and predicting prognosis.
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Affiliation(s)
- Jing Hua
- Department of Hematology, Shandong Provincial Qianfoshan Hospital, Shandong University
- Department of Hematology, Liaocheng People's Hospital
| | - Miaomiao Chu
- Department of Precision Biomedical Laboratory, Liaocheng People's Hospital
| | - Chaohui Wang
- Department of Hematology, Hematology, Qingdao Haici Medical Group
| | - Hangfan Zhang
- Department of Hematology, Liaocheng People's Hospital
| | - Jing Luan
- Department of Hematology, Liaocheng People's Hospital
| | - Yifei Zhang
- Department of Hematology, Liaocheng People's Hospital
| | - Qiang Li
- Department of Hematology, Liaocheng People's Hospital
| | - Taiwu Xiao
- Department of Hematology, Liaocheng People's Hospital
| | - Chuansheng Zhu
- Department of Hematology, Shandong Provincial Qianfoshan Hospital, Shandong University
| | - Xuan Li
- The Key Laboratory of Molecular Pharmacology, Liaocheng People's Hospital, Liaocheng
| | - Bo Fu
- Department of Precision Biomedical Laboratory, Liaocheng People's Hospital
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Rodríguez-Medina C, Stuckey R, Bilbao-Sieyro C, Gómez-Casares MT. Biomarkers of Response to Venetoclax Therapy in Acute Myeloid Leukemia. Int J Mol Sci 2024; 25:1421. [PMID: 38338698 PMCID: PMC10855565 DOI: 10.3390/ijms25031421] [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: 12/12/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Recent progress in the use of massive sequencing technologies has greatly enhanced our understanding of acute myeloid leukemia (AML) pathology. This knowledge has in turn driven the development of targeted therapies, such as venetoclax, a BCL-2 inhibitor approved for use in combination with azacitidine, decitabine, or low-dose cytarabine for the treatment of newly diagnosed adult patients with AML who are not eligible for intensive chemotherapy. However, a significant number of AML patients still face the challenge of disease relapse. In this review, we will explore biomarkers that may predict disease progression in patients receiving venetoclax-based therapy, considering both clinical factors and genetic changes. Despite the many advances, we conclude that the identification of molecular profiles for AML patients who will respond optimally to venetoclax therapy remains an unmet clinical need.
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Affiliation(s)
- Carlos Rodríguez-Medina
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (C.R.-M.); (R.S.); (C.B.-S.)
| | - Ruth Stuckey
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (C.R.-M.); (R.S.); (C.B.-S.)
| | - Cristina Bilbao-Sieyro
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (C.R.-M.); (R.S.); (C.B.-S.)
- Morphology Department, Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain
| | - María Teresa Gómez-Casares
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (C.R.-M.); (R.S.); (C.B.-S.)
- Department of Medical Sciences, Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain
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Zhang W, Zhao M, Xin L, Qi X, Cao P, Wang J, Li X. Bioinformatics-based identification and validation of hub genes associated with aging in patients with coronary artery disease. Aging (Albany NY) 2023; 15:14830-14844. [PMID: 38097358 PMCID: PMC10781473 DOI: 10.18632/aging.205309] [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: 05/17/2023] [Accepted: 11/02/2023] [Indexed: 01/07/2024]
Abstract
Coronary artery disease (CAD) is the most common aging-related disease in adults. We used bioinformatics analysis to study genes associated with aging in patients with CAD. The microarray data of the GSE12288 dataset were downloaded from the Gene Expression Omnibus database to obtain 934 CAD-associated differentially expressed genes. By overlaying them with aging-related genes in the Aging Atlas database, 33 differentially expressed aging-related genes (DEARGs) were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that the 33 DEARGs were mainly enriched in cell adhesion and activation, Th17 and Th1/Th2 cell differentiation, and longevity regulation pathways. Hub genes were further screened using multiple algorithms of Cytoscape software and validation set GSE71226. Clinical samples were then collected, and the expression of hub genes in whole blood was detected by real-time quantitative polymerase chain reaction, enzyme-linked immunosorbent assay, and western blot at the transcription and translation levels. Finally, HSP90AA1 and CEBPA were identified as hub genes. The results of this study suggest that HSP90AA1 and CEBPA are closely related to CAD. These findings provide a theoretical basis for the association between aging effectors and CAD, and indicate that these genes may be promising biomarkers for the diagnosis and treatment of CAD.
