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Nakadai T, Yang L, Kumegawa K, Maruyama R. Estrogen receptor α K303R mutation reorganizes its binding to forkhead box protein A1 regions and induces chromatin opening. Mol Biol Rep 2023; 50:1209-1220. [PMID: 36436079 PMCID: PMC9889408 DOI: 10.1007/s11033-022-08089-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/03/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Estrogen receptor alpha (ERα) is a frequently mutated gene in breast cancer (BC). While many studies have investigated molecular dysregulation by hotspot mutations at Y537 and D538, which exhibit an estrogen-independent constitutively active phenotype, the functional abnormalities of other mutations remain obscure. The K303R mutation in primary invasive BC has been implicated with endocrine resistance, tumor size, and lymph node positivity. However, the impact of the K303R mutation on the cell epigenome is yet unknown. METHODS AND RESULTS We introduced the K303R ERα mutant in ERα-negative MDA-MB-453 cells to monitor ERα-dependent transactivation and to perform epigenomic analyses. ATAC-seq and ChIP-Seq analyses indicated that both wild-type (WT) and the K303R mutant associated with Forkhead box (Fox) protein family motif regions at similar rates, even without an ERα-binding sequence, but only the K303R mutant induced chromatin opening at those regions. Biochemical analyses demonstrated that the WT and the K303R mutant can be tethered on DNA by FoxA1 indirectly, but only the K303R/FoxA1/DNA complex can induce associations with the nuclear receptor cofactor 2 (NCOA2). CONCLUSIONS These findings suggest that the K303R mutant induces chromatin opening at the Fox binding region through the FoxA1-dependent associations of the K303R mutant to NCOA2 and then probably disrupts the regulation of Fox-target genes, resulting in K303R-related BC events.
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Affiliation(s)
- Tomoyoshi Nakadai
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-Ku, Tokyo, 135-8550, Japan.
| | - Liying Yang
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-Ku, Tokyo, 135-8550, Japan
| | - Kohei Kumegawa
- Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-Ku, Tokyo, 135-8550, Japan
- Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
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52
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Bowling GC, Rands MG, Dobi A, Eldhose B. Emerging Developments in ETS-Positive Prostate Cancer Therapy. Mol Cancer Ther 2023; 22:168-178. [PMID: 36511830 DOI: 10.1158/1535-7163.mct-22-0527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/26/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Prostate cancer is a global health concern, which has a low survival rate in its advanced stages. Even though second-generation androgen receptor-axis inhibitors serve as the mainstay treatment options, utmost of the metastatic cases progress into castration-resistant prostate cancer after their initial treatment response with poor prognostic outcomes. Hence, there is a dire need to develop effective inhibitors that aim the causal oncogenes tangled in the prostate cancer initiation and progression. Molecular-targeted therapy against E-26 transformation-specific (ETS) transcription factors, particularly ETS-related gene, has gained wide attention as a potential treatment strategy. ETS rearrangements with the male hormone responsive transmembrane protease serine 2 promoter defines a significant number of prostate cancer cases and is responsible for cancer initiation and progression. Notably, inhibition of ETS activity has shown to reduce tumorigenesis, thus highlighting its potential as a clinical therapeutic target. In this review, we recapitulate the various targeted drug approaches, including small molecules, peptidomimetics, nucleic acids, and many others, aimed to suppress ETS activity. Several inhibitors have demonstrated ERG antagonist activity in prostate cancer, but further investigations into their molecular mechanisms and impacts on nontumor ETS-containing tissues is warranted.
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Affiliation(s)
- Gartrell C Bowling
- School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland.,Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Mitchell G Rands
- School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Albert Dobi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Binil Eldhose
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
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Distinct Prognostic and Immunological Roles of ETS1 and ETS2: A Pan-Cancer Analysis. BIOMED RESEARCH INTERNATIONAL 2023; 2023:4343350. [PMID: 36760475 PMCID: PMC9904892 DOI: 10.1155/2023/4343350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 02/04/2023]
Abstract
Objective ETS1 and ETS2, the main ETS family of transcription factors, have been found to act as downstream effectors of the RAS/MAPK pathway. This study explores the expression and prognostic values of ETS1 and ETS2 across cancers. We also aimed to explore the significance of ETS1 and ETS2 expression in normal immune cells with relation to tumorigenesis. Methods The expression of ETS1 and ETS2 was examined in the HPA and GEPIA2 databases. The KM plotter was applied to examine prognostic value of ETS1 and ETS2. Correlation between ETS1/ETS2 and infiltrating immune cells and immune checkpoints was assessed using TIMER2.0. The mutation landscape of ETS1/ETS2 was explored using the cBioPortal. STRING and GEPIA2 were used to screen ETS1/ETS2 binding and correlated genes. Enrichr was applied to perform GO and KEGG enrichment analyses. Results ETS1 showed enhanced expression in lymphoid tissue, while ETS2 showed low tissue specificity. ETS1 was increased in 12 and decreased in 6 cancers, while ETS2 was increased in 4 and decreased in 13 cancers. Both ETS1 and ETS2 were favorable prognostic markers in LIHC and KIRC, while they showed different prognostic roles in more cancers. ETS1 showed stronger correlation with several infiltrating immune cells and immune checkpoints compared with ETS2. Both ETS1 and ETS2 harbored low mutation ratio. ETS1 interacting and correlated genes were enriched in GO terms in response to cadmium ion and response to oxidative stress, while those of ETS2 were enriched in transcription regulation. Conclusion ETS1 and ETS2 showed different patterns in expression, prognostic values, correlation with immune infiltrating, and immune checkpoints. ETS1 and ETS2 play distinct roles across cancer.
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54
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Wang Z, Coban B, Wu H, Chouaref J, Daxinger L, Paulsen MT, Ljungman M, Smid M, Martens JWM, Danen EHJ. GRHL2-controlled gene expression networks in luminal breast cancer. Cell Commun Signal 2023; 21:15. [PMID: 36691073 PMCID: PMC9869538 DOI: 10.1186/s12964-022-01029-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/24/2022] [Indexed: 01/24/2023] Open
Abstract
Grainyhead like 2 (GRHL2) is an essential transcription factor for development and function of epithelial tissues. It has dual roles in cancer by supporting tumor growth while suppressing epithelial to mesenchymal transitions (EMT). GRHL2 cooperates with androgen and estrogen receptors (ER) to regulate gene expression. We explore genome wide GRHL2 binding sites conserved in three ER⍺/GRHL2 positive luminal breast cancer cell lines by ChIP-Seq. Interaction with the ER⍺/FOXA1/GATA3 complex is observed, however, only for a minor fraction of conserved GRHL2 peaks. We determine genome wide transcriptional dynamics in response to loss of GRHL2 by nascent RNA Bru-seq using an MCF7 conditional knockout model. Integration of ChIP- and Bru-seq pinpoints candidate direct GRHL2 target genes in luminal breast cancer. Multiple connections between GRHL2 and proliferation are uncovered, including transcriptional activation of ETS and E2F transcription factors. Among EMT-related genes, direct regulation of CLDN4 is corroborated but several targets identified in other cells (including CDH1 and ZEB1) are ruled out by both ChIP- and Bru-seq as being directly controlled by GRHL2 in luminal breast cancer cells. Gene clusters correlating positively (including known GRHL2 targets such as ErbB3, CLDN4/7) or negatively (including TGFB1 and TGFBR2) with GRHL2 in the MCF7 knockout model, display similar correlation with GRHL2 in ER positive as well as ER negative breast cancer patients. Altogether, this study uncovers gene sets regulated directly or indirectly by GRHL2 in luminal breast cancer, identifies novel GRHL2-regulated genes, and points to distinct GRHL2 regulation of EMT in luminal breast cancer cells. Video Abstract.
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Affiliation(s)
- Zi Wang
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Bircan Coban
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Haoyu Wu
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Jihed Chouaref
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Michelle T Paulsen
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erik H J Danen
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
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Chen Y, Ying Y, Wang M, Ma C, Jia M, Shi L, Wang S, Zheng X, Chen W, Shu XS. A distal super-enhancer activates oncogenic ETS2 via recruiting MECOM in inflammatory bowel disease and colorectal cancer. Cell Death Dis 2023; 14:8. [PMID: 36609474 PMCID: PMC9822945 DOI: 10.1038/s41419-022-05513-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023]
Abstract
Abnormal activities of distal cis-regulatory elements (CREs) contribute to the initiation and progression of cancer. Gain of super-enhancer (SE), a highly active distal CRE, is essential for the activation of key oncogenes in various cancers. However, the mechanism of action for most tumor-specific SEs still largely remains elusive. Here, we report that a candidate oncogene ETS2 was activated by a distal SE in inflammatory bowel disease (IBD) and colorectal cancer (CRC). The SE physically interacted with the ETS2 promoter and was required for the transcription activation of ETS2. Strikingly, the ETS2-SE activity was dramatically upregulated in both IBD and CRC tissues when compared to normal colon controls and was strongly correlated with the level of ETS2 expression. The tumor-specific activation of ETS2-SE was further validated by increased enhancer RNA transcription from this region in CRC. Intriguingly, a known IBD-risk SNP resides in the ETS2-SE and the genetic variant modulated the level of ETS2 expression through affecting the binding of an oncogenic transcription factor MECOM. Silencing of MECOM induced significant downregulation of ETS2 in CRC cells, and the level of MECOM and ETS2 correlated well with each other in CRC and IBD samples. Functionally, MECOM and ETS2 were both required for maintaining the colony-formation and sphere-formation capacities of CRC cells and MECOM was crucial for promoting migration. Taken together, we uncovered a novel disease-specific SE that distantly drives oncogenic ETS2 expression in IBD and CRC and delineated a mechanistic link between non-coding genetic variation and epigenetic regulation of gene transcription.
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Affiliation(s)
- Yongheng Chen
- Department of Physiology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Ying Ying
- Department of Physiology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
- Marshall Laboratory of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Maolin Wang
- Department of Physiology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Canjie Ma
- Department of Physiology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Min Jia
- Department of Physiology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Liang Shi
- Department of Physiology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Shilan Wang
- Department of Physiology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Xiangyi Zheng
- Department of Physiology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Wei Chen
- Department of Physiology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Xing-Sheng Shu
- Department of Physiology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China.
- Marshall Laboratory of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China.
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Mercher T. ETS Fight Club on Microsatellite Enhancers. Blood Cancer Discov 2023; 4:2-4. [PMID: 36538046 PMCID: PMC9816819 DOI: 10.1158/2643-3230.bcd-22-0177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In this issue of Blood Cancer Discovery, Kodgule, Goldman, Monovichet al. cleverly analyzed the transcription regulatory elements to investigate why the second copy of ETV6 is often lost in ETV6::RUNX1-translocated in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). It turns out that ETV6 suppresses the enhancer activity of GGAA microsatellite repeats, preventing ERG from subverting them to activate aberrant oncogene transcription. See related article by Kodgule, Goldman, Monovich et al., p. 34 (5).
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Affiliation(s)
- Thomas Mercher
- INSERM U1170, Gustave Roussy Cancer Campus, Université Paris Saclay, Program PEDIAC, Villejuif, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,Corresponding Author: Thomas Mercher, U1170, INSERM, 39 rue Camille Desmoulins, Paris 94800, France. Phone: 33-6-34-61-10-58; E-mail:
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57
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Stopsack KH, Su XA, Vaselkiv JB, Graff RE, Ebot EM, Pettersson A, Lis RT, Fiorentino M, Loda M, Penney KL, Lotan TL, Mucci LA. Transcriptomes of Prostate Cancer with TMPRSS2:ERG and Other ETS Fusions. Mol Cancer Res 2023; 21:14-23. [PMID: 36125519 PMCID: PMC9812892 DOI: 10.1158/1541-7786.mcr-22-0446] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/30/2022] [Accepted: 09/15/2022] [Indexed: 02/03/2023]
Abstract
The most common somatic event in primary prostate cancer is a fusion between the androgen-related TMPRSS2 gene and the ERG oncogene. Tumors with these fusions, which occur early in carcinogenesis, have a distinctive etiology. A smaller subset of other tumors harbor fusions between TMPRSS2 and members of the ETS transcription factor family other than ERG. To assess the genomic similarity of tumors with non-ERG ETS fusions and those with fusions involving ERG, this study derived a transcriptomic signature of non-ERG ETS fusions and assessed this signature and ERG-related gene expression in 1,050 men with primary prostate cancer from three independent population-based and hospital-based studies. Although non-ERG ETS fusions involving ETV1, ETV4, ETV5, or FLI1 were individually rare, they jointly accounted for one in seven prostate tumors. Genes differentially regulated between non-ERG ETS tumors and tumors without ETS fusions showed similar differential expression when ERG tumors and tumors without ETS fusions were compared (differences explained: R2 = 69-77%), including ETS-related androgen receptor (AR) target genes. Differences appeared to result from similarities among ETS tumors rather than similarities among non-ETS tumors. Gene sets associated with ERG fusions were consistent with gene sets associated with non-ERG ETS fusions, including fatty acid and amino acid metabolism, an observation that was robust across cohorts. IMPLICATIONS Considering ETS fusions jointly may be useful for etiologic studies on prostate cancer, given that the transcriptome is profoundly impacted by ERG and non-ERG ETS fusions in a largely similar fashion, most notably genes regulating metabolic pathways.
