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Jasani N, Xu X, Posorske B, Kim Y, Vera O, Tsai KY, DeNicola GM, Karreth FA. MAPK-mediated PHGDH induction is essential for melanoma formation and represents an actionable vulnerability. bioRxiv 2024:2024.04.11.589139. [PMID: 38659816 PMCID: PMC11042198 DOI: 10.1101/2024.04.11.589139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Overexpression of PHGDH, the rate-limiting enzyme in the serine synthesis pathway, promotes melanomagenesis, melanoma cell proliferation, and survival of metastases in serine-low environments such as the brain. While PHGDH amplification explains PHGDH overexpression in a subset of melanomas, we find that PHGDH levels are universally increased in melanoma cells due to oncogenic BRAF V600E promoting PHGDH transcription through mTORC1-mediated translation of ATF4. Importantly, PHGDH expression was critical for melanomagenesis as depletion of PHGDH in genetic mouse models blocked melanoma formation. Despite BRAF V600E - mediated upregulation, PHGDH was further induced by exogenous serine restriction. Surprisingly, BRAF V600E inhibition diminished serine restriction-mediated PHGDH expression by preventing ATF4 induction, creating a potential vulnerability whereby melanoma cells could be specifically starved of serine by combining BRAF V600E inhibition with exogenous serine restriction. Indeed, we show that this combination promoted cell death in vitro and attenuated melanoma growth in vivo. This study identified a melanoma cell-specific PHGDH-dependent vulnerability.
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Xu X, Bok I, Jasani N, Wang K, Chadourne M, Mecozzi N, Deng O, Welsh EA, Kinose F, Rix U, Karreth FA. PTEN Lipid Phosphatase Activity Suppresses Melanoma Formation by Opposing an AKT/mTOR/FRA1 Signaling Axis. Cancer Res 2024; 84:388-404. [PMID: 38193852 PMCID: PMC10842853 DOI: 10.1158/0008-5472.can-23-1730] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/27/2023] [Accepted: 11/17/2023] [Indexed: 01/10/2024]
Abstract
Inactivating mutations in PTEN are prevalent in melanoma and are thought to support tumor development by hyperactivating the AKT/mTOR pathway. Conversely, activating mutations in AKT are relatively rare in melanoma, and therapies targeting AKT or mTOR have shown disappointing outcomes in preclinical models and clinical trials of melanoma. This has led to the speculation that PTEN suppresses melanoma by opposing AKT-independent pathways, potentially through noncanonical functions beyond its lipid phosphatase activity. In this study, we examined the mechanisms of PTEN-mediated suppression of melanoma formation through the restoration of various PTEN functions in PTEN-deficient cells or mouse models. PTEN lipid phosphatase activity predominantly inhibited melanoma cell proliferation, invasion, and tumor growth, with minimal contribution from its protein phosphatase and scaffold functions. A drug screen underscored the exquisite dependence of PTEN-deficient melanoma cells on the AKT/mTOR pathway. Furthermore, activation of AKT alone was sufficient to counteract several aspects of PTEN-mediated melanoma suppression, particularly invasion and the growth of allograft tumors. Phosphoproteomics analysis of the lipid phosphatase activity of PTEN validated its potent inhibition of AKT and many of its known targets, while also identifying the AP-1 transcription factor FRA1 as a downstream effector. The restoration of PTEN dampened FRA1 translation by inhibiting AKT/mTOR signaling, and FRA1 overexpression negated aspects of PTEN-mediated melanoma suppression akin to AKT. This study supports AKT as the key mediator of PTEN inactivation in melanoma and identifies an AKT/mTOR/FRA1 axis as a driver of melanomagenesis. SIGNIFICANCE PTEN suppresses melanoma predominantly through its lipid phosphatase function, which when lost, elevates FRA1 levels through AKT/mTOR signaling to promote several aspects of melanomagenesis.
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Affiliation(s)
- Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ilah Bok
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology PhD program, University of South Florida, Tampa, Florida
| | - Neel Jasani
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology PhD program, University of South Florida, Tampa, Florida
| | - Kaizhen Wang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology PhD program, University of South Florida, Tampa, Florida
| | - Manon Chadourne
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Nicol Mecozzi
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology PhD program, University of South Florida, Tampa, Florida
| | - Ou Deng
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Eric A. Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Oncologic Sciences, University of South Florida, Tampa, Florida
| | - Florian A. Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Oncologic Sciences, University of South Florida, Tampa, Florida
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Tasoulas J, Srivastava S, Xu X, Tarasova V, Maniakas A, Karreth FA, Amelio AL. Genetically engineered mouse models of head and neck cancers. Oncogene 2023; 42:2593-2609. [PMID: 37474617 PMCID: PMC10457205 DOI: 10.1038/s41388-023-02783-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Abstract
The head and neck region is one of the anatomic sites commonly afflicted by cancer, with ~1.5 million new diagnoses reported worldwide in 2020 alone. Remarkable progress has been made in understanding the underlying disease mechanisms, personalizing care based on each tumor's individual molecular characteristics, and even therapeutically exploiting the inherent vulnerabilities of these neoplasms. In this regard, genetically engineered mouse models (GEMMs) have played an instrumental role. While progress in the development of GEMMs has been slower than in other major cancer types, several GEMMs are now available that recapitulate most of the heterogeneous characteristics of head and neck cancers such as the tumor microenvironment. Different approaches have been employed in GEMM development and implementation, though each can generally recapitulate only certain disease aspects. As a result, appropriate model selection is essential for addressing specific research questions. In this review, we present an overview of all currently available head and neck cancer GEMMs, encompassing models for head and neck squamous cell carcinoma, nasopharyngeal carcinoma, and salivary and thyroid gland carcinomas.
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Affiliation(s)
- Jason Tasoulas
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sonal Srivastava
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Valentina Tarasova
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Anastasios Maniakas
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Antonio L Amelio
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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DeBlasi JM, Falzone A, Caldwell S, Prieto-Farigua N, Prigge JR, Schmidt EE, Chio IIC, Karreth FA, DeNicola GM. Distinct Nrf2 Signaling Thresholds Mediate Lung Tumor Initiation and Progression. Cancer Res 2023; 83:1953-1967. [PMID: 37062029 PMCID: PMC10267679 DOI: 10.1158/0008-5472.can-22-3848] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 12/08/2022] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023]
Abstract
Mutations in the KEAP1-NRF2 (Kelch-like ECH-associated protein 1-nuclear factor-erythroid 2 p45-related factor 2) pathway occur in up to a third of non-small cell lung cancer (NSCLC) cases and often confer resistance to therapy and poor outcomes. Here, we developed murine alleles of the KEAP1 and NRF2 mutations found in human NSCLC and comprehensively interrogated their impact on tumor initiation and progression. Chronic NRF2 stabilization by Keap1 or Nrf2 mutation was not sufficient to induce tumorigenesis, even in the absence of tumor suppressors, p53 or LKB1. When combined with KrasG12D/+, constitutive NRF2 activation promoted lung tumor initiation and early progression of hyperplasia to low-grade tumors but impaired their progression to advanced-grade tumors, which was reversed by NRF2 deletion. Finally, NRF2 overexpression in KEAP1 mutant human NSCLC cell lines was detrimental to cell proliferation, viability, and anchorage-independent colony formation. Collectively, these results establish the context-dependence and activity threshold for NRF2 during the lung tumorigenic process. SIGNIFICANCE Stabilization of the transcription factor NRF2 promotes oncogene-driven tumor initiation but blocks tumor progression, indicating distinct, threshold-dependent effects of the KEAP1/NRF2 pathway in different stages of lung tumorigenesis.
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Affiliation(s)
- Janine M. DeBlasi
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology PhD Program, University of South Florida, Tampa, Florida
| | - Aimee Falzone
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Samantha Caldwell
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Nicolas Prieto-Farigua
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Justin R. Prigge
- Microbiology & Cell Biology Department, Montana State University, Bozeman, Montana
| | - Edward E. Schmidt
- Microbiology & Cell Biology Department, Montana State University, Bozeman, Montana
| | - Iok In Christine Chio
- Department of Genetics and Development, Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
| | - Florian A. Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Gina M. DeNicola
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
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Reid BM, Chen A, Chen Z, Karreth FA, Kanetsky P, Permuth JB, Saglam O, Teer J, Yu X, Gayther S, Goode E, Pharoah P, Sellers TA, Lawrenson K. Abstract 6065: Patterns of dysregulated coding and noncoding gene expression in high-grade serous ovarian carcinomas. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6065] [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
Purpose: Identifying dysregulated gene expression in ovarian cancers has been limited by a deficit of available normal tissues. Here, we generated the largest set of high-grade serous ovarian cancer (HGSOC) tumors with normal precursor tissues for transcriptome analyses.
Methods: We performed RNA sequencing on 220 primary HGSOCs and 116 benign epithelia (micro-dissected fallopian tube, ovarian surface, and inclusion cysts), and combined samples with 428 HGSOCs from TCGA, 60 HGSOCs from a prior study, and 180 bulk ovary tissues from GTEx. Raw reads were processed with a uniform bioinformatic and quality control pipeline; combined data were batch corrected. We tested for differences in median normalized CPM expression values using the Wilcoxon rank sum test with >2-fold change and a false discovery rate <1% considered statistically significant. We also conducted weighted gene co-expression network analysis in each tissue type. The hypergeometric test was used for enrichment of differentially expressed genes (DEGs) and gene ontologies within modules.
Results: Transcriptomes comprised 27,700 expressed genes (8,202 lncRNAs) across 706 HGSOCs, 180 bulk ovary, and 88 ovarian epithelia tissues. Most (~90%) genes were expressed in all tissues; 5% each showed HGSOC- or normal tissue-specific expression and ≥50% were lncRNA. Comparing HGSOCs to ovarian epithelia and to bulk ovary identified 11,804 DEGs with 4,522 lncRNAs (DElncRNA) of which ~50% were tissue-specific. DEGs included MUC16 and multiple GWAS/TWAS implicated susceptibility genes including RAD51, BRIP1, BNC2, TIPARP-AS1, PRC1, KANSL1, ANKLE1, CHMP4C, ESRP2, and CCNE1. The most highly expressed DElncRNA in HGSOC were upregulated RMRP (P=1.4x10-39), SNHG1 (P=3.0x10-27), and HAGLR (P=2.0x10-24) at the HOXD risk locus. The highest expressed DElncRNA in precursor tissues was the HGSOC-downregulated MEG3 (P=1.7x10-67). DEGs were enriched in HGSOC co-expression modules associated with immune response, cell motility/localization, cell cycle regulation, angiogenesis, reproductive development, transcriptional regulation, and metabolic processes. Tissue-specific DElncRNA tended toward upregulation compared to ovarian epithelia with enriched modules associated with cell cycle regulation (hub=BUB1B; top DElncRNA TRPM2-AS, P=1.5x10-38); and toward downregulation compared to bulk ovary with enriched modules associated with chemokine signaling/response (hub= GADD45B, top DElncRNA RP11-87P3.1, P=1.7x10-113).
