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Shan L, Wang W, Du L, Li D, Wang Y, Xie Y, Li H, Wang J, Shi Z, Zhou Y, Zhu D, Sui G, Liu F. SP1 undergoes phase separation and activates RGS20 expression through super-enhancers to promote lung adenocarcinoma progression. Proc Natl Acad Sci U S A 2024; 121:e2401834121. [PMID: 38976739 DOI: 10.1073/pnas.2401834121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/28/2024] [Indexed: 07/10/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is the leading cause of cancer-related death worldwide, but the underlying molecular mechanisms remain largely unclear. The transcription factor (TF) specificity protein 1 (SP1) plays a crucial role in the development of various cancers, including LUAD. Recent studies have indicated that master TFs may form phase-separated macromolecular condensates to promote super-enhancer (SE) assembly and oncogene expression. In this study, we demonstrated that SP1 undergoes phase separation and that its zinc finger 3 in the DNA-binding domain is essential for this process. Through Cleavage Under Targets & Release Using Nuclease (CUT&RUN) using antibodies against SP1 and H3K27ac, we found a significant correlation between SP1 enrichment and SE elements, identified the regulator of the G protein signaling 20 (RGS20) gene as the most likely target regulated by SP1 through SE mechanisms, and verified this finding using different approaches. The oncogenic activity of SP1 relies on its phase separation ability and RGS20 gene activation, which can be abolished by glycogen synthase kinase J4 (GSK-J4), a demethylase inhibitor. Together, our findings provide evidence that SP1 regulates its target oncogene expression through phase separation and SE mechanisms, thereby promoting LUAD cell progression. This study also revealed an innovative target for LUAD therapies through intervening in SP1-mediated SE formation.
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Affiliation(s)
- Liying Shan
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Lijuan Du
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yunxuan Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Yuyan Xie
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Hongyan Li
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Jiale Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Zhihao Shi
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Yang Zhou
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Daling Zhu
- College of Pharmacy, Harbin Medical University (Daqing), Daqing 163319, China
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Fang Liu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
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Di Marco T, Mazzoni M, Greco A, Cassinelli G. Non-oncogene dependencies: Novel opportunities for cancer therapy. Biochem Pharmacol 2024:116254. [PMID: 38704100 DOI: 10.1016/j.bcp.2024.116254] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Targeting oncogene addictions have changed the history of subsets of malignancies and continues to represent an excellent therapeutic opportunity. Nonetheless, alternative strategies are required to treat malignancies driven by undruggable oncogenes or loss of tumor suppressor genes and to overcome drug resistance also occurring in cancers addicted to actionable drivers. The discovery of non-oncogene addiction (NOA) uncovered novel therapeutically exploitable "Achilles' heels". NOA refers to genes/pathways not oncogenic per sé but essential for the tumor cell growth/survival while dispensable for normal cells. The clinical success of several classes of conventional and molecular targeted agents can be ascribed to their impact on both tumor cell-associated intrinsic as well as microenvironment-related extrinsic NOA. The integration of genetic, computational and pharmacological high-throughput approaches led to the identification of an expanded repertoire of synthetic lethality interactions implicating NOA targets. Only a few of them have been translated into the clinics as most NOA vulnerabilities are not easily druggable or appealing targets. Nonetheless, their identification has provided in-depth knowledge of tumor pathobiology and suggested novel therapeutic opportunities. Here, we summarize conceptual framework of intrinsic and extrinsic NOA providing exploitable vulnerabilities. Conventional and emerging methodological approaches used to disclose NOA dependencies are reported together with their limits. We illustrate NOA paradigmatic and peculiar examples and outline the functional/mechanistic aspects, potential druggability and translational interest. Finally, we comment on difficulties in exploiting the NOA-generated knowledge to develop novel therapeutic approaches to be translated into the clinics and to fully harness the potential of clinically available drugs.
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Affiliation(s)
- Tiziana Di Marco
- Integrated Biology of Rare Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy
| | - Mara Mazzoni
- Integrated Biology of Rare Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy
| | - Angela Greco
- Integrated Biology of Rare Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy
| | - Giuliana Cassinelli
- Molecular Pharmacology Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy.
