1
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Woodworth AM, Hardy K, Taberlay PC, Dickinson JL, Holloway AF. RUNX1 regulates promoter activity in the absence of cognate DNA binding motifs. J Cell Biochem 2024; 125:e30570. [PMID: 38616697 DOI: 10.1002/jcb.30570] [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: 12/21/2023] [Revised: 03/29/2024] [Accepted: 04/06/2024] [Indexed: 04/16/2024]
Abstract
Runt-related transcription factor 1 (RUNX1) plays an important role in normal haematopoietic cell development and function, and its function is frequently disrupted in leukaemia. RUNX1 is widely recognised as a sequence-specific DNA binding factor that recognises the motif 5'-TG(T/C)GGT-3' in promoter and enhancer regions of its target genes. Moreover, RUNX1 fusion proteins, such as RUNX1-ETO formed by the t(8;21) translocation, retain the ability to recognise and bind to this sequence to elicit atypical gene regulatory effects on bona fide RUNX1 targets. However, our analysis of publicly available RUNX1 chromatin immunoprecipitation sequencing (ChIP-Seq) data has provided evidence challenging this dogma, revealing that this motif-specific model of RUNX1 recruitment and function is incomplete. Our analyses revealed that the majority of RUNX1 genomic localisation occurs outside of promoters, that 20% of RUNX1 binding sites lack consensus RUNX motifs, and that binding in the absence of a cognate binding site is more common in promoter regions compared to distal sites. Reporter assays demonstrate that RUNX1 can drive promoter activity in the absence of a recognised DNA binding motif, in contrast to RUNX1-ETO. RUNX1-ETO supresses activity when it is recruited to promoters containing a sequence specific motif, while interestingly, it binds but does not repress promoters devoid of a RUNX1 recognition site. These data suggest that RUNX1 regulation of target genes occurs through multiple mechanisms depending on genomic location, the type of regulatory element and mode of recruitment.
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Affiliation(s)
- Alex M Woodworth
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Kristine Hardy
- Faculty of Education, Science, Technology and Mathematics, Discipline of Biomedical Science, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Adele F Holloway
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
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2
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Manickasamy MK, Sajeev A, BharathwajChetty B, Alqahtani MS, Abbas M, Hegde M, Aswani BS, Shakibaei M, Sethi G, Kunnumakkara AB. Exploring the nexus of nuclear receptors in hematological malignancies. Cell Mol Life Sci 2024; 81:78. [PMID: 38334807 PMCID: PMC10858172 DOI: 10.1007/s00018-023-05085-z] [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: 08/21/2023] [Revised: 11/16/2023] [Accepted: 12/03/2023] [Indexed: 02/10/2024]
Abstract
Hematological malignancies (HM) represent a subset of neoplasms affecting the blood, bone marrow, and lymphatic systems, categorized primarily into leukemia, lymphoma, and multiple myeloma. Their prognosis varies considerably, with a frequent risk of relapse despite ongoing treatments. While contemporary therapeutic strategies have extended overall patient survival, they do not offer cures for advanced stages and often lead to challenges such as acquisition of drug resistance, recurrence, and severe side effects. The need for innovative therapeutic targets is vital to elevate both survival rates and patients' quality of life. Recent research has pivoted towards nuclear receptors (NRs) due to their role in modulating tumor cell characteristics including uncontrolled proliferation, differentiation, apoptosis evasion, invasion and migration. Existing evidence emphasizes NRs' critical role in HM. The regulation of NR expression through agonists, antagonists, or selective modulators, contingent upon their levels, offers promising clinical implications in HM management. Moreover, several anticancer agents targeting NRs have been approved by the Food and Drug Administration (FDA). This review highlights the integral function of NRs in HM's pathophysiology and the potential benefits of therapeutically targeting these receptors, suggesting a prospective avenue for more efficient therapeutic interventions against HM.
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Affiliation(s)
- Mukesh Kumar Manickasamy
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam, 781039, India
| | - Anjana Sajeev
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam, 781039, India
| | - Bandari BharathwajChetty
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam, 781039, India
| | - Mohammed S Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, 61421, Abha, Saudi Arabia
- BioImaging Unit, Space Research Centre, University of Leicester, Michael Atiyah Building, Leicester, LE1 7RH, UK
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, 61421, Abha, Saudi Arabia
| | - Mangala Hegde
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam, 781039, India
| | - Babu Santha Aswani
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam, 781039, India
| | - Mehdi Shakibaei
- Chair of Vegetative Anatomy, Department of Human-Anatomy, Musculoskeletal Research Group and Tumor Biology, Institute of Anatomy, Ludwig-Maximilian-University, 80336, Munich, Germany
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
| | - Ajaikumar B Kunnumakkara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam, 781039, India.
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Layden HM, Johnson AE, Hiebert SW. Chemical-genetics refines transcription factor regulatory circuits. Trends Cancer 2024; 10:65-75. [PMID: 37722945 PMCID: PMC10840957 DOI: 10.1016/j.trecan.2023.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/14/2023] [Accepted: 08/25/2023] [Indexed: 09/20/2023]
Abstract
Transcriptional dysregulation is a key step in oncogenesis, but our understanding of transcriptional control has relied on genetic approaches that are slow and allow for compensation. Chemical-genetic approaches have shortened the time frame for the analysis of transcription factors from days or weeks to minutes. These studies show that while DNA-binding proteins bind to thousands of sites, they are directly required to regulate only a small cadre of genes. Moreover, these transcriptional control networks are far more distinct, with much less overlap and interconnectivity than predicted from DNA binding. The identified direct targets can then be used to dissect the mechanism of action of these factors, which could identify ways to therapeutically manipulate these oncogenic transcriptional control networks.
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Affiliation(s)
- Hillary M Layden
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Anna E Johnson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37027, USA.
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4
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Yan M, Liu M, Davis AG, Stoner SA, Zhang DE. Single-cell RNA sequencing of a new transgenic t(8;21) preleukemia mouse model reveals regulatory networks promoting leukemic transformation. Leukemia 2024; 38:31-44. [PMID: 37838757 PMCID: PMC10776403 DOI: 10.1038/s41375-023-02063-z] [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: 04/24/2023] [Revised: 09/22/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
T(8;21)(q22;q22), which generates the AML1-ETO fusion oncoprotein, is a common chromosomal abnormality in acute myeloid leukemia (AML) patients. Despite having favorable prognosis, 40% of patients will relapse, highlighting the need for innovative models and application of the newest technologies to study t(8;21) leukemogenesis. Currently, available AML1-ETO mouse models have limited utility for studying the pre-leukemic stage because AML1-ETO produces mild hematopoietic phenotypes and no leukemic transformation. Conversely, overexpression of a truncated variant, AML1-ETO9a (AE9a), promotes fully penetrant leukemia and is too potent for studying pre-leukemic changes. To overcome these limitations, we devised a germline-transmitted Rosa26 locus AE9a knock-in mouse model that moderately overexpressed AE9a and developed leukemia with long latency and low penetrance. We observed pre-leukemic alterations in AE9a mice, including skewing of progenitors towards granulocyte/monocyte lineages and replating of stem and progenitor cells. Next, we performed single-cell RNA sequencing to identify specific cell populations that contribute to these pre-leukemic phenotypes. We discovered a subset of common myeloid progenitors that have heightened granulocyte/monocyte bias in AE9a mice. We also observed dysregulation of key hematopoietic transcription factor target gene networks, blocking cellular differentiation. Finally, we identified Sox4 activation as a potential contributor to stem cell self-renewal during the pre-leukemic stage.
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Affiliation(s)
- Ming Yan
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Mengdan Liu
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amanda G Davis
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Samuel A Stoner
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Dong-Er Zhang
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
- Department of Pathology, University of California San Diego, La Jolla, CA, USA.
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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5
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Fang L, Zhang R, Shi L, Xie J, Ma L, Yang Y, Yan X, Fan K. Protein-Nanocaged Selenium Induces t(8;21) Leukemia Cell Differentiation via Epigenetic Regulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300698. [PMID: 37888866 PMCID: PMC10724402 DOI: 10.1002/advs.202300698] [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: 02/01/2023] [Revised: 08/13/2023] [Indexed: 10/28/2023]
Abstract
The success of arsenic in degrading PML-RARα oncoprotein illustrates the great anti-leukemia value of inorganics. Inspired by this, the therapeutic effect of inorganic selenium on t(8; 21) leukemia is studied, which has shown promising anti-cancer effects on solid tumors. A leukemia-targeting selenium nanomedicine is rationally built with bioengineered protein nanocage and is demonstrated to be an effective epigenetic drug for inducing the differentiation of t(8;21) leukemia. The selenium drug significantly induces the differentiation of t(8;21) leukemia cells into more mature myeloid cells. Mechanistic analysis shows that the selenium is metabolized into bioactive forms in cells, which drives the degradation of the AML1-ETO oncoprotein by inhibiting histone deacetylases activity, resulting in the regulation of AML1-ETO target genes. The regulation results in a significant increase in the expression levels of myeloid differentiation transcription factors PU.1 and C/EBPα, and a significant decrease in the expression level of C-KIT protein, a member of the type III receptor tyrosine kinase family. This study demonstrates that this protein-nanocaged selenium is a potential therapeutic drug against t(8;21) leukemia through epigenetic regulation.
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Affiliation(s)
- Long Fang
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing100049China
- CAS Engineering Laboratory for NanozymeKey Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
| | - Ruofei Zhang
- CAS Engineering Laboratory for NanozymeKey Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
| | - Lin Shi
- Department of HematologyPeking University International HospitalBeijing102206China
| | - Jiaying Xie
- CAS Engineering Laboratory for NanozymeKey Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
| | - Long Ma
- CAS Engineering Laboratory for NanozymeKey Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
| | - Yili Yang
- China Regional Research CentreInternational Centre of Genetic Engineering and BiotechnologyTaizhou212200China
| | - Xiyun Yan
- CAS Engineering Laboratory for NanozymeKey Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
- Nanozyme Medical CenterSchool of Basic Medical SciencesZhengzhou UniversityZhengzhou450052China
| | - Kelong Fan
- CAS Engineering Laboratory for NanozymeKey Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
- Nanozyme Medical CenterSchool of Basic Medical SciencesZhengzhou UniversityZhengzhou450052China
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6
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Wang X, Luo X, Wang Z, Wang Y, Zhao J, Bian L. Identification of cancer stemness and M2 macrophage-associated biomarkers in lung adenocarcinoma. Heliyon 2023; 9:e19114. [PMID: 37662825 PMCID: PMC10472008 DOI: 10.1016/j.heliyon.2023.e19114] [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: 02/07/2023] [Revised: 08/06/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
Objective Cancer stemness and M2 macrophages are intimately linked to the prognosis of lung adenocarcinoma (LUAD). For this reason, this investigation sought to identify the key genes relevant to cancer stemness and M2 macrophages, explore the relationship between these genes and clinical characteristics, and determine the potential mechanism. Methods LUAD transcriptomic data was analyzed from The Cancer Genome Atlas (TCGA) as well as the Gene Expression Omnibus databases. Differential expression analysis was performed to discern abnormally expressed genes between LUAD and control samples in TCGA cohort. The Cell type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was applied to determine varyingly infiltrated immune cells in LUAD compared with the control samples in TCGA cohort. Weighted correlation network analysis (WGCNA) was performed to identify genes associated with mRNA expression-based stemness index (mRNAsi) and M2 macrophages. Least absolute shrinkage and selection operator (LASSO), RandomForest (RF) and support vector machine-recursive feature elimination (SVM-RFE) machine learning methods were conducted to detect gene signatures. Global survival evaluation (Kaplan-Meier curve) was applied to investigate the relationship between gene signatures and the survival time of LUAD patients. Receiver operating characteristic (ROC) curves were produced to define biomarkers relevant to diagnosis. Gene Set Enrichment Analysis (GSEA) was performed to probe the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to diagnostic biomarkers. The public single-cell dataset of LUAD (GSE123902) was used to investigate the expression differences of diagnostic biomarkers in various cell types in LUAD. Real-time quantitative PCR (qRT-PCR) was performed to confirm key genes in lung adenocarcinoma cells. Results A total of 5,410 differentialy expressed genes (DEGs) as well as 15 differentially infiltrated immune cells were identified between LUAD and control sepcimens in TCGA cohort. Thirty-seven DEGs were associated with both M2 macrophages and mRNAsi according to the WGCNA analysis. Sixteen common gene signatures were obtained using three diverse algorithms. CBFA2T3, DENND3 and FCAMR were correlated to overall and disease-free survival of LUAD patients. ROC curves revealed that CBFA2T3 and DENND3 expression accurately classified LUAD and control samples. The results of single cell related analysis showed that two diagnostic biomarkers expressions were differed between the different tissue sources in M2-like macrophages. QRT-PCR demonstrated the mRNA expressions of CBFA2T3 and DENND3 were upregulated in lung adenocarcinoma cells A549 and H2122. Conclusion Our study identified CBFA2T3 and DENND3 as key genes associated with mRNAsi and M2 macrophages in LUAD and investigated the potential molecular mechanisms underlying this relationship.
