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Sachs P, Bergmaier P, Treutwein K, Mermoud JE. The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse. Genes (Basel) 2023; 14:1793. [PMID: 37761933 PMCID: PMC10530723 DOI: 10.3390/genes14091793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
In vertebrates, SMARCAD1 participates in transcriptional regulation, heterochromatin maintenance, DNA repair, and replication. The molecular basis underlying its involvement in these processes is not well understood. We identified the RNA polymerase III general transcription factor TFIIIC as an interaction partner of native SMARCAD1 in mouse and human models using endogenous co-immunoprecipitations. TFIIIC has dual functionality, acting as a general transcription factor and as a genome organizer separating chromatin domains. We found that its partnership with SMARCAD1 is conserved across different mammalian cell types, from somatic to pluripotent cells. Using purified proteins, we confirmed that their interaction is direct. A gene expression analysis suggested that SMARCAD1 is dispensable for TFIIIC function as an RNA polymerase III transcription factor in mouse ESCs. The distribution of TFIIIC and SMARCAD1 in the ESC genome is distinct, and unlike in yeast, SMARCAD1 is not enriched at active tRNA genes. Further analysis of SMARCAD1-binding partners in pluripotent and differentiated mammalian cells reveals that SMARCAD1 associates with several factors that have key regulatory roles in chromatin organization, such as cohesin, laminB, and DDX5. Together, our work suggests for the first time that the SMARCAD1 enzyme participates in genome organization in mammalian nuclei through interactions with architectural proteins.
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Affiliation(s)
- Parysatis Sachs
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
- CMC Development, R&D, Sanofi, 65926 Frankfurt, Germany
| | - Philipp Bergmaier
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
- Global Development Operations, R&D, Merck Healthcare, 64293 Darmstadt, Germany
| | - Katrin Treutwein
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
| | - Jacqueline E. Mermoud
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
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2
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Bhandari N, Acharya D, Chatterjee A, Mandve L, Kumar P, Pratap S, Malakar P, Shukla SK. Pan-cancer integrated bioinformatic analysis of RNA polymerase subunits reveal RNA Pol I member CD3EAP regulates cell growth by modulating autophagy. Cell Cycle 2023; 22:1986-2002. [PMID: 37795959 PMCID: PMC10761113 DOI: 10.1080/15384101.2023.2265676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 09/27/2023] [Indexed: 10/06/2023] Open
Abstract
Transcription is a crucial stage in gene expression. An integrated study of 34 RNA polymerase subunits (RNAPS) in the six most frequent cancer types identified several genetic and epigenetic modification. We discovered nine mutant RNAPS with a mutation frequency of more than 1% in at least one tumor type. POLR2K and POLR2H were found to be amplified and overexpressed, whereas POLR3D was deleted and downregulated. Multiple RNAPS were also observed to be regulated by variations in promoter methylation. 5-Aza-2-deoxycytidine mediated re-expression in cell lines verified methylation-driven inhibition of POLR2F and POLR2L expression in BRCA and NSCLC, respectively. Next, we showed that CD3EAP, a Pol I subunit, was overexpressed in all cancer types and was associated with worst survival in breast, liver, lung, and prostate cancers. The knockdown studies showed that CD3EAP is required for cell proliferation and induces autophagy but not apoptosis. Furthermore, autophagy inhibition rescued the cell proliferation in CD3EAP knockdown cells. CD3EAP expression correlated with S and G2 phase cell cycle regulators, and CD3EAP knockdown inhibited the expression of S and G2 CDK/cyclins. We also identified POLR2D, an RNA pol II subunit, as a commonly overexpressed and prognostic gene in multiple cancers. POLR2D knockdown also decreased cell proliferation. POLR2D is related to the transcription of just a subset of RNA POL II transcribe genes, indicating a distinct role. Taken together, we have shown the genetic and epigenetic regulation of RNAPS genes in most common tumors. We have also demonstrated the cancer-specific function of CD3EAP and POLR2D genes.
