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Kim M, Powers CA, Fisher DT, Ku AW, Neznanov N, Safina AF, Wang J, Gautam A, Balachandran S, Krishnamurthy A, Gurova KV, Evans SS, Gudkov AV, Skitzki JJ. Enhancing Anti-PD-1 Immunotherapy by Targeting MDSCs via Hepatic Arterial Infusion in Breast Cancer Liver Metastases. Cancers (Basel) 2024; 16:3711. [PMID: 39518148 PMCID: PMC11545300 DOI: 10.3390/cancers16213711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 10/23/2024] [Accepted: 10/30/2024] [Indexed: 11/16/2024] Open
Abstract
BACKGROUND Surgery, chemotherapy, and radiation often have limited utility for advanced metastatic disease in the liver, and despite its promising activity in select cancers, PD-1 blockade therapy similarly has minimal benefit in this setting. Curaxin, CBL0137, is an experimental anti-cancer drug that disrupts the binding of DNA to histones, destabilizes chromatin, and induces Z-DNA formation which may stimulate anti-tumor immune responses. METHODS Murine cell lines of colon (CT26) and breast (4T1) cancer were interrogated for survival and CBL0137-associated DNA changes in vitro. Immunocompetent models of liver metastases followed by CBL0137 hepatic arterial infusion (HAI) were used to examine in vivo tumor cell DNA alterations, treatment responses, and the immune contexture associated with CBL0137, both alone and in combination with anti-PD-1 therapy. RESULTS CBL0137 induced immediate changes to favor tumor cell death in vitro and in vivo with an efficient tumor uptake via the HAI route. Toxicity to CBL0137 was minimal and anti-tumor treatment effects were more efficient with HAI compared to intravenous delivery. Immune effects were pronounced with CBL0137 HAI with concurrent depletion of a specific population of myeloid-derived suppressor cells and maintenance of effector T cell populations. CONCLUSIONS Combination of CBL0137 HAI with PD-1 blockade improved survival in 4T1 tumors but not in CT26 tumors, and therapeutic efficacy relies on the finding of simultaneous and targeted depletion of myeloid-derived suppressor cells and skewing of T cell populations to produce synergy with PD-1 blockade therapy.
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Affiliation(s)
- Minhyung Kim
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (C.A.P.); (D.T.F.); (A.W.K.)
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Colin A. Powers
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (C.A.P.); (D.T.F.); (A.W.K.)
| | - Daniel T. Fisher
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (C.A.P.); (D.T.F.); (A.W.K.)
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Amy W. Ku
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (C.A.P.); (D.T.F.); (A.W.K.)
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Nickolay Neznanov
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (N.N.); (A.F.S.); (K.V.G.); (A.V.G.)
| | - Alfiya F. Safina
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (N.N.); (A.F.S.); (K.V.G.); (A.V.G.)
| | - Jianmin Wang
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Avishekh Gautam
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (A.G.); (S.B.)
| | - Siddharth Balachandran
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (A.G.); (S.B.)
| | - Anuradha Krishnamurthy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Katerina V. Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (N.N.); (A.F.S.); (K.V.G.); (A.V.G.)
| | - Sharon S. Evans
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Andrei V. Gudkov
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (N.N.); (A.F.S.); (K.V.G.); (A.V.G.)
| | - Joseph J. Skitzki
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (C.A.P.); (D.T.F.); (A.W.K.)
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
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Falbo L, Técher H, Sannino V, Robusto M, Fagà G, Pezzimenti F, Romeo F, Colombo LG, Vultaggio S, Fancelli D, Monzani S, Cecatiello V, Pasqualato S, Varasi M, Mercurio C, Costanzo V. A high-throughput screening identifies MCM chromatin loading inhibitors targeting cells with increased replication origins. iScience 2024; 27:110567. [PMID: 39184446 PMCID: PMC11342271 DOI: 10.1016/j.isci.2024.110567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/25/2024] [Accepted: 07/18/2024] [Indexed: 08/27/2024] Open
Abstract
Replication origin assembly is a pivotal step in chromosomal DNA replication. In this process, the ORC complex binds DNA and, together with the CDC6 and CDT1, promotes the loading of the MCM helicase. Chemicals targeting origin assembly might be useful to sensitize highly proliferative cancer cells. However, identifying such compounds is challenging due to the multistage nature of this process. Here, using Xenopus laevis egg extract we set up a high-throughput screening to isolate MCM chromatin loading inhibitors, which led to the identification of NSC-95397 as a powerful inhibitor of replication origin assembly that targets CDC6 protein and promotes its degradation. Using systems developed to test selective drug-induced lethality we show that NSC-95397 triggers cell death both in human cells and Xenopus embryos that have higher proliferative ability. These findings demonstrate the effectiveness of molecules disrupting DNA replication processes in targeting hyperproliferating cells, highlighting their potential as anti-cancer molecules.
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Affiliation(s)
- Lucia Falbo
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20133 Milan, Italy
| | - Hervé Técher
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Vincenzo Sannino
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Michela Robusto
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Giovanni Fagà
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Francesco Romeo
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20133 Milan, Italy
| | | | | | - Daniele Fancelli
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Silvia Monzani
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20141 Milan, Italy
| | - Valentina Cecatiello
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20141 Milan, Italy
| | - Sebastiano Pasqualato
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20141 Milan, Italy
| | - Mario Varasi
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Ciro Mercurio
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Vincenzo Costanzo
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20133 Milan, Italy
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3
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Artuyants A, Guo G, Flinterman M, Middleditch M, Jacob B, Lee K, Vella L, Su H, Wilson M, Eva L, Shelling AN, Blenkiron C. The tumour-derived extracellular vesicle proteome varies by endometrial cancer histology and is confounded by an obesogenic environment. Proteomics 2024; 24:e2300055. [PMID: 38644352 DOI: 10.1002/pmic.202300055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/23/2024]
Abstract
Endometrial cancer, the most common gynaecological cancer worldwide, is closely linked to obesity and metabolic diseases, particularly in younger women. New circulating biomarkers have the potential to improve diagnosis and treatment selections, which could significantly improve outcomes. Our approach focuses on extracellular vesicle (EV) biomarker discovery by directly profiling the proteome of EVs enriched from frozen biobanked endometrial tumours. We analysed nine tissue samples to compare three clinical subgroups-low BMI (Body Mass Index) Endometrioid, high BMI Endometrioid, and Serous (any BMI)-identifying proteins related to histological subtype, BMI, and shared secreted proteins. Using collagenase digestion and size exclusion chromatography, we successfully enriched generous quantities of EVs (range 204.8-1291.0 µg protein: 1.38 × 1011-1.10 × 1012 particles), characterised by their size (∼150 nm), expression of EV markers (CD63/81), and proposed endometrial cancer markers (L1CAM, ANXA2). Mass spectrometry-based proteomic profiling identified 2075 proteins present in at least one of the 18 samples. Compared to cell lysates, EVs were successfully depleted for mitochondrial and blood proteins and enriched for common EV markers and large secreted proteins. Further analysis highlighted significant differences in EV protein profiles between the high BMI subgroup and others, underlining the impact of comorbidities on the EV secretome. Interestingly, proteins differentially abundant in tissue subgroups were largely not also differential in matched EVs. This research identified secreted proteins known to be involved in endometrial cancer pathophysiology and proposed novel diagnostic biomarkers (EIF6, MUC16, PROM1, SLC26A2).
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Affiliation(s)
- Anastasiia Artuyants
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
| | - George Guo
- Department of Physiology in the School of Medical Sciences, The University of Auckland, Auckland, New Zealand
- Mass Spectrometry Hub, The University of Auckland, Auckland, New Zealand
| | - Marcella Flinterman
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
| | - Martin Middleditch
- Technical Services, Faculty of Science, The University of Auckland, Auckland, New Zealand
| | - Bincy Jacob
- Centre of eResearch, Faculty of Science, The University of Auckland, Auckland, New Zealand
| | - Kate Lee
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
| | - Laura Vella
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Huaqi Su
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Michelle Wilson
- Cancer and Blood, Auckland City Hospital, Auckland, New Zealand
- Department of Oncology, The University of Auckland, Auckland, New Zealand
| | - Lois Eva
- Department of Gynaecological Oncology, Auckland City Hospital, Auckland, New Zealand
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland, New Zealand
| | - Andrew N Shelling
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland, New Zealand
- Centre for Cancer Research, The University of Auckland, Auckland, New Zealand
| | - Cherie Blenkiron
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
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Lyu Y, Yang Y, Talwar V, Lu H, Chen C, Salman S, Wicks EE, Huang TYT, Drehmer D, Wang Y, Zuo Q, Datan E, Jackson W, Dordai D, Wang R, Semenza GL. Hypoxia-inducible factor 1 recruits FACT and RNF20/40 to mediate histone ubiquitination and transcriptional activation of target genes. Cell Rep 2024; 43:113972. [PMID: 38517892 DOI: 10.1016/j.celrep.2024.113972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 02/01/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024] Open
Abstract
Hypoxia-inducible factor 1 (HIF-1) is a transcriptional activator that mediates cellular adaptation to decreased oxygen availability. HIF-1 recruits chromatin-modifying enzymes leading to changes in histone acetylation, citrullination, and methylation at target genes. Here, we demonstrate that hypoxia-inducible gene expression in estrogen receptor (ER)-positive MCF7 and ER-negative SUM159 human breast cancer cells requires the histone H2A/H2B chaperone facilitates chromatin transcription (FACT) and the H2B ubiquitin ligase RING finger protein 20/40 (RNF20/40). Knockdown of FACT or RNF20/40 expression leads to decreased transcription initiation and elongation at HIF-1 target genes. Mechanistically, FACT and RNF20/40 are recruited to hypoxia response elements (HREs) by HIF-1 and stabilize binding of HIF-1 (and each other) at HREs. Hypoxia induces the monoubiquitination of histone H2B at lysine 120 at HIF-1 target genes in an HIF-1-dependent manner. Together, these findings delineate a cooperative molecular mechanism by which FACT and RNF20/40 stabilize multiprotein complex formation at HREs and mediate histone ubiquitination to facilitate HIF-1 transcriptional activity.
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Affiliation(s)
- Yajing Lyu
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yongkang Yang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Varen Talwar
- Johns Hopkins University, Baltimore, MD 21218, USA
| | - Haiquan Lu
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Chelsey Chen
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaima Salman
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elizabeth E Wicks
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tina Yi-Ting Huang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daiana Drehmer
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yufeng Wang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Qiaozhu Zuo
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emmanuel Datan
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Walter Jackson
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dominic Dordai
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ru Wang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gregg L Semenza
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA.
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5
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Patel A, Gulhati P. Molecular Landscape and Therapeutic Strategies against Colorectal Cancer. Cancers (Basel) 2024; 16:1551. [PMID: 38672633 PMCID: PMC11049251 DOI: 10.3390/cancers16081551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer deaths worldwide. Although the overall incidence of CRC is decreasing, the incidence of young-onset CRC, characterized by a diagnosis of CRC before age 50, is increasing. Outcomes for CRC patients are improving, partly due to comprehensive molecular characterization of tumors and novel therapeutic strategies. Advances in genomic and transcriptomic analyses using blood- and tumor-tissue-based sequencing have facilitated identification of distinct tumor subtypes harboring unique biological characteristics and therapeutic vulnerabilities. These insights have led to the development and incorporation of targeted therapies and immunotherapy in CRC treatment. In this review, we discuss the molecular landscape and key oncogenes/tumor suppressors contributing to CRC tumorigenesis, metastasis, and therapeutic resistance. We also discuss personalized therapeutic strategies for subsets of CRC patients and provide an overview of evolving novel treatments being evaluated in clinical trials.
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Affiliation(s)
- Aakash Patel
- Division of Medical Oncology, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
| | - Pat Gulhati
- Division of Medical Oncology, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
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6
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Barman P, Bhaumik SR. Facilitates Chromatin Transcription in Breast and Other Cancers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1465:71-88. [PMID: 39586994 DOI: 10.1007/978-3-031-66686-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2024]
Abstract
Eukaryotic genome is packaged into chromatin. Thus, transcription takes place in the context of chromatin that is an array of nucleosomes. Nucleosome poses a barrier for the gene regulatory factors to access DNA for transcription to occur. Fortunately, eukaryotic cells have evolved mechanisms of nucleosomal disassembly and reassembly for transcription through chromatin. Such nucleosomal alteration in controlling transcription is governed by a heterodimeric chromatin remodeling factor, FACT (facilitates chromatin transcription), which is evolutionarily conserved from yeast to humans. FACT facilitates chromatin disassembly at the promoter and reassembly at the open reading frame. Such chromatin regulatory functions of FACT promote transcription. Likewise, other DNA transacting processes such as DNA replication and repair are also regulated by FACT via modulation of chromatin dynamics. Intriguingly, FACT is found to be upregulated in breast and other cancers with oncogenic potential. Thus, FACT and/or its upstream regulatory pathways/factors can be employed for cancer prognosis and targeted for an effective cancer therapy. Further, FACT is found to be downregulated and/or mutated in various cancers including breast cancer. Here, we describe FACT and its involvement in breast and other cancers with prognostic and targeted therapeutic implications.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, USA.