Conclusion: HGSOC-dysregulated lncRNA expression revealed tissue-specific differences that highlight unique biological pathways in precursor epithelia and the ovarian microenvironment that contribute to HGSOC pathogenesis. Our results provide additional evidence to support previously nominated risk genes. Integration with eQTL and GWAS are underway to further elucidate novel HGSOC susceptibility genes.
Citation Format: Brett M. Reid, Ann Chen, Zhihua Chen, Florian A. Karreth, Peter Kanetsky, Jennifer B. Permuth, Ozlen Saglam, Jamie Teer, Xiaoqing Yu, Simon Gayther, Ellen Goode, Paul Pharoah, Thomas A. Sellers, Kate Lawrenson. Patterns of dysregulated coding and noncoding gene expression in high-grade serous ovarian carcinomas [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 6065.
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Affiliation(s)
| | - Ann Chen
- 1Moffitt Cancer Center, Tampa, FL
| | | | | | | | | | - Ozlen Saglam
- 2Oregon Health and Science University, Portland, OR
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Xu X, Wang K, Vera O, Verma A, Jasani N, Bok I, Elemento O, Du D, Yu X, Karreth FA. Gain of Chromosome 1q Perturbs a Competitive Endogenous RNA Network to Promote Melanoma Metastasis. Cancer Res 2022; 82:3016-3031. [PMID: 36052492 PMCID: PMC9971359 DOI: 10.1158/0008-5472.can-22-0283] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/19/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
Somatic copy-number alterations (CNA) promote cancer, but the underlying driver genes may not be comprehensively identified if only the functions of the encoded proteins are considered. mRNAs can act as competitive endogenous RNAs (ceRNA), which sponge miRNAs to posttranscriptionally regulate gene expression in a protein coding-independent manner. We investigated the contribution of ceRNAs to the oncogenic effects of CNAs. Chromosome 1q gains promoted melanoma progression and metastasis at least in part through overexpression of three mRNAs with ceRNA activity: CEP170, NUCKS1, and ZC3H11A. These ceRNAs enhanced melanoma metastasis by sequestering tumor suppressor miRNAs. Orthogonal genetic assays with miRNA inhibitors and target site blockers, along with rescue experiments, demonstrated that miRNA sequestration is critical for the oncogenic effects of CEP170, NUCKS1, and ZC3H11A mRNAs. Furthermore, chromosome 1q ceRNA-mediated miRNA sequestration alleviated the repression of several prometastatic target genes. This regulatory RNA network was evident in other cancer types, suggesting chromosome 1q ceRNA deregulation as a common driver of cancer progression. Taken together, this work demonstrates that ceRNAs mediate the oncogenicity of somatic CNAs. SIGNIFICANCE The function of CEP170, NUCKS1, and ZC3H11A mRNAs as competitive endogenous RNAs that sequester tumor suppressor microRNAs underlies the oncogenic activity of chromosome 1q gains.
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Affiliation(s)
- Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Kaizhen Wang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
- Cancer Biology PhD program, University of South Florida, Tampa, FL 33612, USA
| | - Olga Vera
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Akanksha Verma
- Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Neel Jasani
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
- Cancer Biology PhD program, University of South Florida, Tampa, FL 33612, USA
| | - Ilah Bok
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
- Cancer Biology PhD program, University of South Florida, Tampa, FL 33612, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Dongliang Du
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Florian A. Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
- Correspondence: Florian A. Karreth, PhD, Moffitt Cancer Center, 12902 Magnolia Drive, Stabile Research Building, Rm 23043, Tampa, FL 33612, USA, , Phone: 813-745-1851
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Li J, Smalley I, Chen Z, Wu JY, Phadke MS, Teer JK, Nguyen T, Karreth FA, Koomen JM, Sarnaik AA, Zager JS, Khushalani NI, Tarhini AA, Sondak VK, Rodriguez PC, Messina JL, Chen YA, Smalley KSM. Single-cell Characterization of the Cellular Landscape of Acral Melanoma Identifies Novel Targets for Immunotherapy. Clin Cancer Res 2022; 28:2131-2146. [PMID: 35247927 PMCID: PMC9106889 DOI: 10.1158/1078-0432.ccr-21-3145] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/10/2021] [Accepted: 03/01/2022] [Indexed: 12/21/2022]
Abstract
PURPOSE Acral melanoma is a rare subtype of melanoma that arises on the non-hair-bearing skin of the palms, soles, and nail beds. In this study, we used single-cell RNA sequencing (scRNA-seq) to map the transcriptional landscape of acral melanoma and identify novel immunotherapeutic targets. EXPERIMENTAL DESIGN We performed scRNA-seq on nine clinical specimens (five primary, four metastases) of acral melanoma. Detailed cell type curation was performed, the immune landscapes were mapped, and key results were validated by analysis of The Cancer Genome Atlas (TCGA) and single-cell datasets. Cell-cell interactions were inferred and compared with those in nonacral cutaneous melanoma. RESULTS Multiple phenotypic subsets of T cells, natural killer (NK) cells, B cells, macrophages, and dendritic cells with varying levels of activation/exhaustion were identified. A comparison between primary and metastatic acral melanoma identified gene signatures associated with changes in immune responses and metabolism. Acral melanoma was characterized by a lower overall immune infiltrate, fewer effector CD8 T cells and NK cells, and a near-complete absence of γδ T cells compared with nonacral cutaneous melanomas. Immune cells associated with acral melanoma exhibited expression of multiple checkpoints including PD-1, LAG-3, CTLA-4, V-domain immunoglobin suppressor of T cell activation (VISTA), TIGIT, and the Adenosine A2A receptor (ADORA2). VISTA was expressed in 58.3% of myeloid cells and TIGIT was expressed in 22.3% of T/NK cells. CONCLUSIONS Acral melanoma has a suppressed immune environment compared with that of cutaneous melanoma from nonacral skin. Expression of multiple, therapeutically tractable immune checkpoints were observed, offering new options for clinical translation.
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Affiliation(s)
- Jiannong Li
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Inna Smalley
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Zhihua Chen
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Jheng-Yu Wu
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Manali S. Phadke
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Jamie K. Teer
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Thanh Nguyen
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Florian A. Karreth
- The Department of Molecular Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - John M. Koomen
- The Department of Molecular Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Amod A. Sarnaik
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Jonathan S. Zager
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Nikhil I. Khushalani
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Ahmad A. Tarhini
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Vernon K. Sondak
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Paulo C. Rodriguez
- The Department of Immunology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Jane L. Messina
- The Department of Immunology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Y. Ann Chen
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Keiran S. M. Smalley
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
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Bok I, Angarita A, Douglass SM, Weeraratna AT, Karreth FA. A Series of BRAF- and NRAS-Driven Murine Melanoma Cell Lines with Inducible Gene Modulation Capabilities. JID Innov 2022; 2:100076. [PMID: 35146482 PMCID: PMC8819036 DOI: 10.1016/j.xjidi.2021.100076] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/30/2021] [Accepted: 11/02/2021] [Indexed: 11/24/2022] Open
Abstract
Murine cancer cell lines are powerful research tools to complement studies in genetically engineered mouse models. We have established 21 melanoma cell lines from embryonic stem cell-genetically engineered mouse models driven by alleles that model the most frequent genetic alterations in human melanoma. In addition, these cell lines harbor regulatory alleles for the genomic integration of transgenes and the regulation of expression of such transgenes. In this study, we report a comprehensive characterization of these cell lines. Specifically, we validated melanocytic origin, driver allele recombination and expression, and activation of the oncogenic MAPK and protein kinase B pathways. We further tested tumor formation in syngeneic immunocompetent recipients as well as the functionality of the integrated Tet-ON system and recombination-mediated cassette exchange homing cassette. Finally, by deleting the transcription factor MAFG with an inducible CRISPR/Cas9 approach, we show the utility of the regulatory alleles for candidate gene modulation. These cell lines will be a valuable resource for studying melanoma biology and therapy.
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Key Words
- BCC, BrafV600E Cdkn2aΔ/Δ
- BPP, BrafV600E PtenΔ/Δ
- CHC, collagen homing cassette
- Dox, doxycycline
- ESC, embryonic stem cell
- FBS, fetal bovine serum
- GEMM, genetically engineered mouse model
- NCC, NrasQ61R Cdkn2aΔ/Δ
- NPP, NrasQ61R PtenΔ/Δ
- RMCE, recombination-mediated cassette exchange
- sgRNA, single-guide RNA
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Affiliation(s)
- Ilah Bok
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Cancer Biology PhD program, Department of Cell Biology, Microbiology and Molecular Biology, College of Arts and Sciences, University of South Florida, Tampa, Florida, USA
| | - Ariana Angarita
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Stephen M. Douglass
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ashani T. Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, University, Baltimore, Maryland, USA
| | - Florian A. Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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Nakamura K, Reid BM, Chen A, Chen Z, Goode EL, Permuth JB, Teer JK, Tyrer J, Yu X, Kanetsky PA, Pharoah PD, Gayther SA, Sellers TA, Lawrenson K, Karreth FA. Functional analysis of the 1p34.3 risk locus implicates GNL2 in high-grade serous ovarian cancer. Am J Hum Genet 2022; 109:116-135. [PMID: 34965383 DOI: 10.1016/j.ajhg.2021.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022] Open
Abstract
The high-grade serous ovarian cancer (HGSOC) risk locus at chromosome 1p34.3 resides within a frequently amplified genomic region signifying the presence of an oncogene. Here, we integrate in silico variant-to-function analysis with functional studies to characterize the oncogenic potential of candidate genes in the 1p34.3 locus. Fine mapping of genome-wide association statistics identified candidate causal SNPs local to H3K27ac-demarcated enhancer regions that exhibit allele-specific binding for CTCF in HGSOC and normal fallopian tube secretory epithelium cells (FTSECs). SNP risk associations colocalized with eQTL for six genes (DNALI1, GNL2, RSPO1, SNIP1, MEAF6, and LINC01137) that are more highly expressed in carriers of the risk allele, and three (DNALI1, GNL2, and RSPO1) were upregulated in HGSOC compared to normal ovarian surface epithelium cells and/or FTSECs. Increased expression of GNL2 and MEAF6 was associated with shorter survival in HGSOC with 1p34.3 amplifications. Despite its activation of β-catenin signaling, RSPO1 overexpression exerted no effects on proliferation or colony formation in our study of ovarian cancer and FTSECs. Instead, GNL2, MEAF6, and SNIP1 silencing impaired in vitro ovarian cancer cell growth. Additionally, GNL2 silencing diminished xenograft tumor formation, whereas overexpression stimulated proliferation and colony formation in FTSECs. GNL2 influences 60S ribosomal subunit maturation and global protein synthesis in ovarian cancer and FTSECs, providing a potential mechanism of how GNL2 upregulation might promote ovarian cancer development and mediate genetic susceptibility of HGSOC.
