1
|
Edtmayer S, Witalisz-Siepracka A, Zdársky B, Heindl K, Weiss S, Eder T, Dutta S, Graichen U, Klee S, Sharif O, Wieser R, Győrffy B, Poli V, Casanova E, Sill H, Grebien F, Stoiber D. A novel function of STAT3β in suppressing interferon response improves outcome in acute myeloid leukemia. Cell Death Dis 2024; 15:369. [PMID: 38806478 PMCID: PMC11133483 DOI: 10.1038/s41419-024-06749-9] [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: 12/14/2023] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024]
Abstract
Signal transducer and activator of transcription 3 (STAT3) is frequently overexpressed in patients with acute myeloid leukemia (AML). STAT3 exists in two distinct alternatively spliced isoforms, the full-length isoform STAT3α and the C-terminally truncated isoform STAT3β. While STAT3α is predominantly described as an oncogenic driver, STAT3β has been suggested to act as a tumor suppressor. To elucidate the role of STAT3β in AML, we established a mouse model of STAT3β-deficient, MLL-AF9-driven AML. STAT3β deficiency significantly shortened survival of leukemic mice confirming its role as a tumor suppressor. Furthermore, RNA sequencing revealed enhanced STAT1 expression and interferon (IFN) signaling upon loss of STAT3β. Accordingly, STAT3β-deficient leukemia cells displayed enhanced sensitivity to blockade of IFN signaling through both an IFNAR1 blocking antibody and the JAK1/2 inhibitor Ruxolitinib. Analysis of human AML patient samples confirmed that elevated expression of IFN-inducible genes correlated with poor overall survival and low STAT3β expression. Together, our data corroborate the tumor suppressive role of STAT3β in a mouse model in vivo. Moreover, they provide evidence that its tumor suppressive function is linked to repression of the STAT1-mediated IFN response. These findings suggest that the STAT3β/α mRNA ratio is a significant prognostic marker in AML and holds crucial information for targeted treatment approaches. Patients displaying a low STAT3β/α mRNA ratio and unfavorable prognosis could benefit from therapeutic interventions directed at STAT1/IFN signaling.
Collapse
MESH Headings
- Animals
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Humans
- STAT3 Transcription Factor/metabolism
- Mice
- Signal Transduction
- Interferons/metabolism
- STAT1 Transcription Factor/metabolism
- STAT1 Transcription Factor/genetics
- Mice, Inbred C57BL
- Receptor, Interferon alpha-beta/metabolism
- Receptor, Interferon alpha-beta/genetics
- Cell Line, Tumor
- Nitriles
- Pyrazoles
- Pyrimidines
Collapse
Affiliation(s)
- Sophie Edtmayer
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Agnieszka Witalisz-Siepracka
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Bernhard Zdársky
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Kerstin Heindl
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Stefanie Weiss
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Thomas Eder
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Uwe Graichen
- Division Biostatistics and Data Science, Department of General Health Studies, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Sascha Klee
- Division Biostatistics and Data Science, Department of General Health Studies, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Omar Sharif
- Institute for Vascular Biology, Centre for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
- Christian Doppler Laboratory for Immunometabolism and Systems Biology of Obesity-Related Diseases (InSpiReD), Vienna, Austria
| | - Rotraud Wieser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
- Cancer Biomarker Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Valeria Poli
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Emilio Casanova
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
- Department of Pharmacology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC), Medical University of Vienna, Vienna, Austria
| | - Heinz Sill
- Division of Hematology, Medical University of Graz, Graz, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Dagmar Stoiber
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria.
| |
Collapse
|
2
|
Wang G, Zhang W, Ren J, Zeng Y, Dang X, Tian X, Yu W, Li Z, Ma Y, Yang P, Lu J, Zheng J, Lu B, Xu J, Liang A. The DNA damage-independent ATM signalling maintains CBP/DOT1L axis in MLL rearranged acute myeloid leukaemia. Oncogene 2024:10.1038/s41388-024-02998-2. [PMID: 38671157 DOI: 10.1038/s41388-024-02998-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 04/28/2024]
Abstract
The long-term maintenance of leukaemia stem cells (LSCs) is responsible for the high degree of malignancy in MLL (mixed-lineage leukaemia) rearranged acute myeloid leukaemia (AML). The DNA damage response (DDR) and DOT1L/H3K79me pathways are required to maintain LSCs in MLLr-AML, but little is known about their interplay. This study revealed that the DDR enzyme ATM regulates the maintenance of LSCs in MLLr-AML with a sequential protein-posttranslational-modification manner via CBP-DOT1L. We identified the phosphorylation of CBP by ATM, which confers the stability of CBP by preventing its proteasomal degradation, and characterised the acetylation of DOT1L by CBP, which mediates the high level of H3K79me2 for the expression of leukaemia genes in MLLr-AML. In addition, we revealed that the regulation of CBP-DOT1L axis in MLLr-AML by ATM was independent of DNA damage activation. Our findings provide insight into the signalling pathways involoved in MLLr-AML and broaden the understanding of the role of DDR enzymes beyond processing DNA damage, as well as identigying them as potent cancer targets.
Collapse
Affiliation(s)
- Guangming Wang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
- East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
- Postdoctoral Station of Clinical Medicine, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200092, China
| | - Wenjun Zhang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Jie Ren
- Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Yu Zeng
- Department of Pathology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Xiuyong Dang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Xiaoxue Tian
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Wenlei Yu
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Zheng Li
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Yuting Ma
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Pingping Yang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Jinyuan Lu
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Junke Zheng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Bing Lu
- East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
| | - Jun Xu
- East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
| | - Aibin Liang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
| |
Collapse
|
3
|
Rao H, Liu C, Wang A, Ma C, Xu Y, Ye T, Su W, Zhou P, Gao WQ, Li L, Ding X. SETD2 deficiency accelerates sphingomyelin accumulation and promotes the development of renal cancer. Nat Commun 2023; 14:7572. [PMID: 37989747 PMCID: PMC10663509 DOI: 10.1038/s41467-023-43378-w] [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: 02/19/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Patients with polycystic kidney disease (PKD) encounter a high risk of clear cell renal cell carcinoma (ccRCC), a malignant tumor with dysregulated lipid metabolism. SET domain-containing 2 (SETD2) has been identified as an important tumor suppressor and an immunosuppressor in ccRCC. However, the role of SETD2 in ccRCC generation in PKD remains largely unexplored. Herein, we perform metabolomics, lipidomics, transcriptomics and proteomics within SETD2 loss induced PKD-ccRCC transition mouse model. Our analyses show that SETD2 loss causes extensive metabolic reprogramming events that eventually results in enhanced sphingomyelin biosynthesis and tumorigenesis. Clinical ccRCC patient specimens further confirm the abnormal metabolic reprogramming and sphingomyelin accumulation. Tumor symptom caused by Setd2 knockout is relieved by myriocin, a selective inhibitor of serine-palmitoyl-transferase and sphingomyelin biosynthesis. Our results reveal that SETD2 deficiency promotes large-scale metabolic reprogramming and sphingomyelin biosynthesis during PKD-ccRCC transition. This study introduces high-quality multi-omics resources and uncovers a regulatory mechanism of SETD2 on lipid metabolism during tumorigenesis.
Collapse
Affiliation(s)
- Hanyu Rao
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Changwei Liu
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Aiting Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Chunxiao Ma
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Xu
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Tianbao Ye
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqiong Su
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Peijun Zhou
- Division of Kidney Transplant, Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Qiang Gao
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Li
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
4
|
Li J, Kalev‐Zylinska ML. Advances in molecular characterization of pediatric acute megakaryoblastic leukemia not associated with Down syndrome; impact on therapy development. Front Cell Dev Biol 2023; 11:1170622. [PMID: 37325571 PMCID: PMC10267407 DOI: 10.3389/fcell.2023.1170622] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/19/2023] [Indexed: 06/17/2023] Open
Abstract
Acute megakaryoblastic leukemia (AMKL) is a rare subtype of acute myeloid leukemia (AML) in which leukemic blasts have megakaryocytic features. AMKL makes up 4%-15% of newly diagnosed pediatric AML, typically affecting young children (less than 2 years old). AMKL associated with Down syndrome (DS) shows GATA1 mutations and has a favorable prognosis. In contrast, AMKL in children without DS is often associated with recurrent and mutually exclusive chimeric fusion genes and has an unfavorable prognosis. This review mainly summarizes the unique features of pediatric non-DS AMKL and highlights the development of novel therapies for high-risk patients. Due to the rarity of pediatric AMKL, large-scale multi-center studies are needed to progress molecular characterization of this disease. Better disease models are also required to test leukemogenic mechanisms and emerging therapies.
