51
|
Harada T, Kalfon J, Perez MW, Eagle K, Braes FD, Batley R, Heshmati Y, Ferrucio JX, Ewers J, Mehta S, Kossenkov A, Ellegast JM, Bowker A, Wickramasinghe J, Nabet B, Paralkar VR, Dharia NV, Stegmaier K, Orkin SH, Pimkin M. Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532438. [PMID: 36993171 PMCID: PMC10054969 DOI: 10.1101/2023.03.13.532438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Lineage-defining transcription factors form densely interconnected circuits in chromatin occupancy assays, but the functional significance of these networks remains underexplored. We reconstructed the functional topology of a leukemia cell transcription network from the direct gene-regulatory programs of eight core transcriptional regulators established in pre-steady state assays coupling targeted protein degradation with nascent transcriptomics. The core regulators displayed narrow, largely non-overlapping direct transcriptional programs, forming a sparsely interconnected functional hierarchy stabilized by incoherent feed-forward loops. BET bromodomain and CDK7 inhibitors disrupted the core regulators' direct programs, acting as mixed agonists/antagonists. The network is predictive of dynamic gene expression behaviors in time-resolved assays and clinically relevant pathway activity in patient populations.
Collapse
Affiliation(s)
- Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Jérémie Kalfon
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Monika W. Perez
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Kenneth Eagle
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Ken Eagle Consulting, Houston, TX, 77494, USA
| | - Flora Dievenich Braes
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Rashad Batley
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Yaser Heshmati
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Juliana Xavier Ferrucio
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Jazmin Ewers
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Stuti Mehta
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | | | - Jana M. Ellegast
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Allyson Bowker
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | | | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Vikram R. Paralkar
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Neekesh V. Dharia
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Kimberly Stegmaier
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Stuart H. Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| |
Collapse
|
52
|
Selvaraj C, Ramalingam KR, Velmurugan D, Singh SK. Transcriptional regulatory mechanisms and signaling networks in cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 134:1-20. [PMID: 36858731 DOI: 10.1016/bs.apcsb.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cancer is a general term that refers to a wide range of illnesses that are characterized by the development of aberrant cells that have the capacity to divide uncontrollably, invade, and harm healthy tissue. It is caused by both genetic and epigenetic changes that suppress abnormal proliferation and prevent cells from surviving outside of their normal niches. Complex protein networks are responsible for the development of a suitable environment via multiple cells signaling pathways. The study of these pathways is essential for analysing network context and developing novel cancer therapies. Transcription factors (TFs) are actively involved in gene expression and maintain the combinatorial on-and-off states of the gene. In addition, the TFs regulate cell identity and state; these TFs cooperate to establish cell-type-specific gene expression. In this chapter, we describe the number of transcription factors and their role in the progression of cancer. The knowledge of transcriptional factors and their network is crucial for emphasizing the specific transcriptional addiction and for designing new anticancer therapies.
Collapse
Affiliation(s)
- Chandrabose Selvaraj
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, India.
| | - Karthik Raja Ramalingam
- Department of Biotechnology, Division of Research and Innovation, Saveetha School of Engineering, SIMATS, Chennai, Tamil Nadu, India
| | - Devadasan Velmurugan
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| |
Collapse
|
53
|
Di Benedetto C, Khan T, Serrano-Saenz S, Rodriguez-Lemus A, Klomsiri C, Beutel TM, Thach A, Walczak H, Betancur P. Enhancer Clusters Drive Type I Interferon-Induced TRAIL Overexpression in Cancer, and Its Intracellular Protein Accumulation Fails to Induce Apoptosis. Cancers (Basel) 2023; 15:967. [PMID: 36765925 PMCID: PMC9913803 DOI: 10.3390/cancers15030967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/14/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a cytokine produced and secreted by immune cells in response to an infection, often in response to interferon (IFN) stimulation. In cancer, it has also been shown that IFN stimulates the production of TRAIL, and it has been proposed that this TRAIL can induce apoptosis in an autocrine or paracrine manner in different cancer cells. Yet, the mechanism mediating TRAIL upregulation and the implications of TRAIL as an apoptotic molecule in cancer cells are still poorly understood. We show here that in certain cancer cells, TRAIL is upregulated by enhancer clusters, potent genomic regulatory regions containing densely packed enhancers that have combinatorial and additive activity and that are usually found to be associated with cancer-promoting genes. Moreover, we found that TRAIL upregulation by IFNα is mediated by these enhancer clusters in breast and lung cancer cells. Surprisingly, IFNα stimulation leads to the intracellular accumulation of TRAIL protein in these cancer cells. Consequently, this TRAIL is not capable of inducing apoptosis. Our study provides novel insights into the mechanism behind the interferon-mediated upregulation of TRAIL and its protein accumulation in cancer cells. Further investigation is required to understand the role of intracellular TRAIL or depict the mechanisms mediating its apoptosis impairment in cancer cells.
Collapse
Affiliation(s)
- Carolina Di Benedetto
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Taimoor Khan
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Santiago Serrano-Saenz
- CECAD Cluster of Excellence, University of Cologne, 50931 Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Anthony Rodriguez-Lemus
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Chananat Klomsiri
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Tim-Mathis Beutel
- CECAD Cluster of Excellence, University of Cologne, 50931 Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Alysia Thach
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Henning Walczak
- CECAD Cluster of Excellence, University of Cologne, 50931 Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Paola Betancur
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| |
Collapse
|
54
|
Lu DY, Ellegast JM, Ross KN, Malone CF, Lin S, Mabe NW, Dharia NV, Meyer A, Conway A, Su AH, Selich-Anderson J, Taslim C, Byrum AK, Seong BKA, Adane B, Gray NS, Rivera MN, Lessnick SL, Stegmaier K. The ETS transcription factor ETV6 constrains the transcriptional activity of EWS-FLI to promote Ewing sarcoma. Nat Cell Biol 2023; 25:285-297. [PMID: 36658220 PMCID: PMC9928584 DOI: 10.1038/s41556-022-01059-8] [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: 11/14/2021] [Accepted: 11/24/2022] [Indexed: 01/21/2023]
Abstract
Transcription factors (TFs) are frequently mutated in cancer. Paediatric cancers exhibit few mutations genome-wide but frequently harbour sentinel mutations that affect TFs, which provides a context to precisely study the transcriptional circuits that support mutant TF-driven oncogenesis. A broadly relevant mechanism that has garnered intense focus involves the ability of mutant TFs to hijack wild-type lineage-specific TFs in self-reinforcing transcriptional circuits. However, it is not known whether this specific type of circuitry is equally crucial in all mutant TF-driven cancers. Here we describe an alternative yet central transcriptional mechanism that promotes Ewing sarcoma, wherein constraint, rather than reinforcement, of the activity of the fusion TF EWS-FLI supports cancer growth. We discover that ETV6 is a crucial TF dependency that is specific to this disease because it, counter-intuitively, represses the transcriptional output of EWS-FLI. This work discovers a previously undescribed transcriptional mechanism that promotes cancer.
Collapse
Affiliation(s)
- Diana Y Lu
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jana M Ellegast
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenneth N Ross
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shan Lin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathaniel W Mabe
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashleigh Meyer
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy Conway
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Angela H Su
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Selich-Anderson
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Andrea K Byrum
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Bo Kyung A Seong
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Biniam Adane
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Miguel N Rivera
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Division of Pediatric Hematology, Oncology and BMT, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
55
|
Zhuang HH, Qu Q, Teng XQ, Dai YH, Qu J. Superenhancers as master gene regulators and novel therapeutic targets in brain tumors. Exp Mol Med 2023; 55:290-303. [PMID: 36720920 PMCID: PMC9981748 DOI: 10.1038/s12276-023-00934-0] [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: 07/24/2022] [Revised: 11/27/2022] [Accepted: 12/04/2022] [Indexed: 02/02/2023] Open
Abstract
Transcriptional deregulation, a cancer cell hallmark, is driven by epigenetic abnormalities in the majority of brain tumors, including adult glioblastoma and pediatric brain tumors. Epigenetic abnormalities can activate epigenetic regulatory elements to regulate the expression of oncogenes. Superenhancers (SEs), identified as novel epigenetic regulatory elements, are clusters of enhancers with cell-type specificity that can drive the aberrant transcription of oncogenes and promote tumor initiation and progression. As gene regulators, SEs are involved in tumorigenesis in a variety of tumors, including brain tumors. SEs are susceptible to inhibition by their key components, such as bromodomain protein 4 and cyclin-dependent kinase 7, providing new opportunities for antitumor therapy. In this review, we summarized the characteristics and identification, unique organizational structures, and activation mechanisms of SEs in tumors, as well as the clinical applications related to SEs in tumor therapy and prognostication. Based on a review of the literature, we discussed the relationship between SEs and different brain tumors and potential therapeutic targets, focusing on glioblastoma.
Collapse
Affiliation(s)
- Hai-Hui Zhuang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410007, PR China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410007, PR China
| | - Xin-Qi Teng
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China
| | - Ying-Huan Dai
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, 410011, PR China
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China.
| |
Collapse
|
56
|
Yang Z, Liu Y, Cheng Q, Chen T. Targeting super enhancers for liver disease: a review. PeerJ 2023; 11:e14780. [PMID: 36726725 PMCID: PMC9885865 DOI: 10.7717/peerj.14780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023] Open
Abstract
Background Super enhancers (SEs) refer to the ultralong regions of a gene accompanied by multiple transcription factors and cofactors and strongly drive the expression of cell-type-related genes. Recent studies have demonstrated that SEs play crucial roles in regulating gene expression related to cell cycle progression and transcription. Aberrant activation of SEs is closely related to the occurrence and development of liver disease. Liver disease, especially liver failure and hepatocellular carcinoma (HCC), constitutes a major class of diseases that seriously endanger human health. Currently, therapeutic strategies targeting SEs can dramatically prevent disease progression and improve the prognosis of animal models. The associated new approaches to the treatment of related liver disease are relatively new and need systematic elaboration. Objectives In this review, we elaborate on the features of SEs and discuss their function in liver disease. Additionally, we review their application prospects in clinical practice in the future. The article would be of interest to hepatologists, molecular biologists, clinicians, and all those concerned with targeted therapy and prognosis of liver disease. Methodology We searched three bibliographic databases (Web of Science Core Collection, Embase, PubMed) from 01/1981 to 06/2022 for peer-reviewed scientific publications focused on (1) gene treatment of liver disease; (2) current status of SE research; and (3) targeting SEs for liver disease. We included English language original studies only. Results The number of published studies considering the role of enhancers in liver disease is considerable. Since SEs were just defined in 2013, the corresponding data on SEs are scarce: approximately 50 papers found in bibliographic databases on the correlation between enhancers (or SEs) and liver disease. Remarkably, half of these papers were published in the past three years, indicating the growing interest of the scientific community in this issue. Studies have shown that treatments targeting components of SEs can improve outcomes in liver disease in animal and clinical trials. Conclusions The treatment of liver disease is facing a bottleneck, and new treatments are needed. Therapeutic regimens targeting SEs have an important role in the treatment of liver disease. However, given the off-target effect of gene therapy and the lack of clinical trials, the available experimental data are still fragmented and controversial.