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Affiliation(s)
- Nikita Bhandari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Disha Acharya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Annesha Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Lakshana Mandve
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Pranjal Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Shreesh Pratap
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Pushkar Malakar
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sudhanshu K. Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
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3
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Seifert-Davila W, Girbig M, Hauptmann L, Hoffmann T, Eustermann S, Müller CW. Structural insights into human TFIIIC promoter recognition. SCIENCE ADVANCES 2023; 9:eadh2019. [PMID: 37418517 DOI: 10.1126/sciadv.adh2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/02/2023] [Indexed: 07/09/2023]
Abstract
Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to most of its target genes. Recognition of intragenic A- and B-box motifs in transfer RNA (tRNA) genes by TFIIIC modules τA and τB is the first critical step for tRNA synthesis but is mechanistically poorly understood. Here, we report cryo-electron microscopy structures of the six-subunit human TFIIIC complex unbound and bound to a tRNA gene. The τB module recognizes the B-box via DNA shape and sequence readout through the assembly of multiple winged-helix domains. TFIIIC220 forms an integral part of both τA and τB connecting the two subcomplexes via a ~550-amino acid residue flexible linker. Our data provide a structural mechanism by which high-affinity B-box recognition anchors TFIIIC to promoter DNA and permits scanning for low-affinity A-boxes and TFIIIB for Pol III activation.
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Affiliation(s)
- Wolfram Seifert-Davila
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Candidate for joint PhD degree from EMBL and Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Mathias Girbig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Luis Hauptmann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thomas Hoffmann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
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4
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The POLR3G Subunit of Human RNA Polymerase III Regulates Tumorigenesis and Metastasis in Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:cancers14235732. [PMID: 36497214 PMCID: PMC9735567 DOI: 10.3390/cancers14235732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
RNA polymerase (Pol) III transcribes short untranslated RNAs that contribute to the regulation of gene expression. Two isoforms of human Pol III have been described that differ by the presence of the POLR3G/RPC32α or POLR3GL/RPC32β subunits. POLR3G was found to be expressed in embryonic stem cells and at least a subset of transformed cells, whereas POLR3GL shows a ubiquitous expression pattern. Here, we demonstrate that POLR3G is specifically overexpressed in clinical samples of triple-negative breast cancer (TNBC) but not in other molecular subtypes of breast cancer. POLR3G KO in the MDA-MB231 TNBC cell line dramatically reduces anchorage-independent growth and invasive capabilities in vitro. In addition, the POLR3G KO impairs tumor growth and metastasis formation of orthotopic xenografts in mice. Moreover, KO of POLR3G induces expression of the pioneer transcription factor FOXA1 and androgen receptor. In contrast, the POLR3G KO neither alters proliferation nor the expression of epithelial-mesenchymal transition marker genes. These data demonstrate that POLR3G expression is required for TNBC tumor growth, invasiveness and dissemination and that its deletion affects triple-negative breast cancer-specific gene expression.
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Lata E, Choquet K, Sagliocco F, Brais B, Bernard G, Teichmann M. RNA Polymerase III Subunit Mutations in Genetic Diseases. Front Mol Biosci 2021; 8:696438. [PMID: 34395528 PMCID: PMC8362101 DOI: 10.3389/fmolb.2021.696438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/21/2021] [Indexed: 12/24/2022] Open
Abstract
RNA polymerase (Pol) III transcribes small untranslated RNAs such as 5S ribosomal RNA, transfer RNAs, and U6 small nuclear RNA. Because of the functions of these RNAs, Pol III transcription is best known for its essential contribution to RNA maturation and translation. Surprisingly, it was discovered in the last decade that various inherited mutations in genes encoding nine distinct subunits of Pol III cause tissue-specific diseases rather than a general failure of all vital functions. Mutations in the POLR3A, POLR3C, POLR3E and POLR3F subunits are associated with susceptibility to varicella zoster virus-induced encephalitis and pneumonitis. In addition, an ever-increasing number of distinct mutations in the POLR3A, POLR3B, POLR1C and POLR3K subunits cause a spectrum of neurodegenerative diseases, which includes most notably hypomyelinating leukodystrophy. Furthermore, other rare diseases are also associated with mutations in genes encoding subunits of Pol III (POLR3H, POLR3GL) and the BRF1 component of the TFIIIB transcription initiation factor. Although the causal relationship between these mutations and disease development is widely accepted, the exact molecular mechanisms underlying disease pathogenesis remain enigmatic. Here, we review the current knowledge on the functional impact of specific mutations, possible Pol III-related disease-causing mechanisms, and animal models that may help to better understand the links between Pol III mutations and disease.