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7
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de Vivo A, Song H, Lee Y, Tirado-Class N, Sanchez A, Westerheide S, Dungrawala H, Kee Y. OTUD5 limits replication fork instability by organizing chromatin remodelers. Nucleic Acids Res 2023; 51:10467-10483. [PMID: 37713620 PMCID: PMC10602872 DOI: 10.1093/nar/gkad732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/01/2023] [Accepted: 08/25/2023] [Indexed: 09/17/2023] Open
Abstract
Proper regulation of replication fork progression is important for genomic maintenance. Subverting the transcription-induced conflicts is crucial in preserving the integrity of replication forks. Various chromatin remodelers, such as histone chaperone and histone deacetylases are known to modulate replication stress, but how these factors are organized or collaborate are not well understood. Here we found a new role of the OTUD5 deubiquitinase in limiting replication stress. We found that OTUD5 is recruited to replication forks, and its depletion causes replication fork stress. Through its C-terminal disordered tail, OTUD5 assembles a complex containing FACT, HDAC1 and HDAC2 at replication forks. A cell line engineered to specifically uncouple FACT interaction with OTUD5 exhibits increases in FACT loading onto chromatin, R-loop formation, and replication fork stress. OTUD5 mediates these processes by recruiting and stabilizing HDAC1 and HDAC2, which decreases H4K16 acetylation and FACT recruitment. Finally, proteomic analysis revealed that the cells with deficient OTUD5-FACT interaction activates the Fanconi Anemia pathway for survival. Altogether, this study identified a new interaction network among OTUD5-FACT-HDAC1/2 that limits transcription-induced replication stress.
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Affiliation(s)
- Angelo de Vivo
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
| | - Hongseon Song
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 333 Techno-Joongang-daero, Dalseong-gun, Daegu 42988, Republic of Korea
| | - Yujin Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 333 Techno-Joongang-daero, Dalseong-gun, Daegu 42988, Republic of Korea
| | - Neysha Tirado-Class
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
| | - Anthony Sanchez
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
| | - Sandy Westerheide
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
| | - Huzefa Dungrawala
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
| | - Younghoon Kee
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 333 Techno-Joongang-daero, Dalseong-gun, Daegu 42988, Republic of Korea
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8
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Klein DC, Lardo SM, McCannell KN, Hainer SJ. FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells. BMC Biol 2023; 21:167. [PMID: 37542287 PMCID: PMC10403911 DOI: 10.1186/s12915-023-01669-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND The FACT complex is a conserved histone chaperone with critical roles in transcription and histone deposition. FACT is essential in pluripotent and cancer cells, but otherwise dispensable for most mammalian cell types. FACT deletion or inhibition can block induction of pluripotent stem cells, yet the mechanism through which FACT regulates cell fate decisions remains unclear. RESULTS To explore the mechanism for FACT function, we generated AID-tagged murine embryonic cell lines for FACT subunit SPT16 and paired depletion with nascent transcription and chromatin accessibility analyses. We also analyzed SPT16 occupancy using CUT&RUN and found that SPT16 localizes to both promoter and enhancer elements, with a strong overlap in binding with OCT4, SOX2, and NANOG. Over a timecourse of SPT16 depletion, nucleosomes invade new loci, including promoters, regions bound by SPT16, OCT4, SOX2, and NANOG, and TSS-distal DNaseI hypersensitive sites. Simultaneously, transcription of Pou5f1 (encoding OCT4), Sox2, Nanog, and enhancer RNAs produced from these genes' associated enhancers are downregulated. CONCLUSIONS We propose that FACT maintains cellular pluripotency through a precise nucleosome-based regulatory mechanism for appropriate expression of both coding and non-coding transcripts associated with pluripotency.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Santana M Lardo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Kurtis N McCannell
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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Pearson S, Blance R, Yan F, Hsieh YC, Geary B, Amaral FMR, Somervaille TCP, Kirschner K, Whetton AD, Pierce A. Identification of curaxin as a potential new therapeutic for JAK2 V617F mutant patients. PLoS One 2023; 18:e0286412. [PMID: 37253035 PMCID: PMC10228771 DOI: 10.1371/journal.pone.0286412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/15/2023] [Indexed: 06/01/2023] Open
Abstract
Myelofibrosis is a myeloproliferative neoplasm (MPN) which typically results in reduced length and quality of life due to systemic symptoms and blood count changes arising from fibrotic changes in the bone marrow. While the JAK2 inhibitor ruxolitinib provides some clinical benefit, there remains a substantial unmet need for novel targeted therapies to better modify the disease process or eradicate the cells at the heart of myelofibrosis pathology. Repurposing drugs bypasses many of the hurdles present in drug development, such as toxicity and pharmacodynamic profiling. To this end we undertook a re-analysis of our pre-existing proteomic data sets to identify perturbed biochemical pathways and their associated drugs/inhibitors to potentially target the cells driving myelofibrosis. This approach identified CBL0137 as a candidate for targeting Jak2 mutation-driven malignancies. CBL0137 is a drug derived from curaxin targeting the Facilitates Chromatin Transcription (FACT) complex. It is reported to trap the FACT complex on chromatin thereby activating p53 and inhibiting NF-kB activity. We therefore assessed the activity of CBL0137 in primary patient samples and murine models of Jak2-mutated MPN and found it preferentially targets CD34+ stem and progenitor cells from myelofibrosis patients by comparison with healthy control cells. Further we investigate its mechanism of action in primary haemopoietic progenitor cells and demonstrate its ability to reduce splenomegaly and reticulocyte number in a transgenic murine model of myeloproliferative neoplasms.
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Affiliation(s)
- Stella Pearson
- Stem Cell and Leukaemia Proteomics Laboratory, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Rognvald Blance
- Stem Cell and Leukaemia Proteomics Laboratory, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Fei Yan
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Ya-Ching Hsieh
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Bethany Geary
- Stoller Biomarker Discovery Centre, University of Manchester, Manchester, United Kingdom
| | - Fabio M. R. Amaral
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Tim C. P. Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Kristina Kirschner
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Anthony D. Whetton
- Stem Cell and Leukaemia Proteomics Laboratory, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Andrew Pierce
- Stem Cell and Leukaemia Proteomics Laboratory, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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10
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Rex EA, Seo D, Chappidi S, Pinkham C, Oliveira SB, Embry A, Heisler D, Liu Y, Luger K, Alto NM, da Fonseca FG, Orchard R, Hancks D, Gammon DB. A FACT-ETS-1 Antiviral Response Pathway Restricts Viral Replication and is Countered by Poxvirus A51R Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527673. [PMID: 36798356 PMCID: PMC9934636 DOI: 10.1101/2023.02.08.527673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The FACT complex is an ancient chromatin remodeling factor comprised of Spt16 and SSRP1 subunits that regulates specific eukaryotic gene expression programs. However, whether FACT regulates host immune responses to infection was unclear. Here, we identify an antiviral pathway mediated by FACT, distinct from the interferon response, that restricts poxvirus replication. We show that early viral gene expression triggers nuclear accumulation of specialized, SUMOylated Spt16 subunits of FACT required for expression of ETS-1, a downstream transcription factor that activates a virus restriction program. However, poxvirus-encoded A51R proteins block ETS-1 expression by outcompeting SSRP1 for binding to SUMOylated Spt16 in the cytosol and by tethering SUMOylated Spt16 to microtubules. Moreover, we show that A51R antagonism of FACT enhances both poxvirus replication in human cells and viral virulence in mice. Finally, we demonstrate that FACT also restricts unrelated RNA viruses, suggesting a broad role for FACT in antiviral immunity. Our study reveals the F ACT- E TS-1 A ntiviral R esponse (FEAR) pathway to be critical for eukaryotic antiviral immunity and describes a unique mechanism of viral immune evasion.
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11
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McCauley MJ, Morse M, Becker N, Hu Q, Botuyan MV, Navarrete E, Huo R, Muthurajan UM, Rouzina I, Luger K, Mer G, Maher LJ, Williams MC. Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes. Cell Rep 2022; 41:111858. [PMID: 36577379 PMCID: PMC9807050 DOI: 10.1016/j.celrep.2022.111858] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/06/2022] [Accepted: 11/30/2022] [Indexed: 12/28/2022] Open
Abstract
The histone chaperone FACT (facilitates chromatin transcription) enhances transcription in eukaryotic cells, targeting DNA-protein interactions. FACT, a heterodimer in humans, comprises SPT16 and SSRP1 subunits. We measure nucleosome stability and dynamics in the presence of FACT and critical component domains. Optical tweezers quantify FACT/subdomain binding to nucleosomes, displacing the outer wrap of DNA, disrupting direct DNA-histone (core site) interactions, altering the energy landscape of unwrapping, and increasing the kinetics of DNA-histone disruption. Atomic force microscopy reveals nucleosome remodeling, while single-molecule fluorescence quantifies kinetics of histone loss for disrupted nucleosomes, a process accelerated by FACT. Furthermore, two isolated domains exhibit contradictory functions; while the SSRP1 HMGB domain displaces DNA, SPT16 MD/CTD stabilizes DNA-H2A/H2B dimer interactions. However, only intact FACT tethers disrupted DNA to the histones and supports rapid nucleosome reformation over several cycles of force disruption/release. These results demonstrate that key FACT domains combine to catalyze both nucleosome disassembly and reassembly.
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Affiliation(s)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Nicole Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Emily Navarrete
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Ran Huo
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Uma M. Muthurajan
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado, Boulder, CO, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA, USA,Lead contact,Correspondence:
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12
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Lu X, He Y, Johnston RL, Nanayakarra D, Sankarasubramanian S, Lopez JA, Friedlander M, Kalimutho M, Hooper JD, Raninga PV, Khanna KK. CBL0137 impairs homologous recombination repair and sensitizes high-grade serous ovarian carcinoma to PARP inhibitors. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:355. [PMID: 36539830 PMCID: PMC9769062 DOI: 10.1186/s13046-022-02570-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND High-grade serous ovarian carcinomas (HGSCs) are a heterogeneous subtype of epithelial ovarian cancers and include serous cancers arising in the fallopian tube and peritoneum. These cancers are now subdivided into homologous recombination repair (HR)-deficient and proficient subgroups as this classification impacts on management and prognosis. PARP inhibitors (PARPi) have shown significant clinical efficacy, particularly as maintenance therapy following response to platinum-based chemotherapy in BRCA-mutant or homologous recombination (HR)-deficient HGSCs in both the 1st and 2nd line settings. However, PARPi have limited clinical benefit in HR-proficient HGSCs which make up almost 50% of HGSC and improving outcomes in these patients is now a high priority due to the poor prognosis with ineffectiveness of the current standard of care. There are a number of potential lines of investigation including efforts in sensitizing HR-proficient tumors to PARPi. Herein, we aimed to develop a novel combination therapy by targeting SSRP1 using a small molecule inhibitor CBL0137 with PARPi in HR-proficient HGSCs. EXPERIMENTAL DESIGN We tested anti-cancer activity of CBL0137 monotherapy using a panel of HGSC cell lines and patient-derived tumor cells in vitro. RNA sequencing was used to map global transcriptomic changes in CBL0137-treated patient-derived HR-proficient HGSC cells. We tested efficacy of CBL0137 in combination with PARPi using HGSC cell lines and patient-derived tumor cells in vitro and in vivo. RESULTS We show that SSRP1 inhibition using a small molecule, CBL0137, that traps SSRP1 onto chromatin, exerts a significant anti-growth activity in vitro against HGSC cell lines and patient-derived tumor cells, and also reduces tumor burden in vivo. CBL0137 induced DNA repair deficiency via inhibition of the HR repair pathway and sensitized SSRP1-high HR-proficient HGSC cell lines and patient-derived tumor cells/xenografts to the PARPi, Olaparib in vitro and in vivo. CBL0137 also enhanced the efficacy of DNA damaging platinum-based chemotherapy in HGSC patient-derived xenografts. CONCLUSION Our findings strongly suggest that combination of CBL0137 and PARP inhibition represents a novel therapeutic strategy for HR-proficient HGSCs that express high levels of SSRP1 and should be investigated in the clinic.