Collapse
|
57
|
Walker FM, Sobral LM, Danis E, Sanford B, Balakrishnan I, Wang D, Pierce A, Karam SD, Serkova NJ, Foreman NK, Venkataraman S, Dowell R, Vibhakar R, Dahl NA. Rapid PTEFb-dependent transcriptional reorganization underpins the glioma adaptive response to radiotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525424. [PMID: 36747867 PMCID: PMC9900817 DOI: 10.1101/2023.01.24.525424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Dynamic regulation of gene expression is fundamental for cellular adaptation to exogenous stressors. PTEFb-mediated pause-release of RNA polymerase II (Pol II) is a conserved regulatory mechanism for synchronous transcriptional induction in response to heat shock, but this pro-survival role has not been examined in the applied context of cancer therapy. Using model systems of pediatric high-grade glioma, we show that rapid genome-wide reorganization of active chromatin facilitates PTEFb-mediated nascent transcriptional induction within hours of exposure to therapeutic ionizing radiation. Concurrent inhibition of PTEFb disrupts this chromatin reorganization and blunts transcriptional induction, abrogating key adaptive programs such as DNA damage repair and cell cycle regulation. This combination demonstrates a potent, synergistic therapeutic potential agnostic of glioma subtype, leading to a marked induction of tumor cell apoptosis and prolongation of xenograft survival. These studies reveal a central role for PTEFb underpinning the early adaptive response to radiotherapy, opening new avenues for combinatorial treatment in these lethal malignancies.
Collapse
|
58
|
Sun X, Wang Y, Wang C, Wang Y, Ren Z, Yang X, Yang X, Liu Y. Genome analysis reveals hepatic transcriptional reprogramming changes mediated by enhancers during chick embryonic development. Poult Sci 2023; 102:102516. [PMID: 36764138 PMCID: PMC9929590 DOI: 10.1016/j.psj.2023.102516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
The liver undergoes a slow process for lipid deposition during chick embryonic period. However, the underlying physiological and molecular mechanisms are still unclear. Therefore, the aim of the current study was to reveal the epigenetic mechanism of hepatic transcriptional reprogramming changes based on the integration analysis of RNA-seq and H3K27ac labeled CUT&Tag. Results showed that lipid contents increased gradually with the embryonic age (E) 11, E15, and E19 based on morphological analysis of Hematoxylin-eosin and Oil Red O staining as well as total triglyceride and cholesterol detection. The hepatic protein level of SREBP-1c was higher in E19 when compared with that in E11 and E15, while H3K27ac and H3K4me2 levels declined from E11 to E19. Differential expression genes (DEGs) among these 3 embryonic ages were determined by transcriptome analysis. A total of 107 and 46 genes were gradually upregulated and downregulated respectively with the embryonic age. Meanwhile, differential H3K27ac occupancy in chromatin was investigated. But the integration analysis of RNA-seq and CUT&Tag data showed that the overlap genes were less between DEGs and target genes of differential peaks in the promoter regions. Further, some KEGG pathways enriched from target genes of typical enhancer were overlapped with those from DEGs in transcriptome analysis such as insulin, FoxO, MAPK signaling pathways which were related to lipid metabolism. DNA motif analysis identify 8 and 10 transcription factors (TFs) based on up and down differential peaks individually among E11, E15, and E19 stages where 7 TFs were overlapped including COUP-TFII, FOXM1, FOXA1, HNF4A, RXR, ERRA, FOXA2. These results indicated that H3K27ac histone modification is involved in the transcriptional reprogramming regulation during embryonic development, which could recruit TFs binding to mediate differential enhancer activation. Differential activated enhancer impels dynamic transcriptional reprogramming towards lipid metabolism to promote the occurrence of special phenotype of hepatic lipid deposition.
Collapse
Affiliation(s)
- Xi Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yumeng Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Chaohui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yibin Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhouzheng Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yanli Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| |
Collapse
|
59
|
Sehgal P, Chaturvedi P. Chromatin and Cancer: Implications of Disrupted Chromatin Organization in Tumorigenesis and Its Diversification. Cancers (Basel) 2023; 15:cancers15020466. [PMID: 36672415 PMCID: PMC9856863 DOI: 10.3390/cancers15020466] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
A hallmark of cancers is uncontrolled cell proliferation, frequently associated with an underlying imbalance in gene expression. This transcriptional dysregulation observed in cancers is multifaceted and involves chromosomal rearrangements, chimeric transcription factors, or altered epigenetic marks. Traditionally, chromatin dysregulation in cancers has been considered a downstream effect of driver mutations. However, here we present a broader perspective on the alteration of chromatin organization in the establishment, diversification, and therapeutic resistance of cancers. We hypothesize that the chromatin organization controls the accessibility of the transcriptional machinery to regulate gene expression in cancerous cells and preserves the structural integrity of the nucleus by regulating nuclear volume. Disruption of this large-scale chromatin in proliferating cancerous cells in conventional chemotherapies induces DNA damage and provides a positive feedback loop for chromatin rearrangements and tumor diversification. Consequently, the surviving cells from these chemotherapies become tolerant to higher doses of the therapeutic reagents, which are significantly toxic to normal cells. Furthermore, the disorganization of chromatin induced by these therapies accentuates nuclear fragility, thereby increasing the invasive potential of these tumors. Therefore, we believe that understanding the changes in chromatin organization in cancerous cells is expected to deliver more effective pharmacological interventions with minimal effects on non-cancerous cells.
Collapse
|
60
|
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.
Collapse
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.
| |
Collapse
|
61
|
Yan A, Chen Y, Bian R, Wang C, Que H, Shen Y, Lu X. The landscape of enhancer RNA identify prognosis-related molecular subtypes in gastric cancer. Cancer Med 2023; 12:2046-2057. [PMID: 35801342 PMCID: PMC9883414 DOI: 10.1002/cam4.4959] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Enhancer RNAs (eRNAs), the transcriptional products of active enhancers, are of great significance in the initial progression of cancers. However, the biological function and bioinformatics profiles of eRNA in gastric cancer remains largely enigmatic. METHODS Firstly, STAD were clustered into three subtypes with the data of eRNA expression from TCeA. Then we explored the difference of the tumor immune microenvironment, transcription levels, and transcription regulation among the three clusters. Finally, samples collected from 12 patients diagnosed with STAD were used to conduct qRT-PCR, verifying the conclusion based on network database. RESULTS The three clusters were detected to have different tumor microenvironments: Cluster A has an immune "cold" microenvironment. While cluster B features as more infiltration of immune cells, accompanied with higher expression of immune checkpoints such as PDCD1, LAG3, and TIGIT. Besides, Cluster C shows a higher stromal feature with B lineage, neutrophils, and fibroblasts. Further analyses indicated that CpG island methylation level of Cluster B is different from the other two clusters. Meanwhile, Cluster A and B showed significant enrichment of TP53 and KRAS mutation respectively while Cluster C has higher tumor mutation burden (TMB) and microsatellite instability (MSI). With the elaboration of transcriptional regulation of epigenetic clustering, we detected that Cluster A enriched in epithelial phenotype pathways. Cluster B enriched in cell-cell adhesion. Cluster C enriched in fibroblast proliferation. The clinical cohort show that Cluster B patients have lower interstitial cell characteristics and CAF infiltration. CONCLUSION We identified three unique epigenetic clusters of STAD through the differential activation of super-enhancers, and identified Cluster B with a higher immune infiltrating and a better prognosis, which provides a novel understanding of eRNAs and potential clinical applicability of eRNA-based molecular subtypes in gastric cancer.
Collapse
Affiliation(s)
- Aiting Yan
- Department of OncologyAffiliated Haian Hospital of Nantong UniversityNantongJiangsuChina
| | - Ying Chen
- Department of OncologyThe Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng Third people's hospitalYanchengJiangsuChina
| | - Rongrong Bian
- Department of Oncology, Nanjing Liuhe People HospitalNanjingJiangsuChina
| | - Cuizhu Wang
- Department of OncologyAffiliated Haian Hospital of Nantong UniversityNantongJiangsuChina
| | - Haitao Que
- Department of OncologyAffiliated Haian Hospital of Nantong UniversityNantongJiangsuChina
| | - Yucheng Shen
- Department of OncologyAffiliated Haian Hospital of Nantong UniversityNantongJiangsuChina
| | - Xiaomin Lu
- Department of OncologyAffiliated Haian Hospital of Nantong UniversityNantongJiangsuChina
| |
Collapse
|
62
|
Zheng M, Wang W, Bu Y, Liu J, Ma J, Wang R, Ren X, Lu Z, Li J, Cai J. Pan-Cancer Analysis of the Roles and Driving Forces of RAB42. Biomolecules 2022; 13:biom13010043. [PMID: 36671428 PMCID: PMC9855782 DOI: 10.3390/biom13010043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
RAB42 is a member of the RAS family. However, the roles and driving forces for RAB42 in tumors remain elusive. In this study, we performed a comprehensive pan-cancer analysis of the roles and regulatory mechanisms of RAB42 using bioinformatics and experiments. Online databases such as Sanger Box, ACLBI and TIDE were used to search for the expression levels, prognostic value and immune features of RAB42. We observed that RAB42 expression was upregulated in most tumors and was closely associated with poor prognosis. Enrichment analysis indicated that RAB42 was related to multiple biological functions, especially the immune process. RAB42 expression had a positive correlation with immune cell infiltration and immune checkpoint gene expression. RAB42 had a high predictive value for immunotherapy efficiency. Our study screened out susceptible drugs for the RAB42 protein by sensitivity analysis and virtual screening. Many key driver genes such as TP53 contributed to RAB42 expression. DNA methylation, super-enhancer and non-coding RNAs were the epigenetic factors responsible for RAB42 expression. In brief, RAB42 could serve as a diagnostic and prognostic biomarker in many tumor types. RAB42 might be a predictive biomarker and a new target for immunotherapy. Genetic and epigenetic factors were essential for RAB42 overexpression in tumors.
Collapse
Affiliation(s)
- Mingzhu Zheng
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Wenhao Wang
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Yulan Bu
- Department of Radiotherapy, Affiliated Hospital of Weifang Medical University, Weifang 261031, China
| | - Jing Liu
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Jingang Ma
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Rui Wang
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Xiaomin Ren
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Zhong Lu
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Jiaqiu Li
- Jinming Yu Academician Workstation of Oncology, Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang 261031, China
- Correspondence: (J.L.); (J.C.)
| | - Jinwei Cai
- Department of Oncology, People’s Hospital of Kecheng District, Quzhou 324000, China
- Correspondence: (J.L.); (J.C.)
| |
Collapse
|
63
|
Super-enhanced MARCO variant drives triple-negative breast cancer progression. Proc Natl Acad Sci U S A 2022; 119:e2217953119. [PMID: 36469785 PMCID: PMC9897437 DOI: 10.1073/pnas.2217953119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
64
|
Luo Y, Xiang S, Feng J. Protein Phase Separation: New Insights into Carcinogenesis. Cancers (Basel) 2022; 14:cancers14235971. [PMID: 36497453 PMCID: PMC9740862 DOI: 10.3390/cancers14235971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Phase separation is now acknowledged as an essential biologic mechanism wherein distinct activated molecules assemble into a different phase from the surrounding constituents of a cell. Condensates formed by phase separation play an essential role in the life activities of various organisms under normal physiological conditions, including the advanced structure and regulation of chromatin, autophagic degradation of incorrectly folded or unneeded proteins, and regulation of the actin cytoskeleton. During malignant transformation, abnormally altered condensate assemblies are often associated with the abnormal activation of oncogenes or inactivation of tumor suppressors, resulting in the promotion of the carcinogenic process. Thus, understanding the role of phase separation in various biological evolutionary processes will provide new ideas for the development of drugs targeting specific condensates, which is expected to be an effective cancer therapy strategy. However, the relationship between phase separation and cancer has not been fully elucidated. In this review, we mainly summarize the main processes and characteristics of phase separation and the main methods for detecting phase separation. In addition, we summarize the cancer proteins and signaling pathways involved in phase separation and discuss their promising future applications in addressing the unmet clinical therapeutic needs of people with cancer. Finally, we explain the means of targeted phase separation and cancer treatment.
