1
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Howard GC, Wang J, Rose KL, Jones C, Patel P, Tsui T, Florian AC, Vlach L, Lorey SL, Grieb BC, Smith BN, Slota MJ, Reynolds EM, Goswami S, Savona MR, Mason FM, Lee T, Fesik S, Liu Q, Tansey WP. Ribosome subunit attrition and activation of the p53-MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition. eLife 2024; 12:RP90683. [PMID: 38682900 PMCID: PMC11057873 DOI: 10.7554/elife.90683] [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] [Indexed: 05/01/2024] Open
Abstract
The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the 'WIN' site that tethers WDR5 to chromatin. WIN site inhibitors (WINi) are active against multiple cancer cell types in vitro, the most notable of which are those derived from MLL-rearranged (MLLr) leukemias. Peptidomimetic WINi were originally proposed to inhibit MLLr cells via dysregulation of genes connected to hematopoietic stem cell expansion. Our discovery and interrogation of small-molecule WINi, however, revealed that they act in MLLr cell lines to suppress ribosome protein gene (RPG) transcription, induce nucleolar stress, and activate p53. Because there is no precedent for an anticancer strategy that specifically targets RPG expression, we took an integrated multi-omics approach to further interrogate the mechanism of action of WINi in human MLLr cancer cells. We show that WINi induce depletion of the stock of ribosomes, accompanied by a broad yet modest translational choke and changes in alternative mRNA splicing that inactivate the p53 antagonist MDM4. We also show that WINi are synergistic with agents including venetoclax and BET-bromodomain inhibitors. Together, these studies reinforce the concept that WINi are a novel type of ribosome-directed anticancer therapy and provide a resource to support their clinical implementation in MLLr leukemias and other malignancies.
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Affiliation(s)
- Gregory Caleb Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical CenterNashvilleUnited States
- Center for Quantitative Sciences, Vanderbilt University Medical CenterNashvilleUnited States
| | - Kristie L Rose
- Mass Spectrometry Research Center, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
| | - Camden Jones
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Purvi Patel
- Mass Spectrometry Research Center, Vanderbilt University School of MedicineNashvilleUnited States
| | - Tina Tsui
- Mass Spectrometry Research Center, Vanderbilt University School of MedicineNashvilleUnited States
| | - Andrea C Florian
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Logan Vlach
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Brian C Grieb
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Brianna N Smith
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Macey J Slota
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Elizabeth M Reynolds
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Soumita Goswami
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Michael R Savona
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Frank M Mason
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Taekyu Lee
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
| | - Stephen Fesik
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Pharmacology, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical CenterNashvilleUnited States
- Center for Quantitative Sciences, Vanderbilt University Medical CenterNashvilleUnited States
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
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2
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Howard GC, Wang J, Rose KL, Jones C, Patel P, Tsui T, Florian AC, Vlach L, Lorey SL, Grieb BC, Smith BN, Slota MJ, Reynolds EM, Goswami S, Savona MR, Mason FM, Lee T, Fesik SW, Liu Q, Tansey WP. Ribosome subunit attrition and activation of the p53-MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.26.550648. [PMID: 37546802 PMCID: PMC10402127 DOI: 10.1101/2023.07.26.550648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the "WIN" site that tethers WDR5 to chromatin. WIN site inhibitors (WINi) are active against multiple cancer cell types in vitro, the most notable of which are those derived from MLL-rearranged (MLLr) leukemias. Peptidomimetic WINi were originally proposed to inhibit MLLr cells via dysregulation of genes connected to hematopoietic stem cell expansion. Our discovery and interrogation of small molecule WIN site inhibitors, however, revealed that they act in MLLr cell lines to suppress ribosome protein gene (RPG) transcription, induce nucleolar stress, and activate p53. Because there is no precedent for an anti-cancer strategy that specifically targets RPG expression, we took an integrated multi-omics approach to further interrogate the mechanism of action of WINi in MLLr cancer cells. We show that WINi induce depletion of the stock of ribosomes, accompanied by a broad yet modest translational choke and changes in alternative mRNA splicing that inactivate the p53 antagonist MDM4. We also show that WINi are synergistic with agents including venetoclax and BET-bromodomain inhibitors. Together, these studies reinforce the concept that WINi are a novel type of ribosome-directed anti-cancer therapy and provide a resource to support their clinical implementation in MLLr leukemias and other malignancies.
