1
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Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. Brief Bioinform 2024; 25:bbae164. [PMID: 38605641 PMCID: PMC11009461 DOI: 10.1093/bib/bbae164] [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: 07/12/2023] [Revised: 01/26/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: Statistics and Mathematics Unit, Indian Statistical Institute, Bengaluru, Karnataka, India
| | - Amruta Naik
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shaon Sengupta
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter S Choi
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology & Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
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2
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Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. bioRxiv 2023:2023.04.21.537847. [PMID: 37162982 PMCID: PMC10168222 DOI: 10.1101/2023.04.21.537847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking, and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully-length mRNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM, or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in PCR amplification, barcode read errors, and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: Statistics and Mathematics Unit, Indian Statistical Institute, Bengaluru, Karnataka, India
| | - Amruta Naik
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shaon Sengupta
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter S Choi
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology & Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
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3
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Tang S, Sethunath V, Metaferia NY, Nogueira MF, Gallant DS, Garner ER, Lairson LA, Penney CM, Li J, Gelbard MK, Alaiwi SA, Seo JH, Hwang JH, Strathdee CA, Baca SC, AbuHammad S, Zhang X, Doench JG, Hahn WC, Takeda DY, Freedman ML, Choi PS, Viswanathan SR. A genome-scale CRISPR screen reveals PRMT1 as a critical regulator of androgen receptor signaling in prostate cancer. Cell Rep 2022; 38:110417. [PMID: 35196489 PMCID: PMC9036938 DOI: 10.1016/j.celrep.2022.110417] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 07/09/2020] [Revised: 12/10/2021] [Accepted: 01/31/2022] [Indexed: 02/08/2023] Open
Abstract
Androgen receptor (AR) signaling is the central driver of prostate cancer across disease states. While androgen deprivation therapy (ADT) is effective in the initial treatment of prostate cancer, resistance to ADT or to next-generation androgen pathway inhibitors invariably arises, most commonly through the re-activation of the AR axis. Thus, orthogonal approaches to inhibit AR signaling in advanced prostate cancer are essential. Here, via genome-scale CRISPR-Cas9 screening, we identify protein arginine methyltransferase 1 (PRMT1) as a critical mediator of AR expression and signaling. PRMT1 regulates the recruitment of AR to genomic target sites and the inhibition of PRMT1 impairs AR binding at lineage-specific enhancers, leading to decreased expression of key oncogenes, including AR itself. In addition, AR-driven prostate cancer cells are uniquely susceptible to combined AR and PRMT1 inhibition. Our findings implicate PRMT1 as a key regulator of AR output and provide a preclinical framework for co-targeting of AR and PRMT1 in advanced prostate cancer.
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Affiliation(s)
- Stephen Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Nebiyou Y Metaferia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marina F Nogueira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Daniel S Gallant
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Emma R Garner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Lauren A Lairson
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher M Penney
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Maya K Gelbard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Justin H Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shatha AbuHammad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xiaoyang Zhang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - David Y Takeda
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Peter S Choi
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Srinivas R Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA.
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4
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Liu Y, Wu Z, Zhou J, Ramadurai DKA, Mortenson KL, Aguilera-Jimenez E, Yan Y, Yang X, Taylor AM, Varley KE, Gertz J, Choi PS, Cherniack AD, Chen X, Bass AJ, Bailey SD, Zhang X. A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer. Nat Commun 2021; 12:7139. [PMID: 34880227 PMCID: PMC8654995 DOI: 10.1038/s41467-021-27055-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/01/2021] [Accepted: 11/01/2021] [Indexed: 02/05/2023] Open
Abstract
Amplification and overexpression of the SOX2 oncogene represent a hallmark of squamous cancers originating from diverse tissue types. Here, we find that squamous cancers selectively amplify a 3' noncoding region together with SOX2, which harbors squamous cancer-specific chromatin accessible regions. We identify a single enhancer e1 that predominantly drives SOX2 expression. Repression of e1 in SOX2-high cells causes collapse of the surrounding enhancers, remarkable reduction in SOX2 expression, and a global transcriptional change reminiscent of SOX2 knockout. The e1 enhancer is driven by a combination of transcription factors including SOX2 itself and the AP-1 complex, which facilitates recruitment of the co-activator BRD4. CRISPR-mediated activation of e1 in SOX2-low cells is sufficient to rebuild the e1-SOX2 loop and activate SOX2 expression. Our study shows that squamous cancers selectively amplify a predominant enhancer to drive SOX2 overexpression, uncovering functional links among enhancer activation, chromatin looping, and lineage-specific copy number amplifications of oncogenes.
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Affiliation(s)
- Yanli Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, Shanxi, China
| | - Zhong Wu
- Department of Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jin Zhou
- Department of Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dinesh K A Ramadurai
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Katelyn L Mortenson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Estrella Aguilera-Jimenez
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Yifei Yan
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Departments of Surgery and Human Genetics, McGill University, Montreal, QC, Canada
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, Shanxi, China
| | - Alison M Taylor
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Katherine E Varley
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Peter S Choi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China
- Yiwu Research Institute of Fudan University, Yiwu, Zhejiang, China
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Swneke D Bailey
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
- Departments of Surgery and Human Genetics, McGill University, Montreal, QC, Canada.
| | - Xiaoyang Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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5
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Abstract
Herculean efforts by the Wellcome Sanger Institute, the National Cancer Institute, and the National Human Genome Research Institute to sequence thousands of tumors representing all major cancer types have yielded more than 700 genes that contribute to neoplastic growth when mutated, amplified, or deleted. While some of these genes (now included in the COSMIC Cancer Gene Census) encode proteins previously identified in hypothesis-driven experiments (oncogenic transcription factors, protein kinases, etc.), additional classes of cancer drivers have emerged, perhaps none more surprisingly than RNA-binding proteins (RBPs). Over 40 RBPs responsible for virtually all aspects of RNA metabolism, from synthesis to degradation, are recurrently mutated in cancer, and just over a dozen are considered major cancer drivers. This Review investigates whether and how their RNA-binding activities pertain to their oncogenic functions. Focusing on several well-characterized steps in RNA metabolism, we demonstrate that for virtually all cancer-driving RBPs, RNA processing activities are either abolished (the loss-of-function phenotype) or carried out with low fidelity (the LoFi phenotype). Conceptually, this suggests that in normal cells, RBPs act as gatekeepers maintaining proper RNA metabolism and the "balanced" proteome. From the practical standpoint, at least some LoFi phenotypes create therapeutic vulnerabilities, which are beginning to be exploited in the clinic.
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6
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Liu Y, Guo B, Aguilera-Jimenez E, Chu VS, Zhou J, Wu Z, Francis JM, Yang X, Choi PS, Bailey SD, Zhang X. Chromatin Looping Shapes KLF5-Dependent Transcriptional Programs in Human Epithelial Cancers. Cancer Res 2020; 80:5464-5477. [PMID: 33115806 DOI: 10.1158/0008-5472.can-20-1287] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/14/2020] [Accepted: 10/19/2020] [Indexed: 12/19/2022]
Abstract
Activation of transcription factors is a key driver event in cancer. We and others have recently reported that the Krüppel-like transcription factor KLF5 is activated in multiple epithelial cancer types including squamous cancer and gastrointestinal adenocarcinoma, yet the functional consequences and the underlying mechanisms of this activation remain largely unknown. Here we demonstrate that activation of KLF5 results in strongly selective KLF5 dependency for these cancer types. KLF5 bound lineage-specific regulatory elements and activated gene expression programs essential to cancer cells. HiChIP analysis revealed that multiple distal KLF5 binding events cluster and synergize to activate individual target genes. Immunoprecipitation-mass spectrometry assays showed that KLF5 interacts with other transcription factors such as TP63 and YAP1, as well as the CBP/EP300 acetyltransferase complex. Furthermore, KLF5 guided the CBP/EP300 complex to increase acetylation of H3K27, which in turn enhanced recruitment of the bromodomain protein BRD4 to chromatin. The 3D chromatin architecture aggregated KLF5-dependent BRD4 binding to activate polymerase II elongation at KLF5 target genes, which conferred a transcriptional vulnerability to proteolysis-targeting chimera-induced degradation of BRD4. Our study demonstrates that KLF5 plays an essential role in multiple epithelial cancers by activating cancer-related genes through 3D chromatin loops, providing an evidence-based rationale for targeting the KLF5 pathway. SIGNIFICANCE: An integrative 3D genomics methodology delineates mechanisms underlying the function of KLF5 in multiple epithelial cancers and suggests potential strategies to target cancers with aberrantly activated KLF5.
