101
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Yang X, Zheng W, Li M, Zhang S. Somatic Super-Enhancer Epigenetic Signature for Overall Survival Prediction in Patients with Breast Invasive Carcinoma. Bioinform Biol Insights 2023; 17:11779322231162767. [PMID: 37020500 PMCID: PMC10068971 DOI: 10.1177/11779322231162767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 02/18/2023] [Indexed: 04/03/2023] Open
Abstract
To analyze genome-wide super-enhancers (SEs) methylation signature of breast invasive carcinoma (BRCA) and its clinical value. Differential methylation sites (DMS) between BRCA and adjacent tissues from The Cancer Genome Atlas (TCGA) database were identified by using ChAMP package in R software. Super-enhancers were identified sing ROSE software. Overlap analysis was used to assess the potential DMS in SEs region. Feature selection was performed by Cox regression and least absolute shrinkage and selection operator (LASSO) algorithm based on TCGA training cohort. Prognosis model validation was performed in TCGA training cohort, TCGA validation cohort, and gene expression omnibus (GEO) test cohort. The gene ontology and KEGG analysis revealed that SEs target genes were significantly enriched in cell-migration-associated processes and pathways. A total of 83 654 DMS were identified between BRCA and adjacent tissues. Around 2397 DMS in SEs region were identified by overlap study and used to feature selection. By using Cox regression and LASSO algorithm, 42 features were selected to develop a clinical prediction model (CPM). Both training (TCGA) and validation cohorts (TCGA and GEO) show that the CPM has ideal discrimination and calibration. The CPM based on DMS at SE regions has ideal discrimination and calibration, which combined with tumor node metastasis (TNM) stage could improve prognostication, and thus contribute to individualized medicine.
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Affiliation(s)
- Xu Yang
- Department of Urology, Fujian Medical
University Union Hospital, Fuzhou, P.R. China
| | - Wenzhong Zheng
- Department of Urology, Fujian Medical
University Union Hospital, Fuzhou, P.R. China
| | - Mengqiang Li
- Department of Urology, Fujian Medical
University Union Hospital, Fuzhou, P.R. China
| | - Shiqiang Zhang
- Department of Urology, Kidney and
Urology Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen,
P.R. China
- Shiqiang Zhang, Department of Urology,
Kidney and Urology Center, The Seventh Affiliated Hospital, Sun Yat-Sen
University, No.628, Zhenyuan Rd, Guangming (New) Dist., Shenzhen 518107, P.R.
China.
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102
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Hu Y, Yang Q, Cai S, Wang W, Fu S. The integrative analysis based on super-enhancer related genes for predicting different subtypes and prognosis of patient with lower-grade glioma. Front Genet 2023; 14:1085584. [PMID: 37091789 PMCID: PMC10119407 DOI: 10.3389/fgene.2023.1085584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Objective: Emerging evidence revealed that super-enhancer plays a crucial role in the transcriptional reprogramming for many cancers. The purpose aimed to explored how the super-enhancer related genes affects the prognosis and tumor immune microenvironment (TIME) of patients with low-grade glioma (LGG). Methods: In this study, the differentially expressed genes (DEGs) between LGG cohorts and normal brain tissue cohort were identified by the comprehensive analysis of the super-enhancer (SE) related genes. Then non-negative matrix factorization was performed to seek the optimal classification based on the DEGs, while investigating prognostic and clinical differences between different subtypes. Subsequently, a prognostic related signature (SERS) was constructed for the comprehensive evaluation in term of individualized prognosis, clinical characteristics, cancer markers, genomic alterations, and immune microenvironment of patients with LGG. Results: Based on the expression profiles of 170 DEGs, we identified three SE subtypes, and the three subtypes showed significant differences in prognostic, clinicopathological features. Then, nine optimal SE-related genes were selected to construct the SERS through the least absolute shrinkage and selection operator Cox regression analysis. Survival analysis showed that SERS had strong and stable predictive ability for the prognosis of LGG patients in the The Cancer Genome Atlas, China Glioma Genome Atlas, and Remdrandt cohorts, respectively. We also found that SERS was highly correlated with clinicopathological features, tumor immune microenvironment, cancer hallmarks, and genomic alterations in LGG patients. In addition, the predictive power of SERS for immune checkpoint inhibitor treatment is also superior. The qRT-PCR results and immunohistochemical results also confirmed the difference in the expression of four key genes in normal cells and tumors, as well as in normal tissues and tumor tissues. Conclusion: The SERS could be suitable to utilize individualized prognosis prediction and immunotherapy options for LGG patients in clinical application.
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Affiliation(s)
- Yungang Hu
- Department of Neurosurgery, Wuhan University of Science and Technology Affiliated Xiaogan Central Hospital, Xiaogan, Hubei, China
| | - Qingqing Yang
- Department of Thyroid and Breast Surgery, Wuhan University of Science and Technology Affiliated Xiaogan Central Hospital, Xiaogan, Hubei, China
| | - Shuzhou Cai
- Department of Neurosurgery, Wuhan University of Science and Technology Affiliated Xiaogan Central Hospital, Xiaogan, Hubei, China
| | - Wei Wang
- Department of Neurosurgery, Wuhan University of Science and Technology Affiliated Xiaogan Central Hospital, Xiaogan, Hubei, China
| | - Shiyin Fu
- Department of Pediatric, Jinchu University of Technology Affiliated Central Hospital, Jingmen, Hubei, China
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103
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Ling X, Liu X, Jiang S, Fan L, Ding J. The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases. CELL REGENERATION (LONDON, ENGLAND) 2022; 11:42. [PMID: 36539553 PMCID: PMC9768101 DOI: 10.1186/s13619-022-00145-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022]
Abstract
Cell fate transition is a fascinating process involving complex dynamics of three-dimensional (3D) chromatin organization and phase separation, which play an essential role in cell fate decision by regulating gene expression. Phase separation is increasingly being considered a driving force of chromatin folding. In this review, we have summarized the dynamic features of 3D chromatin and phase separation during physiological and pathological cell fate transitions and systematically analyzed recent evidence of phase separation facilitating the chromatin structure. In addition, we discuss current advances in understanding how phase separation contributes to physical and functional enhancer-promoter contacts. We highlight the functional roles of 3D chromatin organization and phase separation in cell fate transitions, and more explorations are required to study the regulatory relationship between 3D chromatin organization and phase separation. 3D chromatin organization (shown by Hi-C contact map) and phase separation are highly dynamic and play functional roles during early embryonic development, cell differentiation, somatic reprogramming, cell transdifferentiation and pathogenetic process. Phase separation can regulate 3D chromatin organization directly, but whether 3D chromatin organization regulates phase separation remains unclear.
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Affiliation(s)
- Xiaoru Ling
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Xinyi Liu
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Shaoshuai Jiang
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Lili Fan
- grid.258164.c0000 0004 1790 3548Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong China
| | - Junjun Ding
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.410737.60000 0000 8653 1072Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436 China ,grid.13291.380000 0001 0807 1581West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041 China
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104
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Luo Y, Xiang S, Feng J. Protein Phase Separation: New Insights into Carcinogenesis. Cancers (Basel) 2022; 14:cancers14235971. [PMID: 36497453 PMCID: PMC9740862 DOI: 10.3390/cancers14235971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Phase separation is now acknowledged as an essential biologic mechanism wherein distinct activated molecules assemble into a different phase from the surrounding constituents of a cell. Condensates formed by phase separation play an essential role in the life activities of various organisms under normal physiological conditions, including the advanced structure and regulation of chromatin, autophagic degradation of incorrectly folded or unneeded proteins, and regulation of the actin cytoskeleton. During malignant transformation, abnormally altered condensate assemblies are often associated with the abnormal activation of oncogenes or inactivation of tumor suppressors, resulting in the promotion of the carcinogenic process. Thus, understanding the role of phase separation in various biological evolutionary processes will provide new ideas for the development of drugs targeting specific condensates, which is expected to be an effective cancer therapy strategy. However, the relationship between phase separation and cancer has not been fully elucidated. In this review, we mainly summarize the main processes and characteristics of phase separation and the main methods for detecting phase separation. In addition, we summarize the cancer proteins and signaling pathways involved in phase separation and discuss their promising future applications in addressing the unmet clinical therapeutic needs of people with cancer. Finally, we explain the means of targeted phase separation and cancer treatment.
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105
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Current challenges in understanding the role of enhancers in disease. Nat Struct Mol Biol 2022; 29:1148-1158. [PMID: 36482255 DOI: 10.1038/s41594-022-00896-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/04/2022] [Indexed: 12/13/2022]
Abstract
Enhancers play a central role in the spatiotemporal control of gene expression and tend to work in a cell-type-specific manner. In addition, they are suggested to be major contributors to phenotypic variation, evolution and disease. There is growing evidence that enhancer dysfunction due to genetic, structural or epigenetic mechanisms contributes to a broad range of human diseases referred to as enhanceropathies. Such mechanisms often underlie the susceptibility to common diseases, but can also play a direct causal role in cancer or Mendelian diseases. Despite the recent gain of insights into enhancer biology and function, we still have a limited ability to predict how enhancer dysfunction impacts gene expression. Here we discuss the major challenges that need to be overcome when studying the role of enhancers in disease etiology and highlight opportunities and directions for future studies, aiming to disentangle the molecular basis of enhanceropathies.
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106
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Xu Z, Lee DS, Chandran S, Le VT, Bump R, Yasis J, Dallarda S, Marcotte S, Clock B, Haghani N, Cho CY, Akdemir K, Tyndale S, Futreal PA, McVicker G, Wahl GM, Dixon JR. Structural variants drive context-dependent oncogene activation in cancer. Nature 2022; 612:564-572. [PMID: 36477537 PMCID: PMC9810360 DOI: 10.1038/s41586-022-05504-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Higher-order chromatin structure is important for the regulation of genes by distal regulatory sequences1,2. Structural variants (SVs) that alter three-dimensional (3D) genome organization can lead to enhancer-promoter rewiring and human disease, particularly in the context of cancer3. However, only a small minority of SVs are associated with altered gene expression4,5, and it remains unclear why certain SVs lead to changes in distal gene expression and others do not. To address these questions, we used a combination of genomic profiling and genome engineering to identify sites of recurrent changes in 3D genome structure in cancer and determine the effects of specific rearrangements on oncogene activation. By analysing Hi-C data from 92 cancer cell lines and patient samples, we identified loci affected by recurrent alterations to 3D genome structure, including oncogenes such as MYC, TERT and CCND1. By using CRISPR-Cas9 genome engineering to generate de novo SVs, we show that oncogene activity can be predicted by using 'activity-by-contact' models that consider partner region chromatin contacts and enhancer activity. However, activity-by-contact models are only predictive of specific subsets of genes in the genome, suggesting that different classes of genes engage in distinct modes of regulation by distal regulatory elements. These results indicate that SVs that alter 3D genome organization are widespread in cancer genomes and begin to illustrate predictive rules for the consequences of SVs on oncogene activation.