Collapse
Affiliation(s)
- Jixia Li
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Department of Laboratory Medicine, School of Medicine, Foshan University, Foshan, China
| | - Maggie L. Kalev‐Zylinska
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Haematology Laboratory, Department of Pathology and Laboratory Medicine, Auckland City Hospital, Auckland, New Zealand
| |
Collapse
|
5
|
Walter DM, Gladstein AC, Doerig KR, Natesan R, Baskaran SG, Gudiel AA, Adler KM, Acosta JO, Wallace DC, Asangani IA, Feldser DM. Setd2 inactivation sensitizes lung adenocarcinoma to inhibitors of oxidative respiration and mTORC1 signaling. Commun Biol 2023; 6:255. [PMID: 36899051 PMCID: PMC10006211 DOI: 10.1038/s42003-023-04618-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/21/2023] [Indexed: 03/12/2023] Open
Abstract
SETD2 is a tumor suppressor that is frequently inactivated in several cancer types. The mechanisms through which SETD2 inactivation promotes cancer are unclear, and whether targetable vulnerabilities exist in these tumors is unknown. Here we identify heightened mTORC1-associated gene expression programs and functionally higher levels of oxidative metabolism and protein synthesis as prominent consequences of Setd2 inactivation in KRAS-driven mouse models of lung adenocarcinoma. Blocking oxidative respiration and mTORC1 signaling abrogates the high rates of tumor cell proliferation and tumor growth specifically in SETD2-deficient tumors. Our data nominate SETD2 deficiency as a functional marker of sensitivity to clinically actionable therapeutics targeting oxidative respiration and mTORC1 signaling.
Collapse
Affiliation(s)
- David M Walter
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy C Gladstein
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine R Doerig
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ramakrishnan Natesan
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Saravana G Baskaran
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - A Andrea Gudiel
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Keren M Adler
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonuelle O Acosta
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Irfan A Asangani
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - David M Feldser
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
6
|
Austin S, Mekis R, Mohammed SEM, Scalise M, Wang W, Galluccio M, Pfeiffer C, Borovec T, Parapatics K, Vitko D, Dinhopl N, Demaurex N, Bennett KL, Indiveri C, Nowikovsky K. TMBIM5 is the Ca 2+ /H + antiporter of mammalian mitochondria. EMBO Rep 2022; 23:e54978. [PMID: 36321428 PMCID: PMC9724676 DOI: 10.15252/embr.202254978] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/07/2022] [Accepted: 10/07/2022] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial Ca2+ ions are crucial regulators of bioenergetics and cell death pathways. Mitochondrial Ca2+ content and cytosolic Ca2+ homeostasis strictly depend on Ca2+ transporters. In recent decades, the major players responsible for mitochondrial Ca2+ uptake and release have been identified, except the mitochondrial Ca2+ /H+ exchanger (CHE). Originally identified as the mitochondrial K+ /H+ exchanger, LETM1 was also considered as a candidate for the mitochondrial CHE. Defining the mitochondrial interactome of LETM1, we identify TMBIM5/MICS1, the only mitochondrial member of the TMBIM family, and validate the physical interaction of TMBIM5 and LETM1. Cell-based and cell-free biochemical assays demonstrate the absence or greatly reduced Na+ -independent mitochondrial Ca2+ release in TMBIM5 knockout or pH-sensing site mutants, respectively, and pH-dependent Ca2+ transport by recombinant TMBIM5. Taken together, we demonstrate that TMBIM5, but not LETM1, is the long-sought mitochondrial CHE, involved in setting and regulating the mitochondrial proton gradient. This finding provides the final piece of the puzzle of mitochondrial Ca2+ transporters and opens the door to exploring its importance in health and disease, and to developing drugs modulating Ca2+ exchange.
Collapse
Affiliation(s)
- Shane Austin
- Department of Internal Medicine I and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- Present address:
Department of Biological & Chemical SciencesThe University of the West Indies, Cave Hill CampusCave HillBarbados
| | - Ronald Mekis
- Department of Internal Medicine I and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and BiophysicsUniversity of Veterinary Medicine ViennaViennaAustria
| | - Sami E M Mohammed
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and BiophysicsUniversity of Veterinary Medicine ViennaViennaAustria
| | - Mariafrancesca Scalise
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular BiotechnologyUniversity of CalabriaArcavacata di RendeItaly
| | - Wen‐An Wang
- Department of Cell Physiology & MetabolismUniversity of GenevaGenevaSwitzerland
| | - Michele Galluccio
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular BiotechnologyUniversity of CalabriaArcavacata di RendeItaly
| | - Christina Pfeiffer
- Department of Internal Medicine I and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
| | - Tamara Borovec
- Department of Internal Medicine I and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and BiophysicsUniversity of Veterinary Medicine ViennaViennaAustria
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Dijana Vitko
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Nora Dinhopl
- Department of Pathobiology, Institute of PathologyUniversity of Veterinary MedicineViennaAustria
| | - Nicolas Demaurex
- Department of Cell Physiology & MetabolismUniversity of GenevaGenevaSwitzerland
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular BiotechnologyUniversity of CalabriaArcavacata di RendeItaly
- CNR Institute of BiomembranesBioenergetics and Molecular Biotechnologies (IBIOM)BariItaly
| | - Karin Nowikovsky
- Department of Internal Medicine I and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and BiophysicsUniversity of Veterinary Medicine ViennaViennaAustria
| |
Collapse
|
7
|
Wiedner HJ, Torres EV, Blue RE, Tsai Y, Parker J, Giudice J. SET domain containing 2 (SETD2) influences metabolism and alternative splicing during myogenesis. FEBS J 2022; 289:6799-6816. [PMID: 35724320 PMCID: PMC9796740 DOI: 10.1111/febs.16553] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/13/2022] [Accepted: 06/10/2022] [Indexed: 01/14/2023]
Abstract
Epigenetic regulatory mechanisms are increasingly recognized as crucial determinants of cellular specification and differentiation. During muscle cell differentiation (myogenesis), extensive remodelling of histone acetylation and methylation occurs. Several of these histone modifications aid in the expression of muscle-specific genes and the silencing of genes that block lineage commitment. Therefore, the identification of new epigenetic regulatory mechanisms is of high interest. Still, the functional relevance of numerous histone modifications during myogenesis remain completely uncertain. In this study, we focus on the function of H3K36me3 and its epigenetic writer, SET domain containing 2 (SETD2), in the context of muscle cell differentiation. We first observed that SETD2 expression increases during myogenesis. Targeted depletion of SETD2 in undifferentiated (myoblasts) and differentiated (myotubes) muscle cells reduced H3K36me3 levels and induced profound changes in gene expression and slight alterations in alternative splicing, as determined by deep RNA-sequencing analysis. Enzymes that function in metabolic pathways were upregulated in response to SETD2 depletion. Furthermore, we demonstrated that upregulation of several glycolytic enzymes was associated with an increase in intracellular pyruvate levels in SETD2-depleted cells, indicating a novel role for SETD2 in metabolic programming during myogenesis. Together, our results provide new insight into the signalling pathways controlled by chromatin-modifying enzymes and their associated histone modifications during muscle cell differentiation.
Collapse
Affiliation(s)
- Hannah J. Wiedner
- Department of Cell Biology and PhysiologyThe University of North Carolina at Chapel HillUSA,Curriculum in Genetics and Molecular Biology (GMB)The University of North Carolina at Chapel HillUSA
| | - Eduardo V. Torres
- Department of Cell Biology and PhysiologyThe University of North Carolina at Chapel HillUSA
| | - R. Eric Blue
- Department of Cell Biology and PhysiologyThe University of North Carolina at Chapel HillUSA
| | - Yi‐Hsuan Tsai
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillUSA
| | - Joel Parker
- Curriculum in Genetics and Molecular Biology (GMB)The University of North Carolina at Chapel HillUSA,Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillUSA
| | - Jimena Giudice
- Department of Cell Biology and PhysiologyThe University of North Carolina at Chapel HillUSA,Curriculum in Genetics and Molecular Biology (GMB)The University of North Carolina at Chapel HillUSA,McAllister Heart Institute, School of MedicineThe University of North Carolina at Chapel HillUSA
| |
Collapse
|
8
|
Bajusz D, Keserű GM. Maximizing the integration of virtual and experimental screening in hit discovery. Expert Opin Drug Discov 2022; 17:629-640. [PMID: 35671403 DOI: 10.1080/17460441.2022.2085685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Experimental and virtual screening contributes to the discovery of more than 50% of clinical candidates. Considering the similar concept and goals, early-phase drug discovery would benefit from the effective integration of these approaches. AREAS COVERED After reviewing the recent trends in both experimental and virtual screening, the authors discuss different integration strategies from parallel, focused, sequential, and iterative screening. Strategic considerations are demonstrated in a number of real-life case studies. EXPERT OPINION Experimental and virtual screening are complementary approaches that should be integrated in lead discovery settings. Virtual screening can access extremely large synthetically feasible chemical space that can be effectively searched on GPU clusters or cloud architectures. Experimental screening provides reliable datasets by quantitative HTS applications, and DNA-encoded libraries (DEL) have enlarged the chemical space covered by these technologies. These developments, together with the use of artificial intelligence methods, represent new options for their efficient integration. The case studies discussed here demonstrate the benefits of complementary strategies, such as focused and iterative screening.
Collapse
Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| |
Collapse
|
9
|
Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection. Genome Biol 2022; 23:119. [PMID: 35606795 PMCID: PMC9128273 DOI: 10.1186/s13059-022-02686-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 05/09/2022] [Indexed: 11/21/2022] Open
Abstract
Background The analysis of chromatin binding patterns of proteins in different biological states is a main application of chromatin immunoprecipitation followed by sequencing (ChIP-seq). A large number of algorithms and computational tools for quantitative comparison of ChIP-seq datasets exist, but their performance is strongly dependent on the parameters of the biological system under investigation. Thus, a systematic assessment of available computational tools for differential ChIP-seq analysis is required to guide the optimal selection of analysis tools based on the present biological scenario. Results We created standardized reference datasets by in silico simulation and sub-sampling of genuine ChIP-seq data to represent different biological scenarios and binding profiles. Using these data, we evaluated the performance of 33 computational tools and approaches for differential ChIP-seq analysis. Tool performance was strongly dependent on peak size and shape as well as on the scenario of biological regulation. Conclusions Our analysis provides unbiased guidelines for the optimized choice of software tools in differential ChIP-seq analysis. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02686-y.
