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Zhang Q, Wang S, Li Z, Pan Y, Huang DS. Cross-Species Prediction of Transcription Factor Binding by Adversarial Training of a Novel Nucleotide-Level Deep Neural Network. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405685. [PMID: 39076052 DOI: 10.1002/advs.202405685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Indexed: 07/31/2024]
Abstract
Cross-species prediction of TF binding remains a major challenge due to the rapid evolutionary turnover of individual TF binding sites, resulting in cross-species predictive performance being consistently worse than within-species performance. In this study, a novel Nucleotide-Level Deep Neural Network (NLDNN) is first proposed to predict TF binding within or across species. NLDNN regards the task of TF binding prediction as a nucleotide-level regression task, which takes DNA sequences as input and directly predicts experimental coverage values. Beyond predictive performance, it also assesses model performance by locating potential TF binding regions, discriminating TF-specific single-nucleotide polymorphisms (SNPs), and identifying causal disease-associated SNPs. The experimental results show that NLDNN outperforms the competing methods in these tasks. Then, a dual-path framework is designed for adversarial training of NLDNN to further improve the cross-species prediction performance by pulling the domain space of human and mouse species closer. Through comparison and analysis, it finds that adversarial training not only can improve the cross-species prediction performance between humans and mice but also enhance the ability to locate TF binding regions and discriminate TF-specific SNPs. By visualizing the predictions, it is figured out that the framework corrects some mispredictions by amplifying the coverage values of incorrectly predicted peaks.
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Affiliation(s)
- Qinhu Zhang
- Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo, 315201, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Science, Nanning, 530007, China
| | - Siguo Wang
- Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo, 315201, China
| | - Zhipeng Li
- Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo, 315201, China
| | - Yijie Pan
- Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo, 315201, China
| | - De-Shuang Huang
- Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo, 315201, China
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University, Shanghai, 200092, China
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2
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Iñiguez-Muñoz S, Llinàs-Arias P, Ensenyat-Mendez M, Bedoya-López AF, Orozco JIJ, Cortés J, Roy A, Forsberg-Nilsson K, DiNome ML, Marzese DM. Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements. Cell Mol Life Sci 2024; 81:274. [PMID: 38902506 DOI: 10.1007/s00018-024-05314-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: 07/06/2023] [Revised: 12/07/2023] [Accepted: 06/06/2024] [Indexed: 06/22/2024]
Abstract
Discoveries in the field of genomics have revealed that non-coding genomic regions are not merely "junk DNA", but rather comprise critical elements involved in gene expression. These gene regulatory elements (GREs) include enhancers, insulators, silencers, and gene promoters. Notably, new evidence shows how mutations within these regions substantially influence gene expression programs, especially in the context of cancer. Advances in high-throughput sequencing technologies have accelerated the identification of somatic and germline single nucleotide mutations in non-coding genomic regions. This review provides an overview of somatic and germline non-coding single nucleotide alterations affecting transcription factor binding sites in GREs, specifically involved in cancer biology. It also summarizes the technologies available for exploring GREs and the challenges associated with studying and characterizing non-coding single nucleotide mutations. Understanding the role of GRE alterations in cancer is essential for improving diagnostic and prognostic capabilities in the precision medicine era, leading to enhanced patient-centered clinical outcomes.
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Affiliation(s)
- Sandra Iñiguez-Muñoz
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Pere Llinàs-Arias
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Miquel Ensenyat-Mendez
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Andrés F Bedoya-López
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Javier I J Orozco
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Group, 08017, Barcelona, Spain
- Medica Scientia Innovation Research SL (MEDSIR), 08018, Barcelona, Spain
- Faculty of Biomedical and Health Sciences, Department of Medicine, Universidad Europea de Madrid, 28670, Madrid, Spain
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Maggie L DiNome
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Diego M Marzese
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
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3
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Fan L, Wang H, Ben S, Cheng Y, Chen S, Ding Z, Zhao L, Li S, Wang M, Cheng G. Genetic variant in a BaP-activated super-enhancer increases prostate cancer risk by promoting AhR-mediated FAM227A expression. J Biomed Res 2024; 38:149-162. [PMID: 38410974 PMCID: PMC11001591 DOI: 10.7555/jbr.37.20230049] [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: 03/06/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 02/28/2024] Open
Abstract
Genetic variants in super-enhancers (SEs) are increasingly implicated as a disease risk-driving mechanism. Previous studies have reported an associations between benzo[a]pyrene (BaP) exposure and some malignant tumor risk. Currently, it is unclear whether BaP is involved in the effect of genetic variants in SEs on prostate cancer risk, nor the associated intrinsic molecular mechanisms. In the current study, by using logistic regression analysis, we found that rs5750581T>C in 22q-SE was significantly associated with prostate cancer risk (odds ratio = 1.26, P = 7.61 × 10 -5). We also have found that the rs6001092T>G, in a high linkage disequilibrium with rs5750581T>C ( r 2 = 0.98), is located in a regulatory aryl hydrocarbon receptor (AhR) motif and may interact with the FAM227A promoter in further bioinformatics analysis. We then performed a series of functional and BaP acute exposure experiments to assess biological function of the genetic variant and the target gene. Biologically, the rs6001092-G allele strengthened the transcription factor binding affinity to AhR, thereby upregulating FAM227A, especially upon exposure to BaP, which induced the malignant phenotypes of prostate cancer. The current study highlights that AhR acts as an environmental sensor of BaP and is involved in the SE-mediated prostate cancer risk, which may provide new insights into the etiology of prostate cancer associated with the inherited SE variants under environmental carcinogen stressors.
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Affiliation(s)
- Lulu Fan
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Hao Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Shuai Ben
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yifei Cheng
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Silu Chen
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhutao Ding
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Lingyan Zhao
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Gong Cheng
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, Jiangsu 210029, China
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4
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Wang M, Chen Q, Wang S, Xie H, Liu J, Huang R, Xiang Y, Jiang Y, Tian D, Bian E. Super-enhancers complexes zoom in transcription in cancer. J Exp Clin Cancer Res 2023; 42:183. [PMID: 37501079 PMCID: PMC10375641 DOI: 10.1186/s13046-023-02763-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Super-enhancers (SEs) consist of multiple typical enhancers enriched at high density with transcription factors, histone-modifying enzymes and cofactors. Oncogenic SEs promote tumorigenesis and malignancy by altering protein-coding gene expression and noncoding regulatory element function. Therefore, they play central roles in the treatment of cancer. Here, we review the structural characteristics, organization, identification, and functions of SEs and the underlying molecular mechanism by which SEs drive oncogenic transcription in tumor cells. We then summarize abnormal SE complexes, SE-driven coding genes, and noncoding RNAs involved in tumor development. In summary, we believe that SEs show great potential as biomarkers and therapeutic targets.
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Affiliation(s)
- MengTing Wang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
- School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - QingYang Chen
- Department of Clinical MedicineThe Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - ShuJie Wang
- Department of Clinical MedicineThe Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - Han Xie
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Jun Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - RuiXiang Huang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - YuFei Xiang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - YanYi Jiang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China.
| | - DaSheng Tian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
| | - ErBao Bian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
- School of Pharmacy, Anhui Medical University, Hefei, 230032, China.
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5
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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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6
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Kleinstern G, Slager SL. The inherited genetic contribution and polygenic risk score for risk of CLL and MBL: a narrative review. Leuk Lymphoma 2023; 64:788-798. [PMID: 36576061 PMCID: PMC10121840 DOI: 10.1080/10428194.2022.2157215] [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: 11/04/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/29/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is a neoplasm of B-cells in the blood and monoclonal B-cell lymphocytosis (MBL) is a precursor state to CLL. This narrative review provides an overview of the genetic studies that identified 43 common variants associated with risk of CLL among individuals of European ancestry. Emerging studies found that ∼50% of these variants are associated with MBL risk. Moreover, the polygenic risk score (PRS) calculated from these CLL variants has been shown to be a robust predictor for both CLL and MBL risk among European ancestry individuals but a weak predictor among African ancestry individuals. By summarizing these genetic studies, we conclude that additional studies are needed in other race/ethnic populations to identify race-specific susceptibility variants, that functional studies are needed to validate the biological mechanisms of the variants, and that the clinical utility of the PRS is limited until preventive strategies for CLL are developed.
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Affiliation(s)
- Geffen Kleinstern
- School of Public Health, University of Haifa, Haifa, Israel
- Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Susan L Slager
- Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
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7
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Lampson BL, Gupta A, Tyekucheva S, Mashima K, Petráčková A, Wang Z, Wojciechowska N, Shaughnessy CJ, Baker PO, Fernandes SM, Shupe S, Machado JH, Fardoun R, Kim AS, Brown JR. Rare Germline ATM Variants Influence the Development of Chronic Lymphocytic Leukemia. J Clin Oncol 2023; 41:1116-1128. [PMID: 36315919 PMCID: PMC9928739 DOI: 10.1200/jco.22.00269] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Germline missense variants of unknown significance in cancer-related genes are increasingly being identified with the expanding use of next-generation sequencing. The ataxia telangiectasia-mutated (ATM) gene on chromosome 11 has more than 1,000 germline missense variants of unknown significance and is a tumor suppressor. We aimed to determine if rare germline ATM variants are more frequent in chronic lymphocytic leukemia (CLL) compared with other hematologic malignancies and if they influence the clinical characteristics of CLL. METHODS We identified 3,128 patients (including 825 patients with CLL) in our hematologic malignancy clinic who had received clinical-grade sequencing of the entire coding region of ATM. We ascertained the comparative frequencies of germline ATM variants in categories of hematologic neoplasms, and, in patients with CLL, we determined whether these variants affected CLL-associated characteristics such as somatic 11q deletion. RESULTS Rare germline ATM variants are present in 24% of patients with CLL, significantly greater than that in patients with other lymphoid malignancies (16% prevalence), myeloid disease (15%), or no hematologic neoplasm (14%). Patients with CLL with germline ATM variants are younger at diagnosis and twice as likely to have 11q deletion. The ATM variant p.L2307F is present in 3% of patients with CLL, is associated with a three-fold increase in rates of somatic 11q deletion, and is a hypomorph in cell-based assays. CONCLUSION Germline ATM variants cluster within CLL and affect the phenotype of CLL that develops, implying that some of these variants (such as ATM p.L2307F) have functional significance and should not be ignored. Further studies are needed to determine whether these variants affect the response to therapy or account for some of the inherited risk of CLL.