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Affiliation(s)
- Zhichao Xu
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA,These authors contributed equally
| | - Dong-Sung Lee
- Department of Life Sciences, University of Seoul, Seoul, South Korea,These authors contributed equally
| | - Sahaana Chandran
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Victoria T. Le
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Rosalind Bump
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Jean Yasis
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Sofia Dallarda
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Samantha Marcotte
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Benjamin Clock
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Nicholas Haghani
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Chae Yun Cho
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Kadir Akdemir
- Department of Genomic Medicine; UT MD Anderson Cancer Center; Houston, TX, 77030; USA
| | - Selene Tyndale
- Integrative Biology Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - P. Andrew Futreal
- Department of Genomic Medicine; UT MD Anderson Cancer Center; Houston, TX, 77030; USA
| | - Graham McVicker
- Integrative Biology Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Geoffrey M. Wahl
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Jesse R. Dixon
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA,Correspondence:
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107
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Chen PB, Fiaux PC, Zhang K, Li B, Kubo N, Jiang S, Hu R, Rooholfada E, Wu S, Wang M, Wang W, McVicker G, Mischel PS, Ren B. Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation. Cell Rep 2022; 41:111630. [PMID: 36351387 PMCID: PMC9687083 DOI: 10.1016/j.celrep.2022.111630] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 07/21/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
A scarcity of functionally validated enhancers in the human genome presents a significant hurdle to understanding how these cis-regulatory elements contribute to human diseases. We carry out highly multiplexed CRISPR-based perturbation and sequencing to identify enhancers required for cell proliferation and fitness in 10 human cancer cell lines. Our results suggest that the cell fitness enhancers, unlike their target genes, display high cell-type specificity of chromatin features. They typically adopt a modular structure, comprised of activating elements enriched for motifs of oncogenic transcription factors, surrounded by repressive elements enriched for motifs recognized by transcription factors with tumor suppressor functions. We further identify cell fitness enhancers that are selectively accessible in clinical tumor samples, and the levels of chromatin accessibility are associated with patient survival. These results reveal functional enhancers across multiple cancer cell lines, characterize their context-dependent chromatin organization, and yield insights into altered transcription programs in cancer cells.
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Affiliation(s)
- Poshen B Chen
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore 138672, Singapore
| | - Patrick C Fiaux
- Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Kai Zhang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Bin Li
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Naoki Kubo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Shan Jiang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Rong Hu
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Emma Rooholfada
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Mengchi Wang
- Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Wei Wang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Graham McVicker
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Paul S Mischel
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA; Institute of Genome Medicine, UCSD School of Medicine, La Jolla, CA 92093, USA; Ludwig Institute for Cancer Research, San Diego, La Jolla, CA 92093, USA.
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108
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Markouli M, Strepkos D, Piperi C. Impact of Histone Modifications and Their Therapeutic Targeting in Hematological Malignancies. Int J Mol Sci 2022; 23:13657. [PMID: 36362442 PMCID: PMC9654260 DOI: 10.3390/ijms232113657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Hematologic malignancies are a large and heterogeneous group of neoplasms characterized by complex pathogenetic mechanisms. The abnormal regulation of epigenetic mechanisms and specifically, histone modifications, has been demonstrated to play a central role in hematological cancer pathogenesis and progression. A variety of epigenetic enzymes that affect the state of histones have been detected as deregulated, being either over- or underexpressed, which induces changes in chromatin compaction and, subsequently, affects gene expression. Recent advances in the field of epigenetics have revealed novel therapeutic targets, with many epigenetic drugs being investigated in clinical trials. The present review focuses on the biological impact of histone modifications in the pathogenesis of hematologic malignancies, describing a wide range of therapeutic agents that have been discovered to target these alterations and are currently under investigation in clinical trials.
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Affiliation(s)
| | | | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (M.M.); (D.S.)
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109
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Ren J, Zhang Z, Zong Z, Zhang L, Zhou F. Emerging Implications of Phase Separation in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202855. [PMID: 36117111 PMCID: PMC9631093 DOI: 10.1002/advs.202202855] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Indexed: 05/19/2023]
Abstract
In eukaryotic cells, biological activities are executed in distinct cellular compartments or organelles. Canonical organelles with membrane-bound structures are well understood. Cells also inherently contain versatile membrane-less organelles (MLOs) that feature liquid or gel-like bodies. A biophysical process termed liquid-liquid phase separation (LLPS) elucidates how MLOs form through dynamic biomolecule assembly. LLPS-related molecules often have multivalency, which is essential for low-affinity inter- or intra-molecule interactions to trigger phase separation. Accumulating evidence shows that LLPS concentrates and organizes desired molecules or segregates unneeded molecules in cells. Thus, MLOs have tunable functional specificity in response to environmental stimuli and metabolic processes. Aberrant LLPS is widely associated with several hallmarks of cancer, including sustained proliferative signaling, growth suppressor evasion, cell death resistance, telomere maintenance, DNA damage repair, etc. Insights into the molecular mechanisms of LLPS provide new insights into cancer therapeutics. Here, the current understanding of the emerging concepts of LLPS and its involvement in cancer are comprehensively reviewed.
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Affiliation(s)
- Jiang Ren
- School of MedicineZhejiang University City CollegeHangzhou215123China
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Zhenyu Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan450003China
| | - Zhi Zong
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Long Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
- International Biomed‐X Research Center, Second Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhou215123China
| | - Fangfang Zhou
- School of MedicineZhejiang University City CollegeHangzhou215123China
- Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123China
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110
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Yu CH, Wu G, Chang CC, Jou ST, Lu MY, Lin KH, Chen SH, Wu KH, Huang FL, Cheng CN, Chang HH, Hedges D, Wang JL, Yen HJ, Li MJ, Chou SW, Hung CT, Lin ZS, Lin CY, Chen HY, Ni YL, Hsu YC, Lin DT, Lin SW, Yang JJ, Pui CH, Yu SL, Yang YL. Sequential Approach to Improve the Molecular Classification of Childhood Acute Lymphoblastic Leukemia. J Mol Diagn 2022; 24:1195-1206. [PMID: 35963521 PMCID: PMC9667711 DOI: 10.1016/j.jmoldx.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/27/2022] [Accepted: 08/03/2022] [Indexed: 10/15/2022] Open
Abstract
Identification of specific leukemia subtypes is a key to successful risk-directed therapy in childhood acute lymphoblastic leukemia (ALL). Although RNA sequencing (RNA-seq) is the best approach to identify virtually all specific leukemia subtypes, the routine use of this method is too costly for patients in resource-limited countries. This study enrolled 295 patients with pediatric ALL from 2010 to 2020. Routine screening could identify major cytogenetic alterations in approximately 69% of B-cell ALL (B-ALL) cases by RT-PCR, DNA index, and multiplex ligation-dependent probe amplification. STIL-TAL1 was present in 33% of T-cell ALL (T-ALL) cases. The remaining samples were submitted for RNA-seq. More than 96% of B-ALL cases and 74% of T-ALL cases could be identified based on the current molecular classification using this sequential approach. Patients with Philadelphia chromosome-like ALL constituted only 2.4% of the entire cohort, a rate even lower than those with ZNF384-rearranged (4.8%), DUX4-rearranged (6%), and Philadelphia chromosome-positive (4.4%) ALL. Patients with ETV6-RUNX1, high hyperdiploidy, PAX5 alteration, and DUX4 rearrangement had favorable prognosis, whereas those with hypodiploid and KMT2A and MEF2D rearrangement ALL had unfavorable outcomes. With the use of multiplex ligation-dependent probe amplification, DNA index, and RT-PCR in B-ALL and RT-PCR in T-ALL followed by RNA-seq, childhood ALL can be better classified to improve clinical assessments.
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Affiliation(s)
- Chih-Hsiang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chia-Ching Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shiann-Tarng Jou
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan; Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Yao Lu
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan; Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Kai-Hsin Lin
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Shu-Huey Chen
- Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Kang-Hsi Wu
- Department of Pediatrics, Chung Shan Medical University Hospital and School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Fang-Liang Huang
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chao-Neng Cheng
- Department of Pediatrics, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Hsiu-Hao Chang
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan; Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Dale Hedges
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinn-Li Wang
- Division of Hematology Oncology, Department of Pediatrics, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hsiu-Ju Yen
- Department of Pediatrics, Taipei Veterans General Hospital and National Yang-Ming Chiao-Tung University School of Medicine, Taipei, Taiwan
| | - Meng-Ju Li
- Department of Pediatrics, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
| | - Shu-Wei Chou
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Chen-Ting Hung
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ze-Shiang Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Yu Lin
- Institute of Statistical Science Academia Sinica, Taipei, Taiwan
| | - Hsuan-Yu Chen
- Institute of Statistical Science Academia Sinica, Taipei, Taiwan
| | - Yu-Ling Ni
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yin-Chen Hsu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Dong-Tsamn Lin
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Shu-Wha Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jun J Yang
- Department of Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan; Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Yung-Li Yang
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Laboratory Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
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111
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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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112
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Laukkanen S, Veloso A, Yan C, Oksa L, Alpert EJ, Do D, Hyvärinen N, McCarthy K, Adhikari A, Yang Q, Iyer S, Garcia SP, Pello A, Ruokoranta T, Moisio S, Adhikari S, Yoder JA, Gallagher K, Whelton L, Allen JR, Jin AH, Loontiens S, Heinäniemi M, Kelliher M, Heckman CA, Lohi O, Langenau DM. Therapeutic targeting of LCK tyrosine kinase and mTOR signaling in T-cell acute lymphoblastic leukemia. Blood 2022; 140:1891-1906. [PMID: 35544598 PMCID: PMC10082361 DOI: 10.1182/blood.2021015106] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/19/2022] [Indexed: 11/20/2022] Open
Abstract
Relapse and refractory T-cell acute lymphoblastic leukemia (T-ALL) has a poor prognosis, and new combination therapies are sorely needed. Here, we used an ex vivo high-throughput screening platform to identify drug combinations that kill zebrafish T-ALL and then validated top drug combinations for preclinical efficacy in human disease. This work uncovered potent drug synergies between AKT/mTORC1 (mammalian target of rapamycin complex 1) inhibitors and the general tyrosine kinase inhibitor dasatinib. Importantly, these same drug combinations effectively killed a subset of relapse and dexamethasone-resistant zebrafish T-ALL. Clinical trials are currently underway using the combination of mTORC1 inhibitor temsirolimus and dasatinib in other pediatric cancer indications, leading us to prioritize this therapy for preclinical testing. This combination effectively curbed T-ALL growth in human cell lines and primary human T-ALL and was well tolerated and effective in suppressing leukemia growth in patient-derived xenografts (PDX) grown in mice. Mechanistically, dasatinib inhibited phosphorylation and activation of the lymphocyte-specific protein tyrosine kinase (LCK) to blunt the T-cell receptor (TCR) signaling pathway, and when complexed with mTORC1 inhibition, induced potent T-ALL cell killing through reducing MCL-1 protein expression. In total, our work uncovered unexpected roles for the LCK kinase and its regulation of downstream TCR signaling in suppressing apoptosis and driving continued leukemia growth. Analysis of a wide array of primary human T-ALLs and PDXs grown in mice suggest that combination of temsirolimus and dasatinib treatment will be efficacious for a large fraction of human T-ALLs.