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Affiliation(s)
- Yanli Liu
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.,College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, ShanXi, China
| | - Bingqian Guo
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Estrella Aguilera-Jimenez
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Vivian S Chu
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jin Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Zhong Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Xiaojun Yang
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, ShanXi, China
| | - Peter S Choi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Swneke D Bailey
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada. .,Departments of Surgery and Human Genetics, McGill University, Montreal, QC, Canada
| | - Xiaoyang Zhang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
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7
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Llabata P, Mitsuishi Y, Choi PS, Cai D, Francis JM, Torres-Diz M, Udeshi ND, Golomb L, Wu Z, Zhou J, Svinkina T, Aguilera-Jimenez E, Liu Y, Carr SA, Sanchez-Cespedes M, Meyerson M, Zhang X. Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma. Mol Cancer Res 2019; 18:574-584. [PMID: 31862696 DOI: 10.1158/1541-7786.mcr-19-0657] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/25/2019] [Accepted: 12/18/2019] [Indexed: 01/24/2023]
Abstract
Genomic analysis of lung adenocarcinomas has revealed that the MGA gene, which encodes a heterodimeric partner of the MYC-interacting protein MAX, is significantly mutated or deleted in lung adenocarcinomas. Most of the mutations are loss of function for MGA, suggesting that MGA may act as a tumor suppressor. Here, we characterize both the molecular and cellular role of MGA in lung adenocarcinomas and illustrate its functional relevance in the MYC pathway. Although MGA and MYC interact with the same binding partner, MAX, and recognize the same E-box DNA motif, we show that the molecular function of MGA appears to be antagonistic to that of MYC. Using mass spectrometry-based affinity proteomics, we demonstrate that MGA interacts with a noncanonical PCGF6-PRC1 complex containing MAX and E2F6 that is involved in gene repression, while MYC is not part of this MGA complex, in agreement with previous studies describing the interactomes of E2F6 and PCGF6. Chromatin immunoprecipitation-sequencing and RNA sequencing assays show that MGA binds to and represses genes that are bound and activated by MYC. In addition, we show that, as opposed to the MYC oncoprotein, MGA acts as a negative regulator for cancer cell proliferation. Our study defines a novel MYC/MAX/MGA pathway, in which MYC and MGA play opposite roles in protein interaction, transcriptional regulation, and cellular proliferation. IMPLICATIONS: This study expands the range of key cancer-associated genes whose dysregulation is functionally equivalent to MYC activation and places MYC within a linear pathway analogous to cell-cycle or receptor tyrosine kinase/RAS/RAF pathways in lung adenocarcinomas.
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Affiliation(s)
- Paula Llabata
- Cancer Epigenetics and Biology Program-PEBC (IDIBELL), Barcelona, Spain
| | - Yoichiro Mitsuishi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Peter S Choi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Diana Cai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Joshua M Francis
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Manuel Torres-Diz
- Cancer Epigenetics and Biology Program-PEBC (IDIBELL), Barcelona, Spain
| | - Namrata D Udeshi
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Lior Golomb
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Zhong Wu
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Jin Zhou
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Tanya Svinkina
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Estrella Aguilera-Jimenez
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Yanli Liu
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Steven A Carr
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Matthew Meyerson
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts. .,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Xiaoyang Zhang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
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8
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Cai D, Choi PS, Gelbard M, Meyerson M. Identification and Characterization of Oncogenic SOS1 Mutations in Lung Adenocarcinoma. Mol Cancer Res 2019; 17:1002-1012. [PMID: 30635434 DOI: 10.1158/1541-7786.mcr-18-0316] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/18/2018] [Accepted: 01/04/2019] [Indexed: 12/27/2022]
Abstract
Lung adenocarcinomas are characterized by mutations in the receptor tyrosine kinase (RTK)/Ras/Raf pathway, with up to 75% of cases containing mutations in known driver genes. However, the driver alterations in the remaining cases are yet to be determined. Recent exome sequencing analysis has identified SOS1, encoding a guanine nucleotide exchange factor, as significantly mutated in lung adenocarcinomas lacking canonical oncogenic RTK/Ras/Raf pathway mutations. Here, we demonstrate that ectopic expression of lung adenocarcinoma-derived mutants of SOS1 induces anchorage-independent cell growth in vitro and tumor formation in vivo. Biochemical experiments suggest that these mutations lead to overactivation of the Ras pathway, which can be suppressed by mutations that disrupt either the Ras-GEF or putative Rac-GEF activity of SOS1. Transcriptional profiling reveals that the expression of mutant SOS1 leads to the upregulation of MYC target genes and genes associated with Ras transformation. Furthermore, we demonstrate that an AML cancer cell line harboring a lung adenocarcinoma-associated mutant SOS1 is dependent on SOS1 for survival and is also sensitive to MEK inhibition. Our work provides experimental evidence for the role of SOS1 as an oncogene and suggests a possible therapeutic strategy to target SOS1-mutated cancers. IMPLICATIONS: This study demonstrates that SOS1 mutations found in lung adenocarcinoma are oncogenic and that MEK inhibition may be a therapeutic avenue for the treatment of SOS1-mutant cancers.