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Affiliation(s)
- Benjamin L. Lampson
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Aditi Gupta
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Kiyomi Mashima
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Anna Petráčková
- Department of Immunology, Palacký University, Olomouc, Czech Republic
| | - Zixu Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Natalia Wojciechowska
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Current Address: Wrocław Medical University, Wrocław, Poland
| | - Conner J. Shaughnessy
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Peter O. Baker
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Stacey M. Fernandes
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Samantha Shupe
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - John-Hanson Machado
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Rayan Fardoun
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Annette S. Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Jennifer R. Brown
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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8
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Kulis M, Martin-Subero JI. Integrative epigenomics in chronic lymphocytic leukaemia: Biological insights and clinical applications. Br J Haematol 2023; 200:280-290. [PMID: 36121003 DOI: 10.1111/bjh.18465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/10/2022] [Accepted: 09/05/2022] [Indexed: 01/21/2023]
Abstract
Chronic lymphocytic leukaemia (CLL) is not only characterised by driver genetic alterations but by extensive epigenetic changes. Over the last decade, epigenomic studies have described the DNA methylome, chromatin accessibility, histone modifications and the three-dimensional (3D) genome architecture of CLL. Beyond its regulatory role, the DNA methylome contains imprints of the cellular origin and proliferative history of CLL cells. These two aspects are strong independent prognostic factors. Integrative analyses of chromatin marks have uncovered novel regulatory elements and altered transcription factor networks as non-genetic means mediating gene deregulation in CLL. Additionally, CLL cells display a disease-specific pattern of 3D genome interactions. From the technological perspective, we are currently witnessing a transition from bulk omics to single-cell analyses. This review aims at summarising the major findings from the epigenomics field as well as providing a prospect of the present and future of single-cell analyses in CLL.
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Affiliation(s)
- Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Jose Ignacio Martin-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.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
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9
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Morova T, Ding Y, Huang CCF, Sar F, Schwarz T, Giambartolomei C, Baca S, Grishin D, Hach F, Gusev A, Freedman M, Pasaniuc B, Lack N. Optimized high-throughput screening of non-coding variants identified from genome-wide association studies. Nucleic Acids Res 2022; 51:e18. [PMID: 36546757 PMCID: PMC9943666 DOI: 10.1093/nar/gkac1198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/19/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The vast majority of disease-associated single nucleotide polymorphisms (SNP) identified from genome-wide association studies (GWAS) are localized in non-coding regions. A significant fraction of these variants impact transcription factors binding to enhancer elements and alter gene expression. To functionally interrogate the activity of such variants we developed snpSTARRseq, a high-throughput experimental method that can interrogate the functional impact of hundreds to thousands of non-coding variants on enhancer activity. snpSTARRseq dramatically improves signal-to-noise by utilizing a novel sequencing and bioinformatic approach that increases both insert size and the number of variants tested per loci. Using this strategy, we interrogated known prostate cancer (PCa) risk-associated loci and demonstrated that 35% of them harbor SNPs that significantly altered enhancer activity. Combining these results with chromosomal looping data we could identify interacting genes and provide a mechanism of action for 20 PCa GWAS risk regions. When benchmarked to orthogonal methods, snpSTARRseq showed a strong correlation with in vivo experimental allelic-imbalance studies whereas there was no correlation with predictive in silico approaches. Overall, snpSTARRseq provides an integrated experimental and computational framework to functionally test non-coding genetic variants.
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Affiliation(s)
- Tunc Morova
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Yi Ding
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Funda Sar
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Tommer Schwarz
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Claudia Giambartolomei
- Central RNA Lab, Istituto Italiano di Tecnologia, Genova 16163, Italy,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sylvan C Baca
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Dennis Grishin
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Faraz Hach
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada,Department of Urologic Science, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Alexander Gusev
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Matthew L Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA,The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA,Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nathan A Lack
- To whom correspondence should be addressed. Tel: +1 604 875 4411;
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10
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Shi Y, Wang M, Liu D, Ullah S, Ma X, Yang H, Liu B. Super-enhancers in esophageal carcinoma: Transcriptional addictions and therapeutic strategies. Front Oncol 2022; 12:1036648. [DOI: 10.3389/fonc.2022.1036648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
The tumorigenesis of esophageal carcinoma arises from transcriptional dysregulation would become exceptionally dependent on specific regulators of gene expression, which could be preferentially attributed to the larger non-coding cis-regulatory elements, i.e. super-enhancers (SEs). SEs, large genomic regulatory entity in close genomic proximity, are underpinned by control cancer cell identity. As a consequence, the transcriptional addictions driven by SEs could offer an Achilles’ heel for molecular treatments on patients of esophageal carcinoma and other types of cancer as well. In this review, we summarize the recent findings about the oncogenic SEs upon which esophageal cancer cells depend, and discuss why SEs could be seen as the hallmark of cancer, how transcriptional dependencies driven by SEs, and what opportunities could be supplied based on this cancer-specific SEs.
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11
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Nameki R, Shetty A, Dareng E, Tyrer J, Lin X, Pharoah P, Corona RI, Kar S, Lawrenson K. chromMAGMA: regulatory element-centric interrogation of risk variants. Life Sci Alliance 2022; 5:e202201446. [PMID: 35777959 PMCID: PMC9251535 DOI: 10.26508/lsa.202201446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022] Open
Abstract
Candidate causal risk variants from genome-wide association studies reside almost exclusively in noncoding regions of the genome and innovative approaches are necessary to understand their biological function. Multi-marker analysis of genomic annotation (MAGMA) is a widely used program that nominates candidate risk genes by mapping single-nucleotide polymorphism summary statistics from genome-wide association studies to gene bodies. We augmented MAGMA to create chromatin-MAGMA (chromMAGMA), a method to nominate candidate risk genes based on the presence of risk variants within noncoding regulatory elements (REs). We applied chromMAGMA to a genetic susceptibility dataset for epithelial ovarian cancer (EOC), a rare gynecologic malignancy characterized by high mortality. This identified 155 unique candidate EOC risk genes across five EOC histotypes; 83% (105/127) of high-grade serous ovarian cancer risk genes had not previously been implicated in this EOC histotype. Risk genes nominated by chromMAGMA converged on mRNA splicing and transcriptional dysregulation pathways. chromMAGMA is a pipeline that nominates candidate risk genes through a gene regulation-focused approach and helps interpret the biological mechanism of noncoding risk variants for complex diseases.
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Affiliation(s)
- Robbin Nameki
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anamay Shetty
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Eileen Dareng
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Xianzhi Lin
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Siddhartha Kar
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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12
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Long-Distance Repression by Human Silencers: Chromatin Interactions and Phase Separation in Silencers. Cells 2022; 11:cells11091560. [PMID: 35563864 PMCID: PMC9101175 DOI: 10.3390/cells11091560] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
Three-dimensional genome organization represents an additional layer in the epigenetic regulation of gene expression. Active transcription controlled by enhancers or super-enhancers has been extensively studied. Enhancers or super-enhancers can recruit activators or co-activators to activate target gene expression through long-range chromatin interactions. Chromatin interactions and phase separation play important roles in terms of enhancer or super-enhancer functioning. Silencers are another major type of cis-regulatory element that can mediate gene regulation by turning off or reducing gene expression. However, compared to active transcription, silencer studies are still in their infancy. This review covers the current knowledge of human silencers, especially the roles of chromatin interactions and phase separation in silencers. This review also proposes future directions for human silencer studies.
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13
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Liu Q, Guo L, Lou Z, Xiang X, Shao J. Super-enhancers and novel therapeutic targets in colorectal cancer. Cell Death Dis 2022; 13:228. [PMID: 35277481 PMCID: PMC8917125 DOI: 10.1038/s41419-022-04673-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 12/24/2022]
Abstract
Transcription factors, cofactors, chromatin regulators, and transcription apparatuses interact with transcriptional regulatory elements, including promoters, enhancers, and super-enhancers (SEs), to coordinately regulate the transcription of target genes and thereby control cell behaviors. Among these transcriptional regulatory components and related elements, SEs often play a central role in determining cell identity and tumor initiation and progression. Therefore, oncogenic SEs, which are generated within cancer cells in oncogenes and other genes important in tumor pathogenesis, have emerged as attractive targets for novel cancer therapeutic strategies in recent years. Herein, we review the identification, formation and activation modes, and regulatory mechanisms for downstream genes and pathways of oncogenic SEs. We also review the therapeutic strategies and compounds targeting oncogenic SEs in colorectal cancer and other malignancies.
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Affiliation(s)
- Qian Liu
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lijuan Guo
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhiyuan Lou
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Xueping Xiang
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jimin Shao
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
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14
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Base-resolution prediction of transcription factor binding signals by a deep learning framework. PLoS Comput Biol 2022; 18:e1009941. [PMID: 35263332 PMCID: PMC8982852 DOI: 10.1371/journal.pcbi.1009941] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/05/2022] [Accepted: 02/19/2022] [Indexed: 01/13/2023] Open
Abstract
Transcription factors (TFs) play an important role in regulating gene expression, thus the identification of the sites bound by them has become a fundamental step for molecular and cellular biology. In this paper, we developed a deep learning framework leveraging existing fully convolutional neural networks (FCN) to predict TF-DNA binding signals at the base-resolution level (named as FCNsignal). The proposed FCNsignal can simultaneously achieve the following tasks: (i) modeling the base-resolution signals of binding regions; (ii) discriminating binding or non-binding regions; (iii) locating TF-DNA binding regions; (iv) predicting binding motifs. Besides, FCNsignal can also be used to predict opening regions across the whole genome. The experimental results on 53 TF ChIP-seq datasets and 6 chromatin accessibility ATAC-seq datasets show that our proposed framework outperforms some existing state-of-the-art methods. In addition, we explored to use the trained FCNsignal to locate all potential TF-DNA binding regions on a whole chromosome and predict DNA sequences of arbitrary length, and the results show that our framework can find most of the known binding regions and accept sequences of arbitrary length. Furthermore, we demonstrated the potential ability of our framework in discovering causal disease-associated single-nucleotide polymorphisms (SNPs) through a series of experiments.