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Affiliation(s)
| | | | - ZhiYuan Wang
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - YangHao Wang
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Juan Zhao
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Bian
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
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7
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Chen Y, He Y, Liu S. RUNX1-Regulated Signaling Pathways in Ovarian Cancer. Biomedicines 2023; 11:2357. [PMID: 37760803 PMCID: PMC10525517 DOI: 10.3390/biomedicines11092357] [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: 06/28/2023] [Revised: 07/26/2023] [Accepted: 08/03/2023] [Indexed: 09/29/2023] Open
Abstract
Ovarian cancer is the leading cause of gynecological death worldwide, and its poor prognosis and high mortality seriously affect the life of ovarian cancer patients. Runt-related transcription factor 1 (RUNX1) has been widely studied in hematological diseases and plays an important role in the occurrence and development of hematological diseases. In recent years, studies have reported the roles of RUNX1 in solid tumors, including the significantly increased expression of RUNX1 in ovarian cancer. In ovarian cancer, the dysregulation of the RUNX1 signaling pathway has been implicated in tumor progression, metastasis, and response to therapy. At the same time, the decreased expression of RUNX1 in ovarian cancer can significantly improve the sensitivity of clinical chemotherapy and provide theoretical support for the subsequent diagnosis and treatment target of ovarian cancer, providing prognosis and treatment options to patients with ovarian cancer. However, the role of RUNX1 in ovarian cancer remains unclear. Therefore, this article reviews the relationship between RUNX1 and the occurrence and development of ovarian cancer, as well as the closely regulated signaling pathways, to provide some inspiration and theoretical support for future research on RUNX1 in ovarian cancer and other diseases.
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Affiliation(s)
- Yuanzhi Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingying He
- School of Chemical Science & Technology, Yunnan University, Kunming 650091, China
| | - Shubai Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Lomov NA, Viushkov VS, Rubtsov MA. Mechanisms of Secondary Leukemia Development Caused by Treatment with DNA Topoisomerase Inhibitors. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:892-911. [PMID: 37751862 DOI: 10.1134/s0006297923070040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 09/28/2023]
Abstract
Leukemia is a blood cancer originating in the blood and bone marrow. Therapy-related leukemia is associated with prior chemotherapy. Although cancer therapy with DNA topoisomerase II inhibitors is one of the most effective cancer treatments, its side effects include development of secondary leukemia characterized by the chromosomal rearrangements affecting AML1 or MLL genes. Recurrent chromosomal translocations in the therapy-related leukemia differ from chromosomal rearrangements associated with other neoplasias. Here, we reviewed the factors that drive chromosomal translocations induced by cancer treatment with DNA topoisomerase II inhibitors, such as mobility of ends of double-strand DNA breaks formed before the translocation and gain of function of fusion proteins generated as a result of translocation.
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Affiliation(s)
- Nikolai A Lomov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Vladimir S Viushkov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Mikhail A Rubtsov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Biochemistry, Center for Industrial Technologies and Entrepreneurship Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119435, Russia
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9
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Chianese U, Papulino C, Megchelenbrink W, Tambaro FP, Ciardiello F, Benedetti R, Altucci L. Epigenomic machinery regulating pediatric AML: clonal expansion mechanisms, therapies, and future perspectives. Semin Cancer Biol 2023; 92:84-101. [PMID: 37003397 DOI: 10.1016/j.semcancer.2023.03.009] [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: 12/15/2022] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease with a genetic, epigenetic, and transcriptional etiology mainly presenting somatic and germline abnormalities. AML incidence rises with age but can also occur during childhood. Pediatric AML (pAML) accounts for 15-20% of all pediatric leukemias and differs considerably from adult AML. Next-generation sequencing technologies have enabled the research community to "paint" the genomic and epigenomic landscape in order to identify pathology-associated mutations and other prognostic biomarkers in pAML. Although current treatments have improved the prognosis for pAML, chemoresistance, recurrence, and refractory disease remain major challenges. In particular, pAML relapse is commonly caused by leukemia stem cells that resist therapy. Marked patient-to-patient heterogeneity is likely the primary reason why the same treatment is successful for some patients but, at best, only partially effective for others. Accumulating evidence indicates that patient-specific clonal composition impinges significantly on cellular processes, such as gene regulation and metabolism. Although our understanding of metabolism in pAML is still in its infancy, greater insights into these processes and their (epigenetic) modulation may pave the way toward novel treatment options. In this review, we summarize current knowledge on the function of genetic and epigenetic (mis)regulation in pAML, including metabolic features observed in the disease. Specifically, we describe how (epi)genetic machinery can affect chromatin status during hematopoiesis, leading to an altered metabolic profile, and focus on the potential value of targeting epigenetic abnormalities in precision and combination therapy for pAML. We also discuss the possibility of using alternative epidrug-based therapeutic approaches that are already in clinical practice, either alone as adjuvant treatments and/or in combination with other drugs.
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Affiliation(s)
- Ugo Chianese
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Chiara Papulino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Wout Megchelenbrink
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy; Princess Máxima Center, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands.
| | - Francesco Paolo Tambaro
- Bone Marrow Transplant Unit, Pediatric Oncology Department AORN Santobono Pausilipon, 80129, Naples Italy.
| | - Fortunato Ciardiello
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Rosaria Benedetti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy; Biogem Institute of Molecular and Genetic Biology, 83031 Ariano Irpino, Italy; IEOS, Institute for Endocrinology and Oncology "Gaetano Salvatore" (IEOS), 80131 Naples, Italy.
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10
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Deregulated Gene Expression Profiles and Regulatory Networks in Adult and Pediatric RUNX1/RUNX1T1-Positive AML Patients. Cancers (Basel) 2023; 15:cancers15061795. [PMID: 36980682 PMCID: PMC10046396 DOI: 10.3390/cancers15061795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous and complex disease concerning molecular aberrations and prognosis. RUNX1/RUNX1T1 is a fusion oncogene that results from the chromosomal translocation t(8;21) and plays a crucial role in AML. However, its impact on the transcriptomic profile of different age groups of AML patients is not completely understood. Here, we investigated the deregulated gene expression (DEG) profiles in adult and pediatric RUNX1/RUNX1T1-positive AML patients, and compared their functions and regulatory networks. We retrospectively analyzed gene expression data from two independent Gene Expression Omnibus (GEO) datasets (GSE37642 and GSE75461) and computed their differentially expressed genes and upstream regulators, using limma, GEO2Enrichr, and X2K. For validation purposes, we used the TCGA-LAML (adult) and TARGET-AML (pediatric) patient cohorts. We also analyzed the protein–protein interaction (PPI) networks, as well as those composed of transcription factors (TF), intermediate proteins, and kinases foreseen to regulate the top deregulated genes in each group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses were further performed for the DEGs in each dataset. We found that the top upregulated genes in (both adult and pediatric) RUNX1/RUNX1T1-positive AML patients are enriched in extracellular matrix organization, the cell projection membrane, filopodium membrane, and supramolecular fiber. Our data corroborate that RUNX1/RUNX1T1 reprograms a large transcriptional network to establish and maintain leukemia via intricate PPI interactions and kinase-driven phosphorylation events.
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11
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Bouligny IM, Maher KR, Grant S. Mechanisms of myeloid leukemogenesis: Current perspectives and therapeutic objectives. Blood Rev 2023; 57:100996. [PMID: 35989139 PMCID: PMC10693933 DOI: 10.1016/j.blre.2022.100996] [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: 02/23/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 01/28/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematopoietic neoplasm which results in clonal proliferation of abnormally differentiated hematopoietic cells. In this review, mechanisms contributing to myeloid leukemogenesis are summarized, highlighting aberrations of epigenetics, transcription factors, signal transduction, cell cycling, and the bone marrow microenvironment. The mechanisms contributing to AML are detailed to spotlight recent findings that convey clinical impact. The applications of current and prospective therapeutic targets are accentuated in addition to reviews of treatment paradigms stratified for each characteristic molecular lesion - with a focus on exploring novel treatment approaches and combinations to improve outcomes in AML.
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Affiliation(s)
- Ian M Bouligny
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA.
| | - Keri R Maher
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA.
| | - Steven Grant
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA.
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12
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Chiriches C, Nicolaisen N, Wieske M, Elhaddad H, Mehmetbeyoglu E, Alvares C, Becher D, Hole P, Ottmann OG, Ruthardt M. Understanding a high-risk acute myeloid leukemia by analyzing the interactome of its major driver mutation. PLoS Genet 2022; 18:e1010463. [PMID: 36288392 PMCID: PMC9639852 DOI: 10.1371/journal.pgen.1010463] [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: 03/11/2022] [Revised: 11/07/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022] Open
Abstract
The WHO classifies t(6;9)-positive acute myeloid leukemia (AML) as a subgroup of high-risk AML because of its clinical and biological peculiarities, such as young age and therapy resistance. t(6;9) encodes the DEK/NUP214 fusion oncoprotein that targets only a small subpopulation of bone marrow progenitors for leukemic transformation. This distinguishes DEK/NUP214 from other fusion oncoproteins, such as PML/RARα, RUNX1/ETO, or MLL/AF9, which have a broad target population they block differentiation and increase stem cell capacity. A common theme among most leukemogenic fusion proteins is their aberrant localization compared to their wild-type counterparts. Although the actual consequences are widely unknown, it seems to contribute to leukemogenesis most likely by a sequester of interaction partners. Thus, we applied a global approach to studying the consequences of the aberrant localization of t(6;9)-DEK/NUP214 for its interactome. This study aimed to disclose the role of localization of DEK/NUP214 and the related sequester of proteins interacting with DEK/NUP214 for the determination of the biology of t(6;9)-AML. Here we show the complexity of the biological consequences of the expression of DEK/NUP214 by an in-depth bioinformatic analysis of the interactome of DEK/NUP214 and its biologically dead mutants. DEK/NUP214's interactome points to an essential role for aberrant RNA-regulation and aberrant regulation of apoptosis and leukocyte activation as a significant determinant of the phenotype of t(6;9)-AML. Taken together, we provide evidence that the interactome contributes to the aberrant biology of an oncoprotein, providing opportunities for developing novel targeted therapy approaches.