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Affiliation(s)
- Diana Cai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Program in Genetics and Genomics, Harvard University, Boston, Massachusetts
| | - Peter S Choi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Maya Gelbard
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts. .,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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9
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Li J, Choi PS, Chaffer CL, Labella K, Hwang JH, Giacomelli AO, Kim JW, Ilic N, Doench JG, Ly SH, Dai C, Hagel K, Hong AL, Gjoerup O, Goel S, Ge JY, Root DE, Zhao JJ, Brooks AN, Weinberg RA, Hahn WC. An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. eLife 2018; 7:37184. [PMID: 30059005 PMCID: PMC6103745 DOI: 10.7554/elife.37184] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [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: 04/01/2018] [Accepted: 07/24/2018] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing of mRNA precursors represents a key gene expression regulatory step and permits the generation of distinct protein products with diverse functions. In a genome-scale expression screen for inducers of the epithelial-to-mesenchymal transition (EMT), we found a striking enrichment of RNA-binding proteins. We validated that QKI and RBFOX1 were necessary and sufficient to induce an intermediate mesenchymal cell state and increased tumorigenicity. Using RNA-seq and eCLIP analysis, we found that QKI and RBFOX1 coordinately regulated the splicing and function of the actin-binding protein FLNB, which plays a causal role in the regulation of EMT. Specifically, the skipping of FLNB exon 30 induced EMT by releasing the FOXC1 transcription factor. Moreover, skipping of FLNB exon 30 is strongly associated with EMT gene signatures in basal-like breast cancer patient samples. These observations identify a specific dysregulation of splicing, which regulates tumor cell plasticity and is frequently observed in human cancer. As the human body develops, countless cells change from one state into another. Two important cell states are known as epithelial and mesenchymal. Cells in the epithelial state tend to be tightly connected and form barriers, like skin cells. Mesenchymal state cells are loosely organized, move around more and make up connective tissues. Some cells alternate between these states via an epithelial-to-mesenchymal transition (EMT for short) and back again. Without this transition, certain organs would not develop and wounds would not heal. Yet, cancer cells also use this transition to spread to distant sites of the body. Such cancers are often the most aggressive, and therefore the most deadly. The epithelial-to-mesenchymal transition is dynamically regulated in a reversible manner. For example, the genes for some proteins might only be active in the epithelial state and further reinforce this state by turning on other ‘epithelial genes’. Alternatively, there might be differences in the processing of mRNA molecules – the intermediate molecules between DNA and protein – that result in the production of different proteins in epithelial and mesenchymal cells. Li, Choi et al. wanted to know which of the thousands of human genes can endow epithelial state cells with mesenchymal characteristics. A better understanding of the switch could help to prevent cancers undergoing an epithelial-to-mesenchymal transition. From a large-scale experiment in human breast cancer cells, Li, Choi et al. found that a group of proteins that bind and modify mRNA molecules are important for the epithelial-to-mesenchymal transition. Two proteins in particular promoted the transition, most likely by binding to the mRNA of a third protein called FLNB and removing a small piece of it. FLNB normally works to prevent the epithelial-to-mesenchymal transition, but the smaller protein encoded by the shorter mRNA promoted the transition by turning on ‘mesenchymal genes’. This switching between different FLNB proteins happens in some of the more aggressive breast cancers, which also contain mesenchymal cells. Finding out which FLNB protein is made in a given cancer may provide an indication of its aggressiveness. Also, looking for drugs that can target the mRNA-binding proteins or FLNB may one day lead to new treatments for some of the most aggressive breast cancers.
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Affiliation(s)
- Ji Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Peter S Choi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Christine L Chaffer
- Whitehead Institute for Biomedical Research and MIT, Cambridge, United States.,Garvan Institute of Medical Research, Sydney, Australia
| | - Katherine Labella
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States
| | - Justin H Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Andrew O Giacomelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jong Wook Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Nina Ilic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Seav Huong Ly
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Chao Dai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Kimberly Hagel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States
| | - Andrew L Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Ole Gjoerup
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Shom Goel
- Harvard Medical School, Boston, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States
| | - Jennifer Y Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, United States
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jean J Zhao
- Harvard Medical School, Boston, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States
| | - Angela N Brooks
- University of California, Santa Cruz, Santa Cruz, United States
| | - Robert A Weinberg
- Whitehead Institute for Biomedical Research and MIT, Cambridge, United States
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
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10
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Viswanathan SR, Nogueira MF, Buss CG, Krill-Burger JM, Wawer MJ, Malolepsza E, Berger AC, Choi PS, Shih J, Taylor AM, Tanenbaum B, Pedamallu CS, Cherniack AD, Tamayo P, Strathdee CA, Lage K, Carr SA, Schenone M, Bhatia SN, Vazquez F, Tsherniak A, Hahn WC, Meyerson M. Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer. Nat Genet 2018; 50:937-943. [PMID: 29955178 PMCID: PMC6143899 DOI: 10.1038/s41588-018-0155-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/10/2018] [Indexed: 12/12/2022]
Abstract
Functional redundancy shared by paralog genes may afford protection against genetic perturbations, but it can also result in genetic vulnerabilities due to mutual interdependency1-5. Here, we surveyed genome-scale short hairpin RNA and CRISPR screening data on hundreds of cancer cell lines and identified MAGOH and MAGOHB, core members of the splicing-dependent exon junction complex, as top-ranked paralog dependencies6-8. MAGOHB is the top gene dependency in cells with hemizygous MAGOH deletion, a pervasive genetic event that frequently occurs due to chromosome 1p loss. Inhibition of MAGOHB in a MAGOH-deleted context compromises viability by globally perturbing alternative splicing and RNA surveillance. Dependency on IPO13, an importin-β receptor that mediates nuclear import of the MAGOH/B-Y14 heterodimer9, is highly correlated with dependency on both MAGOH and MAGOHB. Both MAGOHB and IPO13 represent dependencies in murine xenografts with hemizygous MAGOH deletion. Our results identify MAGOH and MAGOHB as reciprocal paralog dependencies across cancer types and suggest a rationale for targeting the MAGOHB-IPO13 axis in cancers with chromosome 1p deletion.
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Affiliation(s)
- Srinivas R Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Marina F Nogueira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Colin G Buss
- Harvard-MIT Department of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Boston, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Mathias J Wawer
- Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Edyta Malolepsza
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Ashton C Berger
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter S Choi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Juliann Shih
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alison M Taylor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | | | - Pablo Tamayo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- UCSD Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Kasper Lage
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Sangeeta N Bhatia
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Harvard-MIT Department of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Boston, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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11
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Zhang X, Choi PS, Francis JM, Gao GF, Campbell JD, Ramachandran A, Mitsuishi Y, Ha G, Shih J, Vazquez F, Tsherniak A, Taylor AM, Zhou J, Wu Z, Berger AC, Giannakis M, Hahn WC, Cherniack AD, Meyerson M. Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor. Cancer Discov 2018; 8:108-125. [PMID: 28963353 PMCID: PMC5760289 DOI: 10.1158/2159-8290.cd-17-0532] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [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: 05/17/2017] [Revised: 09/18/2017] [Accepted: 09/26/2017] [Indexed: 12/23/2022]
Abstract
The Krüppel-like family of transcription factors plays critical roles in human development and is associated with cancer pathogenesis. Krüppel-like factor 5 gene (KLF5) has been shown to promote cancer cell proliferation and tumorigenesis and to be genomically amplified in cancer cells. We recently reported that the KLF5 gene is also subject to other types of somatic coding and noncoding genomic alterations in diverse cancer types. Here, we show that these alterations activate KLF5 by three distinct mechanisms: (i) Focal amplification of superenhancers activates KLF5 expression in squamous cell carcinomas; (ii) Missense mutations disrupt KLF5-FBXW7 interactions to increase KLF5 protein stability in colorectal cancer; (iii) Cancer type-specific hotspot mutations within a zinc-finger DNA binding domain of KLF5 change its DNA binding specificity and reshape cellular transcription. Utilizing data from CRISPR/Cas9 gene knockout screening, we reveal that cancer cells with KLF5 overexpression are dependent on KLF5 for their proliferation, suggesting KLF5 as a putative therapeutic target.Significance: Our observations, together with previous studies that identified oncogenic properties of KLF5, establish the importance of KLF5 activation in human cancers, delineate the varied genomic mechanisms underlying this occurrence, and nominate KLF5 as a putative target for therapeutic intervention in cancer. Cancer Discov; 8(1); 108-25. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Xiaoyang Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Peter S Choi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Joshua M Francis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Galen F Gao
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Joshua D Campbell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Aruna Ramachandran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Yoichiro Mitsuishi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Gavin Ha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Juliann Shih
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Francisca Vazquez
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Aviad Tsherniak
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Alison M Taylor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Jin Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zhong Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ashton C Berger
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
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12
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Li Y, Deutzmann A, Choi PS, Fan AC, Felsher DW. BIM mediates oncogene inactivation-induced apoptosis in multiple transgenic mouse models of acute lymphoblastic leukemia. Oncotarget 2017; 7:26926-34. [PMID: 27095570 PMCID: PMC5053622 DOI: 10.18632/oncotarget.8731] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 03/18/2016] [Accepted: 04/08/2016] [Indexed: 02/07/2023] Open
Abstract
Oncogene inactivation in both clinical targeted therapies and conditional transgenic mouse cancer models can induce significant tumor regression associated with the robust induction of apoptosis. Here we report that in MYC-, RAS-, and BCR-ABL-induced acute lymphoblastic leukemia (ALL), apoptosis upon oncogene inactivation is mediated by the same pro-apoptotic protein, BIM. The induction of BIMin the MYC- and RAS-driven leukemia is mediated by the downregulation of miR-17-92. Overexpression of miR-17-92 blocked the induction of apoptosis upon oncogene inactivation in the MYC and RAS-driven but not in the BCR-ABL-driven ALL leukemia. Hence, our results provide novel insight into the mechanism of apoptosis upon oncogene inactivation and suggest that induction of BIM-mediated apoptosis may be an important therapeutic approach for ALL.
