1
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Tsanov KM, Barriga FM, Ho YJ, Alonso-Curbelo D, Livshits G, Koche RP, Baslan T, Simon J, Tian S, Wuest AN, Luan W, Wilkinson JE, Masilionis I, Dimitrova N, Iacobuzio-Donahue CA, Chaligné R, Pe’er D, Massagué J, Lowe SW. Metastatic site influences driver gene function in pancreatic cancer. bioRxiv 2024:2024.03.17.585402. [PMID: 38562717 PMCID: PMC10983983 DOI: 10.1101/2024.03.17.585402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Driver gene mutations can increase the metastatic potential of the primary tumor1-3, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 - a transcriptional effector of TGFβ signaling - which is a hallmark of multiple gastrointestinal malignancies4,5. SMAD4 inactivation mediates TGFβ's remarkable anti- to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis6-14. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had strikingly opposite effects depending on the tumor's organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis revealed organ-specific differences in the tumor cells' epigenomic state, whereby the liver and lungs harbored chromatin programs respectively dominated by the KLF and RUNX developmental transcription factors, with Klf4 depletion being sufficient to reverse Smad4's tumor-suppressive activity in liver metastases. Our results show how epigenetic states favored by the organ of residence can influence the function of driver genes in metastatic tumors. This organ-specific gene-chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.
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Affiliation(s)
- Kaloyan M. Tsanov
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco M. Barriga
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Yu-Jui Ho
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Direna Alonso-Curbelo
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Geulah Livshits
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timour Baslan
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedical Sciences, School of Veterinary Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Janelle Simon
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sha Tian
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra N. Wuest
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Luan
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John E. Wilkinson
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Ignas Masilionis
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nevenka Dimitrova
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A. Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligné
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe’er
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Joan Massagué
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W. Lowe
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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2
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Leibold J, Tsanov KM, Amor C, Ho YJ, Sánchez-Rivera FJ, Feucht J, Baslan T, Chen HA, Tian S, Simon J, Wuest A, Wilkinson JE, Lowe SW. Somatic mouse models of gastric cancer reveal genotype-specific features of metastatic disease. Nat Cancer 2024; 5:315-329. [PMID: 38177458 PMCID: PMC10899107 DOI: 10.1038/s43018-023-00686-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 11/10/2023] [Indexed: 01/06/2024]
Abstract
Metastatic gastric carcinoma is a highly lethal cancer that responds poorly to conventional and molecularly targeted therapies. Despite its clinical relevance, the mechanisms underlying the behavior and therapeutic response of this disease are poorly understood owing, in part, to a paucity of tractable models. Here we developed methods to somatically introduce different oncogenic lesions directly into the murine gastric epithelium. Genotypic configurations observed in patients produced metastatic gastric cancers that recapitulated the histological, molecular and clinical features of all nonviral molecular subtypes of the human disease. Applying this platform to both wild-type and immunodeficient mice revealed previously unappreciated links between the genotype, organotropism and immune surveillance of metastatic cells, which produced distinct patterns of metastasis that were mirrored in patients. Our results establish a highly portable platform for generating autochthonous cancer models with flexible genotypes and host backgrounds, which can unravel mechanisms of gastric tumorigenesis or test new therapeutic concepts.
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Affiliation(s)
- Josef Leibold
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medical Oncology and Pneumology, University Hospital Tuebingen, Tuebingen, Germany.
- iFIT Cluster of Excellence EXC 2180 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany.