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Affiliation(s)
- Claudia Chiriches
- Division of Cancer and Genetics, Section of Hematology, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Experimental Clinical Medical Center (ECMC) Cardiff, School of Medicine, Cardiff University, Cardiff, United Kingdom
- * E-mail: (CC); (MR)
| | - Nathalie Nicolaisen
- Department of Hematology, Medical Clinic II Goethe University Frankfurt, Germany
| | - Maria Wieske
- Department of Hematology, Medical Clinic II Goethe University Frankfurt, Germany
| | - Heba Elhaddad
- Division of Cancer and Genetics, Section of Hematology, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Experimental Clinical Medical Center (ECMC) Cardiff, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Faculty of Medicine, Department of Clinical Pathology, Mansoura University, Mansoura, Egypt
| | - Ecmel Mehmetbeyoglu
- Division of Cancer and Genetics, Section of Hematology, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Experimental Clinical Medical Center (ECMC) Cardiff, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Caroline Alvares
- Division of Cancer and Genetics, Section of Hematology, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Experimental Clinical Medical Center (ECMC) Cardiff, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Dörte Becher
- Institute of Microbiology, Microbial Proteomics, Ernst Moritz Arndt University, Greifswald, Germany
| | - Paul Hole
- Division of Cancer and Genetics, Section of Hematology, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Experimental Clinical Medical Center (ECMC) Cardiff, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Oliver Gerhard Ottmann
- Division of Cancer and Genetics, Section of Hematology, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Experimental Clinical Medical Center (ECMC) Cardiff, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Martin Ruthardt
- Division of Cancer and Genetics, Section of Hematology, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Experimental Clinical Medical Center (ECMC) Cardiff, School of Medicine, Cardiff University, Cardiff, United Kingdom
- * E-mail: (CC); (MR)
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13
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Zhang YF, Wang XL, Xu CH, Liu N, Zhang L, Zhang YM, Xie YY, Zhang YL, Huang QH, Wang L, Chen Z, Chen SJ, Roeder RG, Shen S, Xue K, Sun XJ. A direct comparison between AML1-ETO and ETO2-GLIS2 leukemia fusion proteins reveals context-dependent binding and regulation of target genes and opposite functions in cell differentiation. Front Cell Dev Biol 2022; 10:992714. [PMID: 36158200 PMCID: PMC9490184 DOI: 10.3389/fcell.2022.992714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
The ETO-family transcriptional corepressors, including ETO, ETO2, and MTGR1, are all involved in leukemia-causing chromosomal translocations. In every case, an ETO-family corepressor acquires a DNA-binding domain (DBD) to form a typical transcription factor—the DBD binds to DNA, while the ETO moiety manifests transcriptional activity. A directly comparative study of these “homologous” fusion transcription factors may clarify their similarities and differences in regulating transcription and leukemogenesis. Here, we performed a side-by-side comparison between AML1-ETO and ETO2-GLIS2, the most common fusion proteins in M2-and M7-subtypes of acute myeloid leukemia, respectively, by inducible expression of them in U937 leukemia cells. We found that, although AML1-ETO and ETO2-GLIS2 can use their own DBDs to bind DNA, they share a large proportion of genome-wide binding regions dependent on other cooperative transcription factors, including the ETS-, bZIP- and bHLH-family proteins. AML1-ETO acts as either transcriptional repressor or activator, whereas ETO2-GLIS2 mainly acts as activator. The repressor-versus-activator functions of AML1-ETO might be determined by the abundance of cooperative transcription factors/cofactors on the target genes. Importantly, AML1-ETO and ETO2-GLIS2 differentially regulate key transcription factors in myeloid differentiation including PU.1 and C/EBPβ. Consequently, AML1-ETO inhibits, but ETO2-GLIS2 facilitates, myeloid differentiation of U937 cells. This function of ETO2-GLIS2 is reminiscent of a similar effect of MLL-AF9 as previously reported. Taken together, this directly comparative study between AML1-ETO and ETO2-GLIS2 in the same cellular context provides insights into context-dependent transcription regulatory mechanisms that may underlie how these seemingly “homologous” fusion transcription factors exert distinct functions to drive different subtypes of leukemia.
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14
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Functional Drug Screening of Small Molecule Inhibitors of Epigenetic Modifiers in Refractory AML Patients. Cancers (Basel) 2022; 14:cancers14174094. [PMID: 36077629 PMCID: PMC9455071 DOI: 10.3390/cancers14174094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/13/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022] Open
Abstract
The use of inhibitors of epigenetic modifiers in the treatment of acute myeloid leukemia (AML) has become increasingly appealing due to the highly epigenetic nature of the disease. We evaluated a library of 164 epigenetic compounds in a cohort of 9 heterogeneous AML patients using an ex vivo drug screen. AML blasts were isolated from bone marrow biopsies according to established protocols and treatment response to the epigenetic library was evaluated. We find that 11 histone deacetylase (HDAC) inhibitors, which act upon mechanisms of cell cycle arrest and apoptotic pathways through inhibition of zinc-dependent classes of HDACs, showed efficacy in all patient-derived samples. Other compounds, including bromodomain and extraterminal domain (BET) protein inhibitors, showed efficacy in most samples. Specifically, HDAC inhibitors are already clinically available and can be repurposed for use in AML. Results in this cohort of AML patient-derived samples reveal several epigenetic compounds with high anti-blast activity in all samples, despite the molecular diversity of the disease. These results further enforce the notion that AML is a predominantly epigenetic disease and that similar epigenetic mechanisms may underlie disease development and progression in all patients, despite differences in genetic mutations.
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15
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Kushwaha K, Garg SS, Gupta J. Targeting epigenetic regulators for treating diabetic nephropathy. Biochimie 2022; 202:146-158. [PMID: 35985560 DOI: 10.1016/j.biochi.2022.08.001] [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: 03/29/2022] [Revised: 07/01/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022]
Abstract
Diabetes is accompanied by the worsening of kidney functions. The reasons for kidney dysfunction mainly include high blood pressure (BP), high blood sugar levels, and genetic makeup. Vascular complications are the leading cause of the end-stage renal disorder (ESRD) and death of diabetic patients. Epigenetics has emerged as a new area to explain the inheritance of non-mendelian conditions like diabetic kidney diseases. Aberrant post-translational histone modifications (PTHMs), DNA methylation (DNAme), and miRNA constitute major epigenetic mechanisms that progress diabetic nephropathy (DN). Increased blood sugar levels alter PTHMs, DNAme, and miRNA in kidney cells results in aberrant gene expression that causes fibrosis, accumulation of extracellular matrix (ECM), increase in reactive oxygen species (ROS), and renal injuries. Histone acetylation (HAc) and histone deacetylation (HDAC) are the most studied epigenetic modifications with implications in the occurrence of kidney disorders. miRNAs induced by hyperglycemia in renal cells are also responsible for ECM accumulation and dysfunction of the glomerulus. In this review, we highlight the role of epigenetic modifications in DN progression and current strategies employed to ameliorate DN.
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Affiliation(s)
- Kriti Kushwaha
- Department of Biotechnology, School of Bioengineering and Bioscience, Lovely Professional University, Phagwara, Punjab, India
| | - Sourbh Suren Garg
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Jeena Gupta
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India.
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16
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Brown RE, Jacobse J, Anant SA, Blunt KM, Chen B, Vega PN, Jones CT, Pilat JM, Revetta F, Gorby AH, Stengel KR, Choksi YA, Palin K, Piazuelo MB, Washington MK, Lau KS, Goettel JA, Hiebert SW, Short SP, Williams CS. MTG16 (CBFA2T3) regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors. JCI Insight 2022; 7:153045. [PMID: 35503250 PMCID: PMC9220854 DOI: 10.1172/jci.insight.153045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/13/2022] [Indexed: 12/04/2022] Open
Abstract
Aberrant epithelial differentiation and regeneration contribute to colon pathologies including inflammatory bowel disease (IBD) and colitis-associated cancer (CAC). MTG16 (CBFA2T3) is a transcriptional corepressor expressed in the colonic epithelium. MTG16 deficiency in mice exacerbates colitis and increases tumor burden in CAC, though the underlying mechanisms remain unclear. Here, we identified MTG16 as a central mediator of epithelial differentiation, promoting goblet and restraining enteroendocrine cell development in homeostasis and enabling regeneration following dextran sulfate sodium (DSS)-induced colitis. Transcriptomic analyses implicated increased E box-binding transcription factor (E protein) activity in MTG16-deficient colon crypts. Using a novel mouse model with a point mutation that attenuates MTG16:E protein interactions (Mtg16P209T), we established that MTG16 exerts control over colonic epithelial differentiation and regeneration by repressing E protein-mediated transcription. Mimicking murine colitis, MTG16 expression was increased in biopsies from patients with active IBD compared to unaffected controls. Finally, uncoupling MTG16:E protein interactions partially phenocopied the enhanced tumorigenicity of Mtg16-/- colon in the azoxymethane(AOM)/DSS-induced model of CAC, indicating that MTG16 protects from tumorigenesis through additional mechanisms. Collectively, our results demonstrate that MTG16, via its repression of E protein targets, is a key regulator of cell fate decisions during colon homeostasis, colitis, and cancer.
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Affiliation(s)
- Rachel E Brown
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Justin Jacobse
- Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Shruti A Anant
- Department of Medicine, Health, and Society, Vanderbilt University, Nashville, United States of America
| | - Koral M Blunt
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Bob Chen
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Paige N Vega
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Chase T Jones
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Jennifer M Pilat
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, United States of America
| | - Aidan H Gorby
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Yash A Choksi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - M Blanca Piazuelo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Mary K Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, United States of America
| | - Ken S Lau
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Jeremy A Goettel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Sarah P Short
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Christopher S Williams
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
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17
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Krivdova G, Voisin V, Schoof EM, Marhon SA, Murison A, McLeod JL, Gabra MM, Zeng AGX, Aigner S, Yee BA, Shishkin AA, Van Nostrand EL, Hermans KG, Trotman-Grant AC, Mbong N, Kennedy JA, Gan OI, Wagenblast E, De Carvalho DD, Salmena L, Minden MD, Bader GD, Yeo GW, Dick JE, Lechman ER. Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML. Cell Rep 2022; 38:110481. [PMID: 35263585 DOI: 10.1016/j.celrep.2022.110481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/03/2021] [Accepted: 02/11/2022] [Indexed: 11/18/2022] Open
Abstract
Gene expression profiling and proteome analysis of normal and malignant hematopoietic stem cells (HSCs) point to shared core stemness properties. However, discordance between mRNA and protein signatures highlights an important role for post-transcriptional regulation by microRNAs (miRNAs) in governing this critical nexus. Here, we identify miR-130a as a regulator of HSC self-renewal and differentiation. Enforced expression of miR-130a impairs B lymphoid differentiation and expands long-term HSCs. Integration of protein mass spectrometry and chimeric AGO2 crosslinking and immunoprecipitation (CLIP) identifies TBL1XR1 as a primary miR-130a target, whose loss of function phenocopies miR-130a overexpression. Moreover, we report that miR-130a is highly expressed in t(8;21) acute myeloid leukemia (AML), where it is critical for maintaining the oncogenic molecular program mediated by the AML1-ETO complex. Our study establishes that identification of the comprehensive miRNA targetome within primary cells enables discovery of genes and molecular networks underpinning stemness properties of normal and leukemic cells.
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Affiliation(s)
- Gabriela Krivdova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Erwin M Schoof
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Jessica L McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Martino M Gabra
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alexander A Shishkin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Karin G Hermans
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Program of Developmental & Stem Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Aaron C Trotman-Grant
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Division of Medical Oncology and Hematology, Sunnybrook Health Sciences Centre, Toronto, ON M4N3M5, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leonardo Salmena
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Gary D Bader
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada.
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
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18
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UBC9 inhibits myeloid differentiation in collaboration with AML1-MTG8. Int J Hematol 2022; 115:686-693. [DOI: 10.1007/s12185-022-03303-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 10/19/2022]
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19
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Vagapova E, Kozlov M, Lebedev T, Ivanenko K, Leonova O, Popenko V, Spirin P, Kochetkov S, Prassolov V. Selective Inhibition of HDAC Class I Sensitizes Leukemia and Neuroblastoma Cells to Anticancer Drugs. Biomedicines 2021; 9:1846. [PMID: 34944663 PMCID: PMC8698907 DOI: 10.3390/biomedicines9121846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
The acquired resistance of neuroblastoma (NB) and leukemia cells to anticancer therapy remains the major challenge in the treatment of patients with these diseases. Although targeted therapy, such as receptor tyrosine kinase (RTK) inhibitors, has been introduced into clinical practice, its efficacy is limited to patients harboring mutant kinases. Through the analysis of transcriptomic data of 701 leukemia and NB patient samples and cell lines, we revealed that the expression of RTK, such as KIT, FLT3, AXL, FGFR3, and NTRK1, is linked with HDAC class I. Although HDAC inhibitors have antitumor activity, they also have high whole-body toxicity. We developed a novel belinostat derivative named hydrazostat, which targets HDAC class I with limited off-target effects. We compared the toxicity of these drugs within the panel of leukemia and NB cell lines. Next, we revealed that HDAC inhibition with hydrazostat reactivates NTRK1, FGFR3, ROR2, KIT, and FLT3 expression. Based on this finding, we tested the efficacy of hydrazostat in combination with RTK inhibitor imatinib. Additionally, we show the ability of hydrazostat to enhance venetoclax-induced apoptosis. Thus, we reveal the connection between HDACs and RTK and describe a useful strategy to overcome the complications of single-agent therapies.