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Affiliation(s)
- Konrad H. Stopsack
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Xiaofeng A. Su
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - J. Bailey Vaselkiv
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Rebecca E. Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA., Division of Research, Kaiser Permanente Northern California, Oakland, CA, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Ericka M. Ebot
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Andreas Pettersson
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Rosina T. Lis
- Department of Pathology and Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA
| | - Michelangelo Fiorentino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, Pathology Unit, Addarii Institute, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Massimo Loda
- Department of Pathology, Weill Cornell Medical College, New York, NY
| | - Kathryn L. Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Tamara L. Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
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58
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Transcriptional Regulation of Siglec-15 by ETS-1 and ETS-2 in Hepatocellular Carcinoma Cells. Int J Mol Sci 2023; 24:ijms24010792. [PMID: 36614238 PMCID: PMC9821606 DOI: 10.3390/ijms24010792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 01/04/2023] Open
Abstract
Sialic acid-binding immunoglobulin-like lectin 15 (Siglec-15) has been identified as a crucial immune suppressor in human cancers, comparable to programmed cell death 1 ligand (PD-L1). However, the regulatory mechanisms underlying its transcriptional upregulation in human cancers remain largely unknown. Here, we show that the transcription factors ETS-1 and ETS-2 bound to the Siglec-15 promoter to enhance transcription and expression of Siglec-15 in hepatocellular carcinoma (HCC) cells and that transforming growth factor β-1 (TGF-β1) upregulated the expression of ETS-1 and ETS-2 and facilitated the binding of ETS-1 and ETS-2 to the Siglec-15 promoter. We further demonstrate that TGF-β1 activated the Ras/C-Raf/MEK/ERK1/2 signaling pathway, leading to phosphorylation of ETS-1 and ETS-2, which consequently upregulates the transcription and expression of Siglec-15. Our study defines a detailed molecular profile of how Siglec-15 is transcriptionally regulated which may offer significant opportunity for therapeutic intervention on HCC immunotherapy.
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The role and application of transcriptional repressors in cancer treatment. Arch Pharm Res 2023; 46:1-17. [PMID: 36645575 DOI: 10.1007/s12272-023-01427-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/03/2023] [Indexed: 01/17/2023]
Abstract
Gene expression is modulated through the integration of many regulatory elements and their associated transcription factors (TFs). TFs bind to specific DNA sequences and either activate or repress transcriptional activity. Through decades of research, it has been established that aberrant expression or functional abnormalities of TFs can lead to uncontrolled cell division and the development of cancer. Initial studies on transcriptional regulation in cancer have focused on TFs as transcriptional activators. However, recent studies have demonstrated several different mechanisms of transcriptional repression in cancer, which could be potential therapeutic targets for the development of specific anti-cancer agents. In the first section of this review, "Emerging roles of transcriptional repressors in cancer development," we summarize the current understanding of transcriptional repressors and their involvement in the molecular processes of cancer progression. In the subsequent section, "Therapeutic applications," we provide an updated overview of the available therapeutic targets for drug discovery and discuss the new frontier of such applications.
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60
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Hasanau TN, Pisarev EP, Kisil OV, Zvereva ME. The TERT Promoter: A Key Player in the Fight for Cancer Cell Immortality. BIOCHEMISTRY (MOSCOW) 2023; 88:S21-S38. [PMID: 37069112 DOI: 10.1134/s000629792314002x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The review describes the role of telomeres and telomerase in tumor progression, as well as various mechanisms of the activation of telomerase reverse transcriptase (TERT) expression in CNS tumors and other cancers. The main mechanism of TERT activation involves acquisition of somatic mutations by the TERT gene promoter (TERTp). The article presents information on the TERTp structure and transcription factors directly interacting with TERTp and regulating its transcription. The prospects of using the mutational status of TERTp as a prognostic marker of CNS malignancies and other tumors with a common profile of TERTp mutations are discussed.
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Affiliation(s)
- Tsimur N Hasanau
- Natural Compounds Department, Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eduard P Pisarev
- Natural Compounds Department, Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Olga V Kisil
- Gause Institute of New Antibiotics, Moscow, 119021, Russia
| | - Maria E Zvereva
- Natural Compounds Department, Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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Wang Z, Liu H, Gong Y, Cheng Y. Establishment and validation of an aging-related risk signature associated with prognosis and tumor immune microenvironment in breast cancer. Eur J Med Res 2022; 27:317. [PMID: 36581948 PMCID: PMC9798726 DOI: 10.1186/s40001-022-00924-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/01/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Breast cancer (BC) is a highly malignant and heterogeneous tumor which is currently the cancer with the highest incidence and seriously endangers the survival and prognosis of patients. Aging, as a research hotspot in recent years, is widely considered to be involved in the occurrence and development of a variety of tumors. However, the relationship between aging-related genes (ARGs) and BC has not yet been fully elucidated. MATERIALS AND METHODS The expression profiles and clinicopathological data were acquired in the Cancer Genome Atlas (TCGA) and the gene expression omnibus (GEO) database. Firstly, the differentially expressed ARGs in BC and normal breast tissues were investigated. Based on these differential genes, a risk model was constructed composed of 11 ARGs via univariate and multivariate Cox analysis. Subsequently, survival analysis, independent prognostic analysis, time-dependent receiver operating characteristic (ROC) analysis and nomogram were performed to assess its ability to sensitively and specifically predict the survival and prognosis of patients, which was also verified in the validation set. In addition, functional enrichment analysis and immune infiltration analysis were applied to reveal the relationship between the risk scores and tumor immune microenvironment, immune status and immunotherapy. Finally, multiple datasets and real-time polymerase chain reaction (RT-PCR) were utilized to verify the expression level of the key genes. RESULTS An 11-gene signature (including FABP7, IGHD, SPIB, CTSW, IGKC, SEZ6, S100B, CXCL1, IGLV6-57, CPLX2 and CCL19) was established to predict the survival of BC patients, which was validated by the GEO cohort. Based on the risk model, the BC patients were divided into high- and low-risk groups, and the high-risk patients showed worse survival. Stepwise ROC analysis and Cox analyses demonstrated the good performance and independence of the model. Moreover, a nomogram combined with the risk score and clinical parameters was built for prognostic prediction. Functional enrichment analysis revealed the robust relationship between the risk model with immune-related functions and pathways. Subsequent immune microenvironment analysis, immunotherapy, etc., indicated that the immune status of patients in the high-risk group decreased, and the anti-tumor immune function was impaired, which was significantly different with those in the low-risk group. Eventually, the expression level of FABP7, IGHD, SPIB, CTSW, IGKC, SEZ6, S100B, CXCL1, IGLV6-57 and CCL19 was identified as down-regulated in tumor cell line, while CPLX2 up-regulated, which was mostly similar with the results in TCGA and Human Protein Atlas (HPA) via RT-PCR. CONCLUSIONS In summary, our study constructed a risk model composed of ARGs, which could be used as a solid model for predicting the survival and prognosis of BC patients. Moreover, this model also played an important role in tumor immunity, providing a new direction for patient immune status assessment and immunotherapy selection.
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Affiliation(s)
- Zitao Wang
- grid.412632.00000 0004 1758 2270Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Hua Liu
- grid.412632.00000 0004 1758 2270Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Yiping Gong
- grid.412632.00000 0004 1758 2270Department of Breast Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Yanxiang Cheng
- grid.412632.00000 0004 1758 2270Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
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Ervin EH, French R, Chang CH, Pauklin S. Inside the stemness engine: Mechanistic links between deregulated transcription factors and stemness in cancer. Semin Cancer Biol 2022; 87:48-83. [PMID: 36347438 DOI: 10.1016/j.semcancer.2022.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/07/2022]
Abstract
Cell identity is largely determined by its transcriptional profile. In tumour, deregulation of transcription factor expression and/or activity enables cancer cell to acquire a stem-like state characterised by capacity to self-renew, differentiate and form tumours in vivo. These stem-like cancer cells are highly metastatic and therapy resistant, thus warranting a more complete understanding of the molecular mechanisms downstream of the transcription factors that mediate the establishment of stemness state. Here, we review recent research findings that provide a mechanistic link between the commonly deregulated transcription factors and stemness in cancer. In particular, we describe the role of master transcription factors (SOX, OCT4, NANOG, KLF, BRACHYURY, SALL, HOX, FOX and RUNX), signalling-regulated transcription factors (SMAD, β-catenin, YAP, TAZ, AP-1, NOTCH, STAT, GLI, ETS and NF-κB) and unclassified transcription factors (c-MYC, HIF, EMT transcription factors and P53) across diverse tumour types, thereby yielding a comprehensive overview identifying shared downstream targets, highlighting unique mechanisms and discussing complexities.
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Affiliation(s)
- Egle-Helene Ervin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Rhiannon French
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Chao-Hui Chang
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
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Wang X, Lv JL, Cheng S, Su ZH, Qin S, Sun X, Tang XD, Liu QN, Li MW, Wang XY. Bombyx mori transcription factor, E74A, beneficially affects BmNPV infection through direct interaction. PEST MANAGEMENT SCIENCE 2022; 78:5302-5312. [PMID: 36054174 DOI: 10.1002/ps.7152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 08/21/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Nucleopolyhedrovirus (NPV), one of the baculoviruses, is a promising biopesticide for pest control. Lepidopteran account for 70% of pests, therefore investigation on highly conserved genes associated with viral infections in the lepidopteran model, the silkworm, will serve as a valuable reference for improving the effectiveness of pest management. BmE74A is a member of the erythroblast transformation-specific (ETS) family of transcription factors in Bombyx mori, which we previously found to be highly conserved and closely associated with BmNPV. This study aimed to elucidate the role of BmE74A in viral infection. RESULTS A significantly high expression of BmE74A in eggs indicated its important role in embryonic development, as did relatively high expressions in the hemolymph and midgut. Significant differences in BmE74A expression in different resistant strains after BmNPV infection suggested its involvement as a response to viral infection. Moreover, RNA interference (RNAi) and overexpression experiments confirmed the important role of BmE74A in promoting viral infection. BmNPV infection was significantly suppressed and enhanced by BmE74A knockdown and overexpression, respectively. Besides, BmE74A was found to regulate the expression of BmMdm2 and Bmp53. Furthermore, the binding of ETS, the functional domain of BmE74A, to occlusion-derived virus proteins was confirmed by far-western blotting, and four viral proteins that may interact with ETS proteins were identified by mass spectrometry. Similarly, a homolog of BmE74A in Spodoptera litura was also found to be involved in larval susceptibility to BmNPV. CONCLUSION BmE74A promotes BmNPV proliferation by directly interacting with the virus, which may be related to the suppression of the p53 pathway. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xin Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Jun-Li Lv
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Shuang Cheng
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhi-Hao Su
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Sheng Qin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
| | - Xia Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
| | - Xu-Dong Tang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Mu-Wang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
| | - Xue-Yang Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
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Gupta N, Song H, Wu W, Ponce RK, Lin YK, Kim JW, Small EJ, Feng FY, Huang FW, Okimoto RA. The CIC-ERF co-deletion underlies fusion-independent activation of ETS family member, ETV1, to drive prostate cancer progression. eLife 2022; 11:e77072. [PMID: 36383412 PMCID: PMC9668335 DOI: 10.7554/elife.77072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 10/16/2022] [Indexed: 11/13/2022] Open
Abstract
Human prostate cancer can result from chromosomal rearrangements that lead to aberrant ETS gene expression. The mechanisms that lead to fusion-independent ETS factor upregulation and prostate oncogenesis remain relatively unknown. Here, we show that two neighboring transcription factors, Capicua (CIC) and ETS2 repressor factor (ERF), which are co-deleted in human prostate tumors can drive prostate oncogenesis. Concurrent CIC and ERF loss commonly occur through focal genomic deletions at chromosome 19q13.2. Mechanistically, CIC and ERF co-bind the proximal regulatory element and mutually repress the ETS transcription factor, ETV1. Targeting ETV1 in CIC and ERF-deficient prostate cancer limits tumor growth. Thus, we have uncovered a fusion-independent mode of ETS transcriptional activation defined by concurrent loss of CIC and ERF.