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Affiliation(s)
- Elisabeth Lata
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Karine Choquet
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Francis Sagliocco
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Bernard Brais
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Geneviève Bernard
- Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Martin Teichmann
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
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6
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Bi G, Bian Y, Liang J, Yin J, Li R, Zhao M, Huang Y, Lu T, Zhan C, Fan H, Wang Q. Pan-cancer characterization of metabolism-related biomarkers identifies potential therapeutic targets. J Transl Med 2021; 19:219. [PMID: 34030708 PMCID: PMC8142489 DOI: 10.1186/s12967-021-02889-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Background Generally, cancer cells undergo metabolic reprogramming to adapt to energetic and biosynthetic requirements that support their uncontrolled proliferation. However, the mutual relationship between two critical metabolic pathways, glycolysis and oxidative phosphorylation (OXPHOS), remains poorly defined. Methods We developed a “double-score” system to quantify glycolysis and OXPHOS in 9668 patients across 33 tumor types from The Cancer Genome Atlas and classified them into four metabolic subtypes. Multi-omics bioinformatical analyses was conducted to detect metabolism-related molecular features. Results Compared with patients with low glycolysis and high OXPHOS (LGHO), those with high glycolysis and low OXPHOS (HGLO) were consistently associated with worse prognosis. We identified common dysregulated molecular features between different metabolic subgroups across multiple cancers, including gene, miRNA, transcription factor, methylation, and somatic alteration, as well as investigated their mutual interfering relationships. Conclusion Overall, this work provides a comprehensive atlas of metabolic heterogeneity on a pan-cancer scale and identified several potential drivers of metabolic rewiring, suggesting corresponding prognostic and therapeutic utility. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02889-0.
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Affiliation(s)
- Guoshu Bi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Yunyi Bian
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Jiacheng Yin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Runmei Li
- Department of Biostatistics, Public Health, Fudan University, Shanghai, 200000, China
| | - Mengnan Zhao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Yiwei Huang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Tao Lu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China.
| | - Hong Fan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China.
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
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7
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Merle C, Lagarde P, Lartigue L, Chibon F. Acquisition of cancer stem cell capacities after spontaneous cell fusion. BMC Cancer 2021; 21:241. [PMID: 33678155 PMCID: PMC7938600 DOI: 10.1186/s12885-021-07979-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
Background Cancer stem/Initiating cell (CS/IC) hypothesis argues that CS/ICs are responsible of tumour initiation, drug resistance, metastasis or disease relapse. Their detection in several cancers supports this concept. However, their origin is still misunderstood. Cell fusion is shown to take part in the formation of CS/ICs, i.e. fusion between mesenchymal stem cell and cancer cell. In a previous paper, we described that fusion leads to hybrids with metastatic capacity. This process triggered genomic rearrangements in hybrid cells together with increased metastasis development. Here, we hypothesize that cell fusion could be strong enough to provoke a cellular reprogramming and the acquisition of CS/IC properties, promoting metastasis formation. Methods After spontaneous cell fusion between E6E7 (IMR90 with the oncogenes E6 and E7) and RST (IMR90 fully transformed) cell lines, hybrid cells were selected by dual antibiotic selection. Cancer stem cells capacities were evaluated regarding capacity to form spheres, expression of stem cell markers and the presence of ALDHhigh cells. Results Our data show that after cell fusion, all hybrids contain a percentage of cells with CS/ICs properties, regarding. Importantly, we lastly showed that NANOG inhibition in H1 hybrid decreases this migration capacity while having no effect on the corresponding parental cells. Conclusions Altogether these results indicate that the combination of CS/ICs properties and genomic rearrangement in hybrids is likely to be key to tumour progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-07979-2.
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Affiliation(s)
- Candice Merle
- INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31037, Toulouse, France.,University of Toulouse 3, Paul Sabatier, 118 route de Narbonne, 31062, Toulouse Cedex 9, France
| | - Pauline Lagarde
- INSERM U1218, 229 cours de l'Argonne, F-33076, Bordeaux, France
| | - Lydia Lartigue
- INSERM U1218, 229 cours de l'Argonne, F-33076, Bordeaux, France.,University of Bordeaux, 146 rue Léo Saignat, F-33000, Bordeaux, France
| | - Frédéric Chibon
- INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31037, Toulouse, France. .,Institut Claudius Régaud, IUCT-Oncopole, Toulouse, France. .,Present address: CRCT-IUCT-O, 2 avenue Hubert Curien, 31037, Toulouse Cedex 1, France.
