101
|
Liang Y, Li L, Xin T, Li B, Zhang D. Superenhancer-transcription factor regulatory network in malignant tumors. Open Med (Wars) 2021; 16:1564-1582. [PMID: 34722892 PMCID: PMC8525661 DOI: 10.1515/med-2021-0326] [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: 11/12/2020] [Revised: 06/02/2021] [Accepted: 06/16/2021] [Indexed: 11/15/2022] Open
Abstract
Objective This study aims to identify superenhancer (SE)-transcriptional factor (TF) regulatory network related to eight common malignant tumors based on ChIP-seq data modified by histone H3K27ac in the enhancer region of the SRA database. Methods H3K27ac ChIP-seq data of eight common malignant tumor samples were downloaded from the SRA database and subjected to comparison with the human reference genome hg19. TFs regulated by SEs were screened with HOMER software. Core regulatory circuitry (CRC) in malignant tumor samples was defined through CRCmapper software and validated by RNA-seq data in TCGA. The findings were substantiated in bladder cancer cell experiments. Results Different malignant tumors could be distinguished through the H3K27ac signal. After SE identification in eight common malignant tumor samples, 35 SE-regulated genes were defined as malignant tumor-specific. SE-regulated specific TFs effectively distinguished the types of malignant tumors. Finally, we obtained 60 CRC TFs, and SMAD3 exhibited a strong H3K27ac signal in eight common malignant tumor samples. In vitro experimental data verified the presence of a SE-TF regulatory network in bladder cancer, and SE-TF regulatory network enhanced the malignant phenotype of bladder cancer cells. Conclusion The SE-TF regulatory network with SMAD3 as the core TF may participate in the carcinogenesis of malignant tumors.
Collapse
Affiliation(s)
- Yuan Liang
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Linlin Li
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Tian Xin
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Binru Li
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Dalin Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, No. 155, Nanjing North Street, Shenyang 110001, Liaoning Province, People's Republic of China
| |
Collapse
|
102
|
Zhang L, Li H, Qiu Y, Liu Y, Liu X, Wang W. Screening and cellular validation of prognostic genes regulated by super enhancers in oral squamous cell carcinoma. Bioengineered 2021; 12:10073-10088. [PMID: 34709988 PMCID: PMC8810015 DOI: 10.1080/21655979.2021.1997089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the leading cause of death in patients with head and neck cancer. Reliable biomarkers to guide treatment decisions for OSCC remain scarce. The purpose of this study was to identify novel prognostic markers regulated by super enhancers in OSCC. Eight modules were obtained by weighted gene co-expression network analysis (WGCNA), among which MEblue module had the highest correlation with tumor stage, alcohol consumption and smoking. There were 41 genes regulated by super enhancers in MEblue module. Functional analysis showed that 41 super enhancer-regulated genes were involved in cancer progression. A total of twenty transcription factors of the 41 genes were predicted. Prognostic analysis of the 41 genes and the top 5 transcription factors showed that patients with high expression of AHCY, KCMF1, MANBAL and TFDP1 had a poor prognosis. Immunohistochemical analysis showed that AHCY, KCMF1 and MANBAL were highly expressed in OSCC tissue. Cellular experiment demonstrated that TFDP1 promoted AHCY, KCMF1 and MANBAL expression by binding to the super enhancers of these genes. Knockdown of TFDP1, AHCY, KCMF1 and MANBAL inhibited the proliferation of OSCC cells. In conclusion, AHCY, KCMF1 and MANBAL were recognized as super enhancer-regulated prognostic biomarkers regulated by TFDP1 in OSCC.
Collapse
Affiliation(s)
- Liru Zhang
- Department of Stomatology, Second Hospital of Shijiazhuang, Shijiazhuang, Hebei 050000, China
| | - Huanju Li
- Department of Surgery, Gucheng County Hospital, Hengshui, Hebei 253800, China
| | - Yongle Qiu
- Department of Stomatology, Fourth Affiliated Hospital, Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Yuanhang Liu
- Department of Stomatology, Second Hospital of Shijiazhuang, Shijiazhuang, Hebei 050000, China
| | - Xin Liu
- Department of Stomatology, Fourth Affiliated Hospital, Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Wenjing Wang
- Department of Stomatology, Fourth Affiliated Hospital, Hebei Medical University, Shijiazhuang, Hebei 050017, China
| |
Collapse
|
103
|
Liu N, Wang X, Zhu Z, Li D, Lv X, Chen Y, Xie H, Guo Z, Song D. Selected ideal natural ligand against TNBC by inhibiting CDC20, using bioinformatics and molecular biology. Aging (Albany NY) 2021; 13:23702-23725. [PMID: 34686627 PMCID: PMC8580355 DOI: 10.18632/aging.203642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/29/2021] [Indexed: 01/14/2023]
Abstract
Object: Find potential therapeutic targets of triple-negative breast cancer (TNBC) patients by bioinformatics. Screen ideal natural ligand that can bind with the potential target and inhibit it by using molecular biology. Methods: Bioinformatics and molecular biology were combined to analyze potential therapeutic targets. Differential expression analysis identified the differentially expressed genes (DEGs) between TNBC tissues and non-TNBC tissues. The functional enrichment analyses of DEGs shown the important gene ontology (GO) terms and pathways of TNBC. Protein-protein interaction (PPI) network construction screened 20 hub genes, while Kaplan website was used to analyze the relationship between the survival curve and expression of hub genes. Then Discovery Studio 4.5 screened ideal natural inhibitors of the potential therapeutic target by LibDock, ADME, toxicity prediction, CDOCKER and molecular dynamic simulation. Results: 1,212 and 353 DEGs were respectively found between TNBC tissues and non-TNBC tissues, including 88 up-regulated and 141 down-regulated DEGs in both databases. 20 hub genes were screened, and the higher expression of CDC20 was associated with a poor prognosis. Therefore, we chose CDC20 as the potential therapeutic target. 7,416 natural ligands were conducted to bind firmly with CDC20, and among these ligands, ZINC000004098930 was regarded as the potential ideal ligand, owing to its non-hepatotoxicity, more solubility level and less carcinogenicity than the reference drug, apcin. The ZINC000004098930-CDC20 could exist stably in natural environment. Conclusion: 20 genes were regarded as hub genes of TNBC and most of them were relevant to the survival curve of breast cancer patients, especially CDC20. ZINC000004098930 was chosen as the ideal natural ligand that can targeted and inhibited CDC20, which may give great contribution to TNBC targeted treatment.
Collapse
Affiliation(s)
- Naimeng Liu
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, China
| | - Xinhui Wang
- Department of Oncology, First People's Hospital of Xinxiang, Xinxiang, China
| | - Zhu Zhu
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, China
| | - Duo Li
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Xiaye Lv
- Department of Hematology, The First Clinical Medical School of Lanzhou University, Lanzhou, Gansu, China
| | - Yichang Chen
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, China
| | - Haoqun Xie
- Clinical College, Jilin University, Changchun, China
| | - Zhen Guo
- Clinical College, Jilin University, Changchun, China
| | - Dong Song
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, China
| |
Collapse
|
104
|
Seachrist DD, Anstine LJ, Keri RA. FOXA1: A Pioneer of Nuclear Receptor Action in Breast Cancer. Cancers (Basel) 2021; 13:cancers13205205. [PMID: 34680352 PMCID: PMC8533709 DOI: 10.3390/cancers13205205] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/26/2022] Open
Abstract
The pioneering function of FOXA1 establishes estrogen-responsive transcriptomes in luminal breast cancer. Dysregulated FOXA1 chromatin occupancy through focal amplification, mutation, or cofactor recruitment modulates estrogen receptor (ER) transcriptional programs and drives endocrine-resistant disease. However, ER is not the sole nuclear receptor (NR) expressed in breast cancers, nor is it the only NR for which FOXA1 serves as a licensing factor. Receptors for androgens, glucocorticoids, and progesterone are also found in the majority of breast cancers, and their functions are also impacted by FOXA1. These NRs interface with ER transcriptional programs and, depending on their activation level, can reprogram FOXA1-ER cistromes. Thus, NR interplay contributes to endocrine therapy response and resistance and may provide a vulnerability for future therapeutic benefit in patients. Herein, we review what is known regarding FOXA1 regulation of NR function in breast cancer in the context of cell identity, endocrine resistance, and NR crosstalk in breast cancer progression and treatment.
Collapse
Affiliation(s)
- Darcie D. Seachrist
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
| | - Lindsey J. Anstine
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ruth A. Keri
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
- Department of Cancer Biology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence:
| |
Collapse
|
105
|
No Need to Stick Together to Be Connected: Multiple Types of Enhancers' Networking. Cancers (Basel) 2021; 13:cancers13205201. [PMID: 34680347 PMCID: PMC8533737 DOI: 10.3390/cancers13205201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Transcription regulation programs require the functional interaction of distal and proximal regulatory regions, interacting by specific 3D chromatin configurations. Enhancers are cis-acting regulatory elements able to promote gene expression regardless their orientation and distance from the transcription starting site. Their systematic mapping by genome-wide chromatin profiling and chromosome conformation analysis, combined with the development of gene-editing approaches to modulate their function, revealed that many enhancers work together to fine-tune the expression of their target genes. This review aim to describe the functions of different types of enhancers and the modalities of enhancers’ interaction, focusing on their role in the regulation of complex biological processes like cancer development. Abstract The control of gene expression at a transcriptional level requires a widespread landscape of regulatory elements. Central to these regulatory circuits are enhancers (ENHs), which are defined as cis-acting DNA elements able to increase the transcription of a target gene in a distance- and orientation-independent manner. ENHs are not independent functional elements but work in a complex and dynamic cooperative network, constituting the building blocks of multimodular domains of gene expression regulation. The information from each of these elements converges on the target promoter, contributing to improving the precision and sharpness of gene modulation. ENHs’ interplay varies in its nature and extent, ranging from an additive to redundant effect depending on contexts. Moving from super-enhancers that drive the high expression levels of identity genes, to shadow-enhancers, whose redundant functions contribute to buffering the variation in gene expression, this review aims to describe the different modalities of ENHs’ interaction and their role in the regulation of complex biological processes like cancer development.
Collapse
|
106
|
Li M, Yang B, Li X, Ren H, Zhang L, Li L, Li W, Wang X, Zhou H, Zhang W. Identification of Prognostic Factors Related to Super Enhancer-Regulated ceRNA Network in Metastatic Lung Adenocarcinoma. Int J Gen Med 2021; 14:6261-6275. [PMID: 34629892 PMCID: PMC8493278 DOI: 10.2147/ijgm.s332317] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/16/2021] [Indexed: 12/18/2022] Open
Abstract
Introduction The regulatory mechanisms of super enhancers (SEs) and ceRNA networks in LUAD progression are not well understood. We aimed to discover the prognostic-related ceRNA network regulated by SEs in metastatic LUAD. Methods RNA-seq data were extracted from The Cancer Genome Atlas (TCGA) database. Differentially expressed (DE) RNAs were identified by edgeR. CeRNA network was predicted and visualized using starBase and Cytoscape. H3K27ac ChIP-seq data were derived from the Gene Expression Omnibus (GEO) database, and used for SE identification. Kaplan–Meier curve and multivariate Cox model were applied for prognostic analysis. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein–protein interaction (PPI) network were performed for functional analysis. SEs of AC074117.1 were verified by ChIP-qPCR in A549 and H1299 cells. MTT assay was performed to analyze cell proliferation. Luciferase activity assay was carried out to validate the target targeting relationships of ceRNA network. Results A total of 2355 DEmRNA, 483 DElncRNA and 155 DEmiRNA were identified between metastatic LUAD and adjacent normal tissues. CeRNA network consisting of 7 DElncRNAs, 18 DEmiRNAs and 15 DEmRNAs was constructed. Among the seven DElncRNAs in ceRNA network, only AC074117.1 was regulated by SEs. SE-regulated prognostic ceRNA sub-network consisting of FKBP3, E2F2, AC074117.1 and hsa-let-7c-5p was screened and verified. The overlapping co-expressed mRNAs of FKBP3, E2F2, AC074117.1 and hsa-let-7c-5p were mainly related to cell division and Fanconi anemia pathway. Genes in the ceRNA sub-network were correlated with DNA mismatch repair markers. Functional experiments proved that AC074117.1 was highly expressed in LUAD cells. AC074117.1 silencing notably inhibited proliferation of A549 and H1299 cells. Luciferase activity assay confirmed the direct relationship in AC074117.1-hsa-let-7c-5p-FKBP3/E2F2 network. Conclusion A novel prognostic ceRNA sub-network regulated by SEs was identified in metastatic LUAD. This study provided potential therapeutic targets and prognostic markers for further study of metastatic LUAD.