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Affiliation(s)
- Nehal Gupta
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Hanbing Song
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Wei Wu
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Rovingaile K Ponce
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Yone K Lin
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Ji Won Kim
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Eric J Small
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
| | - Felix Y Feng
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
- Department of Radiation Oncology, University of CaliforniaSan FranciscoUnited States
| | - Franklin W Huang
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
| | - Ross A Okimoto
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
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Xiong Z, Wu S, Li FJ, Luo C, Jin QY, Connolly ID, Hayden Gephart M, You L. Elevated ETV6 Expression in Glioma Promotes an Aggressive In Vitro Phenotype Associated with Shorter Patient Survival. Genes (Basel) 2022; 13:genes13101882. [PMID: 36292767 PMCID: PMC9656946 DOI: 10.3390/genes13101882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022] Open
Abstract
Background: GBM astrocytes may adopt fetal astrocyte transcriptomic signatures involved in brain development and migration programs to facilitate diffuse tumor infiltration. Our previous data show that ETS variant 6 (ETV6) is highly expressed in human GBM and fetal astrocytes compared to normal mature astrocytes. We hypothesized that ETV6 played a role in GBM tumor progression. Methods: Expression of ETV6 was first examined in two American and three Chinese tissue microarrays. The correlation between ETV6 staining intensity and patient survival was calculated, followed by validation using public databases—TCGA and REMBRANDT. The effect of ETV6 knockdown on glioma cell proliferation (EdU), viability (AnnexinV labeling), clonogenic growth (colony formation), and migration/invasion (transwell assays) in GBM cells was tested. RNA sequencing and Western blot were performed to elucidate the underlying molecular mechanisms. Results: ETV6 was highly expressed in GBM and associated with an unfavorable prognosis. ETV6 silencing in glioma cells led to increased apoptosis or decreased proliferation, clonogenicity, migration, and invasion. RNA-Seq-based gene expression and pathway analyses revealed that ETV6 knockdown in U251 cells led to the upregulation of genes involved in extracellular matrix organization, NF-κB signaling, TNF-mediated signaling, and the downregulation of genes in the regulation of cell motility, cell proliferation, PI3K-AKT signaling, and the Ras pathway. The downregulation of the PI3K-AKT and Ras-MAPK pathways were further validated by immunoblotting. Conclusion: Our findings suggested that ETV6 was highly expressed in GBM and its high expression correlated with poor survival. ETV6 silencing decreased an aggressive in vitro phenotype probably via the PI3K-AKT and Ras-MAPK pathways. The study encourages further investigation of ETV6 as a potential therapeutic target of GBM.
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Affiliation(s)
- Zhang Xiong
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
- Neurosurgical Institute, Fudan University, Shanghai 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai 200040, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai 200040, China
| | - Shuai Wu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
- Neurosurgical Institute, Fudan University, Shanghai 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai 200040, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai 200040, China
| | - Feng-jiao Li
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Chen Luo
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
- Neurosurgical Institute, Fudan University, Shanghai 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai 200040, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai 200040, China
| | - Qiu-yan Jin
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Ian David Connolly
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Melanie Hayden Gephart
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
- Correspondence: to: (M.H.G.); (L.Y.)
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai, Shanghai 200032, China
- Correspondence: to: (M.H.G.); (L.Y.)
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Zhao S, Zhang A, Zhu H, Wen Z. The ETS transcription factor Spi2 regulates hematopoietic cell development in zebrafish. Development 2022; 149:276980. [DOI: 10.1242/dev.200881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/26/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The E26 transformation-specific or E-twenty-six (ETS) genes encode a superfamily of transcription factors involved in diverse biological processes. Here, we report the identification and characterization of a previously unidentified member of the ETS transcription factors, Spi2, that is found exclusively in the ray-finned fish kingdom. We show that the expression of spi2 is restricted to hemogenic endothelial cells (HECs) and to hematopoietic stem and progenitor cells (HSPCs) in zebrafish. Using bacteria artificial chromosome transgenesis, we generate a spi2 reporter line, TgBAC(spi2:P2a-GFP), which manifests the GFP pattern recapitulating the endogenous spi2 expression. Genetic ablation of spi2 has little effect on HEC formation and the endothelial-to-hematopoietic transition, but results in compromised proliferation of HSPCs in the caudal hematopoietic tissue (CHT) during early development and in severe myeloid lineage defect in adulthood. Epistatic analysis shows that spi2 acts downstream of runx1 in regulating HSPC development in the CHT. Our study identifies Spi2 as an essential regulator for definitive hematopoietic cell development and creates a TgBAC(spi2:P2a-GFP) reporter line for tracking HECs, HSPCs, myeloid cells and thrombocytes from early development to adulthood.
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Affiliation(s)
- Shizheng Zhao
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology 1 Division of Life Science , , Clear Water Bay, Hong Kong , China
| | - Ao Zhang
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology 1 Division of Life Science , , Clear Water Bay, Hong Kong , China
| | - Hao Zhu
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology 1 Division of Life Science , , Clear Water Bay, Hong Kong , China
| | - Zilong Wen
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology 1 Division of Life Science , , Clear Water Bay, Hong Kong , China
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen Peking University−Hong Kong University of Science and Technology Medical Center 2 , Shenzhen 518055 , China
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67
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Current and emerging therapies for neuroendocrine prostate cancer. Pharmacol Ther 2022; 238:108255. [DOI: 10.1016/j.pharmthera.2022.108255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022]
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68
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Zhang T, Wang Y, Xie M, Ji X, Luo X, Chen X, Zhang B, Liu D, Feng Y, Sun M, Huang W, Xia L. HGF-mediated elevation of ETV1 facilitates hepatocellular carcinoma metastasis through upregulating PTK2 and c-MET. J Exp Clin Cancer Res 2022; 41:275. [PMID: 36109787 PMCID: PMC9479266 DOI: 10.1186/s13046-022-02475-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/24/2022] [Indexed: 12/14/2022] Open
Abstract
Background Metastasis is a major determinant of death in patients with hepatocellular carcinoma (HCC). Dissecting key molecular mediators that promote this malignant feature may help yield novel therapeutic insights. Here, we investigated the role of E-twenty-six transformation-specific variant 1 (ETV1), a member of the E-twenty-six transformation-specific (ETS) family, in HCC metastasis. Methods The clinical significance of ETV1 and its target genes in two independent cohorts of HCC patients who underwent curative resection were assessed by Kaplan–Meier analysis and Multivariate Cox proportional hazards model. Luciferase reporter assay and chromatin immunoprecipitation assay were used to detect the transcriptional regulation of target gene promoters by ETV1. The effect of ETV1 on invasiveness and metastasis of HCC were detected by transwell assays and the orthotopically metastatic model. Results ETV1 expression was frequently elevated in human HCC specimens. Increased ETV1 expression was associated with the malignant biological characteristics and poor prognosis of HCC patients. ETV1 facilitated invasion and metastasis of HCC cells in vitro and in vivo. Mechanistically, ETV1 promoted HCC metastasis via upregulating metastasis-related genes, including protein tyrosine kinase 2 (PTK2) and MET. Down-regulated the expression of PTK2 or tyrosine protein kinase Met (c-MET) decreased ETV1-mediated HCC metastasis. Hepatocyte growth factor (HGF) upregulated ETV1 expression through activating c-MET-ERK1/2-ELK1 pathway. Notably, in two independent cohorts, patients with positive coexpression of ETV1/PTK2 or ETV1/c-MET had worse prognosis. Furthermore, the combination of PTK2 inhibitor defactinib and c-MET inhibitor capmatinib significantly suppressed HCC metastasis induced by ETV1. Conclusion This study uncovers functional and prognostic roles for ETV1 in HCC and exposes a positive feedback loop of HGF-ERK1/2-ETV1-c-MET. Targeting this pathway may provide a potential therapeutic intervention for ETV1-overexpressing HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02475-2.
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Tsai JW, Cejas P, Wang DK, Patel S, Wu DW, Arounleut P, Wei X, Zhou N, Syamala S, Dubois FP, Crane A, Pelton K, Vogelzang J, Sousa C, Baguette A, Chen X, Condurat AL, Dixon-Clarke SE, Zhou KN, Lu SD, Gonzalez EM, Chacon MS, Digiacomo JJ, Kumbhani R, Novikov D, Hunter J, Tsoli M, Ziegler DS, Dirksen U, Jager N, Balasubramanian GP, Kramm CM, Nathrath M, Bielack S, Baker SJ, Zhang J, McFarland JM, Getz G, Aguet F, Jabado N, Witt O, Pfister SM, Ligon KL, Hovestadt V, Kleinman CL, Long H, Jones DT, Bandopadhayay P, Phoenix TN. FOXR2 Is an Epigenetically Regulated Pan-Cancer Oncogene That Activates ETS Transcriptional Circuits. Cancer Res 2022; 82:2980-3001. [PMID: 35802025 PMCID: PMC9437574 DOI: 10.1158/0008-5472.can-22-0671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/11/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022]
Abstract
Forkhead box R2 (FOXR2) is a forkhead transcription factor located on the X chromosome whose expression is normally restricted to the testis. In this study, we performed a pan-cancer analysis of FOXR2 activation across more than 10,000 adult and pediatric cancer samples and found FOXR2 to be aberrantly upregulated in 70% of all cancer types and 8% of all individual tumors. The majority of tumors (78%) aberrantly expressed FOXR2 through a previously undescribed epigenetic mechanism that involves hypomethylation of a novel promoter, which was functionally validated as necessary for FOXR2 expression and proliferation in FOXR2-expressing cancer cells. FOXR2 promoted tumor growth across multiple cancer lineages and co-opted ETS family transcription circuits across cancers. Taken together, this study identifies FOXR2 as a potent and ubiquitous oncogene that is epigenetically activated across the majority of human cancers. The identification of hijacking of ETS transcription circuits by FOXR2 extends the mechanisms known to active ETS transcription factors and highlights how transcription factor families cooperate to enhance tumorigenesis. SIGNIFICANCE This work identifies a novel promoter that drives aberrant FOXR2 expression and delineates FOXR2 as a pan-cancer oncogene that specifically activates ETS transcriptional circuits across human cancers. See related commentary by Liu and Northcott, p. 2977.
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Affiliation(s)
- Jessica W. Tsai
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, Cancer Program, Broad Institute, Cambridge, Massachusetts
| | - Dayle K. Wang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Smruti Patel
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
- Division of Pediatric Neurosurgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Neurosurgery, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - David W. Wu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Phonepasong Arounleut
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
| | - Xin Wei
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
| | - Ningxuan Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, Cancer Program, Broad Institute, Cambridge, Massachusetts
| | - Sudeepa Syamala
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, Cancer Program, Broad Institute, Cambridge, Massachusetts
| | - Frank P.B. Dubois
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alexander Crane
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kristine Pelton
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jayne Vogelzang
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Cecilia Sousa
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Audrey Baguette
- Quantitative Life Sciences, McGill University, Montreal, Quebec H3A 2A7, Canada
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Alexandra L. Condurat
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Sarah E. Dixon-Clarke
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts
| | - Kevin N. Zhou
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Sophie D. Lu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Elizabeth M. Gonzalez
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Madison S. Chacon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Jeromy J. Digiacomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Rushil Kumbhani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Dana Novikov
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - J'Ya Hunter
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Maria Tsoli
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - David S. Ziegler
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Uta Dirksen
- West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Essen/Düsseldorf, Germany
| | - Natalie Jager
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gnana Prakash Balasubramanian
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christof M. Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Michaela Nathrath
- Department of Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | | | - Suzanne J. Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, H3A 0C7, Canada
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, H4A 3J1, Canada
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology, and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Disease (NCT) Network, Germany
| | - Stefan M. Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology, and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Disease (NCT) Network, Germany
| | - Keith L. Ligon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Volker Hovestadt
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Claudia L. Kleinman
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, H3A 0C7, Canada
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, Cancer Program, Broad Institute, Cambridge, Massachusetts
| | - David T.W. Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Timothy N. Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
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Nabeta R, Katselis GS, Chumala P, Dickinson R, Fernandez NJ, Meachem MD. Identification of potential plasma protein biomarkers for feline pancreatic carcinoma by liquid chromatography tandem mass spectrometry. Vet Comp Oncol 2022; 20:720-731. [PMID: 35514180 DOI: 10.1111/vco.12826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/14/2022] [Accepted: 04/26/2022] [Indexed: 12/01/2022]
Abstract
In both humans and cats, pancreatic carcinoma is an aggressive cancer with a grave prognosis. Proteomics techniques have successfully identified several blood-based biomarkers of human pancreatic neoplasia. Thus, this study aims to investigate whether similar biomarkers can be identified in the plasma of cats with FePAC by using liquid chromatography tandem mass spectrometry (LC-MS/MS). To facilitate evaluation of the low abundance plasma proteome, a human-based immunodepletion device (MARS-2) was first validated for use with feline plasma. Marked reduction and/or complete removal of albumin and immunoglobulins was confirmed by analysis of electrophoretograms and mass spectral data. Subsequently, plasma collected from 9 cats with pancreatic carcinoma (FePAC), 10 cats with symptomatic pancreatitis, and 10 healthy control cats was immunodepleted and subjected to LC-MS/MS. Thirty-seven plasma proteins were found to be differentially expressed (p < .05 in one-way ANOVA, FC >2 in fold change analysis). Among these proteins, ETS variant transcription factor 4 (p < .05) was overexpressed, while gelsolin (p < .01), tryptophan 2,3-dioxygenase (p < .05), serpin family F member 1 (p < .01), apolipoprotein A-IV (p < .01) and phosphatidylinositol-glycan-specific phospholipase D (p < .05) were down-regulated in cats with FePAC. Further studies on these potential biomarkers are needed to investigate their diagnostic value.