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15
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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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16
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Maurya SS. Role of Enhancers in Development and Diseases. EPIGENOMES 2021; 5:epigenomes5040021. [PMID: 34968246 PMCID: PMC8715447 DOI: 10.3390/epigenomes5040021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Enhancers are cis-regulatory elements containing short DNA sequences that serve as binding sites for pioneer/regulatory transcription factors, thus orchestrating the regulation of genes critical for lineage determination. The activity of enhancer elements is believed to be determined by transcription factor binding, thus determining the cell state identity during development. Precise spatio-temporal control of the transcriptome during lineage specification requires the coordinated binding of lineage-specific transcription factors to enhancers. Thus, enhancers are the primary determinants of cell identity. Numerous studies have explored the role and mechanism of enhancers during development and disease, and various basic questions related to the functions and mechanisms of enhancers have not yet been fully answered. In this review, we discuss the recently published literature regarding the roles of enhancers, which are critical for various biological processes governing development. Furthermore, we also highlight that altered enhancer landscapes provide an essential context to understand the etiologies and mechanisms behind numerous complex human diseases, providing new avenues for effective enhancer-based therapeutic interventions.
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Affiliation(s)
- Shailendra S Maurya
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Department of Developmental Biology, School of Medicine, Washington University in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA
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17
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Zboril E, Yoo H, Chen L, Liu Z. Dynamic Interactions of Transcription Factors and Enhancer Reprogramming in Cancer Progression. Front Oncol 2021; 11:753051. [PMID: 34616687 PMCID: PMC8488287 DOI: 10.3389/fonc.2021.753051] [Citation(s) in RCA: 6] [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: 08/04/2021] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
While improved tumor treatment has significantly reduced the overall mortality rates, invasive progression including recurrence, therapy resistance and metastasis contributes to the majority of deaths caused by cancer. Enhancers are essential distal DNA regulatory elements that control temporal- or spatial-specific gene expression patterns during development and other biological processes. Genome-wide sequencing has revealed frequent alterations of enhancers in cancers and reprogramming of distal enhancers has emerged as one of the important features for tumors. In this review, we will discuss tumor progression-associated enhancer dynamics, its transcription factor (TF) drivers and how enhancer reprogramming modulates gene expression during cancer invasive progression. Additionally, we will explore recent advancements in contemporary technology including single-cell sequencing, spatial transcriptomics and CUT&RUN, which have permitted integrated studies of enhancer reprogramming in vivo. Given the essential roles of enhancer dynamics and its drivers in controlling cancer progression and treatment outcome, understanding these changes will be paramount in mitigating invasive events and discovering novel therapeutic targets.
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Affiliation(s)
- Emily Zboril
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Hannah Yoo
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Lizhen Chen
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Department of Cell Systems and Anatomy, Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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18
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Loss of synergistic transcriptional feedback loops drives diverse B-cell cancers. EBioMedicine 2021; 71:103559. [PMID: 34461601 PMCID: PMC8403728 DOI: 10.1016/j.ebiom.2021.103559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/30/2022] Open
Abstract
Background The most common B-cell cancers, chronic lymphocytic leukemia/lymphoma (CLL), follicular and diffuse large B-cell (FL, DLBCL) lymphomas, have distinct clinical courses, yet overlapping “cell-of-origin”. Dynamic changes to the epigenome are essential regulators of B-cell differentiation. Therefore, we reasoned that these distinct cancers may be driven by shared mechanisms of disruption in transcriptional circuitry. Methods We compared purified malignant B-cells from 52 patients with normal B-cell subsets (germinal center centrocytes and centroblasts, naïve and memory B-cells) from 36 donor tonsils using >325 high-resolution molecular profiling assays for histone modifications, open chromatin (ChIP-, FAIRE-seq), transcriptome (RNA-seq), transcription factor (TF) binding, and genome copy number (microarrays). Findings From the resulting data, we identified gains in active chromatin in enhancers/super-enhancers that likely promote unchecked B-cell receptor signaling, including one we validated near the immunoglobulin superfamily receptors FCMR and PIGR. More striking and pervasive was the profound loss of key B-cell identity TFs, tumor suppressors and their super-enhancers, including EBF1, OCT2(POU2F2), and RUNX3. Using a novel approach to identify transcriptional feedback, we showed that these core transcriptional circuitries are self-regulating. Their selective gain and loss form a complex, iterative, and interactive process that likely curbs B-cell maturation and spurs proliferation. Interpretation Our study is the first to map the transcriptional circuitry of the most common blood cancers. We demonstrate that a critical subset of B-cell TFs and their cognate enhancers form self-regulatory transcriptional feedback loops whose disruption is a shared mechanism underlying these diverse subtypes of B-cell lymphoma. Funding National Institute of Health, Siteman Cancer Center, Barnes-Jewish Hospital Foundation, Doris Duke Foundation.
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19
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Yan H, Tian S, Kleinstern G, Wang Z, Lee JH, Boddicker NJ, Cerhan JR, Kay NE, Braggio E, Slager SL. Chronic lymphocytic leukemia (CLL) risk is mediated by multiple enhancer variants within CLL risk loci. Hum Mol Genet 2021; 29:2761-2774. [PMID: 32744316 DOI: 10.1093/hmg/ddaa165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/02/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in Western countries. It has a strong genetic basis, showing a ~ 8-fold increased risk of CLL in first-degree relatives. Genome-wide association studies (GWAS) have identified 41 risk variants across 41 loci. However, for a majority of the loci, the functional variants and the mechanisms underlying their causal roles remain undefined. Here, we examined the genetic and epigenetic features associated with 12 index variants, along with any correlated (r2 ≥ 0.5) variants, at the CLL risk loci located outside of gene promoters. Based on publicly available ChIP-seq and chromatin accessibility data as well as our own ChIP-seq data from CLL patients, we identified six candidate functional variants at six loci and at least two candidate functional variants at each of the remaining six loci. The functional variants are predominantly located within enhancers or super-enhancers, including bi-directionally transcribed enhancers, which are often restricted to immune cell types. Furthermore, we found that, at 78% of the functional variants, the alternative alleles altered the transcription factor binding motifs or histone modifications, indicating the involvement of these variants in the change of local chromatin state. Finally, the enhancers carrying functional variants physically interacted with genes enriched in the type I interferon signaling pathway, apoptosis, or TP53 network that are known to play key roles in CLL. These results support the regulatory roles for inherited noncoding variants in the pathogenesis of CLL.
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Affiliation(s)
- Huihuang Yan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Shulan Tian
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Geffen Kleinstern
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Neil E Kay
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Esteban Braggio
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
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20
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Kasprzyk ME, Sura W, Dzikiewicz-Krawczyk A. Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer. Cancers (Basel) 2021; 13:3270. [PMID: 34210001 PMCID: PMC8269369 DOI: 10.3390/cancers13133270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 01/19/2023] Open
Abstract
B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.
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21
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Xiao S, Huang Q, Ren H, Yang M. The mechanism and function of super enhancer RNA. Genesis 2021; 59:e23422. [PMID: 34028961 DOI: 10.1002/dvg.23422] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/19/2022]
Abstract
Super enhancer (SE) is a cluster of enhancers that has a stronger ability to promote transcription compared to the typical enhancer (TE). Similar to TE, which can transcribe enhancer RNA (eRNA), SE produces super enhancer RNA (seRNA). The activation of SE is cell and tissue-specific, and the SE-associated genes are mostly linked to the cell fate. This is demonstrated by the important role-played by SE in the embryonic stem cell (ESC) and multiple cancer development. SeRNA regulates transcription in both cis and trans configuration, and those located in the cytoplasm mediates various cell activities. However, the functions of seRNAs are unclear, and most of them have a synergistic effect with SE and SE-associated genes. In this mini review, we summarized the mechanisms of seRNA and functions of both SE and seRNA.
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Affiliation(s)
- Shibai Xiao
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qin Huang
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Ren
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Min Yang
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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22
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Enhancer polymorphisms at the IKZF1 susceptibility locus for acute lymphoblastic leukemia impact B-cell proliferation and differentiation in both Down syndrome and non-Down syndrome genetic backgrounds. PLoS One 2021; 16:e0244863. [PMID: 33411777 PMCID: PMC7790404 DOI: 10.1371/journal.pone.0244863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022] Open
Abstract
Children with Down syndrome have an approximately 10-fold increased risk of developing acute lymphoblastic leukemia and this risk is influenced by inherited genetic variation. Genome-wide association studies have identified IKZF1 as a strong acute lymphoblastic leukemia susceptibility locus in children both with and without Down syndrome, with association signals reported at rs4132601 in non-Down syndrome and rs58923657 in individuals with Down syndrome (r2 = 0.98 for these two loci). Expression quantitative trait locus analysis in non-Down syndrome lymphoblastoid cell lines has demonstrated an association between the rs4132601 risk allele and decreased IKZF1 mRNA levels. In this study, we provide further mechanistic evidence linking the region encompassing IKZF1-associated polymorphisms to pro-leukemogenic effects in both human lymphoblastoid cell lines and murine hematopoietic stem cells. CRISPR/Cas9-mediated deletion of the region encompassing the rs17133807 major allele (r2 with rs58923657 = 0.97) resulted in significant reduction of IKZF1 mRNA levels in lymphoblastoid cell lines, with a greater effect in Down syndrome versus non-Down syndrome cells. Since rs17133807 is highly conserved in mammals, we also evaluated the orthologous murine locus at rs263378223, in hematopoietic stem cells from the Dp16(1)Yey mouse model of Down syndrome as well as non-Down syndrome control mice. Homozygous deletion of the region encompassing rs263378223 resulted in significantly reduced Ikzf1 mRNA, confirming that this polymorphism maps to a strong murine Ikzf1 enhancer, and resulted in increased B-lymphoid colony growth and decreased B-lineage differentiation. Our results suggest that both the region encompassing rs17133807 and its conserved orthologous mouse locus have functional effects that may mediate increased leukemia susceptibility in both the Down syndrome and non-Down syndrome genetic backgrounds.