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Mecozzi N, Nenci A, Vera O, Bok I, Falzone A, DeNicola GM, Karreth FA. Genetic tools for the stable overexpression of circular RNAs. RNA Biol 2021; 19:353-363. [PMID: 35289721 PMCID: PMC8928841 DOI: 10.1080/15476286.2022.2043041] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/11/2022] [Indexed: 10/28/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs featuring a covalently closed ring structure formed through backsplicing. circRNAs are broadly expressed and contribute to biological processes through a variety of functions. Standard gain-of-function and loss-of-function approaches to study gene functions have significant limitations when studying circRNAs. Overexpression studies in particular suffer from the lack of efficient genetic tools. While mammalian expression plasmids enable transient circRNA overexpression in cultured cells, most cell biological studies require long-term ectopic expression. Here we report the development and characterization of genetic tools enabling stable circRNA overexpression in vitro and in vivo. We demonstrated that circRNA expression constructs can be delivered to cultured cells via transposons, whereas lentiviral vectors have limited utility for the delivery of circRNA constructs due to viral RNA splicing in virus-producing cells. We further demonstrated ectopic circRNA expression in a hepatocellular carcinoma mouse model upon circRNA transposon delivery via hydrodynamic tail vein injection. Furthermore, we generated genetically engineered mice harbouring circRNA expression constructs. We demonstrated that this approach enables constitutive, global circRNA overexpression as well as inducible circRNA expression directed specifically to melanocytes in a melanoma mouse model. These tools expand the genetic toolkit available for the functional characterization of circRNAs.
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Affiliation(s)
- Nicol Mecozzi
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Cancer Biology PhD Program, University of South Florida, Tampa, FL, USA
| | - Arianna Nenci
- Gene Targeting Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Olga Vera
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Ilah Bok
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Cancer Biology PhD Program, University of South Florida, Tampa, FL, USA
| | - Aimee Falzone
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Gina M. DeNicola
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Florian A. Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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11
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Grammatikakis I, Karreth FA, Panda AC. Editorial: Structural and Functional Characterization of Circular RNAs. Front Mol Biosci 2021; 8:795286. [PMID: 34796203 PMCID: PMC8592900 DOI: 10.3389/fmolb.2021.795286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ioannis Grammatikakis
- National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Florian A Karreth
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
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Abstract
Non-coding RNAs are emerging as critical molecules in the genesis, progression, and therapy resistance of cutaneous melanoma. This includes circular RNAs (circRNAs), a class of non-coding RNAs with distinct characteristics that forms through non-canonical back-splicing. In this review, we summarize the features and functions of circRNAs and introduce the current knowledge of the roles of circRNAs in melanoma. We also highlight the various mechanisms of action of the well-studied circRNA CDR1as and describe how it acts as a melanoma tumor suppressor. We further discuss the utility of circRNAs as biomarkers, therapeutic targets, and therapeutic agents in melanoma and outline challenges that must be overcome to comprehensively characterize circRNA functions.
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Affiliation(s)
- Nicol Mecozzi
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Olga Vera
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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13
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Smalley KSM, Teer JK, Chen YA, Wu JY, Yao J, Koomen JM, Chen WS, Rodriguez-Waitkus P, Karreth FA, Messina JL. A Mutational Survey of Acral Nevi. JAMA Dermatol 2021; 157:831-835. [PMID: 33978681 DOI: 10.1001/jamadermatol.2021.0793] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Importance Acral skin may develop nevi, but their mutational status and association with acral melanoma is unclear. Objective To perform targeted next-generation sequencing on a cohort of acral nevi to determine their mutational spectrum. Design, Setting, and Participants Acral nevi specimens (n = 50) that had been obtained for diagnostic purposes were identified from the pathology archives of a tertiary care academic cancer center and a university dermatology clinic. Next-generation sequencing was performed on DNA extracted from the specimens, and mutations called. A subset of samples was stained immunohistochemically for the BRAF V600E mutation. Results A total of 50 nevi from 49 patients (19 males and 30 females; median [range] age, 48 [13-85] years) were examined. Analysis of the sequencing data revealed a high prevalence of BRAF mutations (n = 43), with a lower frequency of NRAS mutations (n = 5). Mutations in BRAF and NRAS were mutually exclusive. Conclusions and Relevance In this cohort study, nevi arising on mostly sun-protected acral skin showed a rate of BRAF mutation similar to that of acquired nevi on sun-exposed skin but far higher than that of acral melanoma. These findings are in contrast to the well-characterized mutational landscape of acral melanoma.
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Affiliation(s)
- Keiran S M Smalley
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, Florida.,Department of Cutaneous Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jheng-Yu Wu
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jiqiang Yao
- Biostatistics and Bioinformatics Shared Resource, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Wei-Shen Chen
- Department of Dermatology and Cutaneous Surgery, University of South Florida Morsani College of Medicine, Tampa, Florida
| | - Paul Rodriguez-Waitkus
- Department of Dermatology and Cutaneous Surgery, University of South Florida Morsani College of Medicine, Tampa, Florida
| | - Florian A Karreth
- Department of Molecular Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jane L Messina
- Department of Cutaneous Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida
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14
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Patton EE, Mueller KL, Adams DJ, Anandasabapathy N, Aplin AE, Bertolotto C, Bosenberg M, Ceol CJ, Burd CE, Chi P, Herlyn M, Holmen SL, Karreth FA, Kaufman CK, Khan S, Kobold S, Leucci E, Levy C, Lombard DB, Lund AW, Marie KL, Marine JC, Marais R, McMahon M, Robles-Espinoza CD, Ronai ZA, Samuels Y, Soengas MS, Villanueva J, Weeraratna AT, White RM, Yeh I, Zhu J, Zon LI, Hurlbert MS, Merlino G. Melanoma models for the next generation of therapies. Cancer Cell 2021; 39:610-631. [PMID: 33545064 PMCID: PMC8378471 DOI: 10.1016/j.ccell.2021.01.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/12/2022]
Abstract
There is a lack of appropriate melanoma models that can be used to evaluate the efficacy of novel therapeutic modalities. Here, we discuss the current state of the art of melanoma models including genetically engineered mouse, patient-derived xenograft, zebrafish, and ex vivo and in vitro models. We also identify five major challenges that can be addressed using such models, including metastasis and tumor dormancy, drug resistance, the melanoma immune response, and the impact of aging and environmental exposures on melanoma progression and drug resistance. Additionally, we discuss the opportunity for building models for rare subtypes of melanomas, which represent an unmet critical need. Finally, we identify key recommendations for melanoma models that may improve accuracy of preclinical testing and predict efficacy in clinical trials, to help usher in the next generation of melanoma therapies.
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Affiliation(s)
- E Elizabeth Patton
- MRC Human Genetics Unit and Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
| | - Kristen L Mueller
- Melanoma Research Alliance, 730 15th Street NW, Washington, DC 20005, USA.
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Niroshana Anandasabapathy
- Department of Dermatology, Meyer Cancer Center, Program in Immunology and Microbial Pathogenesis, Weill Cornell Medicine, New York, NY 10026, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Corine Bertolotto
- Université Côte d'Azur, Nice, France; INSERM, Biology and Pathologies of Melanocytes, Team 1, Equipe Labellisée Ligue 2020, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Marcus Bosenberg
- Departments of Dermatology, Pathology, and Immunobiology, Yale University, New Haven, CT, USA
| | - Craig J Ceol
- Program in Molecular Medicine and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christin E Burd
- Departments of Molecular Genetics, Cancer Biology, and Genetics, The Ohio State University, Biomedical Research Tower, Room 918, 460 W. 12th Avenue, Columbus, OH 43210, USA
| | - Ping Chi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Sheri L Holmen
- Department of Surgery, University of Utah Health Sciences Center, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Charles K Kaufman
- Washington University School of Medicine, Department of Medicine, Division of Oncology, Department of Developmental Biology, McDonnell Science Building, 4518 McKinley Avenue, St. Louis, MO 63110, USA
| | - Shaheen Khan
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sebastian Kobold
- Center of Integrated Protein Science Munich (CIPS-M) and Division of Clinical Pharmacology, Department of Medicine IV, Klinikum der Universität München, LMU, Munich, Germany; Member of the German Center for Lung Research (DZL), German Center for Translational Cancer Research (DKTK), partner site Munich, Munich, Germany
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, LKI, KU Leuven, 3000 Leuven, Belgium; Trace, Department of Oncology, LKI, KU Leuven, 3000 Leuven, Belgium
| | - Carmit Levy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - David B Lombard
- Department of Pathology, Institute of Gerontology, and Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amanda W Lund
- Ronald O. Perelman Department of Dermatology and Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kerrie L Marie
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Richard Marais
- CRUK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield SK10 4TG, UK
| | - Martin McMahon
- Department of Dermatology & Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, Santiago de Querétaro 76230, Mexico; Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ze'ev A Ronai
- Cancer Center, Sanford Burnham Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Maria S Soengas
- Spanish National Cancer Research Centre, 28029 Madrid, Spain
| | - Jessie Villanueva
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Philadelphia, PA, USA
| | - Ashani T Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, and Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Richard M White
- Department of Cancer Biology & Genetics and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Iwei Yeh
- Departments of Dermatology and Pathology, University of California, San Francisco, CA, USA
| | - Jiyue Zhu
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Marc S Hurlbert
- Melanoma Research Alliance, 730 15th Street NW, Washington, DC 20005, USA
| | - Glenn Merlino
- Center for Cancer Research, NCI, NIH, 37 Convent Drive, Bethesda, MD 20892, USA.