| | - Kaloyan M Tsanov
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Corina Amor
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Yu-Jui Ho
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco J Sánchez-Rivera
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Judith Feucht
- iFIT Cluster of Excellence EXC 2180 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
- Department I-General Paediatrics, Haematology/Oncology, University Children's Hospital Tuebingen, Tuebingen, Germany
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedical Sciences, School of Veterinary Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Hsuan-An Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sha Tian
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Janelle Simon
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra Wuest
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John E Wilkinson
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Sun S, Hong J, You E, Tsanov KM, Chacon-Barahona J, Gioacchino AD, Hoyos D, Li H, Jiang H, Ly H, Marhon S, Murali R, Chanda P, Karacay A, Vabret N, De Carvalho DD, LaCava J, Lowe SW, Ting DT, Iacobuzio-Donahue CA, Solovyov A, Greenbaum BD. Cancer cells co-evolve with retrotransposons to mitigate viral mimicry. bioRxiv 2023:2023.05.19.541456. [PMID: 37292765 PMCID: PMC10245669 DOI: 10.1101/2023.05.19.541456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Overexpression of repetitive elements is an emerging hallmark of human cancers 1 . Diverse repeats can mimic viruses by replicating within the cancer genome through retrotransposition, or presenting pathogen-associated molecular patterns (PAMPs) to the pattern recognition receptors (PRRs) of the innate immune system 2-5 . Yet, how specific repeats affect tumor evolution and shape the tumor immune microenvironment (TME) in a pro- or anti-tumorigenic manner remains poorly defined. Here, we integrate whole genome and total transcriptome data from a unique autopsy cohort of multiregional samples collected in pancreatic ductal adenocarcinoma (PDAC) patients, into a comprehensive evolutionary analysis. We find that more recently evolved S hort I nterspersed N uclear E lements (SINE), a family of retrotransposable repeats, are more likely to form immunostimulatory double-strand RNAs (dsRNAs). Consequently, younger SINEs are strongly co-regulated with RIG-I like receptor associated type-I interferon genes but anti-correlated with pro-tumorigenic macrophage infiltration. We discover that immunostimulatory SINE expression in tumors is regulated by either L ong I nterspersed N uclear E lements 1 (LINE1/L1) mobility or ADAR1 activity in a TP53 mutation dependent manner. Moreover, L1 retrotransposition activity tracks with tumor evolution and is associated with TP53 mutation status. Altogether, our results suggest pancreatic tumors actively evolve to modulate immunogenic SINE stress and induce pro-tumorigenic inflammation. Our integrative, evolutionary analysis therefore illustrates, for the first time, how dark matter genomic repeats enable tumors to co-evolve with the TME by actively regulating viral mimicry to their selective advantage.
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4
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Schwörer S, Cimino FV, Ros M, Tsanov KM, Ng C, Lowe SW, Carmona-Fontaine C, Thompson CB. Hypoxia Potentiates the Inflammatory Fibroblast Phenotype Promoted by Pancreatic Cancer Cell-Derived Cytokines. Cancer Res 2023; 83:1596-1610. [PMID: 36912618 PMCID: PMC10658995 DOI: 10.1158/0008-5472.can-22-2316] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 01/19/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023]
Abstract
Cancer-associated fibroblasts (CAF) are a major cell type in the stroma of solid tumors and can exert both tumor-promoting and tumor-restraining functions. CAF heterogeneity is frequently observed in pancreatic ductal adenocarcinoma (PDAC), a tumor characterized by a dense and hypoxic stroma that features myofibroblastic CAFs (myCAF) and inflammatory CAFs (iCAF) that are thought to have opposing roles in tumor progression. While CAF heterogeneity can be driven in part by tumor cell-produced cytokines, other determinants shaping CAF identity and function are largely unknown. In vivo, we found that iCAFs displayed a hypoxic gene expression and biochemical profile and were enriched in hypoxic regions of PDAC tumors, while myCAFs were excluded from these regions. Hypoxia led fibroblasts to acquire an inflammatory gene expression signature and synergized with cancer cell-derived cytokines to promote an iCAF phenotype in a HIF1α-dependent fashion. Furthermore, HIF1α stabilization was sufficient to induce an iCAF phenotype in stromal cells introduced into PDAC organoid cocultures and to promote PDAC tumor growth. These findings indicate hypoxia-induced HIF1α as a regulator of CAF heterogeneity and promoter of tumor progression in PDAC. SIGNIFICANCE Hypoxia in the tumor microenvironment of pancreatic cancer potentiates the cytokine-induced inflammatory CAF phenotype and promotes tumor growth. See related commentary by Fuentes and Taniguchi, p. 1560.