Collapse
|
10
|
Lam UTF, Tan BKY, Poh JJX, Chen ES. Structural and functional specificity of H3K36 methylation. Epigenetics Chromatin 2022; 15:17. [PMID: 35581654 PMCID: PMC9116022 DOI: 10.1186/s13072-022-00446-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/04/2022] [Indexed: 12/20/2022] Open
Abstract
The methylation of histone H3 at lysine 36 (H3K36me) is essential for maintaining genomic stability. Indeed, this methylation mark is essential for proper transcription, recombination, and DNA damage response. Loss- and gain-of-function mutations in H3K36 methyltransferases are closely linked to human developmental disorders and various cancers. Structural analyses suggest that nucleosomal components such as the linker DNA and a hydrophobic patch constituted by histone H2A and H3 are likely determinants of H3K36 methylation in addition to the histone H3 tail, which encompasses H3K36 and the catalytic SET domain. Interaction of H3K36 methyltransferases with the nucleosome collaborates with regulation of their auto-inhibitory changes fine-tunes the precision of H3K36me in mediating dimethylation by NSD2 and NSD3 as well as trimethylation by Set2/SETD2. The identification of specific structural features and various cis-acting factors that bind to different forms of H3K36me, particularly the di-(H3K36me2) and tri-(H3K36me3) methylated forms of H3K36, have highlighted the intricacy of H3K36me functional significance. Here, we consolidate these findings and offer structural insight to the regulation of H3K36me2 to H3K36me3 conversion. We also discuss the mechanisms that underlie the cooperation between H3K36me and other chromatin modifications (in particular, H3K27me3, H3 acetylation, DNA methylation and N6-methyladenosine in RNAs) in the physiological regulation of the epigenomic functions of chromatin.
Collapse
Affiliation(s)
- Ulysses Tsz Fung Lam
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bryan Kok Yan Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - John Jia Xin Poh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,National University Health System (NUHS), Singapore, Singapore. .,NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Integrative Sciences & Engineering Programme, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
11
|
IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia. NATURE CANCER 2022; 3:595-613. [PMID: 35534777 PMCID: PMC9404532 DOI: 10.1038/s43018-022-00366-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022]
Abstract
Acute myeloid leukemia (AML) remains difficult to treat and requires new therapeutic approaches. Potent inhibitors of the chromatin-associated protein MENIN have recently entered human clinical trials, opening new therapeutic opportunities for some genetic subtypes of this disease. Using genome-scale functional genetic screens, we identified IKAROS (encoded by IKZF1) as an essential transcription factor in KMT2A (MLL1)-rearranged (MLL-r) AML that maintains leukemogenic gene expression while also repressing pathways for tumor suppression, immune regulation and cellular differentiation. Furthermore, IKAROS displays an unexpected functional cooperativity and extensive chromatin co-occupancy with mixed lineage leukemia (MLL)1-MENIN and the regulator MEIS1 and an extensive hematopoietic transcriptional complex involving homeobox (HOX)A10, MEIS1 and IKAROS. This dependency could be therapeutically exploited by inducing IKAROS protein degradation with immunomodulatory imide drugs (IMiDs). Finally, we demonstrate that combined IKAROS degradation and MENIN inhibition effectively disrupts leukemogenic transcriptional networks, resulting in synergistic killing of leukemia cells and providing a paradigm for improved drug targeting of transcription and an opportunity for rapid clinical translation.
Collapse
|
12
|
Bajusz D, Bognár Z, Ebner J, Grebien F, Keserű GM. Discovery of a Non-Nucleoside SETD2 Methyltransferase Inhibitor against Acute Myeloid Leukemia. Int J Mol Sci 2021; 22:ijms221810055. [PMID: 34576219 PMCID: PMC8471172 DOI: 10.3390/ijms221810055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
Histone methyltransferases (HMTs) have attracted considerable attention as potential targets for pharmaceutical intervention in various malignant diseases. These enzymes are known for introducing methyl marks at specific locations of histone proteins, creating a complex system that regulates epigenetic control of gene expression and cell differentiation. Here, we describe the identification of first-generation cell-permeable non-nucleoside type inhibitors of SETD2, the only mammalian HMT that is able to tri-methylate the K36 residue of histone H3. By generating the epigenetic mark H3K36me3, SETD2 is involved in the progression of acute myeloid leukemia. We developed a structure-based virtual screening protocol that was first validated in retrospective studies. Next, prospective screening was performed on a large library of commercially available compounds. Experimental validation of 22 virtual hits led to the discovery of three compounds that showed dose-dependent inhibition of the enzymatic activity of SETD2. Compound C13 effectively blocked the proliferation of two acute myeloid leukemia (AML) cell lines with MLL rearrangements and led to decreased H3K36me3 levels, prioritizing this chemotype as a viable chemical starting point for drug discovery projects.
Collapse
Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (D.B.); (Z.B.)
| | - Zsolt Bognár
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (D.B.); (Z.B.)
| | - Jessica Ebner
- Institute for Medical Biochemistry, University of Veterinary Medicine, 1220 Vienna, Austria; (J.E.); (F.G.)
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, 1220 Vienna, Austria; (J.E.); (F.G.)
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (D.B.); (Z.B.)
- Correspondence:
| |
Collapse
|
13
|
Identification and characterization of relapse-initiating cells in MLL-rearranged infant ALL by single-cell transcriptomics. Leukemia 2021; 36:58-67. [PMID: 34304246 PMCID: PMC8727302 DOI: 10.1038/s41375-021-01341-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 12/17/2022]
Abstract
Infants with MLL-rearranged infant acute lymphoblastic leukemia (MLL-r iALL) undergo intense therapy to counter a highly aggressive malignancy with survival rates of only 30–40%. The majority of patients initially show therapy response, but in two-thirds of cases the leukemia returns, typically during treatment. The glucocorticoid drug prednisone is established as a major player in the treatment of leukemia and the in vivo response to prednisone monotreatment is currently the best indicator of risk for MLL-r iALL. We used two different single-cell RNA sequencing technologies to analyze the expression of a prednisone-dependent signature, derived from an independent study, in diagnostic bone marrow and peripheral blood biopsies. This allowed us to classify individual leukemic cells as either resistant or sensitive to treatment and show that quantification of these two groups can be used to better predict the occurrence of future relapse in individual patients. This work also sheds light on the nature of the therapy-resistant subpopulation of relapse-initiating cells. Leukemic cells associated with high relapse risk are characterized by basal activation of glucocorticoid response, smaller size, and a quiescent gene expression program with cell stemness properties. These results improve current risk stratification and elucidate leukemic therapy-resistant subpopulations at diagnosis.
Collapse
|
14
|
Bajusz D, Wade WS, Satała G, Bojarski AJ, Ilaš J, Ebner J, Grebien F, Papp H, Jakab F, Douangamath A, Fearon D, von Delft F, Schuller M, Ahel I, Wakefield A, Vajda S, Gerencsér J, Pallai P, Keserű GM. Exploring protein hotspots by optimized fragment pharmacophores. Nat Commun 2021; 12:3201. [PMID: 34045440 PMCID: PMC8159961 DOI: 10.1038/s41467-021-23443-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/29/2021] [Indexed: 02/04/2023] Open
Abstract
Fragment-based drug design has introduced a bottom-up process for drug development, with improved sampling of chemical space and increased effectiveness in early drug discovery. Here, we combine the use of pharmacophores, the most general concept of representing drug-target interactions with the theory of protein hotspots, to develop a design protocol for fragment libraries. The SpotXplorer approach compiles small fragment libraries that maximize the coverage of experimentally confirmed binding pharmacophores at the most preferred hotspots. The efficiency of this approach is demonstrated with a pilot library of 96 fragment-sized compounds (SpotXplorer0) that is validated on popular target classes and emerging drug targets. Biochemical screening against a set of GPCRs and proteases retrieves compounds containing an average of 70% of known pharmacophores for these targets. More importantly, SpotXplorer0 screening identifies confirmed hits against recently established challenging targets such as the histone methyltransferase SETD2, the main protease (3CLPro) and the NSP3 macrodomain of SARS-CoV-2.