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15
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Bag AK, Schultz AR, Goala P, Karreth FA, Adeegbe DO. Investigating the role of KLRG1 in regulatory T-cells and implications for anti-tumor immunity in Non-small Cell Lung Cancer. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.57.02] [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] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Abstract
Although it is well established that CD4+CD25+Foxp3+ regulatory T cells (Tregs) dampen anti-tumor T cell responses in cancer, their molecular signature and clonal heterogeneity in NSCLC remains poorly understood. In this study, comparative phenotypic assessment of tumor and lymphoid tissue resident Tregs in KRAS/p53 mutant NSCLC mouse model revealed the presence of a distinct tumor infiltrating Treg population which express KLRG1. Compared to their counterparts, tumor associated KLRG1+ Treg showed higher expression of inhibitory receptors and activation markers, suggesting that KLRG1+ Tregs represent an activated subpopulation which may contribute to immunosuppression. Ex-vivo Treg suppression assay revealed that tumor associated KLGR1+ Tregs exhibited higher suppressive activity compared to KLRG1-Tregs. Although T cell development was normal in in-house generated KLRG1 KO mice including thymic and peripheral Treg numbers, KLRG1 KO Tregs showed less suppressive capacity compared to wild type, implying KLRG1 in Tregs functional program. Furthermore, α-KLRG1 antibody treatment in lung tumor bearing KP mice showed prolonged survival, accompanied by reduced proportion of KLRG1+ Tregs in the tumor. Finally, immunogenomic characterization of KLRG1 KO/wt and tumor infiltrating KLRG1+/− Tregs revealed distinct gene expression patterns and associated immune pathways. Collectively, our findings indicate that KLRG1 is not critical for Treg development and maintenance but may play a non-redundant role in Tregs differentiation and function in inflammatory settings. Therefore, targeting KLRG1 to curtail the inhibitory function of the highly suppressive KLRG1+ Treg subset could facilitate antitumor responses in NSCLC.
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16
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Vera O, Bok I, Jasani N, Nakamura K, Xu X, Mecozzi N, Angarita A, Wang K, Tsai KY, Karreth FA. A MAPK/miR-29 Axis Suppresses Melanoma by Targeting MAFG and MYBL2. Cancers (Basel) 2021; 13:1408. [PMID: 33808771 PMCID: PMC8003541 DOI: 10.3390/cancers13061408] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
The miR-29 family of microRNAs is encoded by two clusters, miR-29b1~a and miR-29b2~c, and is regulated by several oncogenic and tumor suppressive stimuli. While in vitro evidence suggests a tumor suppressor role for miR-29 in melanoma, the mechanisms underlying its deregulation and contribution to melanomagenesis have remained elusive. Using various in vitro systems, we show that oncogenic MAPK signaling paradoxically stimulates transcription of pri-miR-29b1~a and pri-miR-29b2~c, the latter in a p53-dependent manner. Expression analyses in melanocytes, melanoma cells, nevi, and primary melanoma revealed that pri-miR-29b2~c levels decrease during melanoma progression. Inactivation of miR-29 in vivo with a miRNA sponge in a rapid melanoma mouse model resulted in accelerated tumor development and decreased overall survival, verifying tumor suppressive potential of miR-29 in melanoma. Through integrated RNA sequencing, target prediction, and functional assays, we identified the transcription factors MAFG and MYBL2 as bona fide miR-29 targets in melanoma. Our findings suggest that attenuation of miR-29b2~c expression promotes melanoma development, at least in part, by derepressing MAFG and MYBL2.
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Affiliation(s)
- Olga Vera
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (O.V.); (I.B.); (N.J.); (K.N.); (X.X.); (N.M.); (A.A.); (K.W.)
| | - Ilah Bok
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (O.V.); (I.B.); (N.J.); (K.N.); (X.X.); (N.M.); (A.A.); (K.W.)
- Cancer Biology PhD Program, University of South Florida, Tampa, FL 33612, USA
| | - Neel Jasani
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (O.V.); (I.B.); (N.J.); (K.N.); (X.X.); (N.M.); (A.A.); (K.W.)
- Cancer Biology PhD Program, University of South Florida, Tampa, FL 33612, USA
| | - Koji Nakamura
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (O.V.); (I.B.); (N.J.); (K.N.); (X.X.); (N.M.); (A.A.); (K.W.)
| | - Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (O.V.); (I.B.); (N.J.); (K.N.); (X.X.); (N.M.); (A.A.); (K.W.)
| | - Nicol Mecozzi
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (O.V.); (I.B.); (N.J.); (K.N.); (X.X.); (N.M.); (A.A.); (K.W.)
- Department of Biology, University of Pisa, 56126 Pisa, Italy
| | - Ariana Angarita
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (O.V.); (I.B.); (N.J.); (K.N.); (X.X.); (N.M.); (A.A.); (K.W.)
| | - Kaizhen Wang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (O.V.); (I.B.); (N.J.); (K.N.); (X.X.); (N.M.); (A.A.); (K.W.)
- Cancer Biology PhD Program, University of South Florida, Tampa, FL 33612, USA
| | - Kenneth Y. Tsai
- Departments of Anatomic Pathology and Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA;
- Donald A. Adam Melanoma and Skin Cancer Center of Excellence, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Florian A. Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (O.V.); (I.B.); (N.J.); (K.N.); (X.X.); (N.M.); (A.A.); (K.W.)
- Donald A. Adam Melanoma and Skin Cancer Center of Excellence, Moffitt Cancer Center, Tampa, FL 33612, USA
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Bok I, Karreth FA. Strategies to Study the Functions of Pseudogenes in Mouse Models of Cancer. Methods Mol Biol 2021; 2324:287-304. [PMID: 34165722 DOI: 10.1007/978-1-0716-1503-4_18] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Aberrant expression of pseudogenes has been observed in many cancer types. Deregulated pseudogenes engage in a multitude of biological processes at the DNA, RNA, and protein levels and eventually facilitate disease progression. To investigate pseudogene functions in cancer, cell lines and cell line transplantation models have been widely used. However, cancer biology is best studied in the context of an intact organism. Here, we present various strategies to investigate pseudogenes in genetically engineered mouse models and discuss advantages and disadvantages of the different approaches.
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Affiliation(s)
- Ilah Bok
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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18
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Bok I, Reff J, Nenci A, Gonzalez JG, Karreth FA. Abstract A17: A versatile mouse-modeling platform for rapid in vivo melanoma studies. Cancer Res 2020. [DOI: 10.1158/1538-7445.mel2019-a17] [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
Melanoma accounts for about 1% of skin cancers but causes the majority of skin cancer-related deaths. Despite progress in treating melanoma with immunotherapy and targeted therapy, melanoma patients still suffer from relapse due to resistance to these treatments. A better understanding of the molecular mechanisms that contribute to melanomagenesis and resistance may provide novel avenues for the development of improved treatment strategies. To accelerate the speed, increase the throughput, and lower the cost of delineating such mechanisms in vivo, we developed a novel embryonic stem cell-genetically engineered mouse-modeling (ESC-GEMM) platform. We generated ESC lines harboring twelve combinations of four common driver mutations (BRAF-V600E, NRAS-Q61R, loss of PTEN, loss of CDKN2A) that can be efficiently targeted by recombination-mediated cassette exchange (RMCE) to introduce inducible alleles of interest. Importantly, all of our ESC lines are capable of producing high-contribution chimeras, which exhibit the same melanoma kinetics and overall survival as conventionally bred mice. Thus, our platform offers readily adaptable melanoma models whose melanoma phenotypes range from long latency/low penetrance to aggressive melanoma with complete penetrance. We employed our ESC-GEMM approach to compare the efficiency of gene depletion by conditional knockout, CRISPR/Cas9, or RNAi. We found that CRISPR/Cas9 depletion of Pten on a Braf-V600E background produces fewer melanomas but with nearly the same latency as conditional knockout using the Cre-lox system. Silencing of Pten with inducible shRNA resulted in significantly increased latency as well as in melanomas with a distinct macroscopic appearance and widespread lymph node metastases. While inducible shRNAs allowed us to restore Pten expression in established melanomas, depletion of Pten with inducible CRISPR enabled us to control the number of moles/melanomas by limiting the duration of Cas9 expression. We also used inducible CRISPR to sequentially activate Braf-V600E and delete Pten, which more closely mimics the sequence of events in human melanomas. Interestingly, while sequential introduction of these genetic changes had no effect on the overall survival, a subset of mice developed a significantly greater number of tumors. Finally, we established melanoma cell lines from untargeted chimeras, which can be targeted with Tet-inducible expression cassettes and transplanted into syngeneic hosts. Taken together, we have established a speedy mouse-modeling platform that will stimulate and accelerate in vivo melanoma research, provide a powerful resource to investigate the pathobiology of melanomagenesis, and allow the genetic and pharmacologic evaluation of novel treatments.
Citation Format: Ilah Bok, Jordan Reff, Arianna Nenci, Jose G. Gonzalez, Florian A. Karreth. A versatile mouse-modeling platform for rapid in vivo melanoma studies [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr A17.
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Affiliation(s)
- Ilah Bok
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Jordan Reff
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Arianna Nenci
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
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Nakamura K, Reid BM, Sellers TA, Karreth FA. Abstract B34: LINC00886, a risk locus-associated long noncoding RNA, promotes ovarian cancer progression. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.ovca19-b34] [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
Background: Recent genome-wide association studies (GWAS) have identified a plethora of SNPs that cluster at loci associated with increased epithelial ovarian cancer (EOC) risk. The functional validation of genes in such risk loci focused primarily on the protein-coding space while long noncoding RNAs (lncRNAs) were disregarded. Given the emerging evidence that lncRNAs can act as oncogenes and tumor suppressors, we seek to evaluate the functional role of EOC risk locus-associated lncRNAs in EOC development.
Methods: We interrogated GWAS for EOC and the FANTOM-CAT database for lncRNAs to identify EOC risk-associated SNPs that lie within lncRNA regulatory regions. We first prioritized the lncRNAs that are associated with EOC risk loci using public databases including GTEx and TCGA. To assess the oncogenic potential of these lncRNAs, we performed in vitro functional assays such as proliferation, colony formation, anchorage-independent growth and migration by overexpressing and silencing candidate lncRNAs in fallopian tube secretory epithelial and ovarian cancer cells. To validate our findings in vivo, we intraperitoneally injected OVCAR-8 cells into immunocompromised mice and evaluated tumor growth. LncRNA subcellular localization was evaluated based on qPCR from cytoplasmic and nuclear RNA. Further, we investigated expression changes upon lncRNAs overexpression in OVCAR-8 and FT282 cells by RNA sequencing (RNA-seq) and predicted shared microRNAs (miRNA) binding sites using LncBase Predicted v.2 and TargetScanHuman 7.2.