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Zhao M, Yang C, Chai S, Yuan Y, Zhang J, Cao P, Wang Y, Xiao X, Wu K, Yan H, Liu J, Sun S. Curcumol and FTY720 synergistically induce apoptosis and differentiation in chronic myelomonocytic leukemia via multiple signaling pathways. Phytother Res 2020; 35:2157-2170. [PMID: 33274566 DOI: 10.1002/ptr.6968] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
Abstract
Chronic myelomonocytic leukemia (CML) is a myeloid tumor characterized by MDS (myelodysplastic syndrome) and MPN (myeloproliferative neoplasms). Allogeneic hematopoietic stem cell transplantation, chemotherapy, interferon, and targeted therapy are the main treatment methods for CML. Tyrosine kinase inhibitors (TKIs) are also a treatment option, and patients are currently recommended to take these drugs throughout their lives to prevent CML recurrence. Therefore, there is a need to investigate and identify other potential chemotherapy drugs. Currently, research on CML treatment with a single drug has shown little progress. Fingolimod (FTY720), an FDA-approved drug used to treat relapsing multiple sclerosis, has also shown great potential in the treatment of lymphocytic leukemia. In our study, we find that FTY720 and curcumol have a significant inhibitory effect on K562 cells, K562/ADR cells, and CD34+ cells from CML patients. RNAseq data analysis shows that regulation of apoptosis and differentiation pathways are key pathways in this process. Besides, BCR/ABL-Jak2/STAT3 signaling, PI3K/Akt-Jnk signaling, and activation of BH3-only genes are involved in CML inhibition. In a K562 xenograft mouse model, therapy with curcumol and FTY720 led to significant inhibition of tumor growth and induction of apoptosis. To summarize, curcumol and FTY720 synergistically inhibit proliferation involved in differentiation and induce apoptosis in CML cells. Therefore, synergistic treatment with two drugs could be the next choice of treatment for CML.
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Affiliation(s)
- Mingri Zhao
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Chaoying Yang
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Siyu Chai
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Yijun Yuan
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Ji Zhang
- Department of Rheumatology, The First Affiliated Hospital of University of South China, Hengyang, China.,Department of Clinical Laboratory, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Pengfei Cao
- Xiangya Hospital, Central South University, Changsha, China
| | - Yanpeng Wang
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Xiaojuan Xiao
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Kunlu Wu
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Huiwen Yan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Jing Liu
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Shuming Sun
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
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24
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Super-enhancer in prostate cancer: transcriptional disorders and therapeutic targets. NPJ Precis Oncol 2020; 4:31. [PMID: 33299103 PMCID: PMC7677538 DOI: 10.1038/s41698-020-00137-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Abnormal activity of oncogenic and tumor-suppressor signaling pathways contributes to cancer and cancer risk in humans. Transcriptional dysregulation of these pathways is commonly associated with tumorigenesis and the development of cancer. Genetic and epigenetic alterations may mediate dysregulated transcriptional activity. One of the most important epigenetic alternations is the non-coding regulatory element, which includes both enhancers and super-enhancers (SEs). SEs, characterized as large clusters of enhancers with aberrant high levels of transcription factor binding, have been considered as key drivers of gene expression in controlling and maintaining cancer cell identity. In cancer cells, oncogenes acquire SEs and the cancer phenotype relies on these abnormal transcription programs driven by SEs, which leads to cancer cells often becoming addicted to the SEs-related transcription programs, including prostate cancer. Here, we summarize recent findings of SEs and SEs-related gene regulation in prostate cancer and review the potential pharmacological inhibitors in basic research and clinical trials.
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25
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Xu Y, Wu Y, Zhang S, Ma P, Jin X, Wang Z, Yao M, Zhang E, Tao B, Qin Y, Chen H, Liu A, Chen M, Xiao M, Lu C, Mao R, Fan Y. A Tumor-Specific Super-Enhancer Drives Immune Evasion by Guiding Synchronous Expression of PD-L1 and PD-L2. Cell Rep 2020; 29:3435-3447.e4. [PMID: 31825827 DOI: 10.1016/j.celrep.2019.10.093] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 08/10/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
PD-L1 and PD-L2 are important targets for immune checkpoint blockade, but how tumor cells achieve their expression remains to be addressed. Here, we find that PD-L1 and PD-L2 are co-expressed in cancer cell lines and tissues across different cancer types. In breast cancer, MDA-MB-231 and SUM-159 cells show high expression of both PD-L1 and PD-L2. The expression of both PD-L1 and PD-L2 is greatly reduced upon treatment of inhibitors of super-enhancers. Bioinformatic analysis identifies a potential super-enhancer (PD-L1L2-SE) that is located between the CD274 and CD273 genes. Genetic deletion of PD-L1L2-SE profoundly reduces the expression of PD-L1 and PD-L2. PD-L1L2-SE-deficient cancer cells fail to generate immune evasion and are sensitive to T cell-mediated killing. Notably, epigenetic activation of such a region (PD-L1L2-SE) is correlated with PD-L1 and PD-L2. Taken together, we identify a super-enhancer (PD-L1L2-SE) that is responsible for the overexpression of PD-L1 and PD-L2 as well as immune evasion in cancer.
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Affiliation(s)
- Yuanpei Xu
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Yingcheng Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China; Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Siliang Zhang
- The Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Heilongjiang 150086, China
| | - Panpan Ma
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Xinxin Jin
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Zhou Wang
- School of Life Sciences, Nantong University, Jiangsu 226001, China
| | - Min Yao
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Erhao Zhang
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Baorui Tao
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Yongwei Qin
- Department of Pathogenic Biology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Hao Chen
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Aifen Liu
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Miaomiao Chen
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Mingbing Xiao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Cuihua Lu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China.
| | - Yihui Fan
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China; Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China; Department of Pathogenic Biology, School of Medicine, Nantong University, Jiangsu 226001, China; Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China.
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26
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Nadeu F, Diaz-Navarro A, Delgado J, Puente XS, Campo E. Genomic and Epigenomic Alterations in Chronic Lymphocytic Leukemia. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 15:149-177. [PMID: 31977296 DOI: 10.1146/annurev-pathmechdis-012419-032810] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chronic lymphocytic leukemia is a common disease in Western countries and has heterogeneous clinical behavior. The relevance of the genetic basis of the disease has come to the forefront recently, with genome-wide studies that have provided a comprehensive view of structural variants, somatic mutations, and different layers of epigenetic changes. The mutational landscape is characterized by relatively common copy number alterations, a few mutated genes occurring in 10-15% of cases, and a large number of genes mutated in a small number of cases. The epigenomic profile has revealed a marked reprogramming of regulatory regions in tumor cells compared with normal B cells. All of these alterations are differentially distributed in clinical and biological subsets of the disease, indicating that they may underlie the heterogeneous evolution of the disease. These global studies are revealing the molecular complexity of chronic lymphocytic leukemia and provide new perspectives that have helped to understand its pathogenic mechanisms and improve the clinical management of patients.
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Affiliation(s)
- Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; ,
| | - Ander Diaz-Navarro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Hematology Department, Hospital Clinic of Barcelona, University of Barcelona, 08036 Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Hematopathology Section, Laboratory of Pathology, Hospital Clinic of Barcelona, University of Barcelona, 08036 Barcelona, Spain
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27
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Qian FC, Li XC, Guo JC, Zhao JM, Li YY, Tang ZD, Zhou LW, Zhang J, Bai XF, Jiang Y, Pan Q, Wang QY, Li EM, Li CQ, Xu LY, Lin DC. SEanalysis: a web tool for super-enhancer associated regulatory analysis. Nucleic Acids Res 2020; 47:W248-W255. [PMID: 31028388 PMCID: PMC6602466 DOI: 10.1093/nar/gkz302] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/04/2019] [Accepted: 04/18/2019] [Indexed: 01/07/2023] Open
Abstract
Super-enhancers (SEs) have prominent roles in biological and pathological processes through their unique transcriptional regulatory capability. To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analyses of SEs. Pathways, transcription factors (TFs), SEs, and SE-associated genes form complex regulatory networks. Therefore, we designed a novel web server, SEanalysis, which provides comprehensive SE-associated regulatory network analyses. SEanalysis characterizes SE-associated genes, TFs binding to target SEs, and their upstream pathways. The current version of SEanalysis contains more than 330 000 SEs from more than 540 types of cells/tissues, 5042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for ∼700 human TFs and 2880 pathways from 10 databases. SEanalysis supports searching by either SEs, samples, TFs, pathways or genes. The complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a customizable genome browser containing >6000 customizable tracks for visualization. The server is freely available at http://licpathway.net/SEanalysis.