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Affiliation(s)
- Saara Laukkanen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alexandra Veloso
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Chuan Yan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Laura Oksa
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Eric J. Alpert
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Daniel Do
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Noora Hyvärinen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Karin McCarthy
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Abhinav Adhikari
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Qiqi Yang
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Sowmya Iyer
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Sara P. Garcia
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Annukka Pello
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Tanja Ruokoranta
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Sanni Moisio
- The Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Sadiksha Adhikari
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Jeffrey A. Yoder
- Department of Molecular Biomedical Sciences, Comparative Medicine Institute, and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC
| | - Kayleigh Gallagher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Lauren Whelton
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - James R. Allen
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Alex H. Jin
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Siebe Loontiens
- Cancer Research Institute Ghent and Center for Medical Genetics, Ghent, Belgium
| | - Merja Heinäniemi
- The Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Michelle Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Caroline A. Heckman
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Olli Lohi
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere University Hospital, Tays Cancer Center, Tampere, Finland
| | - David M. Langenau
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
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113
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Zhou RW, Xu J, Martin TC, Zachem AL, He J, Ozturk S, Demircioglu D, Bansal A, Trotta AP, Giotti B, Gryder B, Shen Y, Wu X, Carcamo S, Bosch K, Hopkins B, Tsankov A, Steinhagen R, Jones DR, Asara J, Chipuk JE, Brody R, Itzkowitz S, Chio IIC, Hasson D, Bernstein E, Parsons RE. A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma. Nat Commun 2022; 13:6041. [PMID: 36253360 PMCID: PMC9576746 DOI: 10.1038/s41467-022-33377-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/15/2022] [Indexed: 12/24/2022] Open
Abstract
Tumors exhibit enhancer reprogramming compared to normal tissue. The etiology is largely attributed to cell-intrinsic genomic alterations. Here, using freshly resected primary CRC tumors and patient-matched adjacent normal colon, we find divergent epigenetic landscapes between CRC tumors and cell lines. Intriguingly, this phenomenon extends to highly recurrent aberrant super-enhancers gained in CRC over normal. We find one such super-enhancer activated in epithelial cancer cells due to surrounding inflammation in the tumor microenvironment. We restore this super-enhancer and its expressed gene, PDZK1IP1, following treatment with cytokines or xenotransplantation into nude mice, thus demonstrating cell-extrinsic etiology. We demonstrate mechanistically that PDZK1IP1 enhances the reductive capacity CRC cancer cells via the pentose phosphate pathway. We show this activation enables efficient growth under oxidative conditions, challenging the previous notion that PDZK1IP1 acts as a tumor suppressor in CRC. Collectively, these observations highlight the significance of epigenomic profiling on primary specimens.
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Affiliation(s)
- Royce W Zhou
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jia Xu
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tiphaine C Martin
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexis L Zachem
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John He
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sait Ozturk
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Deniz Demircioglu
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ankita Bansal
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew P Trotta
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Berkley Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yao Shen
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xuewei Wu
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Saul Carcamo
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kaitlyn Bosch
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Benjamin Hopkins
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander Tsankov
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Randolph Steinhagen
- Division of Colon and Rectal Surgery, Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Drew R Jones
- Metabolomics Core Resource Laboratory, NYU Langone Health, New York, NY, 10016, USA
| | - John Asara
- Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Jerry E Chipuk
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rachel Brody
- Mount Sinai Biorepository, Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Steven Itzkowitz
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Iok In Christine Chio
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Medical Center, New York, NY, 10032, USA
| | - Dan Hasson
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ramon E Parsons
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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NSMCE2, a novel super-enhancer-regulated gene, is linked to poor prognosis and therapy resistance in breast cancer. BMC Cancer 2022; 22:1056. [PMID: 36224576 PMCID: PMC9555101 DOI: 10.1186/s12885-022-10157-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/07/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Despite today's advances in the treatment of cancer, breast cancer-related mortality remains high, in part due to the lack of effective targeted therapies against breast tumor types that do not respond to standard treatments. Therefore, identifying additional breast cancer molecular targets is urgently needed. Super-enhancers are large regions of open chromatin involved in the overactivation of oncogenes. Thus, inhibition of super-enhancers has become a focus in clinical trials for its therapeutic potential. Here, we aimed to identify novel super-enhancer dysregulated genes highly associated with breast cancer patients' poor prognosis and negative response to treatment. METHODS Using existing datasets containing super-enhancer-associated genes identified in breast tumors and public databases comprising genomic and clinical information for breast cancer patients, we investigated whether highly expressed super-enhancer-associated genes correlate to breast cancer patients' poor prognosis and to patients' poor response to therapy. Our computational findings were experimentally confirmed in breast cancer cells by pharmacological SE disruption and gene silencing techniques. RESULTS We bioinformatically identified two novel super-enhancer-associated genes - NSMCE2 and MAL2 - highly upregulated in breast tumors, for which high RNA levels significantly and specifically correlate with breast cancer patients' poor prognosis. Through in-vitro pharmacological super-enhancer disruption assays, we confirmed that super-enhancers upregulate NSMCE2 and MAL2 transcriptionally, and, through bioinformatics, we found that high levels of NSMCE2 strongly associate with patients' poor response to chemotherapy, especially for patients diagnosed with aggressive triple negative and HER2 positive tumor types. Finally, we showed that decreasing NSMCE2 gene expression increases breast cancer cells' sensitivity to chemotherapy treatment. CONCLUSIONS Our results indicate that moderating the transcript levels of NSMCE2 could improve patients' response to standard chemotherapy consequently improving disease outcome. Our approach offers a new avenue to identify a signature of tumor specific genes that are not frequently mutated but dysregulated by super-enhancers. As a result, this strategy can lead to the discovery of potential and novel pharmacological targets for improving targeted therapy and the treatment of breast cancer.
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115
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Super-enhancers conserved within placental mammals maintain stem cell pluripotency. Proc Natl Acad Sci U S A 2022; 119:e2204716119. [PMID: 36161929 DOI: 10.1073/pnas.2204716119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite pluripotent stem cells sharing key transcription factors, their maintenance involves distinct genetic inputs. Emerging evidence suggests that super-enhancers (SEs) can function as master regulatory hubs to control cell identity and pluripotency in humans and mice. However, whether pluripotency-associated SEs share an evolutionary origin in mammals remains elusive. Here, we performed comprehensive comparative epigenomic and transcription factor binding analyses among pigs, humans, and mice to identify pluripotency-associated SEs. Like typical enhancers, SEs displayed rapid evolution in mammals. We showed that BRD4 is an essential and conserved activator for mammalian pluripotency-associated SEs. Comparative motif enrichment analysis revealed 30 shared transcription factor binding motifs among the three species. The majority of transcriptional factors that bind to identified motifs are known regulators associated with pluripotency. Further, we discovered three pluripotency-associated SEs (SE-SOX2, SE-PIM1, and SE-FGFR1) that displayed remarkable conservation in placental mammals and were sufficient to drive reporter gene expression in a pluripotency-dependent manner. Disruption of these conserved SEs through the CRISPR-Cas9 approach severely impaired stem cell pluripotency. Our study provides insights into the understanding of conserved regulatory mechanisms underlying the maintenance of pluripotency as well as species-specific modulation of the pluripotency-associated regulatory networks in mammals.
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Takayama KI, Inoue S. Targeting phase separation on enhancers induced by transcription factor complex formations as a new strategy for treating drug-resistant cancers. Front Oncol 2022; 12:1024600. [PMID: 36263200 PMCID: PMC9574090 DOI: 10.3389/fonc.2022.1024600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022] Open
Abstract
The limited options for treating patients with drug-resistant cancers have emphasized the need to identify alternative treatment targets. Tumor cells have large super-enhancers (SEs) in the vicinity of important oncogenes for activation. The physical process of liquid-liquid phase separation (LLPS) contributes to the assembly of several membrane-less organelles in mammalian cells. Intrinsically disordered regions (IDRs) of proteins induce LLPS formation by developing condensates. It was discovered that key transcription factors (TFs) undergo LLPS in SEs. In addition, TFs play critical roles in the epigenetic and genetic regulation of cancer progression. Recently, we revealed the essential role of disease-specific TF collaboration changes in advanced prostate cancer (PC). OCT4 confers epigenetic changes by promoting complex formation with TFs, such as Forkhead box protein A1 (FOXA1), androgen receptor (AR) and Nuclear respiratory factor 1 (NRF1), inducing PC progression. It was demonstrated that TF collaboration through LLPS underlying transcriptional activation contributes to cancer aggressiveness and drug resistance. Moreover, the disruption of TF-mediated LLPS inhibited treatment-resistant PC tumor growth. Therefore, we propose that repression of TF collaborations involved in the LLPS of SEs could be a promising strategy for advanced cancer therapy. In this article, we summarize recent evidence highlighting the formation of LLPS on enhancers as a potent therapeutic target in advanced cancers.
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Affiliation(s)
- Ken-ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, Saitama, Japan
- *Correspondence: Satoshi Inoue,
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117
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Summers RJ, Teachey DT. SOHO State of the Art Updates and Next Questions | Novel Approaches to Pediatric T-cell ALL and T-Lymphoblastic Lymphoma. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2022; 22:718-725. [PMID: 35941070 PMCID: PMC9644234 DOI: 10.1016/j.clml.2022.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
While outcomes for children with T-cell acute lymphoblastic leukemia (T-ALL) and T-lymphoblastic lymphoma (T-LL) have improved significantly with contemporary therapy, outcomes for patients with relapsed or refractory (r/r) disease remain dismal. Improved risk stratification and the incorporation of novel therapeutics have the potential to improve outcomes further in T-ALL/T-LL by limiting relapse risk and improving salvage rates for those with r/r disease. In this review we will discuss the challenges and new opportunities for improved risk stratification in T-ALL and T-LL. We will further discuss the recent incorporation of the novel therapeutics nelarabine and bortezomib into front-line therapy for children with T-ALL and T-LL. Finally, we will address new classes of targeted small molecule inhibitors, immunotherapeutics, and chimeric antigen receptor T-cell therapies under investigation in r/r T-ALL and T-LL.