Collapse
|
65
|
Nair RR, Pataki E, Gerst JE. Transperons: RNA operons as effectors of coordinated gene expression in eukaryotes. Trends Genet 2022; 38:1217-1227. [PMID: 35934590 DOI: 10.1016/j.tig.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 01/24/2023]
Abstract
Coordinated gene expression allows spatiotemporal control of cellular processes and is achieved by the cotranscription/translation of functionally related genes/proteins. Prokaryotes evolved polycistronic messages (operons) to confer expression from a single promoter to efficiently cotranslate proteins functioning on the same pathway. Yet, despite having far greater diversity (e.g., gene number, distribution, modes of expression), eukaryotic cells employ individual promoters and monocistronic messages. Although gene expression is modular, it does not account for how eukaryotes achieve coordinated localized translation. The RNA operon theory states that mRNAs derived from different chromosomes assemble into ribonucleoprotein particles (RNPs) that act as functional operons to generate protein cohorts upon cotranslation. Work in yeast has now validated this theory and shown that intergenic associations and noncanonical histone functions create pathway-specific RNA operons (transperons) that regulate cell physiology. Herein the involvement of chromatin organization in transperon formation and programmed gene coexpression is discussed.
Collapse
Affiliation(s)
- Rohini R Nair
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Emese Pataki
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jeffrey E Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|
66
|
Interplay Between the Histone Variant H2A.Z and the Epigenome in Pancreatic Cancer. Arch Med Res 2022; 53:840-858. [PMID: 36470770 DOI: 10.1016/j.arcmed.2022.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/25/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND The oncogenic process is orchestrated by a complex network of chromatin remodeling elements that shape the cancer epigenome. Histone variant H2A.Z regulates DNA control elements such as promoters and enhancers in different types of cancer; however, the interplay between H2A.Z and the pancreatic cancer epigenome is unknown. OBJECTIVE This study analyzed the role of H2A.Z in different DNA regulatory elements. METHODS We performed Chromatin Immunoprecipitation Sequencing assays (ChiP-seq) with total H2A.Z and acetylated H2A.Z (acH2A.Z) antibodies and analyzed published data from ChIP-seq, RNA-seq, bromouridine labeling-UV and sequencing (BruUV-seq), Hi-C and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) in the pancreatic cancer cell line PANC-1. RESULTS The results indicate that total H2A.Z facilitates the recruitment of RNA polymerase II and transcription factors at promoters and enhancers allowing the expression of pro-oncogenic genes. Interestingly, we demonstrated that H2A.Z is enriched in super-enhancers (SEs) contributing to the transcriptional activation of key genes implicated in tumor development. Importantly, we established that H2A.Z contributes to the three-dimensional (3D) genome organization of pancreatic cancer and that it is a component of the Topological Associated Domains (TADs) boundaries in PANC-1 and that total H2A.Z and acH2A.Z are associated with A and B compartments, respectively. CONCLUSIONS H2A.Z participates in the biology and development of pancreatic cancer by generating a pro-oncogenic transcriptome through its posttranslational modifications, interactions with different partners, and regulatory elements, contributing to the oncogenic 3D genome organization. These data allow us to understand the molecular mechanisms that promote an oncogenic transcriptome in pancreatic cancer mediated by H2A.Z.
Collapse
|
67
|
Li H, Muhetaer G, Xie Y, Yao K, Ma Q, Guan H, Xing S, Huang X, Zhou J. Identification of super-enhancer-driven peptidyl arginine deiminases as potential biomarkers and therapeutic targets for osimertinib-resistant non-small cell lung cancer. Front Pharmacol 2022; 13:1071365. [DOI: 10.3389/fphar.2022.1071365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/08/2022] [Indexed: 11/22/2022] Open
Abstract
Resistance to targeted drugs is now a challenging clinical problem in the treatment of non-small cell lung cancer (NSCLC). So far, there are no approved targeted therapeutic drugs for patients with disease progression after the third-generation epidermal growth factor receptor-tyrosine kinase inhibitor osimertinib resistance (OR). Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive gene expression. In this study, we aimed to explore the potential pathogenic SEs and their driven genes in OR NSCLC. OR cell line was established by exposure of H1975 cells to incremental dosing of osimertinib. RNA-sequencing and H3K27ac ChIP-sequencing were used to identify the differential expressed genes (DEGs) and SEs in parental and resistant cells. Gene ontology analysis for the OR-specific SEs-associated genes showed that histone citrullination, protein citrullination, and peptidyl-arginine modification are the top three biological processes, and the DEGs involved in these biological processes, including peptidyl arginine deiminase 1 (PADI1), PADI2, and PADI3. Realtime-PCR and western blot detections confirmed these genes were highly expressed in OR cells. SE inhibitor decreases their expression, ensuring that SEs regulate their transcriptional expressions. The PADI inhibitor inhibited OR cells’ proliferation, invasion, and colony formation. This study demonstrates that SE-driven PADI family genes are potential biomarkers and targets for OR NSCLC.
Collapse
|
68
|
Ren J, Zhang Z, Zong Z, Zhang L, Zhou F. Emerging Implications of Phase Separation in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202855. [PMID: 36117111 PMCID: PMC9631093 DOI: 10.1002/advs.202202855] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Indexed: 05/19/2023]
Abstract
In eukaryotic cells, biological activities are executed in distinct cellular compartments or organelles. Canonical organelles with membrane-bound structures are well understood. Cells also inherently contain versatile membrane-less organelles (MLOs) that feature liquid or gel-like bodies. A biophysical process termed liquid-liquid phase separation (LLPS) elucidates how MLOs form through dynamic biomolecule assembly. LLPS-related molecules often have multivalency, which is essential for low-affinity inter- or intra-molecule interactions to trigger phase separation. Accumulating evidence shows that LLPS concentrates and organizes desired molecules or segregates unneeded molecules in cells. Thus, MLOs have tunable functional specificity in response to environmental stimuli and metabolic processes. Aberrant LLPS is widely associated with several hallmarks of cancer, including sustained proliferative signaling, growth suppressor evasion, cell death resistance, telomere maintenance, DNA damage repair, etc. Insights into the molecular mechanisms of LLPS provide new insights into cancer therapeutics. Here, the current understanding of the emerging concepts of LLPS and its involvement in cancer are comprehensively reviewed.
Collapse
Affiliation(s)
- Jiang Ren
- School of MedicineZhejiang University City CollegeHangzhou215123China
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Zhenyu Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan450003China
| | - Zhi Zong
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Long Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
- International Biomed‐X Research Center, Second Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhou215123China
| | - Fangfang Zhou
- School of MedicineZhejiang University City CollegeHangzhou215123China
- Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123China
| |
Collapse
|
69
|
Insilico exploration of the potential inhibitory activity of DrugBank compounds against CDK7 kinase using structure-based virtual screening, molecular docking, and dynamics simulation approach. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
70
|
Shi Y, Wang M, Liu D, Ullah S, Ma X, Yang H, Liu B. Super-enhancers in esophageal carcinoma: Transcriptional addictions and therapeutic strategies. Front Oncol 2022; 12:1036648. [DOI: 10.3389/fonc.2022.1036648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
The tumorigenesis of esophageal carcinoma arises from transcriptional dysregulation would become exceptionally dependent on specific regulators of gene expression, which could be preferentially attributed to the larger non-coding cis-regulatory elements, i.e. super-enhancers (SEs). SEs, large genomic regulatory entity in close genomic proximity, are underpinned by control cancer cell identity. As a consequence, the transcriptional addictions driven by SEs could offer an Achilles’ heel for molecular treatments on patients of esophageal carcinoma and other types of cancer as well. In this review, we summarize the recent findings about the oncogenic SEs upon which esophageal cancer cells depend, and discuss why SEs could be seen as the hallmark of cancer, how transcriptional dependencies driven by SEs, and what opportunities could be supplied based on this cancer-specific SEs.
Collapse
|
71
|
Kuang C, Tong J, Ermine K, Cai M, Dai F, Hao S, Giles F, Huang Y, Yu J, Zhang L. Dual inhibition of BET and HAT/p300 suppresses colorectal cancer via DR5- and p53/PUMA-mediated cell death. Front Oncol 2022; 12:1018775. [PMID: 36313707 PMCID: PMC9599411 DOI: 10.3389/fonc.2022.1018775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/26/2022] [Indexed: 01/30/2023] Open
Abstract
Background Colorectal cancer (CRC) frequently has a dysregulated epigenome causing aberrant up-regulation of oncogenes such as c-MYC. Bromodomain and extra-terminal domain (BET) proteins and histone acetyltransferases (HAT) are epigenetic regulatory proteins that create and maintain epigenetic states supporting oncogenesis. BET inhibitors and HAT inhibitors are currently being investigated as cancer therapeutics due to their ability to suppress cancer-promoting epigenetic modifiers. Due to the extensive molecular crosstalk between BET proteins and HAT proteins, we hypothesized that dual inhibition of BET and HAT could more potently inhibit CRC cells than inhibition of each individual protein. Methods We investigated the activity and mechanisms of a dual BET and HAT inhibitor, NEO2734, in CRC cell lines and mouse xenografts. MTS, flow cytometry, and microscopy were used to assess cell viability. qPCR, Western blotting, and immunofluorescent staining were used to assess mechanisms of action. Results We found that NEO2734 more potently suppresses CRC cell growth than first generation BET inhibitors, regardless of the status of common CRC driver mutations. We previously showed that BET inhibitors upregulate DR5 to induce extrinsic apoptosis. In the current study, we show that NEO2734 treatment induces CRC cell apoptosis via both the intrinsic and extrinsic apoptosis pathways. NEO2734 increases p53 expression and subsequently increased expression of the p53-upregulated mediator of apoptosis (PUMA), which is a critical mechanism for activating intrinsic apoptosis. We demonstrate that inhibition of either the intrinsic or extrinsic branches of apoptosis partially rescues CRC cells from NEO2734 treatment, while the dual inhibition of both branches of apoptosis more strongly rescues CRC cells from NEO2734 treatment. Finally, we show that NEO2734 monotherapy is able to suppress tumor growth in CRC xenografts by inducing apoptosis. Conclusions Our study demonstrates NEO2734 potently suppresses CRC cells in vitro and in vivo by simultaneously upregulating PUMA and DR5 to induce cell death. Further studies of NEO2734 for treating CRC are warranted.