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Affiliation(s)
- Wangmeng Zhang
- Department of Obstetrics, The Affiliated Tai’an City Central Hospital of Qingdao University, Tai’an 271000, Shandong, China
| | - Minmin Zhao
- Department of Obstetrics, The Affiliated Tai’an City Central Hospital of Qingdao University, Tai’an 271000, Shandong, China
| | - Li Xin
- Department of Cardiology, The Affiliated Tai’an City Central Hospital of Qingdao University, Tai’an 271000, Shandong, China
| | - Ximei Qi
- Department of Cardiology, The Affiliated Tai’an City Central Hospital of Qingdao University, Tai’an 271000, Shandong, China
| | - Ping Cao
- Department of Geriatrics, The Affiliated Tai’an City Central Hospital of Qingdao University, Tai’an 271000, Shandong, China
| | - Jiyan Wang
- Department of Internal Medicine, The Fourth People's Hospital of Tai’an City, Tai’an 271000, Shandong, China
| | - Xin Li
- Department of Obstetrics, Tai’an Maternal and Child Health Care Hospital, Tai’an 271000, Shandong, China
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Sun XH, Wan S, Chai YH, Bai XT, Li HX, Xi YM. Identifying a prognostic model and screening of potential natural compounds for acute myeloid leukemia. Transl Cancer Res 2023; 12:1535-1551. [PMID: 37434693 PMCID: PMC10331709 DOI: 10.21037/tcr-22-2500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/19/2023] [Indexed: 07/13/2023]
Abstract
Background Acute myeloid leukemia (AML) is one of the most common hematologic malignancies with a poor prognosis and high recurrence rate. The discovery of new predictive models and therapeutic agents plays a crucial role. Methods The differentially expressed gene that was explicitly highly expressed in The Cancer Genome Atlas (TCGA) and GSE9476 transcriptome databases were screened and included in the least absolute shrinkage and selection operator (LASSO) regression model to derive risk coefficients and build a risk score model. Functional enrichment analysis was conducted on the screened hub genes to explore the potential mechanisms. Subsequently, critical genes were incorporated into a nomogram model based on risk scores to analyze prognostic value. Finally, this study combined network pharmacology to find potential natural compounds for hub genes and used molecular docking to verify the binding ability of molecular structures to natural compounds to explore drug development for possible efficacy in AML. Results A total of 33 highly expressed genes may be associated with poor prognosis of AML patients. After LASSO and multivariate Cox regression analysis of 33 critical genes, Rho-related BTB domain containing 2 (RHOBTB2), phospholipase A2 (PLA2G4A), interleukin-2 receptor-α (IL2RA), cysteine and glycine-rich protein 1 (CSRP1), and olfactomedin-like 2A (OLFML2A) were found to played a significant role in the prognosis of AML patients. CSRP1 and OLFML2A were independent prognostic factors of AML. The predictive power of these 5 hub genes in combination with clinical features was better than clinical data alone in predicting AML in the column line graphs and had better predictive value at 1, 3, and 5 years. Finally, through network pharmacology and molecular docking, this study found that diosgenin in Guadi docked well with PLA2G4A, beta-sitosterol in Fangji docked well with IL2RA, and OLFML2A docked well with 3,4-di-O-caffeoylquinic acid in Beiliujinu. Conclusions The predictive model of RHOBTB2, PLA2G4A, IL2RA, CSRP1, and OLFML2A combined with clinical features can better guide the prognosis of AML. In addition, the stable docking of PLA2G4A, IL2RA, and OLFML2A with natural compounds may provide new options for treating AML.
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Affiliation(s)
- Xiao-Hong Sun
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Shun Wan
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Yi-Hong Chai
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Xiao-Teng Bai
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Hong-Xing Li
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Ya-Ming Xi
- Division of Hematology, The First Hospital of Lanzhou University, Lanzhou, China
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Targeted Epigenetic Interventions in Cancer with an Emphasis on Pediatric Malignancies. Biomolecules 2022; 13:biom13010061. [PMID: 36671446 PMCID: PMC9855367 DOI: 10.3390/biom13010061] [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: 11/26/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Over the past two decades, novel hallmarks of cancer have been described, including the altered epigenetic landscape of malignant diseases. In addition to the methylation and hyd-roxymethylation of DNA, numerous novel forms of histone modifications and nucleosome remodeling have been discovered, giving rise to a wide variety of targeted therapeutic interventions. DNA hypomethylating drugs, histone deacetylase inhibitors and agents targeting histone methylation machinery are of distinguished clinical significance. The major focus of this review is placed on targeted epigenetic interventions in the most common pediatric malignancies, including acute leukemias, brain and kidney tumors, neuroblastoma and soft tissue sarcomas. Upcoming novel challenges include specificity and potential undesirable side effects. Different epigenetic patterns of pediatric and adult cancers should be noted. Biological significance of epigenetic alterations highly depends on the tissue microenvironment and widespread interactions. An individualized treatment approach requires detailed genetic, epigenetic and metabolomic evaluation of cancer. Advances in molecular technologies and clinical translation may contribute to the development of novel pediatric anticancer treatment strategies, aiming for improved survival and better patient quality of life.
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