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Affiliation(s)
- Ryan J Summers
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA 30322 USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - David T Teachey
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
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118
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Nair SJ, Suter T, Wang S, Yang L, Yang F, Rosenfeld MG. Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures. Trends Genet 2022; 38:1019-1047. [PMID: 35811173 PMCID: PMC9474616 DOI: 10.1016/j.tig.2022.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 02/08/2023]
Abstract
Gene regulation by transcriptional enhancers is the dominant mechanism driving cell type- and signal-specific transcriptional diversity in metazoans. However, over four decades since the original discovery, how enhancers operate in the nuclear space remains largely enigmatic. Recent multidisciplinary efforts combining real-time imaging, genome sequencing, and biophysical strategies provide insightful but conflicting models of enhancer-mediated gene control. Here, we review the discovery and progress in enhancer biology, emphasizing the recent findings that acutely activated enhancers assemble regulatory machinery as mesoscale architectural structures with distinct physical properties. These findings help formulate novel models that explain several mysterious features of the assembly of transcriptional enhancers and the mechanisms of spatial control of gene expression.
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Affiliation(s)
- Sreejith J Nair
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.
| | - Tom Suter
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan Wang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Cellular and Molecular Medicine Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lu Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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119
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Geng K, Merino LG, Wedemann L, Martens A, Sobota M, Sanchez YP, Søndergaard JN, White RJ, Kutter C. Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells. Genome Res 2022; 32:1876-1891. [PMID: 36180232 PMCID: PMC9712622 DOI: 10.1101/gr.276901.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022]
Abstract
The CRISPR-Cas9 system is widely used to permanently delete genomic regions via dual guide RNAs. Genomic rearrangements induced by CRISPR-Cas9 can occur, but continuous technical developments make it possible to characterize complex on-target effects. We combined an innovative droplet-based target enrichment approach with long-read sequencing and coupled it to a customized de novo sequence assembly. This approach enabled us to dissect the sequence content at kilobase scale within an on-target genomic locus. We here describe extensive genomic disruptions by Cas9, involving the allelic co-occurrence of a genomic duplication and inversion of the target region, as well as integrations of exogenous DNA and clustered interchromosomal DNA fragment rearrangements. Furthermore, we found that these genomic alterations led to functional aberrant DNA fragments and can alter cell proliferation. Our findings broaden the consequential spectrum of the Cas9 deletion system, reinforce the necessity of meticulous genomic validations, and introduce a data-driven workflow enabling detailed dissection of the on-target sequence content with superior resolution.
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Affiliation(s)
- Keyi Geng
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Lara G Merino
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Linda Wedemann
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Aniek Martens
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Małgorzata Sobota
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Yerma P Sanchez
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Jonas Nørskov Søndergaard
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Robert J White
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Claudia Kutter
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
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LncRNA SNHG1 regulates neuroblastoma cell fate via interactions with HDAC1/2. Cell Death Dis 2022; 13:809. [PMID: 36130928 PMCID: PMC9492769 DOI: 10.1038/s41419-022-05256-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 01/23/2023]
Abstract
The small nucleolar RNA host gene 1 (SNHG1) is a novel oncogenic long non-coding RNA (lncRNA) aberrantly expressed in different tumor types. We previously found highly expressed SNHG1 was associated with poor prognosis and MYCN status in neuroblastoma (NB). However, the molecular mechanisms of SNHG1 in NB are still unclear. Here, we disrupted endogenous SNHG1 in the MYCN-amplified NB cell line SK-N-BE(2)C using the CRISPR/Cas9 system and demonstrated the proliferation and colony formation ability of SNHG1-knowndown cells were suppressed. The transcriptome analysis and functional assays of SNHG1-knockdown cells revealed SNHG1 was involved in various biological processes including cell growth, migration, apoptosis, cell cycle, and reactive oxygen species (ROS). Interestingly, the expression of core regulatory circuitry (CRC) transcription factors in MYCN-amplified NB, including PHOX2B, HAND2, GATA3, ISL1, TBX1, and MYCN, were decreased in SNHG1-knockdown cells. The chromatin-immunoprecipitation sequencing (ChIP-seq) and transposase-accessible chromatin using sequencing (ATAC-seq) analyses showed that chromatin status of these CRC members was altered, which might stem from interactions between SNHG1 and HDAC1/2. These findings demonstrate that SNHG1 plays a crucial role in maintaining NB identity via chromatin regulation and reveal the function of the lncRNA SNHG1 in NB.
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Sun J, Zhang Q, Sun X, Xue A, Gao X, Shen K. THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours. Cell Commun Signal 2022; 20:138. [PMID: 36076237 PMCID: PMC9454178 DOI: 10.1186/s12964-022-00928-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022] Open
Abstract
Background Gastrointestinal stromal tumours (GISTs) are the most common mesenchymal tumours of the gastrointestinal tract and are characterized by activating mutations of c-KIT or PDGFRa receptor tyrosine kinases (RTKs). Despite the clinical success of tyrosine kinase inhibitors (TKIs), more than half of GIST patients develop resistance due to a second mutation. Cyclin-dependent kinase 7 (CDK7) is the catalytic subunit of CDK-activating kinase (CAK), and it plays an important role in the regulation of cell cycle transitions and gene transcription. THZ1, a CDK7 inhibitor, exhibits a dose-dependent inhibitory effect in various cancers. Methods Data from the public GEO database and tissue microarray were used to analyse the gene expression levels of CDKs in GISTs. The impact of CDK7 knockdown and the CDK7 inhibitor THZ1 on GIST progression was investigated in vitro using CCK-8, colony formation, and flow cytometry assays and in vivo using a xenograft mouse model. RNA sequencing was performed to investigate the mechanism of GIST cell viability impairment mediated by THZ1 treatment. Results Our study demonstrated that CDK7 is relatively overexpressed in high-risk GISTs and predicts a poor outcome. A low concentration of THZ1 exhibited a pronounced antineoplastic effect in GIST cells in vivo and in vitro. Moreover, THZ1 exerted synergistic anticancer effects with imatinib. THZ1 treatment resulted in transcriptional modulation by inhibiting the phosphorylation of Ser2, Ser5, and Ser7 within RNA polymerase II (RNAPII). c-KIT, an oncogene driver of GIST, was transcriptionally repressed by THZ1 treatment or CDK7 knockdown. Transcriptome sequencing analysis showed that OSR1 acts as a downstream target of CDK7 and regulates c-KIT expression. Taken together, our results highlight elevated CDK7 expression as a predictor of poor outcome in GIST and present the combination of CDK7 and RTK inhibitors as a potent therapeutic strategy to improve the efficacy of GIST treatment. Video abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00928-x.
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Affiliation(s)
- Jianyi Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Qiang Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Xiangfei Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Anwei Xue
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Xiaodong Gao
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China.
| | - Kuntang Shen
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China.
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Typical Enhancers, Super-Enhancers, and Cancers. Cancers (Basel) 2022; 14:cancers14184375. [PMID: 36139535 PMCID: PMC9496678 DOI: 10.3390/cancers14184375] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary The cancer genome has been exhaustively studied upon the advent of Next-Generation Sequencing technologies. Coding and non-coding sequences have been defined as hotspots of genomic variations that affect the naïve gene expression programs established in normal cells, thus working as endogenous drivers of carcinogenesis. In this review, we comprehensively summarize fundamental aspects of gene expression regulation, with emphasis on the impact of sequence and structural variations mapped across non-coding cis-acting elements of genes encoding for tumor-related transcription factors. Chromatin architecture, epigenome reprogramming, transcriptional enhancers and Super-enhancers, oncogene regulation, cutting-edge technologies, and pharmacological treatment are substantially highlighted. Abstract Non-coding segments of the human genome are enriched in cis-regulatory modules that constitute functional elements, such as transcriptional enhancers and Super-enhancers. A hallmark of cancer pathogenesis is the dramatic dysregulation of the “archetype” gene expression profiles of normal human cells. Genomic variations can promote such deficiencies when occurring across enhancers and Super-enhancers, since they affect their mechanistic principles, their functional capacity and specificity, and the epigenomic features of the chromatin microenvironment across which these regulatory elements reside. Here, we comprehensively describe: fundamental mechanisms of gene expression dysregulation in cancers that involve genomic abnormalities within enhancers’ and Super-enhancers’ (SEs) sequences, which alter the expression of oncogenic transcription factors (TFs); cutting-edge technologies applied for the analysis of variation-enriched hotspots of the cancer genome; and pharmacological approaches for the treatment of Super-enhancers’ aberrant function. Finally, we provide an intratumor meta-analysis, which highlights that genomic variations in transcription-factor-driven tumors are accompanied overexpression of genes, a portion of which encodes for additional cancer-related transcription factors.
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123
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In APL, noncoding mutations and SNP converge on WT1. Blood 2022; 140:1060-1061. [PMID: 36074531 DOI: 10.1182/blood.2022017214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/15/2022] [Indexed: 11/20/2022] Open
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124
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Song H, Liu Y, Tan Y, Zhang Y, Jin W, Chen L, Wu S, Yan J, Li J, Chen Z, Chen S, Wang K. Recurrent noncoding somatic and germline WT1 variants converge to disrupt MYB binding in acute promyelocytic leukemia. Blood 2022; 140:1132-1144. [PMID: 35653587 PMCID: PMC9461475 DOI: 10.1182/blood.2021014945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/24/2022] [Indexed: 11/22/2022] Open
Abstract
Genetic alternations can occur at noncoding regions, but how they contribute to cancer pathogenesis is poorly understood. Here, we established a mutational landscape of cis-regulatory regions (CREs) in acute promyelocytic leukemia (APL) based on whole-genome sequencing analysis of paired tumor and germline samples from 24 patients and epigenetic profiling of 16 patients. Mutations occurring in CREs occur preferentially in active enhancers bound by the complex of master transcription factors in APL. Among significantly enriched mutated CREs, we found a recurrently mutated region located within the third intron of WT1, an essential regulator of normal and malignant hematopoiesis. Focusing on noncoding mutations within this WT1 intron, an analysis on 169 APL patients revealed that somatic mutations were clustered into a focal hotspot region, including one site identified as a germline polymorphism contributing to APL risk. Significantly decreased WT1 expression was observed in APL patients bearing somatic and/or germline noncoding WT1 variants. Furthermore, biallelic WT1 inactivation was recurrently found in APL patients with noncoding WT1 variants, which resulted in the complete loss of WT1. The high incidence of biallelic inactivation suggested the tumor suppressor activity of WT1 in APL. Mechanistically, noncoding WT1 variants disrupted MYB binding on chromatin and suppressed the enhancer activity and WT1 expression through destroying the chromatin looping formation. Our study highlights the important role of noncoding variants in the leukemogenesis of APL.