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Affiliation(s)
- Simon Schwörer
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Francesco V Cimino
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Manon Ros
- Center for Genomics and Systems Biology, New York University, New York, New York
| | - Kaloyan M Tsanov
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles Ng
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | | | - Craig B Thompson
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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5
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Tsanov KM, Barriga FM, Ho YJ, Alonso-Curbelo D, Livshits G, Koche R, Baslan T, Wuest AN, Simon J, Tian S, Luan W, Lowe SW. Abstract 3512: Organ-specific effects of Smad4 in metastatic pancreatic cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Primary and metastatic tumors typically share the same driver gene mutations, but it is unclear if these mutations are functionally relevant across different anatomical sites. Among such mutations, inactivation of the tumor suppressor gene SMAD4 is a hallmark of pancreatic and other gastrointestinal cancers and has been associated with metastatic disease. Here, we develop a mouse model of pancreatic ductal adenocarcinoma that enables Smad4 depletion in the pre-malignant Kras-mutant pancreas and subsequent Smad4 reactivation in late-stage metastatic tumors. Whereas early Smad4 deficiency facilitated tumor formation, later Smad4 restoration had unexpected organ-specific outcomes: no effect on primary tumor growth, suppression of liver metastases, and promotion of lung metastases. Integrative multiomic analysis revealed a near-universal genomic deletion of the Cdkn2a/b locus and organ-specific changes in the tumor cells’ epigenomic state. In particular, the liver and lung differentially favored KLF vs. RUNX dominated chromatin programs, which were confirmed to underpin the divergent effects of Smad4 restoration in functional studies. Our results show how organ-dependent epigenomic changes lead to altered driver gene function in metastatic disease. This organ-specific gene-chromatin interplay may be a generalizable principle in cancer biology and invites a revised paradigm for precision oncology that considers anatomical site in the interpretation of tumor genetics.
Citation Format: Kaloyan M. Tsanov, Francisco M. Barriga, Yu-Jui Ho, Direna Alonso-Curbelo, Geulah Livshits, Richard Koche, Timour Baslan, Alexandra N. Wuest, Janelle Simon, Sha Tian, Wei Luan, Scott W. Lowe. Organ-specific effects of Smad4 in metastatic pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3512.
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Affiliation(s)
| | | | - Yu-Jui Ho
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Richard Koche
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Timour Baslan
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Janelle Simon
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sha Tian
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wei Luan
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Scott W. Lowe
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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6
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Barriga FM, Tsanov KM, Ho YJ, Sohail N, Zhang A, Baslan T, Wuest AN, Del Priore I, Meškauskaitė B, Livshits G, Alonso-Curbelo D, Simon J, Chaves-Perez A, Bar-Sagi D, Iacobuzio-Donahue CA, Notta F, Chaligne R, Sharma R, Pe'er D, Lowe SW. MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis. Nat Cancer 2022; 3:1367-1385. [PMID: 36344707 PMCID: PMC9701143 DOI: 10.1038/s43018-022-00443-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022]
Abstract
The most prominent homozygous deletions in cancer affect chromosome 9p21.3 and eliminate CDKN2A/B tumor suppressors, disabling a cell-intrinsic barrier to tumorigenesis. Half of 9p21.3 deletions, however, also encompass a type I interferon (IFN) gene cluster; the consequences of this co-deletion remain unexplored. To functionally dissect 9p21.3 and other large genomic deletions, we developed a flexible deletion engineering strategy, MACHETE (molecular alteration of chromosomes with engineered tandem elements). Applying MACHETE to a syngeneic mouse model of pancreatic cancer, we found that co-deletion of the IFN cluster promoted immune evasion, metastasis and immunotherapy resistance. Mechanistically, IFN co-deletion disrupted type I IFN signaling in the tumor microenvironment, leading to marked changes in infiltrating immune cells and escape from CD8+ T-cell surveillance, effects largely driven by the poorly understood interferon epsilon. These results reveal a chromosomal deletion that disables both cell-intrinsic and cell-extrinsic tumor suppression and provide a framework for interrogating large deletions in cancer and beyond.