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Affiliation(s)
- Feng-Cui Qian
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xue-Cang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jin-Cheng Guo
- Institute of Oncologic Pathology, Medical College of Shantou University, Shantou 515041, China
| | - Jian-Mei Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yan-Yu Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Zhi-Dong Tang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Li-Wei Zhou
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xue-Feng Bai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yong Jiang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qi Pan
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qiu-Yu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.,Institute of Oncologic Pathology, Medical College of Shantou University, Shantou 515041, China
| | - En-Min Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chun-Quan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Li-Yan Xu
- Institute of Oncologic Pathology, Medical College of Shantou University, Shantou 515041, China
| | - De-Chen Lin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
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28
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Jia Q, Chen S, Tan Y, Li Y, Tang F. Oncogenic super-enhancer formation in tumorigenesis and its molecular mechanisms. Exp Mol Med 2020; 52:713-723. [PMID: 32382065 PMCID: PMC7272638 DOI: 10.1038/s12276-020-0428-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/08/2020] [Accepted: 03/23/2020] [Indexed: 12/11/2022] Open
Abstract
Super-enhancers (SEs) consist of a cluster of many enhancers bound to a great number of transcription factors. They are critical cis-regulatory elements that determine the identity of various human cell types. During tumorigenesis, DNA mutations and indels, chromosomal rearrangements, three-dimensional chromatin structural changes, and viral infections mediate oncogenic SE activation, and activated SEs have been found to regulate the expression of oncogenic genes. Inhibition specifically targeted to oncogenic SE assembly and activation provides a novel powerful therapeutic strategy for various cancers. In this paper, we first introduce the current understanding of oncogenic SE assembly and activation and then summarize the pathogenic factors and mechanism of oncogenic SE activation. Next, we elaborate on the oncogenic functions of SEs in cancers and the application of SEs as therapeutic targets. Finally, we turn our focus to the use of SEs in basic research and clinical trials. Drugs that block the assembly and activation of large DNA segments involved in enhancing gene expression could help in the treatment of cancer. Faqing Tang of Hunan Cancer Hospital in Changsha, China, and colleagues review the ways in which cancer cells hijack clusters of gene-regulating sequences known as super-enhancers, regulatory gene regions that normally help determine a cell’s unique identity, to drive the aberrant gene activity that fuels tumor growth. The researchers describe how numerous factors, ranging from internal DNA alterations, both large and small, to viral infections and other external assaults, can spur the formation of cancer-causing super-enhancers, leading to out-of-control gene expression. Therapies that selectively target these super-enhancers are now in early clinical testing. However, more studies of super-enhancers and their role in cancer development are needed to inform future drug development.
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Affiliation(s)
- Qunying Jia
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Shuhua Chen
- Department of Otolaryngology, The Second People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Yuan Tan
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Yuejin Li
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Faqing Tang
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China.
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29
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Tan Y, Li Y, Tang F. Oncogenic seRNA functional activation: a novel mechanism of tumorigenesis. Mol Cancer 2020; 19:74. [PMID: 32278350 PMCID: PMC7149907 DOI: 10.1186/s12943-020-01195-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
seRNA is a noncoding RNA (ncRNA) transcribed from active super-enhancer (SE), through which SE exerts biological functions and participates in various physiological and pathological processes. seRNA recruits cofactor, RNA polymerase II and mediator to constitute and stabilize chromatin loop SE and promoter region, which regulates target genes transcription. In tumorigenesis, DNA insertion, deletion, translocation, focal amplification and carcinogen factor mediate oncogenic SE generation, meanwhile, oncogenic SE transcribes into tumor-related seRNA, termed as oncogenic seRNA. Oncogenic seRNA participates in tumorigenesis through activating various signal-pathways. The recent reports showed that oncogenic seRNA implicates in a widespread range of cytopathological processes in cancer progression including cell proliferation, apoptosis, autophagy, epithelial-mesenchymal transition, extracellular matrix stiffness and angiogenesis. In this article, we comprehensively summarized seRNA’s characteristics and functions, and emphatically introduced inducible formation of oncogenic seRNA and its functional mechanisms. Lastly, some research strategies on oncogenic seRNA were introduced, and the perspectives on cancer therapy that targets oncogenic seRNA were also discussed.
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Affiliation(s)
- Yuan Tan
- Department of Clinical Laboratory and Hunan Key Laboratory of Oncotarget gene, Hunan Cancer Hospital & The affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Yuejin Li
- Department of Clinical Laboratory and Hunan Key Laboratory of Oncotarget gene, Hunan Cancer Hospital & The affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Faqing Tang
- Department of Clinical Laboratory and Hunan Key Laboratory of Oncotarget gene, Hunan Cancer Hospital & The affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China.
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30
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Xu C, Liu Q, Zhou J, Xie M, Feng J, Jiang T. Quantifying functional impact of non-coding variants with multi-task Bayesian neural network. Bioinformatics 2020; 36:1397-1404. [PMID: 31693090 DOI: 10.1093/bioinformatics/btz767] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 09/29/2019] [Accepted: 11/04/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Advances in high-throughput genotyping and sequencing technologies during recent years have revealed essential roles of non-coding regions in gene regulation. Genome-wide association studies (GWAS) suggested that a large proportion of risk variants are located in non-coding regions and remain unexplained by current expression quantitative trait loci catalogs. Interpreting the causal effects of these genetic modifications is crucial but difficult owing to our limited knowledge of how regulatory elements function. Although several computational methods have been designed to prioritize regulatory variants that substantially impact human phenotypes, few of them achieve consistently high performance even when large-scale multi-omic data are integrated. RESULTS We propose a novel multi-task framework based on Bayesian deep neural networks, MtBNN, to quantify the deleterious impact of single nucleotide polymorphisms in non-coding genomic regions. With the high-efficiency provided by the multi-task Bayesian framework to integrate information from different sources, MtBNN is capable of extracting features from genomic sequences of large-scale chromatin-profiling data, such as chromatin accessibility and transcript factor binding affinities, and calculating the distribution of the probability that a non-coding variant disrupts regulatory activities. A series of comprehensive experiments show that MtBNN quantifies the functional impact of cis-regulatory variations with high accuracy, including expression quantitative trait locus, DNase I sensitivity quantitative trait locus and functional genetic variants located within ATAC-peaks that affect the accessibility of the corresponding peak and achieves significantly better performance than the existing methods. Moreover, MtBNN has applications in the discovery of potentially causal disease-associated single-nucleotide polymorphisms (SNPs), thus helping fine-map the GWAS SNPs. AVAILABILITY AND IMPLEMENTATION Code can be downloaded from https://github.com/Zoesgithub/MtBNN. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chencheng Xu
- Bioinformatics Division, BNRIST.,Department of Computer Science and Technology
| | - Qiao Liu
- Bioinformatics Division, BNRIST.,Department of Automation, Tsinghua University, Beijing 100084, China
| | - Jianyu Zhou
- Bioinformatics Division, BNRIST.,Department of Computer Science and Technology
| | - Minzhu Xie
- College of Information Science and Engineering, Hunan Normal University, Changsha 410081, China
| | | | - Tao Jiang
- Bioinformatics Division, BNRIST.,Department of Computer Science and Technology.,Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
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31
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Ke J, Tian J, Mei S, Ying P, Yang N, Wang X, Zou D, Peng X, Yang Y, Zhu Y, Gong Y, Wang Z, Gong J, Zhong R, Chang J, Miao X. Genetic Predisposition to Colon and Rectal Adenocarcinoma Is Mediated by a Super-enhancer Polymorphism Coactivating CD9 and PLEKHG6. Cancer Epidemiol Biomarkers Prev 2020; 29:850-859. [PMID: 31988071 DOI: 10.1158/1055-9965.epi-19-1116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/22/2019] [Accepted: 01/21/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified dozens of loci associated with colon and rectal adenocarcinoma risk. As tissue-specific super-enhancers (SE) play important roles in tumorigenesis, we systematically investigate SEs and inner variants in established GWAS loci to decipher the underlying biological mechanisms. METHODS Through a comprehensive bioinformatics analysis on multi-omics data, we screen potential single-nucleotide polymorphisms (SNP) in cancer-specific SEs, and then subject them to a two-stage case-control study containing 4,929 cases and 7,083 controls from the Chinese population. A series of functional assays, including reporter gene assays, electrophoretic mobility shift assays (EMSA), CRISPR-Cas9 genome editing, chromosome conformation capture (3C) assays, and cell proliferation experiments, are performed to characterize the variant's molecular consequence and target genes. RESULTS The SNP rs11064124 in 12p13.31 is found significantly associated with the risk of colon and rectal adenocarcinoma with an odds ratio (OR) of 0.87 [95% confidence interval (CI), 0.82-0.92, P = 8.67E-06]. The protective rs11064124-G weakens the binding affinity with vitamin D receptor (VDR) and increases the enhancer's activity and interactions with two target genes' promoters, thus coactivating the transcription of CD9 and PLEKHG6, which are both putative tumor suppressor genes for colon and rectal adenocarcinoma. CONCLUSIONS Our integrative study highlights an SE polymorphism rs11064124 and two susceptibility genes CD9 and PLEKHG6 in 12p13.31 for colon and rectal adenocarcinoma. IMPACT These findings suggest a novel insight for genetic pathogenesis of colon and rectal adenocarcinoma, involving transcriptional coactivation of diverse susceptibility genes via the SE element as a gene regulation hub.
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Affiliation(s)
- Juntao Ke
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbo Tian
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shufang Mei
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pingting Ying
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nan Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyang Wang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danyi Zou
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiating Peng
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhihua Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Gong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Rong Zhong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Miao
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Abstract
Enhancers are cis-acting elements with many sites bound by transcription factors and activate transcription over long distance. Histone modifications are critical for enhancer activity and utilized as hallmarks for the identification of putative enhancers. Monomethylation of histone H3 lysine 4 (H3K4me1) is the mark for enhancer priming; acetylation of histone H3 lysine 27 (H3K27ac) for active enhancers and trimethylation of histone H3 lysine 27 (H3K27me3) for silent enhancers. Recent studies from multiple groups have provided evidence that enhancer reprogramming, especially gain of enhancer activity, is closely related to tumorigenesis and cancer development. In this review, we will summarize the recent discoveries about enhancer regulation and the mechanisms of enhancer reprogramming in tumorigenesis, and discuss the potential application of enhancer manipulation in precision medicine.