Collapse
Affiliation(s)
- Mingjiang Li
- Department of Thoracic Surgery, Tianjin First Central Hospital, Tianjin, People's Republic of China
| | - Bo Yang
- Department of Thoracic Surgery, Tianjin First Central Hospital, Tianjin, People's Republic of China
| | - Xiaoping Li
- Department of Thoracic Surgery, Tianjin First Central Hospital, Tianjin, People's Republic of China
| | - Haixia Ren
- Department of Pharmacy, Tianjin First Central Hospital, Tianjin, People's Republic of China
| | - Liang Zhang
- Department of Thoracic Surgery, Tianjin First Central Hospital, Tianjin, People's Republic of China
| | - Lei Li
- Department of Thoracic Surgery, Tianjin First Central Hospital, Tianjin, People's Republic of China
| | - Wei Li
- Department of Thoracic Surgery, Tianjin First Central Hospital, Tianjin, People's Republic of China
| | - Xuhui Wang
- Department of Thoracic Surgery, Tianjin First Central Hospital, Tianjin, People's Republic of China
| | - Honggang Zhou
- College of Pharmacy, Nankai University, State Key Laboratory of Medicinal Chemical Biology, Tianjin, People's Republic of China
| | - Weidong Zhang
- Department of Thoracic Surgery, Tianjin First Central Hospital, Tianjin, People's Republic of China
| |
Collapse
|
107
|
Sheng T, Ho SWT, Ooi WF, Xu C, Xing M, Padmanabhan N, Huang KK, Ma L, Ray M, Guo YA, Sim NL, Anene-Nzelu CG, Chang MM, Razavi-Mohseni M, Beer MA, Foo RSY, Sundar R, Chan YH, Tan ALK, Ong X, Skanderup AJ, White KP, Jha S, Tan P. Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer. Genome Med 2021; 13:158. [PMID: 34635154 PMCID: PMC8504099 DOI: 10.1186/s13073-021-00970-3] [Citation(s) in RCA: 9] [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: 03/18/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Enhancers are distal cis-regulatory elements required for cell-specific gene expression and cell fate determination. In cancer, enhancer variation has been proposed as a major cause of inter-patient heterogeneity-however, most predicted enhancer regions remain to be functionally tested. METHODS We analyzed 132 epigenomic histone modification profiles of 18 primary gastric cancer (GC) samples, 18 normal gastric tissues, and 28 GC cell lines using Nano-ChIP-seq technology. We applied Capture-based Self-Transcribing Active Regulatory Region sequencing (CapSTARR-seq) to assess functional enhancer activity. An Activity-by-contact (ABC) model was employed to explore the effects of histone acetylation and CapSTARR-seq levels on enhancer-promoter interactions. RESULTS We report a comprehensive catalog of 75,730 recurrent predicted enhancers, the majority of which are GC-associated in vivo (> 50,000) and associated with lower somatic mutation rates inferred by whole-genome sequencing. Applying CapSTARR-seq to the enhancer catalog, we observed significant correlations between CapSTARR-seq functional activity and H3K27ac/H3K4me1 levels. Super-enhancer regions exhibited increased CapSTARR-seq signals compared to regular enhancers, even when decoupled from native chromatin contexture. We show that combining histone modification and CapSTARR-seq functional enhancer data improves the prediction of enhancer-promoter interactions and pinpointing of germline single nucleotide polymorphisms (SNPs), somatic copy number alterations (SCNAs), and trans-acting TFs involved in GC expression. We identified cancer-relevant genes (ING1, ARL4C) whose expression between patients is influenced by enhancer differences in genomic copy number and germline SNPs, and HNF4α as a master trans-acting factor associated with GC enhancer heterogeneity. CONCLUSIONS Our results indicate that combining histone modification and functional assay data may provide a more accurate metric to assess enhancer activity than either platform individually, providing insights into the relative contribution of genetic (cis) and regulatory (trans) mechanisms to GC enhancer functional heterogeneity.
Collapse
Affiliation(s)
- Taotao Sheng
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Shamaine Wei Ting Ho
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Wen Fong Ooi
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Manjie Xing
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Nisha Padmanabhan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Lijia Ma
- The Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Mohana Ray
- The Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Yu Amanda Guo
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Ngak Leng Sim
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore, 119074, Singapore
- Precision Medicine and Population Genomics (Germline), Genome Institute of Singapore, Singapore, Singapore
- Montreal Heart Institute, Montreal, Canada
- Department of Medicine, University of Montreal, Montreal, Canada
| | - Mei Mei Chang
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Milad Razavi-Mohseni
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA
| | - Roger Sik Yin Foo
- Cardiovascular Research Institute, National University Health System, Singapore, 119074, Singapore
- Precision Medicine and Population Genomics (Germline), Genome Institute of Singapore, Singapore, Singapore
| | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Department of Haematology-Oncology, National University Cancer Institute Singapore, National University Hospital, Singapore, 119074, Singapore
| | - Yiong Huak Chan
- Biostatistics Unit, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Anders Jacobsen Skanderup
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Kevin P White
- The Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA.
- Tempus Labs, Chicago, USA.
| | - Sudhakar Jha
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA.
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, 138672, Singapore.
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, 168752, Singapore.
- Department of Physiology, National University of Singapore, Singapore, 117593, Singapore.
- Singapore Gastric Cancer Consortium, Singapore, 119228, Singapore.
| |
Collapse
|
108
|
Wang C, Li Y, Jia L, Kim JK, Li J, Deng P, Zhang W, Krebsbach PH, Wang CY. CD276 expression enables squamous cell carcinoma stem cells to evade immune surveillance. Cell Stem Cell 2021; 28:1597-1613.e7. [PMID: 33945793 PMCID: PMC8419062 DOI: 10.1016/j.stem.2021.04.011] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/22/2021] [Accepted: 04/12/2021] [Indexed: 01/19/2023]
Abstract
Immunosurveillance is a critical mechanism guarding against tumor development and progression. Checkpoint inhibitors have shown significant success in cancer treatment, but expression of key factors such as PD-L1 in putative cancer stem cell (CSC) populations in squamous cell carcinoma has been inconclusive, suggesting that CSCs may have developed other mechanisms to escape immune surveillance. Here we show that CSCs upregulate the immune checkpoint molecule CD276 (B7-H3) to evade host immune responses. CD276 is highly expressed by CSCs in mouse and human head and neck squamous cell carcinoma (HNSCC) and can be used to prospectively isolate tumorigenic CSCs. Anti-CD276 antibodies eliminate CSCs in a CD8+ T cell-dependent manner, inhibiting tumor growth and lymph node metastases in a mouse HNSCC model. Single-cell RNA sequencing (RNA-seq) showed that CD276 blockade remodels SCC heterogeneity and reduces epithelial-mesenchymal transition. These results show that CSCs utilize CD276 for immune escape and suggest that targeting CD276 may reduce CSCs in HNSCC.
Collapse
Affiliation(s)
- Cheng Wang
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, UCLA, Los Angeles, CA 90095, USA
| | - Yang Li
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, UCLA, Los Angeles, CA 90095, USA
| | - Lingfei Jia
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, UCLA, Los Angeles, CA 90095, USA
| | - Jin koo Kim
- Division of Constitutive and Regenerative Sciences, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Jiong Li
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, UCLA, Los Angeles, CA 90095, USA
| | - Peng Deng
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, UCLA, Los Angeles, CA 90095, USA
| | - Wuchang Zhang
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, UCLA, Los Angeles, CA 90095, USA
| | - Paul H. Krebsbach
- Division of Constitutive and Regenerative Sciences, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Cun-Yu Wang
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, UCLA, Los Angeles, CA 90095, USA,Department of Bioengineering, Henry Samueli School of Engineering and Applied Science, UCLA, Los Angeles, CA 90095, USA,Lead contact,Correspondence:
| |
Collapse
|
109
|
Wang J, Ma X, Ma J. Identification of Four Enhancer-Associated Genes as Risk Signature for Diffuse Glioma Patients. J Mol Neurosci 2021; 72:410-419. [PMID: 34462884 DOI: 10.1007/s12031-021-01861-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/19/2021] [Indexed: 01/21/2023]
Abstract
The abnormal expressions of enhancer-associated genes have been reported to be correlated with poor prognosis of tumors, including glioblastoma (GBM). The objective of the current study is to predict prognosis by identifying enhancer-associated genes (EAGs). The profiles of genome-wide expressions of low-grade glioma (LGG) and GBM tissues in The Cancer Genome Atlas (TCGA) dataset were obtained to explore the expression patterns of EAGs in diffuse glioma. The capacity of prognosis prediction was validated by Rembrandt and GSE16011. Moreover, qPCR was utilized to confirm the effect of JQ1 and THZ1 on the EAGs. We detected 35 differentially expressed EAGs, which were predictive of overall survival. These candidate EAGs were then subjected to the multivariate cox regression analysis and were further scoped down to four signature genes, including TRAM2, SMAGP, KDELC2, and C7ORF25. A total of 662 patients were then stratified according to the expression levels of these four signature genes. The high-risk group accounted for poorer prognosis based on the Rembrandt and GSE16011 databases. The results of qPCR also demonstrated that the expression of the four EAGs could be abolished by JQ1 (bromodomain inhibitor) and THZ1 (CDK7 inhibitor) treatment. Our study not only highlights the potential role of EAGs, which can be used to improve clinical prognosis prediction in patients with diffuse glioma, but also sheds light on the specific biomarkers and therapeutic targets for diffuse glioma patients.
Collapse
Affiliation(s)
- Jiajia Wang
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Xin Ma
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jie Ma
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| |
Collapse
|
110
|
Li L, Wang N, Zhu M, Xiong Y, Wang F, Guo G, Wang X, Gu Y. Aberrant super-enhancer-driven oncogene ENC1 promotes the radio-resistance of breast carcinoma. Cell Death Dis 2021; 12:777. [PMID: 34362881 PMCID: PMC8346480 DOI: 10.1038/s41419-021-04060-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022]
Abstract
Poor response of tumors to radiotherapy is a major clinical obstacle. Because of the dynamic characteristics of the epigenome, identification of possible epigenetic modifiers may be beneficial to confer radio-sensitivity. This research was set to examine the modulation of ectodermal-neural cortex 1 (ENC1) in radio-resistance in breast carcinoma (BC). In silico identification and immunohistochemical staining revealed that overexpression of ENC1 promoted BC metastasis to the bone and brain. Moreover, its overexpression promoted the translocation of YAP1/TAZ into the nucleus and enhanced expression of GLI1, CTGF, and FGF1 through the Hippo pathway. ENC1 expression was controlled by a ~10-kb long SE. ENC1-SEdistal deletion reduced ENC1 expression and inhibited the malignant behavior of BC cells and their resistance to radiotherapy. The binding sites on the ENC1-SE region enriched the shared sequence between TCF4 and ENC1 promoter. Knocking-down TCF4 inhibited luciferase activity and H3K27ac-enriched binding of the ENC1-SE region. Additionally, SE-driven ENC1 overexpression mediated by TCF4 may have clinical implications in radio-resistance in BC patients. Our findings indicated that ENC1 overexpression is mediated by SE and the downstream TCF4 to potentiate the Hippo/YAP1/TAZ pathway. Targeting this axis might be a therapeutic strategy for overcoming BC radio-resistance.