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Affiliation(s)
- Francisco M Barriga
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaloyan M Tsanov
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu-Jui Ho
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Noor Sohail
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Timour Baslan
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra N Wuest
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Isabella Del Priore
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Brigita Meškauskaitė
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Geulah Livshits
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Direna Alonso-Curbelo
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Janelle Simon
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Almudena Chaves-Perez
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dafna Bar-Sagi
- Department of Biochemistry, New York University School of Medicine, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Division of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ronan Chaligne
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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7
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Sánchez-Rivera FJ, Diaz BJ, Kastenhuber ER, Schmidt H, Katti A, Kennedy M, Tem V, Ho YJ, Leibold J, Paffenholz SV, Barriga FM, Chu K, Goswami S, Wuest AN, Simon JM, Tsanov KM, Chakravarty D, Zhang H, Leslie CS, Lowe SW, Dow LE. Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants. Nat Biotechnol 2022; 40:862-873. [PMID: 35165384 PMCID: PMC9232935 DOI: 10.1038/s41587-021-01172-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022]
Abstract
Base editing can be applied to characterize single nucleotide variants of unknown function, yet defining effective combinations of single guide RNAs (sgRNAs) and base editors remains challenging. Here, we describe modular base-editing-activity 'sensors' that link sgRNAs and cognate target sites in cis and use them to systematically measure the editing efficiency and precision of thousands of sgRNAs paired with functionally distinct base editors. By quantifying sensor editing across >200,000 editor-sgRNA combinations, we provide a comprehensive resource of sgRNAs for introducing and interrogating cancer-associated single nucleotide variants in multiple model systems. We demonstrate that sensor-validated tools streamline production of in vivo cancer models and that integrating sensor modules in pooled sgRNA libraries can aid interpretation of high-throughput base editing screens. Using this approach, we identify several previously uncharacterized mutant TP53 alleles as drivers of cancer cell proliferation and in vivo tumor development. We anticipate that the framework described here will facilitate the functional interrogation of cancer variants in cell and animal models.
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Affiliation(s)
- Francisco J Sánchez-Rivera
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bianca J Diaz
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Edward R Kastenhuber
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Henri Schmidt
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alyna Katti
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Margaret Kennedy
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Vincent Tem
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu-Jui Ho
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Josef Leibold
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medical Oncology and Pneumology, University Hospital Tuebingen, Tuebingen, Germany
- iFIT Cluster of Excellence EXC 2180 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Stella V Paffenholz
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Francisco M Barriga
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevan Chu
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Sukanya Goswami
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexandra N Wuest
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Janelle M Simon
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaloyan M Tsanov
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hongxin Zhang
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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8
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Missios P, da Rocha EL, Pearson DS, Philipp J, Aleman MM, Pirouz M, Farache D, Franses JW, Kubaczka C, Tsanov KM, Jha DK, Pepe-Mooney B, Powers JT, Gregory RI, Lee AS, Dominguez D, Ting DT, Daley GQ. LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy. J Clin Invest 2021; 131:145142. [PMID: 34779407 DOI: 10.1172/jci145142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 09/21/2021] [Indexed: 01/21/2023] Open
Abstract
High expression of LIN28B is associated with aggressive malignancy and poor survival. Here, probing MYCN-amplified neuroblastoma as a model system, we showed that LIN28B expression was associated with enhanced cell migration in vitro and invasive and metastatic behavior in murine xenografts. Sequence analysis of the polyribosome fraction of LIN28B-expressing neuroblastoma cells revealed let-7-independent enrichment of transcripts encoding components of the translational and ribosomal apparatus and depletion of transcripts of neuronal developmental programs. We further observed that LIN28B utilizes both its cold shock and zinc finger RNA binding domains to preferentially interact with MYCN-induced transcripts of the ribosomal complex, enhancing their translation. These data demonstrated that LIN28B couples the MYCN-driven transcriptional program to enhanced ribosomal translation, thereby implicating LIN28B as a posttranscriptional driver of the metastatic phenotype.