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Affiliation(s)
- Yulin Li
- Division of Oncology, Department of Medicine and Pathology, Stanford University, Stanford, CA, United States of America
| | - Anja Deutzmann
- Division of Oncology, Department of Medicine and Pathology, Stanford University, Stanford, CA, United States of America
| | - Peter S Choi
- Division of Oncology, Department of Medicine and Pathology, Stanford University, Stanford, CA, United States of America
| | - Alice C Fan
- Division of Oncology, Department of Medicine and Pathology, Stanford University, Stanford, CA, United States of America
| | - Dean W Felsher
- Division of Oncology, Department of Medicine and Pathology, Stanford University, Stanford, CA, United States of America
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13
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Paolella BR, Gibson WJ, Urbanski LM, Alberta JA, Zack TI, Bandopadhayay P, Nichols CA, Agarwalla PK, Brown MS, Lamothe R, Yu Y, Choi PS, Obeng EA, Heckl D, Wei G, Wang B, Tsherniak A, Vazquez F, Weir BA, Root DE, Cowley GS, Buhrlage SJ, Stiles CD, Ebert BL, Hahn WC, Reed R, Beroukhim R. Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. eLife 2017; 6. [PMID: 28177281 PMCID: PMC5357138 DOI: 10.7554/elife.23268] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [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: 11/14/2016] [Accepted: 02/06/2017] [Indexed: 12/13/2022] Open
Abstract
Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent. One of these, the pre-mRNA splicing factor SF3B1, is also frequently mutated in cancer. We validated SF3B1 as a CYCLOPS gene and found that human cancer cells harboring partial SF3B1 copy-loss lack a reservoir of SF3b complex that protects cells with normal SF3B1 copy number from cell death upon partial SF3B1 suppression. These data provide a catalog of copy-number associated gene dependencies and identify partial copy-loss of wild-type SF3B1 as a novel, non-driver cancer gene dependency.
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Affiliation(s)
- Brenton R Paolella
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - William J Gibson
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Laura M Urbanski
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - John A Alberta
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Travis I Zack
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Pratiti Bandopadhayay
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Caitlin A Nichols
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Pankaj K Agarwalla
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Meredith S Brown
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Rebecca Lamothe
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Yong Yu
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Peter S Choi
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Esther A Obeng
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Dirk Heckl
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Guo Wei
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Belinda Wang
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Aviad Tsherniak
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Francisca Vazquez
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Barbara A Weir
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Glenn S Cowley
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Charles D Stiles
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Benjamin L Ebert
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - William C Hahn
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
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14
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Paolella BR, Gibson WJ, Urbanski LM, Alberta JA, Zack TI, Bandopadhayay P, Nichols CA, Agarwalla PK, Brown MS, Lamothe R, Yu Y, Choi PS, Obeng EA, Heckl D, Ebert BL, Wei G, Wang B, Hahn WC, Vazquez F, Weir BA, Stiles CD, Reed R, Beroukhim R. Abstract 4369: Genome-wide copy number dependency analysis identifies partial copy loss of SF3B1 as a novel cancer vulnerability. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4369] [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
Genomic instability is a hallmark of cancer resulting in widespread somatic copy number alterations. We integrated a genome-scale shRNA viability screen and copy number profiles from 179 cancer cell lines to perform an unbiased analysis of copy-number associated gene-dependency interactions. We found most copy-number associated gene dependencies result from losses of genetic material rather than gains. Strikingly, the most enriched class of these dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes. Hemizygous loss of CYCLOPS genes sensitizes cancer cells to their further suppression. One of the “top hits” from the analysis was the pre-mRNA splicing factor SF3B1, which is also frequently mutated in cancer. We then sought to evaluate SF3B1 as a CYCLOPS gene. Cancer cells with hemizygous SF3B1 copy-loss were uniquely sensitive to partial SF3B1 suppression by RNAi compared to cells with normal SF3B1 gene dosage. Mechanistically, cancer cells harboring partial SF3B1 copy-loss lack a reservoir of excess SF3b complex, a precursor complex of the U2 snRNP, which protects cells with normal SF3B1 copy number from cell death upon SF3B1 suppression. Our data highlight the prevalence of CYCLOPS dependencies in cancer and establish the spliceosome as a frequent CYCLOPS target. Further, these data indicate targeting wild-type SF3B1 as a novel cancer dependency in cells with hemizygous SF3B1 copy-loss.
Citation Format: Brenton R. Paolella, William J. Gibson, Laura M. Urbanski, John A. Alberta, Travis I. Zack, Pratiti Bandopadhayay, Caitlin A. Nichols, Pankaj K. Agarwalla, Meredith S. Brown, Rebecca Lamothe, Yong Yu, Peter S. Choi, Esther A. Obeng, Dirk Heckl, Benjamin L. Ebert, Guo Wei, Belinda Wang, William C. Hahn, Francisca Vazquez, Barbara A. Weir, Charles D. Stiles, Robin Reed, Rameen Beroukhim. Genome-wide copy number dependency analysis identifies partial copy loss of SF3B1 as a novel cancer vulnerability. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4369.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Yong Yu
- 3Harvard Medical School, Boston, MA
| | | | | | - Dirk Heckl
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | - Guo Wei
- 4Broad Institute of MIT and Harvard, Cambridge, MA
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15
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de Waal L, Lewis TA, Rees MG, Tsherniak A, Wu X, Choi PS, Gechijian L, Hartigan C, Faloon PW, Hickey MJ, Tolliday N, Carr SA, Clemons PA, Munoz B, Wagner BK, Shamji AF, Koehler AN, Schenone M, Burgin AB, Schreiber SL, Greulich H, Meyerson M. Abstract C136: Identification of selective cancer cytotoxic modulators of phosphodiesterase 3a by predictive chemogenomics. Mol Cancer Ther 2015. [DOI: 10.1158/1535-7163.targ-15-c136] [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
High cancer death rates indicate the need for new anti-cancer therapeutic agents. Approaches to discover new cancer drugs include target-based drug discovery and phenotypic screening. Here, we identify phosphodiesterase 3A modulators as cell-selective cancer cytotoxic compounds by phenotypic compound library screening and target deconvolution by predictive chemogenomics. We found that sensitivity to 6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-one, or DNMDP, across 766 cancer cell lines correlates with expression of the phosphodiesterase 3A gene, PDE3A. Like DNMDP, a subset of known PDE3A inhibitors kill selected cancer cells while others do not. Furthermore, PDE3A depletion leads to DNMDP resistance. We demonstrate that DNMDP binding to PDE3A promotes an interaction between PDE3A and Schlafen 12 (SLFN12), suggesting a neomorphic activity. Co-expression of SLFN12 with PDE3A correlates with DNMDP sensitivity, while depletion of SLFN12 results in decreased sensitivity to DNMDP. Our results implicate PDE3A modulators as candidate cancer therapeutic agents and demonstrate the power of predictive chemogenomics in small-molecule discovery.