Collapse
Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | | | - Grzegorz Satała
- Maj Institute of Pharmacology Polish Academy of Sciences, Kraków, Poland
| | - Andrzej J Bojarski
- Maj Institute of Pharmacology Polish Academy of Sciences, Kraków, Poland
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Jessica Ebner
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Henrietta Papp
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Centre for Medicines Discovery, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Amanda Wakefield
- Department of Chemistry, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Sándor Vajda
- Department of Chemistry, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | | | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary.
| |
Collapse
|
15
|
Rao H, Li X, Liu M, Liu J, Feng W, Tang H, Xu J, Gao WQ, Li L. Multilevel Regulation of β-Catenin Activity by SETD2 Suppresses the Transition from Polycystic Kidney Disease to Clear Cell Renal Cell Carcinoma. Cancer Res 2021; 81:3554-3567. [PMID: 33910928 DOI: 10.1158/0008-5472.can-20-3960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/17/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022]
Abstract
Patients with polycystic kidney disease (PKD) are at a high risk of developing renal cell carcinoma (RCC). However, little is known about genetic alterations or changes in signaling pathways during the transition from PKD to RCC. SET domain-containing 2 (SETD2) is a histone methyltransferase, which catalyzes tri-methylation of H3K36 (H3K36me3) and has been identified as a tumor suppressor in clear cell renal cell carcinoma (ccRCC), but the underlying mechanism remains largely unexplored. Here we report that knockout of SETD2 in a c-MYC-driven PKD mouse model drove the transition to ccRCC. SETD2 inhibited β-catenin activity at transcriptional and posttranscriptional levels by competing with β-catenin for binding promoters of target genes and maintaining transcript levels of members of the β-catenin destruction complex. Thus, SETD2 deficiency enhanced the epithelial-to-mesenchymal transition and tumorigenesis through the hyperactivation of Wnt/β-catenin signaling. Our findings reveal previously unrecognized roles of SETD2-mediated competitive DNA binding and H3K36me3 modification in regulating Wnt/β-catenin signaling during the transition from PKD to ccRCC. The novel autochthonous mouse models of PKD and ccRCC will be useful for preclinical research into disease progression. SIGNIFICANCE: These findings characterize multiple mechanisms by which SETD2 inhibits β-catenin activity during the transition of polycystic kidney disease to renal cell carcinoma, providing a potential therapeutic strategy for high-risk patients. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/13/3554/F1.large.jpg.
Collapse
Affiliation(s)
- Hanyu Rao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxue Li
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Min Liu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Liu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxin Feng
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Huayuan Tang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Jin Xu
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Qiang Gao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China. ; .,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Li Li
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China. ; .,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
16
|
Chen J, Feng J, Fang Z, Ye J, Chen Q, Chen Q, Chen K, Xiong X, Li G, Song H, Xu B. Anlotinib suppresses MLL-rearranged acute myeloid leukemia cell growth by inhibiting SETD1A/AKT-mediated DNA damage response. Am J Transl Res 2021; 13:1494-1504. [PMID: 33841673 PMCID: PMC8014360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Leukemias driven by chromosomal translocation of the mixed-lineage leukemia (MLL) gene are highly prevalent in hematological malignancy. The poor survival rate and lack of effective targeted therapy for patients with MLL-rearranged (MLL-r) leukemias emphasize an urgent need for improved knowledge and novel therapeutic approaches for these malignancies. The present study aimed to investigate the potential effectiveness and mechanism of Anlotinib, a novel receptor tyrosine kinase inhibitor, in MLL-r acute myeloid leukemia (AML). The findings revealed that Anlotinib significantly inhibited the growth of MLL-r AML cells in both in vivo and a murine xenograft model. RNA sequencing identified that multiple genes involved in DNA damage response were responsible for Anlotinib activity. To further elucidate the correlation between the DNA damage response induced by Anlotinib and MLL fusion, Gene Expression Profiling Interactive Analysis (GEPIA) was conducted. It revealed that Anlotinib impaired DNA damage response via inhibiting SETD1A and AKT. In conclusion, Anlotinib exerts anti-leukemia function by inhibiting SETD1A/AKT-mediated DNA damage response and highlights a novel mechanism underlying Anlotinib in the treatment of MLL-r AML.
Collapse
Affiliation(s)
- Jinzhu Chen
- Department of Hematology, The First Hospital of Longhai 363199Fujian, P. R. China
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Juan Feng
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Zhihong Fang
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Jing Ye
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Qinwei Chen
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Qiuling Chen
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Kai Chen
- The First People’s Hospital of Foshan (The Affiliated Foshan Hospital of Sun Yat-sen University)Foshan 528000, Guangdong, P. R. China
| | - Xiaoming Xiong
- Department of Hematology, The First Hospital of Longhai 363199Fujian, P. R. China
| | - Guowei Li
- Department of Hematology, Huizhou Municipal Central HospitalHuizhou 516001, P. R. China
| | - Haihan Song
- Department of Immunology, DICAT Biomedical Computation CentreVancouver, BC, Canada
| | - Bing Xu
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| |
Collapse
|
17
|
CDK6 is an essential direct target of NUP98 fusion proteins in acute myeloid leukemia. Blood 2021; 136:387-400. [PMID: 32344427 DOI: 10.1182/blood.2019003267] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/08/2020] [Indexed: 01/25/2023] Open
Abstract
Fusion proteins involving Nucleoporin 98 (NUP98) are recurrently found in acute myeloid leukemia (AML) and are associated with poor prognosis. Lack of mechanistic insight into NUP98-fusion-dependent oncogenic transformation has so far precluded the development of rational targeted therapies. We reasoned that different NUP98-fusion proteins deregulate a common set of transcriptional targets that might be exploitable for therapy. To decipher transcriptional programs controlled by diverse NUP98-fusion proteins, we developed mouse models for regulatable expression of NUP98/NSD1, NUP98/JARID1A, and NUP98/DDX10. By integrating chromatin occupancy profiles of NUP98-fusion proteins with transcriptome profiling upon acute fusion protein inactivation in vivo, we defined the core set of direct transcriptional targets of NUP98-fusion proteins. Among those, CDK6 was highly expressed in murine and human AML samples. Loss of CDK6 severely attenuated NUP98-fusion-driven leukemogenesis, and NUP98-fusion AML was sensitive to pharmacologic CDK6 inhibition in vitro and in vivo. These findings identify CDK6 as a conserved, critical direct target of NUP98-fusion proteins, proposing CDK4/CDK6 inhibitors as a new rational treatment option for AML patients with NUP98-fusions.
Collapse
|
18
|
SETD2 deficiency accelerates MDS-associated leukemogenesis via S100a9 in NHD13 mice and predicts poor prognosis in MDS. Blood 2021; 135:2271-2285. [PMID: 32202636 DOI: 10.1182/blood.2019001963] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/08/2020] [Indexed: 02/06/2023] Open
Abstract
SETD2, the histone H3 lysine 36 methyltransferase, previously identified by us, plays an important role in the pathogenesis of hematologic malignancies, but its role in myelodysplastic syndromes (MDSs) has been unclear. In this study, low expression of SETD2 correlated with shortened survival in patients with MDS, and the SETD2 levels in CD34+ bone marrow cells of those patients were increased by decitabine. We knocked out Setd2 in NUP98-HOXD13 (NHD13) transgenic mice, which phenocopies human MDS, and found that loss of Setd2 accelerated the transformation of MDS into acute myeloid leukemia (AML). Loss of Setd2 enhanced the ability of NHD13+ hematopoietic stem and progenitor cells (HSPCs) to self-renew, with increased symmetric self-renewal division and decreased differentiation and cell death. The growth of MDS-associated leukemia cells was inhibited though increasing the H3K36me3 level by using epigenetic modifying drugs. Furthermore, Setd2 deficiency upregulated hematopoietic stem cell signaling and downregulated myeloid differentiation pathways in the NHD13+ HSPCs. Our RNA-seq and chromatin immunoprecipitation-seq analysis indicated that S100a9, the S100 calcium-binding protein, is a target gene of Setd2 and that the addition of recombinant S100a9 weakens the effect of Setd2 deficiency in the NHD13+ HSPCs. In contrast, downregulation of S100a9 leads to decreases of its downstream targets, including Ikba and Jnk, which influence the self-renewal and differentiation of HSPCs. Therefore, our results demonstrated that SETD2 deficiency predicts poor prognosis in MDS and promotes the transformation of MDS into AML, which provides a potential therapeutic target for MDS-associated acute leukemia.
Collapse
|
19
|
Terlecki-Zaniewicz S, Humer T, Eder T, Schmoellerl J, Heyes E, Manhart G, Kuchynka N, Parapatics K, Liberante FG, Müller AC, Tomazou EM, Grebien F. Biomolecular condensation of NUP98 fusion proteins drives leukemogenic gene expression. Nat Struct Mol Biol 2021; 28:190-201. [PMID: 33479542 DOI: 10.1038/s41594-020-00550-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/14/2020] [Indexed: 01/15/2023]
Abstract
NUP98 fusion proteins cause leukemia via unknown molecular mechanisms. All NUP98 fusion proteins share an intrinsically disordered region (IDR) in the NUP98 N terminus, featuring repeats of phenylalanine-glycine (FG), and C-terminal fusion partners often function in gene control. We investigated whether mechanisms of oncogenic transformation by NUP98 fusion proteins are hardwired in their protein interactomes. Affinity purification coupled to mass spectrometry (MS) and confocal imaging of five NUP98 fusion proteins expressed in human leukemia cells revealed that shared interactors were enriched for proteins involved in biomolecular condensation and that they colocalized with NUP98 fusion proteins in nuclear puncta. We developed biotinylated isoxazole-mediated condensome MS (biCon-MS) to show that NUP98 fusion proteins alter the global composition of biomolecular condensates. An artificial FG-repeat-containing fusion protein phenocopied the nuclear localization patterns of NUP98 fusion proteins and their capability to drive oncogenic gene expression programs. Thus, we propose that IDR-containing fusion proteins combine biomolecular condensation with transcriptional control to induce cancer.