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Affiliation(s)
- Gregory C. Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Kristie Lindsey Rose
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Camden Jones
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Purvi Patel
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tina Tsui
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrea C. Florian
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Current address: Department of Biology, Belmont University, Nashville, TN 37212, USA
| | - Logan Vlach
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shelly L. Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Brian C. Grieb
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Brianna N. Smith
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Macey J. Slota
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Current address: Department of Urology, University of California San Francisco, San Francisco CA 94143, USA
| | - Elizabeth M. Reynolds
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Soumita Goswami
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Michael R. Savona
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Frank M. Mason
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Taekyu Lee
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - William P. Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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Priyadarshini N, Venkatarama Puppala N, Jayaprakash JP, Khandelia P, Sharma V, Mohannath G. Downregulation of ribosomal RNA (rRNA) genes in human head and neck squamous cell carcinoma (HNSCC) cells correlates with rDNA promoter hypermethylation. Gene 2023; 888:147793. [PMID: 37696422 DOI: 10.1016/j.gene.2023.147793] [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: 07/25/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Eukaryotes carry hundreds of ribosomal RNA (rRNA) genes as tandem arrays, which generate rRNA for protein synthesis. Humans carry ∼ 400 rRNA gene copies and their expression is epigenetically regulated. Dysregulation of rRNA synthesis and ribosome biogenesis are characteristic features of cancers. Targeting aberrant rRNA expression for cancer therapy is being explored. Head and neck squamous cell carcinoma (HNSCC) is among the most prevalent cancers globally. Using quantitative PCR and bisulfite sequencing, we show that rRNA genes are downregulated and their promoters are hypermethylated in HNSCC cell lines. These findings may have relevance for prognosis and diagnosis of HNSCC.
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Affiliation(s)
- Neha Priyadarshini
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Navinchandra Venkatarama Puppala
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Jayasree Peroth Jayaprakash
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Vivek Sharma
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Gireesha Mohannath
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
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4
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Paraqindes H, Mourksi NEH, Ballesta S, Hedjam J, Bourdelais F, Fenouil T, Picart T, Catez F, Combe T, Ferrari A, Kielbassa J, Thomas E, Tonon L, Viari A, Attignon V, Carrere M, Perrossier J, Giraud S, Vanbelle C, Gabut M, Bergeron D, Scott MS, Castro Vega L, Magne N, Huillard E, Sanson M, Meyronet D, Diaz JJ, Ducray F, Marcel V, Durand S. Isocitrate dehydrogenase wt and IDHmut adult-type diffuse gliomas display distinct alterations in ribosome biogenesis and 2'O-methylation of ribosomal RNA. Neuro Oncol 2023; 25:2191-2206. [PMID: 37531290 PMCID: PMC10708943 DOI: 10.1093/neuonc/noad140] [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: 03/01/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND High-grade adult-type diffuse gliomas (HGGs) constitute a heterogeneous group of aggressive tumors that are mostly incurable. Recent advances highlighting the contribution of ribosomes to cancer development have offered new clinical perspectives. Here, we uncovered that isocitrate dehydrogenase (IDH)wt and IDHmut HGGs display distinct alterations of ribosome biology, in terms of rRNA epitranscriptomics and ribosome biogenesis, which could constitute novel hallmarks that can be exploited for the management of these pathologies. METHODS We analyzed (1) the ribosomal RNA 2'O-ribose methylation (rRNA 2'Ome) using RiboMethSeq and in-house developed bioinformatics tools (https://github.com/RibosomeCRCL/ribomethseq-nfandrRMSAnalyzer) on 3 independent cohorts compiling 71 HGGs (IDHwt n = 30, IDHmut n = 41) and 9 non-neoplastic samples, (2) the expression of ribosome biogenesis factors using medium throughput RT-qPCR as a readout of ribosome biogenesis, and (3) the sensitivity of 5 HGG cell lines to RNA Pol I inhibitors (CX5461, BMH-21). RESULTS Unsupervised analysis demonstrated that HGGs could be distinguished based on their rRNA 2'Ome epitranscriptomic profile, with IDHwt glioblastomas displaying the most significant alterations of rRNA 2'Ome at specific sites. In contrast, IDHmut HGGs are largely characterized by an overexpression of ribosome biogenesis factors compared to non-neoplastic tissues or IDHwt glioblastomas. Finally, IDHmut HGG-derived spheroids display higher cytotoxicity to CX5461 than IDHwt glioblastoma, while all HGG spheroids display a similar cytotoxicity to BMH-21. CONCLUSIONS In HGGs, IDH mutational status is associated with specific alterations of the ribosome biology and with distinct sensitivities to RNA Pol I inhibitors.
