1
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Xiong S, Zhou J, Tan TK, Chung TH, Tan TZ, Toh SHM, Tang NXN, Jia Y, See YX, Fullwood MJ, Sanda T, Chng WJ. Super enhancer acquisition drives expression of oncogenic PPP1R15B that regulates protein homeostasis in multiple myeloma. Nat Commun 2024; 15:6810. [PMID: 39122682 PMCID: PMC11316114 DOI: 10.1038/s41467-024-50910-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Multiple myeloma is a hematological malignancy arising from immunoglobulin-secreting plasma cells. It remains poorly understood how chromatin rewiring of regulatory elements contributes to tumorigenesis and therapy resistance in myeloma. Here we generate a high-resolution contact map of myeloma-associated super-enhancers by integrating H3K27ac ChIP-seq and HiChIP from myeloma cell lines, patient-derived myeloma cells and normal plasma cells. Our comprehensive transcriptomic and phenomic analyses prioritize candidate genes with biological and clinical implications in myeloma. We show that myeloma cells frequently acquire SE that transcriptionally activate an oncogene PPP1R15B, which encodes a regulatory subunit of the holophosphatase complex that dephosphorylates translation initiation factor eIF2α. Epigenetic silencing or knockdown of PPP1R15B activates pro-apoptotic eIF2α-ATF4-CHOP pathway, while inhibiting protein synthesis and immunoglobulin production. Pharmacological inhibition of PPP1R15B using Raphin1 potentiates the anti-myeloma effect of bortezomib. Our study reveals that myeloma cells are vulnerable to perturbation of PPP1R15B-dependent protein homeostasis, highlighting a promising therapeutic strategy.
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Affiliation(s)
- Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jianbiao Zhou
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tae-Hoon Chung
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sabrina Hui-Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Nicole Xin Ning Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yunlu Jia
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Yi Xiang See
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Takaomi Sanda
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wee-Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Health System (NUHS), Singapore, Singapore.
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2
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Giannakoulas A, Nikolaidis M, Amoutzias GD, Giannakoulas N. A comparative analysis of transcriptomics of newly diagnosed multiple myeloma: exploring drug repurposing. Front Oncol 2024; 14:1390105. [PMID: 38690165 PMCID: PMC11058662 DOI: 10.3389/fonc.2024.1390105] [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: 02/22/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
Multiple myeloma (MM) is an incurable malignant plasma cell disorder characterized by the infiltration of clonal plasma cells in the bone marrow compartment. Gene Expression Profiling (GEP) has emerged as a powerful investigation tool in modern myeloma research enabling the dissection of the molecular background of MM and allowing the identification of gene products that could potentially serve as targets for therapeutic intervention. In this study we investigated shared transcriptomic abnormalities across newly diagnosed multiple myeloma (NDMM) patient cohorts. In total, publicly available transcriptomic data of 7 studies from CD138+ cells from 281 NDMM patients and 44 healthy individuals were integrated and analyzed. Overall, we identified 28 genes that were consistently differentially expressed (DE) between NDMM patients and healthy donors (HD) across various studies. Of those, 9 genes were over/under-expressed in more than 75% of NDMM patients. In addition, we identified 4 genes (MT1F, PURPL, LINC01239 and LINC01480) that were not previously considered to participate in MM pathogenesis. Meanwhile, by mining three drug databases (ChEMBL, IUPHAR/BPS and DrugBank) we identified 31 FDA-approved and 144 experimental drugs that target 8 of these 28 over/under-expressed MM genes. Taken together, our study offers new insights in MM pathogenesis and importantly, it reveals potential new treatment options that need to be further investigated in future studies.
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Affiliation(s)
- Angelos Giannakoulas
- Department of Hematology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Nikolaos Giannakoulas
- Department of Hematology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
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3
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Chen YJC, Bhaskara GB, Lu Y, Lin K, Dent SYR. The SAGA acetyltransferase module is required for the maintenance of MAF and MYC oncogenic gene expression programs in multiple myeloma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586811. [PMID: 38585845 PMCID: PMC10996596 DOI: 10.1101/2024.03.26.586811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Despite recent advances in therapeutic treatments, multiple myeloma (MM) remains an incurable malignancy. Epigenetic factors contribute to the initiation, progression, relapse, and clonal heterogeneity in MM, but our knowledge on epigenetic mechanisms underlying MM development is far from complete. The SAGA complex serves as a coactivator in transcription and catalyzes acetylation and deubiquitylation. Analyses of datasets in the Cancer Dependency Map Project revealed many SAGA components are selective dependencies in MM. To define SAGA-specific functions, we focused on ADA2B, the only subunit in the lysine acetyltransferase (KAT) module that specifically functions in SAGA. Integration of RNA-seq, ATAC-seq, and CUT&RUN results identified pathways directly regulated by ADA2B include MTORC1 signaling, MYC, E2F, and MM-specific MAF oncogenic programs. We discovered that ADA2B is recruited to MAF and MYC gene targets, and that MAF shares a majority of its targets with MYC in MM cells. Furthermore, we found the SANT domain of ADA2B is required for interaction with both GCN5 and PCAF acetyltransferases, incorporation into SAGA, and ADA2B protein stability. Our findings uncover previously unknown SAGA KAT module-dependent mechanisms controlling MM cell growth, revealing a vulnerability that might be exploited for future development of MM therapy.