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8
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Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states. Nat Struct Mol Biol 2021; 28:210-219. [PMID: 33558764 PMCID: PMC7610652 DOI: 10.1038/s41594-020-00555-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
RNA polymerase III (Pol III) synthesizes transfer RNAs and other short, essential RNAs. Human Pol III misregulation is linked to tumor transformation, neurodegenerative and developmental disorders, and increased sensitivity to viral infections. Here, we present cryo-electron microscopy structures at 2.8 to 3.3 Å resolution of transcribing and unbound human Pol III. We observe insertion of the TFIIS-like subunit RPC10 into the polymerase funnel, providing insights into how RPC10 triggers transcription termination. Our structures resolve elements absent from Saccharomyces cerevisiae Pol III such as the winged-helix domains of RPC5 and an iron-sulfur cluster, which tethers the heterotrimer subcomplex to the core. The cancer-associated RPC7α isoform binds the polymerase clamp, potentially interfering with Pol III inhibition by tumor suppressor MAF1, which may explain why overexpressed RPC7α enhances tumor transformation. Finally, the human Pol III structure allows mapping of disease-related mutations and may contribute to the development of inhibitors that selectively target Pol III for therapeutic interventions.
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9
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Cell-cell fusion of mesenchymal cells with distinct differentiations triggers genomic and transcriptomic remodelling toward tumour aggressiveness. Sci Rep 2020; 10:21634. [PMID: 33303824 PMCID: PMC7729932 DOI: 10.1038/s41598-020-78502-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Cell–cell fusion is a physiological process that is hijacked during oncogenesis and promotes tumour evolution. The main known impact of cell fusion is to promote the formation of metastatic hybrid cells following fusion between mobile leucocytes and proliferating tumour cells. We show here that cell fusion between immortalized myoblasts and transformed fibroblasts, through genomic instability and expression of a specific transcriptomic profile, leads to emergence of hybrid cells acquiring dissemination properties. This is associated with acquisition of clonogenic ability by fused cells. In addition, by inheriting parental properties, hybrid tumours were found to mimic the histological characteristics of a specific histotype of sarcomas: undifferentiated pleomorphic sarcomas with incomplete muscular differentiation. This finding suggests that cell fusion, as macroevolution event, favours specific sarcoma development according to the differentiation lineage of parent cells.
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10
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Dysregulation of Transcription Factor Activity During Formation of Cancer-Associated Fibroblasts. Int J Mol Sci 2020; 21:ijms21228749. [PMID: 33228208 PMCID: PMC7699520 DOI: 10.3390/ijms21228749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/08/2020] [Accepted: 11/17/2020] [Indexed: 01/22/2023] Open
Abstract
The reciprocal interactions between cancer cells and the quiescent fibroblasts leading to the activation of cancer-associated fibroblasts (CAFs) serve an important role in cancer progression. Here, we investigated the activation of transcription factors (TFs) in prostate fibroblasts (WPMY cell line) co-cultured with normal prostate or tumorous cells (RWPE1 and RWPE2 cell lines, respectively). After indirect co-cultures, we performed mRNA-seq and predicted TF activity using mRNA expression profiles with the Systems EPigenomics Inference of Regulatory Activity (SEPIRA) package and the GTEx and mRNA-seq data of 483 cultured fibroblasts. The initial differential expression analysis between time points and experimental conditions showed that co-culture with normal epithelial cells mainly promotes an inflammatory response in fibroblasts, whereas with the cancerous epithelial, it stimulates transformation by changing the expression of the genes associated with microfilaments. TF activity analysis revealed only one positively regulated TF in the RWPE1 co-culture alone, while we observed dysregulation of 45 TFs (7 decreased activity and 38 increased activity) uniquely in co-culture with RWPE2. Pathway analysis showed that these 45 dysregulated TFs in fibroblasts co-cultured with RWPE2 cells may be associated with the RUNX1 and PTEN pathways. Moreover, we showed that observed dysregulation could be associated with FER1L4 expression. We conclude that phenotypic changes in fibroblast responses to co-culturing with cancer epithelium result from orchestrated dysregulation of signaling pathways that favor their transformation and motility rather than proinflammatory status. This dysregulation can be observed both at the TF and transcriptome levels.