Results: We identified 5 candidate risk locus-associated lncRNAs (CATG00000115318.1, HAGLR, LINC00886, CATG00000117550.1, and CTD-2521M24.8). Functional assays showed that LINC00886 promoted cancer cell proliferation and colony formation in vitro. Overexpression of LINC00886 in OVCAR-8 cells significantly promoted peritoneal dissemination in a xenograft model. LINC00886 was mainly localized to the cytoplasm, suggesting it could function by decoying miRNAs. Interestingly, we observed that LINC00886 overexpression increased the levels of several oncogenes, of which several (ROR2, TNFSF14, GPNMB, LTB, and ZBTB20) share miRNA binding sites with LINC00886.
Conclusion: LINC00886, a risk loci-associated lncRNA, promotes an aggressive phenotype in ovarian cancer, suggesting an oncogenic function. We are currently investigating the molecular mechanism of LINC00886 as a ceRNA in ovarian cancer progression.
Citation Format: Koji Nakamura, Brett M. Reid, Thomas A. Sellers, Florian A. Karreth. LINC00886, a risk locus-associated long noncoding RNA, promotes ovarian cancer progression [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B34.
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Affiliation(s)
- Koji Nakamura
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Brett M. Reid
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
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20
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Kang YP, Falzone A, Liu M, González-Sánchez P, Choi BH, Coloff JL, Saller JJ, Karreth FA, DeNicola GM. PHGDH supports liver ceramide synthesis and sustains lipid homeostasis. Cancer Metab 2020; 8:6. [PMID: 32549981 PMCID: PMC7294658 DOI: 10.1186/s40170-020-00212-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/09/2020] [Indexed: 12/21/2022] Open
Abstract
Background d-3-phosphoglycerate dehydrogenase (PHGDH), which encodes the first enzyme in serine biosynthesis, is overexpressed in human cancers and has been proposed as a drug target. However, whether PHGDH is critical for the proliferation or homeostasis of tissues following the postnatal period is unknown. Methods To study PHGDH inhibition in adult animals, we developed a knock-in mouse model harboring a PHGDH shRNA under the control of a doxycycline-inducible promoter. With this model, PHGDH depletion can be globally induced in adult animals, while sparing the brain due to poor doxycycline delivery. Results We found that PHGDH depletion is well tolerated, and no overt phenotypes were observed in multiple highly proliferative cell compartments. Further, despite detectable knockdown and impaired serine synthesis, liver and pancreatic functions were normal. Interestingly, diminished PHGDH expression reduced liver serine and ceramide levels without increasing the levels of deoxysphingolipids. Further, liver triacylglycerol profiles were altered, with an accumulation of longer chain, polyunsaturated tails upon PHGDH knockdown. Conclusions These results suggest that dietary serine is adequate to support the function of healthy, adult murine tissues, but PHGDH-derived serine supports liver ceramide synthesis and sustains general lipid homeostasis.
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Affiliation(s)
- Yun Pyo Kang
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Aimee Falzone
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Min Liu
- Proteomics and Metabolomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Paloma González-Sánchez
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Bo-Hyun Choi
- Department of Physiology and Biophysics, University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL USA
| | - Jonathan L Coloff
- Department of Physiology and Biophysics, University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL USA
| | - James J Saller
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Gina M DeNicola
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
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21
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Bok I, Vera O, Xu X, Jasani N, Nakamura K, Reff J, Nenci A, Gonzalez JG, Karreth FA. A Versatile ES Cell-Based Melanoma Mouse Modeling Platform. Cancer Res 2019; 80:912-921. [PMID: 31744817 DOI: 10.1158/0008-5472.can-19-2924] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/24/2019] [Accepted: 11/13/2019] [Indexed: 01/04/2023]
Abstract
The cumbersome and time-consuming process of generating new mouse strains and multiallelic experimental animals often hinders the use of genetically engineered mouse models (GEMM) in cancer research. Here, we describe the development and validation of an embryonic stem cell (ESC)-GEMM platform for rapid modeling of melanoma in mice. The platform incorporates 12 clinically relevant genotypes composed of combinations of four driver alleles (LSL-BrafV600E, LSL-NrasQ61R, PtenFlox, and Cdkn2aFlox) and regulatory alleles to spatiotemporally control the perturbation of genes of interest. The ESCs produce high-contribution chimeras, which recapitulate the melanoma phenotypes of conventionally bred mice. Using the ESC-GEMM platform to modulate Pten expression in melanocytes in vivo, we highlighted the utility and advantages of gene depletion by CRISPR-Cas9, RNAi, or conditional knockout for melanoma modeling. Moreover, complementary genetic methods demonstrated the impact of Pten restoration on the prevention and maintenance of Pten-deficient melanomas. Finally, we showed that chimera-derived melanoma cell lines retain regulatory allele competency and are a powerful resource to complement ESC-GEMM chimera experiments in vitro and in syngeneic grafts in vivo Thus, when combined with sophisticated genetic tools, the ESC-GEMM platform enables rapid, high-throughput, and versatile studies aimed at addressing outstanding questions in melanoma biology.Significance: This study presents a high-throughput and versatile ES cell-based mouse modeling platform that can be combined with state-of-the-art genetic tools to address unanswered questions in melanoma in vivo See related commentary by Thorkelsson et al., p. 655.
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Affiliation(s)
- Ilah Bok
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Cancer Biology PhD Program, University of South Florida, Tampa, Florida
| | - Olga Vera
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Neel Jasani
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Cancer Biology PhD Program, University of South Florida, Tampa, Florida
| | - Koji Nakamura
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jordan Reff
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Arianna Nenci
- Gene Targeting Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jose G Gonzalez
- Gene Targeting Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
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22
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Eroglu Z, Holmen SL, Chen Q, Khushalani NI, Amaravadi R, Thomas R, Ahmed KA, Tawbi H, Chandra S, Markowitz J, Smalley I, Liu JK, Chen YA, Najjar YG, Karreth FA, Abate-Daga D, Glitza IC, Sosman JA, Sondak VK, Bosenberg M, Herlyn M, Atkins MB, Kluger H, Margolin K, Forsyth PA, Davies MA, Smalley KSM. Melanoma central nervous system metastases: An update to approaches, challenges, and opportunities. Pigment Cell Melanoma Res 2019; 32:458-469. [PMID: 30712316 PMCID: PMC7771318 DOI: 10.1111/pcmr.12771] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Accepted: 01/27/2019] [Indexed: 02/06/2023]
Abstract
In February 2018, the Melanoma Research Foundation and the Moffitt Cancer Center hosted the Second Summit on Melanoma Central Nervous System (CNS) Metastases in Tampa, Florida. In this white paper, we outline the current status of basic science, translational, and clinical research into melanoma brain metastasis development and therapeutic management. We further outline the important challenges that remain for the field and the critical barriers that need to be overcome for continued progress to be made in this clinically difficult area.
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Affiliation(s)
| | - Sheri L. Holmen
- University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Qing Chen
- The Wistar Institute, Philadelphia, Pennsylvania
| | | | - Ravi Amaravadi
- The University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | | | | | | | | | | | | | - Yana G. Najjar
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | | | | | | | | | | | | | | | - Michael B. Atkins
- Georgetown University Cancer Center, Washington, District of Columbia
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23
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Bok I, Karreth FA. Abstract A07: Speedy mouse models to study melanomagenesis. Cancer Res 2018. [DOI: 10.1158/1538-7445.mousemodels17-a07] [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
Melanoma accounts for only about 1% of the skin cancer, but contributes to a vast majority of skin cancer deaths. Despite extensive progress in treating melanoma with immunotherapy and small-molecule inhibitors, melanoma patients still suffer from tumor recurrence, mainly due to inherent or acquired resistance to these treatments. A better understanding of the detailed molecular mechanisms that contribute to melanoma formation and resistance may provide novel avenues for the development of improved treatment strategies. Genetically engineered mouse models (GEMMs) closely recapitulate the genetics and etiology of human malignancies and have significantly contributed to our understanding of the mechanisms underlying melanoma initiation and progression. However, the generation and characterization of GEMMs is often challenging due to their time-consuming, laborious, and expensive nature. To overcome some of these limitations, we sought to develop a melanoma mouse-modeling platform, which allows for accelerated speed, increased throughput, and lower cost of in vivo melanoma studies compared to conventional mouse models. To this end, we established several embryonic stem cell (ESC) lines harboring multiple alleles to aide in creating versatile melanoma mouse models. These alleles include Cre-inducible endogenous BrafV600E or NrasQ61R alleles for melanoma initiation, conditional PTEN knockout alleles for melanoma progression, the melanocyte-specific, tamoxifen-inducible Tyr-CreERt2 allele, a Cags-LSL-rtTA3 allele to activate Tet-inducible expression cassettes, and the collagen homing cassette (CHC) for the efficient delivery of such expression cassettes via recombination-mediated cassette exchange (RMCE). We demonstrated that our newly derived ESCs can be targeted with various constructs via RMCE with extremely high efficiency, thus significantly reducing the number of clones one has to screen for successful targeting. Moreover, we confirmed pluripotency of our ESC lines by Oct4 and Nanog staining, and by demonstrating their ability to generate chimeras via blastocyst injection and completely ESC-derived mice via tetraploid complementation. Topical application of 4-hydroxytamoxifen (4-OHT) on chimeras carrying the BrafV600E and PTENFlox alleles resulted in the development of nevi and melanomas within a few weeks. Importantly, our melanoma ESC-GEMM approach is compatible with novel genetic tools including inducible shRNA and CRISPR, thus providing a versatile and modular platform for the study of gene function in melanomagenesis. Thus, we have established a speedy mouse-modeling platform that will stimulate and accelerate in vivo melanoma research, and will provide a useful resource to investigate the pathobiology of melanomagenesis and to develop and preclinically test novel treatments.
Citation Format: Ilah Bok, Florian A. Karreth. Speedy mouse models to study melanomagenesis [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr A07.