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Affiliation(s)
- Hermes Paraqindes
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Nour-El-Houda Mourksi
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Samantha Ballesta
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Plateforme 3D-ONCO, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon, France
| | - Jordan Hedjam
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Fleur Bourdelais
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Tanguy Fenouil
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Laboratoire de biologie médicale et d’anatomie pathologique, Lyon, France
| | - Thiébaud Picart
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Laboratoire de biologie médicale et d’anatomie pathologique, Lyon, France
| | - Frédéric Catez
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Théo Combe
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Anthony Ferrari
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Janice Kielbassa
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Emilie Thomas
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Laurie Tonon
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Alain Viari
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
- INRIA Grenoble Rhône-Alpes, Montbonnot-Saint-Martin, France
| | - Valéry Attignon
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, Lyon, France
| | - Marjorie Carrere
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, Lyon, France
| | - Jessie Perrossier
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, Lyon, France
| | - Stéphane Giraud
- Plateforme 3D-ONCO, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon, France
| | - Christophe Vanbelle
- Plateforme d’Imagerie Cellulaire, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon, France
| | - Mathieu Gabut
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Danny Bergeron
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Michelle S Scott
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Luis Castro Vega
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Nathalie Magne
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Emmanuelle Huillard
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Marc Sanson
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - David Meyronet
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Laboratoire de biologie médicale et d’anatomie pathologique, Lyon, France
| | - Jean-Jacques Diaz
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - François Ducray
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Service de neuro-oncologie, Hôpital Pierre Wertheimer, Lyon, France
| | - Virginie Marcel
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Sébastien Durand
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
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5
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Kang CW, Blackburn AC, Loh AHP, Hong KC, Goh JY, Hein N, Drygin D, Parish CR, Hannan RD, Hannan KM, Coupland LA. Targeting RNA Polymerase I Transcription Activity in Osteosarcoma: Pre-Clinical Molecular and Animal Treatment Studies. Biomedicines 2023; 11:biomedicines11041133. [PMID: 37189750 DOI: 10.3390/biomedicines11041133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
The survival rate of patients with osteosarcoma (OS) has not improved over the last 30 years. Mutations in the genes TP53, RB1 and c-Myc frequently occur in OS and enhance RNA Polymerase I (Pol I) activity, thus supporting uncontrolled cancer cell proliferation. We therefore hypothesised that Pol I inhibition may be an effective therapeutic strategy for this aggressive cancer. The Pol I inhibitor CX-5461 has demonstrated therapeutic efficacy in different cancers in pre-clinical and phase I clinical trials; thus, the effects were determined on ten human OS cell lines. Following characterisation using genome profiling and Western blotting, RNA Pol I activity, cell proliferation and cell cycle progression were evaluated in vitro, and the growth of TP53 wild-type and mutant tumours was measured in a murine allograft model and in two human xenograft OS models. CX-5461 treatment resulted in reduced ribosomal DNA (rDNA) transcription and Growth 2 (G2)-phase cell cycle arrest in all OS cell lines. Additionally, tumour growth in all allograft and xenograft OS models was effectively suppressed without apparent toxicity. Our study demonstrates the efficacy of Pol I inhibition against OS with varying genetic alterations. This study provides pre-clinical evidence to support this novel therapeutic approach in OS.