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Affiliation(s)
- Ying-Jiun C. Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Govinal Badiger Bhaskara
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharon Y. R. Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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4
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Ang DA, Carter JM, Deka K, Tan JHL, Zhou J, Chen Q, Chng WJ, Harmston N, Li Y. Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma. Nat Commun 2024; 15:2513. [PMID: 38514625 PMCID: PMC10957915 DOI: 10.1038/s41467-024-46728-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 03/07/2024] [Indexed: 03/23/2024] Open
Abstract
In multiple myeloma, abnormal plasma cells establish oncogenic niches within the bone marrow by engaging the NF-κB pathway to nurture their survival while they accumulate pro-proliferative mutations. Under these conditions, many cases eventually develop genetic abnormalities endowing them with constitutive NF-κB activation. Here, we find that sustained NF-κB/p52 levels resulting from such mutations favours the recruitment of enhancers beyond the normal B-cell repertoire. Furthermore, through targeted disruption of p52, we characterise how such enhancers are complicit in the formation of super-enhancers and the establishment of cis-regulatory interactions with myeloma dependencies during constitutive activation of p52. Finally, we functionally validate the pathological impact of these cis-regulatory modules on cell and tumour phenotypes using in vitro and in vivo models, confirming RGS1 as a p52-dependent myeloma driver. We conclude that the divergent epigenomic reprogramming enforced by aberrant non-canonical NF-κB signalling potentiates transcriptional programs beneficial for multiple myeloma progression.
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Affiliation(s)
- Daniel A Ang
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jean-Michel Carter
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Kamalakshi Deka
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Joel H L Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore
- NUS Centre for Cancer Research, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Qingfeng Chen
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore
- NUS Centre for Cancer Research, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Republic of Singapore
| | - Nathan Harmston
- Division of Science, Yale-NUS College, Singapore, 138527, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
- Molecular Biosciences Division, Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Yinghui Li
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
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5
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Abstract
Lymphoid neoplasms represent a heterogeneous group of disease entities and subtypes with markedly different molecular and clinical features. Beyond genetic alterations, lymphoid tumors also show widespread epigenomic changes. These severely affect the levels and distribution of DNA methylation, histone modifications, chromatin accessibility, and three-dimensional genome interactions. DNA methylation stands out as a tracer of cell identity and memory, as B cell neoplasms show epigenetic imprints of their cellular origin and proliferative history, which can be quantified by an epigenetic mitotic clock. Chromatin-associated marks are informative to uncover altered regulatory regions and transcription factor networks contributing to the development of distinct lymphoid tumors. Tumor-intrinsic epigenetic and genetic aberrations cooperate and interact with microenvironmental cells to shape the transcriptome at different phases of lymphoma evolution, and intraclonal heterogeneity can now be characterized by single-cell profiling. Finally, epigenetics offers multiple clinical applications, including powerful diagnostic and prognostic biomarkers as well as therapeutic targets.