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Affiliation(s)
- Rina Nabeta
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - George S Katselis
- Department of Medicine, Division of the Canadian Centre for Health and Safety in Agriculture, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Paulos Chumala
- Department of Medicine, Division of the Canadian Centre for Health and Safety in Agriculture, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ryan Dickinson
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Nicole J Fernandez
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Melissa D Meachem
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Santi MD, Zhang M, Salvo E, Asam K, Viet C, Xie T, Amit M, Aouizerat B, Ye Y. Schwann Cells Induce Phenotypic Changes in Oral Cancer Cells. Adv Biol (Weinh) 2022; 6:e2200187. [PMID: 35925609 PMCID: PMC9474679 DOI: 10.1002/adbi.202200187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/18/2022] [Indexed: 01/28/2023]
Abstract
Head and neck cancer (HNC) is the seventh most common cancer worldwide, the majority being oral squamous cell carcinoma. Despite advances in cancer diagnosis and treatment, the survival rate of patients with HNC remains stagnant. The cancer-nerve interaction has been recognized as an important driver of cancer progression. Schwann cells, a type of peripheral glia, have been implicated in promoting cancer cell growth, migration, dispersion, and invasion into the nerve in many cancers. Here, it is demonstrated that the presence of Schwann cells makes oral cancer cells more aggressive by promoting their proliferation, extracellular matrix breakdown, and altering cell metabolism. Furthermore, oral cancer cells became larger, more circular, with more projections and nuclei following co-culturing with Schwann cells. RNA-sequencing analysis in oral cancer cells following exposure to Schwann cells shows corresponding changes in genes involved in the hallmarks of cancer and cell metabolism; the enriched KEGG pathways are spliceosome, RNA transport, cell cycle, axon guidance, signaling pathways regulating pluripotency of stem cells, cAMP signaling, WNT signaling, proteoglycans in cancer and PI3K-Akt signaling. Taken together, these results suggest a significant role for Schwann cells in facilitating oral cancer progression, highlighting their potential as a target to treat oral cancer progression.
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Affiliation(s)
- Maria Daniela Santi
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
| | - Morgan Zhang
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
| | - Elizabeth Salvo
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
| | - Kesava Asam
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
| | - Chi Viet
- Loma Linda University School of Dentistry, Loma Linda, CA92350
| | - Tongxin Xie
- Head & Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Moran Amit
- Head & Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Bradley Aouizerat
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
| | - Yi Ye
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
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Shen X, Zhou C, Feng H, Li J, Xia T, Cheng X, Zhao R, Zou D. ETV1 Positively Correlated With Immune Infiltration and Poor Clinical Prognosis in Colorectal Cancer. Front Immunol 2022; 13:939806. [PMID: 35860243 PMCID: PMC9291282 DOI: 10.3389/fimmu.2022.939806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveNumerous studies recently suggested that the immune microenvironment could influence the development of colorectal cancer (CRC). These findings implied that the infiltration of immune cells could be a promising prognostic biomarker for CRC.MethodsFurthermore, the Oncomine database and R2 platform analysis were applied in our research to validate CRC clinical prognosis via expression levels of polyoma enhancer activator 3 (PEA3) members. We explored the correlation of ETV1, ETV4, and ETV5 with tumor-infiltrating immune cells (TIICs) in CRC tumor microenvironments via the Tumor Immune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA). Immunohistochemistry (IHC) was used to validate our CRC clinical data.ResultsOur findings indicated that the upregulation of PEA3 members including ETV1 and ETV5 was positively associated with poor prognosis in CRC patients. Meanwhile, ETV1 and ETV5 may play significant roles in the development progress of CRC. Furthermore, ETV1 tends to be associated with immune infiltration of CRC, especially with cancer-associated fibroblasts and M2 macrophages.ConclusionThese findings revealed that ETV1 and ETV5 played significant roles in the development of CRC. Moreover, ETV1 was significantly associated with the infiltration of cancer-associated fibroblasts and M2 macrophages in CRC. Targeting ETV1 can be a potential auspicious approach for CRC treatment.
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Affiliation(s)
- Xiaonan Shen
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunhua Zhou
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoran Feng
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jialu Li
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tianxue Xia
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xi Cheng
- Department of General Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xi Cheng, ; Ren Zhao, ; Duowu Zou,
| | - Ren Zhao
- Department of General Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xi Cheng, ; Ren Zhao, ; Duowu Zou,
| | - Duowu Zou
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xi Cheng, ; Ren Zhao, ; Duowu Zou,
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Biswas A, Rajesh Y, Das S, Banerjee I, Kapoor N, Mitra P, Mandal M. Therapeutic targeting of RBPJ, an upstream regulator of ETV6 gene, abrogates ETV6-NTRK3 fusion gene transformations in glioblastoma. Cancer Lett 2022; 544:215811. [PMID: 35787922 DOI: 10.1016/j.canlet.2022.215811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022]
Abstract
Fusion genes are abnormal genes resulting from chromosomal translocation, insertion, deletion, inversion, etc. ETV6, a rather promiscuous partner forms fusions with several other genes, most commonly, the NTRK3 gene. This fusion leads to the formation of a constitutively activated tyrosine kinase which activates the Ras-Raf-MEK and PI3K/AKT/MAPK pathways, leading the cells through cycles of uncontrolled division and ultimately resulting in cancer. Targeted therapies against this ETV6-NTRK3 fusion protein are much needed. Therefore, to find a targeted approach, a transcription factor RBPJ regulating the ETV6 gene was established and since the ETV6-NTRK3 fusion gene is downstream of the ETV6 promoter/enhancer, this fusion protein is also regulated. The regulation of the ETV6 gene via RBPJ was validated by ChIP analysis in human glioblastoma (GBM) cell lines and patient tissue samples. This study was further followed by the identification of an inhibitor, Furamidine, against transcription factor RBPJ. It was found to be binding with the DNA binding domain of RBPJ with antitumorigenic properties and minimal organ toxicity. Hence, a new target RBPJ, regulating the production of ETV6 and ETV6-NTRK3 fusion protein was found along with a potent RBPJ inhibitor Furamidine.
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Affiliation(s)
- Angana Biswas
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Yetirajam Rajesh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Subhayan Das
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Indranil Banerjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Neelkamal Kapoor
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, 462020, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
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Jin J, Du X, Zhou L, Yao D, Zou Q. SPI1-related protein inhibits cervical cancer cell progression and prevents macrophage cell migration. J Obstet Gynaecol Res 2022; 48:2419-2430. [PMID: 35770729 DOI: 10.1111/jog.15336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022]
Abstract
AIM The functions and molecular mechanisms of SPI1-related protein (SPIB) were examined in cervical cancer (CC) cells. METHODS Genes related to miscarriage and prognosis in CC were identified by Kaplan-Meier and differential expression analysis, respectively. Cell proliferation, apoptosis, migration, and invasion were examined by cell counting kit-8, flow cytometry, transwell migration, and transwell invasion assays, respectively. The potential functions and molecular mechanisms of SPIB in CC were speculated by gene set enrichment analysis (GSEA) analysis. The mRNA and protein levels of genes were examined by RT-qPCR and western blot assays, respectively. The effect of SPIB on macrophage cells was tested by macrophage recruitment assay and bioinformatics analysis. RESULTS A total of 753 dysregulated genes were identified in 88 TCGA CC samples with a history of one or more miscarriages versus 208 CC samples with no miscarriage history. Also, 91 genes related to CC prognosis were identified. SPIB, a gene related to both miscarriage and CC prognosis, inhibited Hela cell proliferation, migration, and invasion, and facilitated Hela cell apoptosis. GSEA analysis disclosed that SPIB might play vital roles in immunity, chemokine signaling pathway, and macrophage chemotaxis/activation in CC. Moreover, SPIB inhibited C-X-C motif chemokine ligand 8 (CXCL8), C-C motif chemokine ligand 17 (CCL17), and C-C motif chemokine ligand 25 (CCL25) expression in Hela cells, and SPIB overexpression in Hela cells hampered THP-1 cell migration. Higher SPIB expression was associated with less M2 macrophage infiltration in CC. CONCLUSIONS SPIB inhibited CC-cell progression and hindered macrophage cell migration in CC.
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Affiliation(s)
- Jing Jin
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan City, PR China
| | - Xin Du
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan City, PR China
| | - Limin Zhou
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan City, PR China
| | - Dongmei Yao
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan City, PR China
| | - Qian Zou
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan City, PR China
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An G, Feng L, Hou L, Li X, Bai J, He L, Gu S, Zhao X. A bioinformatics analysis of zinc finger protein family reveals potential oncogenic biomarkers in breast cancer. Gene 2022; 828:146471. [PMID: 35378249 DOI: 10.1016/j.gene.2022.146471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Zinc finger protein family is the largest transcription factor family in the human genome. Studies have shown that the aberrant expression of zinc finger protein (ZNF) had a potential role in tumorigenesis. However, due to the high complexity of the ZNF family genes, the role of the ZNF family genes in breast cancer (BRCA) is still lacking in systematic understanding. AIM In the study, we aim to understand the expression profile, prognostic value, immune invasion pattern, tumor microenvironment, epigenetic and pathway relationships, and drug sensitivity of ZNFs using multi-omics data from public databases. RESULTS We focused on six members of ZNFs, which were upregulated in a variety of cancers. Notably, ZNF750 and ZNF224 were lower expressed in BRCA, and their expressions were significantly associated with BRCA prognosis. We confirmed the observations obtained by analyzing the clinic-pathological data. Otherwise, the expressions of ZNFs were significantly related to stromal and immune scores, and was significantly different among different immune subtypes in BRCA. Here, we found down-regulated methylation of ZNF217 and ZNF750. The relationship between methylation and survival showed the survival was worse for hypo-methylation of ZNF750 in BRCA, which is consistent with the correlation of high expression of ZNF750 in BRCA with worse survival. CONCLUSIONS Collectively, our results provide clues for a better understanding of the characterization of ZNF family genes in BRCA from a multi-omics perspective and show their potential for use as new tumor markers and therapeutic targets.
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Affiliation(s)
- Gaili An
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China; Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Lu Feng
- Department of Radiotherapy, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Lei Hou
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Xu Li
- Department of Oncology, Shaanxi Provincial Cancer Hospital, Xi'an 712000, Shaanxi, China
| | - Jun Bai
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Li He
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Shanzhi Gu
- Department of College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China.
| | - Xinhan Zhao
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China.