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Affiliation(s)
- Pavlos Missios
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Edroaldo Lummertz da Rocha
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Daniel S Pearson
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Julia Philipp
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA.,Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Maria M Aleman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mehdi Pirouz
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts, USA.,Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Dorian Farache
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Joseph W Franses
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Caroline Kubaczka
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kaloyan M Tsanov
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Deepak K Jha
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Brian Pepe-Mooney
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - John T Powers
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard I Gregory
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Harvard Initiative for RNA Medicine, Boston, Massachusetts, USA
| | - Amy Sy Lee
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - George Q Daley
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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9
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Osborne JK, Kinney MA, Han A, Akinnola KE, Yermalovich AV, Vo LT, Pearson DS, Sousa PM, Ratanasirintrawoot S, Tsanov KM, Barragan J, North TE, Metzger RJ, Daley GQ. Lin28 paralogs regulate lung branching morphogenesis. Cell Rep 2021; 36:109408. [PMID: 34289374 PMCID: PMC8371695 DOI: 10.1016/j.celrep.2021.109408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 03/11/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
The molecular mechanisms that govern the choreographed timing of organ development remain poorly understood. Our investigation of the role of the Lin28a and Lin28b paralogs during the developmental process of branching morphogenesis establishes that dysregulation of Lin28a/b leads to abnormal branching morphogenesis in the lung and other tissues. Additionally, we find that the Lin28 paralogs, which regulate post-transcriptional processing of both mRNAs and microRNAs (miRNAs), predominantly control mRNAs during the initial phases of lung organogenesis. Target mRNAs include Sox2, Sox9, and Etv5, which coordinate lung development and differentiation. Moreover, we find that functional interactions between Lin28a and Sox9 are capable of bypassing branching defects in Lin28a/b mutant lungs. Here, we identify Lin28a and Lin28b as regulators of early embryonic lung development, highlighting the importance of the timing of post-transcriptional regulation of both miRNAs and mRNAs at distinct stages of organogenesis. The timing of organogenesis is poorly understood. Here, Osborne et al. show that the Lin28 paralogs (Lin28a and Lin28b) regulate branching morphogenesis in a let-7-independent manner by directly binding to the mRNAs of Sox2, Sox9, and Etv5 to enhance their post-transcriptional processing.
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Affiliation(s)
- Jihan K Osborne
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Melissa A Kinney
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Areum Han
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kemi E Akinnola
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Alena V Yermalovich
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Linda T Vo
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel S Pearson
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Patricia M Sousa
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA
| | - Sutheera Ratanasirintrawoot
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kaloyan M Tsanov
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica Barragan
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA
| | - Trista E North
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA
| | - Ross J Metzger
- Department of Pediatrics (Cardiology), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - George Q Daley
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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10
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Alonso-Curbelo D, Ho YJ, Burdziak C, Maag JLV, Morris JP, Chandwani R, Chen HA, Tsanov KM, Barriga FM, Luan W, Tasdemir N, Livshits G, Azizi E, Chun J, Wilkinson JE, Mazutis L, Leach SD, Koche R, Pe'er D, Lowe SW. A gene-environment-induced epigenetic program initiates tumorigenesis. Nature 2021; 590:642-648. [PMID: 33536616 PMCID: PMC8482641 DOI: 10.1038/s41586-020-03147-x] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023]
Abstract
Tissue damage increases the risk of cancer through poorly understood mechanisms1. In mouse models of pancreatic cancer, pancreatitis associated with tissue injury collaborates with activating mutations in the Kras oncogene to markedly accelerate the formation of early neoplastic lesions and, ultimately, adenocarcinoma2,3. Here, by integrating genomics, single-cell chromatin assays and spatiotemporally controlled functional perturbations in autochthonous mouse models, we show that the combination of Kras mutation and tissue damage promotes a unique chromatin state in the pancreatic epithelium that distinguishes neoplastic transformation from normal regeneration and is selected for throughout malignant evolution. This cancer-associated epigenetic state emerges within 48 hours of pancreatic injury, and involves an 'acinar-to-neoplasia' chromatin switch that contributes to the early dysregulation of genes that define human pancreatic cancer. Among the factors that are most rapidly activated after tissue damage in the pre-malignant pancreatic epithelium is the alarmin cytokine interleukin 33, which recapitulates the effects of injury in cooperating with mutant Kras to unleash the epigenetic remodelling program of early neoplasia and neoplastic transformation. Collectively, our study demonstrates how gene-environment interactions can rapidly produce gene-regulatory programs that dictate early neoplastic commitment, and provides a molecular framework for understanding the interplay between genetic and environmental cues in the initiation of cancer.