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Affiliation(s)
- Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain;
| | - José Ignacio Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain;
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
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6
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Kumar A, Kumar KV, Kundal K, Sengupta A, Sharma S, R K, Kumar R. MyeloDB: a multi-omics resource for multiple myeloma. Funct Integr Genomics 2024; 24:17. [PMID: 38244111 DOI: 10.1007/s10142-023-01280-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/22/2024]
Abstract
Multiple myeloma (MM) is a common type of blood cancer affecting plasma cells originating from the lymphoid B-cell lineage. It accounts for about 10% of all hematological malignancies and can cause significant end-organ damage. The emergence of genomic technologies such as next-generation sequencing and gene expression analysis has opened new possibilities for early detection of multiple myeloma and identification of personalized treatment options. However, there remain significant challenges to overcome in MM research, including integrating multi-omics data, achieving a comprehensive understanding of the disease, and developing targeted therapies and biomarkers. The extensive data generated by these technologies presents another challenge for data analysis and interpretation. To bridge this gap, we have developed a multi-omics open-access database called MyeloDB. It includes gene expression profiling, high-throughput CRISPR-Cas9 screens, drug sensitivity resources profile, and biomarkers. MyeloDB contains 47 expression profiles, 3 methylation profiles comprising a total of 5630 patient samples and 25 biomarkers which were reported in previous studies. In addition to this, MyeloDB can provide significant insight of gene mutations in MM on drug sensitivity. Furthermore, users can download the datasets and conduct their own analyses. Utilizing this database, we have identified five novel genes, i.e., CBFB, MANF, MBNL1, SEPHS2, and UFM1 as potential drug targets for MM. We hope MyeloDB will serve as a comprehensive platform for researchers and foster novel discoveries in MM. MyeloDB Database URL: https://project.iith.ac.in/cgntlab/myelodb/ .
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Affiliation(s)
- Ambuj Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502284, India
| | - Keerthana Vinod Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502284, India
| | - Kavita Kundal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502284, India
| | - Avik Sengupta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502284, India
| | - Simran Sharma
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502284, India
| | - Kunjulakshmi R
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, Odisha, 760010, India
| | - Rahul Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502284, India.
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7
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Katsarou A, Trasanidis N, Ponnusamy K, Kostopoulos IV, Alvarez-Benayas J, Papaleonidopoulou F, Keren K, Sabbattini PMR, Feldhahn N, Papaioannou M, Hatjiharissi E, Sudbery IM, Chaidos A, Caputo VS, Karadimitris A. MAF functions as a pioneer transcription factor that initiates and sustains myelomagenesis. Blood Adv 2023; 7:6395-6410. [PMID: 37224458 PMCID: PMC10598502 DOI: 10.1182/bloodadvances.2023009772] [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: 01/17/2023] [Revised: 04/17/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
Deregulated expression of lineage-affiliated transcription factors (TFs) is a major mechanism of oncogenesis. However, how the deregulation of nonlineage affiliated TF affects chromatin to initiate oncogenic transcriptional programs is not well-known. To address this, we studied the chromatin effects imposed by oncogenic MAF as the cancer-initiating driver in the plasma cell cancer multiple myeloma. We found that the ectopically expressed MAF endows myeloma plasma cells with migratory and proliferative transcriptional potential. This potential is regulated by the activation of enhancers and superenhancers, previously inactive in healthy B cells and plasma cells, and the cooperation of MAF with the plasma cell-defining TF IRF4. Forced ectopic MAF expression confirms the de novo ability of oncogenic MAF to convert transcriptionally inert chromatin to active chromatin with the features of superenhancers, leading to the activation of the MAF-specific oncogenic transcriptome and the acquisition of cancer-related cellular phenotypes such as CCR1-dependent cell migration. These findings establish oncogenic MAF as a pioneer transcription factor that can initiate as well as sustain oncogenic transcriptomes and cancer phenotypes. However, despite its pioneer function, myeloma cells remain MAF-dependent, thus validating oncogenic MAF as a therapeutic target that would be able to circumvent the challenges of subsequent genetic diversification driving disease relapse and drug resistance.
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Affiliation(s)
- Alexia Katsarou
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Nikolaos Trasanidis
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Kanagaraju Ponnusamy
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Ioannis V. Kostopoulos
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
- Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Jaime Alvarez-Benayas
- Department of the Higher School of Computer Science, Nebrija ARIES Research Group, Universidad Antonio de Nebrija, Madrid, Spain
| | - Foteini Papaleonidopoulou
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Keren Keren
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Pierangela M. R. Sabbattini
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Niklas Feldhahn
- Centre for Haematology, Imperial College London, London, United Kingdom
| | - Maria Papaioannou
- Division of Haematology, First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evdoxia Hatjiharissi
- Division of Haematology, First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ian M. Sudbery
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Aristeidis Chaidos
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Valentina S. Caputo
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
- Cancer Biology and Therapy laboratory, School of Applied Science, London South Bank University, London, United Kingdom
| | - Anastasios Karadimitris
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare National Health Service Trust, London, United Kingdom
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8
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Crump NT, Smith AL, Godfrey L, Dopico-Fernandez AM, Denny N, Harman JR, Hamley JC, Jackson NE, Chahrour C, Riva S, Rice S, Kim J, Basrur V, Fermin D, Elenitoba-Johnson K, Roeder RG, Allis CD, Roberts I, Roy A, Geng H, Davies JOJ, Milne TA. MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia. Nat Commun 2023; 14:5208. [PMID: 37626123 PMCID: PMC10457349 DOI: 10.1038/s41467-023-40981-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Aberrant enhancer activation is a key mechanism driving oncogene expression in many cancers. While much is known about the regulation of larger chromosome domains in eukaryotes, the details of enhancer-promoter interactions remain poorly understood. Recent work suggests co-activators like BRD4 and Mediator have little impact on enhancer-promoter interactions. In leukemias controlled by the MLL-AF4 fusion protein, we use the ultra-high resolution technique Micro-Capture-C (MCC) to show that MLL-AF4 binding promotes broad, high-density regions of enhancer-promoter interactions at a subset of key targets. These enhancers are enriched for transcription elongation factors like PAF1C and FACT, and the loss of these factors abolishes enhancer-promoter contact. This work not only provides an additional model for how MLL-AF4 is able to drive high levels of transcription at key genes in leukemia but also suggests a more general model linking enhancer-promoter crosstalk and transcription elongation.