Collapse
Affiliation(s)
- Stefan Terlecki-Zaniewicz
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria.,Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Theresa Humer
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Eder
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Johannes Schmoellerl
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Elizabeth Heyes
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Gabriele Manhart
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | | | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fabio G Liberante
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Eleni M Tomazou
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria.
| |
Collapse
|
20
|
Bhat KP, Ümit Kaniskan H, Jin J, Gozani O. Epigenetics and beyond: targeting writers of protein lysine methylation to treat disease. Nat Rev Drug Discov 2021; 20:265-286. [PMID: 33469207 DOI: 10.1038/s41573-020-00108-x] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
Protein lysine methylation is a crucial post-translational modification that regulates the functions of both histone and non-histone proteins. Deregulation of the enzymes or 'writers' of protein lysine methylation, lysine methyltransferases (KMTs), is implicated in the cause of many diseases, including cancer, mental health disorders and developmental disorders. Over the past decade, significant advances have been made in developing drugs to target KMTs that are involved in histone methylation and epigenetic regulation. The first of these inhibitors, tazemetostat, was recently approved for the treatment of epithelioid sarcoma and follicular lymphoma, and several more are in clinical and preclinical evaluation. Beyond chromatin, the many KMTs that regulate protein synthesis and other fundamental biological processes are emerging as promising new targets for drug development to treat diverse diseases.
Collapse
Affiliation(s)
- Kamakoti P Bhat
- Department of Biology, Stanford University, Stanford, CA, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
21
|
Zhou Y, Zheng X, Xu B, Deng H, Chen L, Jiang J. Histone methyltransferase SETD2 inhibits tumor growth via suppressing CXCL1-mediated activation of cell cycle in lung adenocarcinoma. Aging (Albany NY) 2020; 12:25189-25206. [PMID: 33223508 PMCID: PMC7803529 DOI: 10.18632/aging.104120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022]
Abstract
The histone H3 lysine 36 methyltransferase SET-domain-containing 2 (SETD2) has been reported to be frequently mutated or deleted in many types of human cancer. However, the role of SETD2 in lung adenocarcinoma (LUAD) has not been well documented. In the present study, we found that SETD2 was significantly down-regulated both in LUAD tissues and cell lines. Functionally, the increased expression of SETD2 significantly attenuated the proliferation of cancer cells by affecting the cell cycle, whereas SETD2 deficiency dramatically improved these proliferative abilities of cancer cells. Through conjoint analysis of RNA-seq and ChIP data, we identified a functional target gene of SETD2, CXCL1, and its expression was negatively correlated with that of SETD2. Moreover, SETD2 deletion stimulated cell cycle-related proteins to promote LUAD. Further mechanistic studies demonstrated that histone H3 lysine 36 trimethylation (H3K36me3) catalyzed by SETD2 interacted with the promoter of CXCL1 to regulate its transcription and downstream signaling pathways, contributing to tumorigenesis in vitro and in vivo. Our findings suggested that SETD2 inhibited tumor growth via suppressing CXCL1-mediated activation of cell cycle, indicating that the regulation of H3K36me3 level by targeting SETD2 and/or the administration of downstream CXCL1 might represent a potential therapeutic way for new treatment in LUAD.
Collapse
Affiliation(s)
- You Zhou
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Xiao Zheng
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Bin Xu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Haifeng Deng
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Lujun Chen
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Jingting Jiang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| |
Collapse
|
22
|
Yang Z, Jiang H. A chromatin perspective on metabolic and genotoxic impacts on hematopoietic stem and progenitor cells. Cell Mol Life Sci 2020; 77:4031-4047. [PMID: 32318759 PMCID: PMC7541408 DOI: 10.1007/s00018-020-03522-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023]
Abstract
Fate determination in self-renewal and differentiation of hematopoietic stem and progenitor cells (HSCs and HPCs) is ultimately controlled by gene expression, which is profoundly influenced by the global and local chromatin state. Cellular metabolism directly influences the chromatin state through the dynamic regulation of the enzymatic activities that modify DNA and histones, but also generates genotoxic metabolites that can damage DNA and thus pose threat to the genome integrity. On the other hand, mechanisms modulating the chromatin state impact metabolism by regulating the expression and activities of key metabolic enzymes. Moreover, through regulating either DNA damage response directly or expression of genes involved in this process, chromatin modulators play active and crucial roles in guarding the genome integrity, breaching of which results in defective HSPC function. Therefore, HSPC function is regulated by the dynamic and two-way interactions between metabolism and chromatin. Here, we review recent advances that provide a chromatin perspective on the major impacts the metabolic and genotoxic factors can have on HSPC function and fate determination.
Collapse
Affiliation(s)
- Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| |
Collapse
|
23
|
Evolving insights on histone methylome regulation in human acute myeloid leukemia pathogenesis and targeted therapy. Exp Hematol 2020; 92:19-31. [PMID: 32950598 DOI: 10.1016/j.exphem.2020.09.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/09/2020] [Accepted: 09/14/2020] [Indexed: 12/25/2022]
Abstract
Acute myeloid leukemia (AML) is an aggressive, disseminated hematological malignancy associated with clonal selection of aberrant self-renewing hematopoietic stem cells and progenitors and poorly differentiated myeloid blasts. The most prevalent form of leukemia in adults, AML is predominantly an age-related disorder and accounts for more than 10,000 deaths per year in the United States alone. In comparison to solid tumors, AML has an overall low mutational burden, albeit more than 70% of AML patients harbor somatic mutations in genes encoding epigenetic modifiers and chromatin regulators. In the past decade, discoveries highlighting the role of DNA and histone modifications in determining cellular plasticity and lineage commitment have attested to the importance of epigenetic contributions to tumor cell de-differentiation and heterogeneity, tumor initiation, maintenance, and relapse. Orchestration in histone methylation levels regulates pluripotency and multicellular development. The increasing number of reversible methylation regulators being identified, including histone methylation writer, reader, and eraser enzymes, and their implications in AML pathogenesis have widened the scope of epigenetic reprogramming, with multiple drugs currently in various stages of preclinical and clinical trials. AML methylome also determines response to conventional chemotherapy, as well as AML cell interaction within a tumor-immune microenvironment ecosystem. Here we summarize the latest developments focusing on molecular derangements in histone methyltransferases (HMTs) and histone demethylases (HDMs) in AML pathogenesis. AML-associated HMTs and HDMs, through intricate crosstalk mechanisms, maintain an altered histone methylation code conducive to disease progression. We further discuss their importance in governing response to therapy, which can be used as a biomarker for treatment efficacy. Finally we deliberate on the therapeutic potential of targeting aberrant histone methylome in AML, examine available small molecule inhibitors in combination with immunomodulating therapeutic approaches and caveats, and discuss how future studies can enable posited epigenome-based targeted therapy to become a mainstay for AML treatment.
Collapse
|
24
|
Wong NHM, So CWE. Novel therapeutic strategies for MLL-rearranged leukemias. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194584. [PMID: 32534041 DOI: 10.1016/j.bbagrm.2020.194584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/27/2020] [Accepted: 05/22/2020] [Indexed: 11/18/2022]
Abstract
MLL rearrangement is one of the key drivers and generally regarded as an independent poor prognostic marker in acute leukemias. The standard of care for MLL-rearranged (MLL-r) leukemias has remained largely unchanged for the past 50 years despite unsatisfying clinical outcomes, so there is an urgent need for novel therapeutic strategies. An increasing body of evidence demonstrates that a vast number of epigenetic regulators are directly or indirectly involved in MLL-r leukemia, and they are responsible for supporting the aberrant gene expression program mediated by MLL-fusions. Unlike genetic mutations, epigenetic modifications can be reversed by pharmacologic targeting of the responsible epigenetic regulators. This leads to significant interest in developing epigenetic therapies for MLL-r leukemia. Intriguingly, many of the epigenetic enzymes also involve in DNA damage response (DDR), which can be potential targets for synthetic lethality-induced therapies. In this review, we will summarize some of the recent advances in the development of epigenetic and DDR therapeutics by targeting epigenetic regulators or protein complexes that mediate MLL-r leukemia gene expression program and key players in DDR that safeguard essential genome integrity. The rationale and molecular mechanisms underpinning the therapeutic effects will also be discussed with a focus on how these treatments can disrupt MLL-fusion mediated transcriptional programs and impair DDR, which may help overcome treatment resistance.
Collapse
Affiliation(s)
- Nok-Hei Mickey Wong
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Chi Wai Eric So
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK.
| |
Collapse
|
25
|
Esse R, Grishok A. Caenorhabditis elegans Deficient in DOT-1.1 Exhibit Increases in H3K9me2 at Enhancer and Certain RNAi-Regulated Regions. Cells 2020; 9:cells9081846. [PMID: 32781660 PMCID: PMC7464606 DOI: 10.3390/cells9081846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 01/06/2023] Open
Abstract
The methylation of histone H3 at lysine 79 is a feature of open chromatin. It is deposited by the conserved histone methyltransferase DOT1. Recently, DOT1 localization and H3K79 methylation (H3K79me) have been correlated with enhancers in C. elegans and mammalian cells. Since earlier research implicated H3K79me in preventing heterochromatin formation both in yeast and leukemic cells, we sought to inquire whether a H3K79me deficiency would lead to higher levels of heterochromatic histone modifications, specifically H3K9me2, at developmental enhancers in C. elegans. Therefore, we used H3K9me2 ChIP-seq to compare its abundance in control and dot-1.1 loss-of-function mutant worms, as well as in rde-4; dot-1.1 and rde-1; dot-1.1 double mutants. The rde-1 and rde-4 genes are components of the RNAi pathway in C. elegans, and RNAi is known to initiate H3K9 methylation in many organisms, including C. elegans. We have previously shown that dot-1.1(-) lethality is rescued by rde-1 and rde-4 loss-of-function. Here we found that H3K9me2 was elevated in enhancer, but not promoter, regions bound by the DOT-1.1/ZFP-1 complex in dot-1.1(-) worms. We also found increased H3K9me2 at genes targeted by the ALG-3/4-dependent small RNAs and repeat regions. Our results suggest that ectopic H3K9me2 in dot-1.1(-) could, in some cases, be induced by small RNAs.