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Affiliation(s)
- Xue Lu
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia ,grid.1022.10000 0004 0437 5432School of Environment and Sciences, Griffith University, Nathan, QLD 4111 Australia
| | - Yaowu He
- grid.489335.00000000406180938Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102 Australia
| | - Rebecca L. Johnston
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - Devathri Nanayakarra
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - Sivanandhini Sankarasubramanian
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - J. Alejandro Lopez
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia ,grid.1022.10000 0004 0437 5432School of Environment and Sciences, Griffith University, Nathan, QLD 4111 Australia
| | - Michael Friedlander
- grid.415193.bUniversity of New South Wales Clinical School, Prince of Wales Hospital, Randwick, NSW 2031 Australia
| | - Murugan Kalimutho
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - John D. Hooper
- grid.489335.00000000406180938Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102 Australia
| | - Prahlad V. Raninga
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - Kum Kum Khanna
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
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13
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Volokh OI, Sivkina AL, Moiseenko AV, Popinako AV, Karlova MG, Valieva ME, Kotova EY, Kirpichnikov MP, Formosa T, Studitsky VM, Sokolova OS. Mechanism of curaxin-dependent nucleosome unfolding by FACT. Front Mol Biosci 2022; 9:1048117. [PMID: 36483541 PMCID: PMC9723464 DOI: 10.3389/fmolb.2022.1048117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/07/2022] [Indexed: 08/27/2023] Open
Abstract
Human FACT (FACT) is a multifunctional histone chaperone involved in transcription, replication and DNA repair. Curaxins are anticancer compounds that induce FACT-dependent nucleosome unfolding and trapping of FACT in the chromatin of cancer cells (c-trapping) through an unknown molecular mechanism. Here, we analyzed the effects of curaxin CBL0137 on nucleosome unfolding by FACT using spFRET and electron microscopy. By itself, FACT adopted multiple conformations, including a novel, compact, four-domain state in which the previously unresolved NTD of the SPT16 subunit of FACT was localized, apparently stabilizing a compact configuration. Multiple, primarily open conformations of FACT-nucleosome complexes were observed during curaxin-supported nucleosome unfolding. The obtained models of intermediates suggest "decision points" in the unfolding/folding pathway where FACT can either promote disassembly or assembly of nucleosomes, with the outcome possibly being influenced by additional factors. The data suggest novel mechanisms of nucleosome unfolding by FACT and c-trapping by curaxins.
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Affiliation(s)
- Olesya I. Volokh
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
| | | | - Andrey V. Moiseenko
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
- Semenov Federal Research Center of Chemical Physics RAS, Moscow, Russia
| | - Anna V. Popinako
- Bach Institute of Biochemistry Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Maria G. Karlova
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
| | - Maria E. Valieva
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
- RG Development & Disease Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | | | - Timothy Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Vasily M. Studitsky
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Olga S. Sokolova
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
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14
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Jeong E, Martina JA, Contreras PS, Lee J, Puertollano R. The FACT complex facilitates expression of lysosomal and antioxidant genes through binding to TFEB and TFE3. Autophagy 2022; 18:2333-2349. [PMID: 35230915 PMCID: PMC9542721 DOI: 10.1080/15548627.2022.2029671] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TFEB (transcription factor EB) and TFE3 (transcription factor binding to IGHM enhancer 3) orchestrate the cellular response to a variety of stressors, including nutrient deprivation, oxidative stress and pathogens. Here we describe a novel interaction of TFEB and TFE3 with the FAcilitates Chromatin Transcription (FACT) complex, a heterodimeric histone chaperone consisting of SSRP1 and SUPT16H that mediates nucleosome disassembly and assembly, thus facilitating transcription. Extracellular stimuli, such as nutrient deprivation or oxidative stress, induce nuclear translocation and activation of TFEB and TFE3, which then associate with the FACT complex to regulate stress-induced gene transcription. Depletion of FACT does not affect TFEB activation, stability, or binding to the promoter of target genes. In contrast, reduction of FACT levels by siRNA or treatment with the FACT inhibitor curaxin, severely impairs induction of numerous antioxidant and lysosomal genes, revealing a crucial role of FACT as a regulator of cellular homeostasis. Furthermore, upregulation of antioxidant genes induced by TFEB over-expression is significantly reduced by curaxin, consistent with a role of FACT as a TFEB transcriptional activator. Together, our data show that chromatin remodeling at the promoter of stress-responsive genes by FACT is important for efficient expression of TFEB and TFE3 targets, thus providing a link between environmental changes, chromatin modifications and transcriptional regulation.Abbreviations: ADNP2, ADNP homeobox 2; ATP6V0D1, ATPase H+ transporting V0 subunit d1; ATP6V1A, ATPase H+ transporting V1 subunit A; ATP6V1C1, ATPase H+ transporting V1 subunit C1; CSNK2/CK2, casein kinase 2; CLCN7, chloride voltage-gated channel 7; CTSD, cathepsin D; CTSZ, cathepsin Z; EBSS, earle's balanced salt solution; FACT complex, facilitates chromatin transcription complex; FOXO3, forkhead box O3; HEXA, hexosaminidase subunit alpha; HIF1A, hypoxia inducible factor 1 subunit alpha; HMOX1, heme oxygenase 1; LAMP1, lysosomal associated membrane protein 1; MAFF, MAF bZIP transcription factor F; MAFG, MAF bZIP transcription factor G; MCOLN1, mucolipin TRP cation channel 1; MTORC1, mechanistic target of rapamycin kinase complex 1; NaAsO2, sodium arsenite; POLR2, RNA polymerase II; PPARGC1A, PPARG coactivator 1 alpha; PYROXD1, pyridine nucleotide-disulfide oxidoreductase domain 1; RRAGC, Ras related GTP binding C; SEC13, SEC13 homolog, nuclear pore and COPII coat complex component; SLC38A9, solute carrier family 38 member 9; SSRP1, structure specific recognition protein 1; SUPT16H, SPT16 homolog, facilitates chromatin remodeling subunit; TFEB, transcription factor EB; TFE3, transcription factor binding to IGHM enhancer 3; TXNRD1, thioredoxin reductase 1; UVRAG, UV radiation resistance associated; WDR59, WD repeat domain 59.
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Affiliation(s)
- Eutteum Jeong
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - José A. Martina
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Pablo S. Contreras
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Juhyung Lee
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rosa Puertollano
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA,CONTACT Rosa Puertollano Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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15
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Aggregative trans-eQTL analysis detects trait-specific target gene sets in whole blood. Nat Commun 2022; 13:4323. [PMID: 35882830 PMCID: PMC9325868 DOI: 10.1038/s41467-022-31845-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/06/2022] [Indexed: 01/13/2023] Open
Abstract
Large scale genetic association studies have identified many trait-associated variants and understanding the role of these variants in the downstream regulation of gene-expressions can uncover important mediating biological mechanisms. Here we propose ARCHIE, a summary statistic based sparse canonical correlation analysis method to identify sets of gene-expressions trans-regulated by sets of known trait-related genetic variants. Simulation studies show that compared to standard methods, ARCHIE is better suited to identify "core"-like genes through which effects of many other genes may be mediated and can capture disease-specific patterns of genetic associations. By applying ARCHIE to publicly available summary statistics from the eQTLGen consortium, we identify gene sets which have significant evidence of trans-association with groups of known genetic variants across 29 complex traits. Around half (50.7%) of the selected genes do not have any strong trans-associations and are not detected by standard methods. We provide further evidence for causal basis of the target genes through a series of follow-up analyses. These results show ARCHIE is a powerful tool for identifying sets of genes whose trans-regulation may be related to specific complex traits.
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16
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Jeronimo C, Robert F. The histone chaperone FACT: a guardian of chromatin structure integrity. Transcription 2022; 13:16-38. [PMID: 35485711 PMCID: PMC9467567 DOI: 10.1080/21541264.2022.2069995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The identification of FACT as a histone chaperone enabling transcription through chromatin in vitro has strongly shaped how its roles are envisioned. However, FACT has been implicated in essentially all aspects of chromatin biology, from transcription to DNA replication, DNA repair, and chromosome segregation. In this review, we focus on recent literature describing the role and mechanisms of FACT during transcription. We highlight the prime importance of FACT in preserving chromatin integrity during transcription and challenge its role as an elongation factor. We also review evidence for FACT's role as a cell-type/gene-specificregulator of gene expression and briefly summarize current efforts at using FACT inhibition as an anti-cancerstrategy.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
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17
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Xiao YF, Li BS, Liu JJ, Wang SM, Liu J, Yang H, Hu YY, Gong CL, Li JL, Yang SM. Role of lncSLCO1C1 in gastric cancer progression and resistance to oxaliplatin therapy. Clin Transl Med 2022; 12:e691. [PMID: 35474446 PMCID: PMC9043116 DOI: 10.1002/ctm2.691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/03/2021] [Accepted: 12/15/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Gastric carcinoma (GC) is one of the most deadly diseases due to tumour metastasis and resistance to therapy. Understanding the molecular mechanism of tumour progression and drug resistance will improve therapeutic efficacy and develop novel intervention strategies. METHODS Differentially expressed long non-coding RNAs (lncRNAs) in clinical specimens were identified by LncRNA microarrays and validated in different clinical cohorts by quantitative real-time polymerase chain reaction (qRT-PCR), in situ hybridisation and bioinformatics analysis. Biological functions of lncRNA were investigated by using cell proliferation assays, migration assays, xenograft tumour models and bioinformatics analysis. Effects of lncSLCO1C1 on GC cell survival were assessed by comet assays and immunofluorescence assays. Underlying molecular mechanisms were further explored by using a number of technologies including RNA pull-down, mass spectrometry analysis, RNA immunoprecipitation, co-immunoprecipitation, miRNA sequencing, luciferase reporter assays and molecular modelling. RESULTS LncSLCO1C1 was highly upregulated in GC tissue samples and associated with GC patients' poor overall survival. Overexpression of lncSLCO1C1 promoted proliferation and migration, whereas decreased lncSLCO1C1 expression produced the opposite effects. lncSLCO1C1 also mediated tumour resistance to chemotherapy with oxaliplatin by reducing DNA damage and increasing cell proliferation. Despite sequence overlapping between lncSLCO1C1 and PDE3A, alternations of PDE3A expression had no effect on the GC cell progression, indicating that lncSLCO1C1, not PDE3A, related with the progression of GC cells. Mechanistically, lncSLCO1C1 serves as a scaffold for the structure-specific recognition protein 1 (SSRP1)/H2A/H2B complex and regulates the function of SSRP1 in reducing DNA damage. Meanwhile, lncSLCO1C1 functions as a sponge to adsorb miR-204-5p and miR-211-5p that target SSRP1 mRNA, and thus increases SSRP1 expression. Patients with high expressions of both lncSLCO1C1 and SSRP1 have poor overall survival, highlighting the role of lncSLCO1C1 in GC progression. CONCLUSIONS LncSLCO1C1 promotes GC progression by enhancing cell growth and preventing DNA damage via interacting and scaffolding the SSRP1/H2A/H2b complex and absorbing both miR-211-5p and miR-204-5p to increase SSRP1 expression.
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Affiliation(s)
- Yu-Feng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Bo-Sheng Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Jing-Jing Liu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Su-Min Wang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Jiao Liu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Huan Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Yi-Yang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Chun-Li Gong
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Ji-Liang Li
- Wenzhou Medical University Eye Hospital and School of Biomedical Engineering, China.,Cancer Research Centre, University of Chinese Academy of Sciences Wenzhou Institute, Wenzhou, China.,Institute of Translational and Stratified Medicine, University of Plymouth Faculty of Medicine and Dentistry, Plymouth, UK
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
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18
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The Current Status of SSRP1 in Cancer: Tribulation and Road Ahead. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:3528786. [PMID: 35463672 PMCID: PMC9020922 DOI: 10.1155/2022/3528786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/21/2022] [Indexed: 12/03/2022]
Abstract
Methods We search PubMed and Web of Sciences with keywords “SSRP1” and “Cancer.” Only English literature was included, and conference papers and abstract were all excluded. Results Transcription factors are classified into three groups based on their DNA binding motifs: simple helix-loop-helix (bHLH), classical zinc fingers (ZF-TFs), and homeodomains. The tumor-suppressive miR-497 (microRNA-497) acted as an undesirable regulator of SSRP1 upregulation, which led to tumor growth. The siRNA (small interfering RNA) knockdown of SSRP1 hindered cell proliferation along with incursion and glioma cell migration. Through the AKT (also known as protein kinase B) signaling pathway, SSRP1 silencing affected cancer apoptosis and cell proliferation. Conclusion The MAPK (mitogen-activated protein kinase) signaling pathway's phosphorylation was suppressed when SSRP1 was depleted. The effect of curaxins on p53 and NF-B (nuclear factor-κB), and their toxicity to cancer cells, is attributable to the FACT (facilitates chromatin transcription) complex's chromatin trapping.