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Affiliation(s)
- Jie Yao
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Ji Chen
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Lian-Yun Li
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Min Wu
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
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Kleinstern G, Yan H, Hildebrandt MAT, Vijai J, Berndt SI, Ghesquières H, McKay J, Wang SS, Nieters A, Ye Y, Monnereau A, Brooks-Wilson AR, Lan Q, Melbye M, Jackson RD, Teras LR, Purdue MP, Vajdic CM, Vermeulen RCH, Giles GG, Cocco PL, Birmann BM, Kraft P, Albanes D, Zeleniuch-Jacquotte A, Crouch S, Zhang Y, Sarangi V, Asmann Y, Offit K, Salles G, Wu X, Smedby KE, Skibola CF, Slager SL, Rothman N, Chanock SJ, Cerhan JR. Inherited variants at 3q13.33 and 3p24.1 are associated with risk of diffuse large B-cell lymphoma and implicate immune pathways. Hum Mol Genet 2020; 29:70-79. [PMID: 31600786 PMCID: PMC7001601 DOI: 10.1093/hmg/ddz228] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/19/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022] Open
Abstract
We previously identified five single nucleotide polymorphisms (SNPs) at four susceptibility loci for diffuse large B-cell lymphoma (DLBCL) in individuals of European ancestry through a large genome-wide association study (GWAS). To further elucidate genetic susceptibility to DLBCL, we sought to validate two loci at 3q13.33 and 3p24.1 that were suggestive in the original GWAS with additional genotyping. In the meta-analysis (5662 cases and 9237 controls) of the four original GWAS discovery scans and three replication studies, the 3q13.33 locus (rs9831894; minor allele frequency [MAF] = 0.40) was associated with DLBCL risk [odds ratio (OR) = 0.83, P = 3.62 × 10-13]. rs9831894 is in linkage disequilibrium (LD) with additional variants that are part of a super-enhancer that physically interacts with promoters of CD86 and ILDR1. In the meta-analysis (5510 cases and 12 817 controls) of the four GWAS discovery scans and four replication studies, the 3p24.1 locus (rs6773363; MAF = 0.45) was also associated with DLBCL risk (OR = 1.20, P = 2.31 × 10-12). This SNP is 29 426-bp upstream of the nearest gene EOMES and in LD with additional SNPs that are part of a highly lineage-specific and tumor-acquired super-enhancer that shows long-range interaction with AZI2 promoter. These loci provide additional evidence for the role of immune function in the etiology of DLBCL, the most common lymphoma subtype.
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Affiliation(s)
| | | | | | - Joseph Vijai
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | | | | | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Sophia S Wang
- City of Hope Beckman Research Institute, Duarte, CA, USA
| | - Alexandra Nieters
- Center for Chronic Immunodeficiency, Medical Center—University of Freiburg, Freiburg, Germany
| | - Yuanqing Ye
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alain Monnereau
- Centre for Research in Epidemiology and Population Health (CESP), Villejuif, France
| | | | - Qing Lan
- National Cancer Institute, Bethesda, MD, USA
| | | | | | | | | | | | | | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Pier Luigi Cocco
- Department of Medical Sciences and Public Health, Occupational Health Section, University of Cagliari, Monserrato, Italy
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter Kraft
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | | | - Yawei Zhang
- Yale School of Public Health, New Haven, CT, USA
| | | | | | - Kenneth Offit
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | | | - Xifeng Wu
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Xanthopoulos C, Kostareli E. Advances in Epigenetics and Epigenomics in Chronic Lymphocytic Leukemia. CURRENT GENETIC MEDICINE REPORTS 2019. [DOI: 10.1007/s40142-019-00178-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abstract
Purpose of Review
The development and progression of chronic lymphocytic leukemia (CLL), a highly heterogenous B cell malignancy, are influenced by both genetic and environmental factors. Environmental factors, including pharmacological interventions, can affect the epigenetic landscape of CLL and thereby determine the CLL phenotype, clonal evolution, and clinical outcome. In this review, we critically present the latest advances in the field of CLL epigenomics/epigenetics in order to provide a systematic overview of to-date achievements and highlight the potential of epigenomics approaches in light of novel treatment therapies.
Recent Findings
Recent technological advances have enabled broad and precise mapping of the CLL epigenome. The identification of CLL-specific DNA methylation patterns has allowed for accurate CLL subtype definition, a better understanding of clonal origin and evolution, and the discovery of reliable biomarkers. More recently, studies have started to unravel the prognostic, predictive, and therapeutic potential of mapping chromatin dynamics and histone modifications in CLL. Finally, analysis of non-coding RNA expression has indicated their contribution to disease pathogenesis and helped to define prognostic subsets in CLL.
Summary
Overall, the potential of CLL epigenomics for predicting treatment response and resistance is mounting, especially with the advent of novel targeted CLL therapies.
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Sud A, Chattopadhyay S, Thomsen H, Sundquist K, Sundquist J, Houlston RS, Hemminki K. Analysis of 153 115 patients with hematological malignancies refines the spectrum of familial risk. Blood 2019; 134:960-969. [PMID: 31395603 PMCID: PMC6789511 DOI: 10.1182/blood.2019001362] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/26/2019] [Indexed: 02/08/2023] Open
Abstract
Estimating familial cancer risks is clinically important in being able to discriminate between individuals in the population at differing risk for malignancy. To gain insight into the familial risk for the different hematological malignancies and their possible inter-relationship, we analyzed data on more than 16 million individuals from the Swedish Family-Cancer Database. After identifying 153 115 patients diagnosed with a primary hematological malignancy, we quantified familial relative risks (FRRs) by calculating standardized incident ratios (SIRs) in 391 131 of their first-degree relatives. The majority of hematological malignancies showed increased FRRs for the same tumor type, with the highest FRRs being observed for mixed cellularity Hodgkin lymphoma (SIR, 16.7), lymphoplasmacytic lymphoma (SIR, 15.8), and mantle cell lymphoma (SIR, 13.3). There was evidence for pleiotropic relationships; notably, chronic lymphocytic leukemia was associated with an elevated familial risk for other B-cell tumors and myeloproliferative neoplasms. Collectively, these data provide evidence for shared etiological factors for many hematological malignancies and provide information for identifying individuals at increased risk, as well as informing future gene discovery initiatives.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Subhayan Chattopadhyay
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Kristina Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Center for Community-based Healthcare Research and Education, Department of Functional Pathology, School of Medicine, Shimane University, Matsue, Japan; and
| | - Jan Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Center for Community-based Healthcare Research and Education, Department of Functional Pathology, School of Medicine, Shimane University, Matsue, Japan; and
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
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36
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Speedy HE, Beekman R, Chapaprieta V, Orlando G, Law PJ, Martín-García D, Gutiérrez-Abril J, Catovsky D, Beà S, Clot G, Puiggròs M, Torrents D, Puente XS, Allan JM, López-Otín C, Campo E, Houlston RS, Martín-Subero JI. Insight into genetic predisposition to chronic lymphocytic leukemia from integrative epigenomics. Nat Commun 2019; 10:3615. [PMID: 31399598 PMCID: PMC6689100 DOI: 10.1038/s41467-019-11582-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 07/23/2019] [Indexed: 12/25/2022] Open
Abstract
Genome-wide association studies have provided evidence for inherited genetic predisposition to chronic lymphocytic leukemia (CLL). To gain insight into the mechanisms underlying CLL risk we analyze chromatin accessibility, active regulatory elements marked by H3K27ac, and DNA methylation at 42 risk loci in up to 486 primary CLLs. We identify that risk loci are significantly enriched for active chromatin in CLL with evidence of being CLL-specific or differentially regulated in normal B-cell development. We then use in situ promoter capture Hi-C, in conjunction with gene expression data to reveal likely target genes of the risk loci. Candidate target genes are enriched for pathways related to B-cell development such as MYC and BCL2 signalling. At 14 loci the analysis highlights 63 variants as the probable functional basis of CLL risk. By integrating genetic and epigenetic information our analysis reveals novel insights into the relationship between inherited predisposition and the regulatory chromatin landscape of CLL.
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MESH Headings
- B-Lymphocytes/metabolism
- Base Sequence
- Chromatin/metabolism
- DNA Methylation
- Epigenesis, Genetic/genetics
- Epigenesis, Genetic/physiology
- Epigenomics
- Gene Expression Regulation, Leukemic
- Genetic Predisposition to Disease/genetics
- Genome-Wide Association Study
- Genotype
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Polymorphism, Single Nucleotide
- Promoter Regions, Genetic
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Proto-Oncogene Proteins c-myc/metabolism
- Transcription Factors
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Affiliation(s)
- Helen E Speedy
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Renée Beekman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Vicente Chapaprieta
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Giulia Orlando
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - David Martín-García
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Jesús Gutiérrez-Abril
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Daniel Catovsky
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Montserrat Puiggròs
- Programa Conjunto de Biología Computacional, Barcelona Supercomputing Center (BSC), Institut de Recerca Biomèdica (IRB), Spanish National Bioinformatics Institute, Universitat de Barcelona, Barcelona, Spain
| | - David Torrents
- Programa Conjunto de Biología Computacional, Barcelona Supercomputing Center (BSC), Institut de Recerca Biomèdica (IRB), Spanish National Bioinformatics Institute, Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - James M Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Carlos López-Otín
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, 08036, Barcelona, Spain
- Hematopathology Section, Hospital Clinic of Barcelona, 08036, Barcelona, Spain
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK.
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, 08036, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain.