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Affiliation(s)
- Ilah Bok
- Moffitt Cancer Center, Tampa, FL
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24
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Vera O, Rodriguez-Antolin C, de Castro J, Karreth FA, Sellers TA, Ibanez de Caceres I. An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells. Epigenetics 2018; 13:251-263. [PMID: 29436261 PMCID: PMC5997141 DOI: 10.1080/15592294.2018.1436364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are critical regulators of cell biology whose alteration can lead to the development of diseases such as cancer. The potential role of lncRNAs and their epigenetic regulation in response to platinum treatment are largely unknown. We analyzed four paired cisplatin-sensitive/resistant non-small cell lung cancer and ovarian cancer cell lines. The epigenetic landscape of overlapping and cis-acting lncRNAs was determined by combining human microarray data on 30,586 lncRNAs and 20,109 protein coding mRNAs with whole-genome bisulfite sequencing. Selected candidate lncRNAs were further characterized by PCR, gene-ontology analysis, and targeted bisulfite sequencing. Differential expression in response to therapy was observed more frequently in cis-acting than in overlapping lncRNAs (78% vs. 22%, fold change ≥1.5), while significantly altered methylation profiles were more commonly associated with overlapping lncRNAs (29% vs. 8%; P value <0.001). Moreover, overlapping lncRNAs contain more CpG islands (CGIs) (25% vs. 17%) and the majority of CGI-containing overlapping lncRNAs share these CGIs with their associated coding genes (84%). The differences in expression between sensitive and resistant cell lines were replicated in 87% of the selected candidates (P<0.05), while our bioinformatics approach identifying differential methylation was confirmed in all of the selected lncRNAs (100%). Five lncRNAs under epigenetic regulation appear to be involved in cisplatin resistance (AC091814.2, AC141928.1, RP11-65J3.1-002, BX641110, and AF198444). These novel findings provide new insights into epigenetic mechanisms and acquired resistance to cisplatin that highlight specific lncRNAs, some with unknown function, that may signal strategies in epigenetic therapies.
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Affiliation(s)
- Olga Vera
- a Cancer Epigenetics Laboratory, INGEMM , La Paz University Hospital , Madrid , Spain.,b Biomarkers and Experimental Therapeutics in Cancer , IdiPAZ , Madrid , Spain
| | - Carlos Rodriguez-Antolin
- a Cancer Epigenetics Laboratory, INGEMM , La Paz University Hospital , Madrid , Spain.,b Biomarkers and Experimental Therapeutics in Cancer , IdiPAZ , Madrid , Spain
| | - Javier de Castro
- a Cancer Epigenetics Laboratory, INGEMM , La Paz University Hospital , Madrid , Spain.,b Biomarkers and Experimental Therapeutics in Cancer , IdiPAZ , Madrid , Spain
| | - Florian A Karreth
- c Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , Tampa , USA
| | - Thomas A Sellers
- d Department of Cancer Epidemiology , H. Lee Moffitt Cancer Center and Research Institute , Tampa , USA
| | - Inmaculada Ibanez de Caceres
- a Cancer Epigenetics Laboratory, INGEMM , La Paz University Hospital , Madrid , Spain.,b Biomarkers and Experimental Therapeutics in Cancer , IdiPAZ , Madrid , Spain
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25
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Liu H, Murphy CJ, Karreth FA, Emdal KB, White FM, Elemento O, Toker A, Wulf GM, Cantley LC. Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer. Cancer Discov 2017; 8:354-369. [PMID: 29203461 DOI: 10.1158/2159-8290.cd-17-0679] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/11/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023]
Abstract
Triple-negative breast cancers (TNBC) are genetically characterized by aberrations in TP53 and a low rate of activating point mutations in common oncogenes, rendering it challenging in applying targeted therapies. We performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) to identify somatic genetic alterations in mouse models of TNBCs driven by loss of Trp53 alone or in combination with Brca1 Amplifications or translocations that resulted in elevated oncoprotein expression or oncoprotein-containing fusions, respectively, as well as frameshift mutations of tumor suppressors were identified in approximately 50% of the tumors evaluated. Although the spectrum of sporadic genetic alterations was diverse, the majority had in common the ability to activate the MAPK/PI3K pathways. Importantly, we demonstrated that approved or experimental drugs efficiently induce tumor regression specifically in tumors harboring somatic aberrations of the drug target. Our study suggests that the combination of WES and RNA-seq on human TNBC will lead to the identification of actionable therapeutic targets for precision medicine-guided TNBC treatment.Significance: Using combined WES and RNA-seq analyses, we identified sporadic oncogenic events in TNBC mouse models that share the capacity to activate the MAPK and/or PI3K pathways. Our data support a treatment tailored to the genetics of individual tumors that parallels the approaches being investigated in the ongoing NCI-MATCH, My Pathway Trial, and ESMART clinical trials. Cancer Discov; 8(3); 354-69. ©2017 AACR.See related commentary by Natrajan et al., p. 272See related article by Matissek et al., p. 336This article is highlighted in the In This Issue feature, p. 253.
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Affiliation(s)
- Hui Liu
- Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Charles J Murphy
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York.,Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kristina B Emdal
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
| | - Forest M White
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Alex Toker
- Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, and Ludwig Center at Harvard, Boston, Massachusetts
| | - Gerburg M Wulf
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York.
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26
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Permuth JB, Chen DT, Yoder SJ, Li J, Smith AT, Choi JW, Kim J, Balagurunathan Y, Jiang K, Coppola D, Centeno BA, Klapman J, Hodul P, Karreth FA, Trevino JG, Merchant N, Magliocco A, Malafa MP, Gillies R. Linc-ing Circulating Long Non-coding RNAs to the Diagnosis and Malignant Prediction of Intraductal Papillary Mucinous Neoplasms of the Pancreas. Sci Rep 2017; 7:10484. [PMID: 28874676 PMCID: PMC5585319 DOI: 10.1038/s41598-017-09754-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/31/2017] [Indexed: 12/20/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease that lacks effective biomarkers for early detection. We hypothesized that circulating long non-coding RNAs (lncRNAs) may act as diagnostic markers of incidentally-detected cystic PDAC precursors known as intraductal papillary mucinous neoplasms (IPMNs) and predictors of their pathology/histological classification. Using NanoString nCounter® technology, we measured the abundance of 28 candidate lncRNAs in pre-operative plasma from a cohort of pathologically-confirmed IPMN cases of various grades of severity and non-diseased controls. Results showed that two lncRNAs (GAS5 and SRA) aided in differentiating IPMNs from controls. An 8-lncRNA signature (including ADARB2-AS1, ANRIL, GLIS3-AS1, LINC00472, MEG3, PANDA, PVT1, and UCA1) had greater accuracy than standard clinical and radiologic features in distinguishing 'aggressive/malignant' IPMNs that warrant surgical removal from 'indolent/benign' IPMNs that can be observed. When the 8-lncRNA signature was combined with plasma miRNA data and quantitative 'radiomic' imaging features, the accuracy of predicting IPMN pathological classification improved. Our findings provide novel information on the ability to detect lncRNAs in plasma from patients with IPMNs and suggest that an lncRNA-based blood test may have utility as a diagnostic adjunct for identifying IPMNs and their pathology, especially when incorporated with biomarkers such as miRNAs, quantitative imaging features, and clinical data.
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Affiliation(s)
- Jennifer B Permuth
- Departments of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA. .,Gastrointestinal Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA.
| | - Dung-Tsa Chen
- Biostatistics and Bioinformatics, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Sean J Yoder
- Molecular Genomics Core Facility, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jiannong Li
- Biostatistics and Bioinformatics, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Andrew T Smith
- Molecular Genomics Core Facility, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jung W Choi
- Diagnostic Imaging and Interventional Radiology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jongphil Kim
- Biostatistics and Bioinformatics, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Yoganand Balagurunathan
- Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Kun Jiang
- Anatomic Pathology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Domenico Coppola
- Anatomic Pathology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Barbara A Centeno
- Anatomic Pathology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jason Klapman
- Gastrointestinal Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Pam Hodul
- Gastrointestinal Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Florian A Karreth
- Molecular Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jose G Trevino
- Department of Surgery, Division of General Surgery, University of Florida Health Sciences Center, Gainesville, Florida, USA
| | - Nipun Merchant
- Department of Surgery, Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Anthony Magliocco
- Anatomic Pathology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Mokenge P Malafa
- Gastrointestinal Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Robert Gillies
- Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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27
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Yoon SO, Shin S, Karreth FA, Buel GR, Jedrychowski MP, Plas DR, Dedhar S, Gygi SP, Roux PP, Dephoure N, Blenis J. Focal Adhesion- and IGF1R-Dependent Survival and Migratory Pathways Mediate Tumor Resistance to mTORC1/2 Inhibition. Mol Cell 2017; 67:512-527.e4. [PMID: 28757207 DOI: 10.1016/j.molcel.2017.06.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 02/13/2017] [Revised: 05/24/2017] [Accepted: 06/27/2017] [Indexed: 01/22/2023]
Abstract
Aberrant signaling by the mammalian target of rapamycin (mTOR) contributes to the devastating features of cancer cells. Thus, mTOR is a critical therapeutic target and catalytic inhibitors are being investigated as anti-cancer drugs. Although mTOR inhibitors initially block cell proliferation, cell viability and migration in some cancer cells are quickly restored. Despite sustained inhibition of mTORC1/2 signaling, Akt, a kinase regulating cell survival and migration, regains phosphorylation at its regulatory sites. Mechanistically, mTORC1/2 inhibition promotes reorganization of integrin/focal adhesion kinase-mediated adhesomes, induction of IGFR/IR-dependent PI3K activation, and Akt phosphorylation via an integrin/FAK/IGFR-dependent process. This resistance mechanism contributes to xenograft tumor cell growth, which is prevented with mTOR plus IGFR inhibitors, supporting this combination as a therapeutic approach for cancers.
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Affiliation(s)
- Sang-Oh Yoon
- Department of Pharmacology, Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA.
| | - Sejeong Shin
- Department of Pharmacology, Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | - Florian A Karreth
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | - Gwen R Buel
- Department of Pharmacology, Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | | | - David R Plas
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Shoukat Dedhar
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Philippe P Roux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - John Blenis
- Department of Pharmacology, Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA.
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Abstract
The use of transposons as insertional mutagens to identify cancer genes in mice has generated a wealth of information over the past decade. Here, we discuss recent major advances in transposon-mediated insertional mutagenesis screens and compare this technology with other screening strategies.
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Affiliation(s)
- Gina M DeNicola
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY, 10021, USA
| | - Florian A Karreth
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY, 10021, USA.
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1HH, UK
| | - Chi C Wong
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1HH, UK. .,Department of Haematology, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK.