Collapse
Affiliation(s)
- Chaoyuan Kuang
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jingshan Tong
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kaylee Ermine
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Manbo Cai
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Fujun Dai
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Suisui Hao
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Francis Giles
- Developmental Therapeutics Consortium, Chicago, IL, United States
| | - Yi Huang
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jian Yu
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Lin Zhang
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States
| |
Collapse
|
72
|
Song X, Zhang T, Ding H, Feng Y, Yang W, Yin X, Chen B, Liang Y, Mao Q, Xia W, Yu G, Xu L, Dong G, Jiang F. Non-genetic stratification reveals epigenetic heterogeneity and identifies vulnerabilities of glycolysis addiction in lung adenocarcinoma subtype. Oncogenesis 2022; 11:61. [PMID: 36216804 PMCID: PMC9550819 DOI: 10.1038/s41389-022-00436-0] [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: 04/15/2022] [Revised: 09/12/2022] [Accepted: 09/26/2022] [Indexed: 11/12/2022] Open
Abstract
Lung adenocarcinoma (LUAD) exhibits high heterogeneity and is well known for its high genetic variation. Recently, the understanding of non-genetic variation provides a new perspective to study the heterogeneity of LUAD. Little is known about whether super-enhancers (SEs) may be primarily responsible for the inter-tumor heterogeneity of LUAD. We used super-enhancer RNA (seRNA) levels of a large-scale clinical well-annotated LUAD cohort to stratify patients into three clusters with different prognosis and other malignant characteristics. Mechanistically, estrogen-related receptor alpha (ERRα) in cluster 3-like cell lines acts as a cofactor of BRD4 to assist SE-promoter loops to activate glycolysis-related target gene expression, thereby promoting glycolysis and malignant progression, which confers a therapeutic vulnerability to glycolytic inhibitors. Our study identified three groups of patients according to seRNA levels, among which patients in cluster 3 have the worst prognosis and vulnerability of glycolysis dependency. We also proposed a 3-TF index model to stratify patients with glycolysis-addicted tumors according to tumor SE stratification.
Collapse
Affiliation(s)
- Xuming Song
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Te Zhang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Hanlin Ding
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Yipeng Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Wenmin Yang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Xuewen Yin
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211198, Nanjing, P. R. China
| | - Bing Chen
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Yingkuan Liang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China
| | - Qixing Mao
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China
| | - Wenjie Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China
| | - Guiping Yu
- Department of Cardiothoracic Surgery, The affiliated Jiangyin Hospital of Southeast University Medical College, 214400, Jiangyin, P. R. China
| | - Lin Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China. .,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China. .,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China. .,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 211116, Nanjing, P. R. China.
| | - Gaochao Dong
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China. .,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China. .,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China. .,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China.
| |
Collapse
|
73
|
Zhao Y. TFSyntax: a database of transcription factors binding syntax in mammalian genomes. Nucleic Acids Res 2022; 51:D306-D314. [PMID: 36200824 PMCID: PMC9825613 DOI: 10.1093/nar/gkac849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/10/2022] [Accepted: 09/21/2022] [Indexed: 01/29/2023] Open
Abstract
In mammals, transcriptional factors (TFs) drive gene expression by binding to regulatory elements in a cooperative manner. Deciphering the rules of such cooperation is crucial to obtain a full understanding of cellular homeostasis and development. Although this is a long-standing topic, there is no comprehensive database for biologists to access the syntax of TF binding sites. Here we present TFSyntax (https://tfsyntax.zhaopage.com), a database focusing on the arrangement of TF binding sites. TFSyntax maps the binding motif of 1299 human TFs and 890 mouse TFs across 382 cells and tissues, representing the most comprehensive TF binding map to date. In addition to location, TFSyntax defines motif positional preference, density and colocalization within accessible elements. Powered by a series of functional modules based on web interface, users can freely search, browse, analyze, and download data of interest. With comprehensive characterization of TF binding syntax across distinct tissues and cell types, TFSyntax represents a valuable resource and platform for studying the mechanism of transcriptional regulation and exploring how regulatory DNA variants cause disease.
Collapse
Affiliation(s)
- Yongbing Zhao
- To whom correspondence should be addressed. Tel: +1 301 480 5852;
| |
Collapse
|
74
|
Liu K, Du Y, Li H, Lin X. Identification of super-enhancer-associated transcription factors regulating glucose metabolism in poorly differentiated thyroid carcinoma. Genet Mol Biol 2022; 45:e20210370. [PMID: 36121916 PMCID: PMC9495016 DOI: 10.1590/1678-4685-gmb-2021-0370] [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: 11/23/2021] [Accepted: 06/05/2022] [Indexed: 12/24/2022] Open
Abstract
This study aimed to uncover transcription factors that regulate super-enhancers involved in glucose metabolism reprogramming in poorly differentiated thyroid carcinoma (PDTC). TCA cycle and pyruvate metabolism were significantly enriched in PDTC. Differentially expressed genes in PDTC vs. normal control tissues were located in key steps in TCA cycle and pyruvate metabolism. A total of 23 upregulated genes localized in TCA cycle and pyruvate metabolism were identified as super-enhancer-controlled genes. Transcription factor analysis of these 23 super-enhancer-controlled genes related to glucose metabolism was performed, and 20 transcription factors were obtained, of which KLF12, ZNF281 and RELA had a significant prognostic impact. Regulatory network of KLF12, ZNF281 and RELA controlled the expression of these four prognostic target genes (LDHA, ACLY, ME2 and IDH2). In vitro validation showed that silencing of KLF12, ZNF281 and RELA suppressed proliferation, glucose uptake, lactate production and ATP level, but increased ADP/ATP ratio in PDTC cells. In conclusion, KLF12, ZNF281 and RELA were identified as the key transcription factors that regulate super-enhancer-controlled genes related to glucose metabolism in PDTC. Our findings contribute to a deeper understanding of the regulatory mechanisms associated with glucose metabolism in PDTC, and advance the theoretical development of PDTC-targeted therapies.
Collapse
Affiliation(s)
- Kun Liu
- Tianjin Hospital, Endocrinology Department, Tianjin, P. R. China
| | - Yongrui Du
- 80th Group Military Hospital, Chinese Peoples Liberation Army, Endocrinology Department, Weifang, Shandong, P. R. China
| | - Hui Li
- XingTai Medical College, Basic Experiment Center, Xingtai, Hebei, P. R. China
| | - Xuexia Lin
- XingTai Medical College, Basic Experiment Center, Xingtai, Hebei, P. R. China
| |
Collapse
|
75
|
Gomez RL, Woods LM, Ramachandran R, Abou Tayoun AN, Philpott A, Ali FR. Super-enhancer associated core regulatory circuits mediate susceptibility to retinoic acid in neuroblastoma cells. Front Cell Dev Biol 2022; 10:943924. [PMID: 36147741 PMCID: PMC9485839 DOI: 10.3389/fcell.2022.943924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
Neuroblastoma is a pediatric tumour that accounts for more than 15% of cancer-related deaths in children. High-risk tumours are often difficult to treat, and patients' survival chances are less than 50%. Retinoic acid treatment is part of the maintenance therapy given to neuroblastoma patients; however, not all tumours differentiate in response to retinoic acid. Within neuroblastoma tumors, two phenotypically distinct cell types have been identified based on their super-enhancer landscape and transcriptional core regulatory circuitries: adrenergic (ADRN) and mesenchymal (MES). We hypothesized that the distinct super-enhancers in these different tumour cells mediate differential response to retinoic acid. To this end, three different neuroblastoma cell lines, ADRN (MYCN amplified and non-amplified) and MES cells, were treated with retinoic acid, and changes in the super-enhancer landscape upon treatment and after subsequent removal of retinoic acid was studied. Using ChIP-seq for the active histone mark H3K27ac, paired with RNA-seq, we compared the super-enhancer landscape in cells that undergo neuronal differentiation in response to retinoic acid versus those that fail to differentiate and identified unique super-enhancers associated with neuronal differentiation. Among the ADRN cells that respond to treatment, MYCN-amplified cells remain differentiated upon removal of retinoic acid, whereas MYCN non-amplified cells revert to an undifferentiated state, allowing for the identification of super-enhancers responsible for maintaining differentiation. This study identifies key super-enhancers that are crucial for retinoic acid-mediated differentiation.
Collapse
Affiliation(s)
- Roshna Lawrence Gomez
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Laura M. Woods
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Revathy Ramachandran
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ahmad N. Abou Tayoun
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | - Anna Philpott
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Fahad R. Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| |
Collapse
|
76
|
Breitenbach T, Schmitt MJ, Dandekar T. Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing. Bioinformatics 2022; 38:4162-4171. [PMID: 35809064 DOI: 10.1093/bioinformatics/btac488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/05/2022] [Accepted: 07/07/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION A recent approach to perform genetic tracing of complex biological problems involves the generation of synthetic deoxyribonucleic acid (DNA) probes that specifically mark cells with a phenotype of interest. These synthetic locus control regions (sLCRs), in turn, drive the expression of a reporter gene, such as fluorescent protein. To build functional and specific sLCRs, it is critical to accurately select multiple bona fide cis-regulatory elements from the target cell phenotype cistrome. This selection occurs by maximizing the number and diversity of transcription factors (TFs) within the sLCR, yet the size of the final sLCR should remain limited. RESULTS In this work, we discuss how optimization, in particular integer programing, can be used to systematically address the construction of a specific sLCR and optimize pre-defined properties of the sLCR. Our presented instance of a linear optimization problem maximizes the activation potential of the sLCR such that its size is limited to a pre-defined length and a minimum number of all TFs deemed sufficiently characteristic for the phenotype of interest is covered. We generated an sLCR to trace the mesenchymal glioblastoma program in patients by solving our corresponding linear program with the software optimizer Gurobi. Considering the binding strength of transcription factor binding sites (TFBSs) with their TFs as a proxy for activation potential, the optimized sLCR scores similarly to an sLCR experimentally validated in vivo, and is smaller in size while having the same coverage of TFBSs. AVAILABILITY AND IMPLEMENTATION We provide a Python implementation of the presented framework in the Supplementary Material with which an optimal selection of cis-regulatory elements can be calculated once the target set of TFs and their binding strength with their TFBSs is known. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Tim Breitenbach
- Biozentrum, Julius-Maximilians-Universität, Würzburg 97074, Germany
| | - Matthias Jürgen Schmitt
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Helmholtz-Gemeinschaft, Berlin 13125, Germany
| | - Thomas Dandekar
- Biozentrum, Julius-Maximilians-Universität, Würzburg 97074, Germany
| |
Collapse
|
77
|
MYCN and Metabolic Reprogramming in Neuroblastoma. Cancers (Basel) 2022; 14:cancers14174113. [PMID: 36077650 PMCID: PMC9455056 DOI: 10.3390/cancers14174113] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Neuroblastoma is a pediatric cancer responsible for approximately 15% of all childhood cancer deaths. Aberrant MYCN activation, as a result of genomic MYCN amplification, is a major driver of high-risk neuroblastoma, which has an overall survival rate of less than 50%, despite the best treatments currently available. Metabolic reprogramming is an integral part of the growth-promoting program driven by MYCN, which fuels cell growth and proliferation by increasing the uptake and catabolism of nutrients, biosynthesis of macromolecules, and production of energy. This reprogramming process also generates metabolic vulnerabilities that can be exploited for therapy. In this review, we present our current understanding of metabolic reprogramming in neuroblastoma, focusing on transcriptional regulation as a key mechanism in driving the reprogramming process. We also highlight some important areas that need to be explored for the successful development of metabolism-based therapy against high-risk neuroblastoma.