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Affiliation(s)
- Huan Song
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yabin Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; and
| | - Li Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shishuang Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinsong Yan
- Department of Hematology, the Second Hospital of Dalian Medical University, Dalian, China
| | - Junmin Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; and
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Gomez RL, Woods LM, Ramachandran R, Abou Tayoun AN, Philpott A, Ali FR. Super-enhancer associated core regulatory circuits mediate susceptibility to retinoic acid in neuroblastoma cells. Front Cell Dev Biol 2022; 10:943924. [PMID: 36147741 PMCID: PMC9485839 DOI: 10.3389/fcell.2022.943924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
Neuroblastoma is a pediatric tumour that accounts for more than 15% of cancer-related deaths in children. High-risk tumours are often difficult to treat, and patients' survival chances are less than 50%. Retinoic acid treatment is part of the maintenance therapy given to neuroblastoma patients; however, not all tumours differentiate in response to retinoic acid. Within neuroblastoma tumors, two phenotypically distinct cell types have been identified based on their super-enhancer landscape and transcriptional core regulatory circuitries: adrenergic (ADRN) and mesenchymal (MES). We hypothesized that the distinct super-enhancers in these different tumour cells mediate differential response to retinoic acid. To this end, three different neuroblastoma cell lines, ADRN (MYCN amplified and non-amplified) and MES cells, were treated with retinoic acid, and changes in the super-enhancer landscape upon treatment and after subsequent removal of retinoic acid was studied. Using ChIP-seq for the active histone mark H3K27ac, paired with RNA-seq, we compared the super-enhancer landscape in cells that undergo neuronal differentiation in response to retinoic acid versus those that fail to differentiate and identified unique super-enhancers associated with neuronal differentiation. Among the ADRN cells that respond to treatment, MYCN-amplified cells remain differentiated upon removal of retinoic acid, whereas MYCN non-amplified cells revert to an undifferentiated state, allowing for the identification of super-enhancers responsible for maintaining differentiation. This study identifies key super-enhancers that are crucial for retinoic acid-mediated differentiation.
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Affiliation(s)
- Roshna Lawrence Gomez
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Laura M. Woods
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Revathy Ramachandran
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ahmad N. Abou Tayoun
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | - Anna Philpott
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Fahad R. Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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126
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Aberrant transcription factors in the cancers of the pancreas. Semin Cancer Biol 2022; 86:28-45. [PMID: 36058426 DOI: 10.1016/j.semcancer.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/15/2022] [Accepted: 08/29/2022] [Indexed: 11/21/2022]
Abstract
Transcription factors (TFs) are essential for proper activation of gene set during the process of organogenesis, differentiation, lineage specificity. Reactivation or dysregulation of TFs regulatory networks could lead to deformation of organs, diseases including various malignancies. Currently, understanding the mechanism of oncogenesis became necessity for the development of targeted therapeutic strategy for different cancer types. It is evident that many TFs go awry in cancers of the pancreas such as pancreatic ductal adenocarcinoma (PDAC) and pancreatic neuroendocrine neoplasms (PanNENs). These mutated or dysregulated TFs abnormally controls various signaling pathways in PDAC and PanNENs including RTK, PI3K-PTEN-AKT-mTOR, JNK, TGF-β/SMAD, WNT/β-catenin, SHH, NOTCH and VEGF which in turn regulate different hallmarks of cancer. Aberrant regulation of such pathways have been linked to the initiation, progression, metastasis, and resistance in pancreatic cancer. As of today, a number of TFs has been identified as crucial regulators of pancreatic cancer and a handful of them shown to have potential as therapeutic targets in pre-clinical and clinical settings. In this review, we have summarized the current knowledge on the role and therapeutic usefulness of TFs in PDAC and PanNENs.
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127
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Downes DJ, Hughes JR. Natural and Experimental Rewiring of Gene Regulatory Regions. Annu Rev Genomics Hum Genet 2022; 23:73-97. [PMID: 35472292 DOI: 10.1146/annurev-genom-112921-010715] [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] [Indexed: 11/09/2022]
Abstract
The successful development and ongoing functioning of complex organisms depend on the faithful execution of the genetic code. A critical step in this process is the correct spatial and temporal expression of genes. The highly orchestrated transcription of genes is controlled primarily by cis-regulatory elements: promoters, enhancers, and insulators. The medical importance of this key biological process can be seen by the frequency with which mutations and inherited variants that alter cis-regulatory elements lead to monogenic and complex diseases and cancer. Here, we provide an overview of the methods available to characterize and perturb gene regulatory circuits. We then highlight mechanisms through which regulatory rewiring contributes to disease, and conclude with a perspective on how our understanding of gene regulation can be used to improve human health.
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Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
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128
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Gibbons MD, Fang Y, Spicola AP, Linzer N, Jones SM, Johnson BR, Li L, Xie M, Bungert J. Enhancer-Mediated Formation of Nuclear Transcription Initiation Domains. Int J Mol Sci 2022; 23:ijms23169290. [PMID: 36012554 PMCID: PMC9409229 DOI: 10.3390/ijms23169290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Enhancers in higher eukaryotes and upstream activating sequences (UASs) in yeast have been shown to recruit components of the RNA polymerase II (Pol II) transcription machinery. At least a fraction of Pol II recruited to enhancers in higher eukaryotes initiates transcription and generates enhancer RNA (eRNA). In contrast, UASs in yeast do not recruit transcription factor TFIIH, which is required for transcription initiation. For both yeast and mammalian systems, it was shown that Pol II is transferred from enhancers/UASs to promoters. We propose that there are two modes of Pol II recruitment to enhancers in higher eukaryotes. Pol II complexes that generate eRNAs are recruited via TFIID, similar to mechanisms operating at promoters. This may involve the binding of TFIID to acetylated nucleosomes flanking the enhancer. The resulting eRNA, together with enhancer-bound transcription factors and co-regulators, contributes to the second mode of Pol II recruitment through the formation of a transcription initiation domain. Transient contacts with target genes, governed by proteins and RNA, lead to the transfer of Pol II from enhancers to TFIID-bound promoters.
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129
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Tsui C, Kretschmer L, Rapelius S, Gabriel SS, Chisanga D, Knöpper K, Utzschneider DT, Nüssing S, Liao Y, Mason T, Torres SV, Wilcox SA, Kanev K, Jarosch S, Leube J, Nutt SL, Zehn D, Parish IA, Kastenmüller W, Shi W, Buchholz VR, Kallies A. MYB orchestrates T cell exhaustion and response to checkpoint inhibition. Nature 2022; 609:354-360. [PMID: 35978192 PMCID: PMC9452299 DOI: 10.1038/s41586-022-05105-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 07/13/2022] [Indexed: 12/29/2022]
Abstract
CD8+ T cells that respond to chronic viral infections or cancer are characterized by the expression of inhibitory receptors such as programmed cell death protein 1 (PD-1) and by the impaired production of cytokines. This state of restrained functionality—which is referred to as T cell exhaustion1,2—is maintained by precursors of exhausted T (TPEX) cells that express the transcription factor T cell factor 1 (TCF1), self-renew and give rise to TCF1− exhausted effector T cells3–6. Here we show that the long-term proliferative potential, multipotency and repopulation capacity of exhausted T cells during chronic infection are selectively preserved in a small population of transcriptionally distinct CD62L+ TPEX cells. The transcription factor MYB is not only essential for the development of CD62L+ TPEX cells and maintenance of the antiviral CD8+ T cell response, but also induces functional exhaustion and thereby prevents lethal immunopathology. Furthermore, the proliferative burst in response to PD-1 checkpoint inhibition originates exclusively from CD62L+ TPEX cells and depends on MYB. Our findings identify CD62L+ TPEX cells as a stem-like population that is central to the maintenance of long-term antiviral immunity and responsiveness to immunotherapy. Moreover, they show that MYB is a transcriptional orchestrator of two fundamental aspects of exhausted T cell responses: the downregulation of effector function and the long-term preservation of self-renewal capacity. CD62L+ precursors of exhausted T cells retain long-term proliferative potential, multipotency and repopulation capacity, and the transcription factor MYB is essential for the development and function of this population of cells.
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Affiliation(s)
- Carlson Tsui
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Lorenz Kretschmer
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Svenja Rapelius
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Sarah S Gabriel
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - David Chisanga
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Konrad Knöpper
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Daniel T Utzschneider
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Simone Nüssing
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Teisha Mason
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Santiago Valle Torres
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen A Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Krystian Kanev
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Justin Leube
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Dietmar Zehn
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Ian A Parish
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Wolfgang Kastenmüller
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany.
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
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The tissue-specificity associated region and motif of an emx2 downstream enhancer CNE2.04 in zebrafish. Gene Expr Patterns 2022; 45:119269. [PMID: 35970322 DOI: 10.1016/j.gep.2022.119269] [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: 03/31/2022] [Revised: 07/04/2022] [Accepted: 07/29/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Expression level of EMX2 plays an important role in the development of nervous system and cancers. CNE2.04, a conserved enhancer downstream of emx2, drives fluorescent protein expression in the similar pattern of emx2. METHODS CNE2.04 truncated or motif-mutated transgenic reporter plasmids were constructed and injected into the zebrafish fertilized egg with Tol2 mRNA at the unicellular stage of zebrafish eggs. The green fluorescence expression patterns were observed at 24, 48, and 72 hpf, and the fluorescence rates of different tissues were counted at 48 hpf. RESULTS Compared to CNE2.04, CNE2.04-R400 had comparable enhancer activity, while the tissue specificity of CNE2.04-L400 was obviously changed. Motif CCCCTC mutation obviously changed the enhancer activity, while motif CCGCTC mutations also changed it. CONCLUSION Due to their correlation with tissue specificity, CNE2.04-R400 is associated with the tissue-specificity of CNE2.04, and motif CCCCTC plays an important role in the enhancer activity of CNE2.04.
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131
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Zhang QX, Zhao DBJ, Gu RY, Zhao XH, Zhao HX, Valenzuela RK, Xi MM, Zhang R, Ma J. Study of a functional SNP rs13423388 in a novel enhancer element of schizophrenia-associated ZNF804A. Asian J Psychiatr 2022; 74:103191. [PMID: 35728455 DOI: 10.1016/j.ajp.2022.103191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/09/2022] [Accepted: 06/13/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Qiao-Xia Zhang
- Department of Electron Microscope, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Dong-Bu-Jia Zhao
- Department of Electron Microscope, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Rui-Ying Gu
- Department of Electron Microscope, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Xiu-Hua Zhao
- Department of Electron Microscope, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Hua-Xiang Zhao
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Robert K Valenzuela
- Center for Precision Medicine Research, Marshfield Clinic, Marshfield, WI 54449, USA
| | - Miao-Miao Xi
- Department of Electron Microscope, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Rui Zhang
- Translational Medicine Center, Hong Hui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710054, China.
| | - Jie Ma
- Department of Electron Microscope, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China.