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, W12 0NN, UK.
| | - Alastair L Smith
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana M Dopico-Fernandez
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nicholas Denny
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joe R Harman
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joseph C Hamley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nicole E Jackson
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Catherine Chahrour
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Simone Riva
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Siobhan Rice
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Damian Fermin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kojo Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK
| | - Anindita Roy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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9
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Sun Z, Fan J, Dang Y, Zhao Y. Enhancer in cancer pathogenesis and treatment. Genet Mol Biol 2023; 46:e20220313. [PMID: 37548349 PMCID: PMC10405138 DOI: 10.1590/1678-4685-gmb-2022-0313] [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: 10/31/2022] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Enhancers are essential cis-acting regulatory elements that determine cell identity and tumor progression. Enhancer function is dependent on the physical interaction between the enhancer and its target promoter inside its local chromatin environment. Enhancer reprogramming is an important mechanism in cancer pathogenesis and can be driven by both cis and trans factors. Super enhancers are acquired at oncogenes in numerous cancer types and represent potential targets for cancer treatment. BET and CDK inhibitors act through mechanisms of enhancer function and have shown promising results in therapy for various types of cancer. Genome editing is another way to reprogram enhancers in cancer treatment. The relationship between enhancers and cancer has been revised by several authors in the past few years, which mainly focuses on the mechanisms by which enhancers can impact cancer. Here, we emphasize SE's role in cancer pathogenesis and the new therapies involving epigenetic regulators (BETi and CDKi). We suggest that understanding mechanisms of activity would aid clinical success for these anti-cancer agents.
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Affiliation(s)
- Zhuo Sun
- Xi’an Medical University, Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Weiyang District, Xi’an, Shaanxi, China
- Institute of Basic Medical Sciences, No.1 XinWang Rd, Weiyang District, Shaanxi, China
| | - Jinbo Fan
- Xi’an Medical University, Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Weiyang District, Xi’an, Shaanxi, China
| | - Yixiong Dang
- Xi’an Medical University, School of Public Health, Weiyang District, Xi’an, 710021 Shaanxi, China
| | - Yufeng Zhao
- Institute of Basic Medical Sciences, No.1 XinWang Rd, Weiyang District, Shaanxi, China
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10
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Di Giorgio E, Benetti R, Kerschbamer E, Xodo L, Brancolini C. Super-enhancer landscape rewiring in cancer: The epigenetic control at distal sites. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 380:97-148. [PMID: 37657861 DOI: 10.1016/bs.ircmb.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Super-enhancers evolve as elements at the top of the hierarchical control of gene expression. They are important end-gatherers of signaling pathways that control stemness, differentiation or adaptive responses. Many epigenetic regulations focus on these regions, and not surprisingly, during the process of tumorigenesis, various alterations can account for their dysfunction. Super-enhancers are emerging as key drivers of the aberrant gene expression landscape that sustain the aggressiveness of cancer cells. In this review, we will describe and discuss about the structure of super-enhancers, their epigenetic regulation, and the major changes affecting their functionality in cancer.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Roberta Benetti
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Emanuela Kerschbamer
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Luigi Xodo
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy.