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19
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Goswami I, Sandlesh P, Stablewski A, Toshkov I, Safina AF, Magnitov M, Wang J, Gurova K. FACT maintains nucleosomes during transcription and stem cell viability in adult mice. EMBO Rep 2022; 23:e53684. [PMID: 35179289 PMCID: PMC8982582 DOI: 10.15252/embr.202153684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/20/2022] [Accepted: 01/28/2022] [Indexed: 12/14/2022] Open
Abstract
Preservation of nucleosomes during replication has been extensively studied, while the maintenance of nucleosomes during transcription has gotten less attention. The histone chaperone FACT has a role in transcription elongation, although whether it disassembles or assembles nucleosomes during this process is unclear. To elucidate the function of FACT in mammals, we deleted the Ssrp1 subunit of FACT in adult mice. FACT loss is lethal, possibly due to the loss of the earliest progenitors in bone marrow and intestine, while more differentiated cells are not affected. Using cells isolated from several tissues, we show that FACT loss reduces the viability of stem cells but not of cells differentiated in vitro. FACT depletion increases chromatin accessibility in a transcription-dependent manner in adipose mesenchymal stem cells, indicating that nucleosomes are lost in these cells during transcription in the absence of FACT. We also observe activation of interferon (IFN) signaling and the accumulation of immunocytes in organs sensitive to FACT loss. Our data indicate that FACT maintains chromatin integrity during transcription in mammalian adult stem cells, suggesting that chromatin transcription in stem cells and differentiated cells is different.
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Affiliation(s)
- Imon Goswami
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | - Poorva Sandlesh
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA,Present address:
Department of Neurological SurgeryUniversity of PittsburghPittsburghPAUSA,Present address:
Department of NeurosurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Aimee Stablewski
- Transgenic Shared FacilityRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | | | - Alfiya F Safina
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | - Mikhail Magnitov
- Institute of Gene BiologyRussian Academy of SciencesMoscowRussia
| | - Jianmin Wang
- Department of Biostatistics and BioinformaticsRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | - Katerina Gurova
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
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20
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Shen J, Yang C, Zhang MS, Chin DWC, Chan FF, Law CT, Wang G, Cheng CLH, Chen M, Wan RTC, Wu M, Kuang Z, Sharma R, Lee TKW, Ng IOL, Wong CCL, Wong CM. Histone chaperone FACT complex coordinates with HIF to mediate an expeditious transcription program to adapt to poorly oxygenated cancers. Cell Rep 2022; 38:110304. [PMID: 35108543 DOI: 10.1016/j.celrep.2022.110304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 11/16/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Cancer cells adapt to hypoxia through HIFs (hypoxia-inducible factors), which initiate the transcription of numerous genes for cancer cell survival in the hypoxia microenvironment. In this study, we find that the FACT (facilitates chromatin transcription) complex works cooperatively with HIFs to facilitate the expeditious expression of HIF targets for hypoxia adaptation. Knockout (KO) of the FACT complex abolishes HIF-mediated transcription by impeding transcription elongation in hypoxic cancer cells. Interestingly, the FACT complex is post-translationally regulated by PHD/VHL-mediated hydroxylation and proteasomal degradation, in similar fashion to HIF-1/2α. Metabolic tracing confirms that FACT KO suppresses glycolytic flux and impairs lactate extrusion, leading to intracellular acidification and apoptosis in cancer cells. Therapeutically, hepatic artery ligation and anti-angiogenic inhibitors adversely induce intratumoral hypoxia, while co-treatment with FACT inhibitor curaxin remarkably hinders the growth of hypoxic tumors. In summary, our findings suggest that the FACT complex is a critical component of hypoxia adaptation and a therapeutic target for hypoxic tumors.
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Affiliation(s)
- Jialing Shen
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Chunxue Yang
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Misty Shuo Zhang
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Don Wai-Ching Chin
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - For-Fan Chan
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Cheuk-Ting Law
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Gengchao Wang
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Carol Lai-Hung Cheng
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Mengnuo Chen
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Rebecca Ting-Chi Wan
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Mengjie Wu
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Zhijian Kuang
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Rakesh Sharma
- Proteomic and Metabolic Core Facility, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Terence Kin Wah Lee
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Irene Oi-Lin Ng
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Carmen Chak-Lui Wong
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
| | - Chun-Ming Wong
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
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Bertuccio SN, Leardini D, Messelodi D, Anselmi L, Manente F, Ragni F, Serravalle S, Masetti R, Pession A. Are Induced Pluripotent Stem Cells a Step towards Modeling Pediatric Leukemias? Cells 2022; 11:cells11030476. [PMID: 35159287 PMCID: PMC8833985 DOI: 10.3390/cells11030476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
Despite enormous improvements in pre-clinical and clinical research, acute leukemia still represents an open challenge for pediatric hematologists; both for a significant relapse rate and for long term therapy-related sequelae. In this context, the use of an innovative technology, such as induced pluripotent stem cells (iPSCs), allows to finely reproduce the primary features of the malignancy and can be exploited as a model to study the onset and development of leukemia in vitro. The aim of this review is to explore the recent literature describing iPSCs as a key tool to study different types of hematological malignancies, comprising acute myeloid leukemia, non-down syndrome acute megakaryoblastic leukemia, B cell acute lymphoblastic leukemia, and juvenile myelomonocytic leukemia. This model demonstrates a positive impact on pediatric hematological diseases, especially in those affecting infants whose onsets is found in fetal hematopoiesis. This evidence highlights the importance of achieving an in vitro representation of the human embryonic hematopoietic development and timing-specific modifications, either genetic or epigenetic. Moreover, further insights into clonal evolution studies shed light in the way of a new precision medicine era, where patient-oriented decisions and therapies could further improve the outcome of pediatric cases. Nonetheless, we will also discuss here the difficulties and limitations of this model.
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Affiliation(s)
- Salvatore Nicola Bertuccio
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (S.N.B.); (F.M.); (F.R.); (R.M.)
| | - Davide Leardini
- Specialty School of Pediatrics, University of Bologna, 40138 Bologna, Italy;
- Pediatric Oncology and Hematology Unit “Lalla Seràgnoli,” Pediatric Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Daria Messelodi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (S.N.B.); (F.M.); (F.R.); (R.M.)
- Correspondence: (D.M.); (L.A.)
| | - Laura Anselmi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (S.N.B.); (F.M.); (F.R.); (R.M.)
- Correspondence: (D.M.); (L.A.)
| | - Francesca Manente
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (S.N.B.); (F.M.); (F.R.); (R.M.)
| | - Federico Ragni
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (S.N.B.); (F.M.); (F.R.); (R.M.)
| | - Salvatore Serravalle
- Pediatric Oncology and Hematology Unit “Lalla Seràgnoli,” Pediatric Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Riccardo Masetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (S.N.B.); (F.M.); (F.R.); (R.M.)
- Pediatric Oncology and Hematology Unit “Lalla Seràgnoli,” Pediatric Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Andrea Pession
- Division of Pediatrics, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
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22
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Hayden E, Holliday H, Lehmann R, Khan A, Tsoli M, Rayner BS, Ziegler DS. Therapeutic Targets in Diffuse Midline Gliomas-An Emerging Landscape. Cancers (Basel) 2021; 13:cancers13246251. [PMID: 34944870 PMCID: PMC8699135 DOI: 10.3390/cancers13246251] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Diffuse midline gliomas (DMGs) remain one of the most devastating childhood brain tumour types, for which there is currently no known cure. In this review we provide a summary of the existing knowledge of the molecular mechanisms underlying the pathogenesis of this disease, highlighting current analyses and novel treatment propositions. Together, the accumulation of these data will aid in the understanding and development of more effective therapeutic options for the treatment of DMGs. Abstract Diffuse midline gliomas (DMGs) are invariably fatal pediatric brain tumours that are inherently resistant to conventional therapy. In recent years our understanding of the underlying molecular mechanisms of DMG tumorigenicity has resulted in the identification of novel targets and the development of a range of potential therapies, with multiple agents now being progressed to clinical translation to test their therapeutic efficacy. Here, we provide an overview of the current therapies aimed at epigenetic and mutational drivers, cellular pathway aberrations and tumor microenvironment mechanisms in DMGs in order to aid therapy development and facilitate a holistic approach to patient treatment.
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Affiliation(s)
- Elisha Hayden
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington 2052, Australia; (E.H.); (H.H.); (R.L.); (A.K.); (M.T.); (B.S.R.)
| | - Holly Holliday
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington 2052, Australia; (E.H.); (H.H.); (R.L.); (A.K.); (M.T.); (B.S.R.)
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Kensington 2052, Australia
| | - Rebecca Lehmann
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington 2052, Australia; (E.H.); (H.H.); (R.L.); (A.K.); (M.T.); (B.S.R.)
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Kensington 2052, Australia
| | - Aaminah Khan
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington 2052, Australia; (E.H.); (H.H.); (R.L.); (A.K.); (M.T.); (B.S.R.)
| | - Maria Tsoli
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington 2052, Australia; (E.H.); (H.H.); (R.L.); (A.K.); (M.T.); (B.S.R.)
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Kensington 2052, Australia
| | - Benjamin S. Rayner
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington 2052, Australia; (E.H.); (H.H.); (R.L.); (A.K.); (M.T.); (B.S.R.)
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Kensington 2052, Australia
| | - David S. Ziegler
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington 2052, Australia; (E.H.); (H.H.); (R.L.); (A.K.); (M.T.); (B.S.R.)
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Kensington 2052, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick 2031, Australia
- Correspondence: ; Tel.: +61-2-9382-1730; Fax: +61-2-9382-1789
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23
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Bhakat KK, Ray S. The FAcilitates Chromatin Transcription (FACT) complex: Its roles in DNA repair and implications for cancer therapy. DNA Repair (Amst) 2021; 109:103246. [PMID: 34847380 DOI: 10.1016/j.dnarep.2021.103246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/07/2021] [Accepted: 11/03/2021] [Indexed: 12/17/2022]
Abstract
Genomic DNA in the nucleus is wrapped around nucleosomes, a repeating unit of chromatin. The nucleosome, consisting of octamer of core histones, is a barrier for several cellular processes that require access to the naked DNA. The FAcilitates Chromatin Transcription (FACT), a histone chaperone complex, is involved in nucleosome remodeling via eviction or assembly of histones during transcription, replication, and DNA repair. Increasing evidence suggests that FACT plays an important role in multiple DNA repair pathways including transcription-coupled nucleotide excision repair (TC-NER) of UV-induced damage, DNA single- and double-strand breaks (DSBs) repair, and base excision repair (BER) of oxidized or alkylated damaged bases. Further, studies have shown overexpression of FACT in multiple types of cancer and its association with drug resistance and patients' poor prognosis. In this review, we discuss how FACT is accumulated at the damage site and what functions it performs. We describe the known mechanisms by which FACT facilitates repair of different types of DNA damage. Further, we highlight the recent advances in a class of FACT inhibitors, called curaxins, which show promise as a new adjuvant therapy to sensitize multiple types of cancer to chemotherapy and radiation.
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Affiliation(s)
- Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198.
| | - Sutapa Ray
- Department of Pediatric, Division of Hematology/oncology, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198
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24
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Ulianov SV, Velichko A, Magnitov MD, Luzhin A, Golov AK, Ovsyannikova N, Kireev II, Gavrikov A, Mishin A, Garaev AK, Tyakht AV, Gavrilov A, Kantidze OL, Razin SV. Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells. Nucleic Acids Res 2021; 49:10524-10541. [PMID: 33836078 PMCID: PMC8501969 DOI: 10.1093/nar/gkab249] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) contributes to the spatial and functional segregation of molecular processes within the cell nucleus. However, the role played by LLPS in chromatin folding in living cells remains unclear. Here, using stochastic optical reconstruction microscopy (STORM) and Hi-C techniques, we studied the effects of 1,6-hexanediol (1,6-HD)-mediated LLPS disruption/modulation on higher-order chromatin organization in living cells. We found that 1,6-HD treatment caused the enlargement of nucleosome clutches and their more uniform distribution in the nuclear space. At a megabase-scale, chromatin underwent moderate but irreversible perturbations that resulted in the partial mixing of A and B compartments. The removal of 1,6-HD from the culture medium did not allow chromatin to acquire initial configurations, and resulted in more compact repressed chromatin than in untreated cells. 1,6-HD treatment also weakened enhancer-promoter interactions and TAD insulation but did not considerably affect CTCF-dependent loops. Our results suggest that 1,6-HD-sensitive LLPS plays a limited role in chromatin spatial organization by constraining its folding patterns and facilitating compartmentalization at different levels.