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132
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Liquid-liquid phase separation in tumor biology. Signal Transduct Target Ther 2022; 7:221. [PMID: 35803926 PMCID: PMC9270353 DOI: 10.1038/s41392-022-01076-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) is a novel principle for explaining the precise spatial and temporal regulation in living cells. LLPS compartmentalizes proteins and nucleic acids into micron-scale, liquid-like, membraneless bodies with specific functions, which were recently termed biomolecular condensates. Biomolecular condensates are executors underlying the intracellular spatiotemporal coordination of various biological activities, including chromatin organization, genomic stability, DNA damage response and repair, transcription, and signal transduction. Dysregulation of these cellular processes is a key event in the initiation and/or evolution of cancer, and emerging evidence has linked the formation and regulation of LLPS to malignant transformations in tumor biology. In this review, we comprehensively summarize the detailed mechanisms of biomolecular condensate formation and biophysical function and review the recent major advances toward elucidating the multiple mechanisms involved in cancer cell pathology driven by aberrant LLPS. In addition, we discuss the therapeutic perspectives of LLPS in cancer research and the most recently developed drug candidates targeting LLPS modulation that can be used to combat tumorigenesis.
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133
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Mikulasova A, Kent D, Trevisan-Herraz M, Karataraki N, Fung KTM, Ashby C, Cieslak A, Yaccoby S, van Rhee F, Zangari M, Thanendrarajan S, Schinke C, Morgan GJ, Asnafi V, Spicuglia S, Brackley CA, Corcoran AE, Hambleton S, Walker BA, Rico D, Russell LJ. Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers. Genome Res 2022; 32:1343-1354. [PMID: 34933939 PMCID: PMC9341503 DOI: 10.1101/gr.276042.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022]
Abstract
Chromosomal translocations are important drivers of haematological malignancies whereby proto-oncogenes are activated by juxtaposition with enhancers, often called enhancer hijacking We analyzed the epigenomic consequences of rearrangements between the super-enhancers of the immunoglobulin heavy locus (IGH) and proto-oncogene CCND1 that are common in B cell malignancies. By integrating BLUEPRINT epigenomic data with DNA breakpoint detection, we characterized the normal chromatin landscape of the human IGH locus and its dynamics after pathological genomic rearrangement. We detected an H3K4me3 broad domain (BD) within the IGH locus of healthy B cells that was absent in samples with IGH-CCND1 translocations. The appearance of H3K4me3-BD over CCND1 in the latter was associated with overexpression and extensive chromatin accessibility of its gene body. We observed similar cancer-specific H3K4me3-BDs associated with hijacking of super-enhancers of other common oncogenes in B cell (MAF, MYC, and FGFR3/NSD2) and T cell malignancies (LMO2, TLX3, and TAL1). Our analysis suggests that H3K4me3-BDs can be created by super-enhancers and supports the new concept of epigenomic translocation, in which the relocation of H3K4me3-BDs from cell identity genes to oncogenes accompanies the translocation of super-enhancers.
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Affiliation(s)
- Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Daniel Kent
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Marco Trevisan-Herraz
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nefeli Karataraki
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Kent T M Fung
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Cody Ashby
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Agata Cieslak
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut National de la Santé et de la Recherche Médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Shmuel Yaccoby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | | | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Gareth J Morgan
- NYU Langone Medical Center, Perlmutter Cancer Center, NYU Langone Health, New York, New York 10016, USA
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut National de la Santé et de la Recherche Médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Chris A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Anne E Corcoran
- Lymphocyte Signalling and Development Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, United Kingdom
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, Indiana 46202, USA
| | - Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Lisa J Russell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
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134
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Bal E, Kumar R, Hadigol M, Holmes AB, Hilton LK, Loh JW, Dreval K, Wong JCH, Vlasevska S, Corinaldesi C, Soni RK, Basso K, Morin RD, Khiabanian H, Pasqualucci L, Dalla-Favera R. Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature 2022; 607:808-815. [PMID: 35794478 PMCID: PMC9583699 DOI: 10.1038/s41586-022-04906-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 05/25/2022] [Indexed: 12/16/2022]
Abstract
Diffuse large B cell lymphoma (DLBCL) is the most common B cell non-Hodgkin lymphoma and remains incurable in around 40% of patients. Efforts to sequence the coding genome identified several genes and pathways that are altered in this disease, including potential therapeutic targets1-5. However, the non-coding genome of DLBCL remains largely unexplored. Here we show that active super-enhancers are highly and specifically hypermutated in 92% of samples from individuals with DLBCL, display signatures of activation-induced cytidine deaminase activity, and are linked to genes that encode B cell developmental regulators and oncogenes. As evidence of oncogenic relevance, we show that the hypermutated super-enhancers linked to the BCL6, BCL2 and CXCR4 proto-oncogenes prevent the binding and transcriptional downregulation of the corresponding target gene by transcriptional repressors, including BLIMP1 (targeting BCL6) and the steroid receptor NR3C1 (targeting BCL2 and CXCR4). Genetic correction of selected mutations restored repressor DNA binding, downregulated target gene expression and led to the counter-selection of cells containing corrected alleles, indicating an oncogenic dependency on the super-enhancer mutations. This pervasive super-enhancer mutational mechanism reveals a major set of genetic lesions deregulating gene expression, which expands the involvement of known oncogenes in DLBCL pathogenesis and identifies new deregulated gene targets of therapeutic relevance.
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Affiliation(s)
- Elodie Bal
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Rahul Kumar
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Mohammad Hadigol
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Laura K Hilton
- Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jui Wan Loh
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Kostiantyn Dreval
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jasper C H Wong
- Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Sofija Vlasevska
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | | | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- Genome Sciences Center, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Hossein Khiabanian
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
- Department of Genetics & Development, Columbia University, New York, NY, USA.
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA.
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135
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Chen Q, Yang B, Liu X, Zhang XD, Zhang L, Liu T. Histone acetyltransferases CBP/p300 in tumorigenesis and CBP/p300 inhibitors as promising novel anticancer agents. Am J Cancer Res 2022; 12:4935-4948. [PMID: 35836809 PMCID: PMC9274749 DOI: 10.7150/thno.73223] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/23/2022] [Indexed: 01/12/2023] Open
Abstract
The histone acetyltransferases CBP and p300, often referred to as CBP/p300 due to their sequence homology and functional overlap and co-operation, are emerging as critical drivers of oncogenesis in the past several years. CBP/p300 induces histone H3 lysine 27 acetylation (H3K27ac) at target gene promoters, enhancers and super-enhancers, thereby activating gene transcription. While earlier studies indicate that CBP/p300 deletion/loss can promote tumorigenesis, CBP/p300 have more recently been shown to be over-expressed in cancer cells and drug-resistant cancer cells, activate oncogene transcription and induce cancer cell proliferation, survival, tumorigenesis, metastasis, immune evasion and drug-resistance. Small molecule CBP/p300 histone acetyltransferase inhibitors, bromodomain inhibitors, CBP/p300 and BET bromodomain dual inhibitors and p300 protein degraders have recently been discovered. The CBP/p300 inhibitors and degraders reduce H3K27ac, down-regulate oncogene transcription, induce cancer cell growth inhibition and cell death, activate immune response, overcome drug resistance and suppress tumor progression in vivo. In addition, CBP/p300 inhibitors enhance the anticancer efficacy of chemotherapy, radiotherapy and epigenetic anticancer agents, including BET bromodomain inhibitors; and the combination therapies exert substantial anticancer effects in mouse models of human cancers including drug-resistant cancers. Currently, two CBP/p300 inhibitors are under clinical evaluation in patients with advanced and drug-resistant solid tumors or hematological malignancies. In summary, CBP/p300 have recently been identified as critical tumorigenic drivers, and CBP/p300 inhibitors and protein degraders are emerging as promising novel anticancer agents for clinical translation.
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Affiliation(s)
- Qingjuan Chen
- Department of Oncology, 3201 Hospital of Xi'an Jiaotong University Health Science Center, Hanzhong, Shaanxi 723000, China
| | - Binhui Yang
- Department of Oncology, 3201 Hospital of Xi'an Jiaotong University Health Science Center, Hanzhong, Shaanxi 723000, China
| | - Xiaochen Liu
- Department of Oncology, 3201 Hospital of Xi'an Jiaotong University Health Science Center, Hanzhong, Shaanxi 723000, China
| | - Xu D. Zhang
- School of Medicine and Public Health, Priority Research Centre for Cancer Research, University of Newcastle, Callaghan, Newcastle, NSW 2308, Australia.,Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China.,✉ Corresponding authors: E-mail: (Xu D. Zhang), (Lirong Zhang); (Tao Liu)
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.,✉ Corresponding authors: E-mail: (Xu D. Zhang), (Lirong Zhang); (Tao Liu)
| | - Tao Liu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China.,Children's Cancer Institute Australia, Randwick, Sydney, NSW 2031, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia.,✉ Corresponding authors: E-mail: (Xu D. Zhang), (Lirong Zhang); (Tao Liu)
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136
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Roth S, Margulis M, Danielli A. Recent Advances in Rapid and Highly Sensitive Detection of Proteins and Specific DNA Sequences Using a Magnetic Modulation Biosensing System. SENSORS (BASEL, SWITZERLAND) 2022; 22:4497. [PMID: 35746278 PMCID: PMC9230956 DOI: 10.3390/s22124497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
In early disease stages, biomolecules of interest exist in very low concentrations, presenting a significant challenge for analytical devices and methods. Here, we provide a comprehensive overview of an innovative optical biosensing technology, termed magnetic modulation biosensing (MMB), its biomedical applications, and its ongoing development. In MMB, magnetic beads are attached to fluorescently labeled target molecules. A controlled magnetic force aggregates the magnetic beads and transports them in and out of an excitation laser beam, generating a periodic fluorescent signal that is detected and demodulated. MMB applications include rapid and highly sensitive detection of specific nucleic acid sequences, antibodies, proteins, and protein interactions. Compared with other established analytical methodologies, MMB provides improved sensitivity, shorter processing time, and simpler protocols.