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Karreth FA, Reschke M, Bjoern C, Shipp M, Chiarle R, Pandolfi PP. Abstract A37: The BRAF pseudogene is a proto-oncogenic competitive endogenous RNA. Clin Cancer Res 2015. [DOI: 10.1158/1557-3265.hemmal14-a37] [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
Noncoding RNAs have long been viewed as non-functional genomic relicts of evolution, but recetn findings have implicated their importance in physiology and disease. Recently, in vitro experiments demonstrated that the pseudogenes of PTEN and KRAS operate as natural miRNA decoys (competitive endogenous RNAs or ceRNAs) that regulate the expression of their parental genes. However, in vivo evidence for a causal role of pseudogenes in cancer development is lacking. To investigate whether the BRAF pseudogene (BRAFps) possesses oncogenic properties we generated transgenic mice carrying a Tet-inducible BRAF pseudogene allele. Global BRAFps overexpression resulted in the development of aggressive B-cell lymphoma after 6-12 months. These tumors were characterized by a profound expansion of B-lymphocytes in the spleen, as well as splenomegaly, lymphadenopathy and infiltration of the kidneys, lungs, and liver by neoplastic cells. The BRAFps-induced lymphoma was polyclonal, transplantable, dependent on continuous BRAFps expression, and cooperated with heterozygous loss of PTEN to accelerate disease onset. Mechanistically, we propose that BRAFps functions as a ceRNA that sequesters miRNAs from BRAF and possibly other targets. Indeed, overexpression of BRAFps results in elevated levels of BRAF in a Dicer-dependent manner. This, in turn, increased BRAF-dependent MAPK signaling and proliferation. To further validate the ceRNA activity of BRAFps, we engineered mice to express only the 3'UTR or CDS of BRAFps as each portion of the pseudogene may individually engage in miRNA-mediated crosstalk with BRAF. Notably, both BRAFps-CDS and BRAFps-3'UTR increased spleen and lymph node weights 6 months after induction. Interestingly, BRAFps-3'UTR elicited a lymphoma phenotype similar to full length BRAFps, while mice expressing BRAFps-CDS developed a more indolent form of this phenotype, suggesting that lymphomagenesis is primarily mediated by the BRAFps 3'UTR. BRAFps transcript was undetectable in primary human B-cells, but was aberrantly expressed in primary human DLBCL and human DLBCL cell lines. Expression of BRAF and BRAFps was positively correlated in human primary DLBCL and human DLBCL cell lines. In addition, gains or amplifications of the genomic locus containing BRAFps were found in various human cancer types. Overexpression of BRAFps in human lymphoma cells elevated BRAF levels, MAPK activation, proliferation and growth in xenografts. Our results demonstrate for the first time the oncogenic potential of a pseudogene in an engineered mouse model and indicate that ceRNA- mediated regulation is an important regulatory mechanism of gene expression in vivo.
Citation Format: Florian A. Karreth, Markus Reschke, Chapuy Bjoern, Margaret Shipp, Roberto Chiarle, Pier Paolo Pandolfi. The BRAF pseudogene is a proto-oncogenic competitive endogenous RNA. [abstract]. In: Proceedings of the AACR Special Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(17 Suppl):Abstract nr A37.
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Karreth FA, Reschke M, Ruocco A, Ng C, Chapuy B, Léopold V, Sjoberg M, Keane TM, Verma A, Ala U, Tay Y, Wu D, Seitzer N, Velasco-Herrera MDC, Bothmer A, Fung J, Langellotto F, Rodig SJ, Elemento O, Shipp MA, Adams DJ, Chiarle R, Pandolfi PP. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell 2015; 161:319-32. [PMID: 25843629 DOI: 10.1016/j.cell.2015.02.043] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 12/19/2014] [Accepted: 02/02/2015] [Indexed: 12/14/2022]
Abstract
Research over the past decade has suggested important roles for pseudogenes in physiology and disease. In vitro experiments demonstrated that pseudogenes contribute to cell transformation through several mechanisms. However, in vivo evidence for a causal role of pseudogenes in cancer development is lacking. Here, we report that mice engineered to overexpress either the full-length murine B-Raf pseudogene Braf-rs1 or its pseudo "CDS" or "3' UTR" develop an aggressive malignancy resembling human diffuse large B cell lymphoma. We show that Braf-rs1 and its human ortholog, BRAFP1, elicit their oncogenic activity, at least in part, as competitive endogenous RNAs (ceRNAs) that elevate BRAF expression and MAPK activation in vitro and in vivo. Notably, we find that transcriptional or genomic aberrations of BRAFP1 occur frequently in multiple human cancers, including B cell lymphomas. Our engineered mouse models demonstrate the oncogenic potential of pseudogenes and indicate that ceRNA-mediated microRNA sequestration may contribute to the development of cancer.
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Affiliation(s)
- Florian A Karreth
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Markus Reschke
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Anna Ruocco
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Christopher Ng
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Bjoern Chapuy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Valentine Léopold
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Marcela Sjoberg
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
| | - Thomas M Keane
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
| | - Akanksha Verma
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Ugo Ala
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yvonne Tay
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David Wu
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10021, USA
| | - Nina Seitzer
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | - Anne Bothmer
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jacqueline Fung
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Fernanda Langellotto
- Department of Pathology, Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Margaret A Shipp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
| | - Roberto Chiarle
- Department of Pathology, Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Molecular Biotechnology and Health Sciences, University of Torino, 10124 Torino, Italy
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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Tay Y, Tan SM, Karreth FA, Lieberman J, Pandolfi PP. Characterization of dual PTEN and p53-targeting microRNAs identifies microRNA-638/Dnm2 as a two-hit oncogenic locus. Cell Rep 2014; 8:714-22. [PMID: 25088422 DOI: 10.1016/j.celrep.2014.06.064] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/30/2014] [Accepted: 06/30/2014] [Indexed: 01/02/2023] Open
Abstract
Tumor suppressor genes (TSGs) are often concomitantly lost or mutated in human cancers and have been shown to act synergistically to promote tumorigenesis. In addition to genomic alterations, posttranscriptional regulation by microRNAs (miRNAs) represents another mechanism by which TSG expression is dysregulated in cancers. Although miRNAs that target critical TSGs such as PTEN or p53 have been identified, little is known about miRNAs that concomitantly regulate both these key TSGs. In this study, we characterize microRNA 518c(∗) (miR-518c(∗)) and miR-638 as dual PTEN- and p53-targeting miRNAs that are upregulated in multiple human cancers. We focus on miR-638 and show that it associates independently with these two tumor suppressor transcripts as well as BRCA1, a known miR-638 target. We find that miR-638 overexpression promotes tumorigenesis and demonstrate cooperativity between miR-638 and its host gene Dnm2, suggesting that the Dnm2 locus encodes two distinct oncogenic components that play important roles in tumorigenesis.
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Affiliation(s)
- Yvonne Tay
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Shen Mynn Tan
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Florian A Karreth
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Judy Lieberman
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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Sadow PM, Priolo C, Nanni S, Karreth FA, Duquette M, Martinelli R, Husain A, Clohessy J, Kutzner H, Mentzel T, Carman CV, Farsetti A, Henske EP, Palescandolo E, Macconaill LE, Chung S, Fadda G, Lombardi CP, De Angelis AM, Durante O, Parker JA, Pontecorvi A, Dvorak HF, Fletcher C, Pandolfi PP, Lawler J, Nucera C. Role of BRAFV600E in the first preclinical model of multifocal infiltrating myopericytoma development and microenvironment. J Natl Cancer Inst 2014; 106:dju182. [PMID: 25063326 DOI: 10.1093/jnci/dju182] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Myopericytoma (MPC) is a rare tumor with perivascular proliferation of pluripotent stem-cell-like pericytes. Although indolent, MPC may be locally aggressive with recurrent disease. The pathogenesis and diagnostic biomarkers of MPC are poorly understood. We discovered that 15% of benign MPCs (thyroid, skin; 3 of 20 samples) harbored BRAF(WT/V600E); 33.3% (1 of 3 samples) of BRAF(WT/V600E)-MPCs were multifocal/infiltrative/recurrent. Patient-MPC and primary MPC cells harbored BRAF(WT/V600E), were clonal and expressed pericytic-differentiation biomarkers crucial for its microenvironment. BRAF(WT/V600E)-positive thyroid MPC primary cells triggered in vitro (8.8-fold increase) and in vivo (3.6-fold increase) angiogenesis. Anti-BRAF(V600E) therapy with vemurafenib disrupted angiogenic and metabolic properties (~3-fold decrease) with down-regulation (~2.2-fold decrease) of some extracellular-matrix (ECM) factors and ECM-associated long non-coding RNA (LincRNA) expression, with no effects in BRAF(WT)-pericytes. Vemurafenib also inhibited (~3-fold decrease) cell viability in vitro and in BRAF(WT/V600E)-positive thyroid MPC patient-derived xenograft (PDX) mice (n = 5 mice per group). We established the first BRAF(WT/V600E)-dependent thyroid MPC cell culture. Our findings identify BRAF(WT/V600E) as a novel genetic aberration in MPC pathogenesis and MPC-associated biomarkers and imply that anti-BRAF(V600E) agents may be useful adjuvant therapy in BRAF(WT/V600E)-MPC patients. Patients with BRAF(WT/V600E)-MPC should be closely followed because of the risk for multifocality/recurrence.
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Affiliation(s)
- Peter M Sadow
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Carmen Priolo
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Simona Nanni
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Florian A Karreth
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Mark Duquette
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Roberta Martinelli
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Amjad Husain
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - John Clohessy
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Heinz Kutzner
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Thomas Mentzel
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Christopher V Carman
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Antonella Farsetti
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Elizabeth Petri Henske
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Emanuele Palescandolo
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Laura E Macconaill
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Seum Chung
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Guido Fadda
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Celestino Pio Lombardi
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Antonina M De Angelis
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Oreste Durante
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - John A Parker
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Alfredo Pontecorvi
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Harold F Dvorak
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Christopher Fletcher
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Pier Paolo Pandolfi
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Jack Lawler
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Carmelo Nucera
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF).
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Abstract
Transcription factor binding sites compete for a limited pool of bioavailable transcription factor molecules to fine tune gene expression.
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Abstract
Pseudogenes may regulate expression of their parental genes as well as other protein-coding genes through various mechanisms. One such mechanism is the ability to act as competitive endogenous RNA (ceRNA) and participate in microRNA-mediated cross-regulation. Here, we outline how to predict the targets of pseudogene ceRNAs bioinformatically and how to validate them experimentally.
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Affiliation(s)
- Florian A Karreth
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, CLS-401, Boston, MA, 02215, USA
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Abstract
UNLABELLED The cancer transcriptome is characterized by aberrant expression of both protein-coding and noncoding transcripts. Similar to mRNAs, a significant portion of the noncoding transcriptome, including long noncoding RNAs and pseudogenes, harbors microRNA (miRNA)-response elements (MRE). The recent discovery of competitive endogenous RNAs (ceRNA), natural decoys that compete for a common pool of miRNAs, provides a framework to systematically functionalize MRE-harboring noncoding RNAs and integrate them with the protein-coding RNA dimension in complex ceRNA networks. Functional interactions in ceRNA networks aid in coordinating a number of biologic processes and, when perturbed, contribute to disease pathogenesis. In this review, we discuss recent discoveries that implicate natural miRNA decoys in the development of cancer. SIGNIFICANCE Cross-talk between ceRNAs through shared miRNAs represents a novel layer of gene regulation that plays important roles in the physiology and development of diseases such as cancer. As cross-talk can be predicted on the basis of the overlap of miRNA-binding sites, we are now one step closer to a complete functionalization of the human transcriptome, especially the noncoding space.