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Affiliation(s)
- Chang-Won Kang
- The Division of Genome Science and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra 2601, Australia
| | - Anneke C Blackburn
- The Division of Genome Science and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra 2601, Australia
| | - Amos Hong Pheng Loh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Kuick Chick Hong
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Jian Yuan Goh
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Nadine Hein
- The Division of Genome Science and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra 2601, Australia
| | - Denis Drygin
- Regulus Therapeutics, 4224 Campus Point C, San Diego, CA 92121, USA
| | - Chris R Parish
- The Division of Genome Science and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra 2601, Australia
| | - Ross D Hannan
- The Division of Genome Science and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra 2601, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3010, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
- School of Biomedical Sciences, University of Queensland, St. Lucia 4067, Australia
| | - Katherine M Hannan
- The Division of Genome Science and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra 2601, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3010, Australia
| | - Lucy A Coupland
- The Division of Genome Science and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra 2601, Australia
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6
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Ni C, Buszczak M. The homeostatic regulation of ribosome biogenesis. Semin Cell Dev Biol 2023; 136:13-26. [PMID: 35440410 PMCID: PMC9569395 DOI: 10.1016/j.semcdb.2022.03.043] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 12/22/2022]
Abstract
The continued integrity of biological systems depends on a balance between interdependent elements at the molecular, cellular, and organismal levels. This is particularly true for the generation of ribosomes, which influence almost every aspect of cell and organismal biology. Ribosome biogenesis (RiBi) is an energetically demanding process that involves all three RNA polymerases, numerous RNA processing factors, chaperones, and the coordinated expression of 79-80 ribosomal proteins (r-proteins). Work over the last several decades has revealed that the dynamic regulation of ribosome production represents a major mechanism by which cells maintain homeostasis in response to changing environmental conditions and acute stress. More recent studies suggest that cells and tissues within multicellular organisms exhibit dramatically different levels of ribosome production and protein synthesis, marked by the differential expression of RiBi factors. Thus, distinct bottlenecks in the RiBi process, downstream of rRNA transcription, may exist within different cell populations of multicellular organisms during development and in adulthood. This review will focus on our current understanding of the mechanisms that link the complex molecular process of ribosome biogenesis with cellular and organismal physiology. We will discuss diverse topics including how different steps in the RiBi process are coordinated with one another, how MYC and mTOR impact RiBi, and how RiBi levels change between stem cells and their differentiated progeny. In turn, we will also review how regulated changes in ribosome production itself can feedback to influence cell fate and function.
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Affiliation(s)
- Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
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7
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Gregori A, Bergonzini C, Capula M, Mantini G, Khojasteh-Leylakoohi F, Comandatore A, Khalili-Tanha G, Khooei A, Morelli L, Avan A, Danen EH, Schmidt T, Giovannetti E. Prognostic Significance of Integrin Subunit Alpha 2 (ITGA2) and Role of Mechanical Cues in Resistance to Gemcitabine in Pancreatic Ductal Adenocarcinoma (PDAC). Cancers (Basel) 2023; 15:cancers15030628. [PMID: 36765586 PMCID: PMC9913151 DOI: 10.3390/cancers15030628] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
INTRODUCTION PDAC is an extremely aggressive tumor with a poor prognosis and remarkable therapeutic resistance. The dense extracellular matrix (ECM) which characterizes PDAC progression is considered a fundamental determinant of chemoresistance, with major contributions from mechanical factors. This study combined biomechanical and pharmacological approaches to evaluate the role of the cell-adhesion molecule ITGA2, a key regulator of ECM, in PDAC resistance to gemcitabine. METHODS The prognostic value of ITGA2 was analysed in publicly available databases and tissue-microarrays of two cohorts of radically resected and metastatic patients treated with gemcitabine. PANC-1 and its gemcitabine-resistant clone (PANC-1R) were analysed by RNA-sequencing and label-free proteomics. The role of ITGA2 in migration, proliferation, and apoptosis was investigated using hydrogel-coated wells, siRNA-mediated knockdown and overexpression, while collagen-embedded spheroids assessed invasion and ECM remodeling. RESULTS High ITGA2 expression correlated with shorter progression-free and overall survival, supporting its impact on prognosis and the lack of efficacy of gemcitabine treatment. These findings were corroborated by transcriptomic and proteomic analyses showing that ITGA2 was upregulated in the PANC-1R clone. The aggressive behavior of these cells was significantly reduced by ITGA2 silencing both in vitro and in vivo, while PANC-1 cells growing under conditions resembling PDAC stiffness acquired resistance to gemcitabine, associated to increased ITGA2 expression. Collagen-embedded spheroids of PANC-1R showed a significant matrix remodeling and spreading potential via increased expression of CXCR4 and MMP2. Additionally, overexpression of ITGA2 in MiaPaCa-2 cells triggered gemcitabine resistance and increased proliferation, both in vitro and in vivo, associated to upregulation of phospho-AKT. CONCLUSIONS ITGA2 emerged as a new prognostic factor, highlighting the relevance of stroma mechanical properties as potential therapeutic targets to counteract gemcitabine resistance in PDAC.