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37
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Li X, Payne DT, Ampolu B, Bland N, Brown JT, Dutton MJ, Fitton CA, Gulliver A, Hale L, Hamza D, Jones G, Lane R, Leach AG, Male L, Merisor EG, Morton MJ, Quy AS, Roberts R, Scarll R, Schulz-Utermoehl T, Stankovic T, Stevenson B, Fossey JS, Agathanggelou A. Derivatisation of parthenolide to address chemoresistant chronic lymphocytic leukaemia. MEDCHEMCOMM 2019; 10:1379-1390. [PMID: 32952998 PMCID: PMC7478165 DOI: 10.1039/c9md00297a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022]
Abstract
Parthenolide is a natural product that exhibits anti-leukaemic activity, however, its clinical use is limited by its poor bioavailability. It may be extracted from feverfew and protocols for growing, extracting and derivatising it are reported. A novel parthenolide derivative with good bioavailability and pharmacological properties was identified through a screening cascade based on in vitro anti-leukaemic activity and calculated "drug-likeness" properties, in vitro and in vivo pharmacokinetics studies and hERG liability testing. In vitro studies showed the most promising derivative to have comparable anti-leukaemic activity to DMAPT, a previously described parthenolide derivative. The newly identified compound was shown to have pro-oxidant activity and in silico molecular docking studies indicate a prodrug mode of action. A synthesis scheme is presented for the production of amine 7 used in the generation of 5f.
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Affiliation(s)
- Xingjian Li
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Daniel T Payne
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Badarinath Ampolu
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Nicholas Bland
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Jane T Brown
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Mark J Dutton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Catherine A Fitton
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Abigail Gulliver
- Winterbourne Botanic Garden, University of Birmingham, 58 Edgbaston Park Road, Edgbaston, Birmingham, West Midlands B15 2RT, UK
| | - Lee Hale
- Winterbourne Botanic Garden, University of Birmingham, 58 Edgbaston Park Road, Edgbaston, Birmingham, West Midlands B15 2RT, UK
| | - Daniel Hamza
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Geraint Jones
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Rebecca Lane
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Andrew G Leach
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Louise Male
- X-Ray Crystallography Facility, School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Elena G Merisor
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Michael J Morton
- ApconiX Ltd, Alderly Park, Nether Alderly, Cheshire, SK10 4TG, UK
| | - Alex S Quy
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Ruth Roberts
- ApconiX Ltd, Alderly Park, Nether Alderly, Cheshire, SK10 4TG, UK
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Rosanna Scarll
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | | | - Tatjana Stankovic
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Brett Stevenson
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - John S Fossey
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Angelo Agathanggelou
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
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38
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Jia Y, Chng WJ, Zhou J. Super-enhancers: critical roles and therapeutic targets in hematologic malignancies. J Hematol Oncol 2019; 12:77. [PMID: 31311566 PMCID: PMC6636097 DOI: 10.1186/s13045-019-0757-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022] Open
Abstract
Super-enhancers (SEs) in a broad range of human cell types are large clusters of enhancers with aberrant high levels of transcription factor binding, which are central to drive expression of genes in controlling cell identity and stimulating oncogenic transcription. Cancer cells acquire super-enhancers at oncogene and cancerous phenotype relies on these abnormal transcription propelled by SEs. Furthermore, specific inhibitors targeting SEs assembly and activation have offered potential targets for treating various tumors including hematological malignancies. Here, we first review the identification, functional significance of SEs. Next, we summarize recent findings of SEs and SE-driven gene regulation in normal hematopoiesis and hematologic malignancies. The importance and various modes of SE-mediated MYC oncogene amplification are illustrated. Finally, we highlight the progress of SEs as selective therapeutic targets in basic research and clinical trials. Some open questions regarding functional significance and future directions of targeting SEs in the clinic will be discussed too.
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Affiliation(s)
- Yunlu Jia
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore.,Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - 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.,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
| | - 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.
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39
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He Y, Long W, Liu Q. Targeting Super-Enhancers as a Therapeutic Strategy for Cancer Treatment. Front Pharmacol 2019; 10:361. [PMID: 31105558 PMCID: PMC6499164 DOI: 10.3389/fphar.2019.00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/22/2019] [Indexed: 01/09/2023] Open
Abstract
Super-enhancers (SEs) refer to large clusters of enhancers that drive gene expressions. Recent data has provided novel insights in elucidating the roles of SEs in many diseases, including cancer. Many mechanisms involved in tumorigenesis and progression, ranging from internal gene mutation and rearrangement to external damage and inducement, have been demonstrated to be highly associated with SEs. Moreover, translocation, formation, deletion, or duplication of SEs themselves could lead to tumor development. It has been reported that various oncogenic molecules and pathways are tightly regulated by SEs. Moreover, several clinical trials on novel SEs blockers, such as BET inhibitor and CDK7i, have indicated the potential roles of SEs in cancer therapy. In this review, we highlighted the underlying mechanism of action of SEs in cancer development and the corresponding novel potential therapeutic strategies. It is speculated that targeting SEs could complement the traditional approaches and lead to more effective treatment for cancer patients.
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Affiliation(s)
- Yi He
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wenyong Long
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Qing Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
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40
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Abstract
Cancer is fueled by the aberrant activity of oncogenic and tumor suppressive pathways. Transcriptional dysregulation of these pathways play a major role both in the genesis and development of cancer. Dysregulation of transcriptional programs can be mediated by genetic and epigenetic alterations targeting both protein coding genes and non-coding regulatory elements like enhancers and super-enhancers. Super-enhancers, characterized as large clusters of enhancers in close proximity, have been identified as essential oncogenic drivers required for the maintenance of cancer cell identity. As a result, cancer cells are often addicted to the super-enhancer driven transcriptional programs. Furthermore, pharmacological inhibitors targeting key components of super-enhancer assembly and activation have shown great promise in reducing tumor growth and proliferation in several pre-clinical tumor models. This article reviews the current understanding of super-enhancer assembly and activation, the different mechanisms by which cancer cells acquire oncogenic super-enhancers and, finally, the potential of targeting super-enhancers as future therapeutics.
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Affiliation(s)
- Palaniraja Thandapani
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
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Jiang Y, Qian F, Bai X, Liu Y, Wang Q, Ai B, Han X, Shi S, Zhang J, Li X, Tang Z, Pan Q, Wang Y, Wang F, Li C. SEdb: a comprehensive human super-enhancer database. Nucleic Acids Res 2019; 47:D235-D243. [PMID: 30371817 PMCID: PMC6323980 DOI: 10.1093/nar/gky1025] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/12/2018] [Accepted: 10/17/2018] [Indexed: 12/21/2022] Open
Abstract
Super-enhancers are important for controlling and defining the expression of cell-specific genes. With research on human disease and biological processes, human H3K27ac ChIP-seq datasets are accumulating rapidly, creating the urgent need to collect and process these data comprehensively and efficiently. More importantly, many studies showed that super-enhancer-associated single nucleotide polymorphisms (SNPs) and transcription factors (TFs) strongly influence human disease and biological processes. Here, we developed a comprehensive human super-enhancer database (SEdb, http://www.licpathway.net/sedb) that aimed to provide a large number of available resources on human super-enhancers. The database was annotated with potential functions of super-enhancers in the gene regulation. The current version of SEdb documented a total of 331 601 super-enhancers from 542 samples. Especially, unlike existing super-enhancer databases, we manually curated and classified 410 available H3K27ac samples from >2000 ChIP-seq samples from NCBI GEO/SRA. Furthermore, SEdb provides detailed genetic and epigenetic annotation information on super-enhancers. Information includes common SNPs, motif changes, expression quantitative trait locus (eQTL), risk SNPs, transcription factor binding sites (TFBSs), CRISPR/Cas9 target sites and Dnase I hypersensitivity sites (DHSs) for in-depth analyses of super-enhancers. SEdb will help elucidate super-enhancer-related functions and find potential biological effects.
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Affiliation(s)
- Yong Jiang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Fengcui Qian
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xuefeng Bai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yuejuan Liu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qiuyu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xiaole Han
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Shanshan Shi
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xuecang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Zhidong Tang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qi Pan
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yuezhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Fan Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
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Fagnocchi L, Poli V, Zippo A. Enhancer reprogramming in tumor progression: a new route towards cancer cell plasticity. Cell Mol Life Sci 2018; 75:2537-2555. [PMID: 29691590 PMCID: PMC11105402 DOI: 10.1007/s00018-018-2820-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/11/2018] [Accepted: 04/17/2018] [Indexed: 12/13/2022]
Abstract
Cancer heterogeneity arises during tumor progression as a consequence of genetic insults, environmental cues, and reversible changes in the epigenetic state, favoring tumor cell plasticity. The role of enhancer reprogramming is emerging as a relevant field in cancer biology as it supports adaptation of cancer cells to those environmental changes encountered during tumor progression and metastasis seeding. In this review, we describe the cancer-related alterations that drive oncogenic enhancer activity, leading to dysregulated transcriptional programs. We discuss the molecular mechanisms of both cis- and trans-factors in overriding the regulatory circuits that maintain cell-type specificity and imposing an alternative, de-regulated enhancer activity in cancer cells. We further comment on the increasing evidence which implicates stress response and aging-signaling pathways in the enhancer landscape reprogramming during tumorigenesis. Finally, we focus on the potential therapeutic implications of these enhancer-mediated subverted transcriptional programs, putting particular emphasis on the lack of information regarding tumor progression and the metastatic outgrowth, which still remain the major cause of mortality related to cancer.
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Affiliation(s)
- Luca Fagnocchi
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy.
| | - Vittoria Poli
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Alessio Zippo
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy.
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, 20122, Milan, Italy.