Collapse
|
78
|
Zhang T, Xia W, Song X, Mao Q, Huang X, Chen B, Liang Y, Wang H, Chen Y, Yu X, Zhang Z, Yang W, Xu L, Dong G, Jiang F. Super-enhancer hijacking LINC01977 promotes malignancy of early-stage lung adenocarcinoma addicted to the canonical TGF-β/SMAD3 pathway. J Hematol Oncol 2022; 15:114. [PMID: 35982471 PMCID: PMC9389757 DOI: 10.1186/s13045-022-01331-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the leading cause of death worldwide. However, the roles of long noncoding RNAs (lncRNAs) hijacked by super-enhancers (SEs), vital regulatory elements of the epigenome, remain elusive in the progression of LUAD metastasis. METHODS SE-associated lncRNA microarrays were used to identify the dysregulated lncRNAs in LUAD. ChIP-seq, Hi-C data analysis, and luciferase reporter assays were utilized to confirm the hijacking of LINC01977 by SE. The functions and mechanisms of LINC01977 in LUAD were explored by a series of in vitro and in vivo assays. RESULTS We found that LINC01977, a cancer-testis lncRNA, was hijacked by SE, which promoted proliferation and invasion both in vitro and in vivo. LINC01977 interacted with SMAD3 to induce its nuclear transport, which facilitated the interaction between SMAD3 and CBP/P300, thereby regulating the downstream target gene ZEB1. Additionally, SMAD3 up-regulated LINC09177 transcription by simultaneously binding the promoter and SE, which was induced by the infiltration of M2-like tumor-associated macrophages (TAM2), subsequently activating the TGF-β/SMAD3 pathway. Moreover, LINC01977 expression was positively correlated with TAM2 infiltration and SMAD3 expression, especially in early-stage LUAD. Higher chromatin accessibility in the SE region of LINC01977 was observed with high expression of TGF-β. Early-stage LUAD patients with high LIN01977 expression had a shorter disease-free survival. CONCLUSIONS TAM2 infiltration induced a rich TGF-β microenvironment, activating SMAD3 to bind the promoter and the SE of LINC01977, which up-regulated LINC01977 expression. LINC01977 also promoted malignancy via the canonical TGF-β/SMAD3 pathway. LINC01977 hijacked by SE could be a valuable therapeutic target, especially for the treatment of early-stage LUAD.
Collapse
Affiliation(s)
- Te Zhang
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, China
| | - Wenjie Xia
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China
| | - Xuming Song
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, China
| | - Qixing Mao
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China
| | - Xing Huang
- Department of Pathology, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China
| | - Bing Chen
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China
| | - Yingkuan Liang
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China
| | - Hui Wang
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China
| | - Yuzhong Chen
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China
| | - Xinnian Yu
- Department of Oncology, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China
| | - Zeyu Zhang
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China
| | - Wenmin Yang
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China
| | - Lin Xu
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China. .,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China. .,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, China.
| | - Gaochao Dong
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China. .,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.
| | - Feng Jiang
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China. .,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, 210009, China.
| |
Collapse
|
79
|
Yang Y, Qian F, Li X, Li Y, Zhou L, Wang Q, Zhou X, Zhang J, Song C, Yu Z, Cui T, Feng C, Zhu J, Shang D, Liu J, Sun M, Zhang Y, Tang H, Li C. GREAP: a comprehensive enrichment analysis software for human genomic regions. Brief Bioinform 2022; 23:6663640. [PMID: 35959979 DOI: 10.1093/bib/bbac329] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 12/12/2022] Open
Abstract
The rapid development of genomic high-throughput sequencing has identified a large number of DNA regulatory elements with abundant epigenetics markers, which promotes the rapid accumulation of functional genomic region data. The comprehensively understanding and research of human functional genomic regions is still a relatively urgent work at present. However, the existing analysis tools lack extensive annotation and enrichment analytical abilities for these regions. Here, we designed a novel software, Genomic Region sets Enrichment Analysis Platform (GREAP), which provides comprehensive region annotation and enrichment analysis capabilities. Currently, GREAP supports 85 370 genomic region reference sets, which cover 634 681 107 regions across 11 different data types, including super enhancers, transcription factors, accessible chromatins, etc. GREAP provides widespread annotation and enrichment analysis of genomic regions. To reflect the significance of enrichment analysis, we used the hypergeometric test and also provided a Locus Overlap Analysis. In summary, GREAP is a powerful platform that provides many types of genomic region sets for users and supports genomic region annotations and enrichment analyses. In addition, we developed a customizable genome browser containing >400 000 000 customizable tracks for visualization. The platform is freely available at http://www.liclab.net/Greap/view/index.
Collapse
Affiliation(s)
- Yongsan Yang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.,West China Biomedical Big Data Center, West China Hospital, Sichuan University, China
| | - Fengcui Qian
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Xuecang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Yanyu Li
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Liwei Zhou
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Qiuyu Wang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Xinyuan Zhou
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Chao Song
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Zhengmin Yu
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Ting Cui
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Desi Shang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Jiaqi Liu
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Mengfei Sun
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Yuexin Zhang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Huifang Tang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Chunquan Li
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| |
Collapse
|
80
|
HSF1 Stimulates Glutamine Transport by Super-Enhancer-Driven lncRNA LINC00857 in Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14163855. [PMID: 36010849 PMCID: PMC9406190 DOI: 10.3390/cancers14163855] [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: 07/01/2022] [Revised: 08/02/2022] [Accepted: 08/06/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Based on the latest research, cancer cells prefer glutamine to glucose. Therefore, it is more worthwhile to explore the regulatory mechanism of glutamine metabolism in cancer cells. Super enhancers are critical for the gene transcriptional programs responsible for cell fate by interacting with various transcription factors. The transcription factor HSF1 exerts a multifaced role in tumorigenesis. However, the relevance of HSF1 to super enhancers in tumors remains obscure. Therefore, this study focused on the mechanism underlying super-enhancer activation and its relationship to HSF1 in CRC. Here, we performed a super-enhancer landscape in CRC and we screened out an HSF1-mediated super enhancer, lncRNA-LINC00857, by lncRNA microarray. We discovered that HSF1 could stimulate acetyltransferase P300-mediated super-enhancer activity to facilitate LINC00857 expression, contributing to SLC1A5/ASCT2-mediated glutamine transport. In addition, we validated that targeting the HSF1/LINC00857/ANXA11 axis may provide a valuable therapeutic strategy against CRC. Abstract Super enhancers are critical for the gene transcription responsible for cell fate by interacting with transcription factors. However, the relevance of HSF1 to super enhancers in tumors remains obscure. We profiled H3K27ac enrichment by chromatin immunoprecipitation sequencing. HSF1-mediated lncRNAs were identified by lncRNA microarray. The characteristics of LINC00857 were explored by in vitro and in vivo assays. The mechanism was studied via chromatin immunoprecipitation, RNA immunoprecipitation, and HSF1/ANXA11 knockout mice. We found that super enhancers occupied multiple gene loci in colorectal cancer. We screened out an HSF1-mediated super enhancer, lncRNA-LINC00857, which exerts its characteristics in promoting cell growth via regulating glutamine metabolism. Notably, HSF1 could stimulate the super-enhancer activity of LINC00857 by the enrichment of acetyltransferase P300 to its gene loci, contributing to LINC00857 transcription. In turn, nuclear LINC00857 cooperated with HSF1 to promote ANXA11 transcription, which modulated SLC1A5/ASCT2 protein expression by binding competitively to miR-122-5p. The knockout of ANXA11 attenuated colorectal cancer formation in vivo. Collectively, we shed light on a closely cooperative machinery between HSF1 and super enhancers. HSF1 could stimulate acetyltransferase P300-mediated super-enhancer activity to facilitate LINC00857 expression, contributing to SLC1A5-mediated glutamine transport. Targeting the HSF1/LINC00857/ANXA11 axis may provide a valuable therapeutic strategy against colorectal cancer.
Collapse
|
81
|
Zhu Y, Zhou Z, Huang T, Zhang Z, Li W, Ling Z, Jiang T, Yang J, Yang S, Xiao Y, Charlier C, Georges M, Yang B, Huang L. Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1517-1534. [PMID: 35122624 DOI: 10.1007/s11427-021-2034-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022]
Abstract
The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted ChIP-Seq and RNA-Seq in fetal (prenatal days 74-75) and adult (postnatal days 132-150) tissues (brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521 promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages (which could indicate safe harbor locus for exogenous gene insertion) and tissue- and developmental stage-specific peaks (which regulate gene pathways matching tissue- and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of the XIST gene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results ( http://segtp.jxau.edu.cn/pencode/?genome=susScr11 ).
Collapse
Affiliation(s)
- Yaling Zhu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
- Laboratory Animal Research Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Zhimin Zhou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Tao Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhen Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wanbo Li
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Tao Jiang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiawen Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Siyu Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yanyuan Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Carole Charlier
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
- Unit of Animal Genomics, GIGA-Institute and Faculty of Veterinary Medicine, University of Liege, 4000, Liege, Belgium
| | - Michel Georges
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
- Unit of Animal Genomics, GIGA-Institute and Faculty of Veterinary Medicine, University of Liege, 4000, Liege, Belgium
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| |
Collapse
|
82
|
Li H, Li J, Xiao T, Hu Y, Yang Y, Gu X, Jin G, Cao H, Zhou H, Yang C. Nintedanib Alleviates Experimental Colitis by Inhibiting CEBPB/PCK1 and CEBPB/EFNA1 Pathways. Front Pharmacol 2022; 13:904420. [PMID: 35910380 PMCID: PMC9331303 DOI: 10.3389/fphar.2022.904420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/13/2022] [Indexed: 11/22/2022] Open
Abstract
The super-enhancer, a cluster of enhancers with strong transcriptional activity, has become one of the most interesting topics in recent years. This study aimed to investigate pathogenic super-enhancer–driven genes in IBD and screen therapeutic drugs based on the results. In this study, through the analysis of differentially expressed genes in colitis patients from the GEO database and the analysis of the super-enhancer–associated database, we found that the super-enhancer pathogenic genes PCK1 and EFNA1 were simultaneously regulated by transcription factor CEBPB through two super-enhancers (sc-CHR20-57528535 and sc-CHR1-155093980). Silencing CEBPB could significantly inhibit the expression of PCK1 and EFNA1 and enhance the expression of epithelial barrier proteins claudin-1, occludin, and ZO-1. In LPS-induced Caco-2 cells, drugs commonly used in clinical colitis including tofacitinib, oxalazine, mesalazine, and sulfasalazine inhibited mRNA levels of CEBPB, PCK1, and EFNA1. In the drug screening, we found that nintedanib significantly inhibited the mRNA and protein levels of CEBPB, PCK1, and EFNA1. In vivo experiments, nintedanib significantly alleviated DSS-induced colitis in mice by inhibiting CEBPB/PCK1 and CEBPB/EFNA1 signaling pathways. At the genus level, nintedanib improved the composition of the gut microbiota in mice with DSS-induced experimental colitis. In conclusion, we found that PCK1 and EFNA1 are highly expressed in colitis and they are regulated by CEBPB through two super-enhancers, and we further demonstrate their role in vivo and in vitro. Nintedanib may be a potential treatment for IBD. Super-enhancers may be a new way to explore the pathogenesis of colitis.