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Abstract
In this review, Yeganeh et al. summarize different human diseases that have been linked to defects in the Pol III transcription apparatus or to Pol III products imbalance and discuss the possible underlying mechanisms. RNA polymerase (Pol) III is responsible for transcription of different noncoding genes in eukaryotic cells, whose RNA products have well-defined functions in translation and other biological processes for some, and functions that remain to be defined for others. For all of them, however, new functions are being described. For example, Pol III products have been reported to regulate certain proteins such as protein kinase R (PKR) by direct association, to constitute the source of very short RNAs with regulatory roles in gene expression, or to control microRNA levels by sequestration. Consistent with these many functions, deregulation of Pol III transcribed genes is associated with a large variety of human disorders. Here we review different human diseases that have been linked to defects in the Pol III transcription apparatus or to Pol III products imbalance and discuss the possible underlying mechanisms.
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Affiliation(s)
- Meghdad Yeganeh
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
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12
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Liu X, Zhang W, Wang H, Lai CH, Xu K, Hu H. Increased expression of POLR3G predicts poor prognosis in transitional cell carcinoma. PeerJ 2020; 8:e10281. [PMID: 33194434 PMCID: PMC7646299 DOI: 10.7717/peerj.10281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/09/2020] [Indexed: 11/20/2022] Open
Abstract
Background Previous studies have shown that RNA Polymerase III Subunit G (POLR3G) has oncogenic effects in cultured cells and mice. However, the role of POLR3G in transitional cell carcinoma (TCC) has not been reported. This study explores the potential of POLR3G as a novel molecular marker for TCC. Methods The RNA sequencing data and clinical information of patients with TCC were downloaded from The Cancer Genome Atlas official website. Transcriptome analysis was performed as implemented in the edgeR package to explore whether POLR3G was up-regulated in TCC tissues compared to normal bladder tissues. The expression of POLR3G in bladder cancer cell line T24 and human uroepithelial cell line SV-HUC-1 were detected via quantitative real time polymerase chain reaction (qRT-PCR). Correlations between POLR3G expression and clinicopathological characteristics were analyzed using Mann-Whitney U test or Kruskal-Wallis H test. Clinicopathological characteristics associated with overall survival were explored using the Kaplan-Meier method and Cox regression analyses. Gene set enrichment analysis (GSEA) was performed to explore the associated gene sets enriched in different POLR3G expression phenotypes and the online tool Tumor IMmune Estimation Resource (TIMER) was used to explore the correlation between POLR3G expression and tumor immune infiltration in TCC. Results Transcriptome analysis showed that POLR3G was significantly up-regulated in TCC tissues compared to normal bladder tissues. Furthermore, qRT-PCR revealed high expression of POLR3G in T24 cells compared to SV-HUC-1 cells. Overall, POLR3G expression was associated with race, tumor status, tumor subtype, T classification, and pathological stage. Kaplan-Meier survival analysis revealed that higher POLR3G expression was associated with lower overall survival. The univariate Cox regression model revealed that age at diagnosis, pathological stage, and POLR3G expression were associated with prognosis of TCC patients. Further multivariate analyses identified these three clinicopathological characteristics as independent prognostic factors for overall survival. GSEA analysis showed that several gene sets associated with tumor development and metastasis, including TGF-β signaling, PI3K-AKT-mTOR signaling, and IL6-JAK-STAT3 signaling, were significantly enriched in POLR3G high expression phenotype. Immune infiltration analysis revealed that the expression of POLR3G was significantly correlated with infiltrating levels of immune cells, including CD8+ T cells, neutrophils, and dendritic cells; and the expression of POLR3G was also significantly correlated with the expression of immune checkpoint molecules, such as PD1, PD-L1, PD-L2, CTLA4, LAG3, HAVCR2, and TIGIT. Conclusions POLR3G was up-regulated in TCC and high POLR3G expression correlated with poor prognosis. POLR3G can potentially be used as a prognostic marker for TCC and might be of great value in predicting the response to immunotherapy.