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Affiliation(s)
- Sergey V Ulianov
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Artem K Velichko
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Mikhail D Magnitov
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
| | - Artem V Luzhin
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Arkadiy K Golov
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
| | - Natalia Ovsyannikova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Igor I Kireev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology, and Perinatology, 117997 Moscow, Russia
| | - Alexey S Gavrikov
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexander S Mishin
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Azat K Garaev
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
| | - Alexander V Tyakht
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Alexey A Gavrilov
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Omar L Kantidze
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
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25
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Histone chaperone FACT complex inhibitor CBL0137 interferes with DNA damage repair and enhances sensitivity of medulloblastoma to chemotherapy and radiation. Cancer Lett 2021; 520:201-212. [PMID: 34271103 DOI: 10.1016/j.canlet.2021.07.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 06/24/2021] [Accepted: 07/09/2021] [Indexed: 11/21/2022]
Abstract
Medulloblastoma (MB) is a malignant pediatric brain tumor with a poor prognosis. Post-surgical radiation and cisplatin-based chemotherapy have been a mainstay of treatment, which often leads to substantial neurocognitive impairments and morbidity, highlighting the need for a novel therapeutic target to enhance the sensitivity of MB tumors to cytotoxic therapies. We performed a comprehensive study using a cohort of 71 MB patients' samples and pediatric MB cell lines and found that MB tumors have elevated levels of nucleosome remodeling FACT (FAcilitates Chromatin Transcription) complex and DNA repair enzyme AP-endonuclease1 (APE1). FACT interacts with APE1 and facilitates recruitment and acetylation of APE1 to promote repair of radiation and cisplatin-induced DNA damage. Further, levels of FACT and acetylated APE1 both are correlate strongly with MB patients' survival. Targeting FACT complex with CBL0137 inhibits DNA repair and alters expression of a subset of genes, and significantly improves the potency of cisplatin and radiation in vitro and in MB xenograft. Notably, combination of CBL0137 and cisplatin significantly suppressed MB tumor growth in an intracranial orthotopic xenograft model. We conclude that FACT complex promotes chemo-radiation resistance in MB, and FACT inhibitor CBL0137 can be used as a chemo-radiation sensitizer to augment treatment efficacy and reduce therapy-related toxicity in high-risk pediatric patients.
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26
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Andronikou C, Rottenberg S. Studying PAR-Dependent Chromatin Remodeling to Tackle PARPi Resistance. Trends Mol Med 2021; 27:630-642. [PMID: 34030964 DOI: 10.1016/j.molmed.2021.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022]
Abstract
Histone eviction and chromatin relaxation are important processes for efficient DNA repair. Poly(ADP) ribose (PAR) polymerase 1 (PARP1) is a key mediator of this process, and disruption of PARP1 activity has a direct impact on chromatin structure. PARP inhibitors (PARPis) have been established as a treatment for BRCA1- or BRCA2-deficient tumors. Unfortunately, PARPi resistance occurs in many patients and the underlying mechanisms are not fully understood. In particular, it remains unclear how chromatin remodelers and histone chaperones compensate for the loss of the PARylation signal. In this Opinion article, we summarize currently known mechanisms of PARPi resistance. We discuss how the study of PARP1-mediated chromatin remodeling may help in further understanding PARPi resistance and finding new therapeutic approaches to overcome it.
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Affiliation(s)
- Christina Andronikou
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sven Rottenberg
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Bern Center for Precision Medicine, University of Bern, Bern, Switzerland.
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27
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Song H, Zeng J, Lele S, LaGrange CA, Bhakat KK. APE1 and SSRP1 is overexpressed in muscle invasive bladder cancer and associated with poor survival. Heliyon 2021; 7:e06756. [PMID: 33948507 PMCID: PMC8080038 DOI: 10.1016/j.heliyon.2021.e06756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/18/2021] [Accepted: 04/06/2021] [Indexed: 12/22/2022] Open
Abstract
Background Human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) plays a critical role in DNA base excision repair (BER) pathway and has been reported to be overexpressed in multiple cancers. Previously, we have shown that histone chaperone FACT complex (Facilitates Chromatin Transcription, a heterodimer of SSRP1 and SPT16 proteins) facilitates the chromatin access and DNA repair function of APE1, and their expression levels are correlated with promoting drug resistance in cancer. FACT inhibitor has been introduced in phase I and II clinical trials for chemosensitization of advanced solid cancers. However, the expression profile and prognostic significance of APE1 and FACT complex in bladder cancer remains largely unknown. Methods Retrospectively, 69 bladder cancer samples were retrieved and submitted for immunohistochemical staining of APE1 and SSRP1. Expression profile including cytoplasmic and nuclear staining of APE1 and expression level of SSRP1 was examined and semi-quantified to render a H-score. The prognostic significance of APE1 and SSRP1 was evaluated by Kaplan-Meier survival analysis in our cohort and R2 database. Results APE1 expression is elevated in bladder cancer compared to normal adjacent tissues. Compared with low grade tumors, high grade tumors show a shift in the staining pattern including higher intensity and positive cytoplasmic staining. Carcinoma in situ has a similar staining pattern to high grade tumors. APE1 and SSRP1 staining intensity increases as tumor progresses with stage. There is a correlation between APE1 and SSRP1 staining in invasive bladder cancer (Spearman r = 0.5466, p < 0.0001). The increased expression of APE1 and SSRP1 is associated with poor survival in Kaplan-Meier analysis in our cohort and in R2-TCGA bladder cancer database. Conclusions The expression levels of APE1 and SSRP1 are significantly elevated in bladder cancer as compared to normal adjacent tissues. APE1 correlates with SSRP1 expression in high grade tumors. Overexpression of APE1 and SSRP1 is associated with poor survival in bladder cancer. This suggests the usage of FACT inhibitor curaxins in muscle invasive bladder cancer to target FACT complex and APE1 to improve chemosensitization after further validation.
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Affiliation(s)
- Heyu Song
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Jiping Zeng
- College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Urology, University of Arizona College of Medicine, Tucson, AZ, United States
| | - Subodh Lele
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Chad A LaGrange
- Division of Urologic Surgery, Department of Surgery, University of Nebraska Medical Center, Omaha, NE, United States.,Fred & Pamela Buffett Cancer Center, Omaha, NE, United States
| | - Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States.,Fred & Pamela Buffett Cancer Center, Omaha, NE, United States
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28
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Mo J, Liu F, Sun X, Huang H, Tan K, Zhao X, Li R, Jiang W, Sui Y, Chen X, Shen K, Zhang L, Ma J, Zhao K, Tang Y. Inhibition of the FACT Complex Targets Aberrant Hedgehog Signaling and Overcomes Resistance to Smoothened Antagonists. Cancer Res 2021; 81:3105-3120. [PMID: 33853831 DOI: 10.1158/0008-5472.can-20-3186] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/05/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022]
Abstract
Hedgehog signaling is aberrantly activated in hematologic malignancies and solid tumors, and targeting it is a promising therapeutic strategy against these cancers. Resistance to clinically available hedgehog-targeted Smoothened inhibitor (SMOi) drugs has become a critical issue in hedgehog-driven cancer treatment. Our previous studies identified inhibition of BET and CDK7 as two epigenetic/transcriptional-targeted therapeutic strategies for overcoming SMOi resistance, providing a promising direction for anti-hedgehog drug development. To uncover additional strategies for inhibiting aberrant hedgehog activity, here we performed CRISPR-Cas9 screening with an single-guide RNA library targeting epigenetic and transcriptional modulators in hedgehog-driven medulloblastoma cells, combined with tumor dataset analyses. Structure specific recognition protein 1 (SSRP1), a subunit of facilitates chromatin transcription (FACT) complex, was identified as a hedgehog-induced essential oncogene and therapeutic target in hedgehog-driven cancer. The FACT inhibitor CBL0137, which has entered clinical trials for cancer, effectively suppressed in vitro and in vivo growth of multiple SMOi-responsive and SMOi-resistant hedgehog-driven cancer models. Mechanistically, CBL0137 exerted anti-hedgehog activity by targeting transcription of GLI1 and GLI2, which are core transcription factors of the hedgehog pathway. SSRP1 bound the promoter regions of GLI1 and GLI2, while CBL0137 treatment substantially disrupted these interactions. Moreover, CBL0137 synergized with BET or CDK7 inhibitors to antagonize aberrant hedgehog pathway and growth of hedgehog-driven cancer models. Taken together, these results identify FACT inhibition as a promising epigenetic/transcriptional-targeted therapeutic strategy for treating hedgehog-driven cancers and overcoming SMOi resistance. SIGNIFICANCE: This study identifies FACT inhibition as an anti-hedgehog therapeutic strategy for overcoming resistance to Smoothened inhibitors and provides preclinical support for initiating clinical trials of FACT-targeted drug CBL0137 against hedgehog-driven cancers.
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Affiliation(s)
- Jialin Mo
- Research Center of Translational Medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Fang Liu
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Xi Sun
- Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Hongting Huang
- Department of Hepatic Surgery and Liver Transplantation Center, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Kezhe Tan
- Research Center of Translational Medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Xiaojing Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, P.R. China
| | - Rui Li
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Wenyan Jiang
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Yi Sui
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Xiaosong Chen
- Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Kunwei Shen
- Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, P.R. China
| | - Jie Ma
- Department of Pediatric Neurosurgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
| | - Kewen Zhao
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
| | - Yujie Tang
- Research Center of Translational Medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
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29
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Abstract
Cancer is a complex disease characterized by loss of cellular homeostasis through genetic and epigenetic alterations. Emerging evidence highlights a role for histone variants and their dedicated chaperones in cancer initiation and progression. Histone variants are involved in processes as diverse as maintenance of genome integrity, nuclear architecture and cell identity. On a molecular level, histone variants add a layer of complexity to the dynamic regulation of transcription, DNA replication and repair, and mitotic chromosome segregation. Because these functions are critical to ensure normal proliferation and maintenance of cellular fate, cancer cells are defined by their capacity to subvert them. Hijacking histone variants and their chaperones is emerging as a common means to disrupt homeostasis across a wide range of cancers, particularly solid tumours. Here we discuss histone variants and histone chaperones as tumour-promoting or tumour-suppressive players in the pathogenesis of cancer.
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Affiliation(s)
| | - Dan Filipescu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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30
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Ehteda A, Simon S, Franshaw L, Giorgi FM, Liu J, Joshi S, Rouaen JRC, Pang CNI, Pandher R, Mayoh C, Tang Y, Khan A, Ung C, Tolhurst O, Kankean A, Hayden E, Lehmann R, Shen S, Gopalakrishnan A, Trebilcock P, Gurova K, Gudkov AV, Norris MD, Haber M, Vittorio O, Tsoli M, Ziegler DS. Dual targeting of the epigenome via FACT complex and histone deacetylase is a potent treatment strategy for DIPG. Cell Rep 2021; 35:108994. [PMID: 33852836 DOI: 10.1016/j.celrep.2021.108994] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/24/2020] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is an aggressive and incurable childhood brain tumor for which new treatments are needed. CBL0137 is an anti-cancer compound developed from quinacrine that targets facilitates chromatin transcription (FACT), a chromatin remodeling complex involved in transcription, replication, and DNA repair. We show that CBL0137 displays profound cytotoxic activity against a panel of patient-derived DIPG cultures by restoring tumor suppressor TP53 and Rb activity. Moreover, in an orthotopic model of DIPG, treatment with CBL0137 significantly extends animal survival. The FACT subunit SPT16 is found to directly interact with H3.3K27M, and treatment with CBL0137 restores both histone H3 acetylation and trimethylation. Combined treatment of CBL0137 with the histone deacetylase inhibitor panobinostat leads to inhibition of the Rb/E2F1 pathway and induction of apoptosis. The combination of CBL0137 and panobinostat significantly prolongs the survival of mice bearing DIPG orthografts, suggesting a potential treatment strategy for DIPG.
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Affiliation(s)
- Anahid Ehteda
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Sandy Simon
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Laura Franshaw
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Jie Liu
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Swapna Joshi
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Jourdin R C Rouaen
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Chi Nam Ignatius Pang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ruby Pandher
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Yujie Tang
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Aaminah Khan
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Caitlin Ung
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Ornella Tolhurst
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Anne Kankean
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Elisha Hayden
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Rebecca Lehmann
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Sylvie Shen
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Anjana Gopalakrishnan
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Peter Trebilcock
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Andrei V Gudkov
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Murray D Norris
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia; Centre for Childhood Cancer Research, University of New South Wales, Sydney, NSW, Australia
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Orazio Vittorio
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Maria Tsoli
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia.
| | - David S Ziegler
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia; Kid's Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia.