Collapse
Affiliation(s)
- Hailong Li
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Jinhe Li
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- High-throughput Molecular Drug Screening Centre, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Ting Xiao
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Yayue Hu
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- High-throughput Molecular Drug Screening Centre, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Ying Yang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Xiaoting Gu
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Ge Jin
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
- *Correspondence: Hailong Cao, ; Honggang Zhou, ; Cheng Yang,
| | - Honggang Zhou
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- High-throughput Molecular Drug Screening Centre, Tianjin International Joint Academy of Biomedicine, Tianjin, China
- *Correspondence: Hailong Cao, ; Honggang Zhou, ; Cheng Yang,
| | - Cheng Yang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- High-throughput Molecular Drug Screening Centre, Tianjin International Joint Academy of Biomedicine, Tianjin, China
- *Correspondence: Hailong Cao, ; Honggang Zhou, ; Cheng Yang,
| |
Collapse
|
83
|
Peng A, Peng W, Wang R, Zhao H, Yu X, Sun Y. Regulation of 3D Organization and Its Role in Cancer Biology. Front Cell Dev Biol 2022; 10:879465. [PMID: 35757006 PMCID: PMC9213882 DOI: 10.3389/fcell.2022.879465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Three-dimensional (3D) genomics is the frontier field in the post-genomics era, its foremost content is the relationship between chromatin spatial conformation and regulation of gene transcription. Cancer biology is a complex system resulting from genetic alterations in key tumor oncogenes and suppressor genes for cell proliferation, DNA replication, cell differentiation, and homeostatic functions. Although scientific research in recent decades has revealed how the genome sequence is mutated in many cancers, high-order chromosomal structures involved in the development and fate of cancer cells represent a crucial but rarely explored aspect of cancer genomics. Hence, dissection of the 3D genome conformation of cancer helps understand the unique epigenetic patterns and gene regulation processes that distinguish cancer biology from normal physiological states. In recent years, research in tumor 3D genomics has grown quickly. With the rapid progress of 3D genomics technology, we can now better determine the relationship between cancer pathogenesis and the chromatin structure of cancer cells. It is becoming increasingly explicit that changes in 3D chromatin structure play a vital role in controlling oncogene transcription. This review focuses on the relationships between tumor gene expression regulation, tumor 3D chromatin structure, and cancer phenotypic plasticity. Furthermore, based on the functional consequences of spatial disorganization in the cancer genome, we look forward to the clinical application prospects of 3D genomic biomarkers.
Collapse
Affiliation(s)
- Anghui Peng
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Wang Peng
- Department of Oncology, Liuzhou People's Hospital, Liuzhou, China
| | - Ruiqi Wang
- Department of Pharmacy, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Hao Zhao
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Xinyang Yu
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yihao Sun
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| |
Collapse
|
84
|
Super-Enhancers, Phase-Separated Condensates, and 3D Genome Organization in Cancer. Cancers (Basel) 2022; 14:cancers14122866. [PMID: 35740532 PMCID: PMC9221043 DOI: 10.3390/cancers14122866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 01/27/2023] Open
Abstract
3D chromatin organization plays an important role in transcription regulation and gene expression. The 3D genome is highly maintained by several architectural proteins, such as CTCF, Yin Yang 1, and cohesin complex. This structural organization brings regulatory DNA elements in close proximity to their target promoters. In this review, we discuss the 3D chromatin organization of super-enhancers and their relationship to phase-separated condensates. Super-enhancers are large clusters of DNA elements. They can physically contact with their target promoters by chromatin looping during transcription. Multiple transcription factors can bind to enhancer and promoter sequences and recruit a complex array of transcriptional co-activators and RNA polymerase II to effect transcriptional activation. Phase-separated condensates of transcription factors and transcriptional co-activators have been implicated in assembling the transcription machinery at particular enhancers. Cancer cells can hijack super-enhancers to drive oncogenic transcription to promote cell survival and proliferation. These dysregulated transcriptional programs can cause cancer cells to become highly dependent on transcriptional regulators, such as Mediator and BRD4. Moreover, the expression of oncogenes that are driven by super-enhancers is sensitive to transcriptional perturbation and often occurs in phase-separated condensates, supporting therapeutic rationales of targeting SE components, 3D genome organization, or dysregulated condensates in cancer.
Collapse
|
85
|
PRRX1 is a master transcription factor of stromal fibroblasts for myofibroblastic lineage progression. Nat Commun 2022; 13:2793. [PMID: 35589735 PMCID: PMC9120014 DOI: 10.1038/s41467-022-30484-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/04/2022] [Indexed: 12/01/2022] Open
Abstract
Although stromal fibroblasts play a critical role in cancer progression, their identities remain unclear as they exhibit high heterogeneity and plasticity. Here, a master transcription factor (mTF) constructing core-regulatory circuitry, PRRX1, which determines the fibroblast lineage with a myofibroblastic phenotype, is identified for the fibroblast subgroup. PRRX1 orchestrates the functional drift of fibroblasts into myofibroblastic phenotype via TGF-β signaling by remodeling a super-enhancer landscape. Such reprogrammed fibroblasts have myofibroblastic functions resulting in markedly enhanced tumorigenicity and aggressiveness of cancer. PRRX1 expression in cancer-associated fibroblast (CAF) has an unfavorable prognosis in multiple cancer types. Fibroblast-specific PRRX1 depletion induces long-term and sustained complete remission of chemotherapy-resistant cancer in genetically engineered mice models. This study reveals CAF subpopulations based on super-enhancer profiles including PRRX1. Therefore, mTFs, including PRRX1, provide another opportunity for establishing a hierarchical classification system of fibroblasts and cancer treatment by targeting fibroblasts. Cancer associated fibroblasts are an important and highly heterogeneous component of the tumor microenvironment. Here the authors identify PRRX1 as a master transcription factor determining a fibroblast lineage with myofibroblastic phenotype, associated with unfavourable prognosis in several cancer types.
Collapse
|
86
|
Wan L, Li W, Meng Y, Hou Y, Chen M, Xu B. Inflammatory Immune-Associated eRNA: Mechanisms, Functions and Therapeutic Prospects. Front Immunol 2022; 13:849451. [PMID: 35514959 PMCID: PMC9063412 DOI: 10.3389/fimmu.2022.849451] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid development of multiple high-throughput sequencing technologies has made it possible to explore the critical roles and mechanisms of functional enhancers and enhancer RNAs (eRNAs). The inflammatory immune response, as a fundamental pathological process in infectious diseases, cancers and immune disorders, coordinates the balance between the internal and external environment of the organism. It has been shown that both active enhancers and intranuclear eRNAs are preferentially expressed over inflammation-related genes in response to inflammatory stimuli, suggesting that enhancer transcription events and their products influence the expression and function of inflammatory genes. Therefore, in this review, we summarize and discuss the relevant inflammatory roles and regulatory mechanisms of eRNAs in inflammatory immune cells, non-inflammatory immune cells, inflammatory immune diseases and tumors, and explore the potential therapeutic effects of enhancer inhibitors affecting eRNA production for diseases with inflammatory immune responses.
Collapse
Affiliation(s)
- Lilin Wan
- Medical School, Southeast University, Nanjing, China
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Wenchao Li
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Yuan Meng
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Yue Hou
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| |
Collapse
|
87
|
Mehta S, Zhang J. Liquid-liquid phase separation drives cellular function and dysfunction in cancer. Nat Rev Cancer 2022; 22:239-252. [PMID: 35149762 PMCID: PMC10036213 DOI: 10.1038/s41568-022-00444-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2022] [Indexed: 12/11/2022]
Abstract
Cancer is a disease of uncontrollably reproducing cells. It is governed by biochemical pathways that have escaped the regulatory bounds of normal homeostatic balance. This balance is maintained through precise spatiotemporal regulation of these pathways. The formation of biomolecular condensates via liquid-liquid phase separation (LLPS) has recently emerged as a widespread mechanism underlying the spatiotemporal coordination of biological activities in cells. Biomolecular condensates are widely observed to directly regulate key cellular processes involved in cancer cell pathology, and the dysregulation of LLPS is increasingly implicated as a previously hidden driver of oncogenic activity. In this Perspective, we discuss how LLPS shapes the biochemical landscape of cancer cells.
Collapse
Affiliation(s)
- Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
88
|
Ponzoni M, Bachetti T, Corrias MV, Brignole C, Pastorino F, Calarco E, Bensa V, Giusto E, Ceccherini I, Perri P. Recent advances in the developmental origin of neuroblastoma: an overview. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:92. [PMID: 35277192 PMCID: PMC8915499 DOI: 10.1186/s13046-022-02281-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 02/06/2022] [Indexed: 02/04/2023]
Abstract
Neuroblastoma (NB) is a pediatric tumor that originates from neural crest-derived cells undergoing a defective differentiation due to genomic and epigenetic impairments. Therefore, NB may arise at any final site reached by migrating neural crest cells (NCCs) and their progeny, preferentially in the adrenal medulla or in the para-spinal ganglia. NB shows a remarkable genetic heterogeneity including several chromosome/gene alterations and deregulated expression of key oncogenes that drive tumor initiation and promote disease progression. NB substantially contributes to childhood cancer mortality, with a survival rate of only 40% for high-risk patients suffering chemo-resistant relapse. Hence, NB remains a challenge in pediatric oncology and the need of designing new therapies targeted to specific genetic/epigenetic alterations become imperative to improve the outcome of high-risk NB patients with refractory disease or chemo-resistant relapse. In this review, we give a broad overview of the latest advances that have unraveled the developmental origin of NB and its complex epigenetic landscape. Single-cell RNA sequencing with spatial transcriptomics and lineage tracing have identified the NCC progeny involved in normal development and in NB oncogenesis, revealing that adrenal NB cells transcriptionally resemble immature neuroblasts or their closest progenitors. The comparison of adrenal NB cells from patients classified into risk subgroups with normal sympatho-adrenal cells has highlighted that tumor phenotype severity correlates with neuroblast differentiation grade. Transcriptional profiling of NB tumors has identified two cell identities that represent divergent differentiation states, i.e. undifferentiated mesenchymal (MES) and committed adrenergic (ADRN), able to interconvert by epigenetic reprogramming and to confer intra-tumoral heterogeneity and high plasticity to NB. Chromatin immunoprecipitation sequencing has disclosed the existence of two super-enhancers and their associated transcription factor networks underlying MES and ADRN identities and controlling NB gene expression programs. The discovery of NB-specific regulatory circuitries driving oncogenic transformation and maintaining the malignant state opens new perspectives on the design of innovative therapies targeted to the genetic and epigenetic determinants of NB. Remodeling the disrupted regulatory networks from a dysregulated expression, which blocks differentiation and enhances proliferation, toward a controlled expression that prompts the most differentiated state may represent a promising therapeutic strategy for NB.
Collapse
Affiliation(s)
- Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Tiziana Bachetti
- U.O. Proteomica e Spettrometria di Massa, IRCSS Ospedale Policlinico San Martino, Genoa, Italy
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Chiara Brignole
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Fabio Pastorino
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Enzo Calarco
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Veronica Bensa
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Elena Giusto
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Isabella Ceccherini
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Patrizia Perri
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy.
| |
Collapse
|
89
|
Liu Q, Guo L, Lou Z, Xiang X, Shao J. Super-enhancers and novel therapeutic targets in colorectal cancer. Cell Death Dis 2022; 13:228. [PMID: 35277481 PMCID: PMC8917125 DOI: 10.1038/s41419-022-04673-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 12/24/2022]
Abstract
Transcription factors, cofactors, chromatin regulators, and transcription apparatuses interact with transcriptional regulatory elements, including promoters, enhancers, and super-enhancers (SEs), to coordinately regulate the transcription of target genes and thereby control cell behaviors. Among these transcriptional regulatory components and related elements, SEs often play a central role in determining cell identity and tumor initiation and progression. Therefore, oncogenic SEs, which are generated within cancer cells in oncogenes and other genes important in tumor pathogenesis, have emerged as attractive targets for novel cancer therapeutic strategies in recent years. Herein, we review the identification, formation and activation modes, and regulatory mechanisms for downstream genes and pathways of oncogenic SEs. We also review the therapeutic strategies and compounds targeting oncogenic SEs in colorectal cancer and other malignancies.