Collapse
Affiliation(s)
- Lin Li
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Nan Wang
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Mingzhi Zhu
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Youyi Xiong
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Fang Wang
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Guangcheng Guo
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Xinxing Wang
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Yuanyan Gu
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China.
| |
Collapse
|
111
|
Inhibitors Targeting CDK9 Show High Efficacy against Osimertinib and AMG510 Resistant Lung Adenocarcinoma Cells. Cancers (Basel) 2021; 13:cancers13153906. [PMID: 34359807 PMCID: PMC8345430 DOI: 10.3390/cancers13153906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Non-small cell lung cancer accounts for 80% of all lung cancer cases. While a subset of non-small cell lung cancer patients respond to immunotherapy, those who are treated with chemotherapy or targeted therapy develop resistance to the drugs. Thus, novel therapeutic strategies are needed to combat this disease. Here we show that inhibitors of the cyclin-dependent kinase 9 are highly effective in preventing the growth of a variety of lung cancer cell lines and lung cancer organoids with high potency. These inhibitors suppressed the expression of several genes like Sox2, Sox9, and Mcl1 that promote tumor growth, facilitating growth arrest. Since inhibitors of cyclin-dependent kinase 9 are undergoing clinical trials for hematological malignancies, our studies suggest that these inhibitors would be attractive candidates to combat non-small cell lung cancer. Abstract Non-small cell lung cancer has a 5-year survival rate of less than 12–15%, calling for the development of additional therapeutic strategies to combat this disease. Here we tested the efficacy of inhibiting cyclin-dependent kinase 9 (CDK9) on lung cancer cell lines with K-Ras and EGFR mutations and on lung cancer organoids. Three different CDK9 inhibitors reduced the viability and anchorage-independent growth of lung cancer cell lines at very low nanomolar to micromolar concentrations. CDK9 inhibition suppressed the expression of the anti-apoptotic protein, Mcl1, as well as the embryonic stem cell transcription factors, Sox2 and Sox9, which are pro-tumorigenic. In contrast, treatment with CDK9 inhibitors increased the levels of WT p53 and its downstream target p21 in K-Ras mutant cell lines. Furthermore, the CDK9 inhibitors could markedly reduce the viability of Osimertinib-resistant PC9 and AMG510-resistant H23 and H358 cells with comparable efficacy as the parental cells. CDK9 inhibitors could also significantly reduce the growth and viability of lung cancer organoids with high potency. Taken together, the data presented here strongly suggest that CDK9 inhibitors would be efficacious against K-Ras mutant and EGFR mutant NSCLCs, including those that develop resistance to targeted therapies.
Collapse
|
112
|
Yang Y, Jiang D, Zhou Z, Xiong H, Yang X, Peng G, Xia W, Wang S, Lei H, Zhao J, Qian Z, Wu S, Pang J. CDK7 blockade suppresses super-enhancer-associated oncogenes in bladder cancer. Cell Oncol (Dordr) 2021; 44:871-887. [PMID: 33905040 DOI: 10.1007/s13402-021-00608-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/08/2021] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Transcriptional addiction plays a pivotal role in maintaining the hallmarks of cancer cells. Thus, targeting super-enhancers (SEs), which modulate the transcriptional activity of oncogenes, has become an attractive strategy for cancer therapy. As yet, however, the molecular mechanisms of this process in bladder cancer (BC) remain to be elucidated. Here, we aimed to provide detailed information regarding the SE landscape in BC and to investigate new potential pharmaceutical targets for BC therapy. METHODS We employed THZ1 as a potent and specific CDK7 inhibitor. In vitro and in vivo studies were carried out to investigate the anticancer and apoptosis-inducing effects of THZ1 on BC cells. Whole-transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) were performed to investigate the mechanism and function of SE-linked oncogenic transcription in BC cells. RESULTS We found that THZ1 serves as an effective and potent inhibitor with suppressive activity against BC cells. An integrative analysis of THZ1-sensitive and SE-associated oncogenes yielded potential new pharmaceutical targets, including DDIT4, B4GALT5, PSRC1 and MED22. Combination treatment with THZ1 and the DDIT4 inhibitor rapamycin effectively suppressed BC cell growth. In addition, we found that THZ1 and rapamycin sensitized BC cells to conventional chemotherapy. CONCLUSIONS Our data indicate that exploring BC gene regulatory mechanisms associated with SEs through integrating RNA-seq and ChIP-seq data improves our understanding of BC biology and provides a basis for innovative therapies.
Collapse
Affiliation(s)
- Yafei Yang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, China
| | - Donggen Jiang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, China
| | - Ziyu Zhou
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China
- Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, 518000, China
| | - Haiyun Xiong
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, China
| | - Xiangwei Yang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, China
| | - Guoyu Peng
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China
- Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, 518000, China
| | - Wuchao Xia
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China
- Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, 518000, China
| | - Shang Wang
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China
- Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, 518000, China
| | - Hanqi Lei
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, China
| | - Jing Zhao
- Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Zhirong Qian
- Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Song Wu
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China.
- Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, 518000, China.
| | - Jun Pang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, China.
| |
Collapse
|
113
|
Lara-Ureña N, García-Domínguez M. Relevance of BET Family Proteins in SARS-CoV-2 Infection. Biomolecules 2021; 11:1126. [PMID: 34439792 PMCID: PMC8391731 DOI: 10.3390/biom11081126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
The recent pandemic we are experiencing caused by the coronavirus disease 2019 (COVID-19) has put the world's population on the rack, with more than 191 million cases and more than 4.1 million deaths confirmed to date. This disease is caused by a new type of coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A massive proteomic analysis has revealed that one of the structural proteins of the virus, the E protein, interacts with BRD2 and BRD4 proteins of the Bromodomain and Extra Terminal domain (BET) family of proteins. BETs are essential to cell cycle progression, inflammation and immune response and have also been strongly associated with infection by different types of viruses. The fundamental role BET proteins play in transcription makes them appropriate targets for the propagation strategies of some viruses. Recognition of histone acetylation by BET bromodomains is essential for transcription control. The development of drugs mimicking acetyl groups, and thereby able to displace BET proteins from chromatin, has boosted interest on BETs as attractive targets for therapeutic intervention. The success of these drugs against a variety of diseases in cellular and animal models has been recently enlarged with promising results from SARS-CoV-2 infection studies.
Collapse
Affiliation(s)
| | - Mario García-Domínguez
- Andalusian Centre for Molecular Biology and Regenerative Medicine (CABIMER), CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain;
| |
Collapse
|
114
|
Yu D, Yang X, Lin J, Cao Z, Lu C, Yang Z, Zheng M, Pan R, Cai W. Super-Enhancer Induced IL-20RA Promotes Proliferation/Metastasis and Immune Evasion in Colorectal Cancer. Front Oncol 2021; 11:724655. [PMID: 34336707 PMCID: PMC8319729 DOI: 10.3389/fonc.2021.724655] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/02/2021] [Indexed: 12/15/2022] Open
Abstract
Unveiling key oncogenic events in malignancies is the key to improving the prognosis and therapeutic outcome of malignancies. Lines of evidence have shown that super-enhancers control the expression of genes that determine the cell fate, but the oncogenic super-enhancers in colorectal cancer (CRC) and their impact on carcinogens remain largely unexplored. Here, we identified a new oncogenic super-enhancer-regulated gene, IL-20RA, in CRC. Using the integrative analysis of H3K27ac ChIP-seq and RNA-seq in CRC tumors and normal colon tissues, we obtained a series of oncogenic super-enhancers in CRC. We found that super-enhancer inhibition by JQ-1 or iBET-151 suppressed the growth of tumor cells and inhibited the expression of IL-20RA. We found that IL-20RA was highly expressed in the tumor tissue of CRC and related to the advanced stage. Further functional studies showed that knockdown of IL-20RA inhibited the growth and metastasis of CRC. In addition, we found that IL-20RA was involved in regulating oncogenic and immune pathways and affecting the expression of genes related to cell proliferation and immune evasion in CRC. Together, our study demonstrated a novel oncogene in CRC and shed new light on oncogenic super-enhancer contributions to cell proliferation and immune escape.
Collapse
Affiliation(s)
- Dingye Yu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiao Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jianwei Lin
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zichao Cao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chenghao Lu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zheyu Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Minhua Zheng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ruijun Pan
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wei Cai
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| |
Collapse
|
115
|
Beacon TH, Delcuve GP, López C, Nardocci G, Kovalchuk I, van Wijnen AJ, Davie JR. The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes. Clin Epigenetics 2021; 13:138. [PMID: 34238359 PMCID: PMC8264473 DOI: 10.1186/s13148-021-01126-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4 (H3K4me3) located after first exons and around transcription start sites. This epigenetic mark is typically restricted to narrow regions at the 5`end of the gene body, though a small subset of genes have a broad H3K4me3 domain which extensively covers the coding region. Although most studies focus on the H3K4me3 mark, the broad H3K4me3 domain is associated with a plethora of histone modifications (e.g., H3 acetylated at K27) and is therein termed broad epigenetic domain. Genes marked with the broad epigenetic domain are involved in cell identity and essential cell functions and have clinical potential as biomarkers for patient stratification. Reducing expression of genes with the broad epigenetic domain may increase the metastatic potential of cancer cells. Enhancers and super-enhancers interact with the broad epigenetic domain marked genes forming a hub of interactions involving nucleosome-depleted regions. Together, the regulatory elements coalesce with transcription factors, chromatin modifying/remodeling enzymes, coactivators, and the Mediator and/or Integrator complex into a transcription factory which may be analogous to a liquid–liquid phase-separated condensate. The broad epigenetic domain has a dynamic chromatin structure which supports frequent transcription bursts. In this review, we present the current knowledge of broad epigenetic domains.
Collapse
Affiliation(s)
- Tasnim H Beacon
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Geneviève P Delcuve
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Camila López
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Gino Nardocci
- Faculty of Medicine, Universidad de Los Andes, Santiago, Chile.,Molecular Biology and Bioinformatics Lab, Program in Molecular Biology and Bioinformatics, Center for Biomedical Research and Innovation (CIIB), Universidad de Los Andes, Santiago, Chile
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - James R Davie
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada. .,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada.
| |
Collapse
|
116
|
The MLL3/4 H3K4 methyltransferase complex in establishing an active enhancer landscape. Biochem Soc Trans 2021; 49:1041-1054. [PMID: 34156443 PMCID: PMC8286814 DOI: 10.1042/bst20191164] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/23/2022]
Abstract
Enhancers are cis-regulatory elements that play essential roles in tissue-specific gene expression during development. Enhancer function in the expression of developmental genes requires precise regulation, while deregulation of enhancer function could be the main cause of tissue-specific cancer development. MLL3/KMT2C and MLL4/KMT2D are two paralogous histone modifiers that belong to the SET1/MLL (also named COMPASS) family of lysine methyltransferases and play critical roles in enhancer-regulated gene activation. Importantly, large-scale DNA sequencing studies have revealed that they are amongst the most frequently mutated genes associated with human cancers. MLL3 and MLL4 form identical multi-protein complexes for modifying mono-methylation of histone H3 lysine 4 (H3K4) at enhancers, which together with the p300/CBP-mediated H3K27 acetylation can generate an active enhancer landscape for long-range target gene activation. Recent studies have provided a better understanding of the possible mechanisms underlying the roles of MLL3/MLL4 complexes in enhancer regulation. Moreover, accumulating studies offer new insights into our knowledge of the potential role of MLL3/MLL4 in cancer development. In this review, we summarize recent evidence on the molecular mechanisms of MLL3/MLL4 in the regulation of active enhancer landscape and long-range gene expression, and discuss their clinical implications in human cancers.
Collapse
|
117
|
Lu J, Qian J, Xu Z, Yin S, Zhou L, Zheng S, Zhang W. Emerging Roles of Liquid-Liquid Phase Separation in Cancer: From Protein Aggregation to Immune-Associated Signaling. Front Cell Dev Biol 2021; 9:631486. [PMID: 34235141 PMCID: PMC8255971 DOI: 10.3389/fcell.2021.631486] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/14/2021] [Indexed: 12/12/2022] Open
Abstract
Liquid-liquid Phase Separation (LLPS) of proteins and nucleic acids has emerged as a new paradigm in the study of cellular activities. It drives the formation of liquid-like condensates containing biomolecules in the absence of membrane structures in living cells. In addition, typical membrane-less condensates such as nuclear speckles, stress granules and cell signaling clusters play important roles in various cellular activities, including regulation of transcription, cellular stress response and signal transduction. Previous studies highlighted the biophysical and biochemical principles underlying the formation of these liquid condensates. The studies also showed how these principles determine the molecular properties, LLPS behavior, and composition of liquid condensates. While the basic rules driving LLPS are continuously being uncovered, their function in cellular activities is still unclear, especially within a pathological context. Therefore, the present review summarizes the recent progress made on the existing roles of LLPS in cancer, including cancer-related signaling pathways, transcription regulation and maintenance of genome stability. Additionally, the review briefly introduces the basic rules of LLPS, and cellular signaling that potentially plays a role in cancer, including pathways relevant to immune responses and autophagy.