Collapse
|
26
|
Giurgiu M, Reinhard J, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Ruepp A. CORUM: the comprehensive resource of mammalian protein complexes-2019. Nucleic Acids Res 2020; 47:D559-D563. [PMID: 30357367 PMCID: PMC6323970 DOI: 10.1093/nar/gky973] [Citation(s) in RCA: 373] [Impact Index Per Article: 93.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/18/2018] [Indexed: 12/17/2022] Open
Abstract
CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (67%), mouse (15%) and rat (10%). Given the vital functions of these macromolecular machines, their identification and functional characterization is foundational to our understanding of normal and disease biology. The new CORUM 3.0 release encompasses 4274 protein complexes offering the largest and most comprehensive publicly available dataset of mammalian protein complexes. The CORUM dataset is built from 4473 different genes, representing 22% of the protein coding genes in humans. Protein complexes are described by a protein complex name, subunit composition, cellular functions as well as the literature references. Information about stoichiometry of subunits depends on availability of experimental data. Recent developments include a graphical tool displaying known interactions between subunits. This allows the prediction of structural interconnections within protein complexes of unknown structure. In addition, we present a set of 58 protein complexes with alternatively spliced subunits. Those were found to affect cellular functions such as regulation of apoptotic activity, protein complex assembly or define cellular localization. CORUM is freely accessible at http://mips.helmholtz-muenchen.de/corum/.
Collapse
Affiliation(s)
- Madalina Giurgiu
- Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Julian Reinhard
- Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Barbara Brauner
- Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Irmtraud Dunger-Kaltenbach
- Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Gisela Fobo
- Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Goar Frishman
- Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Corinna Montrone
- Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Andreas Ruepp
- Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| |
Collapse
|
27
|
de Bessa Garcia SA, Araújo M, Pereira T, Mouta J, Freitas R. HOX genes function in Breast Cancer development. Biochim Biophys Acta Rev Cancer 2020; 1873:188358. [PMID: 32147544 DOI: 10.1016/j.bbcan.2020.188358] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 02/07/2023]
Abstract
Breast cancer develops in the mammary glands during mammalian adulthood and is considered the second most common type of human carcinoma and the most incident and mortal in the female population. In contrast to other human structures, the female mammary glands continue to develop after birth, undergoing various modifications during pregnancy, lactation and involution under the regulation of hormones and transcription factors, including those encoded by the HOX clusters (A, B, C, and D). Interestingly, HOX gene deregulation is often associated to breast cancer development. Within the HOXB cluster, 8 out of the 10 genes present altered expression levels in breast cancer with an impact in its aggressiveness and resistance to hormone therapy, which highlights the importance of HOXB genes as potential therapeutic targets used to overcome the limitations of tamoxifen-resistant cancer treatments. Here, we review the current state of knowledge on the role of HOX genes in breast cancer, specially focus on HOXB, discussing the causes and consequences of HOXB gene deregulation and their relevance as prognostic factors and therapeutic targets.
Collapse
Affiliation(s)
- Simone Aparecida de Bessa Garcia
- IBMC- Institute for Molecular and Cell Biology, I3S- Institute for Innovation and Health Research, Universidade do Porto, Portugal
| | - Mafalda Araújo
- IBMC- Institute for Molecular and Cell Biology, I3S- Institute for Innovation and Health Research, Universidade do Porto, Portugal
| | - Tiago Pereira
- IBMC- Institute for Molecular and Cell Biology, I3S- Institute for Innovation and Health Research, Universidade do Porto, Portugal
| | - João Mouta
- IBMC- Institute for Molecular and Cell Biology, I3S- Institute for Innovation and Health Research, Universidade do Porto, Portugal
| | - Renata Freitas
- IBMC- Institute for Molecular and Cell Biology, I3S- Institute for Innovation and Health Research, Universidade do Porto, Portugal.; ICBAS- Institute of Biomedical Sciences Abel Salazar, Universidade do Porto, Portugal..
| |
Collapse
|
28
|
Slany RK. MLL fusion proteins and transcriptional control. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194503. [PMID: 32061883 DOI: 10.1016/j.bbagrm.2020.194503] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/17/2019] [Accepted: 02/11/2020] [Indexed: 12/20/2022]
Abstract
The highly leukemogenic MLL fusion proteins have a unique mechanism of action. This review summarizes the current knowledge of how MLL fusions interact with the transcriptional machinery and it proposes a hypothesis how these proteins modify transcriptional control to act as transcriptional amplifiers causing runaway production of certain RNAs that transform hematopoietic cells.
Collapse
Affiliation(s)
- Robert K Slany
- Department of Genetics, Friedrich-Alexander-University Erlangen-Nürnberg, Germany.
| |
Collapse
|
29
|
Sun Z, Zhang Y, Jia J, Fang Y, Tang Y, Wu H, Fang D. H3K36me3, message from chromatin to DNA damage repair. Cell Biosci 2020; 10:9. [PMID: 32021684 PMCID: PMC6995143 DOI: 10.1186/s13578-020-0374-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022] Open
Abstract
Histone marks control many cellular processes including DNA damage repair. This review will focus primarily on the active histone mark H3K36me3 in the regulation of DNA damage repair and the maintenance of genomic stability after DNA damage. There are diverse clues showing H3K36me3 participates in DNA damage response by directly recruiting DNA repair machinery to set the chromatin at a “ready” status, leading to a quick response upon damage. Reduced H3K36me3 is associated with low DNA repair efficiency. This review will also place a main emphasis on the H3K36me3-mediated DNA damage repair in the tumorigenesis of the newly found oncohistone mutant tumors. Gaining an understanding of different aspects of H3K36me3 in DNA damage repair, especially in cancers, would share the knowledge of chromatin and DNA repair to serve to the drug discovery and patient care.
Collapse
Affiliation(s)
- Zhongxing Sun
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Yanjun Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Junqi Jia
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Yuan Fang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Yin Tang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Hongfei Wu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Dong Fang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| |
Collapse
|
30
|
MacPherson L, Anokye J, Yeung MM, Lam EYN, Chan YC, Weng CF, Yeh P, Knezevic K, Butler MS, Hoegl A, Chan KL, Burr ML, Gearing LJ, Willson T, Liu J, Choi J, Yang Y, Bilardi RA, Falk H, Nguyen N, Stupple PA, Peat TS, Zhang M, de Silva M, Carrasco-Pozo C, Avery VM, Khoo PS, Dolezal O, Dennis ML, Nuttall S, Surjadi R, Newman J, Ren B, Leaver DJ, Sun Y, Baell JB, Dovey O, Vassiliou GS, Grebien F, Dawson SJ, Street IP, Monahan BJ, Burns CJ, Choudhary C, Blewitt ME, Voss AK, Thomas T, Dawson MA. HBO1 is required for the maintenance of leukaemia stem cells. Nature 2020; 577:266-270. [PMID: 31827282 DOI: 10.1038/s41586-019-1835-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/12/2019] [Indexed: 02/07/2023]
Abstract
Acute myeloid leukaemia (AML) is a heterogeneous disease characterized by transcriptional dysregulation that results in a block in differentiation and increased malignant self-renewal. Various epigenetic therapies aimed at reversing these hallmarks of AML have progressed into clinical trials, but most show only modest efficacy owing to an inability to effectively eradicate leukaemia stem cells (LSCs)1. Here, to specifically identify novel dependencies in LSCs, we screened a bespoke library of small hairpin RNAs that target chromatin regulators in a unique ex vivo mouse model of LSCs. We identify the MYST acetyltransferase HBO1 (also known as KAT7 or MYST2) and several known members of the HBO1 protein complex as critical regulators of LSC maintenance. Using CRISPR domain screening and quantitative mass spectrometry, we identified the histone acetyltransferase domain of HBO1 as being essential in the acetylation of histone H3 at K14. H3 acetylated at K14 (H3K14ac) facilitates the processivity of RNA polymerase II to maintain the high expression of key genes (including Hoxa9 and Hoxa10) that help to sustain the functional properties of LSCs. To leverage this dependency therapeutically, we developed a highly potent small-molecule inhibitor of HBO1 and demonstrate its mode of activity as a competitive analogue of acetyl-CoA. Inhibition of HBO1 phenocopied our genetic data and showed efficacy in a broad range of human cell lines and primary AML cells from patients. These biological, structural and chemical insights into a therapeutic target in AML will enable the clinical translation of these findings.