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137
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Histone H3K36me2 demethylase KDM2A promotes bladder cancer progression through epigenetically silencing RARRES3. Cell Death Dis 2022; 13:547. [PMID: 35697678 PMCID: PMC9192503 DOI: 10.1038/s41419-022-04983-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 01/21/2023]
Abstract
Epigenetic dysregulation contributes to bladder cancer tumorigenesis. H3K36me2 demethylase KDM2A functions as an important epigenetic regulator of cell fate in many types of tumors. However, its role in bladder cancer remains unknown. Here, we revealed a positive correlation between KDM2A gene copy number gain and upregulation of KDM2A mRNA expression in bladder cancer. Moreover, a super-enhancer (SE) driving KDM2A transcription was found in high-grade bladder cancer, resulting in a significantly higher expression of KDM2A mRNA compared to that in low-grade bladder tumors. KDM2A knockdown (KD) decreased the proliferation, invasion, and spheroid formation of high-grade bladder cancer cells and inhibited tumor growth in mouse xenograft models. Furthermore, we identified RARRES3 as a key KDM2A target gene. KDM2A suppresses RARRES3 expression via demethylation of H3K36me2 in the RARRES3 promoter. Intriguingly, RARRES3 KD attenuated the inhibitory effects of KDM2A depletion on the malignant phenotypes of high-grade bladder cancer cells. The combination of the KDM2A inhibitor IOX1 and the RARRES3 agonist all-trans retinoic acid (ATRA) synergistically inhibited the proliferation of high-grade bladder cancer cells, suggesting that the KDM2A/RARRES3 axis may be a promising therapeutic target for the treatment of high-grade bladder cancer.
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138
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Correia L, Magno R, Xavier JM, de Almeida BP, Duarte I, Esteves F, Ghezzo M, Eldridge M, Sun C, Bosma A, Mittempergher L, Marreiros A, Bernards R, Caldas C, Chin SF, Maia AT. Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant. NPJ Breast Cancer 2022; 8:71. [PMID: 35676284 PMCID: PMC9177727 DOI: 10.1038/s41523-022-00435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
PIK3CA mutations are the most common in breast cancer, particularly in the estrogen receptor-positive cohort, but the benefit of PI3K inhibitors has had limited success compared with approaches targeting other less common mutations. We found a frequent allelic expression imbalance between the missense mutant and wild-type PIK3CA alleles in breast tumors from the METABRIC (70.2%) and the TCGA (60.1%) projects. When considering the mechanisms controlling allelic expression, 27.7% and 11.8% of tumors showed imbalance due to regulatory variants in cis, in the two studies respectively. Furthermore, preferential expression of the mutant allele due to cis-regulatory variation is associated with poor prognosis in the METABRIC tumors (P = 0.031). Interestingly, ER-, PR-, and HER2+ tumors showed significant preferential expression of the mutated allele in both datasets. Our work provides compelling evidence to support the clinical utility of PIK3CA allelic expression in breast cancer in identifying patients of poorer prognosis, and those with low expression of the mutated allele, who will unlikely benefit from PI3K inhibitors. Furthermore, our work proposes a model of differential regulation of a critical cancer-promoting gene in breast cancer.
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Affiliation(s)
- Lizelle Correia
- Faculty of Medicine and Biomedical Sciences (FMCB), Universidade do Algarve, Faro, Portugal
| | - Ramiro Magno
- Center for Research in Health Technologies and Information Systems (CINTESIS), Universidade do Algarve, Faro, Portugal
| | - Joana M Xavier
- Center for Research in Health Technologies and Information Systems (CINTESIS), Universidade do Algarve, Faro, Portugal
| | - Bernardo P de Almeida
- Faculty of Medicine and Biomedical Sciences (FMCB), Universidade do Algarve, Faro, Portugal
- The Research Institute of Molecular Pathology, Vienna, Austria
| | - Isabel Duarte
- Center for Research in Health Technologies and Information Systems (CINTESIS), Universidade do Algarve, Faro, Portugal
| | - Filipa Esteves
- Faculty of Medicine and Biomedical Sciences (FMCB), Universidade do Algarve, Faro, Portugal
- ProRegeM-PhD Program in Mechanisms of Disease and Regenerative Medicine, Universidade do Algarve, Faro, Portugal
| | - Marinella Ghezzo
- Center for Research in Health Technologies and Information Systems (CINTESIS), Universidade do Algarve, Faro, Portugal
| | - Matthew Eldridge
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, UK
| | - Chong Sun
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- DKFZ, Heidelberg, Germany
| | - Astrid Bosma
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lorenza Mittempergher
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ana Marreiros
- Faculty of Medicine and Biomedical Sciences (FMCB), Universidade do Algarve, Faro, Portugal
| | - Rene Bernards
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Cancer Centre, Cambridge, UK
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
| | - Ana-Teresa Maia
- Faculty of Medicine and Biomedical Sciences (FMCB), Universidade do Algarve, Faro, Portugal.
- Center for Research in Health Technologies and Information Systems (CINTESIS), Universidade do Algarve, Faro, Portugal.
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139
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Mulero Hernández J, Fernández-Breis JT. Analysis of the landscape of human enhancer sequences in biological databases. Comput Struct Biotechnol J 2022; 20:2728-2744. [PMID: 35685360 PMCID: PMC9168495 DOI: 10.1016/j.csbj.2022.05.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/01/2022] Open
Abstract
The process of gene regulation extends as a network in which both genetic sequences and proteins are involved. The levels of regulation and the mechanisms involved are multiple. Transcription is the main control mechanism for most genes, being the downstream steps responsible for refining the transcription patterns. In turn, gene transcription is mainly controlled by regulatory events that occur at promoters and enhancers. Several studies are focused on analyzing the contribution of enhancers in the development of diseases and their possible use as therapeutic targets. The study of regulatory elements has advanced rapidly in recent years with the development and use of next generation sequencing techniques. All this information has generated a large volume of information that has been transferred to a growing number of public repositories that store this information. In this article, we analyze the content of those public repositories that contain information about human enhancers with the aim of detecting whether the knowledge generated by scientific research is contained in those databases in a way that could be computationally exploited. The analysis will be based on three main aspects identified in the literature: types of enhancers, type of evidence about the enhancers, and methods for detecting enhancer-promoter interactions. Our results show that no single database facilitates the optimal exploitation of enhancer data, most types of enhancers are not represented in the databases and there is need for a standardized model for enhancers. We have identified major gaps and challenges for the computational exploitation of enhancer data.
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Affiliation(s)
- Juan Mulero Hernández
- Dept. Informática y Sistemas, Universidad de Murcia, CEIR Campus Mare Nostrum, IMIB-Arrixaca, Spain
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140
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Shendy NAM, Zimmerman MW, Abraham BJ, Durbin AD. Intrinsic transcriptional heterogeneity in neuroblastoma guides mechanistic and therapeutic insights. Cell Rep Med 2022; 3:100632. [PMID: 35584622 PMCID: PMC9133465 DOI: 10.1016/j.xcrm.2022.100632] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/24/2022] [Accepted: 04/20/2022] [Indexed: 12/20/2022]
Abstract
Cell state is controlled by master transcription factors (mTFs) that determine the cellular gene expression program. Cancer cells acquire dysregulated gene expression programs by mutational and non-mutational processes. Intratumoral heterogeneity can result from cells displaying distinct mTF-regulated cell states, which co-exist within the tumor. One archetypal tumor associated with transcriptionally regulated heterogeneity is high-risk neuroblastoma (NB). Patients with NB have poor overall survival despite intensive therapies, and relapsed patients are commonly refractory to treatment. The cellular populations that comprise NB are marked by different cohorts of mTFs and differential sensitivity to conventional therapies. Recent studies have highlighted mechanisms by which NB cells dynamically shift the cell state with treatment, revealing new opportunities to control the cellular response to treatment by manipulating cell-state-defining transcriptional programs. Here, we review recent advances in understanding transcriptionally defined cancer heterogeneity. We offer challenges to the field to encourage translation of basic science into clinical benefit.
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Affiliation(s)
- Noha A M Shendy
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mark W Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian J Abraham
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adam D Durbin
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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141
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Genescà E, González-Gil C. Latest Contributions of Genomics to T-Cell Acute Lymphoblastic Leukemia (T-ALL). Cancers (Basel) 2022; 14:2474. [PMID: 35626077 PMCID: PMC9140158 DOI: 10.3390/cancers14102474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 12/04/2022] Open
Abstract
As for many neoplasms, initial genetic data about T-cell acute lymphoblastic leukemia (T-ALL) came from the application of cytogenetics. This information helped identify some recurrent chromosomal alterations in T-ALL at the time of diagnosis, although it was difficult to determine their prognostic impact because of their low incidence in the specific T-ALL cohort analyzed. Genetic knowledge accumulated rapidly following the application of genomic techniques, drawing attention to the importance of using high-resolution genetic techniques to detect cryptic aberrations present in T-ALL, which are not usually detected by cytogenetics. We now have a clearer appreciation of the genetic landscape of the different T-ALL subtypes at diagnosis, explaining the particular oncogenetic processes taking place in each T-ALL, and we have begun to understand relapse-specific mechanisms. This review aims to summarize the latest advances in our knowledge of the genome in T-ALL. We highlight areas where the research in this subtype of ALL is progressing with the aim of identifying key questions that need to be answered in the medium-long term if this knowledge is to be applied in clinics.
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Affiliation(s)
- Eulàlia Genescà
- Institut d’Investigació Contra la Leucemia Josep Carreras (IJC), Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain;
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142
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Parriott G, Kee BL. E Protein Transcription Factors as Suppressors of T Lymphocyte Acute Lymphoblastic Leukemia. Front Immunol 2022; 13:885144. [PMID: 35514954 PMCID: PMC9065262 DOI: 10.3389/fimmu.2022.885144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
T Lymphocyte Acute Lymphoblastic Leukemia (ALL) is an aggressive disease arising from transformation of T lymphocytes during their development. The mutation spectrum of T-ALL has revealed critical regulators of the growth and differentiation of normal and leukemic T lymphocytes. Approximately, 60% of T-ALLs show aberrant expression of the hematopoietic stem cell-associated helix-loop-helix transcription factors TAL1 and LYL1. TAL1 and LYL1 function in multiprotein complexes that regulate gene expression in T-ALL but they also antagonize the function of the E protein homodimers that are critical regulators of T cell development. Mice lacking E2A, or ectopically expressing TAL1, LYL1, or other inhibitors of E protein function in T cell progenitors, also succumb to an aggressive T-ALL-like disease highlighting that E proteins promote T cell development and suppress leukemogenesis. In this review, we discuss the role of E2A in T cell development and how alterations in E protein function underlie leukemogenesis. We focus on the role of TAL1 and LYL1 and the genes that are dysregulated in E2a-/- T cell progenitors that contribute to human T-ALL. These studies reveal novel mechanisms of transformation and provide insights into potential therapeutic targets for intervention in this disease.