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11
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Molecular Crosstalk between Chromatin Remodeling and Tumor Microenvironment in Multiple Myeloma. Curr Oncol 2022; 29:9535-9549. [PMID: 36547163 PMCID: PMC9777166 DOI: 10.3390/curroncol29120749] [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: 10/26/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Multiple myeloma (MM) is a complex disease driven by numerous genetic and epigenetic alterations that are acquired over time. Despite recent progress in the understanding of MM pathobiology and the availability of innovative drugs, which have pronounced clinical outcome, this malignancy eventually progresses to a drug-resistant lethal stage and, thus, novel therapeutic drugs/models always play an important role in effective management of MM. Modulation of tumor microenvironment is one of the hallmarks of cancer biology, including MM, which affects the myeloma genomic architecture and disease progression subtly through chromatin modifications. The bone marrow niche has a prime role in progression, survival, and drug resistance of multiple myeloma cells. Therefore, it is important to develop means for targeting the ecosystem between multiple myeloma bone marrow microenvironment and chromatin remodeling. Extensive gene expression profile analysis has indeed provided the framework for new risk stratification of MM patients and identifying novel molecular targets and therapeutics. However, key tumor microenvironment factors/immune cells and their interactions with chromatin remodeling complex proteins that drive MM cell growth and progression remain grossly undefined.
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12
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Wu T, Huang H, Wang X. Dissecting super-enhancer heterogeneity: time to re-examine cancer subtypes? Trends Genet 2022; 38:1199-1203. [PMID: 35803787 DOI: 10.1016/j.tig.2022.06.006] [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: 05/09/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 01/24/2023]
Abstract
The heterogeneity of transcriptional regulations by super-enhancers (SEs) is poorly understood in human cancers. Herein, we summarize a bioinformatics workflow for genome-wide SE profiling and identification of subtype-specific SEs and regulatory networks. Dissecting SE heterogeneity provides new insights into cancer biology and alternative therapeutic strategies for cancer precision medicine.
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Affiliation(s)
- Tan Wu
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, SAR, China; Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, SAR, China
| | - Hao Huang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, SAR, China.
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13
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Nussinov R, Zhang M, Maloney R, Liu Y, Tsai CJ, Jang H. Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs. J Mol Biol 2022; 434:167569. [PMID: 35378118 PMCID: PMC9398924 DOI: 10.1016/j.jmb.2022.167569] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/11/2022] [Accepted: 03/25/2022] [Indexed: 01/12/2023]
Abstract
Here, we discuss the principles of allosteric activating mutations, propagation downstream of the signals that they prompt, and allosteric drugs, with examples from the Ras signaling network. We focus on Abl kinase where mutations shift the landscape toward the active, imatinib binding-incompetent conformation, likely resulting in the high affinity ATP outcompeting drug binding. Recent pharmacological innovation extends to allosteric inhibitor (GNF-5)-linked PROTAC, targeting Bcr-Abl1 myristoylation site, and broadly, allosteric heterobifunctional degraders that destroy targets, rather than inhibiting them. Designed chemical linkers in bifunctional degraders can connect the allosteric ligand that binds the target protein and the E3 ubiquitin ligase warhead anchor. The physical properties and favored conformational state of the engineered linker can precisely coordinate the distance and orientation between the target and the recruited E3. Allosteric PROTACs, noncompetitive molecular glues, and bitopic ligands, with covalent links of allosteric ligands and orthosteric warheads, increase the effective local concentration of productively oriented and placed ligands. Through covalent chemical or peptide linkers, allosteric drugs can collaborate with competitive drugs, degrader anchors, or other molecules of choice, driving innovative drug discovery.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Yonglan Liu
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
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14
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Sprang M, Andrade-Navarro MA, Fontaine JF. Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality. BMC Bioinformatics 2022; 23:279. [PMID: 35836114 PMCID: PMC9284682 DOI: 10.1186/s12859-022-04775-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 11/26/2022] Open
Abstract
Background The constant evolving and development of next-generation sequencing techniques lead to high throughput data composed of datasets that include a large number of biological samples. Although a large number of samples are usually experimentally processed by batches, scientific publications are often elusive about this information, which can greatly impact the quality of the samples and confound further statistical analyzes. Because dedicated bioinformatics methods developed to detect unwanted sources of variance in the data can wrongly detect real biological signals, such methods could benefit from using a quality-aware approach. Results We recently developed statistical guidelines and a machine learning tool to automatically evaluate the quality of a next-generation-sequencing sample. We leveraged this quality assessment to detect and correct batch effects in 12 publicly available RNA-seq datasets with available batch information. We were able to distinguish batches by our quality score and used it to correct for some batch effects in sample clustering. Overall, the correction was evaluated as comparable to or better than the reference method that uses a priori knowledge of the batches (in 10 and 1 datasets of 12, respectively; total = 92%). When coupled to outlier removal, the correction was more often evaluated as better than the reference (comparable or better in 5 and 6 datasets of 12, respectively; total = 92%). Conclusions In this work, we show the capabilities of our software to detect batches in public RNA-seq datasets from differences in the predicted quality of their samples. We also use these insights to correct the batch effect and observe the relation of sample quality and batch effect. These observations reinforce our expectation that while batch effects do correlate with differences in quality, batch effects also arise from other artifacts and are more suitably corrected statistically in well-designed experiments. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04775-y.