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Hostallero DE, Li Y, Emad A. Looking at the BiG Picture: Incorporating bipartite graphs in drug response prediction. Bioinformatics 2022; 38:3609-3620. [PMID: 35674359 DOI: 10.1093/bioinformatics/btac383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 04/17/2022] [Accepted: 06/01/2022] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION The increasing number of publicly available databases containing drugs' chemical structures, their response in cell lines, and molecular profiles of the cell lines has garnered attention to the problem of drug response prediction. However, many existing methods do not fully leverage the information that is shared among cell lines and drugs with similar structure. As such, drug similarities in terms of cell line responses and chemical structures could prove to be useful in forming drug representations to improve drug response prediction accuracy. RESULTS We present two deep learning approaches, BiG-DRP and BiG-DRP+, for drug response prediction. Our models take advantage of the drugs' chemical structure and the underlying relationships of drugs and cell lines through a bipartite graph and a heterogenous graph convolutional network that incorporate sensitive and resistant cell line information in forming drug representations. Evaluation of our methods and other state-of-the-art models in different scenarios shows that incorporating this bipartite graph significantly improves the prediction performance. Additionally, genes that contribute significantly to the performance of our models also point to important biological processes and signaling pathways. Analysis of predicted drug response of patients' tumors using our model revealed important associations between mutations and drug sensitivity, illustrating the utility of our model in pharmacogenomics studies. AVAILABILITY AND IMPLEMENTATION An implementation of the algorithms in Python is provided in https://github.com/ddhostallero/BiG-DRP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David Earl Hostallero
- Department of Electrical and Computer Engineering, McGill University, Montreal, QC H3A 0E9, Canada
- Mila, Quebec AI Institute, Montreal, QC H2S 3H1, Canada
| | - Yihui Li
- Department of Electrical and Computer Engineering, McGill University, Montreal, QC H3A 0E9, Canada
| | - Amin Emad
- Department of Electrical and Computer Engineering, McGill University, Montreal, QC H3A 0E9, Canada
- Mila, Quebec AI Institute, Montreal, QC H2S 3H1, Canada
- The Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
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Du L, Liu Y, Li C, Deng J, Sang Y. The interaction between ETS transcription factor family members and microRNAs: A novel approach to cancer therapy. Biomed Pharmacother 2022; 150:113069. [PMID: 35658214 DOI: 10.1016/j.biopha.2022.113069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/18/2022] Open
Abstract
In cancer biology, ETS transcription factors promote tumorigenesis by mediating transcriptional regulation of numerous genes via the conserved ETS DNA-binding domain. MicroRNAs (miRNAs) act as posttranscriptional regulators to regulate various tumor-promoting or tumor-suppressing factors. Interactions between ETS factors and miRNAs regulate complex tumor-promoting and tumor-suppressing networks. This review discusses the progress of ETS factors and miRNAs in cancer research in detail. We focused on characterizing the interaction of the miRNA/ETS axis with competing endogenous RNAs (ceRNAs) and its regulation in posttranslational modifications (PTMs) and the tumor microenvironment (TME). Finally, we explore the prospect of ETS factors and miRNAs in therapeutic intervention. Generally, interactions between ETS factors and miRNAs provide fresh perspectives into tumorigenesis and development and novel therapeutic approaches for malignant tumors.
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Affiliation(s)
- Liwei Du
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China
| | - Yuchen Liu
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China; Stomatology College of Nanchang University, Nanchang, China
| | - Chenxi Li
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China
| | - Jinkuang Deng
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China
| | - Yi Sang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China.
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Elucidating the importance and regulation of key enhancers for human MEIS1 expression. Leukemia 2022; 36:1980-1989. [PMID: 35624144 PMCID: PMC9343249 DOI: 10.1038/s41375-022-01602-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 11/20/2022]
Abstract
Myeloid ecotropic virus insertion site 1 (MEIS1) is essential for normal hematopoiesis and is a critical factor in the pathogenesis of a large subset of acute myeloid leukemia (AML). Despite the clinical relevance of MEIS1, its regulation is largely unknown. To understand the transcriptional regulatory mechanisms contributing to human MEIS1 expression, we created a knock-in green florescent protein (GFP) reporter system at the endogenous MEIS1 locus in a human AML cell line. Using this model, we have delineated and dissected a critical enhancer region of the MEIS1 locus for transcription factor (TF) binding through in silico prediction in combination with oligo pull-down, mass-spectrometry and knockout analysis leading to the identification of FLI1, an E-twenty-six (ETS) transcription factor, as an important regulator of MEIS1 transcription. We further show direct binding of FLI1 to the MEIS1 locus in human AML cell lines as well as enrichment of histone acetylation in MEIS1-high healthy and leukemic cells. We also observe a positive correlation between high FLI1 transcript levels and worse overall survival in AML patients. Our study expands the role of ETS factors in AML and our model constitutes a feasible tool for a more detailed understanding of transcriptional regulatory elements and their interactome.
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Fang Z, Zhang N, Yuan X, Xing X, Li X, Qin X, Liu Z, Neo S, Liu C, Kong F, Björkholm M, Fan Y, Xu D. GABPA-activated TGFBR2 transcription inhibits aggressiveness but is epigenetically erased by oncometabolites in renal cell carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:173. [PMID: 35549739 PMCID: PMC9097325 DOI: 10.1186/s13046-022-02382-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/04/2022] [Indexed: 01/20/2023]
Abstract
Background The ETS transcription factor GABPA has long been thought of as an oncogenic factor and recently suggested as a target for cancer therapy due to its critical effect on telomerase activation, but the role of GABPA in clear cell renal cell carcinoma (ccRCC) is unclear. In addition, ccRCC is characterized by metabolic reprograming with aberrant accumulation of L-2-hydroxyglurate (L-2HG), an oncometabolite that has been shown to promote ccRCC development and progression by inducing DNA methylation, however, its downstream effectors remain poorly defined. Methods siRNAs and expression vectors were used to manipulate the expression of GABPA and other factors and to determine cellular/molecular and phenotypic alterations. RNA sequencing and ChIP assays were performed to identify GABPA target genes. A human ccRCC xenograft model in mice was used to evaluate the effect of GABPA overexpression on in vivo tumorigenesis and metastasis. ccRCC cells were incubated with L-2-HG to analyze GABPA expression and methylation. We carried out immunohistochemistry on patient specimens and TCGA dataset analyses to assess the effect of GABPA on ccRCC survival. Results GABPA depletion, although inhibiting telomerase expression, robustly enhanced proliferation, invasion and stemness of ccRCC cells, whereas GABPA overexpression exhibited opposite effects, strongly inhibiting in vivo metastasis and carcinogenesis. TGFBR2 was identified as the GABPA target gene through which GABPA governed the TGFβ signaling to dictate ccRCC phenotypes. GABPA and TGFBR2 phenocopies each other in ccRCC cells. Higher GABPA or TGFBR2 expression predicted longer survival in patients with ccRCC. Incubation of ccRCC cells with L-2-HG mimics GABPA-knockdown-mediated phenotypic alterations. L-2-HG silenced the expression of GABPA in ccRCC cells by increasing its methylation. Conclusions GABPA acts as a tumor suppressor by stimulating TGFBR2 expression and TGFβ signaling, while L-2-HG epigenetically inhibits GABPA expression, disrupting the GABPA-TGFβ loop to drive ccRCC aggressiveness. These results exemplify how oncometabolites erase tumor suppressive function for cancer development/progression. Restoring GABPA expression using DNA methylation inhibitors or other approaches, rather than targeting it, may be a novel strategy for ccRCC therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02382-6.
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Affiliation(s)
- Zhiqing Fang
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China.,Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Ning Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China.
| | - Xiaotian Yuan
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden.,Laboratory Animal Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xiangling Xing
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Xiaofeng Li
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Xin Qin
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Zhengfang Liu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Shiyong Neo
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Cheng Liu
- Department of Urology, the Third Hospital of Peking University, Beijing, People's Republic of China
| | - Feng Kong
- Renal Regeneration Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Magnus Björkholm
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Yidong Fan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China.
| | - Dawei Xu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden.
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80
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Xiao FH, Yu Q, Deng ZL, Yang K, Ye Y, Ge MX, Yan D, Wang HT, Chen XQ, Yang LQ, Yang BY, Lin R, Zhang W, Yang XL, Dong L, He Y, Zhou J, Cai WW, Li J, Kong QP. ETS1 acts as a regulator of human healthy aging via decreasing ribosomal activity. SCIENCE ADVANCES 2022; 8:eabf2017. [PMID: 35476452 PMCID: PMC9045719 DOI: 10.1126/sciadv.abf2017] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/27/2022] [Indexed: 05/25/2023]
Abstract
Adaptation to reduced energy production during aging is a fundamental issue for maintaining healthspan or prolonging life span. Currently, however, the underlying mechanism in long-lived people remains poorly understood. Here, we analyzed transcriptomes of 185 long-lived individuals (LLIs) and 86 spouses of their children from two independent Chinese longevity cohorts and found that the ribosome pathway was significantly down-regulated in LLIs. We found that the down-regulation is likely controlled by ETS1 (ETS proto-oncogene 1), a transcription factor down-regulated in LLIs and positively coexpressed with most ribosomal protein genes (RPGs). Functional assays showed that ETS1 can bind to RPG promoters, while ETS1 knockdown reduces RPG expression and alleviates cellular senescence in human dermal fibroblast (HDF) and embryonic lung fibroblast (IMR-90) cells. As protein synthesis/turnover in ribosomes is an energy-intensive cellular process, the decline in ribosomal biogenesis governed by ETS1 in certain female LLIs may serve as an alternative mechanism to achieve energy-saving and healthy aging.
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Affiliation(s)
- Fu-Hui Xiao
- State Key Laboratory of Genetic Resources and
Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming
Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming Key Laboratory of Healthy Aging Study,
Kunming 650201, China
| | - Qin Yu
- State Key Laboratory of Genetic Resources and
Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming
Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming Key Laboratory of Healthy Aging Study,
Kunming 650201, China
| | - Zhi-Li Deng
- Department of Dermatology/National Clinical Research
Center for Geriatric Disorders, Xiangya Hospital, Central South University,
Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya
Hospital, Central South University, Changsha 410000, China
- Department of Dermatology, Second affiliated Hospital
of Xinjiang Medical University, Urumqi 830000, China
| | - Ke Yang
- Kunming Key Laboratory of Healthy Aging Study,
Kunming 650201, China
- Kunming College of Life Science, University of
Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology,
Kunming 650223, China
| | - Yunshuang Ye
- Kunming Key Laboratory of Healthy Aging Study,
Kunming 650201, China
- Kunming College of Life Science, University of
Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology,
Kunming 650223, China
| | - Ming-Xia Ge
- State Key Laboratory of Genetic Resources and
Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming
Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming Key Laboratory of Healthy Aging Study,
Kunming 650201, China
- Kunming College of Life Science, University of
Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Animal Evolution and
Genetics, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and
Molecular Research in Common Diseases, Kunming 650223, China
| | - Dongjing Yan
- Department of Biochemistry and Molecular Biology,
Hainan Medical College, Haikou 571199, China
| | - Hao-Tian Wang
- State Key Laboratory of Genetic Resources and
Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming
Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming Key Laboratory of Healthy Aging Study,
Kunming 650201, China
- Kunming College of Life Science, University of
Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Animal Evolution and
Genetics, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and
Molecular Research in Common Diseases, Kunming 650223, China
| | - Xiao-Qiong Chen
- State Key Laboratory of Genetic Resources and
Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming
Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and
Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming
Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Bin-Yu Yang
- State Key Laboratory of Genetic Resources and
Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming
Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Rong Lin
- Department of Biology, Hainan Medical College,
Haikou 571199, China
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology,
Hainan Medical College, Haikou 571199, China
| | - Xing-Li Yang
- State Key Laboratory of Genetic Resources and
Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming
Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Lei Dong
- State Key Laboratory of Genetic Resources and
Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming
Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yonghan He
- State Key Laboratory of Genetic Resources and
Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming
Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Jumin Zhou
- Kunming Key Laboratory of Healthy Aging Study,
Kunming 650201, China
- Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology,
Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and
Molecular Research in Common Diseases, Kunming 650223, China
| | - Wang-Wei Cai
- Department of Biochemistry and Molecular Biology,
Hainan Medical College, Haikou 571199, China
| | - Ji Li
- Department of Dermatology/National Clinical Research
Center for Geriatric Disorders, Xiangya Hospital, Central South University,
Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya
Hospital, Central South University, Changsha 410000, China
- Department of Dermatology, Second affiliated Hospital
of Xinjiang Medical University, Urumqi 830000, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and
Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming
Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming Key Laboratory of Healthy Aging Study,
Kunming 650201, China
- CAS Center for Excellence in Animal Evolution and
Genetics, Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and
Molecular Research in Common Diseases, Kunming 650223, China
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81
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Telomerase gene therapy: a remission toward cancer. Med Oncol 2022; 39:105. [DOI: 10.1007/s12032-022-01702-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/02/2022] [Indexed: 12/21/2022]
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82
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Starita N, Pezzuto F, Sarno S, Losito NS, Perdonà S, Buonaguro L, Buonaguro FM, Tornesello ML. Mutations in the telomerase reverse transcriptase promoter and
PIK3CA
gene are common events in penile squamous cell carcinoma of Italian and Ugandan patients. Int J Cancer 2022; 150:1879-1888. [PMID: 35253909 PMCID: PMC9310576 DOI: 10.1002/ijc.33990] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/20/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022]
Abstract
Penile carcinoma develops either through human papillomavirus (HPV) related or unrelated carcinogenic pathways. Genetic alterations and nucleotide changes in coding regions (ie, TP53, CDKN2A, PIK3CA and NOTCH1) are main cancer driver events either in HPV positive or in HPV negative tumours. We investigated the presence of hotspot nucleotide mutations in TERT promoter (TERTp) and PIK3CA exon 9 and their relationship with HPV status in 69 penile cancer cases from Italian and Ugandan patients. Genetic variations and viral sequences have been characterised by end‐point polymerase chain reaction (PCR) and Sanger sequencing. The mutant allele frequencies (MAFs) of TERTp −124A/−146A and PIK3CA E545K have been determined by droplet digital PCR (ddPCR) assays. The results showed that TERTp mutations are highly prevalent in penile carcinoma (53.6%) and significantly more frequent in HPV negative (67.6%) than HPV positive (32.4%) cases (P = .0482). PIK3CA mutations were similarly distributed in virus‐related and unrelated cases (25.9% and 26.7%, respectively) and coexisted with TERTp changes in 15.8% of penile carcinoma samples. Notably, MAFs of co‐occurring mutations were frequently discordant indicating that PIK3CA E545K nucleotide changes are subsequent genetic events occurring in subclones of TERTp mutated cells. The frequencies of TERTp and PIK3CA mutations were higher among Italian compared to Ugandan cases and inversely correlated with the HPV status. In conclusion, TERTp mutations are very common in penile carcinoma and their coexistence with PIK3CA in a substantial number of cases may represent a novel oncogenic synergy relevant for patient stratification and use of therapeutic strategies against new actionable targets.