Citation Format: Lucian de Waal, Timothy A. Lewis, Matthew G. Rees, Aviad Tsherniak, Xiaoyun Wu, Peter S. Choi, Lara Gechijian, Christina Hartigan, Patrick W. Faloon, Mark J. Hickey, Nicola Tolliday, Steven A. Carr, Paul A. Clemons, Benito Munoz, Bridget K. Wagner, Alykhan F. Shamji, Angela N. Koehler, Monica Schenone, Alex B. Burgin, Stuart L. Schreiber, Heidi Greulich, Matthew Meyerson. Identification of selective cancer cytotoxic modulators of phosphodiesterase 3a by predictive chemogenomics. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C136.
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Affiliation(s)
| | | | | | | | - Xiaoyun Wu
- 2Broad Institute of Harvard and MIT, Cambridge, MA
| | | | | | | | | | | | | | | | | | - Benito Munoz
- 2Broad Institute of Harvard and MIT, Cambridge, MA
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Li Y, Choi PS, Casey SC, Dill DL, Felsher DW. Abstract PR13: miR-17-92 mediates MYC oncogene addiction. Mol Cancer Res 2015. [DOI: 10.1158/1557-3125.myc15-pr13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The MYC oncogene is frequently overexpressed in human cancers. MYC can transcriptionally and translationally regulate the expression of thousands of genes. However, it was unclear which specific genes are responsible for MYC to maintain a neoplastic state. The microRNA cluster miR-17-92 is a major MYC target gene known to regulate proliferation, survival, and angiogenesis, which are several of the key phenotypes associated with MYC oncogene addiction. The resemblance of biological functions between MYC and miR-17-92 thus evoked the hypothesis that miR-17-92 is causally responsible for at least part of the mechanism by which MYC maintains a neoplastic state. We have found that miR-17-92 regulates multiple histone modifiers, such as Sin3b, Hbp1, Suv420h1, and Btg1, as well as the apoptosis regulator Bim, to maintain autonomous proliferation, survival, and self-renewal of MYC-driven tumors. Conversely, MYC inactivation downregulates the expression of miR-17-92 and results in the loss of neoplastic features as a consequence of restoration of senescence, apoptosis, and differentiation. Thus, the expression of miR-17-92 can dictate the cellular fates of MYC-driven tumors between survival versus apoptosis and proliferation versus senescence. Our findings provide a mechanistic insight into why tumors are dependent on or addicted to MYC.
Citation Format: Yulin Li, Peter S. Choi, Stephanie C. Casey, David L. Dill, Dean W. Felsher. miR-17-92 mediates MYC oncogene addiction. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr PR13.
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Affiliation(s)
- Yulin Li
- Stanford University, Stanford, CA
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Li Y, Casey SC, Choi PS, Felsher DW. miR-17-92 explains MYC oncogene addiction. Mol Cell Oncol 2014; 1:e970092. [PMID: 27308380 DOI: 10.4161/23723548.2014.970092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 09/06/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 11/19/2022]
Abstract
MYC regulates tumorigenesis by coordinating the expression of thousands of genes. We found that MYC appears to regulate the decisions between cell survival versus death and self-renewal versus senescence through the microRNA miR-17-92 cluster. Addiction to the MYC oncogene may therefore in fact be an addiction to miR-17-92.
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Affiliation(s)
- Yulin Li
- Division of Oncology; Departments of Medicine and Pathology; Stanford University ; Stanford, CA USA
| | - Stephanie C Casey
- Division of Oncology; Departments of Medicine and Pathology; Stanford University ; Stanford, CA USA
| | - Peter S Choi
- Division of Oncology; Departments of Medicine and Pathology; Stanford University ; Stanford, CA USA
| | - Dean W Felsher
- Division of Oncology; Departments of Medicine and Pathology; Stanford University ; Stanford, CA USA
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Abstract
The Cre/loxP system is a powerful tool for generating conditional genomic recombination and is often used to examine the mechanistic role of specific genes in tumorigenesis. However, Cre toxicity due to its non-specific endonuclease activity has been a concern. Here, we report that tamoxifen-mediated Cre activation in vivo induced the regression of primary lymphomas in p53−/− mice. Our findings illustrate that Cre activation alone can induce the regression of established tumors.
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Affiliation(s)
- Yulin Li
- Department of Medicine, Division of Oncology, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Peter S. Choi
- Department of Medicine, Division of Oncology, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Stephanie C. Casey
- Department of Medicine, Division of Oncology, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Dean W. Felsher
- Department of Medicine, Division of Oncology, School of Medicine, Stanford University, Stanford, California, United States of America
- * E-mail:
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Li Y, Choi PS, Casey SC, Dill DL, Felsher DW. MYC through miR-17-92 suppresses specific target genes to maintain survival, autonomous proliferation, and a neoplastic state. Cancer Cell 2014; 26:262-72. [PMID: 25117713 PMCID: PMC4191901 DOI: 10.1016/j.ccr.2014.06.014] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [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: 12/12/2013] [Revised: 03/23/2014] [Accepted: 06/17/2014] [Indexed: 01/04/2023]
Abstract
The MYC oncogene regulates gene expression through multiple mechanisms, and its overexpression culminates in tumorigenesis. MYC inactivation reverses turmorigenesis through the loss of distinguishing features of cancer, including autonomous proliferation and survival. Here we report that MYC via miR-17-92 maintains a neoplastic state through the suppression of chromatin regulatory genes Sin3b, Hbp1, Suv420h1, and Btg1, as well as the apoptosis regulator Bim. The enforced expression of miR-17-92 prevents MYC suppression from inducing proliferative arrest, senescence, and apoptosis and abrogates sustained tumor regression. Knockdown of the five miR-17-92 target genes blocks senescence and apoptosis while it modestly delays proliferative arrest, thus partially recapitulating miR-17-92 function. We conclude that MYC, via miR-17-92, maintains a neoplastic state by suppressing specific target genes.
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Affiliation(s)
- Yulin Li
- Division of Oncology, Department of Medicine and Pathology, Stanford University, Stanford, CA 94305, USA
| | - Peter S Choi
- Division of Oncology, Department of Medicine and Pathology, Stanford University, Stanford, CA 94305, USA
| | - Stephanie C Casey
- Division of Oncology, Department of Medicine and Pathology, Stanford University, Stanford, CA 94305, USA
| | - David L Dill
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Dean W Felsher
- Division of Oncology, Department of Medicine and Pathology, Stanford University, Stanford, CA 94305, USA.
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Abstract
Genomic rearrangements are frequently observed in cancer cells but have been difficult to generate in a highly specific manner for functional analysis. Here we report the application of CRISPR/Cas technology to successfully generate several types of chromosomal rearrangements implicated as driver events in lung cancer, including the CD74-ROS1 translocation event and the EML4-ALK and KIF5B-RET inversion events. Our results demonstrate that Cas9-induced DNA breaks promote efficient rearrangement between pairs of targeted loci, providing a highly tractable approach for the study of genomic rearrangements.