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Affiliation(s)
- Alessandro Gregori
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
- Department of Cancer Biology and Immunology, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Cecilia Bergonzini
- Leiden Academic Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Mjriam Capula
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
- Institute of Life Sciences, Sant’Anna School of Advanced Studies, 56127 Pisa, Italy
- Cancer Pharmacology Lab, Fondazione Pisana per La Scienza, 56017 San Giuliano, Italy
| | - Giulia Mantini
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
- Department of Cancer Biology and Immunology, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
- Cancer Pharmacology Lab, Fondazione Pisana per La Scienza, 56017 San Giuliano, Italy
| | | | - Annalisa Comandatore
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
- Department of Cancer Biology and Immunology, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56100 Pisa, Italy
| | - Ghazaleh Khalili-Tanha
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad 91886-17871, Iran
| | - Alireza Khooei
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 91886-17871, Iran
| | - Luca Morelli
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56100 Pisa, Italy
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad 91886-17871, Iran
- Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 91886-17871, Iran
| | - Erik H. Danen
- Leiden Academic Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Thomas Schmidt
- Physics of Life Processes, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2333 CA Leiden, The Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
- Department of Cancer Biology and Immunology, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
- Cancer Pharmacology Lab, Fondazione Pisana per La Scienza, 56017 San Giuliano, Italy
- Correspondence:
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8
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Hossen MB, Islam MA, Reza MS, Kibria MK, Horaira MA, Tuly KF, Faruqe MO, Kabir F, Mollah MNH. Robust identification of common genomic biomarkers from multiple gene expression profiles for the prognosis, diagnosis, and therapies of pancreatic cancer. Comput Biol Med 2023; 152:106411. [PMID: 36502691 DOI: 10.1016/j.compbiomed.2022.106411] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/17/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
Pancreatic cancer (PC) is one of the leading causes of cancer-related death globally. So, identification of potential molecular signatures is required for diagnosis, prognosis, and therapies of PC. In this study, we detected 71 common differentially expressed genes (cDEGs) between PC and control samples from four microarray gene-expression datasets (GSE15471, GSE16515, GSE71989, and GSE22780) by using robust statistical and machine learning approaches, since microarray gene-expression datasets are often contaminated by outliers due to several steps involved in the data generating processes. Then we detected 8 cDEGs (ADAM10, COL1A2, FN1, P4HB, ITGB1, ITGB5, ANXA2, and MYOF) as the PC-causing key genes (KGs) by the protein-protein interaction (PPI) network analysis. We validated the expression patterns of KGs between case and control samples by box plot analysis with the TCGA and GTEx databases. The proposed KGs showed high prognostic power with the random forest (RF) based prediction model and Kaplan-Meier-based survival probability curve. The KGs regulatory network analysis detected few transcriptional and post-transcriptional regulators for KGs. The cDEGs-set enrichment analysis revealed some crucial PC-causing molecular functions, biological processes, cellular components, and pathways that are associated with KGs. Finally, we suggested KGs-guided five repurposable drug molecules (Linsitinib, CX5461, Irinotecan, Timosaponin AIII, and Olaparib) and a new molecule (NVP-BHG712) against PC by molecular docking. The stability of the top three protein-ligand complexes was confirmed by molecular dynamic (MD) simulation studies. The cross-validation and some literature reviews also supported our findings. Therefore, the finding of this study might be useful resources to the researchers and medical doctors for diagnosis, prognosis and therapies of PC by the wet-lab validation.