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Affiliation(s)
- Geoffrey Parriott
- Committee on Immunology, University of Chicago, Chicago, IL, United States
| | - Barbara L Kee
- Committee on Immunology, University of Chicago, Chicago, IL, United States.,Committee on Cancer Biology, University of Chicago, Chicago, IL, United States.,Department of Pathology, University of Chicago, Chicago, IL, United States
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143
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Pich O, Bailey C, Watkins TBK, Zaccaria S, Jamal-Hanjani M, Swanton C. The translational challenges of precision oncology. Cancer Cell 2022; 40:458-478. [PMID: 35487215 DOI: 10.1016/j.ccell.2022.04.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/16/2022] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
Abstract
The translational challenges in the field of precision oncology are in part related to the biological complexity and diversity of this disease. Technological advances in genomics have facilitated large sequencing efforts and discoveries that have further supported this notion. In this review, we reflect on the impact of these discoveries on our understanding of several concepts: cancer initiation, cancer prevention, early detection, adjuvant therapy and minimal residual disease monitoring, cancer drug resistance, and cancer evolution in metastasis. We discuss key areas of focus for improving cancer outcomes, from biological insights to clinical application, and suggest where the development of these technologies will lead us. Finally, we discuss practical challenges to the wider adoption of molecular profiling in the clinic and the need for robust translational infrastructure.
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Affiliation(s)
- Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
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144
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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: 7] [Impact Index Per Article: 3.5] [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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145
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Yoshino S, Suzuki HI. The molecular understanding of super-enhancer dysregulation in cancer. NAGOYA JOURNAL OF MEDICAL SCIENCE 2022; 84:216-229. [PMID: 35967935 PMCID: PMC9350580 DOI: 10.18999/nagjms.84.2.216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Abnormalities in the regulation of gene expression are associated with various pathological conditions. Among the distal regulatory elements in the genome, the activation of target genes by enhancers plays a central role in the formation of cell type-specific gene expression patterns. Super-enhancers are a subclass of enhancers that frequently contain multiple enhancer-like elements and are characterized by dense binding of master transcription factors and Mediator complexes and high signals of active histone marks. Super-enhancers have been studied in detail as important regulatory regions that control cell identity and contribute to the pathogenesis of diverse diseases. In cancer, super-enhancers have multifaceted roles by activating various oncogenes and other cancer-related genes and shaping characteristic gene expression patterns in cancer cells. Alterations in super-enhancer activities in cancer involve multiple mechanisms, including the dysregulation of transcription factors and the super-enhancer-associated genomic abnormalities. The study of super-enhancers could contribute to the identification of effective biomarkers and the development of cancer therapeutics targeting transcriptional addiction. In this review, we summarize the roles of super-enhancers in cancer biology, with a particular focus on hematopoietic malignancies, in which multiple super-enhancer alteration mechanisms have been reported.
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Affiliation(s)
- Seiko Yoshino
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
,Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
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146
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Zeng Z, Bromberg Y. Inferring Potential Cancer Driving Synonymous Variants. Genes (Basel) 2022; 13:778. [PMID: 35627162 PMCID: PMC9140830 DOI: 10.3390/genes13050778] [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: 03/25/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023] Open
Abstract
Synonymous single nucleotide variants (sSNVs) are often considered functionally silent, but a few cases of cancer-causing sSNVs have been reported. From available databases, we collected four categories of sSNVs: germline, somatic in normal tissues, somatic in cancerous tissues, and putative cancer drivers. We found that screening sSNVs for recurrence among patients, conservation of the affected genomic position, and synVep prediction (synVep is a machine learning-based sSNV effect predictor) recovers cancer driver variants (termed proposed drivers) and previously unknown putative cancer genes. Of the 2.9 million somatic sSNVs found in the COSMIC database, we identified 2111 proposed cancer driver sSNVs. Of these, 326 sSNVs could be further tagged for possible RNA splicing effects, RNA structural changes, and affected RBP motifs. This list of proposed cancer driver sSNVs provides computational guidance in prioritizing the experimental evaluation of synonymous mutations found in cancers. Furthermore, our list of novel potential cancer genes, galvanized by synonymous mutations, may highlight yet unexplored cancer mechanisms.
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Affiliation(s)
- Zishuo Zeng
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
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147
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Wan L, Li W, Meng Y, Hou Y, Chen M, Xu B. Inflammatory Immune-Associated eRNA: Mechanisms, Functions and Therapeutic Prospects. Front Immunol 2022; 13:849451. [PMID: 35514959 PMCID: PMC9063412 DOI: 10.3389/fimmu.2022.849451] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid development of multiple high-throughput sequencing technologies has made it possible to explore the critical roles and mechanisms of functional enhancers and enhancer RNAs (eRNAs). The inflammatory immune response, as a fundamental pathological process in infectious diseases, cancers and immune disorders, coordinates the balance between the internal and external environment of the organism. It has been shown that both active enhancers and intranuclear eRNAs are preferentially expressed over inflammation-related genes in response to inflammatory stimuli, suggesting that enhancer transcription events and their products influence the expression and function of inflammatory genes. Therefore, in this review, we summarize and discuss the relevant inflammatory roles and regulatory mechanisms of eRNAs in inflammatory immune cells, non-inflammatory immune cells, inflammatory immune diseases and tumors, and explore the potential therapeutic effects of enhancer inhibitors affecting eRNA production for diseases with inflammatory immune responses.
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Affiliation(s)
- Lilin Wan
- Medical School, Southeast University, Nanjing, China
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Wenchao Li
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Yuan Meng
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Yue Hou
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
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148
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LaFave LM, Savage RE, Buenrostro JD. Single-Cell Epigenomics Reveals Mechanisms of Cancer Progression. ANNUAL REVIEW OF CANCER BIOLOGY 2022. [DOI: 10.1146/annurev-cancerbio-070620-094453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cancer initiation is driven by the cooperation between genetic and epigenetic aberrations that disrupt gene regulatory programs critical to maintaining specialized cellular functions. After initiation, cells acquire additional genetic and epigenetic alterations influenced by tumor-intrinsic and -extrinsic mechanisms, which increase intratumoral heterogeneity, reshape the cell's underlying gene regulatory networks and promote cancer evolution. Furthermore, environmental or therapeutic insults drive the selection of heterogeneous cell states, with implications for cancer initiation, maintenance, and drug resistance. The advancement of single-cell genomics has begun to uncover the full repertoire of chromatin and gene expression states (cell states) that exist within individual tumors. These single-cell analyses suggest that cells diversify in their regulatory states upon transformation by co-opting damage-induced and nonlineage regulatory programs that can lead to epigenomic plasticity. Here, we review these recent studies related to regulatory state changes in cancer progression and highlight the growing single-cell epigenomics toolkit poised to address unresolved questions in the field.
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Affiliation(s)
- Lindsay M. LaFave
- Department of Cell Biology and Albert Einstein Cancer Center, Albert Einstein College of Medicine, Montefiore Health System, Bronx, NY, USA
| | - Rachel E. Savage
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jason D. Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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149
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Biyanee A, Yusenko MV, Klempnauer KH. Src-Family Protein Kinase Inhibitors Suppress MYB Activity in a p300-Dependent Manner. Cells 2022; 11:1162. [PMID: 35406726 PMCID: PMC8997952 DOI: 10.3390/cells11071162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 02/05/2023] Open
Abstract
Recent studies have disclosed transcription factor MYB as a potential drug target for malignancies that are dependent on deregulated MYB function, including acute myeloid leukemia (AML) and adenoid cystic carcinoma (ACC). Although transcription factors are often regarded as undruggable, successful targeting of MYB by low-molecular-weight compounds has recently been demonstrated. In an attempt to repurpose known drugs as novel MYB-inhibitory agents, we have screened libraries of approved drugs and drug-like compounds for molecules with MYB-inhibitory potential. Here, we present initial evidence for the MYB-inhibitory activity of the protein kinase inhibitors bosutinib, PD180970 and PD161570, that we identified in a recent screen. We show that these compounds interfere with the activity of the MYB transactivation domain, apparently by disturbing the ability of MYB to cooperate with the coactivator p300. We show that treatment of the AML cell line HL60 with these compounds triggers the up-regulation of the myeloid differentiation marker CD11b and induces cell death. Importantly, we show that these effects are significantly dampened by forced expression of an activated version of MYB, confirming that the ability to suppress MYB function is a relevant activity of these compounds. Overall, our work identifies several protein kinase inhibitors as novel MYB-inhibitory agents and suggests that the inhibition of MYB function may play a role in their pharmacological impact on leukemic cells.
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Affiliation(s)
| | | | - Karl-Heinz Klempnauer
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany; (A.B.); (M.V.Y.)
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150
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Schmidt TJ, Klempnauer KH. Natural Products with Antitumor Potential Targeting the MYB-C/EBPβ-p300 Transcription Module. Molecules 2022; 27:molecules27072077. [PMID: 35408476 PMCID: PMC9000602 DOI: 10.3390/molecules27072077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022] Open
Abstract
The transcription factor MYB is expressed predominantly in hematopoietic progenitor cells, where it plays an essential role in the development of most lineages of the hematopoietic system. In the myeloid lineage, MYB is known to cooperate with members of the CCAAT box/enhancer binding protein (C/EBP) family of transcription factors. MYB and C/EBPs interact with the co-activator p300 or its paralog CREB-binding protein (CBP), to form a transcriptional module involved in myeloid-specific gene expression. Recent work has demonstrated that MYB is involved in the development of human leukemia, especially in acute T-cell leukemia (T-ALL) and acute myeloid leukemia (AML). Chemical entities that inhibit the transcriptional activity of the MYB-C/EBPβ-p300 transcription module may therefore be of use as potential anti-tumour drugs. In searching for small molecule inhibitors, studies from our group over the last 10 years have identified natural products belonging to different structural classes, including various sesquiterpene lactones, a steroid lactone, quinone methide triterpenes and naphthoquinones that interfere with the activity of this transcriptional module in different ways. This review gives a comprehensive overview on the various classes of inhibitors and the inhibitory mechanisms by which they affect the MYB-C/EBPβ-p300 transcriptional module as a potential anti-tumor target. We also focus on the current knowledge on structure-activity relationships underlying these biological effects and on the potential of these compounds for further development.
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Affiliation(s)
- Thomas J. Schmidt
- Institute of Pharmaceutical Biology and Phytochemistry (IPBP), University of Münster, PharmaCampus-Corrensstraße 48, D-48149 Munster, Germany
- Correspondence: (T.J.S.); (K.-H.K.)
| | - Karl-Heinz Klempnauer
- Institute of Biochemistry, University of Münster, Corrensstraße 36, D-48149 Munster, Germany
- Correspondence: (T.J.S.); (K.-H.K.)
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