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Affiliation(s)
- Xianhui Liu
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Weiyu Zhang
- Department of Urology, Peking University People's Hospital, Beijing, China.,Peking University Applied Lithotripsy Institute, Peking University People's Hospital, Beijing, China
| | - Huanrui Wang
- Department of Urology, Peking University People's Hospital, Beijing, China.,Peking University Applied Lithotripsy Institute, Peking University People's Hospital, Beijing, China
| | - Chin-Hui Lai
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Kexin Xu
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Hao Hu
- Department of Urology, Peking University People's Hospital, Beijing, China
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13
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Genome remodeling upon mesenchymal tumor cell fusion contributes to tumor progression and metastatic spread. Oncogene 2020; 39:4198-4211. [PMID: 32242148 DOI: 10.1038/s41388-020-1276-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 12/17/2022]
Abstract
Cell fusion in tumor progression mostly refers to the merging of a cancer cell with a cell that has migration and immune escape capabilities such as macrophages. Here we show that spontaneous hybrids made from the fusion of transformed mesenchymal cells with partners from the same lineage undergo nonrecurrent large-scale genomic rearrangements, leading to the creation of highly aneuploid cells with novel phenotypic traits, including metastatic spreading capabilities. Moreover, in contrast to their parents, hybrids were the only cells able to recapitulate in vivo all features of human pleomorphic sarcomas, a rare and genetically complex mesenchymal tumor. Hybrid tumors not only displayed specific mesenchymal markers, but also combined a complex genetic profile with a highly metastatic behavior, like their human counterparts. Finally, we provide evidence that patient-derived pleomorphic sarcoma cells are inclined to spontaneous cell fusion. The resulting hybrids also gain in aggressiveness, exhibiting superior growth capacity in mouse models. Altogether, these results indicate that cell fusion has the potential to promote cancer progression by increasing growth and/or metastatic capacities, regardless of the nature of the companion cell. Moreover, such events likely occur upon sarcoma development, paving the way for better understanding of the biology, and aggressiveness of these tumors.
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Ayoubi LE, Dumay-Odelot H, Chernev A, Boissier F, Minvielle-Sébastia L, Urlaub H, Fribourg S, Teichmann M. The hRPC62 subunit of human RNA polymerase III displays helicase activity. Nucleic Acids Res 2019; 47:10313-10326. [PMID: 31529052 PMCID: PMC6821166 DOI: 10.1093/nar/gkz788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 11/20/2022] Open
Abstract
In Eukaryotes, tRNAs, 5S RNA and U6 RNA are transcribed by RNA polymerase (Pol) III. Human Pol III is composed of 17 subunits. Three specific Pol III subunits form a stable ternary subcomplex (RPC62-RPC39-RPC32α/β) being involved in pre-initiation complex formation. No paralogues for subunits of this subcomplex subunits have been found in Pols I or II, but hRPC62 was shown to be structurally related to the general Pol II transcription factor hTFIIEα. Here we show that these structural homologies extend to functional similarities. hRPC62 as well as hTFIIEα possess intrinsic ATP-dependent 3′-5′ DNA unwinding activity. The ATPase activities of both proteins are stimulated by single-stranded DNA. Moreover, the eWH domain of hTFIIEα can replace the first eWH (eWH1) domain of hRPC62 in ATPase and DNA unwinding assays. Our results identify intrinsic enzymatic activities in hRPC62 and hTFIIEα.
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Affiliation(s)
- Leyla El Ayoubi
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | - Hélène Dumay-Odelot
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
- Correspondence may also be addressed to Hélène Dumay-Odelot.
| | - Aleksandar Chernev
- Max Planck Institute for Biophysical Chemistry, Research group Mass Spectrometry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Fanny Boissier
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | | | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Research group Mass Spectrometry, Am Faßberg 11, 37077 Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center, Robert-Koch-Strasse 420, 37075 Göttingen, Germany
| | - Sébastien Fribourg
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | - Martin Teichmann
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
- To whom correspondence should be addressed. Tel: +33 5 5757 4647;
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15
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Petrie JL, Swan C, Ingram RM, Frame FM, Collins AT, Dumay-Odelot H, Teichmann M, Maitland NJ, White RJ. Effects on prostate cancer cells of targeting RNA polymerase III. Nucleic Acids Res 2019; 47:3937-3956. [PMID: 30820548 PMCID: PMC6486637 DOI: 10.1093/nar/gkz128] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
RNA polymerase (pol) III occurs in two forms, containing either the POLR3G subunit or the related paralogue POLR3GL. Whereas POLR3GL is ubiquitous, POLR3G is enriched in undifferentiated cells. Depletion of POLR3G selectively triggers proliferative arrest and differentiation of prostate cancer cells, responses not elicited when POLR3GL is depleted. A small molecule pol III inhibitor can cause POLR3G depletion, induce similar differentiation and suppress proliferation and viability of cancer cells. This response involves control of the fate-determining factor NANOG by small RNAs derived from Alu short interspersed nuclear elements. Tumour initiating activity in vivo can be reduced by transient exposure to the pol III inhibitor. Untransformed prostate cells appear less sensitive than cancer cells to pol III depletion or inhibition, raising the possibility of a therapeutic window.