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Affiliation(s)
- Peter S Choi
- 1] Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, Massachusetts 02215, USA [2] Broad Institute of MIT and Harvard, Cancer Program, Cambridge, Massachusetts 02142, USA
| | - Matthew Meyerson
- 1] Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, Massachusetts 02215, USA [2] Broad Institute of MIT and Harvard, Cancer Program, Cambridge, Massachusetts 02142, USA [3] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Ahn JS, Kim KM, Nam DS, Kang KU, Choi PS, Jeong SY. Preparation of Lacosamide Sustained-release Tablets and Their Pharmacokinetics in Beagles and Mini-pigs. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.2.557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M. A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events. PLoS One 2014; 9:e87361. [PMID: 24498085 PMCID: PMC3909098 DOI: 10.1371/journal.pone.0087361] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 12/20/2013] [Indexed: 01/23/2023] Open
Abstract
Although recurrent somatic mutations in the splicing factor U2AF1 (also known as U2AF35) have been identified in multiple cancer types, the effects of these mutations on the cancer transcriptome have yet to be fully elucidated. Here, we identified splicing alterations associated with U2AF1 mutations across distinct cancers using DNA and RNA sequencing data from The Cancer Genome Atlas (TCGA). Using RNA-Seq data from 182 lung adenocarcinomas and 167 acute myeloid leukemias (AML), in which U2AF1 is somatically mutated in 3-4% of cases, we identified 131 and 369 splicing alterations, respectively, that were significantly associated with U2AF1 mutation. Of these, 30 splicing alterations were statistically significant in both lung adenocarcinoma and AML, including three genes in the Cancer Gene Census, CTNNB1, CHCHD7, and PICALM. Cell line experiments expressing U2AF1 S34F in HeLa cells and in 293T cells provide further support that these altered splicing events are caused by U2AF1 mutation. Consistent with the function of U2AF1 in 3' splice site recognition, we found that S34F/Y mutations cause preferences for CAG over UAG 3' splice site sequences. This report demonstrates consistent effects of U2AF1 mutation on splicing in distinct cancer cell types.
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Affiliation(s)
- Angela N. Brooks
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Peter S. Choi
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Luc de Waal
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Tanaz Sharifnia
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Marcin Imielinski
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Gordon Saksena
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Chandra Sekhar Pedamallu
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Andrey Sivachenko
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Mara Rosenberg
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Juliann Chmielecki
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Michael S. Lawrence
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - David S. DeLuca
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Gad Getz
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Matthew Meyerson
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
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van Riggelen J, Müller J, Otto T, Beuger V, Yetil A, Choi PS, Kosan C, Möröy T, Felsher DW, Eilers M. The interaction between Myc and Miz1 is required to antagonize TGFbeta-dependent autocrine signaling during lymphoma formation and maintenance. Genes Dev 2010; 24:1281-94. [PMID: 20551174 PMCID: PMC2885663 DOI: 10.1101/gad.585710] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [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] [Indexed: 01/28/2023]
Abstract
The Myc protein suppresses the transcription of several cyclin-dependent kinase inhibitors (CKIs) via binding to Miz1; whether this interaction is important for Myc's ability to induce or maintain tumorigenesis is not known. Here we show that the oncogenic potential of a point mutant of Myc (MycV394D) that is selectively deficient in binding to Miz1 is greatly attenuated. Binding of Myc to Miz1 is continuously required to repress CKI expression and inhibit accumulation of trimethylated histone H3 at Lys 9 (H3K9triMe), a hallmark of cellular senescence, in T-cell lymphomas. Lymphomas that arise express high amounts of transforming growth factor beta-2 (TGFbeta-2) and TGFbeta-3. Upon Myc suppression, TGFbeta signaling is required to induce CKI expression and cellular senescence and suppress tumor recurrence. Binding of Myc to Miz1 is required to antagonize growth suppression and induction of senescence by TGFbeta. We demonstrate that, since lymphomas express high levels of TGFbeta, they are poised to elicit an autocrine program of senescence upon Myc inactivation, demonstrating that TGFbeta is a key factor that establishes oncogene addiction of T-cell lymphomas.
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Affiliation(s)
- Jan van Riggelen
- Department of Medicine, Division of Oncology, Stanford University, School of Medicine, Stanford, California 94304, USA
- Department of Pathology, Division of Oncology, Stanford University, School of Medicine, Stanford, California 94304, USA
| | - Judith Müller
- Theodor Boveri Institute, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Tobias Otto
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Vincent Beuger
- Theodor Boveri Institute, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- TaconicArtemis GmbH, 51063 Koeln, Germany
| | - Alper Yetil
- Department of Medicine, Division of Oncology, Stanford University, School of Medicine, Stanford, California 94304, USA
- Department of Pathology, Division of Oncology, Stanford University, School of Medicine, Stanford, California 94304, USA
| | - Peter S. Choi
- Department of Medicine, Division of Oncology, Stanford University, School of Medicine, Stanford, California 94304, USA
- Department of Pathology, Division of Oncology, Stanford University, School of Medicine, Stanford, California 94304, USA
| | - Christian Kosan
- Institut de Recherches Cliniques de Montreal, Université de Montréal, Montreal, Québec H2W 1R7, Canada
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montreal, Université de Montréal, Montreal, Québec H2W 1R7, Canada
| | - Dean W. Felsher
- Department of Medicine, Division of Oncology, Stanford University, School of Medicine, Stanford, California 94304, USA
- Department of Pathology, Division of Oncology, Stanford University, School of Medicine, Stanford, California 94304, USA
- E-MAIL ; FAX (650) 725-1420
| | - Martin Eilers
- Theodor Boveri Institute, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- Corresponding authors.E-MAIL ; FAX 49-9031-3184113
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Choi PS, Bernstein HD. Sequential translocation of an Escherchia coli two-partner secretion pathway exoprotein across the inner and outer membranes. Mol Microbiol 2009; 75:440-51. [PMID: 19968793 DOI: 10.1111/j.1365-2958.2009.06993.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In Gram-negative bacteria, a variety of high molecular weight 'exoproteins' are translocated across the outer membrane (OM) via the two-partner secretion (TPS) pathway by interacting with a dedicated transporter. It is unclear, however, whether the translocation of exoproteins across the OM is coupled to their translocation across the inner membrane (IM). To address this question, we separated the production of an Escherichia coli O157:H7 exoprotein (OtpA) and its transporter (OtpB) temporally by placing otpA and otpB under the control of distinct regulatable promoters. We found that when both full-length and truncated forms of OtpA were expressed prior to OtpB, a significant fraction of the exoprotein was secreted. The results indicate that OtpA can be translocated into the periplasm and briefly remain secretion-competent. Furthermore, by engineering cysteine residues into OtpA and using disulphide bond formation as a reporter of periplasmic localization, we obtained additional evidence that the C-terminus of OtpA enters the periplasm before the N-terminus is translocated across the OM even when OtpA and OtpB are expressed simultaneously. Taken together, our results demonstrate that the translocation of a TPS exoprotein across the OM can occur independently from its translocation across the IM.
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Affiliation(s)
- Peter S Choi
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0538, USA
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25
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Abstract
Gram-negative bacteria contain multiple secretion pathways that facilitate the translocation of proteins across the outer membrane. The two-partner secretion (TPS) system is composed of two essential components, a secreted exoprotein and a pore-forming beta barrel protein that is thought to transport the exoprotein across the outer membrane. A putative TPS system was previously described in the annotation of the genome of Escherichia coli O157:H7 strain EDL933. We found that the two components of this system, which we designate OtpA and OtpB, are not predicted to belong to either of the two major subtypes of TPS systems (hemolysins and adhesins) based on their sequences. Nevertheless, we obtained direct evidence that OtpA and OtpB constitute a bona fide TPS system. We found that secretion of OtpA into the extracellular environment in E. coli O157:H7 requires OtpB and that when OtpA was produced in an E. coli K-12 strain, its secretion was strictly dependent on the production of OtpB. Furthermore, using OtpA/OtpB as a model system, we show that protein secretion via the TPS pathway is extremely rapid.