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Affiliation(s)
- Elmira Vagapova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia; (M.K.); (T.L.); (K.I.); (O.L.); (V.P.); (P.S.); (S.K.); (V.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia
| | - Maxim Kozlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia; (M.K.); (T.L.); (K.I.); (O.L.); (V.P.); (P.S.); (S.K.); (V.P.)
| | - Timofey Lebedev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia; (M.K.); (T.L.); (K.I.); (O.L.); (V.P.); (P.S.); (S.K.); (V.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia
| | - Karina Ivanenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia; (M.K.); (T.L.); (K.I.); (O.L.); (V.P.); (P.S.); (S.K.); (V.P.)
| | - Olga Leonova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia; (M.K.); (T.L.); (K.I.); (O.L.); (V.P.); (P.S.); (S.K.); (V.P.)
| | - Vladimir Popenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia; (M.K.); (T.L.); (K.I.); (O.L.); (V.P.); (P.S.); (S.K.); (V.P.)
| | - Pavel Spirin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia; (M.K.); (T.L.); (K.I.); (O.L.); (V.P.); (P.S.); (S.K.); (V.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia
| | - Sergey Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia; (M.K.); (T.L.); (K.I.); (O.L.); (V.P.); (P.S.); (S.K.); (V.P.)
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia; (M.K.); (T.L.); (K.I.); (O.L.); (V.P.); (P.S.); (S.K.); (V.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia
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20
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Trinh BQ, Ummarino S, Zhang Y, Ebralidze AK, Bassal MA, Nguyen TM, Heller G, Coffey R, Tenen DE, van der Kouwe E, Fabiani E, Gurnari C, Wu CS, Angarica VE, Yang H, Chen S, Zhang H, Thurm AR, Marchi F, Levantini E, Staber PB, Zhang P, Voso MT, Pandolfi PP, Kobayashi SS, Chai L, Di Ruscio A, Tenen DG. Myeloid lncRNA LOUP mediates opposing regulatory effects of RUNX1 and RUNX1-ETO in t(8;21) AML. Blood 2021; 138:1331-1344. [PMID: 33971010 PMCID: PMC8525335 DOI: 10.1182/blood.2020007920] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 04/18/2021] [Indexed: 11/20/2022] Open
Abstract
The mechanism underlying cell type-specific gene induction conferred by ubiquitous transcription factors as well as disruptions caused by their chimeric derivatives in leukemia is not well understood. Here, we investigate whether RNAs coordinate with transcription factors to drive myeloid gene transcription. In an integrated genome-wide approach surveying for gene loci exhibiting concurrent RNA and DNA interactions with the broadly expressed Runt-related transcription factor 1 (RUNX1), we identified the long noncoding RNA (lncRNA) originating from the upstream regulatory element of PU.1 (LOUP). This myeloid-specific and polyadenylated lncRNA induces myeloid differentiation and inhibits cell growth, acting as a transcriptional inducer of the myeloid master regulator PU.1. Mechanistically, LOUP recruits RUNX1 to both the PU.1 enhancer and the promoter, leading to the formation of an active chromatin loop. In t(8;21) acute myeloid leukemia (AML), wherein RUNX1 is fused to ETO, the resulting oncogenic fusion protein, RUNX1-ETO, limits chromatin accessibility at the LOUP locus, causing inhibition of LOUP and PU.1 expression. These findings highlight the important role of the interplay between cell-type-specific RNAs and transcription factors, as well as their oncogenic derivatives in modulating lineage-gene activation and raise the possibility that RNA regulators of transcription factors represent alternative targets for therapeutic development.
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Affiliation(s)
- Bon Q Trinh
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
| | - Simone Ummarino
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
| | - Yanzhou Zhang
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
| | - Alexander K Ebralidze
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
| | - Mahmoud A Bassal
- Harvard Stem Cell Institute, Harvard University, Boston, MA
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tuan M Nguyen
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Gerwin Heller
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Rory Coffey
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
| | - Danielle E Tenen
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Emiel van der Kouwe
- Division of Hematology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Emiliano Fabiani
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Saint Camillus International University of Health Sciences, Rome, Italy
| | - Carmelo Gurnari
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Chan-Shuo Wu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Sisi Chen
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
| | - Hong Zhang
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
| | - Abby R Thurm
- Harvard Stem Cell Institute, Harvard University, Boston, MA
- Stanford University School of Medicine, Stanford, CA
| | - Francisco Marchi
- Harvard Stem Cell Institute, Harvard University, Boston, MA
- University of Florida, Gainesville, FL
| | - Elena Levantini
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
- Harvard Stem Cell Institute, Harvard University, Boston, MA
- Institute of Biomedical Technologies, National Research Council (CNR), Area della Ricerca di Pisa, Pisa, Italy
| | - Philipp B Staber
- Division of Hematology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Pu Zhang
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
| | - Maria Teresa Voso
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Pier Paolo Pandolfi
- Department of Pathology, Beth Israel Deaconess Cancer Center, Harvard Medical School Boston, MA
| | - Susumu S Kobayashi
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
- Harvard Stem Cell Institute, Harvard University, Boston, MA
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
| | - Li Chai
- Harvard Stem Cell Institute, Harvard University, Boston, MA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Annalisa Di Ruscio
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA; and
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Daniel G Tenen
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
- Stanford University School of Medicine, Stanford, CA
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21
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Rejeski K, Duque-Afonso J, Lübbert M. AML1/ETO and its function as a regulator of gene transcription via epigenetic mechanisms. Oncogene 2021; 40:5665-5676. [PMID: 34331016 PMCID: PMC8460439 DOI: 10.1038/s41388-021-01952-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 06/11/2021] [Accepted: 07/07/2021] [Indexed: 01/10/2023]
Abstract
The chromosomal translocation t(8;21) and the resulting oncofusion gene AML1/ETO have long served as a prototypical genetic lesion to model and understand leukemogenesis. In this review, we describe the wide-ranging role of AML1/ETO in AML leukemogenesis, with a particular focus on the aberrant epigenetic regulation of gene transcription driven by this AML-defining mutation. We begin by analyzing how structural changes secondary to distinct genomic breakpoints and splice changes, as well as posttranscriptional modifications, influence AML1/ETO protein function. Next, we characterize how AML1/ETO recruits chromatin-modifying enzymes to target genes and how the oncofusion protein alters chromatin marks, transcription factor binding, and gene expression. We explore the specific impact of these global changes in the epigenetic network facilitated by the AML1/ETO oncofusion on cellular processes and leukemic growth. Furthermore, we define the genetic landscape of AML1/ETO-positive AML, presenting the current literature concerning the incidence of cooperating mutations in genes such as KIT, FLT3, and NRAS. Finally, we outline how alterations in transcriptional regulation patterns create potential vulnerabilities that may be exploited by epigenetically active agents and other therapeutics.
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Affiliation(s)
- Kai Rejeski
- Department of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, Freiburg, Germany.,Department of Hematology and Oncology, University Hospital of the LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK) Freiburg Partner Site, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jesús Duque-Afonso
- Department of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, Freiburg, Germany. .,German Cancer Consortium (DKTK) Freiburg Partner Site, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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22
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Saikia S, Pal U, Kalita DJ, Rai AK, Sarma A, Kataki AC, Limaye AM. RUNX1T1, a potential prognostic marker in breast cancer, is co-ordinately expressed with ERα, and regulated by estrogen receptor signalling in breast cancer cells. Mol Biol Rep 2021; 48:5399-5409. [PMID: 34264479 DOI: 10.1007/s11033-021-06542-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/02/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND RUNX1T1 is extensively studied in the context of AML1-RUNX1T1 fusion protein in acute myeloid leukemia. Little is known about the function of RUNX1T1 itself, although data on its function and regulation have begun to emerge from clinical, and in vitro studies. It is a putative tumor suppressor, whose expression is altered in a variety of solid tumors. Recently, reduced expression of RUNX1T1 in triple-negative breast tumors, and its influence on prognosis was reported. METHODS AND RESULTS The Kaplan-Meier Plotter online tool was used to study the relationship between RUNX1T1 expression and survival of breast cancer patients. High RUNX1T1 expression was associated with longer overall survival (OS), relapse-free survival (RFS) and distant metastasis free survival (DMFS). RUNX1T1 expression positively and negatively influenced OS of patients with ERα-positive and ERα-negative breast tumors, respectively. It was also associated with prolonged RFS, and DMFS in tamoxifen-treated patients. Expression of RUNX1T1 and ERα mRNA was analyzed in 40 breast tumor samples, and breast cancer cell lines using RT-PCR. TCGA-BRCA data was mined to study the relationship between RUNX1T1 and ERα mRNA expression. ERα-positive breast tumors showed significantly higher RUNX1T1 mRNA expression compared to ERα-negative tumors. RUNX1T1 mRNA expression was analyzed by qRT-PCR in MCF-7 or T47D cells, which were treated with 17β-estradiol, or the ERα agonist PPT, alone or in combination with 4-hydroxytamoxifen. Effect of ERα knockdown was also investigated. Results indicate that estrogen downmodulated RUNX1T1 mRNA expression via ERα. CONCLUSION Higher expression of RUNX1T1 in breast tumors is associated with favourable prognosis. RUNX1T1 and ERα show co-ordinated expression in breast tumors, and breast cancer cell lines. Estrogen-ERα signalling downmodulates the expression of RUNX1T1 mRNA in ERα-positive breast cancer cells. In-depth investigations on the interaction between RUNX1T1 and ERα are warranted to unravel the role and relevance of RUNX1T1 in breast cancer.
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Affiliation(s)
- Snigdha Saikia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Uttariya Pal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Deep Jyoti Kalita
- Department of Surgical Oncology, Dr. Bhubaneswar Borooah Cancer Institute, Guwahati, Assam, 781016, India
| | - Avdhesh Kumar Rai
- DBT Centre for Molecular Biology and Cancer Research, Dr. Bhubaneswar Borooah Cancer Institute, Guwahati, Assam, 781016, India
| | - Anupam Sarma
- Department of Oncopathology, Dr. Bhubaneswar Borooah Cancer Institute, Guwahati, Assam, 781016, India
| | - Amal Chandra Kataki
- Department of Gynecologic Oncology, Dr. Bhubaneswar Borooah Cancer Institute, Guwahati, Assam, 781016, India
| | - Anil Mukund Limaye
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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23
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An update on the molecular pathogenesis and potential therapeutic targeting of AML with t(8;21)(q22;q22.1);RUNX1-RUNX1T1. Blood Adv 2021; 4:229-238. [PMID: 31935293 DOI: 10.1182/bloodadvances.2019000168] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023] Open
Abstract
Acute myeloid leukemia (AML) with t(8;21)(q22;q22.1);RUNX1-RUNX1T1, one of the core-binding factor leukemias, is one of the most common subtypes of AML with recurrent genetic abnormalities and is associated with a favorable outcome. The translocation leads to the formation of a pathological RUNX1-RUNX1T1 fusion that leads to the disruption of the normal function of the core-binding factor, namely, its role in hematopoietic differentiation and maturation. The consequences of this alteration include the recruitment of repressors of transcription, thus blocking the expression of genes involved in hematopoiesis, and impaired apoptosis. A number of concurrent and cooperating mutations clearly play a role in modulating the proliferative potential of cells, including mutations in KIT, FLT3, and possibly JAK2. RUNX1-RUNX1T1 also appears to interact with microRNAs during leukemogenesis. Epigenetic factors also play a role, especially with the recruitment of histone deacetylases. A better understanding of the concurrent mutations, activated pathways, and epigenetic modulation of the cellular processes paves the way for exploring a number of approaches to achieve cure. Potential approaches include the development of small molecules targeting the RUNX1-RUNX1T1 protein, the use of tyrosine kinase inhibitors such as dasatinib and FLT3 inhibitors to target mutations that lead to a proliferative advantage of the leukemic cells, and experimentation with epigenetic therapies. In this review, we unravel some of the recently described molecular pathways and explore potential therapeutic strategies.