Collapse
Affiliation(s)
- Jiahua Lu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China
| | - Junjie Qian
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China.,Organ Transplantation Institute, Zhejiang University, Hangzhou, China
| | - Zhentian Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China
| | - Shengyong Yin
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China.,Organ Transplantation Institute, Zhejiang University, Hangzhou, China
| | - Lin Zhou
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China.,Organ Transplantation Institute, Zhejiang University, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China.,Organ Transplantation Institute, Zhejiang University, Hangzhou, China.,Shulan (Hangzhou) Hospital Affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Wu Zhang
- Organ Transplantation Institute, Zhejiang University, Hangzhou, China.,Shulan (Hangzhou) Hospital Affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| |
Collapse
|
118
|
BRD4 inhibition boosts the therapeutic effects of epidermal growth factor receptor-targeted chimeric antigen receptor T cells in glioblastoma. Mol Ther 2021; 29:3011-3026. [PMID: 34058385 PMCID: PMC8531146 DOI: 10.1016/j.ymthe.2021.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/30/2021] [Accepted: 05/25/2021] [Indexed: 11/21/2022] Open
Abstract
Glioblastoma (GBM) is the deadliest brain malignancy without effective treatments. Here, we reported that epidermal growth factor receptor-targeted chimeric antigen receptor T cells (EGFR CAR-T) were effective in suppressing the growth of GBM cells in vitro and xenografts derived from GBM cell lines and patients in mice. However, mice soon acquired resistance to EGFR CAR-T cell treatment, limiting its potential use in the clinic. To find ways to improve the efficacy of EGFR CAR-T cells, we performed genomics and transcriptomics analysis for GBM cells incubated with EGFR CAR-T cells and found that a large cohort of genes, including immunosuppressive genes, as well as enhancers in vicinity are activated. BRD4, an epigenetic modulator functioning on both promoters and enhancers, was required for the activation of these immunosuppressive genes. Accordingly, inhibition of BRD4 by JQ1 blocked the activation of these immunosuppressive genes. Combination therapy with EGFR CAR-T cells and JQ1 suppressed the growth and metastasis of GBM cells and prolonged survival in mice. We demonstrated that transcriptional modulation by targeting epigenetic regulators could improve the efficacy of immunotherapy including CAR-T, providing a therapeutic avenue for treating GBM in the clinic.
Collapse
|
119
|
Wood S, Willbanks A, Cheng JX. The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance. Curr Cancer Drug Targets 2021; 21:326-352. [PMID: 33504307 DOI: 10.2174/1568009621666210127092828] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
The advent of new genome-wide sequencing technologies has uncovered abnormal RNA modifications and RNA editing in a variety of human cancers. The discovery of reversible RNA N6-methyladenosine (RNA: m6A) by fat mass and obesity-associated protein (FTO) demethylase has led to exponential publications on the pathophysiological functions of m6A and its corresponding RNA modifying proteins (RMPs) in the past decade. Some excellent reviews have summarized the recent progress in this field. Compared to the extent of research into RNA: m6A and DNA 5-methylcytosine (DNA: m5C), much less is known about other RNA modifications and their associated RMPs, such as the role of RNA: m5C and its RNA cytosine methyltransferases (RCMTs) in cancer therapy and drug resistance. In this review, we will summarize the recent progress surrounding the function, intramolecular distribution and subcellular localization of several major RNA modifications, including 5' cap N7-methylguanosine (m7G) and 2'-O-methylation (Nm), m6A, m5C, A-to-I editing, and the associated RMPs. We will then discuss dysregulation of those RNA modifications and RMPs in cancer and their role in cancer therapy and drug resistance.
Collapse
Affiliation(s)
- Shaun Wood
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Amber Willbanks
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Jason X Cheng
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| |
Collapse
|
120
|
Adhikary S, Roy S, Chacon J, Gadad SS, Das C. Implications of Enhancer Transcription and eRNAs in Cancer. Cancer Res 2021; 81:4174-4182. [PMID: 34016622 DOI: 10.1158/0008-5472.can-20-4010] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/03/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022]
Abstract
Despite extensive progress in developing anticancer therapies, therapy resistance remains a major challenge that promotes disease relapse. The changes that lead to therapy resistance can be intrinsically present or may be initiated during treatment. Genetic and epigenetic heterogeneity in tumors make it more challenging to deal with therapy resistance. Recent advances in genome-wide analyses have revealed that the deregulation of distal gene regulatory elements, such as enhancers, appears in several pathophysiological conditions, including cancer. Beyond the conventional function of enhancers in recruiting transcription factors to gene promoters, enhancer elements are also transcribed into noncoding RNAs known as enhancer RNAs (eRNA). Accumulating evidence suggests that uncontrolled enhancer activity with aberrant eRNA expression promotes oncogenesis. Interestingly, tissue-specific, transcribed eRNAs from active enhancers can serve as potential therapeutic targets or biomarkers in several cancer types. This review provides a comprehensive overview of the mechanisms of enhancer transcription and eRNAs as well as their potential roles in cancer and drug resistance.
Collapse
Affiliation(s)
- Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jessica Chacon
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas
| | - Shrikanth S Gadad
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas. .,Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas.,Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, Texas.,Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynaecology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India. .,Homi Bhaba National Institute, Mumbai, Maharashtra, India
| |
Collapse
|
121
|
Li GH, Qu Q, Qi TT, Teng XQ, Zhu HH, Wang JJ, Lu Q, Qu J. Super-enhancers: a new frontier for epigenetic modifiers in cancer chemoresistance. J Exp Clin Cancer Res 2021; 40:174. [PMID: 34011395 PMCID: PMC8132395 DOI: 10.1186/s13046-021-01974-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/05/2021] [Indexed: 02/06/2023] Open
Abstract
Although new developments of surgery, chemotherapy, radiotherapy, and immunotherapy treatments for cancer have improved patient survival, the emergence of chemoresistance in cancer has significant impacts on treatment effects. The development of chemoresistance involves several polygenic, progressive mechanisms at the molecular and cellular levels, as well as both genetic and epigenetic heterogeneities. Chemotherapeutics induce epigenetic reprogramming in cancer cells, converting a transient transcriptional state into a stably resistant one. Super-enhancers (SEs) are central to the maintenance of identity of cancer cells and promote SE-driven-oncogenic transcriptions to which cancer cells become highly addicted. This dependence on SE-driven transcription to maintain chemoresistance offers an Achilles' heel for chemoresistance. Indeed, the inhibition of SE components dampens oncogenic transcription and inhibits tumor growth to ultimately achieve combined sensitization and reverse the effects of drug resistance. No reviews have been published on SE-related mechanisms in the cancer chemoresistance. In this review, we investigated the structure, function, and regulation of chemoresistance-related SEs and their contributions to the chemotherapy via regulation of the formation of cancer stem cells, cellular plasticity, the microenvironment, genes associated with chemoresistance, noncoding RNAs, and tumor immunity. The discovery of these mechanisms may aid in the development of new drugs to improve the sensitivity and specificity of cancer cells to chemotherapy drugs.
Collapse
Affiliation(s)
- Guo-Hua Li
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Ting-Ting Qi
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Xin-Qi Teng
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Hai-Hong Zhu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Jiao-Jiao Wang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Qiong Lu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China.
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China.
| |
Collapse
|
122
|
Ma Q, Yang F, Mackintosh C, Jayani RS, Oh S, Jin C, Nair SJ, Merkurjev D, Ma W, Allen S, Wang D, Almenar-Queralt A, Garcia-Bassets I. Super-Enhancer Redistribution as a Mechanism of Broad Gene Dysregulation in Repeatedly Drug-Treated Cancer Cells. Cell Rep 2021; 31:107532. [PMID: 32320655 DOI: 10.1016/j.celrep.2020.107532] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/07/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
Cisplatin is an antineoplastic drug administered at suboptimal and intermittent doses to avoid life-threatening effects. Although this regimen shortly improves symptoms in the short term, it also leads to more malignant disease in the long term. We describe a multilayered analysis ranging from chromatin to translation-integrating chromatin immunoprecipitation sequencing (ChIP-seq), global run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and ribosome profiling-to understand how cisplatin confers (pre)malignant features by using a well-established ovarian cancer model of cisplatin exposure. This approach allows us to segregate the human transcriptome into gene modules representing distinct regulatory principles and to characterize that the most cisplatin-disrupted modules are associated with underlying events of super-enhancer plasticity. These events arise when cancer cells initiate without ultimately ending the program of drug-stimulated death. Using a PageRank-based algorithm, we predict super-enhancer regulator ISL1 as a driver of this plasticity and validate this prediction by using CRISPR/dCas9-KRAB inhibition (CRISPRi) and CRISPR/dCas9-VP64 activation (CRISPRa) tools. Together, we propose that cisplatin reprograms cancer cells when inducing them to undergo near-to-death experiences.
Collapse
Affiliation(s)
- Qi Ma
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Feng Yang
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carlos Mackintosh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ranveer Singh Jayani
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Soohwan Oh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chunyu Jin
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sreejith Janardhanan Nair
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daria Merkurjev
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wubin Ma
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Allen
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dong Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China
| | - Angels Almenar-Queralt
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
123
|
C646 inhibits G2/M cell cycle-related proteins and potentiates anti-tumor effects in pancreatic cancer. Sci Rep 2021; 11:10078. [PMID: 33980911 PMCID: PMC8115044 DOI: 10.1038/s41598-021-89530-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/27/2021] [Indexed: 12/19/2022] Open
Abstract
The activity of histone acetyltransferases (HATs) plays a central role in an epigenetic modification in cooperation with HDACs (histone deacetyl transferases). It is likely that malfunction of this enzymatic machinery controlling epigenetic modification is relevant to carcinogenesis and tumor progression. However, in pancreatic cancer, the clinical relevance of HAT activity and histone acetylation has remained unclear. We identified that H3 acetylation was expressed in all pancreatic cancer patients, indicating that H3 acetylation may be essential in pancreatic cancer cells. We also found that the HAT inhibitor C646 augmented anti-tumor effects in vitro by inhibiting cell proliferation and cell cycle progression concomitantly with suppression of acetylated H3K9 and H3K27 expression. C646 or p300 and CBP (CREB-binding protein)-specific siRNA treatment inhibited the transcription of the G2/M cell cycle regulatory proteins cyclin B1 and CDK1 (cyclin-dependent kinase 1). C646 treatment also inhibited tumor growth in vivo in a xenograft mouse model. C646 could be an effective therapeutic agent for pancreatic cancer. The epigenetic status of pancreatic cancers based on their level of histone H3 acetylation may influence patient survival. Epigenetic stratification according to H3K27 acetylation could be useful for predicting disease prognosis as well as the therapeutic efficacy of C646 in pancreatic cancer.
Collapse
|
124
|
Grosveld F, van Staalduinen J, Stadhouders R. Transcriptional Regulation by (Super)Enhancers: From Discovery to Mechanisms. Annu Rev Genomics Hum Genet 2021; 22:127-146. [PMID: 33951408 DOI: 10.1146/annurev-genom-122220-093818] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Accurate control of gene expression in the right cell at the right moment is of fundamental importance to animal development and homeostasis. At the heart of gene regulation lie the enhancers, a class of gene regulatory elements that ensures precise spatiotemporal activation of gene transcription. Mammalian genomes are littered with enhancers, which are frequently organized in cooperative clusters such as locus control regions and superenhancers. Here, we discuss our current knowledge of enhancer biology, including an overview of the discovery of the various enhancer subsets and the mechanistic models used to explain their gene regulatory function.