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Affiliation(s)
- Noemy Starita
- Molecular Biology and Viral Oncology UnitIstituto Nazionale Tumori IRCCS Fondazione G. PascaleNaplesItaly
| | - Francesca Pezzuto
- Molecular Biology and Viral Oncology UnitIstituto Nazionale Tumori IRCCS Fondazione G. PascaleNaplesItaly
| | - Sabrina Sarno
- Department of PathologyIstituto Nazionale Tumori IRCCS Fondazione G. PascaleNaplesItaly
| | - Nunzia Simona Losito
- Department of PathologyIstituto Nazionale Tumori IRCCS Fondazione G. PascaleNaplesItaly
| | - Sisto Perdonà
- Urology UnitIstituto Nazionale Tumori IRCCS Fondazione G. PascaleNaplesItaly
| | - Luigi Buonaguro
- Innovative Immunological ModelsIstituto Nazionale Tumori IRCCS Fondazione G. PascaleNaplesItaly
| | - Franco M. Buonaguro
- Molecular Biology and Viral Oncology UnitIstituto Nazionale Tumori IRCCS Fondazione G. PascaleNaplesItaly
| | - Maria Lina Tornesello
- Molecular Biology and Viral Oncology UnitIstituto Nazionale Tumori IRCCS Fondazione G. PascaleNaplesItaly
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83
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Wang Y, Xue H, Aglave M, Lainé A, Gallopin M, Gautheret D. The contribution of uncharted RNA sequences to tumor identity in lung adenocarcinoma. NAR Cancer 2022; 4:zcac001. [PMID: 35118386 PMCID: PMC8807116 DOI: 10.1093/narcan/zcac001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/18/2021] [Accepted: 01/10/2022] [Indexed: 11/12/2022] Open
Abstract
The identity of cancer cells is defined by the interplay between genetic, epigenetic transcriptional and post-transcriptional variation. A lot of this variation is present in RNA-seq data and can be captured at once using reference-free, k-mer analysis. An important issue with k-mer analysis, however, is the difficulty of distinguishing signal from noise. Here, we use two independent lung adenocarcinoma datasets to identify all reproducible events at the k-mer level, in a tumor versus normal setting. We find reproducible events in many different locations (introns, intergenic, repeats) and forms (spliced, polyadenylated, chimeric etc.). We systematically analyze events that are ignored in conventional transcriptomics and assess their value as biomarkers and for tumor classification, survival prediction, neoantigen prediction and correlation with the immune microenvironment. We find that unannotated lincRNAs, novel splice variants, endogenous HERV, Line1 and Alu repeats and bacterial RNAs each contribute to different, important aspects of tumor identity. We argue that differential RNA-seq analysis of tumor/normal sample collections would benefit from this type k-mer analysis to cast a wider net on important cancer-related events. The code is available at https://github.com/Transipedia/dekupl-lung-cancer-inter-cohort.
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Affiliation(s)
- Yunfeng Wang
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 1 avenue de la Terrasse, 91190, Gif-sur-Yvette, France
- Annoroad Gene Technology Co., Ltd, 100176 Beijing, China
| | - Haoliang Xue
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 1 avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Marine Aglave
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 1 avenue de la Terrasse, 91190, Gif-sur-Yvette, France
- Gustave Roussy, 114 rue Edouard Vaillant, 94800, Villejuif, France
| | - Antoine Lainé
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 1 avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Mélina Gallopin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 1 avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 1 avenue de la Terrasse, 91190, Gif-sur-Yvette, France
- Gustave Roussy, 114 rue Edouard Vaillant, 94800, Villejuif, France
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84
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Neveu B, Richer C, Cassart P, Caron M, Jimenez-Cortes C, St-Onge P, Fuchs C, Garnier N, Gobeil S, Sinnett D. Identification of new ETV6 modulators through a high-throughput functional screening. iScience 2022; 25:103858. [PMID: 35198911 PMCID: PMC8851229 DOI: 10.1016/j.isci.2022.103858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/01/2022] [Accepted: 01/28/2022] [Indexed: 12/02/2022] Open
Abstract
ETV6 transcriptional activity is critical for proper blood cell development in the bone marrow. Despite the accumulating body of evidence linking ETV6 malfunction to hematological malignancies, its regulatory network remains unclear. To uncover genes that modulate ETV6 repressive transcriptional activity, we performed a specifically designed, unbiased genome-wide shRNA screen in pre-B acute lymphoblastic leukemia cells. Following an extensive validation process, we identified 13 shRNAs inducing overexpression of ETV6 transcriptional target genes. We showed that the silencing of AKIRIN1, COMMD9, DYRK4, JUNB, and SRP72 led to an abrogation of ETV6 repressive activity. We identified critical modulators of the ETV6 function which could participate in cellular transformation through the ETV6 transcriptional network. We develop a genome-wide shRNAs screen for ETV6 modulators The screen uncovered 13 novel putative ETV6 modulator genes The modulators demonstrated a broad impact on the ETV6 transcriptional network T-ALL cells results suggest modulators are conserved in other cellular contexts
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Affiliation(s)
- Benjamin Neveu
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Chantal Richer
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Pauline Cassart
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Maxime Caron
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Camille Jimenez-Cortes
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Molecular Biology Program, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Pascal St-Onge
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Claire Fuchs
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Nicolas Garnier
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Stéphane Gobeil
- CHU de Québec-Université Laval Research Center, Quebec City, QC G1V 4G2, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Corresponding author
| | - Daniel Sinnett
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
- Corresponding author
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85
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Lorenzin F, Demichelis F. Past, Current, and Future Strategies to Target ERG Fusion-Positive Prostate Cancer. Cancers (Basel) 2022; 14:cancers14051118. [PMID: 35267426 PMCID: PMC8909394 DOI: 10.3390/cancers14051118] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 12/27/2022] Open
Abstract
Simple Summary In addition to its role in development and in the vascular and hematopoietic systems, ERG plays a central role in prostate cancer. Approximately 40–50% of prostate cancer cases are characterized by ERG gene fusions, which lead to ERG overexpression. Importantly, inhibition of ERG activity in prostate cancer cells decreases their viability. Therefore, inhibiting ERG might represent an important step to improve treatment efficacy for patients with ERG-positive prostate tumors. Here, we summarize the attempts made over the past years to repress ERG activity, the current use of ERG fusion detection and the strategies that might be utilized in the future to treat ERG fusion-positive tumors. Abstract The ETS family member ERG is a transcription factor with physiological roles during development and in the vascular and hematopoietic systems. ERG oncogenic activity characterizes several malignancies, including Ewing’s sarcoma, leukemia and prostate cancer (PCa). In PCa, ERG rearrangements with androgen-regulated genes—mostly TMPRSS2—characterize a large subset of patients across disease progression and result in androgen receptor (AR)-mediated overexpression of ERG in the prostate cells. Importantly, PCa cells overexpressing ERG are dependent on ERG activity for survival, further highlighting its therapeutic potential. Here, we review the current understanding of the role of ERG and its partners in PCa. We discuss the strategies developed in recent years to inhibit ERG activity, the current therapeutic utility of ERG fusion detection in PCa patients, and the possible future approaches to target ERG fusion-positive tumors.
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Affiliation(s)
- Francesca Lorenzin
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy
- Correspondence: (F.L.); (F.D.)
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Correspondence: (F.L.); (F.D.)
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86
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Vervoort SJ, Devlin JR, Kwiatkowski N, Teng M, Gray NS, Johnstone RW. Targeting transcription cycles in cancer. Nat Rev Cancer 2022; 22:5-24. [PMID: 34675395 DOI: 10.1038/s41568-021-00411-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Accurate control of gene expression is essential for normal development and dysregulation of transcription underpins cancer onset and progression. Similar to cell cycle regulation, RNA polymerase II-driven transcription can be considered as a unidirectional multistep cycle, with thousands of unique transcription cycles occurring in concert within each cell. Each transcription cycle comprises recruitment, initiation, pausing, elongation, termination and recycling stages that are tightly controlled by the coordinated action of transcriptional cyclin-dependent kinases and their cognate cyclins as well as the opposing activity of transcriptional phosphatases. Oncogenic dysregulation of transcription can entail defective control of gene expression, either at select loci or more globally, impacting a large proportion of the genome. The resultant dependency on the core-transcriptional machinery is believed to render 'transcriptionally addicted' cancers sensitive to perturbation of transcription. Based on these findings, small molecules targeting transcriptional cyclin-dependent kinases and associated proteins hold promise for the treatment of cancer. Here, we utilize the transcription cycles concept to explain how dysregulation of these finely tuned gene expression processes may drive tumorigenesis and how therapeutically beneficial responses may arise from global or selective transcriptional perturbation. This conceptual framework helps to explain tumour-selective transcriptional dependencies and facilitates the rational design of combination therapies.
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Affiliation(s)
- Stephin J Vervoort
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jennifer R Devlin
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas Kwiatkowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mingxing Teng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, CHEM-H and SCI, Stanford Medical School, Stanford University, Stanford, CA, USA.
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
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87
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TERT Promoter Mutations Increase Sense and Antisense Transcription from the TERT Promoter. Biomedicines 2021; 9:biomedicines9121773. [PMID: 34944589 PMCID: PMC8698883 DOI: 10.3390/biomedicines9121773] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/21/2022] Open
Abstract
Background: Chief among mechanisms of telomerase reverse transcriptase (TERT) reactivation is the appearance of mutations in the TERT promoter. The two main TERT promoter mutations are C>T transitions located −146C>T and −124C>T upstream from the translational start site. They generate a novel Ets/TCF binding site. Both mutations are mutually exclusive and −124C>T is strikingly overrepresented in most cancers. We investigated whether this mutational bias and mutual exclusion could be due to transcriptional constraints. Methods: We compared sense and antisense transcription of a panel of TERT promoter-luciferase vectors harboring the −124C>T and -146C>T mutations alone or together. lncRNA TAPAS levels were measured by RT-PCR. Results: Both mutations generally increased TERT transcription by 2–4-fold regardless of upstream and downstream regulatory elements. The double mutant increased transcription in an additive fashion, arguing against a direct transcriptional constraint. The −146C>T mutation, alone or in combination with −124C>T, also unleashed antisense transcription. In line with this finding, lncRNA TAPAS was higher in cells with mutated TERT promoter (T98G and U87) than in cells with wild-type promoter, suggesting that lncRNA TAPAS may balance the effect of TERT promoter mutations. Conclusions: −146C>T and −124C>T TERT promoter mutations increase TERT sense and antisense transcription, and the double mutant features higher transcription levels. Increased antisense transcription may contain TERT expression within sustainable levels.