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24
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Heimbruch KE, Meyer AE, Agrawal P, Viny AD, Rao S. A cohesive look at leukemogenesis: The cohesin complex and other driving mutations in AML. Neoplasia 2021; 23:337-347. [PMID: 33621854 PMCID: PMC7905235 DOI: 10.1016/j.neo.2021.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023]
Abstract
Acute myeloid leukemia (AML) affects tens of thousands of patients a year, yet survival rates are as low as 25% in certain populations. This poor survival rate is partially due to the vast genetic diversity of the disease. Rarely do 2 patients with AML have the same mutational profile, which makes the development of targeted therapies particularly challenging. However, a set of recurrent mutations in chromatin modifiers have been identified in many patients, including mutations in the cohesin complex, which have been identified in up to 20% of cases. Interestingly, the canonical function of the cohesin complex in establishing sister chromatid cohesin during mitosis is unlikely to be the affected role in leukemogenesis. Instead, the cohesin complex's role in DNA looping and gene regulation likely facilitates disease. The epigenetic mechanisms by which cohesin complex mutations promote leukemia are not completely elucidated, but alterations of enhancer-promoter interactions and differential histone modifications have been shown to drive oncogenic gene expression changes. Such changes commonly include HoxA upregulation, which may represent a common pathway that could be therapeutically targeted. As cohesin mutations rarely occur alone, examining the impact of common co-occurring mutations, including those in NPM1, the core-binding factor complex, FLT3, and ASXL1, will yield additional insight. While further study of these mutational interactions is required, current research suggests that the use of combinatorial genetics could be the key to uncovering new targets, allowing for the treatment of AML patients based on their individual genetic profiles.
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Affiliation(s)
- Katelyn E Heimbruch
- Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Puja Agrawal
- Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Aaron D Viny
- Department of Medicine, Division of Hematology and Oncology, and Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Sridhar Rao
- Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA; Department of Pediatrics, Division of Hematology, Oncology, and Bone Marrow Transplantation, Medical College of Wisconsin, Milwaukee, WI, USA.
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25
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Johnson DT, Davis AG, Zhou JH, Ball ED, Zhang DE. MicroRNA let-7b downregulates AML1-ETO oncogene expression in t(8;21) AML by targeting its 3'UTR. Exp Hematol Oncol 2021; 10:8. [PMID: 33531067 PMCID: PMC7856722 DOI: 10.1186/s40164-021-00204-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/22/2021] [Indexed: 01/06/2023] Open
Abstract
Background Acute myeloid leukemia (AML) with the t(8;21)(q22;q22) chromosomal translocation is among the most common subtypes of AML and produces the AML1-ETO (RUNX1-ETO, RUNX1-RUNX1T1) oncogenic fusion gene. AML1-ETO functions as an aberrant transcription factor which plays a key role in blocking normal hematopoiesis. Thus, the expression of AML1-ETO is critical to t(8;21) AML leukemogenesis and maintenance. Post-transcriptional regulation of gene expression is often mediated through interactions between trans-factors and cis-elements within transcript 3′-untranslated regions (UTR). AML1-ETO uses the 3′UTR of the ETO gene, which is not normally expressed in hematopoietic cells. Therefore, the mechanisms regulating AML1-ETO expression via the 3’UTR are attractive therapeutic targets. Methods We used RNA-sequencing of t(8;21) patients and cell lines to examine the 3′UTR isoforms used by AML1-ETO transcripts. Using luciferase assay approaches, we test the relative contribution of 3′UTR cis elements to AML1-ETO expression. We further use let-7b microRNA mimics and anti-let-7b sponges for functional studies of t(8;21) AML cell lines. Results In this study, we examine the regulation of AML1-ETO via the 3’UTR. We demonstrate that AML1-ETO transcripts primarily use a 3.7 kb isoform of the ETO 3′UTR in both t(8;21) patients and cell lines. We identify a negative regulatory element within the AML1-ETO 3′UTR. We further demonstrate that the let-7b microRNA directly represses AML1-ETO through this site. Finally, we find that let-7b inhibits the proliferation of t(8;21) AML cell lines, rescues expression of AML1-ETO target genes, and promotes differentiation. Conclusions AML1-ETO is post-transcriptionally regulated by let-7b, which contributes to the leukemic phenotype of t(8;21) AML and may be important for t(8;21) leukemogenesis and maintenance.
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Affiliation(s)
- Daniel T Johnson
- Moores Cancer Center, University of California, La Jolla, San Diego, CA, USA.,Biological Sciences Graduate Program, University of California San Diego, La Jolla, San Diego, CA, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Amanda G Davis
- Moores Cancer Center, University of California, La Jolla, San Diego, CA, USA.,Biological Sciences Graduate Program, University of California San Diego, La Jolla, San Diego, CA, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Jie-Hua Zhou
- Moores Cancer Center, University of California, La Jolla, San Diego, CA, USA.,BMT Division, Department of Medicine, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Edward D Ball
- Moores Cancer Center, University of California, La Jolla, San Diego, CA, USA.,BMT Division, Department of Medicine, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Dong-Er Zhang
- Moores Cancer Center, University of California, La Jolla, San Diego, CA, USA. .,Biological Sciences Graduate Program, University of California San Diego, La Jolla, San Diego, CA, USA. .,Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA, USA. .,Department of Pathology, University of California San Diego, La Jolla, San Diego, CA, USA.
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26
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Swart LE, Heidenreich O. The RUNX1/RUNX1T1 network: translating insights into therapeutic options. Exp Hematol 2021; 94:1-10. [PMID: 33217477 PMCID: PMC7854360 DOI: 10.1016/j.exphem.2020.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022]
Abstract
RUNX1/RUNX1T1 is the most common fusion gene found in acute myeloid leukemia. Seminal contributions by many different research groups have revealed a complex regulatory network promoting leukemic self-renewal and propagation. Perturbation of RUNX1/RUNX1T1 levels and its DNA binding affects chromatin accessibility and transcription factor occupation at multiple gene loci associated with changes in gene expression levels. Exploration of this transcriptional program by targeted RNAi screens uncovered a crucial role of RUNX1/RUNX1T1 in cell cycle progression by regulating CCND2. This dependency results in a high vulnerability toward inhibitors of CDK4 and CDK6 and suggests new avenues for therapeutic intervention against acute myeloid leukemia.
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MESH Headings
- Animals
- Cell Cycle
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Protein Interaction Maps
- RUNX1 Translocation Partner 1 Protein/genetics
- RUNX1 Translocation Partner 1 Protein/metabolism
- Transcriptional Activation
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Affiliation(s)
- Laura E Swart
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Olaf Heidenreich
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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27
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Transcription Factor RBPJ as a Molecular Switch in Regulating the Notch Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1287:9-30. [PMID: 33034023 DOI: 10.1007/978-3-030-55031-8_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Notch signal transduction cascade requires cell-to-cell contact and results in the proteolytic processing of the Notch receptor and subsequent assembly of a transcriptional coactivator complex containing the Notch intracellular domain (NICD) and transcription factor RBPJ. In the absence of a Notch signal, RBPJ remains at Notch target genes and dampens transcriptional output. Like in other signaling pathways, RBPJ is able to switch from activation to repression by associating with corepressor complexes containing several chromatin-modifying enzymes. Here, we focus on the recent advances concerning RBPJ-corepressor functions, especially in regard to chromatin regulation. We put this into the context of one of the best-studied model systems for Notch, blood cell development. Alterations in the RBPJ-corepressor functions can contribute to the development of leukemia, especially in the case of acute myeloid leukemia (AML). The versatile role of transcription factor RBPJ in regulating pivotal target genes like c-MYC and HES1 may contribute to the better understanding of the development of leukemia.
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28
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Stengel KR, Ellis JD, Spielman CL, Bomber ML, Hiebert SW. Definition of a small core transcriptional circuit regulated by AML1-ETO. Mol Cell 2020; 81:530-545.e5. [PMID: 33382982 DOI: 10.1016/j.molcel.2020.12.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/19/2020] [Accepted: 12/02/2020] [Indexed: 12/21/2022]
Abstract
Transcription factors regulate gene networks controlling normal hematopoiesis and are frequently deregulated in acute myeloid leukemia (AML). Critical to our understanding of the mechanism of cellular transformation by oncogenic transcription factors is the ability to define their direct gene targets. However, gene network cascades can change within minutes to hours, making it difficult to distinguish direct from secondary or compensatory transcriptional changes by traditional methodologies. To overcome this limitation, we devised cell models in which the AML1-ETO protein could be quickly degraded upon addition of a small molecule. The rapid kinetics of AML1-ETO removal, when combined with analysis of transcriptional output by nascent transcript analysis and genome-wide AML1-ETO binding by CUT&RUN, enabled the identification of direct gene targets that constitute a core AML1-ETO regulatory network. Moreover, derepression of this gene network was associated with RUNX1 DNA binding and triggered a transcription cascade ultimately resulting in myeloid differentiation.
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Affiliation(s)
- Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| | - Jacob D Ellis
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Clare L Spielman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Monica L Bomber
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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29
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Regulating the Regulators: The Role of Histone Deacetylase 1 (HDAC1) in Erythropoiesis. Int J Mol Sci 2020; 21:ijms21228460. [PMID: 33187090 PMCID: PMC7696854 DOI: 10.3390/ijms21228460] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylases (HDACs) play important roles in transcriptional regulation in eukaryotic cells. Class I deacetylase HDAC1/2 often associates with repressor complexes, such as Sin3 (Switch Independent 3), NuRD (Nucleosome remodeling and deacetylase) and CoREST (Corepressor of RE1 silencing transcription factor) complexes. It has been shown that HDAC1 interacts with and modulates all essential transcription factors for erythropoiesis. During erythropoiesis, histone deacetylase activity is dramatically reduced. Consistently, inhibition of HDAC activity promotes erythroid differentiation. The reduction of HDAC activity not only results in the activation of transcription activators such as GATA-1 (GATA-binding factor 1), TAL1 (TAL BHLH Transcription Factor 1) and KLF1 (Krüpple-like factor 1), but also represses transcription repressors such as PU.1 (Putative oncogene Spi-1). The reduction of histone deacetylase activity is mainly through HDAC1 acetylation that attenuates HDAC1 activity and trans-repress HDAC2 activity through dimerization with HDAC1. Therefore, the acetylation of HDAC1 can convert the corepressor complex to an activator complex for gene activation. HDAC1 also can deacetylate non-histone proteins that play a role on erythropoiesis, therefore adds another layer of gene regulation through HDAC1. Clinically, it has been shown HDACi can reactivate fetal globin in adult erythroid cells. This review will cover the up to date research on the role of HDAC1 in modulating key transcription factors for erythropoiesis and its clinical relevance.
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30
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Hontecillas-Prieto L, Flores-Campos R, Silver A, de Álava E, Hajji N, García-Domínguez DJ. Synergistic Enhancement of Cancer Therapy Using HDAC Inhibitors: Opportunity for Clinical Trials. Front Genet 2020; 11:578011. [PMID: 33024443 PMCID: PMC7516260 DOI: 10.3389/fgene.2020.578011] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/26/2020] [Indexed: 12/25/2022] Open
Abstract
Chemotherapy is one of the most established and effective treatments for almost all types of cancer. However, the elevated toxicity due to the non-tumor-associated effects, development of secondary malignancies, infertility, radiation-induced fibrosis and resistance to treatment limit the effectiveness and safety of treatment. In addition, these multiple factors significantly impact quality of life. Over the last decades, our increased understanding of cancer epigenetics has led to new therapeutic approaches and the promise of improved patient outcomes. Epigenetic alterations are commonly found in cancer, especially the increased expression and activity of histone deacetylases (HDACs). Dysregulation of HDACs are critical to the development and progression of the majority of tumors. Hence, HDACs inhibitors (HDACis) were developed and now represent a very promising treatment strategy. The use of HDACis as monotherapy has shown very positive pre-clinical results, but clinical trials have had only limited success. However, combinatorial regimens with other cancer drugs have shown synergistic effects both in pre-clinical and clinical studies. At the same time, these combinations have enhanced the efficacy, reduced the toxicity and tumor resistance to therapy. In this review, we will examine examples of HDACis used in combination with other cancer drugs and highlight the synergistic effects observed in recent preclinical and clinical studies.