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Affiliation(s)
- Florian A Karreth
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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Ala U, Karreth FA, Bosia C, Pagnani A, Taulli R, Léopold V, Tay Y, Provero P, Zecchina R, Pandolfi PP. Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments. Proc Natl Acad Sci U S A 2013; 110:7154-9. [PMID: 23536298 PMCID: PMC3645534 DOI: 10.1073/pnas.1222509110] [Citation(s) in RCA: 264] [Impact Index Per Article: 24.0] [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] [Indexed: 12/16/2022] Open
Abstract
Competitive endogenous (ce)RNAs cross-regulate each other through sequestration of shared microRNAs and form complex regulatory networks based on their microRNA signature. However, the molecular requirements for ceRNA cross-regulation and the extent of ceRNA networks remain unknown. Here, we present a mathematical mass-action model to determine the optimal conditions for ceRNA activity in silico. This model was validated using phosphatase and tensin homolog (PTEN) and its ceRNA VAMP (vesicle-associated membrane protein)-associated protein A (VAPA) as paradigmatic examples. A computational assessment of the complexity of ceRNA networks revealed that transcription factor and ceRNA networks are intimately intertwined. Notably, we found that ceRNA networks are responsive to transcription factor up-regulation or their aberrant expression in cancer. Thus, given optimal molecular conditions, alterations of one ceRNA can have striking effects on integrated ceRNA and transcriptional networks.
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Affiliation(s)
- Ugo Ala
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215
| | - Florian A. Karreth
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215
| | - Carla Bosia
- Human Genetics Foundation, Via Nizza 52, 10126 Turin, Italy
| | - Andrea Pagnani
- Human Genetics Foundation, Via Nizza 52, 10126 Turin, Italy
- Department of Applied Science and Technology and Center for Computational Studies, Politecnico di Torino, Corsa Duca degli Abruzzi 24, 10129 Turin, Italy; and
| | - Riccardo Taulli
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215
| | - Valentine Léopold
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215
| | - Yvonne Tay
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215
| | - Paolo Provero
- Molecular Biotechnology Center and Department of Molecular Biotechnology and Health Sciences, University of Torino, 10124 Torino, Italy
| | - Riccardo Zecchina
- Human Genetics Foundation, Via Nizza 52, 10126 Turin, Italy
- Department of Applied Science and Technology and Center for Computational Studies, Politecnico di Torino, Corsa Duca degli Abruzzi 24, 10129 Turin, Italy; and
| | - Pier Paolo Pandolfi
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215
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Gopinathan A, Denicola GM, Frese KK, Cook N, Karreth FA, Mayerle J, Lerch MM, Reinheckel T, Tuveson DA. Cathepsin B promotes the progression of pancreatic ductal adenocarcinoma in mice. Gut 2012; 61:877-84. [PMID: 22157328 DOI: 10.1136/gutjnl-2011-300850] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The lysosomal protease cathepsin B is upregulated in human pancreatic ductal adenocarcinoma (PDA) and represents a potential therapeutic target. Loss of cathepsin B delays tumour progression in mouse models of islet, mammary and intestinal carcinoma and decreases invasion and metastasis. This study examines the role of cathepsin B in the initiation, progression and metastasis of PDA. METHODS Cathepsin B germline knockout mice were crossed with animals expressing an endogenous Kras(G12D) allele in the pancreas, and mice were aged to evaluate the role of cathepsin B in pancreatic intraepithelial neoplasia (PanIN). A survival study was also performed with mice carrying an additional heterozygous conditional Trp53(R172H) allele. Cell lines derived from tumours were used to investigate the role of cathepsin B in vitro, and subcutaneous allografts investigated the cell autonomous and non-cell autonomous roles of cathepsin B in pancreatic cancer. RESULTS Constitutive cathepsin B loss resulted in delayed progression of both PanIN and PDA and a significant survival advantage in mice. Cathepsin B-deficient PDA cells and PanIN showed decreased proliferation and mitogen-activated protein (MAP) kinase signalling. The reconstitution of deficient cells with cathepsin B reversed these findings, which correlated with decreased levels of the active forms of the related protease cathepsin L. Conversely, acute ablation of cathepsin L activated the MAP kinase cascade in PDA cells. CONCLUSIONS These results confirm that cathepsin B plays an important cell autonomous role in the progression of PDA and suggest that the regulation of cathepsin L by cathepsin B may be a means of stimulating cell proliferation in neoplasia.
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Affiliation(s)
- Aarthi Gopinathan
- Li Ka Shing Centre, Cancer Research UK Cambridge Research Institute, Cambridge, UK
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38
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Abstract
The Ras/Raf/MEK/ERK (extracellular signal-regulated kinase) pathway is primarily responsible for mitogenesis in metazoans, and mutational activation of this pathway is common in cancer. A variety of selective chemical inhibitors directed against the mitogen-activated protein kinase pathway are now available for clinical investigation and thus the determination of the importance of each of the kinases in oncogenesis is paramount. We investigated the role of two Raf kinases, B-Raf and C-Raf, in Ras oncogenesis, and found that although B-Raf and C-Raf have overlapping functions in primary mesenchymal cells, C-Raf but not B-Raf is required for the proliferative effects of K-Ras(G12D) in primary epithelial cells. Furthermore, in a lung cancer mouse model, C-Raf is essential for tumor initiation by oncogenic K-Ras(G12D), whereas B-Raf is dispensable for this process. Our findings reveal that K-Ras(G12D) elicits its oncogenic effects primarily through C-Raf and suggest that selective C-Raf inhibition could be explored as a therapeutic strategy for K-Ras-dependent cancers.
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Affiliation(s)
- Florian A Karreth
- Li Ka Shing Centre, Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom
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39
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Skoulidis F, Cassidy LD, Pisupati V, Jonasson JG, Bjarnason H, Eyfjord JE, Karreth FA, Lim M, Barber LM, Clatworthy SA, Davies SE, Olive KP, Tuveson DA, Venkitaraman AR. Germline Brca2 heterozygosity promotes Kras(G12D) -driven carcinogenesis in a murine model of familial pancreatic cancer. Cancer Cell 2010; 18:499-509. [PMID: 21056012 DOI: 10.1016/j.ccr.2010.10.015] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 08/25/2010] [Accepted: 10/18/2010] [Indexed: 12/17/2022]
Abstract
Inherited heterozygous BRCA2 mutations predispose carriers to tissue-specific cancers, but somatic deletion of the wild-type allele is considered essential for carcinogenesis. We find in a murine model of familial pancreatic cancer that germline heterozygosity for a pathogenic Brca2 truncation suffices to promote pancreatic ductal adenocarcinomas (PDACs) driven by Kras(G12D), irrespective of Trp53 status. Unexpectedly, tumor cells retain a functional Brca2 allele. Correspondingly, three out of four PDACs from patients inheriting BRCA2(999del5) did not exhibit loss-of-heterozygosity (LOH). Three tumors from these patients displaying LOH were acinar carcinomas, which also developed only in mice with biallelic Brca2 inactivation. We suggest a revised model for tumor suppression by BRCA2 with implications for the therapeutic strategy targeting BRCA2 mutant cancer cells.
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Affiliation(s)
- Ferdinandos Skoulidis
- Department of Oncology and the Medical Research Council Cancer Cell Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
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40
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Karreth FA, DeNicola GM, Winter SP, Tuveson DA. C-Raf inhibits MAPK activation and transformation by B-Raf(V600E). Mol Cell 2010; 36:477-86. [PMID: 19917255 DOI: 10.1016/j.molcel.2009.10.017] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 08/10/2009] [Accepted: 09/17/2009] [Indexed: 10/20/2022]
Abstract
Activating B-Raf mutations that deregulate the MAPK pathway commonly occur in cancer. Whether additional proteins modulate the enzymatic activity of oncogenic B-Raf is unknown. Here we show that the proto-oncogene C-Raf paradoxically inhibits B-Raf(V600E) kinase activity through the formation of B-Raf(V600E)-C-Raf complexes. Although all Raf family members associate with oncogenic B-Raf, this inhibitory effect is specific to C-Raf. Indeed, a B-Raf(V600E) isoform with impaired ability to interact with C-Raf exhibits elevated oncogenic potential. Human melanoma cells expressing B-Raf(V600E) display a reduced C-Raf:B-Raf ratio, and further suppression of C-Raf increases MAPK activation and proliferation. Conversely, ectopic C-Raf expression lowers ERK phosphorylation and proliferation. Moreover, both oncogenic Ras and Sorafenib stabilize B-Raf(V600E)-C-Raf complexes, thereby impairing MAPK activation. This inhibitory function of C-Raf on B-Raf(V600E)-mediated MAPK activation may explain the lack of co-occurrence of B-Raf(V600E) and oncogenic Ras mutations, and influence the successful clinical development of small molecule inhibitors for B-Raf(V600E)-driven cancers.
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Affiliation(s)
- Florian A Karreth
- Li Ka Shing Centre, Cambridge Research Institute, Cancer Research UK, Robinson Way, Cambridge CB2 0RE, UK
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41
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Karreth FA, Tuveson DA. Modelling oncogenic Ras/Raf signalling in the mouse. Curr Opin Genet Dev 2009; 19:4-11. [PMID: 19201597 DOI: 10.1016/j.gde.2008.12.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 12/19/2008] [Accepted: 12/19/2008] [Indexed: 12/14/2022]
Abstract
The Ras/Raf/MEK/ERK (or MAPK) signalling pathway relays extracellular stimuli to the nucleus, thereby regulating diverse cellular responses such as proliferation, growth, differentiation and apoptosis. Perturbation of these processes by aberrant MAPK signalling often leads to malignant transformation as indicated by the frequent occurrence in human cancers of genetic alterations affecting this pathway. In recent years, genetically modified mouse models have proven instrumental in unravelling how deregulated MAPK signalling leads to disease. Indeed, conditional activation of oncogenic K-Ras or B-Raf in mice resulted in neoplasms that closely resemble the human disease. Such tractable mouse models will enable the pursuit of basic biological mechanisms and translational applications regarding the MAPK pathway.
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Affiliation(s)
- Florian A Karreth
- Li Ka Shing Centre, Cambridge Research Institute, Cancer Research UK, Robinson Way, Cambridge, United Kingdom
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