Collapse
Affiliation(s)
- Qian Liu
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lijuan Guo
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhiyuan Lou
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Xueping Xiang
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jimin Shao
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
| |
Collapse
|
90
|
Harada T, Heshmati Y, Kalfon J, Perez MW, Xavier Ferrucio J, Ewers J, Hubbell Engler B, Kossenkov A, Ellegast JM, Yi JS, Bowker A, Zhu Q, Eagle K, Liu T, Kai Y, Dempster JM, Kugener G, Wickramasinghe J, Herbert ZT, Li CH, Vrabič Koren J, Weinstock DM, Paralkar VR, Nabet B, Lin CY, Dharia NV, Stegmaier K, Orkin SH, Pimkin M. A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia. Genes Dev 2022; 36:368-389. [PMID: 35301220 PMCID: PMC8973843 DOI: 10.1101/gad.349284.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/22/2022] [Indexed: 12/12/2022]
Abstract
In this study, Harada et al. identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. This study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes. Acute myeloid leukemia with KMT2A (MLL) rearrangements is characterized by specific patterns of gene expression and enhancer architecture, implying unique core transcriptional regulatory circuitry. Here, we identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. Rapid transcription factor degradation followed by measurements of genome-wide transcription rates and superresolution microscopy revealed that MEF2D and IRF8 form a distinct core regulatory module with a narrow direct transcriptional program that includes activation of the key oncogenes MYC, HOXA9, and BCL2. Our study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes.
Collapse
Affiliation(s)
- Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yaser Heshmati
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jérémie Kalfon
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Monika W Perez
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Juliana Xavier Ferrucio
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jazmin Ewers
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Benjamin Hubbell Engler
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | | | - Jana M Ellegast
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Joanna S Yi
- Baylor College of Medicine, Houston, Texas 77030, USA
| | - Allyson Bowker
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Qian Zhu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Kenneth Eagle
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Ken Eagle Consulting, Houston, Texas 77494, USA
| | - Tianxin Liu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yan Kai
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Joshua M Dempster
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Guillaume Kugener
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Zachary T Herbert
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | | | - David M Weinstock
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Vikram R Paralkar
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Charles Y Lin
- Baylor College of Medicine, Houston, Texas 77030, USA
| | - Neekesh V Dharia
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kimberly Stegmaier
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Stuart H Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02215, USA
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| |
Collapse
|
91
|
Benbarche S, Lopez CK, Salataj E, Aid Z, Thirant C, Laiguillon MC, Lecourt S, Belloucif Y, Vaganay C, Antonini M, Hu J, da Silva Babinet A, Ndiaye-Lobry D, Pardieu B, Petit A, Puissant A, Chaumeil J, Mercher T, Lobry C. Screening of ETO2-GLIS2-induced Super Enhancers identifies targetable cooperative dependencies in acute megakaryoblastic leukemia. SCIENCE ADVANCES 2022; 8:eabg9455. [PMID: 35138899 PMCID: PMC8827662 DOI: 10.1126/sciadv.abg9455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Super Enhancers (SEs) are clusters of regulatory elements associated with cell identity and disease. However, whether these elements are induced by oncogenes and can regulate gene modules cooperating for cancer cell transformation or maintenance remains elusive. To address this question, we conducted a genome-wide CRISPRi-based screening of SEs in ETO2-GLIS2+ acute megakaryoblastic leukemia. This approach revealed SEs essential for leukemic cell growth and survival that are induced by ETO2-GLIS2 expression. In particular, we identified a de novo SE specific of this leukemia subtype and regulating expression of tyrosine kinase-associated receptors KIT and PDGFRA. Combined expression of these two receptors was required for leukemic cell growth, and CRISPRi-mediated inhibition of this SE or treatment with tyrosine kinase inhibitors impaired progression of leukemia in vivo in patient-derived xenografts experiments. Our results show that fusion oncogenes, such as ETO2-GLIS2, can induce activation of SEs regulating essential gene modules synergizing for leukemia progression.
Collapse
Affiliation(s)
- Salima Benbarche
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
| | - Cécile K. Lopez
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
| | - Eralda Salataj
- Université de Paris, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Zakia Aid
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
| | - Cécile Thirant
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
| | | | - Séverine Lecourt
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
| | - Yannis Belloucif
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Camille Vaganay
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Marion Antonini
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
| | - Jiang Hu
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | | | | | - Bryann Pardieu
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Arnaud Petit
- Hôpital Trousseau, Sorbonne Université, Assistance Publique - Hôpitaux de Paris CONECT-AML, Paris F-75012, France
| | - Alexandre Puissant
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
| | - Julie Chaumeil
- Université de Paris, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Thomas Mercher
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris F-75013, France
- Corresponding author. (C.L.); (T.M.)
| | - Camille Lobry
- INSERM U1170, Gustave Roussy Cancer Center and Université Paris Saclay, Villejuif F-94800, France
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis and Université de Paris, Paris F-75010, France
- Corresponding author. (C.L.); (T.M.)
| |
Collapse
|
92
|
Super enhancers as master gene regulators in the pathogenesis of hematologic malignancies. Biochim Biophys Acta Rev Cancer 2022; 1877:188697. [PMID: 35150791 DOI: 10.1016/j.bbcan.2022.188697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/20/2022] [Accepted: 02/04/2022] [Indexed: 12/17/2022]
Abstract
Transcriptional deregulation of multiple oncogenes, tumor suppressors and survival pathways is a cancer cell hallmark. Super enhancers (SE) are long stretches of active enhancers in close linear proximity that ensure extraordinarily high expression levels of key genes associated with cell lineage, function and survival. SE landscape is intrinsically prone to changes and reorganization during the course of normal cell differentiation. This functional plasticity is typically utilized by cancer cells, which remodel their SE landscapes to ensure oncogenic transcriptional reprogramming. Multiple recent studies highlighted structural genetic mechanisms in non-coding regions that create new SE or hijack already existing ones. In addition, alterations in abundance/activity of certain SE-associated proteins or certain viral infections can elicit new super enhancers and trigger SE-driven transcriptional changes. For these reasons, SE profiling emerged as a powerful tool for discovering the core transcriptional regulatory circuits in tumor cells. This, in turn, provides new insights into cancer cell biology, and identifies main nodes of key cellular pathways to be potentially targeted. Since SEs are susceptible to inhibition, their disruption results in exponentially amassing 'butterfly' effect on gene expression and cell function. Moreover, many of SE elements are druggable, opening new therapeutic opportunities. Indeed, SE targeting drugs have been studied preclinically in various hematologic malignancies with promising effects. Herein, we review the unique features of SEs, present different cis- and trans-acting mechanisms through which hematologic tumor cells acquire SEs, and finally, discuss the potential of SE targeting in the therapy of hematologic malignancies.
Collapse
|
93
|
Du F, Peng L, Wang Q, Dong K, Pei W, Zhuo H, Xu T, Jing C, Li L, Zhang J. CCDC12 promotes tumor development and invasion through the Snail pathway in colon adenocarcinoma. Cell Death Dis 2022; 13:187. [PMID: 35217636 PMCID: PMC8881494 DOI: 10.1038/s41419-022-04617-y] [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: 08/09/2021] [Revised: 01/10/2022] [Accepted: 02/09/2022] [Indexed: 12/02/2022]
Abstract
Integrative expression Quantitative Trait Loci (eQTL) analysis found that rs8180040 was significantly associated with Coiled-coil domain containing 12 (CCDC12) in colon adenocarcinoma (COAD) patients. Immunohistochemical staining and western blotting confirmed CCDC12 was highly expressed in COAD tissues, which was consistent with RNA-Seq data from the TCGA database. Knockdown of CCDC12 could significantly reduce proliferation, migration, invasion, and tumorigenicity of colon cancer cells, while exogenous overexpression of CCDC12 had the opposite effect. Four plex Isobaric Tags for Relative and Absolute Quantitation assays were performed to determine its function and potential regulatory mechanism and demonstrated that overexpression of CCDC12 would change proteins on the adherens junction pathway. Overexpressed Snail and knocked down CCDC12 subsequently in SW480 cells, and we found that overexpression of Snail did not significantly change CCDC12 levels in SW480 cells, while knockdown of CCDC12 reduced that of Snail. CCDC12 plays a significant role in tumorigenesis, development, and invasion of COAD and may affect the epithelial to mesenchymal transformation process of colon cancer cells by regulating the Snail pathway.
Collapse
|
94
|
Qiu Z, Zhao L, Shen JZ, Liang Z, Wu Q, Yang K, Min L, Gimple RC, Yang Q, Bhargava S, Jin C, Kim C, Hinz D, Dixit D, Bernatchez JA, Prager BC, Zhang G, Dong Z, Lv D, Wang X, Kim LJ, Zhu Z, Jones KA, Zheng Y, Wang X, Siqueira-Neto JL, Chavez L, Fu XD, Spruck C, Rich JN. Transcription Elongation Machinery Is a Druggable Dependency and Potentiates Immunotherapy in Glioblastoma Stem Cells. Cancer Discov 2022; 12:502-521. [PMID: 34615656 PMCID: PMC8831451 DOI: 10.1158/2159-8290.cd-20-1848] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 07/03/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022]
Abstract
Glioblastoma (GBM) is the most lethal primary brain cancer characterized by therapeutic resistance, which is promoted by GBM stem cells (GSC). Here, we interrogated gene expression and whole-genome CRISPR/Cas9 screening in a large panel of patient-derived GSCs, differentiated GBM cells (DGC), and neural stem cells (NSC) to identify master regulators of GSC stemness, revealing an essential transcription state with increased RNA polymerase II-mediated transcription. The YY1 and transcriptional CDK9 complex was essential for GSC survival and maintenance in vitro and in vivo. YY1 interacted with CDK9 to regulate transcription elongation in GSCs. Genetic or pharmacologic targeting of the YY1-CDK9 complex elicited RNA m6A modification-dependent interferon responses, reduced regulatory T-cell infiltration, and augmented efficacy of immune checkpoint therapy in GBM. Collectively, these results suggest that YY1-CDK9 transcription elongation complex defines a targetable cell state with active transcription, suppressed interferon responses, and immunotherapy resistance in GBM. SIGNIFICANCE: Effective strategies to rewire immunosuppressive microenvironment and enhance immunotherapy response are still lacking in GBM. YY1-driven transcriptional elongation machinery represents a druggable target to activate interferon response and enhance anti-PD-1 response through regulating the m6A modification program, linking epigenetic regulation to immunomodulatory function in GBM.This article is highlighted in the In This Issue feature, p. 275.