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
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Chronic lymphocytic leukemia and mantle cell lymphoma: crossroads of genetic and microenvironment interactions. Blood 2018; 131:2283-2296. [PMID: 29666114 DOI: 10.1182/blood-2017-10-764373] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/03/2018] [Indexed: 02/07/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) are 2 well-defined entities that diverge in their basic pathogenic mechanisms and clinical evolution but they share epidemiological characteristics, cells of origin, molecular alterations, and clinical features that differ from other lymphoid neoplasms. CLL and MCL are classically considered indolent and aggressive neoplasms, respectively. However, the clinical evolution of both tumors is very heterogeneous, with subsets of patients having stable disease for a long time whereas others require immediate intervention. Both CLL and MCL include 2 major molecular subtypes that seem to derive from antigen-experienced CD5+ B cells that retain a naive or memory-like epigenetic signature and carry a variable load of immunoglobulin heavy-chain variable region somatic mutations from truly unmutated to highly mutated, respectively. These 2 subtypes of tumors differ in their molecular pathways, genomic alterations, and clinical behavior, being more aggressive in naive-like than memory-like-derived tumors in both CLL and MCL. The pathogenesis of the 2 entities integrates the relevant influence of B-cell receptor signaling, tumor cell microenvironment interactions, genomic alterations, and epigenome modifications that configure the evolution of the tumors and offer new possibilities for therapeutic intervention. This review will focus on the similarities and differences of these 2 tumors based on recent studies that are enhancing the understanding of their pathogenesis and creating solid bases for new management strategies.
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Vijayakrishnan J, Studd J, Broderick P, Kinnersley B, Holroyd A, Law PJ, Kumar R, Allan JM, Harrison CJ, Moorman AV, Vora A, Roman E, Rachakonda S, Kinsey SE, Sheridan E, Thompson PD, Irving JA, Koehler R, Hoffmann P, Nöthen MM, Heilmann-Heimbach S, Jöckel KH, Easton DF, Pharaoh PDP, Dunning AM, Peto J, Canzian F, Swerdlow A, Eeles RA, Kote-Jarai ZS, Muir K, Pashayan N, Greaves M, Zimmerman M, Bartram CR, Schrappe M, Stanulla M, Hemminki K, Houlston RS. Genome-wide association study identifies susceptibility loci for B-cell childhood acute lymphoblastic leukemia. Nat Commun 2018; 9:1340. [PMID: 29632299 PMCID: PMC5890276 DOI: 10.1038/s41467-018-03178-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/25/2018] [Indexed: 01/19/2023] Open
Abstract
Genome-wide association studies (GWAS) have advanced our understanding of susceptibility to B-cell precursor acute lymphoblastic leukemia (BCP-ALL); however, much of the heritable risk remains unidentified. Here, we perform a GWAS and conduct a meta-analysis with two existing GWAS, totaling 2442 cases and 14,609 controls. We identify risk loci for BCP-ALL at 8q24.21 (rs28665337, P = 3.86 × 10-9, odds ratio (OR) = 1.34) and for ETV6-RUNX1 fusion-positive BCP-ALL at 2q22.3 (rs17481869, P = 3.20 × 10-8, OR = 2.14). Our findings provide further insights into genetic susceptibility to ALL and its biology.
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Affiliation(s)
- Jayaram Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - James Studd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, 69120, Heidelberg, Germany
| | - James M Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Christine J Harrison
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Anthony V Moorman
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Ajay Vora
- Department of Haematology, Great Ormond Street Hospital, London, WC1N 3JH, UK
| | - Eve Roman
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | | | - Sally E Kinsey
- Department of Paediatric and Adolescent Haematology and Oncology, Leeds General Infirmary, Leeds, LS1 3EX, UK
| | - Eamonn Sheridan
- Medical Genetics Research Group, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK
| | - Pamela D Thompson
- Paediatric and Familial Cancer Research Group, Institute of Cancer Sciences, St. Mary's Hospital, Manchester, M13 9WL, UK
| | - Julie A Irving
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Rolf Koehler
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Per Hoffmann
- Department of Genomics, Institute of Human Genetics, Life & Brain Centre, University of Bonn, D-53012, Bonn, Germany
- Department of Biomedicine, Human Genomics Research Group, University Hospital and University of Basel, 4031, Basel, Switzerland
| | - Markus M Nöthen
- Department of Genomics, Institute of Human Genetics, Life & Brain Centre, University of Bonn, D-53012, Bonn, Germany
| | - Stefanie Heilmann-Heimbach
- Department of Genomics, Institute of Human Genetics, Life & Brain Centre, University of Bonn, D-53012, Bonn, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Douglas F Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul D P Pharaoh
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Laboratory, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Frederico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Nora Pashayan
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Mel Greaves
- Centre for Evolution and Cancer, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Martin Zimmerman
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Claus R Bartram
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Martin Schrappe
- General Paediatrics, University Hospital Schleswig-Holstein, 24105, Kiel, Germany
| | - Martin Stanulla
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, 221 00, Lund, Sweden
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK.
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Abstract
Hematopoietic cancers are often initiated by deregulation of the transcriptional machinery. Prominent among such regulators are the sequence-specific DNA-binding transcription factors (TFs), which bind to enhancer and promoter elements in the genome to control gene expression through the recruitment of cofactors. Remarkably, perturbing the function of even a single TF or cofactor can modulate the active enhancer landscape of a cell; conversely, knowledge of the enhancer configuration can be used to discover functionally important TFs in a given cellular process. Our expanding insight into enhancer function can be attributed to the emergence of genome-scale measurements of enhancer activity, which can be applied to virtually any cell type to expose regulatory mechanisms. Such approaches are beginning to reveal the abnormal enhancer configurations present in cancer cells, thereby providing a framework for understanding how transcriptional dysregulation can lead to malignancy. Here, we review the evidence for alterations in enhancer landscapes contributing to the pathogenesis of leukemia, a malignancy in which enhancer-binding proteins and enhancer DNA itself are altered via genetic mutation. We will also highlight examples of small molecules that reprogram the enhancer landscape of leukemia cells in association with therapeutic benefit.
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Mansouri L, Wierzbinska JA, Plass C, Rosenquist R. Epigenetic deregulation in chronic lymphocytic leukemia: Clinical and biological impact. Semin Cancer Biol 2018; 51:1-11. [PMID: 29427646 DOI: 10.1016/j.semcancer.2018.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 12/12/2017] [Accepted: 02/05/2018] [Indexed: 01/01/2023]
Abstract
Deregulated transcriptional control caused by aberrant DNA methylation and/or histone modifications is a hallmark of cancer cells. In chronic lymphocytic leukemia (CLL), the most common adult leukemia, the epigenetic 'landscape' has added a new layer of complexity to our understanding of this clinically and biologically heterogeneous disease. Early studies identified aberrant DNA methylation, often based on single gene promoter analysis with both biological and clinical impact. Subsequent genome-wide profiling studies revealed differential DNA methylation between CLLs and controls and in prognostics subgroups of the disease. From these studies, it became apparent that DNA methylation in regions outside of promoters, such as enhancers, is important for the regulation of coding genes as well as for the regulation of non-coding RNAs. Although DNA methylation profiles are reportedly stable over time and in relation to therapy, a higher epigenetic heterogeneity or 'burden' is seen in more aggressive CLL subgroups, albeit as non-recurrent 'passenger' events. More recently, DNA methylation profiles in CLL analyzed in relation to differentiating normal B-cell populations revealed that the majority of the CLL epigenome reflects the epigenomes present in the cell of origin and that only a small fraction of the epigenetic alterations represents truly CLL-specific changes. Furthermore, CLL patients can be grouped into at least three clinically relevant epigenetic subgroups, potentially originating from different cells at various stages of differentiation and associated with distinct outcomes. In this review, we summarize the current understanding of the DNA methylome in CLL, the role of histone modifying enzymes, highlight insights derived from animal models and attempts made to target epigenetic regulators in CLL along with the future directions of this rapidly advancing field.
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Affiliation(s)
- Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Sweden
| | - Justyna Anna Wierzbinska
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Sweden.
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48
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Mediator complex components are frequent targets for genetic alterations in various types of human cancer. J Genet Genomics 2017; 44:587-591. [PMID: 29246864 DOI: 10.1016/j.jgg.2017.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/26/2017] [Accepted: 08/25/2017] [Indexed: 11/22/2022]
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49
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Ghamlouch H, Nguyen-Khac F, Bernard OA. Chronic lymphocytic leukaemia genomics and the precision medicine era. Br J Haematol 2017; 178:852-870. [DOI: 10.1111/bjh.14719] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hussein Ghamlouch
- Institut National De La Santé Et De La Recherche Médicale (INSERM) U1170; Villejuif France
- Gustave Roussy; Villejuif France
- Université Paris Saclay; Paris France
- Equipe Labellisée Ligue Nationale Contre Le Cancer; Paris France
| | - Florence Nguyen-Khac
- INSERM U1138; Université Pierre et Marie Curie-Paris 6; Service d'Hématologie Biologique; Hôpital Pitié-Salpêtrière; APHP; Paris France
| | - Olivier A. Bernard
- Institut National De La Santé Et De La Recherche Médicale (INSERM) U1170; Villejuif France
- Gustave Roussy; Villejuif France
- Université Paris Saclay; Paris France
- Equipe Labellisée Ligue Nationale Contre Le Cancer; Paris France
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50
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Sengupta S, George RE. Super-Enhancer-Driven Transcriptional Dependencies in Cancer. Trends Cancer 2017; 3:269-281. [PMID: 28718439 DOI: 10.1016/j.trecan.2017.03.006] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 11/24/2022]
Abstract
Transcriptional deregulation is one of the core tenets of cancer biology and is underpinned by alterations in both protein-coding genes and noncoding regulatory elements. Large regulatory elements, so-called super-enhancers (SEs), are central to the maintenance of cancer cell identity and promote oncogenic transcription to which cancer cells become highly addicted. Such dependence on SE-driven transcription for proliferation and survival offers an Achilles heel for the therapeutic targeting of cancer cells. Indeed, inhibition of the cellular machinery required for the assembly and maintenance of SEs dampens oncogenic transcription and inhibits tumor growth. In this article, we review the organization, function, and regulation of oncogenic SEs and their contribution to the cancer cell state.
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Affiliation(s)
- Satyaki Sengupta
- Department of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Rani E George
- Department of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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