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Affiliation(s)
- Maximilian Sprang
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Jean-Fred Fontaine
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
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15
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Nussinov R, Tsai CJ, Jang H. Allostery, and how to define and measure signal transduction. Biophys Chem 2022; 283:106766. [PMID: 35121384 PMCID: PMC8898294 DOI: 10.1016/j.bpc.2022.106766] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/15/2022]
Abstract
Here we ask: What is productive signaling? How to define it, how to measure it, and most of all, what are the parameters that determine it? Further, what determines the strength of signaling from an upstream to a downstream node in a specific cell? These questions have either not been considered or not entirely resolved. The requirements for the signal to propagate downstream to activate (repress) transcription have not been considered either. Yet, the questions are pivotal to clarify, especially in diseases such as cancer where determination of signal propagation can point to cell proliferation and to emerging drug resistance, and to neurodevelopmental disorders, such as RASopathy, autism, attention-deficit/hyperactivity disorder (ADHD), and cerebral palsy. Here we propose a framework for signal transduction from an upstream to a downstream node addressing these questions. Defining cellular processes, experimentally measuring them, and devising powerful computational AI-powered algorithms that exploit the measurements, are essential for quantitative science.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
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16
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Trasanidis N, Katsarou A, Ponnusamy K, Shen YA, Kostopoulos IV, Bergonia B, Keren K, Reema P, Xiao X, Szydlo RM, Sabbattini PMR, Roberts IAG, Auner HW, Naresh KN, Chaidos A, Wang TL, Magnani L, Caputo VS, Karadimitris A. Systems medicine dissection of chr1q-amp reveals a novel PBX1-FOXM1 axis for targeted therapy in multiple myeloma. Blood 2022; 139:1939-1953. [PMID: 35015835 DOI: 10.1182/blood.2021014391] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/20/2021] [Indexed: 11/20/2022] Open
Abstract
Understanding the biological and clinical impact of copy number aberrations (CNAs) on the development of precision therapies in cancer remains an unmet challenge. Genetic amplification of chromosome 1q (chr1q-amp) is a major CNA conferring an adverse prognosis in several types of cancer, including in the blood cancer multiple myeloma (MM). Although several genes across chromosome 1 (chr1q) portend high-risk MM disease, the underpinning molecular etiology remains elusive. Here, with reference to the 3-dimensional (3D) chromatin structure, we integrate multi-omics data sets from patients with MM with genetic variables to obtain an associated clinical risk map across chr1q and to identify 103 adverse prognosis genes in chr1q-amp MM. Prominent among these genes, the transcription factor PBX1 is ectopically expressed by genetic amplification and epigenetic activation of its own preserved 3D regulatory domain. By binding to reprogrammed superenhancers, PBX1 directly regulates critical oncogenic pathways and a FOXM1-dependent transcriptional program. Together, PBX1 and FOXM1 activate a proliferative gene signature that predicts adverse prognosis across multiple types of cancer. Notably, pharmacological disruption of the PBX1-FOXM1 axis with existing agents (thiostrepton) and a novel PBX1 small molecule inhibitor (T417) is selectively toxic against chr1q-amp myeloma and solid tumor cells. Overall, our systems medicine approach successfully identifies CNA-driven oncogenic circuitries, links them to clinical phenotypes, and proposes novel CNA-targeted therapy strategies in MM and other types of cancer.