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Affiliation(s)
- Peter S Choi
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0538, USA
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Choi PS, Naal Z, Moore C, Casado-Rivera E, Abruña HD, Helmann JD, Shapleigh JP. Assessing the impact of denitrifier-produced nitric oxide on other bacteria. Appl Environ Microbiol 2006; 72:2200-5. [PMID: 16517672 PMCID: PMC1393196 DOI: 10.1128/aem.72.3.2200-2205.2006] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [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: 08/15/2005] [Accepted: 01/09/2006] [Indexed: 11/20/2022] Open
Abstract
A series of experiments was undertaken to learn more about the impact on other bacteria of nitric oxide (NO) produced during denitrification. The denitrifier Rhodobacter sphaeroides 2.4.3 was chosen as a denitrifier for these experiments. To learn more about NO production by this bacterium, NO levels during denitrification were measured by using differential mass spectrometry. This revealed that NO levels produced during nitrate respiration by this bacterium were in the low muM range. This concentration of NO is higher than that previously measured in denitrifiers, including Achromobacter cycloclastes and Paracoccus denitrificans. Therefore, both 2.4.3 and A. cycloclastes were used in this work to compare the effects of various NO levels on nondenitrifying bacteria. By use of bacterial overlays, it was found that the NO generated by A. cycloclastes and 2.4.3 cells during denitrification inhibited the growth of both Bacillus subtilis and R. sphaeroides 2.4.1 but that R. sphaeroides 2.4.3 caused larger zones of inhibition in the overlays than A. cycloclastes. Both R. sphaeroides 2.4.3 and A. cycloclastes induced the expression of the NO stress response gene hmp in B. subtilis. Taken together, these results indicate that there is variability in the NO concentrations produced by denitrifiers, but, irrespective of the NO levels produced, microbes in the surrounding environment were responsive to the NO produced during denitrification.
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Affiliation(s)
- Peter S Choi
- Cornell University, Department of Microbiology, Wing Hall, Ithaca, NY 14853, USA
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Abstract
Cytochrome c' (Cyt c') is a c-type cytochrome with a pentacoordinate heme iron. The gene encoding this protein in Rhodobacter sphaeroides 2.4.3, designated cycP, was isolated and sequenced. Northern blot analysis and beta-galactosidase assays demonstrated that cycP transcription increased as oxygen levels decreased and was not repressed under denitrifying conditions as observed in another Rhodobacter species. CO difference spectra performed with extracts of cells grown under different conditions revealed that Cyt c' levels were highest during photosynthetic denitrifying growth conditions. The increase in Cyt c' under this condition was higher than would be predicted from transcriptional studies. Electron paramagnetic resonance analysis of whole cells demonstrated that Cyt c' binds NO during denitrification. Mass spectrometric analysis of nitrogen oxides produced by cells and purified protein did not indicate that Cyt c' has NO reductase activity. Taken together, these results suggest a model where Cyt c' in R. sphaeroides 2.4.3 may shuttle NO to the membrane, where it can be reduced.
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Affiliation(s)
- Peter S Choi
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853, USA
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Kim SW, Ban SH, Chung H, Cho S, Chung HJ, Choi PS, Yoo OJ, Liu JR. Taxonomic discrimination of flowering plants by multivariate analysis of Fourier transform infrared spectroscopy data. Plant Cell Rep 2004; 23:246-50. [PMID: 15248083 DOI: 10.1007/s00299-004-0811-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2003] [Revised: 04/19/2004] [Accepted: 04/20/2004] [Indexed: 05/11/2023]
Abstract
Fourier transform infrared spectroscopy (FTIR) provides biochemical profiles containing overlapping signals from a majority of the compounds that are present when whole cells are analyzed. Leaf samples of seven higher plant species and varieties were subjected to FTIR to determine whether plants can be discriminated phylogenetically on the basis of biochemical profiles. A hierarchical dendrogram based on principal component analysis (PCA) of FTIR data showed relationships between plants that were in agreement with known plant taxonomy. Genetic programming (GP) analysis determined the top three to five biomarkers from FTIR data that discriminated plants at each hierarchical level of the dendrogram. Most biomarkers determined by GP analysis at each hierarchical level were specific to the carbohydrate fingerprint region (1,200-800 cm(-1)) of the FTIR spectrum. Our results indicate that differences in cell-wall composition and structure can provide the basis for chemotaxonomy of flowering plants.
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Affiliation(s)
- S W Kim
- Laboratory of Plant Genomic Services, Korea Research Institute of Bioscience and Biotechnology, 52 Eoun-dong, Yuseong-gu, 305-333, Daejeon, South Korea
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Craiu A, Saito Y, Limon A, Eppich HM, Olson DP, Rodrigues N, Adams GB, Dombkowski D, Richardson P, Schlossman R, Choi PS, Grogins J, O'Connor PG, Cohen K, Attar EC, Freshman J, Rich R, Mangano JA, Gribben JG, Anderson KC, Scadden DT. Flowing cells through pulsed electric fields efficiently purges stem cell preparations of contaminating myeloma cells while preserving stem cell function. Blood 2004; 105:2235-8. [PMID: 15292069 DOI: 10.1182/blood-2003-12-4399] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [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: 11/20/2022] Open
Abstract
Autologous stem cell transplantation, in the setting of hematologic malignancies such as lymphoma, improves disease-free survival if the graft has undergone tumor purging. Here we show that flowing hematopoietic cells through pulsed electric fields (PEFs) effectively purges myeloma cells without sacrificing functional stem cells. Electric fields can induce irreversible cell membrane pores in direct relation to cell diameter, an effect we exploit in a flowing system appropriate for clinical scale. Multiple myeloma (MM) cell lines admixed with human bone marrow (BM) or peripheral blood (PB) cells were passed through PEFs at 1.35 kV/cm to 1.4 kV/cm, resulting in 3- to 4-log tumor cell depletion by flow cytometry and 4.5- to 6-log depletion by tumor regrowth cultures. Samples from patients with MM gave similar results by cytometry. Stem cell engraftment into nonobese diabetic-severe combined immunodeficient (NOD/SCID)/beta2m-/- mice was unperturbed by PEFs. Flowing cells through PEFs is a promising technology for rapid tumor cell purging of clinical progenitor cell preparations.
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Affiliation(s)
- Abie Craiu
- Science Research Laboratory Inc, Somerville, MA, USA
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Choi PS, Kim YD, Choi KM, Chung HJ, Choi DW, Liu JR. Plant regeneration from hairy-root cultures transformed by infection with Agrobacterium rhizogenes in Catharanthus roseus. Plant Cell Rep 2004. [PMID: 14963692 DOI: 10.1007/s00299-004-0765-763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Hypocotyl explants of Catharanthus roseus produced hairy roots when cultured on Murashige and Skoog (MS) basal medium after infection by Agrobacterium rhizogenes. Explants gave rise to adventitious shoots at a frequency of up to 80% when cultured on MS medium supplemented with 31.1 microM 6-benzyladenine and 5.4 microM alpha-naphthaleneacetic acid. There was a significant difference in the frequency of adventitious shoot formation for each hairy-root line derived from a different cultivar. Plants derived from hairy roots exhibited prolific rooting and had shortened internodes. Approximately half of the plants had wrinkled leaves and an abundant root mass with extensive lateral branching, but otherwise appeared morphologically normal. Plants with hairy roots that were derived from the cultivar Cooler Apricot developed flowers with petals that were white in the proximal region, whereas the wild-type flower petals are red. PCR and Southern blot analyses revealed that plants derived from hairy roots retained the Ri TL-DNA.