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Affiliation(s)
- Direna Alonso-Curbelo
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu-Jui Ho
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cassandra Burdziak
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jesper L V Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John P Morris
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rohit Chandwani
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA
| | - Hsuan-An Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaloyan M Tsanov
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco M Barriga
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Luan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nilgun Tasdemir
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Geulah Livshits
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elham Azizi
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jaeyoung Chun
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John E Wilkinson
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Linas Mazutis
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven D Leach
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Dartmouth Norris Cotton Cancer Center, Hanover, NH, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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11
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Leibold J, Ruscetti M, Cao Z, Ho YJ, Baslan T, Zou M, Abida W, Feucht J, Han T, Barriga FM, Tsanov KM, Zamechek L, Kulick A, Amor C, Tian S, Rybczyk K, Salgado NR, Sánchez-Rivera FJ, Watson PA, de Stanchina E, Wilkinson JE, Dow LE, Abate-Shen C, Sawyers CL, Lowe SW. Somatic Tissue Engineering in Mouse Models Reveals an Actionable Role for WNT Pathway Alterations in Prostate Cancer Metastasis. Cancer Discov 2020; 10:1038-1057. [PMID: 32376773 DOI: 10.1158/2159-8290.cd-19-1242] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/26/2020] [Accepted: 05/01/2020] [Indexed: 11/16/2022]
Abstract
To study genetic factors influencing the progression and therapeutic responses of advanced prostate cancer, we developed a fast and flexible system that introduces genetic alterations relevant to human disease directly into the prostate glands of mice using tissue electroporation. These electroporation-based genetically engineered mouse models (EPO-GEMM) recapitulate features of traditional germline models and, by modeling genetic factors linked to late-stage human disease, can produce tumors that are metastatic and castration-resistant. A subset of tumors with Trp53 alterations acquired spontaneous WNT pathway alterations, which are also associated with metastatic prostate cancer in humans. Using the EPO-GEMM approach and an orthogonal organoid-based model, we show that WNT pathway activation drives metastatic disease that is sensitive to pharmacologic WNT pathway inhibition. Thus, by leveraging EPO-GEMMs, we reveal a functional role for WNT signaling in driving prostate cancer metastasis and validate the WNT pathway as therapeutic target in metastatic prostate cancer. SIGNIFICANCE: Our understanding of the factors driving metastatic prostate cancer is limited by the paucity of models of late-stage disease. Here, we develop EPO-GEMMs of prostate cancer and use them to identify and validate the WNT pathway as an actionable driver of aggressive metastatic disease.This article is highlighted in the In This Issue feature, p. 890.
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Affiliation(s)
- Josef Leibold
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marcus Ruscetti
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zhen Cao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York
| | - Yu-Jui Ho
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timour Baslan
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Min Zou
- Departments of Pharmacology, Urology, Medicine, Pathology and Cell Biology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Judith Feucht
- Center for Cell Engineering and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Teng Han
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Francisco M Barriga
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kaloyan M Tsanov
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leah Zamechek
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amanda Kulick
- Department of Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Corina Amor
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sha Tian
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katarzyna Rybczyk
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nelson R Salgado
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Philip A Watson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Department of Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John E Wilkinson
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Cory Abate-Shen
- Departments of Pharmacology, Urology, Medicine, Pathology and Cell Biology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. .,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York. .,Howard Hughes Medical Institute, Chevy Chase, Maryland
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12
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Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ. A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell 2019; 22:575-588.e7. [PMID: 29625070 DOI: 10.1016/j.stem.2018.03.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 10/10/2017] [Accepted: 03/14/2018] [Indexed: 12/21/2022]
Abstract
While gene expression dynamics have been extensively cataloged during hematopoietic differentiation in the adult, less is known about transcriptome diversity of human hematopoietic stem cells (HSCs) during development. To characterize transcriptional and post-transcriptional changes in HSCs during development, we leveraged high-throughput genomic approaches to profile miRNAs, lincRNAs, and mRNAs. Our findings indicate that HSCs manifest distinct alternative splicing patterns in key hematopoietic regulators. Detailed analysis of the splicing dynamics and function of one such regulator, HMGA2, identified an alternative isoform that escapes miRNA-mediated targeting. We further identified the splicing kinase CLK3 that, by regulating HMGA2 splicing, preserves HMGA2 function in the setting of an increase in let-7 miRNA levels, delineating how CLK3 and HMGA2 form a functional axis that influences HSC properties during development. Collectively, our study highlights molecular mechanisms by which alternative splicing and miRNA-mediated post-transcriptional regulation impact the molecular identity and stage-specific developmental features of human HSCs.