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31
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Proteasomal Regulation of Mammalian SPT16 in Controlling Transcription. Mol Cell Biol 2021; 41:MCB.00452-20. [PMID: 33526453 DOI: 10.1128/mcb.00452-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
FACT (facilitates chromatin transcription), an essential and evolutionarily conserved heterodimer from yeast to humans, controls transcription and is found to be upregulated in various cancers. However, the basis for such upregulation is not clearly understood. Our recent results deciphering a new ubiquitin-proteasome system regulation of the FACT subunit SPT16 in orchestrating transcription in yeast hint at the involvement of the proteasome in controlling FACT in humans, with a link to cancer. To test this, we carried out experiments in human embryonic kidney (HEK293) cells, which revealed that human SPT16 undergoes ubiquitylation and that its abundance is increased following inhibition of the proteolytic activity of the proteasome, thus implying proteasomal regulation of human SPT16. Furthermore, we find that the increased abundance/expression of SPT16 in HEK293 cells alters the transcription of genes, including ones associated with cancer, and that the proteasomal degradation of SPT16 is impaired in kidney cancer (Caki-2) cells to upregulate SPT16. Like human SPT16, murine SPT16 in C2C12 cells also undergoes ubiquitylation and proteasomal degradation to regulate transcription. Collectively, our results reveal a proteasomal regulation of mammalian SPT16, with physiological relevance in controlling transcription, and implicate such proteasomal control in the upregulation of SPT16 in cancer.
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32
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Nayak A, Dutta M, Roychowdhury A. Emerging oncogene ATAD2: Signaling cascades and therapeutic initiatives. Life Sci 2021; 276:119322. [PMID: 33711386 DOI: 10.1016/j.lfs.2021.119322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/12/2021] [Accepted: 02/27/2021] [Indexed: 12/11/2022]
Abstract
ATAD2 is a promising oncoprotein with tumor-promoting functions in many cancers. It is a valid cancer drug-target and a potential cancer-biomarker for multiple malignancies. As a cancer/testis antigen (CTA), ATAD2 could also be a probable candidate for immunotherapy. It is a unique CTA that belongs to both AAA+ ATPase and bromodomain family proteins. Since 2007, several research groups have been reported on the pleiotropic oncogenic functions of ATAD2 in diverse signaling pathways, including Rb/E2F-cMyc pathway, steroid hormone signaling pathway, p53 and p38-MAPK-mediated apoptotic pathway, AKT pathway, hedgehog signaling pathway, HIF1α signaling pathway, and Epithelial to Mesenchymal Transition (EMT) pathway in various cancers. In all these pathways, ATAD2 participates in chromatin dynamics, DNA replication, and gene transcription, demonstrating its role as an epigenetic reader and transcription factor or coactivator to promote tumorigenesis. However, despite the progress, an overall mechanism of ATAD2-mediated oncogenesis in diverse origin is elusive. In this review, we summarize the accumulated evidence to envision the overall ATAD2 signaling networks during carcinogenesis and highlight the area where missing links await further research. Besides, the structure-function aspect of ATAD2 is also discussed. Since the efforts have already been initiated to explore targeted drug molecules and RNA-based therapeutic alternatives against ATAD2, their potency and prospects have been elucidated. Together, we believe this is a well-rounded review on ATAD2, facilitating a new drift in ATAD2 research, essential for its clinical implication as a biomarker and/or cancer drug-target.
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Affiliation(s)
- Aditi Nayak
- Biochemistry and Cell Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha 752050, India
| | - Madhuri Dutta
- Biochemistry and Cell Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha 752050, India
| | - Anasuya Roychowdhury
- Biochemistry and Cell Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha 752050, India.
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33
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Das B, Kundu CN. Anti-Cancer Stem Cells Potentiality of an Anti-Malarial Agent Quinacrine: An Old Wine in a New Bottle. Anticancer Agents Med Chem 2021; 21:416-427. [PMID: 32698746 DOI: 10.2174/1871520620666200721123046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/23/2020] [Accepted: 05/24/2020] [Indexed: 11/22/2022]
Abstract
Quinacrine (QC) is a tricyclic compound and a derivative of 9-aminoacridine. It has been widely used to treat malaria and other parasitic diseases since the last century. Interestingly, studies have revealed that it also displays anti-cancer activities. Here, we have discussed the anti-cancer mechanism of QC along with its potentiality to specifically target cancer stem cells. The anti-cancer action of this drug includes DNA intercalation, inhibition of DNA repair mechanism, prevention of cellular growth, cell cycle arrest, inhibition of DNA and RNA polymerase activity, induction of autophagy, promotion of apoptosis, deregulation of cell signaling in cancer cells and cancer stem cells, inhibition of metastasis and angiogenesis. In addition, we have also emphasized on the synergistic effect of this drug with other potent chemotherapeutic agents and mentioned its different applications in anti-cancer therapy.
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Affiliation(s)
- Biswajit Das
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha 751024, India
| | - Chanakya N Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha 751024, India
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34
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Positioning of nucleosomes containing γ-H2AX precedes active DNA demethylation and transcription initiation. Nat Commun 2021; 12:1072. [PMID: 33594057 PMCID: PMC7886895 DOI: 10.1038/s41467-021-21227-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 01/12/2021] [Indexed: 01/09/2023] Open
Abstract
In addition to nucleosomes, chromatin contains non-histone chromatin-associated proteins, of which the high-mobility group proteins are the most abundant. Chromatin-mediated regulation of transcription involves DNA methylation and histone modifications. However, the order of events and the precise function of high-mobility group proteins during transcription initiation remain unclear. Here we show that high-mobility group AT-hook 2 protein (HMGA2) induces DNA nicks at the transcription start site, which are required by the histone chaperone FACT complex to incorporate nucleosomes containing the histone variant H2A.X. Further, phosphorylation of H2A.X at S139 (γ-H2AX) is required for repair-mediated DNA demethylation and transcription activation. The relevance of these findings is demonstrated within the context of TGFB1 signaling and idiopathic pulmonary fibrosis, suggesting therapies against this lethal disease. Our data support the concept that chromatin opening during transcriptional initiation involves intermediates with DNA breaks that subsequently require DNA repair mechanisms to ensure genome integrity. The order of DNA methylation and histone modifications during transcription remained unclear. Here the authors show that HMGA2 induces DNA nicks at TGFB1-responsive genes, promoting nucleosome incorporation containing γ-H2AX, which is required for repair-mediated DNA demethylation and transcription.
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35
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Wang P, Yang W, Zhao S, Nashun B. Regulation of chromatin structure and function: insights into the histone chaperone FACT. Cell Cycle 2021; 20:465-479. [PMID: 33590780 DOI: 10.1080/15384101.2021.1881726] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In eukaryotic cells, changes in chromatin accessibility are necessary for chromatin to maintain its highly dynamic nature at different times during the cell cycle. Histone chaperones interact with histones and regulate chromatin dynamics. Facilitates chromatin transcription (FACT) is an important histone chaperone that plays crucial roles during various cellular processes. Here, we analyze the structural characteristics of FACT, discuss how FACT regulates nucleosome/chromatin reorganization and summarize possible functions of FACT in transcription, replication, and DNA repair. The possible involvement of FACT in cell fate determination is also discussed.Abbreviations: FACT: facilitates chromatin transcription, Spt16: suppressor of Ty16, SSRP1: structure-specific recognition protein-1, NTD: N-terminal domain, DD: dimerization domain, MD: middle domain, CTD: C-terminus domain, IDD: internal intrinsically disordered domain, HMG: high mobility group, CID: C-terminal intrinsically disordered domain, Nhp6: non-histone chromosomal protein 6, RNAPII: RNA polymerase II, CK2: casein kinase 2, AID: acidic inner disorder, PIC: pre-initiation complex, IR: ionizing radiation, DDSB: DNA double-strand break, PARlation: poly ADP-ribosylation, BER: base-excision repair, UVSSA: UV-stimulated scaffold protein A, HR: homologous recombination, CAF-1: chromatin assembly factor 1, Asf1: anti-silencing factor 1, Rtt106: regulator of Ty1 transposition protein 106, H3K56ac: H3K56 acetylation, KD: knock down, SETD2: SET domain containing 2, H3K36me3: trimethylation of lysine36 in histone H3, H2Bub: H2B ubiquitination, iPSCs: induced pluripotent stem cells, ESC: embryonic stem cell, H3K4me3: trimethylation of lysine 4 on histone H3 protein subunit, CHD1: chromodomain protein.
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Affiliation(s)
- Peijun Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Wanting Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Shuxin Zhao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Buhe Nashun
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
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36
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Lu K, Liu C, Liu Y, Luo A, Chen J, Lei Z, Kong J, Xiao X, Zhang S, Wang YZ, Ma L, Dou SX, Wang PY, Li M, Li G, Li W, Chen P. Curaxin-Induced DNA Topology Alterations Trigger the Distinct Binding Response of CTCF and FACT at the Single-Molecule Level. Biochemistry 2021; 60:494-499. [PMID: 33570402 DOI: 10.1021/acs.biochem.1c00014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The candidate anticancer drug curaxins can insert into DNA base pairs and efficiently inhibit the growth of various cancers. However, how curaxins alter the genomic DNA structure and affect the DNA binding property of key proteins remains to be clarified. Here, we first showed that curaxin CBL0137 strongly stabilizes the interaction between the double strands of DNA and reduces DNA bending and twist rigidity simultaneously, by single-molecule magnetic tweezers. More importantly, we found that CBL0137 greatly impairs the binding of CTCF but facilitates trapping FACT on DNA. We revealed that CBL0137 clamps the DNA double helix that may induce a huge barrier for DNA unzipping during replication and transcription and causes the distinct binding response of CTCF and FACT on DNA. Our work provides a novel mechanical insight into CBL0137's anticancer mechanisms at the nucleic acid level.
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Affiliation(s)
- Ke Lu
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yinuo Liu
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Anfeng Luo
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Jun Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Zhichao Lei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, and iChEM, Xiamen University, Xiamen 361005, China
| | - Jingwei Kong
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Xiao
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuming Zhang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Yi-Zhou Wang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Lu Ma
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuo-Xing Dou
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Ye Wang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Ming Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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37
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Amjadi-Moheb F, Paniri A, Akhavan-Niaki H. Insights into the Links between MYC and 3D Chromatin Structure and Epigenetics Regulation: Implications for Cancer Therapy. Cancer Res 2021; 81:1925-1936. [PMID: 33472888 DOI: 10.1158/0008-5472.can-20-3613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/21/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
MYC is embedded in the transcriptional oasis of the 8q24 gene desert. A plethora of genomic elements has roles in MYC aberrant expression in cancer development by interacting with transcription factors and epigenetics regulators as well as altering the structure of chromatin at the MYC locus and tissue-specific long-range enhancer-promoter contacts. Furthermore, MYC is a master regulator of several human cancers by modulating the transcription of numerous cancer-related genes through epigenetic mechanisms. This review provides a comprehensive overview of the three-dimensional genomic organization around MYC and the role of epigenetic machinery in transcription and function of MYC as well as discusses various epigenetic-targeted therapeutic strategies in MYC-driven cancers.
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Affiliation(s)
- Fatemeh Amjadi-Moheb
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Alireza Paniri
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Haleh Akhavan-Niaki
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
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38
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Falbo L, Costanzo V. Epigenetic regulation of replication origin assembly: A role for histone H1 and chromatin remodeling factors. Bioessays 2020; 43:e2000181. [PMID: 33165968 DOI: 10.1002/bies.202000181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 12/18/2022]
Abstract
During early embryonic development in several metazoans, accurate DNA replication is ensured by high number of replication origins. This guarantees rapid genome duplication coordinated with fast cell divisions. In Xenopus laevis embryos this program switches to one with a lower number of origins at a developmental stage known as mid-blastula transition (MBT) when cell cycle length increases and gene transcription starts. Consistent with this regulation, somatic nuclei replicate poorly when transferred to eggs, suggesting the existence of an epigenetic memory suppressing replication assembly origins at all available sites. Recently, it was shown that histone H1 imposes a non-permissive chromatin configuration preventing replication origin assembly on somatic nuclei. This somatic state can be erased by SSRP1, a subunit of the FACT complex. Here, we further develop the hypothesis that this novel form of epigenetic memory might impact on different areas of vertebrate biology going from nuclear reprogramming to cancer development.