Collapse
Affiliation(s)
- Frank Grosveld
- Department of Cell Biology, Erasmus MC, 3000 CA Rotterdam, The Netherlands; ,
| | | | - Ralph Stadhouders
- Department of Cell Biology, Erasmus MC, 3000 CA Rotterdam, The Netherlands; , .,Department of Pulmonary Medicine, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| |
Collapse
|
125
|
Xia L, Zheng Z, Liu JY, Chen YJ, Ding J, Hu GS, Hu YH, Liu S, Luo WX, Xia NS, Liu W. Targeting Triple-Negative Breast Cancer with Combination Therapy of EGFR CAR T Cells and CDK7 Inhibition. Cancer Immunol Res 2021; 9:707-722. [PMID: 33875483 DOI: 10.1158/2326-6066.cir-20-0405] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 01/22/2021] [Accepted: 04/15/2021] [Indexed: 11/16/2022]
Abstract
EGFR-targeted chimeric antigen receptor (CAR) T cells are potent and specific in suppressing the growth of triple-negative breast cancer (TNBC) in vitro and in vivo. However, in this study, a subset of mice soon acquired resistance, which limits the potential use of EGFR CAR T cells. We aimed to find a way to overcome the observed resistance. Transcriptomic analysis results revealed that EGFR CAR T-cell treatment induced a set of immunosuppressive genes, presumably through IFNγ signaling, in EGFR CAR T-cell-resistant TNBC tumors. The EGFR CAR T-cell-induced immunosuppressive genes were associated with EGFR CAR T-cell-activated enhancers and were especially sensitive to THZ1, a CDK7 inhibitor we screened out of a panel of small molecules targeting epigenetic modulators. Accordingly, combination therapy with THZ1 and EGFR CAR T cells suppressed immune resistance, tumor growth, and metastasis in TNBC tumor models, including human MDA-MB-231 cell-derived and TNBC patient-derived xenografts, and mouse EMT6 cell-derived allografts. Taken together, we demonstrated that transcriptional modulation using epigenetic inhibitors could overcome CAR T-cell therapy-induced immune resistance, thus providing a therapeutic avenue for treating TNBC in the clinic.
Collapse
Affiliation(s)
- Lin Xia
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China
| | - Zaozao Zheng
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jun-Yi Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China
| | - Yu-Jie Chen
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jiancheng Ding
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Guo-Sheng Hu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ya-Hong Hu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Suling Liu
- Shanghai Cancer Hospital, Xuhui District, Shanghai, China
| | - Wen-Xin Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China
| | - Ning-Shao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China
| | - Wen Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China. .,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China.,State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| |
Collapse
|
126
|
Han C, Gao X, Li Y, Zhang J, Yang E, Zhang L, Yu L. Characteristics of Cohesin Mutation in Acute Myeloid Leukemia and Its Clinical Significance. Front Oncol 2021; 11:579881. [PMID: 33928020 PMCID: PMC8076553 DOI: 10.3389/fonc.2021.579881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 03/18/2021] [Indexed: 12/18/2022] Open
Abstract
The occurrence of gene mutation is a major contributor to the initiation and propagation of acute myeloid leukemia (AML). Accumulating evidence suggests that genes encoding cohesin subunits have a high prevalence of mutations in AML, especially in the t(8;21) subtype. Therefore, it is important to understand how cohesin mutations contribute to leukemogenesis. However, the fundamental understanding of cohesin mutation in clonal expansion and myeloid transformation in hematopoietic cells remains ambiguous. Previous studies briefly introduced the cohesin mutation in AML; however, an in-depth summary of mutations in AML was not provided, and the correlation between cohesin and AML1-ETO in t (8;21) AML was also not analyzed. By summarizing the major findings regarding the cohesin mutation in AML, this review aims to define the characteristics of the cohesin complex mutation, identify its relationships with co-occurring gene mutations, assess its roles in clonal evolution, and discuss its potential for the prognosis of AML. In particular, we focus on the function of cohesin mutations in RUNX1-RUNX1T1 fusion.
Collapse
Affiliation(s)
- Caixia Han
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Xuefeng Gao
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Yonghui Li
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Juan Zhang
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Erna Yang
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Li Zhang
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Li Yu
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| |
Collapse
|
127
|
Grady WM. Epigenetic alterations in the gastrointestinal tract: Current and emerging use for biomarkers of cancer. Adv Cancer Res 2021; 151:425-468. [PMID: 34148620 DOI: 10.1016/bs.acr.2021.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Colorectal cancer is a leading cause of cancer related deaths worldwide. One of the hallmarks of cancer and a fundamental trait of virtually all gastrointestinal cancers is genomic and epigenomic DNA alterations. Cancer cells acquire genetic and epigenetic alterations that drive the initiation and progression of the cancers by altering the molecular and cell biological process of the cells. These alterations, as well as other host and microenvironment factors, ultimately mediate the initiation and progression of cancers, including colorectal cancer. Epigenetic alterations, which include changes affecting DNA methylation, histone modifications, chromatin structure, and noncoding RNA expression, have emerged as a major class of molecular alteration in colon polyps and colorectal cancer. The classes of epigenetic alterations, their status in colorectal polyps and cancer, their effects on neoplasm biology, and their application to clinical care will be discussed.
Collapse
Affiliation(s)
- William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States; Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA, United States.
| |
Collapse
|
128
|
Li X, Duan Y, Hao Y. Identification of super enhancer-associated key genes for prognosis of germinal center B-cell type diffuse large B-cell lymphoma by integrated analysis. BMC Med Genomics 2021; 14:69. [PMID: 33663517 PMCID: PMC7934469 DOI: 10.1186/s12920-021-00916-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/21/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The pathogenesis of germinal center B-cell type diffuse large B-cell lymphoma (GCB-DLBCL) is not fully elucidated. This study aims to explore the regulation of super enhancers (SEs) on GCB-DLBCL by identifying specific SE-target gene. METHODS Weighted gene co-expression network analysis (WGCNA) was used to screen modules associated with GCB subtype. Functional analysis was performed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. H3K27ac peaks were used to identify SEs. Overall survival analysis was performed using Kaplan-Meier curve with log-rank and Breslow test. The effect of ADNP, ANKRD28 and RTN4IP1 knockdown on Karpas 422 and SUDHL-4 cells proliferation was analyzed by CCK-8. Karpas 422 and SUDHL-4 cells were treated with bromodomain and extra-terminal domain (BET) inhibitor JQ1, and the expression of ADNP, ANKRD28 and RTN4IP1was measured by qRT-PCR. RESULTS A total of 26 modules were screened in DLBCL. Turquoise module was closely related to GCB-DLBCL, and its eigengenes were mainly related to autophagy. There were 971 SEs in Karpas 422 cell and 1088 SEs in SUDHL-4 cell. Function of the nearest genes of overall SEs were related to cancer. Six SE-related genes associated with GCB-DLBCL were identified as prognostic markers. Knockdown of ADNP, ANKRD28 and RTN4IP1 inhibited the proliferation of Karpas 422 and SUDHL-4 cells. JQ1 treatment suppressed ADNP, ANKRD28 and RTN4IP1 expression in Karpas 422 and SUDHL-4 cells. CONCLUSIONS A total of 6 SE-related genes associated with GCB-DLBCL overall survival were identified in this study. These results will serve as a theoretical basis for further study of gene regulation and function of GCB-DLBCL.
Collapse
Affiliation(s)
- Xi Li
- Department of Lymphoma, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Taiyuan, Shanxi, People's Republic of China
| | - Yan Duan
- Department of Critical Care Medicine, Shanxi Provincial Cancer Hospital, Taiyuan, Shanxi, People's Republic of China
| | - Yuxia Hao
- Department of Gastroenterology, Shanxi Provincial People's Hospital, 29 shuangtasi Rd, Taiyuan, 030012, People's Republic of China.
| |
Collapse
|
129
|
Lee Z, Raabe M, Hu WS. Epigenomic features revealed by ATAC-seq impact transgene expression in CHO cells. Biotechnol Bioeng 2021; 118:1851-1861. [PMID: 33521928 DOI: 10.1002/bit.27701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/15/2022]
Abstract
Different regions of a mammalian genome have different accessibilities to transcriptional machinery. The integration site of a transgene affects how actively it is transcribed. Highly accessible genomic regions called super-enhancers have been recently described as strong regulatory elements that shape cell identity. Super-enhancers have been identified in Chinese hamster ovary (CHO) cells using the Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq). Genes near super-enhancer regions had high transcript levels and were enriched for oncogenic signaling and proliferation functions, consistent with an immortalized phenotype. Inaccessible regions in the genome with low ATAC signal also had low transcriptional activity. Genes in inaccessible regions were enriched for remote tissue functions such as taste, smell, and neuronal activation. A lentiviral reporter integration assay showed integration into super-enhancer regions conferred higher reporter expression than insertion into inaccessible regions. Targeted integration of an IgG vector into the Plec super-enhancer region yielded clones that expressed the immunoglobulin light chain gene mostly in the top 20% of all transcripts with the majority in the top 5%. The results suggest the epigenomic landscape of CHO cells can guide the selection of integration sites in the development of cell lines for therapeutic protein production.
Collapse
Affiliation(s)
- Zion Lee
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Marina Raabe
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| |
Collapse
|
130
|
Liu Z, Chen SS, Clarke S, Veschi V, Thiele CJ. Targeting MYCN in Pediatric and Adult Cancers. Front Oncol 2021; 10:623679. [PMID: 33628735 PMCID: PMC7898977 DOI: 10.3389/fonc.2020.623679] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/14/2020] [Indexed: 12/18/2022] Open
Abstract
The deregulation of the MYC family of oncogenes, including c-MYC, MYCN and MYCL occurs in many types of cancers, and is frequently associated with a poor prognosis. The majority of functional studies have focused on c-MYC due to its broad expression profile in human cancers. The existence of highly conserved functional domains between MYCN and c-MYC suggests that MYCN participates in similar activities. MYC encodes a basic helix-loop-helix-leucine zipper (bHLH-LZ) transcription factor (TF) whose central oncogenic role in many human cancers makes it a highly desirable therapeutic target. Historically, as a TF, MYC has been regarded as “undruggable”. Thus, recent efforts focus on investigating methods to indirectly target MYC to achieve anti-tumor effects. This review will primarily summarize the recent progress in understanding the function of MYCN. It will explore efforts at targeting MYCN, including strategies aimed at suppression of MYCN transcription, destabilization of MYCN protein, inhibition of MYCN transcriptional activity, repression of MYCN targets and utilization of MYCN overexpression dependent synthetic lethality.
Collapse
Affiliation(s)
- Zhihui Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Samuel S Chen
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Saki Clarke
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Veronica Veschi
- Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Carol J Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| |
Collapse
|
131
|
Grady WM, Yu M, Markowitz SD. Epigenetic Alterations in the Gastrointestinal Tract: Current and Emerging Use for Biomarkers of Cancer. Gastroenterology 2021; 160:690-709. [PMID: 33279516 PMCID: PMC7878343 DOI: 10.1053/j.gastro.2020.09.058] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer, liver cancer, stomach cancer, pancreatic cancer, and esophageal cancer are leading causes of cancer-related deaths worldwide. A fundamental trait of virtually all gastrointestinal cancers is genomic and epigenomic DNA alterations. Cancer cells acquire genetic and epigenetic alterations that drive the initiation and progression of the cancers by altering the molecular and cell biological processes of the cells. These alterations, as well as other host and microenvironment factors, ultimately mediate the clinical behavior of the precancers and cancers and can be used as biomarkers for cancer risk determination, early detection of cancer and precancer, determination of the prognosis of cancer and prediction of the response to therapy. Epigenetic alterations have emerged as one of most robust classes of biomarkers and are the basis for a growing number of clinical tests for cancer screening and surveillance.
Collapse
Affiliation(s)
- William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | | |
Collapse
|
132
|
Bruter AV, Rodionova MD, Varlamova EA, Shtil AA. Super-Enhancers in the Regulation of Gene Transcription: General Aspects and Antitumor Targets. Acta Naturae 2021; 13:4-15. [PMID: 33959383 PMCID: PMC8084300 DOI: 10.32607/actanaturae.11067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/07/2020] [Indexed: 01/18/2023] Open
Abstract
Super-enhancers (genome elements that activate gene transcription) are DNA regions with an elevated concentration of transcriptional complexes. These multiprotein structures contain, among other components, the cyclin-dependent kinases 8 and 19. These and other transcriptional protein kinases are regarded as novel targets for pharmacological inhibition by antitumor drug candidates.