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Affiliation(s)
- Nikolaos Trasanidis
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Alexia Katsarou
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
| | - Kanagaraju Ponnusamy
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Yao-An Shen
- Department of Pathology
- Department of Oncology
- Department of Gynecology and Obstetrics, and
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ioannis V Kostopoulos
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Bien Bergonia
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Keren Keren
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Paudel Reema
- Imperial Experimental Cancer Medicine Centre and Cancer Research UK Imperial Centre, London, United Kingdom
| | - Xiaolin Xiao
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Richard M Szydlo
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Pierangela M R Sabbattini
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Irene A G Roberts
- Department of Paediatrics and Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
- Oxford Biomedical Research Centre Blood Theme, National Institute for Health Research Oxford Biomedical Centre, Oxford, United Kingdom
| | - Holger W Auner
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
| | - Kikkeri N Naresh
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
- Imperial Experimental Cancer Medicine Centre and Cancer Research UK Imperial Centre, London, United Kingdom
| | - Aristeidis Chaidos
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
| | - Tian-Li Wang
- Department of Pathology
- Department of Oncology
- Department of Gynecology and Obstetrics, and
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom; and
| | - Valentina S Caputo
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Cancer Biology and Therapy Laboratory, School of Applied Science, London South Bank University, London, United Kingdom
| | - Anastasios Karadimitris
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
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17
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Watt SM, Hua P, Roberts I. Increasing Complexity of Molecular Landscapes in Human Hematopoietic Stem and Progenitor Cells during Development and Aging. Int J Mol Sci 2022; 23:3675. [PMID: 35409034 PMCID: PMC8999121 DOI: 10.3390/ijms23073675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
The past five decades have seen significant progress in our understanding of human hematopoiesis. This has in part been due to the unprecedented development of advanced technologies, which have allowed the identification and characterization of rare subsets of human hematopoietic stem and progenitor cells and their lineage trajectories from embryonic through to adult life. Additionally, surrogate in vitro and in vivo models, although not fully recapitulating human hematopoiesis, have spurred on these scientific advances. These approaches have heightened our knowledge of hematological disorders and diseases and have led to their improved diagnosis and therapies. Here, we review human hematopoiesis at each end of the age spectrum, during embryonic and fetal development and on aging, providing exemplars of recent progress in deciphering the increasingly complex cellular and molecular hematopoietic landscapes in health and disease. This review concludes by highlighting links between chronic inflammation and metabolic and epigenetic changes associated with aging and in the development of clonal hematopoiesis.
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Affiliation(s)
- Suzanne M. Watt
- Stem Cell Research, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9BQ, UK
- Myeloma Research Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide 5005, Australia
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide 5001, Australia
| | - Peng Hua
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China;
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, and NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK;
- Department of Paediatrics and NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford OX3 9DU, UK
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18
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Dziadowicz SA, Wang L, Akhter H, Aesoph D, Sharma T, Adjeroh DA, Hazlehurst LA, Hu G. Bone Marrow Stroma-Induced Transcriptome and Regulome Signatures of Multiple Myeloma. Cancers (Basel) 2022; 14:927. [PMID: 35205675 PMCID: PMC8870223 DOI: 10.3390/cancers14040927] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/01/2023] Open
Abstract
Multiple myeloma (MM) is a hematological cancer with inevitable drug resistance. MM cells interacting with bone marrow stromal cells (BMSCs) undergo substantial changes in the transcriptome and develop de novo multi-drug resistance. As a critical component in transcriptional regulation, how the chromatin landscape is transformed in MM cells exposed to BMSCs and contributes to the transcriptional response to BMSCs remains elusive. We profiled the transcriptome and regulome for MM cells using a transwell coculture system with BMSCs. The transcriptome and regulome of MM cells from the upper transwell resembled MM cells that coexisted with BMSCs from the lower chamber but were distinctive to monoculture. BMSC-induced genes were enriched in the JAK2/STAT3 signaling pathway, unfolded protein stress, signatures of early plasma cells, and response to proteasome inhibitors. Genes with increasing accessibility at multiple regulatory sites were preferentially induced by BMSCs; these genes were enriched in functions linked to responses to drugs and unfavorable clinic outcomes. We proposed JUNB and ATF4::CEBPβ as candidate transcription factors (TFs) that modulate the BMSC-induced transformation of the regulome linked to the transcriptional response. Together, we characterized the BMSC-induced transcriptome and regulome signatures of MM cells to facilitate research on epigenetic mechanisms of BMSC-induced multi-drug resistance in MM.