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Affiliation(s)
- Lourdes Hontecillas-Prieto
- Institute of Biomedicine of Seville, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla/CIBERONC, Seville, Spain
| | - Rocío Flores-Campos
- Institute of Biomedicine of Seville, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla/CIBERONC, Seville, Spain
| | - Andrew Silver
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Enrique de Álava
- Institute of Biomedicine of Seville, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla/CIBERONC, Seville, Spain.,Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, Seville, Spain
| | - Nabil Hajji
- Division of Brain Sciences, Imperial College London, London, United Kingdom
| | - Daniel J García-Domínguez
- Institute of Biomedicine of Seville, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla/CIBERONC, Seville, Spain
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31
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Fukunaga J, Nomura Y, Tanaka Y, Torigoe H, Nakamura Y, Sakamoto T, Kozu T. A G-quadruplex-forming RNA aptamer binds to the MTG8 TAFH domain and dissociates the leukemic AML1-MTG8 fusion protein from DNA. FEBS Lett 2020; 594:3477-3489. [PMID: 32870501 DOI: 10.1002/1873-3468.13914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 11/11/2022]
Abstract
MTG8 (RUNX1T1) is a fusion partner of AML1 (RUNX1) in the leukemic chromosome translocation t(8;21). The AML1-MTG8 fusion gene encodes a chimeric transcription factor. One of the highly conserved domains of MTG8 is TAFH which possesses homology with human TAF4 [TATA-box binding protein-associated factor]. To obtain specific inhibitors of the AML1-MTG8 fusion protein, we isolated RNA aptamers against the MTG8 TAFH domain using systematic evolution of ligands by exponential enrichment. All TAF aptamers contained guanine-rich sequences. Analyses of a TAF aptamer by NMR, CD, and mutagenesis revealed that it forms a parallel G-quadruplex structure in the presence of K+ . Furthermore, the aptamer could bind to the AML1-MTG8 fusion protein and dissociate the AML1-MTG8/DNA complex, suggesting that it can inhibit the dominant negative effects of AML1-MTG8 against normal AML1 function and serve as a potential therapeutic agent for leukemia.
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Affiliation(s)
- Junichi Fukunaga
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Japan
| | - Yusuke Nomura
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino, Japan.,Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Japan
| | - Yoichiro Tanaka
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Japan.,Facility for RI Research and Education, Instrumental Analysis Center, Research Initiatives and Promotion Organization, Yokohama National University, Hodogaya-ku, Japan
| | - Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Japan
| | - Yoshikazu Nakamura
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Minato-ku, Japan.,Ribomic Inc., Minato-ku, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Japan
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32
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Steinauer N, Guo C, Zhang J. The transcriptional corepressor CBFA2T3 inhibits all- trans-retinoic acid-induced myeloid gene expression and differentiation in acute myeloid leukemia. J Biol Chem 2020; 295:8887-8900. [PMID: 32434928 PMCID: PMC7335779 DOI: 10.1074/jbc.ra120.013042] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/17/2020] [Indexed: 01/10/2023] Open
Abstract
CBFA2/RUNX1 partner transcriptional co-repressor 3 (CBFA2T3, also known as MTG16 or ETO2) is a myeloid translocation gene family protein that functions as a master transcriptional corepressor in hematopoiesis. Recently, it has been shown that CBFA2T3 maintains leukemia stem cell gene expression and promotes relapse in acute myeloid leukemia (AML). However, a role for CBFA2T3 in myeloid differentiation of AML has not been reported. Here, we show that CBFA2T3 represses retinoic acid receptor (RAR) target gene expression and inhibits all-trans-retinoic acid (ATRA)-induced myeloid differentiation of AML cells. ChIP-Seq revealed that CBFA2T3 targets the RARα/RXRα cistrome in U937 AML cells, predominantly at myeloid-specific enhancers associated with terminal differentiation. CRISPR/Cas9-mediated abrogation of CBFA2T3 resulted in spontaneous and ATRA-induced activation of myeloid-specific genes in a manner correlated with myeloid differentiation. Importantly, these effects were reversed by CBFA2T3 re-expression. Mechanistic studies showed that CBFA2T3 inhibits RAR target gene transcription by acting at an early step to regulate histone acetyltransferase recruitment, histone acetylation, and chromatin accessibility at RARα target sites, independently of the downstream, RAR-mediated steps of transcription. Finally, we validated the inhibitory effect of CBFA2T3 on RAR in multiple AML subtypes and patient samples. To our knowledge, this is the first study to show that CBFA2T3 down-regulation is both necessary and sufficient for enhancing ATRA-induced myeloid gene expression and differentiation of AML cells. Our findings suggest that CBFA2T3 can serve as a potential target for enhancing AML responsiveness to ATRA differentiation therapies.
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Affiliation(s)
- Nickolas Steinauer
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Chun Guo
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Jinsong Zhang
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.
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33
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Zou L, Li H, Han X, Qin J, Song G. Runx1t1 promotes the neuronal differentiation in rat hippocampus. Stem Cell Res Ther 2020; 11:160. [PMID: 32321587 PMCID: PMC7178948 DOI: 10.1186/s13287-020-01667-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/20/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022] Open
Abstract
Background Runt-related transcription factor 1 translocated to 1 (Runx1t1) is one of the members of the myeloid translocation gene family. Our previous work showed that Runx1t1 induced the neuronal differentiation of radial glia cells in vitro. Methods To better uncover the role of Runx1t1 in hippocampal neurogenesis, in this study, we further explore its localization and function during the hippocampal neurogenesis. Results Our results showed that insufficient expression of Runx1t1 reduced the neuronal differentiation, and overexpression of Runx1t1 promoted the neuronal differentiation in vitro. We also found that Runx1t1 localized in neurons but not astrocytes both in vivo and in vitro. Furthermore, we found that Runx1t1 overexpression elevated the number of newborn neurons in the hippocampal dentate gyrus. Conclusions Taken together, our results further proved that Runx1t1 could be worked as a regulator in the process of hippocampal neurogenesis.
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Affiliation(s)
- Linqing Zou
- Department of Human Anatomy, Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, 226001, Jiangsu, China.,Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Haoming Li
- Department of Human Anatomy, Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, 226001, Jiangsu, China.,Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Xiao Han
- Department of Human Anatomy, Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, 226001, Jiangsu, China
| | - Jianbing Qin
- Department of Human Anatomy, Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, 226001, Jiangsu, China
| | - Guoqi Song
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China. .,Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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34
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Guo C, Li J, Steinauer N, Wong M, Wu B, Dickson A, Kalkum M, Zhang J. Histone deacetylase 3 preferentially binds and collaborates with the transcription factor RUNX1 to repress AML1-ETO-dependent transcription in t(8;21) AML. J Biol Chem 2020; 295:4212-4223. [PMID: 32071087 PMCID: PMC7105303 DOI: 10.1074/jbc.ra119.010707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 02/11/2020] [Indexed: 01/26/2023] Open
Abstract
In up to 15% of acute myeloid leukemias (AMLs), a recurring chromosomal translocation, termed t(8;21), generates the AML1-eight-twenty-one (ETO) leukemia fusion protein, which contains the DNA-binding domain of Runt-related transcription factor 1 (RUNX1) and almost all of ETO. RUNX1 and the AML1-ETO fusion protein are coexpressed in t(8;21) AML cells and antagonize each other's gene-regulatory functions. AML1-ETO represses transcription of RUNX1 target genes by competitively displacing RUNX1 and recruiting corepressors such as histone deacetylase 3 (HDAC3). Recent studies have shown that AML1-ETO and RUNX1 co-occupy the binding sites of AML1-ETO-activated genes. How this joined binding allows RUNX1 to antagonize AML1-ETO-mediated transcriptional activation is unclear. Here we show that RUNX1 functions as a bona fide repressor of transcription activated by AML1-ETO. Mechanistically, we show that RUNX1 is a component of the HDAC3 corepressor complex and that HDAC3 preferentially binds to RUNX1 rather than to AML1-ETO in t(8;21) AML cells. Studying the regulation of interleukin-8 (IL8), a newly identified AML1-ETO-activated gene, we demonstrate that RUNX1 and HDAC3 collaboratively repress AML1-ETO-dependent transcription, a finding further supported by results of genome-wide analyses of AML1-ETO-activated genes. These and other results from the genome-wide studies also have important implications for the mechanistic understanding of gene-specific coactivator and corepressor functions across the AML1-ETO/RUNX1 cistrome.
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MESH Headings
- Cell Line, Tumor
- Core Binding Factor Alpha 2 Subunit/genetics
- Gene Expression Regulation, Neoplastic
- Genome, Human/genetics
- Histone Deacetylases/genetics
- Humans
- Interleukin-8/genetics
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Oncogene Proteins, Fusion/genetics
- Promoter Regions, Genetic
- RUNX1 Translocation Partner 1 Protein/genetics
- Transcriptional Activation/genetics
- Translocation, Genetic/genetics
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Affiliation(s)
- Chun Guo
- Department of Pharmacology and Physiology, Saint Louis University, School of Medicine, St. Louis, Missouri 63104
| | - Jian Li
- Department of Pharmacology and Physiology, Saint Louis University, School of Medicine, St. Louis, Missouri 63104
| | - Nickolas Steinauer
- Department of Pharmacology and Physiology, Saint Louis University, School of Medicine, St. Louis, Missouri 63104
| | - Madeline Wong
- Department of Pharmacology and Physiology, Saint Louis University, School of Medicine, St. Louis, Missouri 63104
| | - Brent Wu
- Department of Pharmacology and Physiology, Saint Louis University, School of Medicine, St. Louis, Missouri 63104
| | - Alexandria Dickson
- Department of Pharmacology and Physiology, Saint Louis University, School of Medicine, St. Louis, Missouri 63104
| | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Jinsong Zhang
- Department of Pharmacology and Physiology, Saint Louis University, School of Medicine, St. Louis, Missouri 63104.
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35
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RUNX1 mutations enhance self-renewal and block granulocytic differentiation in human in vitro models and primary AMLs. Blood Adv 2020; 3:320-332. [PMID: 30709863 DOI: 10.1182/bloodadvances.2018024422] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/24/2018] [Indexed: 12/21/2022] Open
Abstract
To unravel molecular mechanisms by which Runt-related transcription factor 1 (RUNX1) mutations contribute to leukemic transformation, we introduced the RUNX1-S291fs300X mutation in human CD34+ stem/progenitor cells and in human induced pluripotent stem cells (iPSCs). In both models, RUNX1mut overexpression strongly impaired myeloid commitment. Instead, self-renewal was enhanced, as shown, by increased long-term culture-initiating cell frequencies and enhanced colony-forming cell replating capacity. Long-term suspension cultures with RUNX1mut-transduced cord blood (CB) CD34+ cells continued for more than 100 days, during which the cells displayed an immature granulocyte-macrophage progenitor-like CD34+/CD123+/CD45RA+ phenotype. The CD34+/CD38- hematopoietic stem cell (HSC) population most likely acted as cell of origin, as HSCs provided the best long-term proliferative potential on overexpression of RUNX1mut. CEBPA expression was reduced in RUNX1mut cells, and reexpression of CEBPA partly restored differentiation. RNA-seq analysis on CB/iPSC systems and on primary patient samples confirmed that RUNX1 mutations induce a myeloid differentiation block, and that a common set of RUNX1mut-upregulated target genes was strongly enriched for gene ontology terms associated with nucleosome assembly and chromatin structure. Interestingly, in comparison with AML1-ETO binding in acute myeloid leukemias (AMLs), we found significantly distinct genomic distribution and differential expression for RUNX1mut of genes such as TCF4, MEIS1, and HMGA2 that may potentially contribute to the underlying difference in clinical outcomes between RUNX1mut and AML1-ETO patients. In conclusion, RUNX1mut appears to induce a specific transcriptional program that contributes to leukemic transformation.