Collapse
Affiliation(s)
- Laura MacPherson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Juliana Anokye
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Miriam M Yeung
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chen-Fang Weng
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paul Yeh
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kathy Knezevic
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Miriam S Butler
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Annabelle Hoegl
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kah-Lok Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Marian L Burr
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Linden J Gearing
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tracy Willson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Joy Liu
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Jarny Choi
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yuqing Yang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca A Bilardi
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Hendrik Falk
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Nghi Nguyen
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Paul A Stupple
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Thomas S Peat
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Ming Zhang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Melanie de Silva
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Catalina Carrasco-Pozo
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Vicky M Avery
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Poh Sim Khoo
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Children's Cancer Institute, Kensington, New South Wales, Australia
| | - Olan Dolezal
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Matthew L Dennis
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Stewart Nuttall
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Regina Surjadi
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Janet Newman
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Bin Ren
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - David J Leaver
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Yuxin Sun
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jonathan B Baell
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Oliver Dovey
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian P Street
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Brendon J Monahan
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Christopher J Burns
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
| |
Collapse
|
31
|
Byun WS, Kim WK, Han HJ, Chung HJ, Jang K, Kim HS, Kim S, Kim D, Bae ES, Park S, Lee J, Park HG, Lee SK. Targeting Histone Methyltransferase DOT1L by a Novel Psammaplin A Analog Inhibits Growth and Metastasis of Triple-Negative Breast Cancer. Mol Ther Oncolytics 2019; 15:140-152. [PMID: 31720371 PMCID: PMC6838941 DOI: 10.1016/j.omto.2019.09.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/19/2019] [Indexed: 01/24/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is the most intractable cancer in women with a high risk of metastasis. While hyper-methylation of histone H3 catalyzed by disruptor of telomeric silencing 1-like (DOT1L), a specific methyltransferase for histone H3 at lysine residue 79 (H3K79), is reported as a potential target for TNBCs, early developed nucleoside-type DOT1L inhibitors are not sufficient for effective inhibition of growth and metastasis of TNBC cells. We found that TNBC cells had a high expression level of DOT1L and a low expression level of E-cadherin compared to normal breast epithelial cells and non-TNBC cells. Here, a novel psammaplin A analog (PsA-3091) exhibited a potent inhibitory effect of DOT1L-mediated H3K79 methylation. Consistently, PsA-3091 also significantly inhibited the proliferation, migration, and invasion of TNBC cells along with the augmented expression of E-cadherin and the suppression of N-cadherin, ZEB1, and vimentin expression. In an orthotopic mouse model, PsA-3091 effectively inhibited lung metastasis and tumor growth by the regulation of DOT1L activity and EMT biomarkers. Together, we report here a new template of DOT1L inhibitor and suggest that targeting DOT1L-mediated H3K79 methylation by a novel PsA analog may be a promising strategy for the treatment of metastatic breast cancer patients.
Collapse
Affiliation(s)
- Woong Sub Byun
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Won Kyung Kim
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Hae Ju Han
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hwa-Jin Chung
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyungkuk Jang
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Han Sun Kim
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghwa Kim
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Donghwa Kim
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun Seo Bae
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghyouk Park
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeeyeon Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyeung-geun Park
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| |
Collapse
|
32
|
Abstract
Comprehensive cataloguing of the acute myeloid leukaemia (AML) genome has revealed a high frequency of mutations and deletions in epigenetic factors that are frequently linked to treatment resistance and poor patient outcome. In this review, we discuss how the epigenetic mechanisms that underpin normal haematopoiesis are subverted in AML, and in particular how these processes are altered in childhood and adolescent leukaemias. We also provide a brief summary of the burgeoning field of epigenetic-based therapies, and how AML treatment might be improved through provision of better conceptual frameworks for understanding the pleiotropic molecular effects of epigenetic disruption.
Collapse
Affiliation(s)
- Luke Jones
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland
| | - Peter McCarthy
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Jonathan Bond
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| |
Collapse
|
33
|
Histone lysine methyltransferases in biology and disease. Nat Struct Mol Biol 2019; 26:880-889. [PMID: 31582846 DOI: 10.1038/s41594-019-0298-7] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/24/2022]
Abstract
The precise temporal and spatial coordination of histone lysine methylation dynamics across the epigenome regulates virtually all DNA-templated processes. A large number of histone lysine methyltransferase (KMT) enzymes catalyze the various lysine methylation events decorating the core histone proteins. Mutations, genetic translocations and altered gene expression involving these KMTs are frequently observed in cancer, developmental disorders and other pathologies. Therapeutic compounds targeting specific KMTs are currently being tested in the clinic, although overall drug discovery in the field is relatively underdeveloped. Here we review the biochemical and biological activities of histone KMTs and their connections to human diseases, focusing on cancer. We also discuss the scientific and clinical challenges and opportunities in studying KMTs.
Collapse
|
34
|
Bilokapic S, Halic M. Nucleosome and ubiquitin position Set2 to methylate H3K36. Nat Commun 2019; 10:3795. [PMID: 31439846 PMCID: PMC6706414 DOI: 10.1038/s41467-019-11726-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/01/2019] [Indexed: 12/19/2022] Open
Abstract
Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes cancer progression, however, mechanisms of H3K36me are poorly understood. Set2 enzymes show spurious activity on histones and histone tails, and it is unknown how they obtain specificity to methylate H3K36 on the nucleosome. In this study, we present 3.8 Å cryo-EM structure of Set2 bound to the mimic of H2B ubiquitinated nucleosome. Our structure shows that Set2 makes extensive interactions with the H3 αN, the H3 tail, the H2A C-terminal tail and stabilizes DNA in the unwrapped conformation, which positions Set2 to specifically methylate H3K36. Moreover, we show that ubiquitin contributes to Set2 positioning on the nucleosome and stimulates the methyltransferase activity. Notably, our structure uncovers interfaces that can be targeted by small molecules for development of future cancer therapies.
Collapse
Affiliation(s)
- Silvija Bilokapic
- Department of Structural Biology, St. Jude Children's Research Hospital, 263 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, 263 Danny Thomas Place, Memphis, TN, 38105, USA.
| |
Collapse
|
35
|
Li J, Ahn JH, Wang GG. Understanding histone H3 lysine 36 methylation and its deregulation in disease. Cell Mol Life Sci 2019; 76:2899-2916. [PMID: 31147750 PMCID: PMC11105573 DOI: 10.1007/s00018-019-03144-y] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/13/2022]
Abstract
Methylation of histone H3 lysine 36 (H3K36) plays crucial roles in the partitioning of chromatin to distinctive domains and the regulation of a wide range of biological processes. Trimethylation of H3K36 (H3K36me3) demarcates body regions of the actively transcribed genes, providing signals for modulating transcription fidelity, mRNA splicing and DNA damage repair; and di-methylation of H3K36 (H3K36me2) spreads out within large intragenic regions, regulating distribution of histone H3 lysine 27 trimethylation (H3K27me3) and possibly DNA methylation. These H3K36 methylation-mediated events are biologically crucial and controlled by different classes of proteins responsible for either 'writing', 'reading' or 'erasing' of H3K36 methylation marks. Deregulation of H3K36 methylation and related regulatory factors leads to pathogenesis of disease such as developmental syndrome and cancer. Additionally, recurrent mutations of H3K36 and surrounding histone residues are detected in human tumors, further highlighting the importance of H3K36 in biology and medicine. This review will elaborate on current advances in understanding H3K36 methylation and related molecular players during various chromatin-templated cellular processes, their crosstalks with other chromatin factors, as well as their deregulations in the diseased contexts.
Collapse
Affiliation(s)
- Jie Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| |
Collapse
|
36
|
Zhang HH, Wang HS, Qian XW, Fan CQ, Li J, Miao H, Zhu XH, Yu Y, Meng JH, Cao P, Le J, Jiang JY, Jiang WJ, Wang P, Zhai XW. Genetic variants and clinical significance of pediatric acute lymphoblastic leukemia. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:296. [PMID: 31475166 DOI: 10.21037/atm.2019.04.80] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background Acute lymphoblastic leukemia (ALL), the most common childhood malignancy, is characterized by molecular aberrations. Recently, genetic profiling has been fully investigated on ALL; however, the interaction between its genetic alterations and clinical features is still unclear. Therefore, we investigated the effects of genetic variants on ALL phenotypes and clinical outcomes. Methods Targeted exome sequencing technology was used to detect molecular profiling of 140 Chinese pediatric patients with ALL. Correlation of genetic features and clinical outcomes was analyzed. Results T-cell ALL (T-ALL) patients had higher initial white blood cell (WBC) count (34.8×109/L), higher incidence of mediastinal mass (26.9%), more relapse (23.1%), and enriched NOTCH1 (23.1%), FBXW7 (23.1%) and PHF6 (11.5%) mutations. Among the 18 recurrently mutated genes, SETD2 and TP53 mutations occurred more in female patients (P=0.041), NOTCH1 and SETD2 mutants were with higher initial WBC counts (≥50×109/L) (P=0.047 and P=0.041), JAK1 mutants were with higher minimal residual disease (MRD) level both on day 19 and day 46 (day 19 MRD ≥1%, P=0.039; day 46 MRD ≥0.01%, P=0.031) after induction chemotherapy. Multivariate analysis revealed that initial WBC counts (≥50×109/L), MLLr, and TP53 mutations were independent risk factors for 3-year relapse free survival (RFS) in ALL. Furthermore, TP53 mutations, age (<1 year or ≥10 years), and MLLr were independently associated with adverse outcome in B-cell ALL (B-ALL). Conclusions MLLr and TP53 mutations are powerful predictors for adverse outcome in pediatric B-ALL and ALL. Genetic profiling can contribute to the improvement of prognostication and management in ALL patients.