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Affiliation(s)
- Marcella Cesana
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Michael H Guo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA; Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Davide Cacchiarelli
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli 80078, Italy; Department of Translational Medicine, University of Naples "Federico II", Naples 80131, Italy
| | - Lara Wahlster
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jessica Barragan
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sergei Doulatov
- Division of Hematology, University of Washington, Seattle, WA 98195, USA
| | - Linda T Vo
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Beatrice Salvatori
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98115, USA
| | - Kendell Clement
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kaloyan M Tsanov
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Patricia M Sousa
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Barbara Tazon-Vega
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adriano Bolondi
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Federico M Giorgi
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Departments of Biomedical Informatics, Biochemistry and Molecular Biophysics, JP Sulzberger Columbia Genome Center, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - John L Rinn
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; University of Colorado Boulder Biofrontiers, Boulder, CO 80301, USA
| | - Alexander Meissner
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA; Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - George Q Daley
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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13
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Affiliation(s)
- Kaloyan M Tsanov
- a Stem Cell Transplantation Program, Division of Hematology/Oncology , Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana Farber Cancer Institute , Boston , MA , USA.,b Department of Biological Chemistry and Molecular Pharmacology , Harvard Stem Cell Institute, Harvard Medical School, Howard Hughes Medical Institute , Boston , MA , USA
| | - George Q Daley
- a Stem Cell Transplantation Program, Division of Hematology/Oncology , Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana Farber Cancer Institute , Boston , MA , USA.,b Department of Biological Chemistry and Molecular Pharmacology , Harvard Stem Cell Institute, Harvard Medical School, Howard Hughes Medical Institute , Boston , MA , USA
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14
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Powers JT, Tsanov KM, Pearson DS, Roels F, Spina CS, Ebright R, Seligson M, de Soysa Y, Cahan P, Theiβen J, Tu HC, Han A, Kurek KC, LaPier GS, Osborne JK, Ross SJ, Cesana M, Collins JJ, Berthold F, Daley GQ. Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma. Nature 2016; 535:246-51. [PMID: 27383785 PMCID: PMC4947006 DOI: 10.1038/nature18632] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/08/2016] [Indexed: 02/06/2023]
Abstract
Poor prognosis in neuroblastoma is associated with genetic amplification of MYCN. MYCN is itself a target of let-7, a tumour suppressor family of microRNAs implicated in numerous cancers. LIN28B, an inhibitor of let-7 biogenesis, is overexpressed in neuroblastoma and has been reported to regulate MYCN. Here we show, however, that LIN28B is dispensable in MYCN-amplified neuroblastoma cell lines, despite de-repression of let-7. We further demonstrate that MYCN messenger RNA levels in amplified disease are exceptionally high and sufficient to sponge let-7, which reconciles the dispensability of LIN28B. We found that genetic loss of let-7 is common in neuroblastoma, inversely associated with MYCN amplification, and independently associated with poor outcomes, providing a rationale for chromosomal loss patterns in neuroblastoma. We propose that let-7 disruption by LIN28B, MYCN sponging, or genetic loss is a unifying mechanism of neuroblastoma development with broad implications for cancer pathogenesis.