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Affiliation(s)
- Lucia Falbo
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, Milan, 20139, Italy
| | - Vincenzo Costanzo
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, Milan, 20139, Italy.,Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
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39
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Pavlova II, Tsvetkov VB, Isaakova EA, Severov VV, Khomyakova EA, Lacis IA, Lazarev VN, Lagarkova MA, Pozmogova GE, Varizhuk AM. Transcription-facilitating histone chaperons interact with genomic and synthetic G4 structures. Int J Biol Macromol 2020; 160:1144-1157. [PMID: 32454109 DOI: 10.1016/j.ijbiomac.2020.05.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/11/2020] [Accepted: 05/21/2020] [Indexed: 01/26/2023]
Abstract
Affinity for G-quadruplex (G4) structures may be a common feature of transcription-facilitating histone chaperons (HCs). This assumption is based on previous unmatched studies of HCs FACT, nucleolin (NCL), BRD3, and ATRX. We verified this assumption and considered its implications for the therapeutic applications of synthetic (exogenous) G4s and the biological significance of genomic G4s. First, we questioned whether exogenous G4s that recognize cell-surface NCL and could trap other HCs in the nucleus are usable as anticancer agents. We performed in vitro binding assays and selected leading multi-targeted G4s. They exhibited minor effects on cell viability. The presumed NCL-regulated intracellular transport of G4s was inefficient or insufficient for tumor-specific G4 delivery. Next, to clarify whether G4s in the human genome could recruit HCs, we compared available HC ChIP-seq data with G4-seq/G4-ChIP-seq data. Several G4s, including the well-known c-Myc quadruplex structure, were found to be colocalized with HC occupancy sites in cancer cell lines. As evidenced by our molecular modeling data, c-Myc G4 might interfere with the HC function of BRD3 but is unlikely to prevent the BRD3-driven assembly of the chromatin remodeling complex. The c-Myc case illustrates the intricate role of genomic G4s in chromatin remodeling, nucleosome remodeling, and transcription.
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Affiliation(s)
- Iulia I Pavlova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Vladimir B Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Computational Oncology Group, I.M. Sechenov First Moscow State Medical University, Trubetskaya str, 8/2, Moscow 119146, Russia; A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky prospect str. 29, Moscow 119991, Russia
| | - Ekaterina A Isaakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Vyacheslav V Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Ekaterina A Khomyakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Ivan A Lacis
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Vassilii N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Maria A Lagarkova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Galina E Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia; Engelhardt Institute of Molecular Biology, Vavilova str. 32, Moscow 119991, Russia.
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40
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Yang L, Wang X, Jiao X, Tian B, Zhang M, Zhou C, Wang R, Chen H, Wang B, Li J, Liu J, Zhang G, Liu P. Suppressor of Ty 16 promotes lung cancer malignancy and is negatively regulated by miR-1227-5p. Cancer Sci 2020; 111:4075-4087. [PMID: 32860308 PMCID: PMC7648015 DOI: 10.1111/cas.14627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 07/03/2020] [Accepted: 07/27/2020] [Indexed: 01/01/2023] Open
Abstract
Suppressor of Ty 16 (Spt16) is a component of the facilitates chromatin transcription (FACT) complex, which is a histone chaperone and involved in gene transcription, DNA replication, and DNA repair. Previous studies showed that FACT is highly expressed in cancer, and cancer cells are more reliant on FACT than normal cells. However, the relationship between Spt16 and lung cancer remains unclear. In this study, we explored the functions of Spt16 in lung cancer cells. The effects of Spt16 on lung cancer cell proliferation, cell cycle progression, apoptosis, migration, and invasion were examined. We found that knockdown of Spt16 led to obvious decreases of both Rb and MCM7, and further activated the DNA damage response (DDR) pathway. In addition, a novel micro‐RNA, miR‐1227‐5p, directly targeted the 3′‐UTR of Spt16 and regulated the mRNA levels of Spt16. Furthermore, we found that CBL0137, the functional inhibitor of FACT, showed similar effects as loss of Spt16. Together, our data indicated that Spt16 is likely to be an essential regulator for lung cancer malignancy and is negatively regulated by miR‐1227‐5p.
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Affiliation(s)
- Lu Yang
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xing Wang
- Department of Pathology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Xinyan Jiao
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bixia Tian
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Miao Zhang
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Can Zhou
- Department of Breast Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ruiqi Wang
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - He Chen
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bo Wang
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Juan Li
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jie Liu
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Guanjun Zhang
- Department of Pathology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Peijun Liu
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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41
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Azevedo H, Pessoa GC, de Luna Vitorino FN, Nsengimana J, Newton-Bishop J, Reis EM, da Cunha JPC, Jasiulionis MG. Gene co-expression and histone modification signatures are associated with melanoma progression, epithelial-to-mesenchymal transition, and metastasis. Clin Epigenetics 2020; 12:127. [PMID: 32831131 PMCID: PMC7444266 DOI: 10.1186/s13148-020-00910-9] [Citation(s) in RCA: 5] [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: 06/09/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND We have previously developed a murine cellular system that models the transformation from melanocytes to metastatic melanoma cells. This model was established by cycles of anchorage impediment of melanocytes and consists of four cell lines: differentiated melanocytes (melan-a), pre-malignant melanocytes (4C), malignant (4C11-), and metastasis-prone (4C11+) melanoma cells. Here, we searched for transcriptional and epigenetic signatures associated with melanoma progression and metastasis by performing a gene co-expression analysis of transcriptome data and a mass-spectrometry-based profiling of histone modifications in this model. RESULTS Eighteen modules of co-expressed genes were identified, and some of them were associated with melanoma progression, epithelial-to-mesenchymal transition (EMT), and metastasis. The genes in these modules participate in biological processes like focal adhesion, cell migration, extracellular matrix organization, endocytosis, cell cycle, DNA repair, protein ubiquitination, and autophagy. Modules and hub signatures related to EMT and metastasis (turquoise, green yellow, and yellow) were significantly enriched in genes associated to patient survival in two independent melanoma cohorts (TCGA and Leeds), suggesting they could be sources of novel prognostic biomarkers. Clusters of histone modifications were also linked to melanoma progression, EMT, and metastasis. Reduced levels of H4K5ac and H4K8ac marks were seen in the pre-malignant and tumorigenic cell lines, whereas the methylation patterns of H3K4, H3K56, and H4K20 were related to EMT. Moreover, the metastatic 4C11+ cell line showed higher H3K9me2 and H3K36me3 methylation, lower H3K18me1, H3K23me1, H3K79me2, and H3K36me2 marks and, in agreement, downregulation of the H3K36me2 methyltransferase Nsd1. CONCLUSIONS We uncovered transcriptional and histone modification signatures that may be molecular events driving melanoma progression and metastasis, which can aid in the identification of novel prognostic genes and drug targets for treating the disease.
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Affiliation(s)
- Hátylas Azevedo
- Division of Urology, Department of Surgery, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Guilherme Cavalcante Pessoa
- Department of Pharmacology, Universidade Federal de São Paulo (UNIFESP), Rua Pedro de Toledo 669 5 andar, Vila Clementino, São Paulo, SP, 04039032, Brazil
| | | | - Jérémie Nsengimana
- Institute of Medical Research at St James's, University of Leeds School of Medicine, Leeds, UK
- Biostatistics Research Group, Population Health Sciences Institute, Newcastle University, Newcastle, United Kingdom
| | - Julia Newton-Bishop
- Institute of Medical Research at St James's, University of Leeds School of Medicine, Leeds, UK
| | - Eduardo Moraes Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Júlia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, Brazil
| | - Miriam Galvonas Jasiulionis
- Department of Pharmacology, Universidade Federal de São Paulo (UNIFESP), Rua Pedro de Toledo 669 5 andar, Vila Clementino, São Paulo, SP, 04039032, Brazil.
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42
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Tettey TT, Gao X, Shao W, Li H, Story BA, Chitsazan AD, Glaser RL, Goode ZH, Seidel CW, Conaway RC, Zeitlinger J, Blanchette M, Conaway JW. A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing. Cell Rep 2020; 27:3770-3779.e7. [PMID: 31242411 DOI: 10.1016/j.celrep.2019.05.099] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 04/22/2019] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
FACT (facilitates chromatin transcription) is an evolutionarily conserved histone chaperone that was initially identified as an activity capable of promoting RNA polymerase II (Pol II) transcription through nucleosomes in vitro. In this report, we describe a global analysis of FACT function in Pol II transcription in Drosophila. We present evidence that loss of FACT has a dramatic impact on Pol II elongation-coupled processes including histone H3 lysine 4 (H3K4) and H3K36 methylation, consistent with a role for FACT in coordinating histone modification and chromatin architecture during Pol II transcription. Importantly, we identify a role for FACT in the maintenance of promoter-proximal Pol II pausing, a key step in transcription activation in higher eukaryotes. These findings bring to light a broader role for FACT in the regulation of Pol II transcription.
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Affiliation(s)
- Theophilus T Tettey
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; The Open University, Walton Hall, Milton Keynes, Buckinghamshire MK7 6AA, UK
| | - Xin Gao
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Wanqing Shao
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Benjamin A Story
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Alex D Chitsazan
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Robert L Glaser
- Wadsworth Center, New York State Department of Health, PO Box 509, Albany, NY 12201, USA
| | - Zach H Goode
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Christopher W Seidel
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Marco Blanchette
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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43
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Histone chaperone FACT is essential to overcome replication stress in mammalian cells. Oncogene 2020; 39:5124-5137. [PMID: 32533099 PMCID: PMC7343669 DOI: 10.1038/s41388-020-1346-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 05/11/2020] [Accepted: 06/01/2020] [Indexed: 12/15/2022]
Abstract
The histone chaperone FACT is upregulated during mammary tumorigenesis and necessary for the viability and growth of breast tumor cells. We established that only proliferating tumor cells are sensitive to FACT knockdown, suggesting that FACT functions during DNA replication in tumor cells but not in normal cells. We hypothesized that the basal level of replication stress defines the FACT dependence of cells. Using genetic and chemical tools, we demonstrated that FACT is needed to overcome replication stress. In the absence of FACT during replication stress, the MCM2-7 helicase dissociates from chromatin, resulting in the absence of ssDNA accumulation, RPA binding, and activation of the ATR/CHK1 checkpoint response. Without this response, stalled replication forks are not stabilized, and new origin firing cannot be prevented, leading to the accumulation of DNA damage and cell death. Thus, we propose a novel role for FACT as a factor preventing helicase dissociation from chromatin during replication stress.
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44
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Sandlesh P, Safina A, Goswami I, Prendergast L, Rosario S, Gomez EC, Wang J, Gurova KV. Prevention of Chromatin Destabilization by FACT Is Crucial for Malignant Transformation. iScience 2020; 23:101177. [PMID: 32498018 PMCID: PMC7267732 DOI: 10.1016/j.isci.2020.101177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 03/23/2020] [Accepted: 05/14/2020] [Indexed: 01/09/2023] Open
Abstract
Histone chaperone FACT is commonly expressed and essential for the viability of transformed but not normal cells, and its expression levels correlate with poor prognosis in patients with cancer. FACT binds several components of nucleosomes and has been viewed as a factor destabilizing nucleosomes to facilitate RNA polymerase passage. To connect FACT's role in transcription with the viability of tumor cells, we analyzed genome-wide FACT binding to chromatin in conjunction with transcription in mouse and human cells with different degrees of FACT dependence. Genomic distribution and density of FACT correlated with the intensity of transcription. However, FACT knockout or knockdown was unexpectedly accompanied by the elevation, rather than suppression, of transcription and with the destabilization of chromatin in transformed, but not normal cells. These data suggest that FACT stabilizes and reassembles nucleosomes disturbed by transcription. This function is vital for tumor cells because malignant transformation is accompanied by chromatin destabilization. FACT is essential for viability of the tumor, but not for normal cells FACT level depends on transcription, but transcription does not depend on FACT FACT preserves nucleosomes during transcription to maintain chromatin integrity FACT maintains chromatin in destabilized state during malignant transformation
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Affiliation(s)
- Poorva Sandlesh
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Alfiya Safina
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Imon Goswami
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Laura Prendergast
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Spenser Rosario
- Department of Cancer Genetics, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Eduardo C Gomez
- Department of Bioinformatics, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Jianmin Wang
- Department of Bioinformatics, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA.