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36
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Wang P, Wang Z, Liu J. Role of HDACs in normal and malignant hematopoiesis. Mol Cancer 2020; 19:5. [PMID: 31910827 PMCID: PMC6945581 DOI: 10.1186/s12943-019-1127-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/26/2019] [Indexed: 01/09/2023] Open
Abstract
Normal hematopoiesis requires the accurate orchestration of lineage-specific patterns of gene expression at each stage of development, and epigenetic regulators play a vital role. Disordered epigenetic regulation has emerged as a key mechanism contributing to hematological malignancies. Histone deacetylases (HDACs) are a series of key transcriptional cofactors that regulate gene expression by deacetylation of lysine residues on histone and nonhistone proteins. In normal hematopoiesis, HDACs are widely involved in the development of various lineages. Their functions involve stemness maintenance, lineage commitment determination, cell differentiation and proliferation, etc. Deregulation of HDACs by abnormal expression or activity and oncogenic HDAC-containing transcriptional complexes are involved in hematological malignancies. Currently, HDAC family members are attractive targets for drug design, and a variety of HDAC-based combination strategies have been developed for the treatment of hematological malignancies. Drug resistance and limited therapeutic efficacy are key issues that hinder the clinical applications of HDAC inhibitors (HDACis). In this review, we summarize the current knowledge of how HDACs and HDAC-containing complexes function in normal hematopoiesis and highlight the etiology of HDACs in hematological malignancies. Moreover, the implication and drug resistance of HDACis are also discussed. This review presents an overview of the physiology and pathology of HDACs in the blood system.
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Affiliation(s)
- Pan Wang
- The Xiangya Hospital, Central South University, Changsha, 410005, Hunan, China.,Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zi Wang
- The Xiangya Hospital, Central South University, Changsha, 410005, Hunan, China. .,Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
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37
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Schoenherr C, Wohlan K, Dallmann I, Pich A, Hegermann J, Ganser A, Hilfiker-Kleiner D, Heidenreich O, Scherr M, Eder M. Stable depletion of RUNX1-ETO in Kasumi-1 cells induces expression and enhanced proteolytic activity of Cathepsin G and Neutrophil Elastase. PLoS One 2019; 14:e0225977. [PMID: 31826021 PMCID: PMC6905530 DOI: 10.1371/journal.pone.0225977] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/15/2019] [Indexed: 01/24/2023] Open
Abstract
The oncogenic fusion protein RUNX1-ETO is a product of the t(8;21) translocation and consists of the hematopoietic transcriptional master regulator RUNX1 and the repressor ETO. RUNX1-ETO is found in 10–15% of acute myeloid leukemia and interferes with the expression of genes that are essential for myeloid differentiation. The neutrophil serine protease Cathepsin G is one of the genes suppressed by RUNX1-ETO, but little is known about its impact on the regulation of other lysosomal proteases. By lentiviral transduction of the t(8;21) positive cell line Kasumi-1 with an RUNX1-ETO specific shRNA, we analyzed long-term effects of stable RUNX1-ETO silencing on cellular phenotypes and target gene expression. Stable anti RUNX1-ETO RNAi reduces both proliferation and apoptosis in Kasumi-1 cells. In addition, long-term knockdown of RUNX1-ETO leads to an upregulation of proteolytic activity in Kasumi-1 cells, which may be released in vitro upon cell lysis leading to massive degradation of cellular proteins. We therefore propose that protein expression data of RUNX1-ETO-silenced Kasumi-1 cells must be analyzed with caution, as cell lysis conditions can heavily influence the results of studies on protein expression. Next, a mass spectrometry-based approach was used to identify protease cleavage patterns in RUNX1-ETO-depleted Kasumi-1 cells and Neutrophil Elastase has been identified as a RUNX1-ETO candidate target. Finally, proteolytic activity of Neutrophil Elastase and Cathepsin G was functionally confirmed by si/shRNA-mediated knockdown in Kasumi-1 cells.
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Affiliation(s)
- Caroline Schoenherr
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Katharina Wohlan
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Iris Dallmann
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Andreas Pich
- Department of Toxicology, Research Core Unit Proteomics, Hannover Medical School, Hannover, Germany
| | - Jan Hegermann
- Department of Functional and Applied Anatomy, Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | | | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, United Kingdom
- Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Michaela Scherr
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- * E-mail: (MS); (ME)
| | - Matthias Eder
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- * E-mail: (MS); (ME)
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38
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Retinoic Acid Receptors in Acute Myeloid Leukemia Therapy. Cancers (Basel) 2019; 11:cancers11121915. [PMID: 31805753 PMCID: PMC6966485 DOI: 10.3390/cancers11121915] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022] Open
Abstract
Retinoic acid (RA) signaling pathways regulate fundamental biological processes, such as cell proliferation, development, differentiation, and apoptosis. Retinoid receptors (RARs and RXRs) are ligand-dependent transcription factors. All-trans retinoic acid (ATRA) is the principal endogenous ligand for the retinoic acid receptor alpha (RARA) and is produced by the enzymatic oxidation of dietary vitamin A, whose deficiency is associated with several pathological conditions. Differentiation therapy using ATRA revolutionized the outcome of acute promyelocytic leukemia (APL), although attempts to replicate these results in other cancer types have been met with more modest results. A better knowledge of RA signaling in different leukemia contexts is required to improve initial designs. Here, we will review the RA signaling pathway in normal and malignant hematopoiesis, and will discuss the advantages and the limitations related to retinoid therapy in acute myeloid leukemia.
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39
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Sampathi S, Acharya P, Zhao Y, Wang J, Stengel KR, Liu Q, Savona MR, Hiebert SW. The CDK7 inhibitor THZ1 alters RNA polymerase dynamics at the 5' and 3' ends of genes. Nucleic Acids Res 2019; 47:3921-3936. [PMID: 30805632 PMCID: PMC6486546 DOI: 10.1093/nar/gkz127] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/22/2019] [Indexed: 01/01/2023] Open
Abstract
The t(8;21) is one of the most frequent chromosomal translocations associated with acute myeloid leukemia (AML). We found that t(8;21) AML were extremely sensitive to THZ1, which triggered apoptosis after only 4 h. We used precision nuclear run-on transcription sequencing (PROseq) to define the global effects of THZ1 and other CDK inhibitors on RNA polymerase II dynamics. Inhibition of CDK7 using THZ1 caused wide-spread loss of promoter-proximal paused RNA polymerase. This loss of 5′ pausing was associated with accumulation of polymerases in the body of a large number of genes. However, there were modest effects on genes regulated by ‘super-enhancers’. At the 3′ ends of genes, treatment with THZ1 suppressed RNA polymerase ‘read through’ at the end of the last exon, which resembled a phenotype associated with a mutant RNA polymerase with slower elongation rates. Consistent with this hypothesis, polyA site-sequencing (PolyA-seq) did not detect differences in poly A sites after THZ1 treatment. PROseq analysis after short treatments with THZ1 suggested that these 3′ effects were due to altered CDK7 activity at the 5′ end of long genes, and were likely to be due to slower rates of elongation.
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Affiliation(s)
- Shilpa Sampathi
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Pankaj Acharya
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yue Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Michael R Savona
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37027.,Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37027
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40
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Thoms JAI, Beck D, Pimanda JE. Transcriptional networks in acute myeloid leukemia. Genes Chromosomes Cancer 2019; 58:859-874. [PMID: 31369171 DOI: 10.1002/gcc.22794] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/16/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease characterized by a diverse range of recurrent molecular aberrations that occur in many different combinations. Components of transcriptional networks are a common target of these aberrations, leading to network-wide changes and deployment of novel or developmentally inappropriate transcriptional programs. Genome-wide techniques are beginning to reveal the full complexity of normal hematopoietic stem cell transcriptional networks and the extent to which they are deregulated in AML, and new understandings of the mechanisms by which AML cells maintain self-renewal and block differentiation are starting to emerge. The hope is that increased understanding of the network architecture in AML will lead to identification of key oncogenic dependencies that are downstream of multiple network aberrations, and that this knowledge will be translated into new therapies that target these dependencies. Here, we review the current state of knowledge of network perturbation in AML with a focus on major mechanisms of transcription factor dysregulation, including mutation, translocation, and transcriptional dysregulation, and discuss how these perturbations propagate across transcriptional networks. We will also review emerging mechanisms of network disruption, and briefly discuss how increased knowledge of network disruption is already being used to develop new therapies.
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Affiliation(s)
- Julie A I Thoms
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Dominik Beck
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - John E Pimanda
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia.,Department of Haematology, Prince of Wales Hospital, Sydney, New South Wales, Australia
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41
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Hong D, Fritz AJ, Gordon JA, Tye CE, Boyd JR, Tracy KM, Frietze SE, Carr FE, Nickerson JA, Van Wijnen AJ, Imbalzano AN, Zaidi SK, Lian JB, Stein JL, Stein GS. RUNX1-dependent mechanisms in biological control and dysregulation in cancer. J Cell Physiol 2019; 234:8597-8609. [PMID: 30515788 PMCID: PMC6395522 DOI: 10.1002/jcp.27841] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/12/2018] [Indexed: 01/02/2023]
Abstract
The RUNX1 transcription factor has recently been shown to be obligatory for normal development. RUNX1 controls the expression of genes essential for proper development in many cell lineages and tissues including blood, bone, cartilage, hair follicles, and mammary glands. Compromised RUNX1 regulation is associated with many cancers. In this review, we highlight evidence for RUNX1 control in both invertebrate and mammalian development and recent novel findings of perturbed RUNX1 control in breast cancer that has implications for other solid tumors. As RUNX1 is essential for definitive hematopoiesis, RUNX1 mutations in hematopoietic lineage cells have been implicated in the etiology of several leukemias. Studies of solid tumors have revealed a context-dependent function for RUNX1 either as an oncogene or a tumor suppressor. These RUNX1 functions have been reported for breast, prostate, lung, and skin cancers that are related to cancer subtypes and different stages of tumor development. Growing evidence suggests that RUNX1 suppresses aggressiveness in most breast cancer subtypes particularly in the early stage of tumorigenesis. Several studies have identified RUNX1 suppression of the breast cancer epithelial-to-mesenchymal transition. Most recently, RUNX1 repression of cancer stem cells and tumorsphere formation was reported for breast cancer. It is anticipated that these new discoveries of the context-dependent diversity of RUNX1 functions will lead to innovative therapeutic strategies for the intervention of cancer and other abnormalities of normal tissues.
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Affiliation(s)
- Deli Hong
- Dana Farber Cancer Institute, Boston, Massachusetts
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, Vermont
| | - Jonathan A Gordon
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, Vermont
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, Vermont
| | - Joseph R Boyd
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, Vermont
| | - Kirsten M Tracy
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, Vermont
| | - Seth E Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - Frances E. Carr
- Department of Pharmacology, University of Vermont, Burlington, Vermont
| | | | - Andre J. Van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Anthony N. Imbalzano
- Graduate Program in Cell Biology and Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts
| | - Sayyed K. Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, Vermont
| | - Jane B. Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, Vermont
| | - Janet L. Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, Vermont
| | - Gary S. Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, Vermont
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42
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RUNX family: Oncogenes or tumor suppressors (Review). Oncol Rep 2019; 42:3-19. [PMID: 31059069 PMCID: PMC6549079 DOI: 10.3892/or.2019.7149] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Runt-related transcription factor (RUNX) proteins belong to a transcription factors family known as master regulators of important embryonic developmental programs. In the last decade, the whole family has been implicated in the regulation of different oncogenic processes and signaling pathways associated with cancer. Furthermore, a suppressor tumor function has been also reported, suggesting the RUNX family serves key role in all different types of cancer. In this review, the known biological characteristics, specific regulatory abilities and experimental evidence of RUNX proteins will be analyzed to demonstrate their oncogenic potential and tumor suppressor abilities during oncogenic processes, suggesting their importance as biomarkers of cancer. Additionally, the importance of continuing with the molecular studies of RUNX proteins' and its dual functions in cancer will be underlined in order to apply it in the future development of specific diagnostic methods and therapies against different types of cancer.