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Affiliation(s)
- Sebastian A. Dziadowicz
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
| | - Lei Wang
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
| | - Halima Akhter
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
- Lane Department of Computer Science & Electrical Engineering, West Virginia University, Morgantown, WV 26506, USA;
| | - Drake Aesoph
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
- Lane Department of Computer Science & Electrical Engineering, West Virginia University, Morgantown, WV 26506, USA;
| | - Tulika Sharma
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
| | - Donald A. Adjeroh
- Lane Department of Computer Science & Electrical Engineering, West Virginia University, Morgantown, WV 26506, USA;
| | - Lori A. Hazlehurst
- WVU Cancer Institute, West Virginia University, Morgantown, WV 26506, USA;
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morganton, WV 26506, USA
| | - Gangqing Hu
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
- WVU Cancer Institute, West Virginia University, Morgantown, WV 26506, USA;
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19
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Super enhancers as master gene regulators in the pathogenesis of hematologic malignancies. Biochim Biophys Acta Rev Cancer 2022; 1877:188697. [PMID: 35150791 DOI: 10.1016/j.bbcan.2022.188697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/20/2022] [Accepted: 02/04/2022] [Indexed: 12/17/2022]
Abstract
Transcriptional deregulation of multiple oncogenes, tumor suppressors and survival pathways is a cancer cell hallmark. Super enhancers (SE) are long stretches of active enhancers in close linear proximity that ensure extraordinarily high expression levels of key genes associated with cell lineage, function and survival. SE landscape is intrinsically prone to changes and reorganization during the course of normal cell differentiation. This functional plasticity is typically utilized by cancer cells, which remodel their SE landscapes to ensure oncogenic transcriptional reprogramming. Multiple recent studies highlighted structural genetic mechanisms in non-coding regions that create new SE or hijack already existing ones. In addition, alterations in abundance/activity of certain SE-associated proteins or certain viral infections can elicit new super enhancers and trigger SE-driven transcriptional changes. For these reasons, SE profiling emerged as a powerful tool for discovering the core transcriptional regulatory circuits in tumor cells. This, in turn, provides new insights into cancer cell biology, and identifies main nodes of key cellular pathways to be potentially targeted. Since SEs are susceptible to inhibition, their disruption results in exponentially amassing 'butterfly' effect on gene expression and cell function. Moreover, many of SE elements are druggable, opening new therapeutic opportunities. Indeed, SE targeting drugs have been studied preclinically in various hematologic malignancies with promising effects. Herein, we review the unique features of SEs, present different cis- and trans-acting mechanisms through which hematologic tumor cells acquire SEs, and finally, discuss the potential of SE targeting in the therapy of hematologic malignancies.
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20
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Salpini R, D’Anna S, Benedetti L, Piermatteo L, Gill U, Svicher V, Kennedy PTF. Hepatitis B virus DNA integration as a novel biomarker of hepatitis B virus-mediated pathogenetic properties and a barrier to the current strategies for hepatitis B virus cure. Front Microbiol 2022; 13:972687. [PMID: 36118192 PMCID: PMC9478028 DOI: 10.3389/fmicb.2022.972687] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic infection with Hepatitis B Virus (HBV) is a major cause of liver-related morbidity and mortality worldwide. HBV-DNA integration into the human genome is recognized as a frequent event occurring during the early phases of HBV infection and characterizing the entire course of HBV natural history. The development of refined molecular biology technologies sheds new light on the functional implications of HBV-DNA integration into the human genome, including its role in the progression of HBV-related pathogenesis and in triggering the establishment of pro-oncogenic mechanisms, promoting the development of hepatocellular carcinoma. The present review provides an updated and comprehensive overview of the current body of knowledge on HBV-DNA integration, focusing on the molecular mechanisms underlying HBV-DNA integration and its occurrence throughout the different phases characterizing the natural history of HBV infection. Furthermore, here we discuss the main clinical implications of HBV integration as a biomarker of HBV-related pathogenesis, particularly in reference to hepatocarcinogenesis, and how integration may act as a barrier to the achievement of HBV cure with current and novel antiviral therapies. Overall, a more refined insight into the mechanisms and functionality of HBV integration is paramount, since it can potentially inform the design of ad hoc diagnostic tools with the ability to reveal HBV integration events perturbating relevant intracellular pathways and for identifying novel therapeutic strategies targeting alterations directly related to HBV integration.
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Affiliation(s)
- Romina Salpini
- Department of Experimental Medicine, University of Rome Tor Vergata, Roma, Italy
| | - Stefano D’Anna
- Department of Experimental Medicine, University of Rome Tor Vergata, Roma, Italy
| | - Livia Benedetti
- Department of Experimental Medicine, University of Rome Tor Vergata, Roma, Italy
| | - Lorenzo Piermatteo
- Department of Experimental Medicine, University of Rome Tor Vergata, Roma, Italy
| | - Upkar Gill
- Barts Liver Centre, Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Valentina Svicher
- Department of Biology, University of Rome Tor Vergata, Roma, Italy
- *Correspondence: Valentina Svicher,
| | - Patrick T. F. Kennedy
- Barts Liver Centre, Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, United Kingdom
- Patrick T. F. Kennedy,
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