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88
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Di M, Zhang Y, Zeng R, Liu X, Chen W, Zhang M, Zhang C, Li M, Zhang M. The pro-angiogenesis effect of miR33a-5p/Ets-1/DKK1 signaling in ox-LDL induced HUVECs. Int J Biol Sci 2021; 17:4122-4139. [PMID: 34803487 PMCID: PMC8579465 DOI: 10.7150/ijbs.60302] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/21/2021] [Indexed: 12/22/2022] Open
Abstract
Objective: Angiogenesis is involved in multiple biological processes, including atherosclerosis (AS) and cancer. Dickkopf1 (DKK1) plays many roles in both tumors and AS and has emerged as a potential biomarker of cancer progression and prognosis. Targeting DKK1 is a good choice for oncological treatments. Many anticancer therapies are associated with specific cardiovascular toxicity. However, the effects of DKK1 neutralizing therapy on AS are unclear. We focused on how DKK1 affected angiogenesis in AS and ox-LDL-induced human umbilical vein endothelial cells (HUVECs). Methods: ApoE-/- mice were fed a high-fat diet and then injected with DKK1i or DKK1 lentivirus to study the effects of DKK1. In vitro, promoter assays, protein analysis, database mining, dual-luciferase reporter assay (DLR), electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP), and coimmunoprecipitation (co-IP) were used to study the mechanism of DKK1 biogenesis. Cell migration and angiogenesis assays were performed to investigate the function and regulatory mechanisms of DKK1. Results: DKK1 participated in angiogenesis both in the plaques of ApoE-/- mice by knockdown or overexpression of DKK1 and ox-LDL-induced HUVECs. DKK1 induced angiogenesis (increasing migration and capillary formation, inducing expression of VEGFR-2/VEGF-A/MMP) via the CKAP4/PI3K pathway, independent of Wnt/β-catenin. ox-LDL increased the expression and nuclear transfer of Ets-1 and c-jun, and induced the transcriptional activity of DKK1 in HUVECs. Ets-1, along with c-jun and CBP, could bind to the promoter of DKK1 and enhance DKK1 transcription. MiR33a-5p was downregulated in ox-LDL induced HUVECs and aortic artery of high-fat diet ApoE-/- mice. Ets-1 was a direct target of miR33a-5p. MiR33a-5p/Ets-1/ DKK1 axis contributed to angiogenesis. Conclusions: MiR33a-5p/Ets-1/DKK1 signaling participated in ox-LDL-induced angiogenesis of HUVECs via the CKAP4/PI3K pathway. These new findings provide a rationale and notable method for tumor therapy and cardiovascular protection.
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Affiliation(s)
- Mingxue Di
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China.,Department of Gerontology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital
| | - Yu Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Renya Zeng
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Xiaolin Liu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Weijia Chen
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Meng Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Cheng Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Mengmeng Li
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Mei Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
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89
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Lee JS, Choi YE, Kim S, Han JY, Goh SH. ELF3 Is a Target That Promotes Therapeutic Efficiency in EGFR Tyrosine Kinase Inhibitor-Resistant Non-Small Cell Lung Cancer Cells via Inhibiting PKCί. Int J Mol Sci 2021; 22:ijms222212287. [PMID: 34830169 PMCID: PMC8620479 DOI: 10.3390/ijms222212287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Mutations in epidermal growth factor receptor (EGFR) proteins account for many non-small cell lung cancers (NSCLCs), and EGFR tyrosine kinase inhibitors (TKIs) are being used as targeted therapeutics. However, resistance to TKIs continues to increase owing to additional mutations in more than half of the patients receiving EGFR TKI therapy. In addition to targeting new mutations with next-generation therapeutics, it is necessary to find an alternative target to overcome the challenges associated with resistance. (2) Methods: To identify potential alternative targets in patients with NSCLC undergoing targeted therapy, putative targets were identified by transcriptome profiling and validated for their biological and therapeutic effects in vitro and in vivo. (3) Results: ELF3 was found to be differentially expressed in NSCLC, and ELF3 knockdown significantly increased cell death in K-Ras mutant as well as in EGFR L858R/T790M mutation harboring lung cancer cells. We also found that auranofin, an inhibitor of protein kinase C iota (PKCί), a protein upstream of ELF3, effectively induced cell death. (4) Conclusions: Our study suggests that blocking ELF3 is an effective way to induce cell death in NSCLC with K-Ras and EGFR T790M/L858R mutations and thus advocates the use of auranofin as an effective alternative drug to overcome EGFR TKI resistance.
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Affiliation(s)
- Jeon-Soo Lee
- Division of Cancer Biology, Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang 10408, Korea; (J.-S.L.); (Y.E.C.)
| | - Young Eun Choi
- Division of Cancer Biology, Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang 10408, Korea; (J.-S.L.); (Y.E.C.)
| | - Sunshin Kim
- Division of Rare and Refractory Cancer, Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang 10408, Korea; (S.K.); (J.-Y.H.)
| | - Ji-Youn Han
- Division of Rare and Refractory Cancer, Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang 10408, Korea; (S.K.); (J.-Y.H.)
| | - Sung-Ho Goh
- Division of Cancer Biology, Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang 10408, Korea; (J.-S.L.); (Y.E.C.)
- Correspondence: ; Tel.: +82-31-920-2477
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90
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Abstract
Undifferentiated small round cell sarcomas represent a heterogeneous group of mesenchymal neoplasms. While imprecise, this term nevertheless provides a useful framework for conceptualizing these tumors. This article highlights current trends in their classification based on morphology, immunohistochemistry, and advanced molecular techniques. As next-generation sequencing becomes commonplace in diagnostic laboratories pathologists can expect to differentiate these tumors with increasing confidence, and actively contribute to related discoveries. Ultimately, when synthesized with rigorous clinical outcome data and other investigative techniques, a more robust landscape for the molecular diagnosis and classification of undifferentiated small round cell sarcomas is expected to emerge in the future.
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91
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Hunter MV, Moncada R, Weiss JM, Yanai I, White RM. Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface. Nat Commun 2021; 12:6278. [PMID: 34725363 PMCID: PMC8560802 DOI: 10.1038/s41467-021-26614-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 10/06/2021] [Indexed: 12/24/2022] Open
Abstract
During tumor progression, cancer cells come into contact with various non-tumor cell types, but it is unclear how tumors adapt to these new environments. Here, we integrate spatially resolved transcriptomics, single-cell RNA-seq, and single-nucleus RNA-seq to characterize tumor-microenvironment interactions at the tumor boundary. Using a zebrafish model of melanoma, we identify a distinct "interface" cell state where the tumor contacts neighboring tissues. This interface is composed of specialized tumor and microenvironment cells that upregulate a common set of cilia genes, and cilia proteins are enriched only where the tumor contacts the microenvironment. Cilia gene expression is regulated by ETS-family transcription factors, which normally act to suppress cilia genes outside of the interface. A cilia-enriched interface is conserved in human patient samples, suggesting it is a conserved feature of human melanoma. Our results demonstrate the power of spatially resolved transcriptomics in uncovering mechanisms that allow tumors to adapt to new environments.
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Affiliation(s)
- Miranda V Hunter
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Reuben Moncada
- Institute for Computational Medicine, NYU Langone Health, New York, NY, USA
| | - Joshua M Weiss
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Itai Yanai
- Institute for Computational Medicine, NYU Langone Health, New York, NY, USA.
| | - Richard M White
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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92
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Finesso GE, McDevitt RA, Roy R, Brinster LR, Di Francesco A, Meade T, de Cabo R, Ferrucci L, Perdue KA. Impact of large granular lymphocyte leukemia on blood DNA methylation and epigenetic clock modeling in Fischer 344 rats. J Gerontol A Biol Sci Med Sci 2021; 77:956-963. [PMID: 34718551 DOI: 10.1093/gerona/glab328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Indexed: 11/14/2022] Open
Abstract
Age-dependent differences in methylation at specific cytosine-guanosine sites (CpGs) have been used in "epigenetic clock" formulas to predict age. Deviations of epigenetic age from chronological age are informative of health status and are associated with adverse health outcomes, including mortality. In most cases, epigenetic clocks are performed on methylation from DNA extracted from circulating blood cells. However, the effect of neoplastic cells in the circulation on estimation and interpretation of epigenetic clocks is not well understood. Here, we explored this using Fischer 344 (F344) rats, a strain that often develops large granular lymphocyte leukemia (LGL). We found clear histological markers of LGL pathology in the spleens and livers of 27 out of 61 rats aged 17-27 months. We assessed DNA methylation by reduced representation bisulfite sequencing with coverage of 3 million cytosine residues. Although LGL broadly increased DNA methylation variability, it did not change epigenetic aging. Despite this, inclusion of rats with LGL in clock training sets significantly altered predictor selection probability at 83 of 121 commonly utilized CpGs. Furthermore, models trained on rat samples that included individuals with LGL had greater absolute age error than those trained exclusively on LGL-free rats (39% increase; p<0.0001). We conclude that the epigenetic signals for aging and LGL are distinct, such that LGL assessment is not necessary for valid measures of epigenetic age in F344 rats. The precision and architecture of constructed epigenetic clock formulas, however, can be influenced by the presence of neoplastic hematopoietic cells in training set populations.
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Affiliation(s)
- Giovanni E Finesso
- Comparative Medicine Section, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Ross A McDevitt
- Comparative Medicine Section, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Roshni Roy
- Laboratory of Molecular Biology and Immunology, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Lauren R Brinster
- Office of Research Services, Division of Veterinary Resources, National Institutes of Health, Bethesda, MD
| | - Andrea Di Francesco
- Translational Gerontology Branch, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD.,Calico Life Sciences, South San Francisco, CA
| | - Theresa Meade
- Comparative Medicine Section, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Kathy A Perdue
- Comparative Medicine Section, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
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93
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Hawley JR, Zhou S, Arlidge C, Grillo G, Kron KJ, Hugh-White R, van der Kwast TH, Fraser M, Boutros PC, Bristow RG, Lupien M. Reorganization of the 3D genome pinpoints non-coding drivers of primary prostate tumors. Cancer Res 2021; 81:5833-5848. [PMID: 34642184 DOI: 10.1158/0008-5472.can-21-2056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/13/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022]
Abstract
Prostate cancer is a heterogeneous disease whose progression is linked to genome instability. However, the impact of this instability on the non-coding genome and its three-dimensional organization to aid progression is unclear. Using primary benign and tumor tissue, we find a high concordance in higher order three-dimensional genome organization. This concordance argues for constraints to the topology of prostate tumor genomes. Nonetheless, we identified changes in focal chromatin interactions, typical of loops bridging non-coding cis-regulatory elements, and showed how structural variants can induce these changes to guide cis-regulatory element hijacking. Such events resulted in opposing differential expression of genes found at antipodes of rearrangements. Collectively, these results argue that changes to focal chromatin interactions, as opposed to higher order genome organization, allow for aberrant gene regulation and are repeatedly mediated by structural variants in primary prostate cancer.
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Affiliation(s)
- James R Hawley
- Medical Biophysics, University of Toronto, Princess Margaret Cancer Center-University Health Network, Ontario Institute for Cancer Research
| | - Stanley Zhou
- Medical Biophysics, University of Toronto, Princess Margaret Cancer Center-University Health Network, Ontario Institute for Cancer Research
| | | | - Giacomo Grillo
- Medical Biophysics, University of Toronto, Princess Margaret Cancer Center-University Health Network, Ontario Institute for Cancer Research
| | | | | | | | | | | | | | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network
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94
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Oliveira TT, Fontes-Dantas FL, de Medeiros Oliveira RK, Pinheiro DML, Coutinho LG, da Silva VL, de Souza SJ, Agnez-Lima LF. Chemical Inhibition of Apurinic-Apyrimidinic Endonuclease 1 Redox and DNA Repair Functions Affects the Inflammatory Response via Different but Overlapping Mechanisms. Front Cell Dev Biol 2021; 9:731588. [PMID: 34616737 PMCID: PMC8488223 DOI: 10.3389/fcell.2021.731588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/27/2021] [Indexed: 01/21/2023] Open
Abstract
The presence of oxidized DNA lesions, such as 7,8-dihydro-8-oxoguanine (8-oxoG) and apurinic/apyrimidinic sites (AP sites), has been described as epigenetic signals that are involved in gene expression control. In mammals, Apurinic-apyrimidinic endonuclease 1/Redox factor-1 (APE1/Ref-1) is the main AP endonuclease of the base excision repair (BER) pathway and is involved in active demethylation processes. In addition, APE1/Ref-1, through its redox function, regulates several transcriptional factors. However, the transcriptional control targets of each APE1 function are not completely known. In this study, a transcriptomic approach was used to investigate the effects of chemical inhibition of APE1/Ref-1 redox or DNA repair functions by E3330 or methoxyamine (MX) in an inflammatory cellular model. Under lipopolysaccharide (LPS) stimulation, both E3330 and MX reduced the expression of some cytokines and chemokines. Interestingly, E3330 treatment reduced cell viability after 48 h of the treatment. Genes related to inflammatory response and mitochondrial processes were downregulated in both treatments. In the E3330 treatment, RNA processing and ribosome biogenesis genes were downregulated, while they were upregulated in the MX treatment. Furthermore, in the E3330 treatment, the cellular stress response was the main upregulated process, while the cellular macromolecule metabolic process was observed in MX-upregulated genes. Nuclear respiratory factor 1 (NRF1) was predicted to be a master regulator of the downregulated genes in both treatments, while the ETS transcription factor ELK1 (ELK1) was predicted to be a master regulator only for E3330 treatment. Decreased expression of ELK1 and its target genes and a reduced 28S/18S ratio were observed, suggesting impaired rRNA processing. In addition, both redox and repair functions can affect the expression of NRF1 and GABPA target genes. The master regulators predicted for upregulated genes were YY1 and FLI1 for the E3330 and MX treatments, respectively. In summary, the chemical inhibition of APE1/Ref-1 affects gene expression regulated mainly by transcriptional factors of the ETS family, showing partial overlap of APE1 redox and DNA repair functions, suggesting that these activities are not entirely independent. This work provides a new perspective on the interaction between APE1 redox and DNA repair activity in inflammatory response modulation and transcription.