Collapse
Affiliation(s)
- A. V. Bruter
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Blokhin National Medical Research Center of Oncology, Moscow, 115478 Russia
| | | | - E. A. Varlamova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Blokhin National Medical Research Center of Oncology, Moscow, 115478 Russia
| | - A. A. Shtil
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Blokhin National Medical Research Center of Oncology, Moscow, 115478 Russia
| |
Collapse
|
133
|
Watt AC, Cejas P, DeCristo MJ, Metzger-Filho O, Lam EYN, Qiu X, BrinJones H, Kesten N, Coulson R, Font-Tello A, Lim K, Vadhi R, Daniels VW, Montero J, Taing L, Meyer CA, Gilan O, Bell CC, Korthauer KD, Giambartolomei C, Pasaniuc B, Seo JH, Freedman ML, Ma C, Ellis MJ, Krop I, Winer E, Letai A, Brown M, Dawson MA, Long HW, Zhao JJ, Goel S. CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity. NATURE CANCER 2021; 2:34-48. [PMID: 33997789 PMCID: PMC8115221 DOI: 10.1038/s43018-020-00135-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023]
Abstract
Pharmacologic inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) were designed to induce cancer cell cycle arrest. Recent studies have suggested that these agents also exert other effects, influencing cancer cell immunogenicity, apoptotic responses, and differentiation. Using cell-based and mouse models of breast cancer together with clinical specimens, we show that CDK4/6 inhibitors induce remodeling of cancer cell chromatin characterized by widespread enhancer activation, and that this explains many of these effects. The newly activated enhancers include classical super-enhancers that drive luminal differentiation and apoptotic evasion, as well as a set of enhancers overlying endogenous retroviral elements that is enriched for proximity to interferon-driven genes. Mechanistically, CDK4/6 inhibition increases the level of several Activator Protein-1 (AP-1) transcription factor proteins, which are in turn implicated in the activity of many of the new enhancers. Our findings offer insights into CDK4/6 pathway biology and should inform the future development of CDK4/6 inhibitors.
Collapse
Affiliation(s)
- April C Watt
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Oncology Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
- CIBERONC CB16/12/00398, La Paz University Hospital, Madrid, Spain
| | - Molly J DeCristo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Otto Metzger-Filho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Haley BrinJones
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikolas Kesten
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rhiannon Coulson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Alba Font-Tello
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Raga Vadhi
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Veerle W Daniels
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joan Montero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute for Bioengineering of Catalonia, Barcelona, Spain
| | - Len Taing
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Clifford A Meyer
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Omer Gilan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Keegan D Korthauer
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Claudia Giambartolomei
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cynthia Ma
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Ian Krop
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eric Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Parkville, Victoria, Australia
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Jean J Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Shom Goel
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
134
|
Li S, Liu N, Piao J, Meng F, Li Y. CCNB1 Expedites the Progression of Cervical Squamous Cell Carcinoma via the Regulation by FOXM1. Onco Targets Ther 2020; 13:12383-12395. [PMID: 33299327 PMCID: PMC7721124 DOI: 10.2147/ott.s279951] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
Background Cervical squamous cell carcinoma (CSCC) is responsible for 80-85% of cervical cancer. Cyclin B1 (CCNB1) represents a hub gene during the development of cervical cancer. However, the oncogenic role of CCNB1 in CSCC remains unclear. Our study aims to explore the mechanism underlying CCNB1 regulation on cell cycle progression in CSCC cells. Methods First, we analyzed differentially expressed genes from CSCC dataset GSE63678 and conducted gene function enrichment analysis. Subsequently, CCNB1 expression was knocked down in CSCC cell lines to assess cell proliferation, apoptosis, and cell cycle distribution. After the validation of the binding relationship between forkhead box protein M1 (FOXM1) and the promoter of CCNB1, the effect of FOXM1 on CCNB1 expression and on CSCC cell growth and apoptosis was verified. We further analyzed the histone ChIP-Seq data of CCNB1 in CSCC cells and measured the acetylation levels of the CCNB1 promoter histones. Results CCNB1 was overexpressed in CSCC tissues and cells, and CCNB1 silencing inhibited the growth of CSCC cells, and promoted cell cycle arrest and apoptosis. FOXM1 potentiated CCNB1 transcription by binding to its promoter and recruiting CBP/P300, a histone acetyltransferase. Further increasing FOXM1 expression or increasing P300 activity in CSCC cells with CCNB1 knockdown elevated CCNB1 expression and proliferation and cell cycle progression of CSCC cells. Knockdown of CCNB1 activated the p53 pathway in cells. Conclusion FOXM1 inhibited the activation of the p53 pathway by recruiting CBP/P300, which promoted the transcription of CCNB1, resulting in the growth and cell cycle progression of CSCC cells.
Collapse
Affiliation(s)
- Shufeng Li
- Department 1 of Gynecological Oncology, Jilin Cancer Hospital, Changchun 130012, Jilin, People's Republic of China
| | - Ning Liu
- Department of Gynecology and Oncology, The Second Hospital of Jilin University, Changchun 130041, Jilin, People's Republic of China
| | - Jinxia Piao
- Department 1 of Gynecological Oncology, Jilin Cancer Hospital, Changchun 130012, Jilin, People's Republic of China
| | - Fanxu Meng
- Department of Radiotherapy, Jilin Cancer Hospital, Changchun 130012, Jilin, People's Republic of China
| | - Yanyan Li
- Department 1 of Gynecological Oncology, Jilin Cancer Hospital, Changchun 130012, Jilin, People's Republic of China
| |
Collapse
|
135
|
Epstein-Barr Virus Episome Physically Interacts with Active Regions of the Host Genome in Lymphoblastoid Cells. J Virol 2020; 94:JVI.01390-20. [PMID: 32999023 DOI: 10.1128/jvi.01390-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022] Open
Abstract
The Epstein-Barr virus (EBV) episome is known to interact with the three-dimensional structure of the human genome in infected cells. However, the exact locations of these interactions and their potential functional consequences remain unclear. Recently, high-resolution chromatin conformation capture (Hi-C) assays in lymphoblastoid cells have become available, enabling us to precisely map the contacts between the EBV episome(s) and the human host genome. Using available Hi-C data at a 10-kb resolution, we have identified 15,000 reproducible contacts between EBV episome(s) and the human genome. These contacts are highly enriched in chromatin regions denoted by typical or super enhancers and active markers, including histone H3K27ac and H3K4me1. Additionally, these contacts are highly enriched at loci bound by host transcription factors that regulate B cell growth (e.g., IKZF1 and RUNX3), factors that enhance cell proliferation (e.g., HDGF), or factors that promote viral replication (e.g., NBS1 and NFIC). EBV contacts show nearly 2-fold enrichment in host regions bound by EBV nuclear antigen 2 (EBNA2) and EBNA3 transcription factors. Circular chromosome conformation capture followed by sequencing (4C-seq) using the EBV origin of plasmid replication (oriP) as a "bait" in lymphoblastoid cells further confirmed contacts with active chromatin regions. Collectively, our analysis supports interactions between EBV episome(s) and active regions of the human genome in lymphoblastoid cells.IMPORTANCE EBV is associated with ∼200,000 cancers each year. In vitro, EBV can transform primary human B lymphocytes into immortalized cell lines. EBV-encoded proteins, along with noncoding RNAs and microRNAs, hijack cellular proteins and pathways to control cell growth. EBV nuclear proteins usurp normal transcriptional programs to activate the expression of key oncogenes, including MYC, to provide a proliferation signal. EBV nuclear antigens also repress CDKN2A to suppress senescence. EBV membrane protein activates NF-κB to provide survival signals. EBV genomes are maintained by EBNA1, which tethers EBV episomes to the host chromosomes during mitosis. However, little is known about where EBV episomes are located in interphase cells. In interphase cells, EBV promoters drive the expression of latency genes, while oriP functions as an enhancer for these promoters. In this study, integrative analyses of published lymphoblastoid cell line (LCL) Hi-C data and our 4C-seq experiments position EBV episomes to host genomes with active epigenetic marks. These contact points were significantly enriched for super enhancers. The close proximity of EBV episomes and the super enhancers that are enriched for transcription cofactors or mediators in lymphoblasts may benefit EBV gene expression, suggesting a novel mechanism of transcriptional activation.
Collapse
|
136
|
Okazaki K, Anzawa H, Liu Z, Ota N, Kitamura H, Onodera Y, Alam MM, Matsumaru D, Suzuki T, Katsuoka F, Tadaka S, Motoike I, Watanabe M, Hayasaka K, Sakurada A, Okada Y, Yamamoto M, Suzuki T, Kinoshita K, Sekine H, Motohashi H. Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers. Nat Commun 2020; 11:5911. [PMID: 33219226 PMCID: PMC7679411 DOI: 10.1038/s41467-020-19593-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/21/2020] [Indexed: 01/05/2023] Open
Abstract
Transcriptional dysregulation, which can be caused by genetic and epigenetic alterations, is a fundamental feature of many cancers. A key cytoprotective transcriptional activator, NRF2, is often aberrantly activated in non-small cell lung cancers (NSCLCs) and supports both aggressive tumorigenesis and therapeutic resistance. Herein, we find that persistently activated NRF2 in NSCLCs generates enhancers at gene loci that are not normally regulated by transiently activated NRF2 under physiological conditions. Elevated accumulation of CEBPB in NRF2-activated NSCLCs is found to be one of the prerequisites for establishment of the unique NRF2-dependent enhancers, among which the NOTCH3 enhancer is shown to be critical for promotion of tumor-initiating activity. Enhancer remodeling mediated by NRF2-CEBPB cooperativity promotes tumor-initiating activity and drives malignancy of NRF2-activated NSCLCs via establishment of the NRF2-NOTCH3 regulatory axis. Aberrant activation of NRF2 in cancer cells contributes to tumorigenicity and therapeutic resistance. Here, the authors show that NRF2 cooperates with CEBPB and remodels enhancers to confer tumor-initiating activity on NRF2- activated non-small cell lung cancers.
Collapse
Affiliation(s)
- Keito Okazaki
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Hayato Anzawa
- Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, 980-8579, Sendai, Japan
| | - Zun Liu
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Nao Ota
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Hiroshi Kitamura
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Yoshiaki Onodera
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Md Morshedul Alam
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Daisuke Matsumaru
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Takuma Suzuki
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Shu Tadaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Ikuko Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Mika Watanabe
- Department of Pathology, Tohoku University Hospital, Sendai, 980-8575, Japan
| | - Kazuki Hayasaka
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan.,Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Akira Sakurada
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Yoshinori Okada
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Kengo Kinoshita
- Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, 980-8579, Sendai, Japan.,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Hiroki Sekine
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan.
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan.
| |
Collapse
|
137
|
Noel P, Hussein S, Ng S, Antal CE, Lin W, Rodela E, Delgado P, Naveed S, Downes M, Lin Y, Evans RM, Von Hoff DD, Han H. Triptolide targets super-enhancer networks in pancreatic cancer cells and cancer-associated fibroblasts. Oncogenesis 2020; 9:100. [PMID: 33168807 PMCID: PMC7653036 DOI: 10.1038/s41389-020-00285-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
The tumor microenvironment in pancreatic ductal adenocarcinoma (PDAC) is highly heterogeneous, fibrotic, and hypovascular, marked by extensive desmoplasia and maintained by the tumor cells, cancer-associated fibroblasts (CAFs) and other stromal cells. There is an urgent need to identify and develop treatment strategies that not only target the tumor cells but can also modulate the stromal cells. A growing number of studies implicate the role of regulatory DNA elements called super-enhancers (SE) in maintaining cell-type-specific gene expression networks in both normal and cancer cells. Using chromatin activation marks, we first mapped SE networks in pancreatic CAFs and epithelial tumor cells and found them to have distinct SE profiles. Next, we explored the role of triptolide (TPL), a natural compound with antitumor activity, in the context of modulating cell-type-specific SE signatures in PDAC. We found that TPL, cytotoxic to both pancreatic tumor cells and CAFs, disrupted SEs in a manner that resulted in the downregulation of SE-associated genes (e.g., BRD4, MYC, RNA Pol II, and Collagen 1) in both cell types at mRNA and protein levels. Our observations suggest that TPL acts as a SE interactive agent and may elicit its antitumor activity through SE disruption to re-program cellular cross talk and signaling in PDAC. Based on our findings, epigenetic reprogramming of transcriptional regulation using SE modulating compounds such as TPL may provide means for effective treatment options for pancreatic cancer patients.