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3
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Pandini C, Pagani G, Tassinari M, Vitale E, Bezzecchi E, Saadeldin MK, Doldi V, Giannuzzi G, Mantovani R, Chiara M, Ciarrocchi A, Gandellini P. The pancancer overexpressed NFYC Antisense 1 controls cell cycle mitotic progression through in cis and in trans modes of action. Cell Death Dis 2024; 15:206. [PMID: 38467619 PMCID: PMC10928104 DOI: 10.1038/s41419-024-06576-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024]
Abstract
Antisense RNAs (asRNAs) represent an underappreciated yet crucial layer of gene expression regulation. Generally thought to modulate their sense genes in cis through sequence complementarity or their act of transcription, asRNAs can also regulate different molecular targets in trans, in the nucleus or in the cytoplasm. Here, we performed an in-depth molecular characterization of NFYC Antisense 1 (NFYC-AS1), the asRNA transcribed head-to-head to NFYC subunit of the proliferation-associated NF-Y transcription factor. Our results show that NFYC-AS1 is a prevalently nuclear asRNA peaking early in the cell cycle. Comparative genomics suggests a narrow phylogenetic distribution, with a probable origin in the common ancestor of mammalian lineages. NFYC-AS1 is overexpressed pancancer, preferentially in association with RB1 mutations. Knockdown of NFYC-AS1 by antisense oligonucleotides impairs cell growth in lung squamous cell carcinoma and small cell lung cancer cells, a phenotype recapitulated by CRISPR/Cas9-deletion of its transcription start site. Surprisingly, expression of the sense gene is affected only when endogenous transcription of NFYC-AS1 is manipulated. This suggests that regulation of cell proliferation is at least in part independent of the in cis transcription-mediated effect on NFYC and is possibly exerted by RNA-dependent in trans effects converging on the regulation of G2/M cell cycle phase genes. Accordingly, NFYC-AS1-depleted cells are stuck in mitosis, indicating defects in mitotic progression. Overall, NFYC-AS1 emerged as a cell cycle-regulating asRNA with dual action, holding therapeutic potential in different cancer types, including the very aggressive RB1-mutated tumors.
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Affiliation(s)
- Cecilia Pandini
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Giulia Pagani
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Martina Tassinari
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Emanuele Vitale
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Via Università 4, 41121, Modena, Italy
| | - Eugenia Bezzecchi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Mona Kamal Saadeldin
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
- Biology Department, School of Science and Engineering, The American University in Cairo, New Cairo, 11835, Egypt
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Valentina Doldi
- Molecular Pharmacology Unit, Department of Experimental Oncology, Fondazione IRCSS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133, Milan, Italy
| | - Giuliana Giannuzzi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Roberto Mantovani
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy.
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AGBEKTAS T, ZONTUL C, OZTURK A, HUSEYNZADA A, GANBAROVA R, HASANOVA U, CINAR G, TAS A, KAYA S, CHTITA S, SİLİG Y. EFFECT of AZOMETHINE GROUP CONTAINING COMPOUNDS on GENE PROFILES in Wnt and MAPK SIGNAL PATTERNS in LUNG CANCER CELL LINE: In Silico and In Vitro ANALYSES. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Kawabata A, Hayashi T, Akasu-Nagayoshi Y, Yamada A, Shimizu N, Yokota N, Nakato R, Shirahige K, Okamoto A, Akiyama T. CRISPR/Cas9 Screening for Identification of Genes Required for the Growth of Ovarian Clear Cell Carcinoma Cells. Curr Issues Mol Biol 2022; 44:1587-1596. [PMID: 35723366 PMCID: PMC9164056 DOI: 10.3390/cimb44040108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022] Open
Abstract
Epithelial ovarian cancer is classified into four major histological subtypes: serous, clear cell, endometrioid and mucinous. Ovarian clear cell carcinoma (OCCC) responds poorly to conventional chemotherapies and shows poor prognosis. Thus, there is a need to develop new drugs for the treatment of OCCC. In this study, we performed CRISPR/Cas9 screens against OCCC cell lines and identified candidate genes important for their proliferation. We found that quite different genes are required for the growth of ARID1A and PIK3CA mutant and wild-type OCCC cell lines, respectively. Furthermore, we found that the epigenetic regulator KDM2A and the translation regulator PAIP1 may play important roles in the growth of ARID1A and PIK3CA mutant, but not wild-type, OCCC cells. The results of our CRISPR/Cas9 screening may be useful in elucidating the molecular mechanism of OCCC tumorigenesis and in developing OCCC-targeted drugs.
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Affiliation(s)
- Ayako Kawabata
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan;
| | - Tomoatsu Hayashi
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
| | - Yoko Akasu-Nagayoshi
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan;
| | - Ai Yamada
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
| | - Naomi Shimizu
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
| | - Naoko Yokota
- Laboratory of Computational Genetics, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (N.Y.); (R.N.)
| | - Ryuichiro Nakato
- Laboratory of Computational Genetics, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (N.Y.); (R.N.)
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan;
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan;
| | - Tetsu Akiyama
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; (A.K.); (Y.A.-N.); (A.Y.); (N.S.)
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