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van der Kouwe E, Staber PB. RUNX1-ETO: Attacking the Epigenome for Genomic Instable Leukemia. Int J Mol Sci 2019; 20:E350. [PMID: 30654457 PMCID: PMC6358732 DOI: 10.3390/ijms20020350] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 12/29/2022] Open
Abstract
Oncogenic fusion protein RUNX1-ETO is the product of the t(8;21) translocation, responsible for the most common cytogenetic subtype of acute myeloid leukemia. RUNX1, a critical transcription factor in hematopoietic development, is fused with almost the entire ETO sequence with the ability to recruit a wide range of repressors. Past efforts in providing a comprehensive picture of the genome-wide localization and the target genes of RUNX1-ETO have been inconclusive in understanding the underlying mechanism by which it deregulates native RUNX1. In this review; we dissect the current data on the epigenetic impact of RUNX1 and RUNX1-ETO. Both share similarities however, in recent years, research focused on epigenetic factors to explain their differences. RUNX1-ETO impairs DNA repair mechanisms which compromises genomic stability and favors a mutator phenotype. Among an increasing pool of mutated factors, regulators of DNA methylation are frequently found in t(8;21) AML. Together with the alteration of both, histone markers and distal enhancer regulation, RUNX1-ETO might specifically disrupt normal chromatin structure. Epigenetic studies on the fusion protein uncovered new mechanisms contributing to leukemogenesis and hopefully will translate into clinical applications.
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Affiliation(s)
- Emiel van der Kouwe
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria.
| | - Philipp Bernhard Staber
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria.
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Different roles of E proteins in t(8;21) leukemia: E2-2 compromises the function of AETFC and negatively regulates leukemogenesis. Proc Natl Acad Sci U S A 2018; 116:890-899. [PMID: 30593567 DOI: 10.1073/pnas.1809327116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The AML1-ETO fusion protein, generated by the t(8;21) chromosomal translocation, is causally involved in nearly 20% of acute myeloid leukemia (AML) cases. In leukemic cells, AML1-ETO resides in and functions through a stable protein complex, AML1-ETO-containing transcription factor complex (AETFC), that contains multiple transcription (co)factors. Among these AETFC components, HEB and E2A, two members of the ubiquitously expressed E proteins, directly interact with AML1-ETO, confer new DNA-binding capacity to AETFC, and are essential for leukemogenesis. However, the third E protein, E2-2, is specifically silenced in AML1-ETO-expressing leukemic cells, suggesting E2-2 as a negative factor of leukemogenesis. Indeed, ectopic expression of E2-2 selectively inhibits the growth of AML1-ETO-expressing leukemic cells, and this inhibition requires the bHLH DNA-binding domain. RNA-seq and ChIP-seq analyses reveal that, despite some overlap, the three E proteins differentially regulate many target genes. In particular, studies show that E2-2 both redistributes AETFC to, and activates, some genes associated with dendritic cell differentiation and represses MYC target genes. In AML patients, the expression of E2-2 is relatively lower in the t(8;21) subtype, and an E2-2 target gene, THPO, is identified as a potential predictor of relapse. In a mouse model of human t(8;21) leukemia, E2-2 suppression accelerates leukemogenesis. Taken together, these results reveal that, in contrast to HEB and E2A, which facilitate AML1-ETO-mediated leukemogenesis, E2-2 compromises the function of AETFC and negatively regulates leukemogenesis. The three E proteins thus define a heterogeneity of AETFC, which improves our understanding of the precise mechanism of leukemogenesis and assists development of diagnostic/therapeutic strategies.
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Kibler CE, Milligan SL, Farris TR, Zhu B, Mitra S, McBride JW. Ehrlichia chaffeensis TRP47 enters the nucleus via a MYND-binding domain-dependent mechanism and predominantly binds enhancers of host genes associated with signal transduction, cytoskeletal organization, and immune response. PLoS One 2018; 13:e0205983. [PMID: 30408047 PMCID: PMC6224051 DOI: 10.1371/journal.pone.0205983] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 10/04/2018] [Indexed: 12/14/2022] Open
Abstract
Ehrlichia chaffeensis is an obligately intracellular bacterium that establishes infection in mononuclear phagocytes through largely undefined reprogramming strategies including modulation of host gene transcription. In this study, we demonstrate that the E. chaffeensis effector TRP47 enters the host cell nucleus and binds regulatory regions of host genes relevant to infection. TRP47 was observed in the nucleus of E. chaffeensis-infected host cells, and nuclear localization was dependent on a variant MYND-binding domain. An electrophoretic mobility shift assay (EMSA) demonstrated that TRP47 directly binds host DNA via its tandem repeat domain. Utilizing chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) with E. chaffeensis-infected cells, TRP47 was found to bind at multiple sites in the human genome (n = 2,051 at p < 10-30). Ontology analysis identified genes involved in functions such as immune response, cytoskeletal organization, and signal transduction. TRP47-bound genes included RNA-coding genes, many of these linked to cell proliferation or apoptosis. Comparison of TRP47 binding sites with those of previously-identified E. chaffeensis nucleomodulins identified multiple genes and gene functional categories in common including intracellular transport, cell signaling, and transcriptional regulation. Further, motif analysis followed by EMSA with synthetic oligonucleotides containing discovered motifs revealed a conserved TRP47 DNA-binding motif. This study reveals that TRP47 is a nucleomodulin that enters the nucleus via a MYND-binding domain and appears to play a role in host cell reprogramming by regulation of transcription.
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Affiliation(s)
- Clayton E. Kibler
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sarah L. Milligan
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tierra R. Farris
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Bing Zhu
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Shubhajit Mitra
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jere W. McBride
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
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Martinez-Soria N, McKenzie L, Draper J, Ptasinska A, Issa H, Potluri S, Blair HJ, Pickin A, Isa A, Chin PS, Tirtakusuma R, Coleman D, Nakjang S, Assi S, Forster V, Reza M, Law E, Berry P, Mueller D, Osborne C, Elder A, Bomken SN, Pal D, Allan JM, Veal GJ, Cockerill PN, Wichmann C, Vormoor J, Lacaud G, Bonifer C, Heidenreich O. The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation. Cancer Cell 2018; 34:626-642.e8. [PMID: 30300583 PMCID: PMC6179967 DOI: 10.1016/j.ccell.2018.08.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/20/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
Oncogenic transcription factors such as the leukemic fusion protein RUNX1/ETO, which drives t(8;21) acute myeloid leukemia (AML), constitute cancer-specific but highly challenging therapeutic targets. We used epigenomic profiling data for an RNAi screen to interrogate the transcriptional network maintaining t(8;21) AML. This strategy identified Cyclin D2 (CCND2) as a crucial transmitter of RUNX1/ETO-driven leukemic propagation. RUNX1/ETO cooperates with AP-1 to drive CCND2 expression. Knockdown or pharmacological inhibition of CCND2 by an approved drug significantly impairs leukemic expansion of patient-derived AML cells and engraftment in immunodeficient murine hosts. Our data demonstrate that RUNX1/ETO maintains leukemia by promoting cell cycle progression and identifies G1 CCND-CDK complexes as promising therapeutic targets for treatment of RUNX1/ETO-driven AML.
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Affiliation(s)
- Natalia Martinez-Soria
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Lynsey McKenzie
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Julia Draper
- Cancer Research UK Manchester Institute, Manchester M20 4GJ, UK
| | - Anetta Ptasinska
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Hasan Issa
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Sandeep Potluri
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Helen J Blair
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Anna Pickin
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Asmida Isa
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Paulynn Suyin Chin
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ricky Tirtakusuma
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Daniel Coleman
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Sirintra Nakjang
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Salam Assi
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Victoria Forster
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Mojgan Reza
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Ed Law
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Philip Berry
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dorothee Mueller
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Cameron Osborne
- Department of Medical & Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Alex Elder
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Simon N Bomken
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Deepali Pal
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - James M Allan
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gareth J Veal
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Peter N Cockerill
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilian University Hospital, Munich 80539, Germany
| | - Josef Vormoor
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK; Princess Maxima Center for Pediatric Oncology, Utrecht 3584CS, the Netherlands
| | - Georges Lacaud
- Cancer Research UK Manchester Institute, Manchester M20 4GJ, UK
| | - Constanze Bonifer
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK; Princess Maxima Center for Pediatric Oncology, Utrecht 3584CS, the Netherlands.
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Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly. Sci Rep 2018; 8:13712. [PMID: 30209338 PMCID: PMC6135828 DOI: 10.1038/s41598-018-32009-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/24/2018] [Indexed: 01/27/2023] Open
Abstract
HDAC1 and HDAC2 are components of several corepressor complexes (NuRD, Sin3, CoREST and MiDAC) that regulate transcription by deacetylating histones resulting in a more compact chromatin environment. This limits access of transcriptional machinery to genes and silences transcription. While using an AP-MS approach to map HDAC1/2 protein interaction networks, we noticed that N-terminally tagged versions of HDAC1 and HDAC2 did not assemble into HDAC corepressor complexes as expected, but instead appeared to be stalled with components of the prefoldin-CCT chaperonin pathway. These N-terminally tagged HDACs were also catalytically inactive. In contrast to the N-terminally tagged HDACs, C-terminally tagged HDAC1 and HDAC2 captured complete histone deacetylase complexes and the purified proteins had deacetylation activity that could be inhibited by SAHA (Vorinostat), a Class I/II HDAC inhibitor. This tag-mediated reprogramming of the HDAC1/2 protein interaction network suggests a mechanism whereby HDAC1 is first loaded into the CCT complex by prefoldin to complete folding, and then assembled into active, functional HDAC complexes. Imaging revealed that the prefoldin subunit VBP1 colocalises with nuclear HDAC1, suggesting that delivery of HDAC1 to the CCT complex happens in the nucleus.
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49
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Newcombe AA, Gibson BES, Keeshan K. Harnessing the potential of epigenetic therapies for childhood acute myeloid leukemia. Exp Hematol 2018; 63:1-11. [PMID: 29608923 DOI: 10.1016/j.exphem.2018.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/19/2018] [Accepted: 03/27/2018] [Indexed: 12/31/2022]
Abstract
There is a desperate need for new and effective therapeutic approaches to acute myeloid leukemia (AML) in both children and adults. Epigenetic aberrations are common in adult AML, and many novel epigenetic compounds that may improve patient outcomes are in clinical development. Mutations in epigenetic regulators occur less frequently in AML in children than in adults. Investigating the potential benefits of epigenetic therapy in pediatric AML is an important issue and is discussed in this review.
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Affiliation(s)
| | - Brenda E S Gibson
- Department of Paediatric Haematology, Royal Hospital for Children, Glasgow, UK
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
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50
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Takada K, Amano R, Nomura Y, Tanaka Y, Sugiyama S, Nagata T, Katahira M, Nakamura Y, Kozu T, Sakamoto T. Characterisation of an aptamer against the Runt domain of AML1 (RUNX1) by NMR and mutational analyses. FEBS Open Bio 2018; 8:264-270. [PMID: 29435416 PMCID: PMC5794459 DOI: 10.1002/2211-5463.12368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/20/2017] [Accepted: 12/02/2017] [Indexed: 01/15/2023] Open
Abstract
Since the invention of systematic evolution of ligands by exponential enrichment, many short oligonucleotides (or aptamers) have been reported that can bind to a wide range of target molecules with high affinity and specificity. Previously, we reported an RNA aptamer that shows high affinity to the Runt domain (RD) of the AML1 protein, a transcription factor with roles in haematopoiesis and immune function. From kinetic and thermodynamic studies, it was suggested that the aptamer recognises a large surface area of the RD, using numerous weak interactions. In this study, we identified the secondary structure by nuclear magnetic resonance spectroscopy and performed a mutational study to reveal the residue critical for binding to the RD. It was suggested that the large contact area was formed by a DNA‐mimicking motif and a multibranched loop, which confers the high affinity and specificity of binding.
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Affiliation(s)
- Kenta Takada
- Department of Life and Environmental Sciences Faculty of Engineering Chiba Institute of Technology Narashino Japan
| | - Ryo Amano
- Department of Life and Environmental Sciences Faculty of Engineering Chiba Institute of Technology Narashino Japan
| | - Yusuke Nomura
- Division of Medical Devices National Institute of Health Sciences Tokyo Japan
| | - Yoichiro Tanaka
- Facility for RI Research and Education Instrumental Analysis Center Yokohama National University Japan
| | | | | | | | - Yoshikazu Nakamura
- RIBOMIC Inc.Tokyo Japan.,Department of Basic Medical Sciences Institute of Medical Science University of Tokyo Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology Saitama Cancer CenterIna Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences Faculty of Engineering Chiba Institute of Technology Narashino Japan
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