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Affiliation(s)
- Md Bayazid Hossen
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Ariful Islam
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Selim Reza
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Kaderi Kibria
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Abu Horaira
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Khanis Farhana Tuly
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Firoz Kabir
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Md Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
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9
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Targeting Ribosome Biogenesis in Cancer: Lessons Learned and Way Forward. Cancers (Basel) 2022; 14:cancers14092126. [PMID: 35565259 PMCID: PMC9100539 DOI: 10.3390/cancers14092126] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Cells need to produce ribosomes to sustain continuous proliferation and expand in numbers, a feature that is even more prominent in uncontrollably proliferating cancer cells. Certain cancer cell types are expected to depend more on ribosome biogenesis based on their genetic background, and this potential vulnerability can be exploited in designing effective, targeted cancer therapies. This review provides information on anti-cancer molecules that target the ribosome biogenesis machinery and indicates avenues for future research. Abstract Rapid growth and unrestrained proliferation is a hallmark of many cancers. To accomplish this, cancer cells re-wire and increase their biosynthetic and metabolic activities, including ribosome biogenesis (RiBi), a complex, highly energy-consuming process. Several chemotherapeutic agents used in the clinic impair this process by interfering with the transcription of ribosomal RNA (rRNA) in the nucleolus through the blockade of RNA polymerase I or by limiting the nucleotide building blocks of RNA, thereby ultimately preventing the synthesis of new ribosomes. Perturbations in RiBi activate nucleolar stress response pathways, including those controlled by p53. While compounds such as actinomycin D and oxaliplatin effectively disrupt RiBi, there is an ongoing effort to improve the specificity further and find new potent RiBi-targeting compounds with improved pharmacological characteristics. A few recently identified inhibitors have also become popular as research tools, facilitating our advances in understanding RiBi. Here we provide a comprehensive overview of the various compounds targeting RiBi, their mechanism of action, and potential use in cancer therapy. We discuss screening strategies, drug repurposing, and common problems with compound specificity and mechanisms of action. Finally, emerging paths to discovery and avenues for the development of potential biomarkers predictive of therapeutic outcomes across cancer subtypes are also presented.
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10
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Kang CW, Hannan KM, Blackburn AC, Loh AHP, Hong KC, Yuan GJ, Hein N, Drygin D, Hannan RD, Coupland LA. The therapeutic potential of RNA Polymerase I transcription inhibitor, CX-5461, in uterine leiomyosarcoma. Invest New Drugs 2022; 40:529-536. [PMID: 35201535 PMCID: PMC9098598 DOI: 10.1007/s10637-022-01222-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 02/07/2022] [Indexed: 12/01/2022]
Abstract
Background. Uterine leiomyosarcoma is a rare aggressive smooth muscle cancer with poor survival rates. RNA Polymerase I (Pol I) activity is elevated in many cancers supporting tumour growth and prior studies in uterine leiomyosarcoma revealed enlarged nucleoli and upregulated Pol I activity-related genes. This study aimed to investigate the anti-tumour potential of CX-5461, a Pol I transcription inhibitor currently being evaluated in clinical trials for several cancers, against the human uterine leiomyosarcoma cell line, SK-UT-1. Methods. SK-UT-1 was characterised using genome profiling and western blotting. The anti-tumour effects of CX-5461 were investigated using cell proliferation assays, expression analysis using qRT-PCR, and BrdU/PI based cell cycle analysis. Results. Genetic analysis of SK-UT-1 revealed mutations in TP53, RB1, PTEN, APC and TSC1 & 2, all potentially associated with increased Pol I activity. Protein expression analysis showed dysregulated p53, RB1 and c-Myc. CX-5461 treatment resulted in an anti-proliferation response, G2 phase cell-cycle arrest and on-target activity demonstrated by reduced ribosomal DNA transcription. Conclusions. SK-UT-1 was confirmed as a representative model of uterine leiomyosarcoma and CX-5461 has significant potential as a novel adjuvant for this rare cancer.
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Affiliation(s)
- Chang-Won Kang
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Katherine M Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, 3010, Australia
| | - Anneke C Blackburn
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Amos H P Loh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, KK Women's and Children's Hospital, Bukit Timah, Singapore
| | - Kuick Chik Hong
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Bukit Timah, Singapore
| | - Goh Jian Yuan
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Bukit Timah, Singapore
| | - Nadine Hein
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Denis Drygin
- Regulus Therapeutics, 4224 Campus Point C, San Diego, CA, USA
| | - Ross D Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, 3010, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800, Australia.,School of Biomedical Sciences, University of Queensland, 4067, St Lucia, Australia
| | - Lucy A Coupland
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
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11
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Jacobs RQ, Huffines AK, Laiho M, Schneider DA. The small-molecule BMH-21 directly inhibits transcription elongation and DNA occupancy of RNA polymerase I in vivo and in vitro. J Biol Chem 2021; 298:101450. [PMID: 34838819 PMCID: PMC8683726 DOI: 10.1016/j.jbc.2021.101450] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 12/11/2022] Open
Abstract
Cancer cells are dependent upon an abundance of ribosomes to maintain rapid cell growth and proliferation. The rate-limiting step of ribosome biogenesis is ribosomal RNA (rRNA) synthesis by RNA polymerase I (Pol I). Therefore, a goal of the cancer therapeutic field is to develop and characterize Pol I inhibitors. Here, we elucidate the mechanism of Pol I inhibition by a first-in-class small-molecule BMH-21. To characterize the effects of BMH-21 on Pol I transcription, we leveraged high-resolution in vitro transcription assays and in vivo native elongating transcript sequencing (NET-seq). We find that Pol I transcription initiation, promoter escape, and elongation are all inhibited by BMH-21 in vitro. In particular, the transcription elongation phase is highly sensitive to BMH-21 treatment, as it causes a decrease in transcription elongation rate and an increase in paused Pols on the ribosomal DNA (rDNA) template. In vivo NET-seq experiments complement these findings by revealing a reduction in Pol I occupancy on the template and an increase in sequence-specific pausing upstream of G-rich rDNA sequences after BMH-21 treatment. Collectively, these data reveal the mechanism of action of BMH-21, which is a critical step forward in the development of this compound and its derivatives for clinical use.