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45
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Gao H, Zhang F, Liang S, Zhang Q, Lyu M, Qian L, Liu W, Ge W, Chen C, Yi X, Zhu J, Lu C, Sun P, Liu K, Zhu Y, Guo T. Accelerated Lysis and Proteolytic Digestion of Biopsy-Level Fresh-Frozen and FFPE Tissue Samples Using Pressure Cycling Technology. J Proteome Res 2020; 19:1982-1990. [PMID: 32182071 DOI: 10.1021/acs.jproteome.9b00790] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Pressure cycling technology (PCT)-assisted tissue lysis and digestion have facilitated reproducible and high-throughput proteomic studies of both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tissue of biopsy scale for biomarker discovery. Here, we present an improved PCT method accelerating the conventional procedures by about two-fold without sacrificing peptide yield, digestion efficiency, peptide, and protein identification. The time required for processing 16 tissue samples from tissues to peptides is reduced from about 6 to about 3 h. We analyzed peptides prepared from FFPE hepatocellular carcinoma (HCC) tissue samples by the accelerated PCT method using multiple MS acquisition methods, including short-gradient SWATH-MS, PulseDIA-MS, and 10-plex TMT-based shotgun MS. The data showed that up to 8541 protein groups could be reliably quantified from the thus prepared peptide samples. We applied the accelerated sample preparation method to 25 pairs (tumorous and matched benign) of HCC samples followed by a single-shot, 15 min gradient SWATH-MS analysis. An average of 18 453 peptides from 2822 proteins were quantified in at least 20% samples in this cohort, while 1817 proteins were quantified in at least 50% samples. The data not only identified the previously known dysregulated proteins such as MCM7, MAPRE1, and SSRP1 but also discovered promising novel protein markers, including DRAP1 and PRMT5. In summary, we present an accelerated PCT protocol that effectively doubles the throughput of PCT-assisted sample preparation of biopsy-level FF and FFPE samples without compromising protein digestion efficiency, peptide yield, and protein identification.
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Affiliation(s)
- Huanhuan Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Fangfei Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Shuang Liang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Qiushi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Mengge Lyu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Liujia Qian
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Wei Liu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 200335, Liaoning, China
| | - Weigang Ge
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | | | - Xiao Yi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Jiang Zhu
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Cong Lu
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Ping Sun
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Kexin Liu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 200335, Liaoning, China
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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46
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SSRP1-mediated histone H1 eviction promotes replication origin assembly and accelerated development. Nat Commun 2020; 11:1345. [PMID: 32165637 PMCID: PMC7067836 DOI: 10.1038/s41467-020-15180-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 02/24/2020] [Indexed: 12/17/2022] Open
Abstract
In several metazoans, the number of active replication origins in embryonic nuclei is higher than in somatic ones, ensuring rapid genome duplication during synchronous embryonic cell divisions. High replication origin density can be restored by somatic nuclear reprogramming. However, mechanisms underlying high replication origin density formation coupled to rapid cell cycles are poorly understood. Here, using Xenopus laevis, we show that SSRP1 stimulates replication origin assembly on somatic chromatin by promoting eviction of histone H1 through its N-terminal domain. Histone H1 removal derepresses ORC and MCM chromatin binding, allowing efficient replication origin assembly. SSRP1 protein decays at mid-blastula transition (MBT) when asynchronous somatic cell cycles start. Increasing levels of SSRP1 delay MBT and, surprisingly, accelerate post-MBT cell cycle speed and embryo development. These findings identify a major epigenetic mechanism regulating DNA replication and directly linking replication origin assembly, cell cycle duration and embryo development in vertebrates. During embryonic development, it is vital to maintain rapid genome duplication. Here, the authors shed light on the mechanism by revealing that SSRP1 stimulates replication origin assembly on somatic nuclei in Xenopus laevis egg extract by promoting histone H1 eviction from somatic chromatin.
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47
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The 3D Genome as a Target for Anticancer Therapy. Trends Mol Med 2020; 26:141-149. [PMID: 31679987 PMCID: PMC9929230 DOI: 10.1016/j.molmed.2019.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/23/2019] [Accepted: 09/23/2019] [Indexed: 01/08/2023]
Abstract
The role of 3D genome organization in the precise regulation of gene expression is well established. Accordingly, the mechanistic connections between 3D genome alterations and disease development are becoming increasingly apparent. This opinion article provides a snapshot of our current understanding of the 3D genome alterations associated with cancers. We discuss potential connections of the 3D genome and cancer transcriptional addiction phenomenon as well as molecular mechanisms of action of 3D genome-disrupting drugs. Finally, we highlight issues and perspectives raised by the discovery of the first pharmaceutical strongly affecting 3D genome organization.
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48
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Bi L, Xie C, Jiao L, Jin S, Hnit SST, Mu Y, Wang Y, Wang Q, Ge G, Wang Y, Zhao X, Shi X, Kang Y, De Souza P, Liu T, Zhou J, Xu L, Dong Q. CPF impedes cell cycle re-entry of quiescent lung cancer cells through transcriptional suppression of FACT and c-MYC. J Cell Mol Med 2020; 24:2229-2239. [PMID: 31960591 PMCID: PMC7011132 DOI: 10.1111/jcmm.14897] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/24/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
Blockade of cell cycle re‐entry in quiescent cancer cells is a strategy to prevent cancer progression and recurrence. We investigated the action and mode of action of CPF mixture (Coptis chinensis, Pinellia ternata and Fructus trichosanthis) in impeding a proliferative switch in quiescent lung cancer cells. The results indicated that CPF impeded cell cycle re‐entry in quiescent lung cancer cells by reduction of FACT and c‐MYC mRNA and protein levels, with concomitant decrease in H3K4 tri‐methylation and RNA polymerase II occupancy at FACT and c‐MYC promoter regions. Animals implanted with quiescent cancer cells that had been exposed to CPF had reduced tumour volume/weight. Thus, CPF suppresses proliferative switching through transcriptional suppression of FACT and the c‐MYC, providing a new insight into therapeutic target and intervention method in impeding cancer recurrence.
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Affiliation(s)
- Ling Bi
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chanlu Xie
- School of Science and Health, National Institute of Complementary Medicine, Western Sydney University, Penrith South, NSW, Australia.,Chinese Medicine Anti-cancer Evaluation Program, Greg Brown Laboratory, Central Clinical School and Charles Perkins Center, The University of Sydney, Sydney, NSW, Australia.,Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Lijing Jiao
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shenyi Jin
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Su Su Thae Hnit
- School of Science and Health, National Institute of Complementary Medicine, Western Sydney University, Penrith South, NSW, Australia.,Chinese Medicine Anti-cancer Evaluation Program, Greg Brown Laboratory, Central Clinical School and Charles Perkins Center, The University of Sydney, Sydney, NSW, Australia.,Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Yao Mu
- Chinese Medicine Anti-cancer Evaluation Program, Greg Brown Laboratory, Central Clinical School and Charles Perkins Center, The University of Sydney, Sydney, NSW, Australia.,Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Yilun Wang
- Chinese Medicine Anti-cancer Evaluation Program, Greg Brown Laboratory, Central Clinical School and Charles Perkins Center, The University of Sydney, Sydney, NSW, Australia.,Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Qian Wang
- Origins of Cancer Program, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, the University of Sydney, Sydney, NSW, Australia
| | - Guangbo Ge
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yaqiao Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaodong Zhao
- Shanghai Center for Systems Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinglong Shi
- Shanghai Center for Systems Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yani Kang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Paul De Souza
- School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, Sydney, NSW, Australia.,Center for Childhood Cancer Research, UNSW Medicine, Sydney, NSW, Australia
| | - Jia Zhou
- Department of Thoracic Surgery, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ling Xu
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qihan Dong
- School of Science and Health, National Institute of Complementary Medicine, Western Sydney University, Penrith South, NSW, Australia.,Chinese Medicine Anti-cancer Evaluation Program, Greg Brown Laboratory, Central Clinical School and Charles Perkins Center, The University of Sydney, Sydney, NSW, Australia.,Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
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49
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Pearson S, Guo B, Pierce A, Azadbakht N, Brazzatti JA, Patassini S, Mulero-Navarro S, Meyer S, Flotho C, Gelb BD, Whetton AD. Proteomic Analysis of an Induced Pluripotent Stem Cell Model Reveals Strategies to Treat Juvenile Myelomonocytic Leukemia. J Proteome Res 2020; 19:194-203. [PMID: 31657576 PMCID: PMC6942217 DOI: 10.1021/acs.jproteome.9b00495] [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] [Indexed: 12/31/2022]
Abstract
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Juvenile
myelomonocytic leukemia (JMML) is an aggressive myeloproliferative
neoplasm of early childhood with a poor survival rate, thus there
is a requirement for improved treatment strategies. Induced pluripotent
stem cells offer the ability to model disease and develop new treatment
strategies. JMML is frequently associated with mutations in PTPN11. Children with Noonan syndrome, a development disorder,
have an increased incidence of JMML associated with specific germline
mutations in PTPN11. We undertook a proteomic assessment
of myeloid cells derived from induced pluripotent stem cells obtained
from Noonan syndrome patients with PTPN11 mutations,
either associated or not associated with an increased incidence of
JMML. We report that the proteomic perturbations induced by the leukemia-associated PTPN11 mutations are associated with TP53 and NF-Kκb
signaling. We have previously shown that MYC is involved in the differential
gene expression observed in Noonan syndrome patients associated with
an increased incidence of JMML. Thus, we employed drugs to target
these pathways and demonstrate differential effects on clonogenic
hematopoietic cells derived from Noonan syndrome patients, who develop
JMML and those who do not. Further, we demonstrated these small molecular
inhibitors, JQ1 and CBL0137, preferentially extinguish primitive hematopoietic
cells from sporadic JMML patients as opposed to cells from healthy
individuals.
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Affiliation(s)
- Stella Pearson
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre , The University of Manchester, Wolfson Molecular Imaging Centre , 27 Palatine Road , Withington, Manchester M20 3LJ , U.K
| | - Baoqiang Guo
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre , The University of Manchester, Wolfson Molecular Imaging Centre , 27 Palatine Road , Withington, Manchester M20 3LJ , U.K
| | - Andrew Pierce
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre , The University of Manchester, Wolfson Molecular Imaging Centre , 27 Palatine Road , Withington, Manchester M20 3LJ , U.K
| | - Narges Azadbakht
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre , The University of Manchester, Wolfson Molecular Imaging Centre , 27 Palatine Road , Withington, Manchester M20 3LJ , U.K
| | - Julie A Brazzatti
- Stoller Biomarker Discovery Centre, Manchester Academic Health Science Centre , University of Manchester , Manchester M13 9NQ , U.K
| | - Stefano Patassini
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre , The University of Manchester, Wolfson Molecular Imaging Centre , 27 Palatine Road , Withington, Manchester M20 3LJ , U.K
| | | | - Stefan Meyer
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre , The University of Manchester, Wolfson Molecular Imaging Centre , 27 Palatine Road , Withington, Manchester M20 3LJ , U.K
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine , University of Freiburg , 79106 Freiburg , Germany
| | - Bruce D Gelb
- The Mindich Child Health and Development Institute , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Anthony D Whetton
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre , The University of Manchester, Wolfson Molecular Imaging Centre , 27 Palatine Road , Withington, Manchester M20 3LJ , U.K.,Stoller Biomarker Discovery Centre, Manchester Academic Health Science Centre , University of Manchester , Manchester M13 9NQ , U.K
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50
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Chang HW, Nizovtseva EV, Razin SV, Formosa T, Gurova KV, Studitsky VM. Histone Chaperone FACT and Curaxins: Effects on Genome Structure and Function. ACTA ACUST UNITED AC 2019; 5. [PMID: 31853507 DOI: 10.20517/2394-4722.2019.31] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The histone chaperone FACT plays important roles in essentially every chromatin-associated process and is an important indirect target of the curaxin class of anti-cancer drugs. Curaxins are aromatiс compounds that intercalate into DNA and can trap FACT in bulk chromatin, thus interfering with its distribution and its functions in cancer cells. Recent studies have provided mechanistic insight into how FACT and curaxins cooperate to promote unfolding of nucleosomes and chromatin fibers, resulting in genome-wide disruption of contact chromatin domain boundaries, perturbation of higher order chromatin organization, and global disregulation of gene expression. Here, we discuss the implications of these insights for cancer biology.
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Affiliation(s)
- Han-Wen Chang
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Ekaterina V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Sergey V Razin
- Institute of Gene Biology RAS, 34/5 Vavilov Str., 119334 Moscow, Russia.,Biology Faculty, Lomonosov Moscow State University, 1 Leninskie Gory, 119992 Moscow, Russia
| | - Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo, NY14263, USA
| | - Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Biology Faculty, Lomonosov Moscow State University, 1 Leninskie Gory, 119992 Moscow, Russia
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