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Affiliation(s)
- John L Petrie
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Caroline Swan
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Richard M Ingram
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Fiona M Frame
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Anne T Collins
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hélène Dumay-Odelot
- Université de Bordeaux, ARNA Laboratory, F-33076 Bordeaux, France INSERM, U1212 - CNRS UMR 5320, ARNA Laboratory, F-33000 Bordeaux, France
| | - Martin Teichmann
- Université de Bordeaux, ARNA Laboratory, F-33076 Bordeaux, France INSERM, U1212 - CNRS UMR 5320, ARNA Laboratory, F-33000 Bordeaux, France
| | - Norman J Maitland
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Robert J White
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
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16
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Yeganeh M, Praz V, Carmeli C, Villeneuve D, Rib L, Guex N, Herr W, Delorenzi M, Hernandez N. Differential regulation of RNA polymerase III genes during liver regeneration. Nucleic Acids Res 2019; 47:1786-1796. [PMID: 30597109 PMCID: PMC6393285 DOI: 10.1093/nar/gky1282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/22/2018] [Accepted: 12/14/2018] [Indexed: 12/23/2022] Open
Abstract
Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcription. Our results broadly define a class of genes close to H3K4me3 and Pol II peaks, whose Pol III occupancy is high and stable, and another class, distant from Pol II peaks, whose Pol III occupancy strongly increases after partial hepatectomy. Pol III regulation in the liver thus entails both highly expressed housekeeping genes and genes whose expression can adapt to increased demand.
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Affiliation(s)
- Meghdad Yeganeh
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Viviane Praz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Cristian Carmeli
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland.,Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Dominic Villeneuve
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Leonor Rib
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Guex
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Winship Herr
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Mauro Delorenzi
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Fundamental Oncology and the Ludwig Center for Cancer research, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
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17
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Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts. Int J Mol Sci 2019; 20:ijms20133315. [PMID: 31284509 PMCID: PMC6651528 DOI: 10.3390/ijms20133315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. Alu RNAs, being able to act as gene expression modulators, may be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of Alu RNAs, we generated IMR90 fibroblasts and HeLa cell lines stably overexpressing two slightly different Alu RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-sequencing. Among the genes that were upregulated or downregulated in response to Alu overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry. Accordingly, Alu overexpression was found to promote transition from G1 to S phase, as revealed by flow cytometry. Therefore, increased Alu RNA may contribute to sustained cell proliferation, which is an important factor of cancer development and progression.
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18
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Fusion-mediated chromosomal instability promotes aneuploidy patterns that resemble human tumors. Oncogene 2019; 38:6083-6094. [PMID: 31270395 DOI: 10.1038/s41388-019-0859-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/04/2019] [Accepted: 04/12/2019] [Indexed: 12/11/2022]
Abstract
Oncogenesis is considered to result from chromosomal instability, in addition to oncogene and tumor-suppressor alterations. Intermediate to aneuploidy and chromosomal instability, genome doubling is a frequent event in tumor development but the mechanisms driving tetraploidization and its impact remain unexplored. Cell fusion, one of the pathways to tetraploidy, is a physiological process involved in mesenchymal cell differentiation. Besides simple genome doubling, cell fusion results in the merging of two different genomes that can be destabilized upon proliferation. By testing whether cell fusion is involved in mesenchymal oncogenesis, we provide evidence that it induces genomic instability and mediates tumor initiation. After a latency period, the tumor emerges with the cells most suited for its development. Furthermore, hybrid tumor genomes were stabilized after this selection process and were very close to those of human pleomorphic mesenchymal tumors. Thus genome restructuring triggered by cell fusion may account for the chromosomal instability involved in oncogenesis.
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19
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Dieci G, Ferrari R. The third (III) road to cell transformation. Cell Cycle 2017; 17:410-411. [PMID: 29258395 DOI: 10.1080/15384101.2017.1419903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Giorgio Dieci
- a Department of Chemistry, Life Sciences and Environmental Sustainability , University of Parma , Parma , Italy
| | - Roberto Ferrari
- b Centre de Regulació Genòmica (CRG) , The Barcelona Institute for Science and Technology (BIST) , Barcelona , Spain
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