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Affiliation(s)
- Ruth Q Jacobs
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Abigail K Huffines
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA.
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12
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Cornelison R, Biswas K, Llaneza DC, Harris AR, Sosale NG, Lazzara MJ, Landen CN. CX-5461 Treatment Leads to Cytosolic DNA-Mediated STING Activation in Ovarian Cancer. Cancers (Basel) 2021; 13:cancers13205056. [PMID: 34680204 PMCID: PMC8533980 DOI: 10.3390/cancers13205056] [Citation(s) in RCA: 3] [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: 08/31/2021] [Revised: 09/29/2021] [Accepted: 10/07/2021] [Indexed: 12/23/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is the deadliest of the gynecologic malignancies, with an overall survival rate of <30%. Recent research has suggested that targeting RNA polymerase I (POL I) with small-molecule inhibitors may be a viable therapeutic approach to combating EOC, even when chemoresistance is present. CX-5461 is one of the most promising POL I inhibitors currently being investigated, and previous reports have shown that CX-5461 treatment induces DNA damage response (DDR) through ATM/ATR kinase. Investigation into downstream effects of CX-5461 led us to uncovering a previously unreported phenotype. Treatment with CX-5461 induces a rapid accumulation of cytosolic DNA. This accumulation leads to transcriptional upregulation of 'STimulator of Interferon Genes' (STING) in the same time frame, phosphorylation of IRF3, and activation of type I interferon response both in vitro and in vivo. This activation is mediated and dependent on cyclic GMP-AMP synthase (cGAS). Here, we show THAT CX-5461 leads to an accumulation of cytosolic dsDNA and thereby activates the cGAS-STING-TBK1-IRF3 innate immune pathway, which induces type I IFN. CX-5461 treatment-mediated immune activation may be a powerful mechanism of action to exploit, leading to novel drug combinations with a chance of increasing immunotherapy efficacy, possibly with some cancer specificity limiting deleterious toxicities.
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Affiliation(s)
- Robert Cornelison
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, VA 22908, USA; (R.C.); (K.B.); (D.C.L.); (A.R.H.)
| | - Kuntal Biswas
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, VA 22908, USA; (R.C.); (K.B.); (D.C.L.); (A.R.H.)
| | - Danielle C. Llaneza
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, VA 22908, USA; (R.C.); (K.B.); (D.C.L.); (A.R.H.)
| | - Alexandra R. Harris
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, VA 22908, USA; (R.C.); (K.B.); (D.C.L.); (A.R.H.)
| | - Nisha G. Sosale
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22908, USA; (N.G.S.); (M.J.L.)
| | - Matthew J. Lazzara
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22908, USA; (N.G.S.); (M.J.L.)
| | - Charles N. Landen
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, VA 22908, USA; (R.C.); (K.B.); (D.C.L.); (A.R.H.)