Collapse
Affiliation(s)
- Zhixin Qiu
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.,Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Linjie Zhao
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.,Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jia Z. Shen
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Zhengyu Liang
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qiulian Wu
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.,Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Lihua Min
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Ryan C. Gimple
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Qiyuan Yang
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shruti Bhargava
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Chunyu Jin
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cheryl Kim
- Flow Cytometry Core Facility, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Denise Hinz
- Flow Cytometry Core Facility, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Deobrat Dixit
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jean A. Bernatchez
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Briana C. Prager
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Guoxin Zhang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Zhen Dong
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Deguan Lv
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.,Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Xujun Wang
- SJTU-Yale Joint Center for Biostatistics, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Leo J.Y. Kim
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Zhe Zhu
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Katherine A. Jones
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ye Zheng
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Xiuxing Wang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.,School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jair L. Siqueira-Neto
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Lukas Chavez
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Charles Spruck
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.
| | - Jeremy N. Rich
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.,Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA.,Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA.,Corresponding Authors: Jeremy N. Rich: ; +1(412) 623-3364; Address: UPMC Hillman Cancer Center, 5115 Centre Ave, Pittsburgh, PA 15232; Charles Spruck: ; +1(858) 401-3459; Address: 10901 N Torrey Pines Rd, La Jolla, CA 92037
| |
Collapse
|
95
|
CDK7 Predicts Worse Outcome in Head and Neck Squamous-Cell Cancer. Cancers (Basel) 2022; 14:cancers14030492. [PMID: 35158760 PMCID: PMC8833595 DOI: 10.3390/cancers14030492] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/03/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
HNSCC is the sixth most common cancer worldwide and the prognosis is still poor. Here, we investigated the prognostic implications of CDK7 and pMED1. Both proteins affect transcription, and their expression is altered throughout different tumor entities. pMED1 is phosphorylated by CDK7. Importantly, CDK7 and MED1 have been ascribed prognostic implications by various studies. However, their prognostic value in head and neck squamous-cell cancer (HNSCC) remains elusive. We applied immunohistochemical staining of CDK7 and pMED1 on our large and clinically well-characterized HNSCC tissue cohort comprising 419 patients. Software-aided quantification of staining intensity was performed as a measure of protein expression. The following results were linked to the clinicopathological features of our cohort and correlated in different tissue types (primary tumor, lymph node metastasis, distant metastasis, recurrence). Upregulation CDK7 was associated with worse 5-year overall survival as well as disease-free survival in HNSCC while being independent of other known prognostic factors such as p16-status. Also, CDK7 expression was significantly elevated in immune cell infiltrated tumors. In HNSCC CDK7 might serve as a novel prognostic marker to indicate the prognosis of patients. Furthermore, in vitro studies proved the feasibility of CDK7 inhibition with attenuating effects on cell proliferation underlining its remarkable translational potential for future therapeutic regimes.
Collapse
|
96
|
Yuan J, Li X, Yu S. CDK7-dependent transcriptional addiction in bone and soft tissue sarcomas: Present and Future. Biochim Biophys Acta Rev Cancer 2022; 1877:188680. [PMID: 35051528 DOI: 10.1016/j.bbcan.2022.188680] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/25/2022]
Abstract
Cancer arises from genetic alterations that invariably contribute to dysregulated transcriptional programs. These dysregulated programs establish and maintain specific cancer cell states, leading to an intensive dependence on a set of certain regulators of gene expression. The CDK7 functions as the core of transcription, and governs RNA polymerase II and the downstream oncogenes expression in cancers. CDK7 inhibition leads to reduced recruitment of super-enhancers-driven oncogenic transcription factors, and the depression of these associated oncogenes expression, which indicates the dependence of transcriptional addiction of cancers on CDK7. Given that specified oncoproteins of sarcomas commonly function at oncogenic transcription, targeting CDK7-denpendent transcriptional addiction may be of guiding significance for the treatment of sarcomas. In this review, we summarize the advances in mechanism of targeted CDK7-dependent transcriptional addiction and discuss the path ahead to potential application discovery in bone and soft tissue sarcomas, providing theoretical considerations for bio-orthogonal therapeutic strategies.
Collapse
Affiliation(s)
- Jin Yuan
- Department of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyang Li
- Department of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical sciences and Peking Union Medical College, Beijing, China.
| | - Shengji Yu
- Department of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical sciences and Peking Union Medical College, Beijing, China.
| |
Collapse
|
97
|
Belloucif Y, Lobry C. Super-Enhancers Dysregulations in Hematological Malignancies. Cells 2022; 11:196. [PMID: 35053311 PMCID: PMC8774084 DOI: 10.3390/cells11020196] [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: 11/15/2021] [Revised: 12/17/2021] [Accepted: 12/27/2021] [Indexed: 01/27/2023] Open
Abstract
Hematological malignancies affecting either the lymphoid or the myeloid lineages involve epigenetic mutations or dysregulation in the majority of cases. These epigenetic abnormalities can affect regulatory elements in the genome and, particularly, enhancers. Recently, large regulatory elements known as super-enhancers, initially identified for their critical roles in cell-type specific expression regulation of genes controlling cell identity, have been shown to also be involved in tumorigenesis in many cancer types and hematological malignancies via the regulation of numerous oncogenes, including MYC. In this review, we highlight the existing links between super-enhancers and hematological malignancies, with a particular focus on acute myeloid leukemia, a clonal hematopoietic neoplasm with dismal outcomes, resulting in an uncontrolled proliferation of myeloblasts, abnormally blocked during differentiation and accumulating within the patient's bone marrow. We report recent works, performed during the last few years, treating this subject and consider the possibility of targeting oncogenic regulatory elements, as well as the effectiveness and limitations reported so far for such strategies.
Collapse
Affiliation(s)
| | - Camille Lobry
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis, Université de Paris, 75010 Paris, France;
| |
Collapse
|
98
|
Takeda T, Yokoyama Y, Takahashi H, Okuzaki D, Asai K, Itakura H, Miyoshi N, Kobayashi S, Uemura M, Fujita T, Ueno H, Mori M, Doki Y, Fujii H, Eguchi H, Yamamoto H. A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells. Br J Cancer 2022; 126:109-119. [PMID: 34707247 PMCID: PMC8727571 DOI: 10.1038/s41416-021-01579-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND KLF5 plays a crucial role in stem cells of colorectum in cooperation with Lgr5 gene. In this study, we aimed to explicate a regulatory mechanism of the KLF5 gene product from a view of three-dimensional genome structure in colorectal cancer (CRC). METHODS In vitro engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP)-seq method was used to identify the regions that bind to the KLF5 promoter. RESULTS We revealed that the KLF5 promoter region interacted with the KLF5 enhancer region as well as the transcription start site (TSS) region of the Colon Cancer Associated Transcript 1 (CCAT1) gene. Notably, the heterodeletion mutants of KLF5 enhancer impaired the cancer stem-like properties of CRC cells. The KLF5 protein participated in the core-regulatory circuitry together with co-factors (BRD4, MED1, and RAD21), which constructs the three-dimensional genome structures consisting of KLF5 promoter, enhancer and CCAT1 TSS region. In vitro analysis indicated that KLF5 regulated CCAT1 expression and we found that CCAT1 expression was highly correlated with KLF5 expression in CRC clinical samples. CONCLUSIONS Our data propose the mechanistic insight that the KLF5 protein constructs the core-regulatory circuitry with co-factors in the three-dimensional genome structure and coordinately regulates KLF5 and CCAT1 expression in CRC.
Collapse
Affiliation(s)
- Takashi Takeda
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuhki Yokoyama
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, 1-7, Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Hidekazu Takahashi
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Daisuke Okuzaki
- Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, 3-1, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kaho Asai
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, 1-7, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroaki Itakura
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Norikatsu Miyoshi
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shogo Kobayashi
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mamoru Uemura
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Hiroo Ueno
- Department of Stem Cell Pathology, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
| | - Masaki Mori
- School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Yuichiro Doki
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Hidetoshi Eguchi
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hirofumi Yamamoto
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, 1-7, Yamadaoka, Suita, Osaka, 565-0871, Japan
| |
Collapse
|
99
|
Nuñez-Olvera SI, Puente-Rivera J, Ramos-Payán R, Pérez-Plasencia C, Salinas-Vera YM, Aguilar-Arnal L, López-Camarillo C. Three-Dimensional Genome Organization in Breast and Gynecological Cancers: How Chromatin Folding Influences Tumorigenic Transcriptional Programs. Cells 2021; 11:75. [PMID: 35011637 PMCID: PMC8750285 DOI: 10.3390/cells11010075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/15/2021] [Accepted: 12/24/2021] [Indexed: 12/19/2022] Open
Abstract
A growing body of research on the transcriptome and cancer genome has demonstrated that many gynecological tumor-specific gene mutations are located in cis-regulatory elements. Through chromosomal looping, cis-regulatory elements interact which each other to control gene expression by bringing distant regulatory elements, such as enhancers and insulators, into close proximity with promoters. It is well known that chromatin connections may be disrupted in cancer cells, promoting transcriptional dysregulation and the expression of abnormal tumor suppressor genes and oncogenes. In this review, we examine the roles of alterations in 3D chromatin interactions. This includes changes in CTCF protein function, cancer-risk single nucleotide polymorphisms, viral integration, and hormonal response as part of the mechanisms that lead to the acquisition of enhancers or super-enhancers. The translocation of existing enhancers, as well as enhancer loss or acquisition of insulator elements that interact with gene promoters, is also revised. Remarkably, similar processes that modify 3D chromatin contacts in gene promoters may also influence the expression of non-coding RNAs, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), which have emerged as key regulators of gene expression in a variety of cancers, including gynecological malignancies.
Collapse
Affiliation(s)
- Stephanie I. Nuñez-Olvera
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Jonathan Puente-Rivera
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico;
| | - Rosalio Ramos-Payán
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacan City 80030, Mexico;
| | | | - Yarely M. Salinas-Vera
- Departamento de Bioquímica, Centro de Investigación y Estudios Avanzados, Mexico City 07360, Mexico;
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico;
| |
Collapse
|
100
|
Perri P, Ponzoni M, Corrias MV, Ceccherini I, Candiani S, Bachetti T. A Focus on Regulatory Networks Linking MicroRNAs, Transcription Factors and Target Genes in Neuroblastoma. Cancers (Basel) 2021; 13:5528. [PMID: 34771690 PMCID: PMC8582685 DOI: 10.3390/cancers13215528] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/17/2022] Open
Abstract
Neuroblastoma (NB) is a tumor of the peripheral sympathetic nervous system that substantially contributes to childhood cancer mortality. NB originates from neural crest cells (NCCs) undergoing a defective sympathetic neuronal differentiation and although the starting events leading to the development of NB remain to be fully elucidated, the master role of genetic alterations in key oncogenes has been ascertained: (1) amplification and/or over-expression of MYCN, which is strongly associated with tumor progression and invasion; (2) activating mutations, amplification and/or over-expression of ALK, which is involved in tumor initiation, angiogenesis and invasion; (3) amplification and/or over-expression of LIN28B, promoting proliferation and suppression of neuroblast differentiation; (4) mutations and/or over-expression of PHOX2B, which is involved in the regulation of NB differentiation, stemness maintenance, migration and metastasis. Moreover, altered microRNA (miRNA) expression takes part in generating pathogenetic networks, in which the regulatory loops among transcription factors, miRNAs and target genes lead to complex and aberrant oncogene expression that underlies the development of a tumor. In this review, we have focused on the circuitry linking the oncogenic transcription factors MYCN and PHOX2B with their transcriptional targets ALK and LIN28B and the tumor suppressor microRNAs let-7, miR-34 and miR-204, which should act as down-regulators of their expression. We have also looked at the physiologic role of these genetic and epigenetic determinants in NC development, as well as in terminal differentiation, with their pathogenic dysregulation leading to NB oncogenesis.
Collapse
Affiliation(s)
- Patrizia Perri
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.P.); (M.V.C.)
| | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.P.); (M.V.C.)
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.P.); (M.V.C.)
| | - Isabella Ceccherini
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Simona Candiani
- Department of Earth, Environment and Life Sciences, University of Genoa, 16132 Genoa, Italy;
| | - Tiziana Bachetti
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
- Department of Earth, Environment and Life Sciences, University of Genoa, 16132 Genoa, Italy;
| |
Collapse
|