Collapse
Affiliation(s)
- Pawan Noel
- Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Shaimaa Hussein
- Baylor Scott and White Research Institute, Baylor Institute for Immunology Research, Dallas, TX, USA
| | - Serina Ng
- Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Corina E Antal
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Wei Lin
- Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Emily Rodela
- Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, USA.,Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Priscilla Delgado
- Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Sanna Naveed
- Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Yin Lin
- Baylor Scott and White Research Institute, Baylor Institute for Immunology Research, Dallas, TX, USA
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA.,Howard Hughes Medical Institute, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Daniel D Von Hoff
- Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Haiyong Han
- Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
| |
Collapse
|
138
|
Wengner AM, Scholz A, Haendler B. Targeting DNA Damage Response in Prostate and Breast Cancer. Int J Mol Sci 2020; 21:E8273. [PMID: 33158305 PMCID: PMC7663807 DOI: 10.3390/ijms21218273] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
Steroid hormone signaling induces vast gene expression programs which necessitate the local formation of transcription factories at regulatory regions and large-scale alterations of the genome architecture to allow communication among distantly related cis-acting regions. This involves major stress at the genomic DNA level. Transcriptionally active regions are generally instable and prone to breakage due to the torsional stress and local depletion of nucleosomes that make DNA more accessible to damaging agents. A dedicated DNA damage response (DDR) is therefore essential to maintain genome integrity at these exposed regions. The DDR is a complex network involving DNA damage sensor proteins, such as the poly(ADP-ribose) polymerase 1 (PARP-1), the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), the ataxia-telangiectasia-mutated (ATM) kinase and the ATM and Rad3-related (ATR) kinase, as central regulators. The tight interplay between the DDR and steroid hormone receptors has been unraveled recently. Several DNA repair factors interact with the androgen and estrogen receptors and support their transcriptional functions. Conversely, both receptors directly control the expression of agents involved in the DDR. Impaired DDR is also exploited by tumors to acquire advantageous mutations. Cancer cells often harbor germline or somatic alterations in DDR genes, and their association with disease outcome and treatment response led to intensive efforts towards identifying selective inhibitors targeting the major players in this process. The PARP-1 inhibitors are now approved for ovarian, breast, and prostate cancer with specific genomic alterations. Additional DDR-targeting agents are being evaluated in clinical studies either as single agents or in combination with treatments eliciting DNA damage (e.g., radiation therapy, including targeted radiotherapy, and chemotherapy) or addressing targets involved in maintenance of genome integrity. Recent preclinical and clinical findings made in addressing DNA repair dysfunction in hormone-dependent and -independent prostate and breast tumors are presented. Importantly, the combination of anti-hormonal therapy with DDR inhibition or with radiation has the potential to enhance efficacy but still needs further investigation.
Collapse
Affiliation(s)
| | | | - Bernard Haendler
- Preclinical Research, Research & Development, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany; (A.M.W.); (A.S.)
| |
Collapse
|
139
|
Jiang S, Fagman JB, Chen C, Alberti S, Liu B. Protein phase separation and its role in tumorigenesis. eLife 2020; 9:60264. [PMID: 33138914 PMCID: PMC7609067 DOI: 10.7554/elife.60264] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer is a disease characterized by uncontrolled cell proliferation, but the precise pathological mechanisms underlying tumorigenesis often remain to be elucidated. In recent years, condensates formed by phase separation have emerged as a new principle governing the organization and functional regulation of cells. Increasing evidence links cancer-related mutations to aberrantly altered condensate assembly, suggesting that condensates play a key role in tumorigenesis. In this review, we summarize and discuss the latest progress on the formation, regulation, and function of condensates. Special emphasis is given to emerging evidence regarding the link between condensates and the initiation and progression of cancers.
Collapse
Affiliation(s)
- Shan Jiang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johan Bourghardt Fagman
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Changyan Chen
- Department of Oncology at the Department of Clinical Sciences, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Simon Alberti
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Center for Large-scale cell-based screening, Faculty of Science, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
140
|
Wang Y, Nie H, He X, Liao Z, Zhou Y, Zhou J, Ou C. The emerging role of super enhancer-derived noncoding RNAs in human cancer. Theranostics 2020; 10:11049-11062. [PMID: 33042269 PMCID: PMC7532672 DOI: 10.7150/thno.49168] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/23/2020] [Indexed: 02/06/2023] Open
Abstract
Super enhancers (SEs) are large clusters of adjacent enhancers that drive the expression of genes which regulate cellular identity; SE regions can be enriched with a high density of transcription factors, co-factors, and enhancer-associated epigenetic modifications. Through enhanced activation of their target genes, SEs play an important role in various diseases and conditions, including cancer. Recent studies have shown that SEs not only activate the transcriptional expression of coding genes to directly regulate biological functions, but also drive the transcriptional expression of non-coding RNAs (ncRNAs) to indirectly regulate biological functions. SE-derived ncRNAs play critical roles in tumorigenesis, including malignant proliferation, metastasis, drug resistance, and inflammatory response. Moreover, the abnormal expression of SE-derived ncRNAs is closely related to the clinical and pathological characterization of tumors. In this review, we summarize the functions and roles of SE-derived ncRNAs in tumorigenesis and discuss their prospective applications in tumor therapy. A deeper understanding of the potential mechanism underlying the action of SE-derived ncRNAs in tumorigenesis may provide new strategies for the early diagnosis of tumors and targeted therapy.
Collapse
|
141
|
Yi M, Tan Y, Wang L, Cai J, Li X, Zeng Z, Xiong W, Li G, Li X, Tan P, Xiang B. TP63 links chromatin remodeling and enhancer reprogramming to epidermal differentiation and squamous cell carcinoma development. Cell Mol Life Sci 2020; 77:4325-4346. [PMID: 32447427 PMCID: PMC7588389 DOI: 10.1007/s00018-020-03539-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/21/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022]
Abstract
Squamous cell carcinoma (SCC) is an aggressive malignancy that can originate from various organs. TP63 is a master regulator that plays an essential role in epidermal differentiation. It is also a lineage-dependent oncogene in SCC. ΔNp63α is the prominent isoform of TP63 expressed in epidermal cells and SCC, and overexpression promotes SCC development through a variety of mechanisms. Recently, ΔNp63α was highlighted to act as an epidermal-specific pioneer factor that binds closed chromatin and enhances chromatin accessibility at epidermal enhancers. ΔNp63α coordinates chromatin-remodeling enzymes to orchestrate the tissue-specific enhancer landscape and three-dimensional high-order architecture of chromatin. Moreover, ΔNp63α establishes squamous-like enhancer landscapes to drive oncogenic target expression during SCC development. Importantly, ΔNp63α acts as an upstream regulator of super enhancers to activate a number of oncogenic transcripts linked to poor prognosis in SCC. Mechanistically, ΔNp63α activates genes transcription through physically interacting with a number of epigenetic modulators to establish enhancers and enhance chromatin accessibility. In contrast, ΔNp63α also represses gene transcription via interacting with repressive epigenetic regulators. ΔNp63α expression is regulated at multiple levels, including transcriptional, post-transcriptional, and post-translational levels. In this review, we summarize recent advances of p63 in epigenomic and transcriptional control, as well as the mechanistic regulation of p63.
Collapse
Affiliation(s)
- Mei Yi
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Yixin Tan
- Department of Dermatology, The Second Xiangya Hospital, The Central South University, Changsha, 410011, Hunan, China
| | - Li Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jing Cai
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Xiaoling Li
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
| | - Pingqing Tan
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- Department of Head and Neck Surgery, Hunan Provincial Cancer Hospital and Cancer Hospital Affiliated to Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China.
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China.
| |
Collapse
|
142
|
Fóthi Á, Biró O, Erdei Z, Apáti Á, Orbán TI. Tissue-specific and transcription-dependent mechanisms regulate primary microRNA processing efficiency of the human chromosome 19 MicroRNA cluster. RNA Biol 2020; 18:1170-1180. [PMID: 33052778 DOI: 10.1080/15476286.2020.1836457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
One of the longest human microRNA (miRNA) clusters is located on chromosome 19 (C19MC), containing 46 miRNA genes, which were considered to be expressed simultaneously and at similar levels from a common long noncoding transcript. Investigating the two tissue types where C19MC is exclusively expressed, we could show that there is a tissue-specific and chromosomal position-dependent decrease in mature miRNA levels towards the 3' end of the cluster in embryonic stem cells but not in placenta. Although C19MC transcription level is significantly lower in stem cells, this gradual decrease is not present at the primary miRNA levels, indicating that a difference in posttranscriptional processing could explain this observation. By depleting Drosha, the nuclease component of the Microprocessor complex, we could further enhance the positional decrease in stem cells, demonstrating that a tissue-specific, local availability of the Microprocessor complex could lie behind the phenomenon. Moreover, we could describe a tissue-specific promoter being exclusively active in placenta, and the epigenetic mark analysis suggested the presence of several putative enhancer sequences in this region. Performing specific chromatin immunoprecipitation followed by quantitative real-time PCR experiments we could show a strong association of Drosha with selected enhancer regions in placenta, but not in embryonic stem cells. These enhancers could provide explanation for a more efficient co-transcriptional recruitment of the Microprocessor, and therefore a more efficient processing of pri-miRNAs throughout the cluster in placenta. Our results point towards a new model where tissue-specific, posttranscriptional 'fine-tuning' can differentiate among miRNAs that are expressed simultaneously from a common precursor.
Collapse
Affiliation(s)
- Ábel Fóthi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Orsolya Biró
- Department of Obstetrics and Gynaecology, Semmelweis University, Budapest, Hungary
| | - Zsuzsa Erdei
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ágota Apáti
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| |
Collapse
|
143
|
Aberrant super-enhancer landscape reveals core transcriptional regulatory circuitry in lung adenocarcinoma. Oncogenesis 2020; 9:92. [PMID: 33070167 PMCID: PMC7568720 DOI: 10.1038/s41389-020-00277-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/25/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
Lung adenocarcinoma (LUAD) relies on dysregulated gene expression to sustain its infinite growth and progression. Emerging evidence indicates that aberrant transcriptional program results from core transcriptional regulatory circuitry (CRC) which is driven by super-enhancers (SEs). In this study, by integrating profiles of H3K27Ac chromatin immunoprecipitation sequencing (ChIP-seq) from normal adult lung and LUAD cell lines, we revealed that widespread alterations of the super-enhancer were presence during lung carcinogenesis. With SE-based modeling of regulatory circuits and assessments of transcription factor (TF) dependencies, we reconstructed an interconnected transcriptional regulation network formed by three master TFs, including ELF3, EHF, and TGIF1, all of which promoted each other’s expression that confirmed by ChIP-qPCR and western blot. Loss-of function assay revealed that each of them is essential for LUAD cells survival, invasion and metastasis. Meanwhile, the rescue assay also illustrated the transacting transcriptional regulatory circuitry. In addition, the mRNA levels of ELF3, EHF, and TGIF1 were differentially expressed in LUAD tumors and peritumoral tissue. IHC of serial sections revealed that high expressions of CRC (ELF3/EHF/TGIF1-High) were closely associated with high proliferative activity in tumor tissue and poor prognosis on patients with LUAD. Finally, we used small molecular inhibitors to perturb the transcriptional circuitry, also exhibited a prominent anti-cancer effect in vitro. Our findings reveal the mechanism of the transcriptional dysregulation and addiction of LUAD.