Collapse
Affiliation(s)
- Hong-Hong Zhang
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Hong-Sheng Wang
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiao-Wen Qian
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Cui-Qing Fan
- Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Jun Li
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Hui Miao
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiao-Hua Zhu
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Yi Yu
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Jian-Hua Meng
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Ping Cao
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Jun Le
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Jun-Ye Jiang
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Wen-Jing Jiang
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Ping Wang
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiao-Wen Zhai
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| |
Collapse
|
37
|
Ettel M, Zhao L, Schechter S, Shi J. Expression and prognostic value of NSD1 and SETD2 in pancreatic ductal adenocarcinoma and its precursor lesions. Pathology 2019; 51:392-398. [PMID: 31060750 DOI: 10.1016/j.pathol.2019.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/21/2019] [Accepted: 02/28/2019] [Indexed: 02/07/2023]
Abstract
Epigenetic regulation is emerging as a critical mechanism for pancreatic ductal adenocarcinoma (PDA) development. Histone methylation is an important regulatory mechanism, altering chromatin structure and promoter accessibility and causing aberrant gene expression. NSD1 and SETD2 genes encoding two histone H3K36 methyltransferases, are mutated or altered in 8-10% of PDA cases. However, whether there is altered protein expression of NSD1 or SETD2 in PDA and its precursors, and whether they have diagnostic or prognostic utility is unknown. Tissue microarrays composed of a total of 190 and 192 duplicated cases of PDA (n=74 and 75), metastatic PDA (n=17 and 18), pancreatic intraepithelial neoplasia (PanIN; n=19 and 24), intraductal papillary mucinous neoplasm (IPMN; n=36), mucinous cystic neoplasm (MCN; n=12) and benign pancreatic tissues (n=27 and 32) were analysed for expression of NSD1 and SETD2 by immunohistochemistry. We assessed intensity and percentage of positive cells. NSD1 expression was significantly increased in metastatic PDA compared to benign ducts, primary PDA, and all other lesions combined (p=0.03, 0.02, and 0.03 respectively). Additionally, significantly decreased SETD2 protein expression was found in metastatic PDA and PanIN lesions compared to benign ducts (p=0.04 and 0.007, respectively). High NSD1 expression was associated with clinical stage III/IV disease (p=0.026), tumour grade 2 (p=0.022), use of neoadjuvant therapy (p=0.037), and overall higher clinical stage (p=0.022). There is no significant difference in overall and progression-free survival between NSD1/SETD2 high and low PDA. Expression of NSD1 and SETD2 is specifically altered in metastatic PDA and some of the PDA precursor lesions, supporting their important role in PDA development and metastasis. In addition, increased NSD1 expression is significantly associated with higher clinical stage and neoadjuvant therapy, suggesting that NSD1 may be a useful prognostic marker.
Collapse
Affiliation(s)
- Mark Ettel
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, NY, USA
| | - Lili Zhao
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Shula Schechter
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jiaqi Shi
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
38
|
Skucha A, Ebner J, Grebien F. Roles of SETD2 in Leukemia-Transcription, DNA-Damage, and Beyond. Int J Mol Sci 2019; 20:ijms20051029. [PMID: 30818762 PMCID: PMC6429614 DOI: 10.3390/ijms20051029] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/15/2019] [Accepted: 02/20/2019] [Indexed: 01/07/2023] Open
Abstract
The non-redundant histone methyltransferase SETD2 (SET domain containing 2; KMT3A) is responsible for tri-methylation of lysine 36 on histone H3 (H3K36me3). Presence of the H3K36me3 histone mark across the genome has been correlated with transcriptional activation and elongation, but also with the regulation of DNA mismatch repair, homologous recombination and alternative splicing. The role of SETD2 and the H3K36me3 histone mark in cancer is controversial. SETD2 is lost or mutated in various cancers, supporting a tumor suppressive role of the protein. Alterations in the SETD2 gene are also present in leukemia patients, where they are associated with aggressive disease and relapse. In line, heterozygous SETD2 loss caused chemotherapy resistance in leukemia cell lines and mouse models. In contrast, other studies indicate that SETD2 is critically required for the proliferation of leukemia cells. Thus, although studies of SETD2-dependent processes in cancer have contributed to a better understanding of the SETD2⁻H3K36me3 axis, many open questions remain regarding its specific role in leukemia. Here, we review the current literature about critical functions of SETD2 in the context of hematopoietic malignancies.
Collapse
Affiliation(s)
- Anna Skucha
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria.
| | - Jessica Ebner
- Ludwig Boltzmann Institute for Cancer Research, Waehringer Strasse 13A, 1090 Vienna, Austria.
| | - Florian Grebien
- Ludwig Boltzmann Institute for Cancer Research, Waehringer Strasse 13A, 1090 Vienna, Austria.
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
| |
Collapse
|
39
|
Yokoyama A. RNA Polymerase II-Dependent Transcription Initiated by Selectivity Factor 1: A Central Mechanism Used by MLL Fusion Proteins in Leukemic Transformation. Front Genet 2019; 9:722. [PMID: 30693017 PMCID: PMC6339877 DOI: 10.3389/fgene.2018.00722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/21/2018] [Indexed: 11/13/2022] Open
Abstract
Cancer cells transcribe RNAs in a characteristic manner in order to maintain their oncogenic potentials. In eukaryotes, RNA is polymerized by three distinct RNA polymerases, RNA polymerase I, II, and III (RNAP1, RNAP2, and RNAP3, respectively). The transcriptional machinery that initiates each transcription reaction has been purified and characterized. Selectivity factor 1 (SL1) is the complex responsible for RNAP1 pre-initiation complex formation. However, whether it plays any role in RNAP2-dependent transcription remains unclear. Our group previously found that SL1 specifically associates with AF4 family proteins. AF4 family proteins form the AEP complex with ENL family proteins and the P-TEFb elongation factor. Similar complexes have been independently characterized by several different laboratories and are often referred to as super elongation complex. The involvement of AEP in RNAP2-dependent transcription indicates that SL1 must play an important role in RNAP2-dependent transcription. To date, this role of SL1 has not been appreciated. In leukemia, AF4 and ENL family genes are frequently rearranged to form chimeric fusion genes with MLL. The resultant MLL fusion genes produce chimeric MLL fusion proteins comprising MLL and AEP components. The MLL portion functions as a targeting module, which specifically binds chromatin containing di-/tri-methylated histone H3 lysine 36 and non-methylated CpGs. This type of chromatin is enriched at the promoters of transcriptionally active genes which allows MLL fusion proteins to selectively bind to transcriptionally-active/CpG-rich gene promoters. The fusion partner portion, which recruits other AEP components and SL1, is responsible for activation of RNAP2-dependent transcription. Consequently, MLL fusion proteins constitutively activate the transcription of previously-transcribed MLL target genes. Structure/function analysis has shown that the ability of MLL fusion proteins to transform hematopoietic progenitors depends on the recruitment of AEP and SL1. Thus, the AEP/SL1-mediated gene activation pathway appears to be the central mechanism of MLL fusion-mediated transcriptional activation. However, the molecular mechanism by which SL1 activates RNAP2-dependent transcription remains largely unclear. This review aims to cover recent discoveries of the mechanism of transcriptional activation by MLL fusion proteins and to introduce novel roles of SL1 in RNAP2-dependent transcription by discussing how the RNAP1 machinery may be involved in RNAP2-dependent gene regulation.
Collapse
Affiliation(s)
- Akihiko Yokoyama
- Tsuruoka Meatabolomics Laboratory, National Cancer Center, Yamagata, Japan
| |
Collapse
|
40
|
Abstract
Introduction: Epigenetic dysregulation drives or supports numerous human cancers. The chromatin landscape in cancer cells is often marked by abnormal histone post-translational modification (PTM) patterns and by aberrant assembly and recruitment of protein complexes to specific genomic loci. Mass spectrometry-based proteomic analyses can support the discovery and characterization of both phenomena. Areas covered: We broadly divide this literature into two parts: 'modification-centric' analyses that link histone PTMs to cancer biology; and 'complex-centric' analyses that examine protein-protein interactions that occur de novo as a result of oncogenic mutations. We also discuss proteomic studies of oncohistones. We highlight relevant examples, discuss limitations, and speculate about forthcoming innovations regarding each application. Expert commentary: 'Modification-centric' analyses have been used to further understanding of cancer's histone code and to identify associated therapeutic vulnerabilities. 'Complex-centric' analyses have likewise revealed insights into mechanisms of oncogenesis and suggested potential therapeutic targets, particularly in MLL-associated leukemia. Proteomic experiments have also supported some of the pioneering studies of oncohistone-mediated tumorigenesis. Additional applications of proteomics that may benefit cancer epigenetics research include middle-down and top-down histone PTM analysis, chromatin reader profiling, and genomic locus-specific protein identification. In the coming years, proteomic approaches will remain powerful ways to interrogate the biology of cancer.
Collapse
Affiliation(s)
- Dylan M Marchione
- a Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Benjamin A Garcia
- a Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - John Wojcik
- b Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| |
Collapse
|
41
|
Skucha A, Ebner J, Grebien F. SETD2 in MLL-rearranged leukemia - a complex case. Mol Cell Oncol 2018; 5:e1503492. [PMID: 30250934 DOI: 10.1080/23723556.2018.1503492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 10/28/2022]
Abstract
Oncogenic MLL-fusion proteins often hijack essential molecular mechanisms during leukemogenesis. The histone methyltransferase SETD2 was implicated in the regulation of transcription, DNA damage and other cellular processes. Recent studies identified a critical role for SETD2 in MLL-rearranged leukemia. These results may help to unravel important functions of SETD2 in hematopoiesis.
Collapse
Affiliation(s)
- Anna Skucha
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria
| | - Jessica Ebner
- Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria
| | - Florian Grebien
- Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria.,Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
| |
Collapse
|