- Correspondence: ; Tel.: +1-434-243-6131
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13
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Zhang W, Cheng W, Parlato R, Guo X, Cui X, Dai C, Xu L, Zhu J, Zhu M, Luo K, Zhang W, Dong B, Wang J, Jiang F. Nucleolar stress induces a senescence-like phenotype in smooth muscle cells and promotes development of vascular degeneration. Aging (Albany NY) 2020; 12:22174-22198. [PMID: 33146634 PMCID: PMC7695416 DOI: 10.18632/aging.104094] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/31/2020] [Indexed: 12/24/2022]
Abstract
Senescence of smooth muscle cells (SMCs) has a crucial role in the pathogenesis of abdominal aortic aneurysm (AAA), a disease of vascular degeneration. Perturbation of cellular ribosomal DNA (rDNA) transcription triggers nucleolar stress response. Previously we demonstrated that induction of nucleolar stress in SMCs elicited cell cycle arrest via the ataxia-telangiectasia mutated (ATM)/ATM- and Rad3-related (ATR)-p53 axis. However, the specific roles of nucleolar stress in vascular degeneration remain unexplored. In the present study, we demonstrated for the first time that in both human and animal AAA tissues, there were non-coordinated changes in the expression of RNA polymerase I machinery components, including a downregulation of transcription initiation factor-IA (TIF-IA). Genetic deletion of TIF-IA in SMCs in mice (smTIF-IA-/-) caused spontaneous aneurysm-like lesions in the aorta. In vitro, induction of nucleolar stress triggered a non-canonical DNA damage response, leading to p53 phosphorylation and a senescence-like phenotype in SMCs. In human AAA tissues, there was increased nucleolar stress in medial cells, accompanied by localized DNA damage response within the nucleolar compartment. Our data suggest that perturbed rDNA transcription and induction of nucleolar stress contribute to the pathogenesis of AAA. Moreover, smTIF-IA-/- mice may be a novel animal model for studying spontaneous AAA-like vascular degenerations.
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Affiliation(s)
- Wenjing Zhang
- Department of Physiology and Pathophysiology, School of Basic Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China.,Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
| | - Wen Cheng
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Rosanna Parlato
- Institute of Applied Physiology, University of Ulm, Ulm, Germany.,Institute of Anatomy and Cell Biology, University of Heidelberg, Heidelberg, Germany
| | - Xiaosun Guo
- Department of Physiology and Pathophysiology, School of Basic Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Xiaopei Cui
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
| | - Chaochao Dai
- Department of Physiology and Pathophysiology, School of Basic Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China.,Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
| | - Lei Xu
- Department of Vascular Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jiankang Zhu
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Min Zhu
- Department of Transplant Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Kun Luo
- Department of Vascular Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Wencheng Zhang
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Bo Dong
- Department of Cardiology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong Province, China
| | - Jianli Wang
- Department of Physiology and Pathophysiology, School of Basic Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China.,Current address: Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, China
| | - Fan Jiang
- Department of Physiology and Pathophysiology, School of Basic Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China.,Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
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14
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El Hassouni B, Franczak M, Capula M, Vonk CM, Gomez VM, Smolenski RT, Granchi C, Peters GJ, Minutolo F, Giovannetti E. Lactate dehydrogenase A inhibition by small molecular entities: steps in the right direction. Oncoscience 2020; 7:76-80. [PMID: 33195739 PMCID: PMC7640902 DOI: 10.18632/oncoscience.519] [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: 06/30/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022] Open
Abstract
Direct targeting of energy metabolism to defeat cancer is not a recent strategy. Although quite a few drugs use cellular metabolism for their antitumor effect, no direct inhibitors of energy metabolism have been approved by the FDA. Currently, several inhibitors of lactate dehydrogenase A (LDH-A), a key player in glycolysis, are in development. Earlier, we demonstrated the efficacy of N-hydroxyindole-based LDH-A inhibitors in different cancer types. In this study we describe the efficacy of NHI-Glc-2, which is designed to dual target cancer cells, by exploiting a simultaneous enhanced glucose uptake by overexpressed glucose transporter 1 (GLUT1) and by inhibition of LDH-A. NHI-Glc-2 inhibits LDH-A enzyme activity, PANC-1 cell growth and disrupts spheroid integrity, with an overall effect that is more pronounced when combined with gemcitabine.
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Affiliation(s)
- Btissame El Hassouni
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, Netherlands
| | - Marika Franczak
- Department of Biochemistry, Medical University of Gdansk, Gdansk, Poland
| | | | - Christian M Vonk
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, Netherlands
| | - Valentina M Gomez
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, Netherlands
| | | | | | - Godefridus J Peters
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, Netherlands.,Department of Biochemistry, Medical University of Gdansk, Gdansk, Poland
| | | | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, Netherlands.,Fondazione Pisana per la Scienza, Pisa, Italy
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