Collapse
|
144
|
Komar D, Juszczynski P. Rebelled epigenome: histone H3S10 phosphorylation and H3S10 kinases in cancer biology and therapy. Clin Epigenetics 2020; 12:147. [PMID: 33054831 PMCID: PMC7556946 DOI: 10.1186/s13148-020-00941-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background With the discovery that more than half of human cancers harbor mutations in chromatin proteins, deregulation of epigenetic mechanisms has been recognized a hallmark of malignant transformation. Post-translational modifications (PTMs) of histone proteins, as main components of epigenetic regulatory machinery, are also broadly accepted as therapeutic target. Current “epigenetic” therapies target predominantly writers, erasers and readers of histone acetylation and (to a lesser extent) methylation, leaving other types of PTMs largely unexplored. One of them is the phosphorylation of serine 10 on histone H3 (H3S10ph). Main body H3S10ph is emerging as an important player in the initiation and propagation of cancer, as it facilitates cellular malignant transformation and participates in fundamental cellular functions. In normal cells this histone mark dictates the hierarchy of additional histone modifications involved in the formation of protein binding scaffolds, transcriptional regulation, blocking repressive epigenetic information and shielding gene regions from heterochromatin spreading. During cell division, this mark is essential for chromosome condensation and segregation. It is also involved in the function of specific DNA–RNA hybrids, called R-loops, which modulate transcription and facilitate chromosomal instability. Increase in H3S10ph is observed in numerous cancer types and its abundance has been associated with inferior prognosis. Many H3S10-kinases, including MSK1/2, PIM1, CDK8 and AURORA kinases, have been long considered targets in cancer therapy. However, since these proteins also participate in other critical processes, including signal transduction, apoptotic signaling, metabolic fitness and transcription, their chromatin functions are often neglected. Conclusions H3S10ph and enzymes responsible for deposition of this histone modification are important for chromatin activity and oncogenesis. Epigenetic-drugs targeting this axis of modifications, potentially in combination with conventional or targeted therapy, provide a promising angle in search for knowledge-driven therapeutic strategies in oncology.
Collapse
Affiliation(s)
- Dorota Komar
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Gandhi 14 Str, 02-776, Warsaw, Poland.
| | - Przemyslaw Juszczynski
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Gandhi 14 Str, 02-776, Warsaw, Poland
| |
Collapse
|
145
|
Syafruddin SE, Mohtar MA, Wan Mohamad Nazarie WF, Low TY. Two Sides of the Same Coin: The Roles of KLF6 in Physiology and Pathophysiology. Biomolecules 2020; 10:biom10101378. [PMID: 32998281 PMCID: PMC7601070 DOI: 10.3390/biom10101378] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/26/2020] [Accepted: 09/26/2020] [Indexed: 12/12/2022] Open
Abstract
The Krüppel-like factors (KLFs) family of proteins control several key biological processes that include proliferation, differentiation, metabolism, apoptosis and inflammation. Dysregulation of KLF functions have been shown to disrupt cellular homeostasis and contribute to disease development. KLF6 is a relevant example; a range of functional and expression assays suggested that the dysregulation of KLF6 contributes to the onset of cancer, inflammation-associated diseases as well as cardiovascular diseases. KLF6 expression is either suppressed or elevated depending on the disease, and this is largely due to alternative splicing events producing KLF6 isoforms with specialised functions. Hence, the aim of this review is to discuss the known aspects of KLF6 biology that covers the gene and protein architecture, gene regulation, post-translational modifications and functions of KLF6 in health and diseases. We put special emphasis on the equivocal roles of its full-length and spliced variants. We also deliberate on the therapeutic strategies of KLF6 and its associated signalling pathways. Finally, we provide compelling basic and clinical questions to enhance the knowledge and research on elucidating the roles of KLF6 in physiological and pathophysiological processes.
Collapse
Affiliation(s)
- Saiful E. Syafruddin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia; (M.A.M.); (T.Y.L.)
- Correspondence: ; Tel.: +60-3-9145-9040
| | - M. Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia; (M.A.M.); (T.Y.L.)
| | - Wan Fahmi Wan Mohamad Nazarie
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia;
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia; (M.A.M.); (T.Y.L.)
| |
Collapse
|
146
|
Xu Y, Wu Y, Zhang S, Ma P, Jin X, Wang Z, Yao M, Zhang E, Tao B, Qin Y, Chen H, Liu A, Chen M, Xiao M, Lu C, Mao R, Fan Y. A Tumor-Specific Super-Enhancer Drives Immune Evasion by Guiding Synchronous Expression of PD-L1 and PD-L2. Cell Rep 2020; 29:3435-3447.e4. [PMID: 31825827 DOI: 10.1016/j.celrep.2019.10.093] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 08/10/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
PD-L1 and PD-L2 are important targets for immune checkpoint blockade, but how tumor cells achieve their expression remains to be addressed. Here, we find that PD-L1 and PD-L2 are co-expressed in cancer cell lines and tissues across different cancer types. In breast cancer, MDA-MB-231 and SUM-159 cells show high expression of both PD-L1 and PD-L2. The expression of both PD-L1 and PD-L2 is greatly reduced upon treatment of inhibitors of super-enhancers. Bioinformatic analysis identifies a potential super-enhancer (PD-L1L2-SE) that is located between the CD274 and CD273 genes. Genetic deletion of PD-L1L2-SE profoundly reduces the expression of PD-L1 and PD-L2. PD-L1L2-SE-deficient cancer cells fail to generate immune evasion and are sensitive to T cell-mediated killing. Notably, epigenetic activation of such a region (PD-L1L2-SE) is correlated with PD-L1 and PD-L2. Taken together, we identify a super-enhancer (PD-L1L2-SE) that is responsible for the overexpression of PD-L1 and PD-L2 as well as immune evasion in cancer.
Collapse
Affiliation(s)
- Yuanpei Xu
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Yingcheng Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China; Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Siliang Zhang
- The Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Heilongjiang 150086, China
| | - Panpan Ma
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Xinxin Jin
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Zhou Wang
- School of Life Sciences, Nantong University, Jiangsu 226001, China
| | - Min Yao
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Erhao Zhang
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Baorui Tao
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Yongwei Qin
- Department of Pathogenic Biology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Hao Chen
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Aifen Liu
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Miaomiao Chen
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Mingbing Xiao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Cuihua Lu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China.
| | - Yihui Fan
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China; Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China; Department of Pathogenic Biology, School of Medicine, Nantong University, Jiangsu 226001, China; Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China.
| |
Collapse
|
147
|
Aberrant activation of super enhancer and choline metabolism drive antiandrogen therapy resistance in prostate cancer. Oncogene 2020; 39:6556-6571. [PMID: 32917955 DOI: 10.1038/s41388-020-01456-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/20/2020] [Accepted: 09/02/2020] [Indexed: 12/28/2022]
Abstract
Next generation antiandrogens such as enzalutamide (Enz) are effective initially for the treatment of castration-resistant prostate cancer (CRPC). However, the disease often relapses and the underlying mechanisms remain elusive. By performing H3-lysine-27 acetylation (H3K27ac) ChIP-seq in Enz-resistant CRPC cells, we identified a group of super enhancers (SEs) that are abnormally activated in Enz-resistant CRPC cells and associated with enhanced transcription of a subset of tumor promoting genes such as CHPT1, which catalyzes phosphatidylcholine (PtdCho) synthesis and regulates choline metabolism. Increased CHPT1 conferred CRPC resistance to Enz in vitro and in mice. While androgen receptor (AR) primarily binds to a putative CHPT1 enhancer and mediates androgen-dependent expression of CHPT1 gene in Enz-sensitive prostate cancer cells, AR binds to a different enhancer within the CHPT1 SE locus and facilities androgen-independent expression of CHPT1 in Enz-resistant cells. We further identified a long-non coding RNA transcribed at CHPT1 enhancer (also known as enhancer RNA) that binds to the H3K27ac reader BRD4 and participates in regulating CHPT1 SE activity and CHPT1 gene expression. Our findings demonstrate that aberrantly activated SE upregulates CHPT1 expression and confers Enz resistance in CRPC, suggesting that SE-mediated expression of downstream effectors such as CHPT1 can be viable targets to overcome Enz resistance in PCa.
Collapse
|
148
|
Mun J, Choi G, Lim B. A guide for bioinformaticians: 'omics-based drug discovery for precision oncology. Drug Discov Today 2020; 25:S1359-6446(20)30335-4. [PMID: 32828947 DOI: 10.1016/j.drudis.2020.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/19/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
Bioinformatics-centric drug development is inevitable in the era of precision medicine. Clinical 'omics information, including genomics, epigenomics, transcriptomics, and proteomics, provides the most comprehensive molecular landscape in which each patient's pathological history is delineated. Hence, the capability of bioinformaticians to manage integrative 'omics data is crucial to current drug development. Bioinformatics can accelerate drug development from initial time-consuming discoveries to the clinical stage by providing information-guided solutions. However, many bioinformaticians do not have opportunities to participate in drug discovery programs. As a starting point for bioinformaticians with no prior drug development experience, here we discuss bioinformatics applications during drug development with a focus on working-level omics-based methodologies.
Collapse
Affiliation(s)
- Jihyeob Mun
- Center for Supercomputing Applications, Division of National Supercomputing R&D, Korea Institute of Science and Technology Information (KISTI), Daejeon, Republic of Korea
| | - Gildon Choi
- Research Center for Drug Discovery Technology, Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.
| | - Byungho Lim
- Research Center for Drug Discovery Technology, Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.
| |
Collapse
|
149
|
Abstract
The hierarchical three-dimensional folding of the mammalian genome constitutes an important regulatory layer of gene expression and cell fate control during processes such as development and tumorigenesis. Accumulating evidence supports the existence of complex topological assemblies in which multiple genes and regulatory elements are frequently interacting with each other in the 3D nucleus. Here, we will discuss the nature, organizational principles, and potential function of such assemblies, including the recently reported enhancer “hubs,” “cliques,” and FIREs (frequently interacting regions) as well as multi-contact hubs. We will also review recent studies that investigate the role of transcription factors (TFs) in driving the topological genome reorganization and hub formation in the context of cell fate transitions and cancer. Finally, we will highlight technological advances that enabled these studies, current limitations, and future directions necessary to advance our understating in the field.
Collapse
Affiliation(s)
- Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine , New York, NY, USA
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine , New York, NY, USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine , New York, NY, USA
| |
Collapse
|
150
|
Marques JG, Gryder BE, Pavlovic B, Chung Y, Ngo QA, Frommelt F, Gstaiger M, Song Y, Benischke K, Laubscher D, Wachtel M, Khan J, Schäfer BW. NuRD subunit CHD4 regulates super-enhancer accessibility in rhabdomyosarcoma and represents a general tumor dependency. eLife 2020; 9:54993. [PMID: 32744500 PMCID: PMC7438112 DOI: 10.7554/elife.54993] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/02/2020] [Indexed: 12/15/2022] Open
Abstract
The NuRD complex subunit CHD4 is essential for fusion-positive rhabdomyosarcoma (FP-RMS) survival, but the mechanisms underlying this dependency are not understood. Here, a NuRD-specific CRISPR screen demonstrates that FP-RMS is particularly sensitive to CHD4 amongst the NuRD members. Mechanistically, NuRD complex containing CHD4 localizes to super-enhancers where CHD4 generates a chromatin architecture permissive for the binding of the tumor driver and fusion protein PAX3-FOXO1, allowing downstream transcription of its oncogenic program. Moreover, CHD4 depletion removes HDAC2 from the chromatin, leading to an increase and spread of histone acetylation, and prevents the positioning of RNA Polymerase 2 at promoters impeding transcription initiation. Strikingly, analysis of genome-wide cancer dependency databases identifies CHD4 as a general cancer vulnerability. Our findings describe CHD4, a classically defined repressor, as positive regulator of transcription and super-enhancer accessibility as well as establish this remodeler as an unexpected broad tumor susceptibility and promising drug target for cancer therapy.
Collapse
Affiliation(s)
- Joana G Marques
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Berkley E Gryder
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Blaz Pavlovic
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Yeonjoo Chung
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Quy A Ngo
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Young Song
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Katharina Benischke
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Dominik Laubscher
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Marco Wachtel
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| |
Collapse
|