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Affiliation(s)
- Thais Teixeira Oliveira
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | - Fabrícia Lima Fontes-Dantas
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | | | | | - Leonam Gomes Coutinho
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil.,Instituto Federal de Educação Tecnológica do Rio Grande do Norte, IFRN, São Paulo do Potengi, Brazil
| | - Vandeclecio Lira da Silva
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), IMD, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Sandro José de Souza
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), IMD, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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95
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Jiang W, Xu Y, Chen X, Pan S, Zhu X. E26 transformation-specific variant 4 as a tumor promotor in human cancers through specific molecular mechanisms. Mol Ther Oncolytics 2021; 22:518-527. [PMID: 34553037 PMCID: PMC8433062 DOI: 10.1016/j.omto.2021.07.012] [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] [Indexed: 01/16/2023] Open
Abstract
E26 transformation-specific (ETS) variant 4 (ETV4) is an important transcription factor that belongs to the ETS transcription factor family and is essential for much cellular physiology. Recent evidence has revealed that ETV4 is aberrantly expressed in many types of tumors, and its overexpression is related to poor prognosis of cancer patients. Additionally, increasing studies have identified that ETV4 promotes cancer growth, invasion, metastasis, and drug resistance. Mechanistically, the level of ETV4 is regulated by some post-translation modulations in a broad spectrum of cancers. However, little progress has been made to comprehensively summarize the critical roles of ETV4 in different human cancers. Hence, this review mainly focuses on the physiological functions of ETV4 in various human tumors. In addition, the molecular mechanisms of ETV4-mediated cancer progression were elucidated, including how ETV4 modulates its downstream signaling pathways and how ETV4 is regulated by some factors. On this basis, the present review may provide a valuable therapeutics strategy for future cancer treatment by targeting ETV4-related pathways.
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Affiliation(s)
- Wenxiao Jiang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Yichi Xu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Xin Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Shuya Pan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
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96
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Planterose Jiménez B, Kayser M, Vidaki A. Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implications. Genome Biol 2021; 22:274. [PMID: 34548083 PMCID: PMC8454075 DOI: 10.1186/s13059-021-02484-y] [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: 04/29/2021] [Accepted: 09/01/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Illumina DNA methylation microarrays enable epigenome-wide analysis vastly used for the discovery of novel DNA methylation variation in health and disease. However, the microarrays' probe design cannot fully consider the vast human genetic diversity, leading to genetic artifacts. Distinguishing genuine from artifactual genetic influence is of particular relevance in the study of DNA methylation heritability and methylation quantitative trait loci. But despite its importance, current strategies to account for genetic artifacts are lagging due to a limited mechanistic understanding on how such artifacts operate. RESULTS To address this, we develop and benchmark UMtools, an R-package containing novel methods for the quantification and qualification of genetic artifacts based on fluorescence intensity signals. With our approach, we model and validate known SNPs/indels on a genetically controlled dataset of monozygotic twins, and we estimate minor allele frequency from DNA methylation data and empirically detect variants not included in dbSNP. Moreover, we identify examples where genetic artifacts interact with each other or with imprinting, X-inactivation, or tissue-specific regulation. Finally, we propose a novel strategy based on co-methylation that can discern between genetic artifacts and genuine genomic influence. CONCLUSIONS We provide an atlas to navigate through the huge diversity of genetic artifacts encountered on DNA methylation microarrays. Overall, our study sets the ground for a paradigm shift in the study of the genetic component of epigenetic variation in DNA methylation microarrays.
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Affiliation(s)
- Benjamin Planterose Jiménez
- Erasmus MC, University Medical Center Rotterdam, Department of Genetic Identification, Rotterdam, the Netherlands
| | - Manfred Kayser
- Erasmus MC, University Medical Center Rotterdam, Department of Genetic Identification, Rotterdam, the Netherlands
| | - Athina Vidaki
- Erasmus MC, University Medical Center Rotterdam, Department of Genetic Identification, Rotterdam, the Netherlands
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97
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Zhao X, Li L, Yuan S, Zhang Q, Jiang X, Luo T. SPIB acts as a tumor suppressor by activating the NFkB and JNK signaling pathways through MAP4K1 in colorectal cancer cells. Cell Signal 2021; 88:110148. [PMID: 34530056 DOI: 10.1016/j.cellsig.2021.110148] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 01/03/2023]
Abstract
Spi-B transcription factor (SPIB) is a member of the E-twenty-six (ETS) transcription factor family. Previous studies have shown that the expression of SPIB is downregulated in human colorectal cancer tissues. The purpose of our study was to explore the biological function and related mechanism of SPIB in colorectal cancer cells. Our study found that SPIB could inhibit the proliferation, migration and invasion of CRC cells; inhibit angiogenesis; and induce CRC cells cycle arrest in G2/M phase and promote the apoptosis of CRC cells. We also found that compared with the control group, the 50% inhibitory concentration (IC50) values of oxaliplatin and 5-FU in the SPIB overexpression group were significantly reduced. Western blot results showed that the overexpression of SPIB upregulated cleaved-PARP(c-PARP), nuclear factor kB p65 (NFkB p65), phospho-NFkB p65 (p-NFkB P65), JNK1, and C-Jun protein expression levels compared with the control group. The silence of SPIB downregulated c-PARP, NFκB p65, p-NFκB p65, JNK1, and C-Jun protein expression levels. A dual-luciferase reporter assay showed that SPIB could activate the promoter of MAP4K1 and enhance the expression of MAP4K1. After silencing MAP4K1, the protein expression levels of c-PARP, NFkB P65, p-NFkB P65, JNK1, and C-Jun were downregulated. In summary, we found that SPIB is a tumor suppressor in colorectal cancer cells and that SPIB sensitizes colorectal cancer cells to oxaliplatin and 5-FU, SPIB exerts its anti-colorectal cancer effect by activating the NFkB and JNK signaling pathways through MAP4K1. The above findings may provide a reference for new molecular markers and therapeutic targets for CRC.
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Affiliation(s)
- Xunping Zhao
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Lin Li
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Shiyun Yuan
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Qia Zhang
- Department of Medical Oncology, Yongchuan Hospital of Chongqing Medical University, Chongqing 404000, People's Republic of China
| | - Xianyao Jiang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Tao Luo
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.
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98
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Boone MA, Taslim C, Crow JC, Selich-Anderson J, Watson M, Heppner P, Hamill J, Wood AC, Lessnick SL, Winstanley M. Identification of a Novel FUS/ETV4 Fusion and Comparative Analysis with Other Ewing Sarcoma Fusion Proteins. Mol Cancer Res 2021; 19:1795-1801. [PMID: 34465585 DOI: 10.1158/1541-7786.mcr-21-0354] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/20/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022]
Abstract
Ewing sarcoma is a pediatric bone cancer defined by a chromosomal translocation fusing one of the FET family members to an ETS transcription factor. There have been seven reported chromosomal translocations, with the most recent reported over a decade ago. We now report a novel FET/ETS translocation involving FUS and ETV4 detected in a patient with Ewing sarcoma. Here, we characterized FUS/ETV4 by performing genomic localization and transcriptional regulatory studies on numerous FET/ETS fusions in a Ewing sarcoma cellular model. Through this comparative analysis, we demonstrate significant similarities across these fusions, and in doing so, validate FUS/ETV4 as a bona fide Ewing sarcoma translocation. This study presents the first genomic comparison of Ewing sarcoma-associated translocations and reveals that the FET/ETS fusions share highly similar, but not identical, genomic localization and transcriptional regulation patterns. These data strengthen the notion that FET/ETS fusions are key drivers of, and thus pathognomonic for, Ewing sarcoma. IMPLICATIONS: Identification and initial characterization of the novel Ewing sarcoma fusion, FUS/ETV4, expands the family of Ewing fusions and extends the diagnostic possibilities for this aggressive tumor of adolescents and young adults.
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Affiliation(s)
- Megann A Boone
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, Ohio
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Jesse C Crow
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Julia Selich-Anderson
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Mike Watson
- LabPLUS, Auckland City Hospital, Grafton, Auckland, New Zealand
| | - Peter Heppner
- Starship Children's Hospital, Grafton, Auckland, New Zealand
| | - James Hamill
- Starship Children's Hospital, Grafton, Auckland, New Zealand
| | - Andrew C Wood
- Starship Children's Hospital, Grafton, Auckland, New Zealand
- University of Auckland, Private Bag, Auckland, New Zealand
| | - Stephen L Lessnick
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, Ohio.
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Mark Winstanley
- Starship Children's Hospital, Grafton, Auckland, New Zealand
- University of Auckland, Private Bag, Auckland, New Zealand
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99
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Liu Y, Wang S, Zhou R, Li W, Zhang G. Overexpression of E74-like transformation-specific transcription factor 3 promotes cellular proliferation and predicts poor prognosis in ovarian cancer. Oncol Lett 2021; 22:710. [PMID: 34457065 PMCID: PMC8358619 DOI: 10.3892/ol.2021.12971] [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: 01/03/2021] [Accepted: 07/12/2021] [Indexed: 01/24/2023] Open
Abstract
E74-like E26 transformation-specific (ETS) transcription factor 3 (ELF3), is a member of the ETS transcription factor family, and has been characterized as an epithelial cell-specific transcription factor. The role of ELF3 in tumor progression remains to be elucidated. Previous studies have indicated that loss of ELF3 mRNA and protein expression was associated with poor outcomes in ovarian cancer (OC). By contrast, the present study demonstrated that ELF3 was upregulated in OC, using data from The Cancer Genome Atlas, and elevated expression levels of ELF3 were associated with a poor prognosis. ELF3 promoted OC cell proliferation in vitro and in vivo. The present study revealed that ELF3 inhibited apoptosis and reduced the cisplatin sensitivity of OC cells. Furthermore, the mTOR pathway was found to be activated by ELF3. Collectively, the results of the present study indicated the role of ELF3 in the development and pathogenesis of OC.
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Affiliation(s)
- Yao Liu
- Department of Gynecology and Obstetrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Shourong Wang
- Department of Gynecology and Obstetrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Ruiqi Zhou
- Department of Gynecology and Obstetrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Wenxue Li
- Department of Gynecology and Obstetrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Guiyu Zhang
- Department of Gynecology and Obstetrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
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100
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Simeonov KP, Byrns CN, Clark ML, Norgard RJ, Martin B, Stanger BZ, Shendure J, McKenna A, Lengner CJ. Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states. Cancer Cell 2021; 39:1150-1162.e9. [PMID: 34115987 PMCID: PMC8782207 DOI: 10.1016/j.ccell.2021.05.005] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 04/01/2021] [Accepted: 05/13/2021] [Indexed: 12/20/2022]
Abstract
The underpinnings of cancer metastasis remain poorly understood, in part due to a lack of tools for probing their emergence at high resolution. Here we present macsGESTALT, an inducible CRISPR-Cas9-based lineage recorder with highly efficient single-cell capture of both transcriptional and phylogenetic information. Applying macsGESTALT to a mouse model of metastatic pancreatic cancer, we recover ∼380,000 CRISPR target sites and reconstruct dissemination of ∼28,000 single cells across multiple metastatic sites. We find that cells occupy a continuum of epithelial-to-mesenchymal transition (EMT) states. Metastatic potential peaks in rare, late-hybrid EMT states, which are aggressively selected from a predominately epithelial ancestral pool. The gene signatures of these late-hybrid EMT states are predictive of reduced survival in both human pancreatic and lung cancer patients, highlighting their relevance to clinical disease progression. Finally, we observe evidence for in vivo propagation of S100 family gene expression across clonally distinct metastatic subpopulations.
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Affiliation(s)
- Kamen P Simeonov
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - China N Byrns
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Megan L Clark
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert J Norgard
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Ben Z Stanger
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell & Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Aaron McKenna
- Department of Molecular & Systems Biology, Dartmouth Geisel School of Medicine, Lebanon, NH, USA.
| | - Christopher J Lengner
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell & Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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