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Affiliation(s)
- John T Powers
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Kaloyan M Tsanov
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Daniel S Pearson
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Frederik Roels
- Department of Pediatric Oncology, University Hospital Koln, Cologne, Germany
| | - Catherine S Spina
- Department of Biological Engineering, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard; Wyss Institute for Biologically Inspired Engineering; Boston, MA 02115, USA
| | - Richard Ebright
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Marc Seligson
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Yvanka de Soysa
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Patrick Cahan
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Jessica Theiβen
- Department of Pediatric Oncology, University Hospital Koln, Cologne, Germany
| | - Ho-Chou Tu
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Areum Han
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Kyle C Kurek
- Department of Pathology, Boston Children’s Hospital, Boston MA 02215, USA
| | - Grace S LaPier
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Jihan K Osborne
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Samantha J Ross
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Marcella Cesana
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard; Wyss Institute for Biologically Inspired Engineering; Boston, MA 02115, USA
| | - Frank Berthold
- Department of Pediatric Oncology, University Hospital Koln, Cologne, Germany
| | - George Q Daley
- Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Howard Hughes Medical Institute, Boston Children’s Hospital and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Boston, MA 02115, USA Harvard Stem Cell Institute, Boston, MA 02115, USA
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Powers JT, Tsanov KM, Roles F, Ebright R, Seligson M, de Soysa Y, Cahan P, Theissen J, LaPier GS, Pearson DS, Berthold F, Daley GQ. Abstract LB-290: Multiple distinct mechanisms disrupt let-7 miRNA biogenesis and function in neuroblastoma. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The let-7 microRNA family are known tumor suppressors often deregulated in cancer, yet the underlying mechanisms of let-7 disruption remain poorly understood. Neuroblastoma, a neural crest derived tumor, is defined in part by poor prognosis associated with genetic amplification of MYCN, itself a let-7 target. The let-7 biogenesis inhibitor LIN28B has recently been implicated as a critical regulator of MYCN, but we have employed siRNA and CRISPR-mediated gene disruption to show that LIN28B is dispensable for both MYCN protein expression and growth of MYCN-amplified neuroblastoma cell lines despite robust de-repression of let-7, which prompted us to explore additional mechanisms for let-7 disruption. Consequently, we have found that amplified MYCN mRNA is a potent let-7 sponge that through exceptionally high expression defines a sub-class of self-sponging amplified-competing-endogenous-RNA (aceRNA), which reconciles the dispensability of LIN28B in NB cell lines. In addition, by analyzing a large cohort of tumor samples from patients, we observe frequent genomic loss of let-7 that inversely associates with MYCN-amplification, providing a functional explanation for the known MYCN-amplification-independent pattern of chromosome 3p and 11q loss, which harbor let-7g and let-7a2, respectively. We thus propose a model whereby let-7 disruption by genetic loss, LIN28B expression, or aceRNA sponging is a unifying mechanism of neuroblastoma pathogenesis. Indeed, our data show that the majority of neuroblastomas have at least one let-7 disruption event and that genetic loss in non-MYCN-amplified tumors marks decreased survival, further underscoring its importance. The inverse selective relationship between allelic loss and sponging of let-7 from highly expressed or amplified oncogenes may have broad implications for oncogenesis.
Note: This abstract was not presented at the meeting.
Citation Format: John T. Powers, Kaloyan M. Tsanov, Frederik Roles, Richard Ebright, Marc Seligson, Yvanka de Soysa, Patrick Cahan, Jessica Theissen, Grace S. LaPier, Dan S. Pearson, Frank Berthold, George Q. Daley. Multiple distinct mechanisms disrupt let-7 miRNA biogenesis and function in neuroblastoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-290. doi:10.1158/1538-7445.AM2015-LB-290
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Tsanov KM, Nishi Y, Peterson KA, Liu J, Baetscher M, McMahon AP. An embryonic stem cell-based system for rapid analysis of transcriptional enhancers. Genesis 2012; 50:443-50. [PMID: 22083581 DOI: 10.1002/dvg.20820] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/19/2011] [Accepted: 10/26/2011] [Indexed: 11/07/2022]
Abstract
With the growing use of genome-wide screens for cis-regulatory elements, there is a pressing need for platforms that enable fast and cost-effective experimental validation of identified hits in relevant developmental and tissue contexts. Here, we describe a murine embryonic stem cell (ESC)-based system that facilitates rapid analysis of putative transcriptional enhancers. Candidate enhancers are targeted with high efficiency to a defined genomic locus via recombinase-mediated cassette exchange. Targeted ESCs are subsequently differentiated in vitro into desired cell types, where enhancer activity is monitored by reporter gene expression. As a proof of principle, we analyzed a previously characterized, Sonic hedgehog (Shh)-dependent, V3 interneuron progenitor (pV3)-specific enhancer for the Nkx2.2 gene, and observed highly specific enhancer activity. Given the broad potential of ESCs to generate a spectrum of cell types, this system can serve as an effective platform for the characterization of gene regulatory networks controlling cell fate specification and cell function.
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Affiliation(s)
- Kaloyan M Tsanov
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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