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Affiliation(s)
- P S Choi
- Laboratory of Functional Genomics for Plant Secondary Metabolism (National Research Laboratory), Eugentech Inc., P.O. Box 115, Yuseong, 305-333 Daejeon, Korea
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Choi PS, Kim YD, Choi KM, Chung HJ, Choi DW, Liu JR. Plant regeneration from hairy-root cultures transformed by infection with Agrobacterium rhizogenes in Catharanthus roseus. Plant Cell Rep 2004; 22:828-31. [PMID: 14963692 DOI: 10.1007/s00299-004-0765-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2003] [Accepted: 01/06/2004] [Indexed: 05/07/2023]
Abstract
Hypocotyl explants of Catharanthus roseus produced hairy roots when cultured on Murashige and Skoog (MS) basal medium after infection by Agrobacterium rhizogenes. Explants gave rise to adventitious shoots at a frequency of up to 80% when cultured on MS medium supplemented with 31.1 microM 6-benzyladenine and 5.4 microM alpha-naphthaleneacetic acid. There was a significant difference in the frequency of adventitious shoot formation for each hairy-root line derived from a different cultivar. Plants derived from hairy roots exhibited prolific rooting and had shortened internodes. Approximately half of the plants had wrinkled leaves and an abundant root mass with extensive lateral branching, but otherwise appeared morphologically normal. Plants with hairy roots that were derived from the cultivar Cooler Apricot developed flowers with petals that were white in the proximal region, whereas the wild-type flower petals are red. PCR and Southern blot analyses revealed that plants derived from hairy roots retained the Ri TL-DNA.
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Affiliation(s)
- P S Choi
- Laboratory of Functional Genomics for Plant Secondary Metabolism (National Research Laboratory), Eugentech Inc., P.O. Box 115, Yuseong, 305-333 Daejeon, Korea
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Kim SW, Ban SH, Chung HJ, Choi DW, Choi PS, Yoo OJ, Liu JR. Taxonomic discrimination of higher plants by pyrolysis mass spectrometry. Plant Cell Rep 2004; 22:519-522. [PMID: 14520500 DOI: 10.1007/s00299-003-0714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2003] [Revised: 08/22/2003] [Accepted: 08/22/2003] [Indexed: 05/24/2023]
Abstract
Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum and has been widely applied to the discrimination of closely related microbial strains. Leaf samples of six species and one variety of higher plants (Rosa multiflora, R. multiflora var. platyphylla, Sedum kamtschaticum, S. takesimense, S. sarmentosum, Hepatica insularis, and H. asiatica) were subjected to PyMS for spectral fingerprinting. Principal component analysis of PyMS data was not able to discriminate these plants in discrete clusters. However, canonical variate analysis of PyMS data separated these plants from one another. A hierarchical dendrogram based on canonical variate analysis was in agreement with the known taxonomy of the plants at the variety level. These results indicate that PyMS is able to discriminate higher plants based on taxonomic classification at the family, genus, species, and variety level.
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Affiliation(s)
- S W Kim
- Laboratory of Plant Genomics Services, Korea Research Institute of Bioscience and Biotechnology, 52 Eoun-dong, Yuseong-gu, 305-333 Daejeon, Korea
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Lee BC, Cheng T, Adams GB, Attar EC, Miura N, Lee SB, Saito Y, Olszak I, Dombkowski D, Olson DP, Hancock J, Choi PS, Haber DA, Luster AD, Scadden DT. P2Y-like receptor, GPR105 (P2Y14), identifies and mediates chemotaxis of bone-marrow hematopoietic stem cells. Genes Dev 2003; 17:1592-604. [PMID: 12842911 PMCID: PMC196132 DOI: 10.1101/gad.1071503] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [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: 11/24/2022]
Abstract
Hematopoiesis in mammals undergoes a developmental shift in location from fetal liver to bone marrow accompanied by a gradual transition from highly proliferative to deeply quiescent stem cell populations. P2Y receptors are G-protein-coupled nucleotide receptors participating in vascular and immune responses to injury. We identified a P2Y-like receptor for UDP-conjugated sugars, GPR105 (P2Y14), with restricted expression on primitive cells in the hematopoietic lineage. Anti-GPR105 antibody selectively isolated a subset of hematopoietic cells within the fetal bone marrow, but not in the fetal liver, that was enriched for G0 cell cycle status and for in vitro stem-cell-like multipotential long-term culture capability. Conditioned media from bone marrow stroma induced receptor activation and chemotaxis that was sensitive to G alpha i and anti-receptor antibody inhibition. GPR105 is a G-protein-coupled receptor identifying a quiescent, primitive population of hematopoietic cells restricted to bone marrow. It mediates primitive cell responses to specific hematopoietic microenvironments and extends the known immune system functions of P2Y receptors to the stem cell level. These data suggest a new class of receptors participating in the regulation of the stem cell compartment.
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MESH Headings
- ADP-ribosyl Cyclase/analysis
- ADP-ribosyl Cyclase 1
- Amino Acid Sequence
- Animals
- Antigens, CD/analysis
- Antigens, CD34/analysis
- COS Cells
- Cell Cycle
- Cell Lineage
- Cell Separation
- Cells, Cultured
- Chemotaxis
- Colony-Forming Units Assay
- Culture Media, Conditioned
- Flow Cytometry
- Hematopoiesis
- Hematopoietic Stem Cells/chemistry
- Hematopoietic Stem Cells/physiology
- Humans
- Immunophenotyping
- Liver/chemistry
- Liver/embryology
- Membrane Glycoproteins
- Mice
- Molecular Sequence Data
- Receptors, G-Protein-Coupled
- Receptors, Purinergic P2/analysis
- Receptors, Purinergic P2/chemistry
- Receptors, Purinergic P2/genetics
- Receptors, Purinergic P2/physiology
- Receptors, Purinergic P2Y
- Resting Phase, Cell Cycle
- Transfection
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Affiliation(s)
- Byeong-Chel Lee
- Center for Regenerative Medicine and Technology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129, USA
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Laratta WP, Choi PS, Tosques IE, Shapleigh JP. Involvement of the PrrB/PrrA two-component system in nitrite respiration in Rhodobacter sphaeroides 2.4.3: evidence for transcriptional regulation. J Bacteriol 2002; 184:3521-9. [PMID: 12057946 PMCID: PMC135133 DOI: 10.1128/jb.184.13.3521-3529.2002] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodobacter sphaeroides strain 2.4.3 is capable of diverse metabolic lifestyles, including denitrification. The regulation of many Rhodobacter genes involved in redox processes is controlled, in part, by the PrrBA two-component sensor-regulator system, where PrrB serves as the sensor kinase and PrrA is the response regulator. Four strains of 2.4.3 carrying mutations within the prrB gene were isolated in a screen for mutants unable to grow anaerobically on medium containing nitrite. Studies revealed that the expression of nirK, the structural gene encoding nitrite reductase, in these strains was significantly decreased compared to its expression in 2.4.3. Disruption of prrA also eliminated the ability to grow both photosynthetically and anaerobically in the dark on nitrite-amended medium. Complementation with prrA restored the wild-type phenotype. The PrrA strain exhibited a severe decrease in both nitrite reductase activity and expression of a nirK-lacZ fusion. Nitrite reductase activity in the PrrA strain could be restored to wild-type levels by using nirK expressed from a heterologous promoter, suggesting that the loss of nitrite reductase activity in the PrrA and PrrB mutants was not due to problems with enzyme assembly or the supply of reductant. Inactivation of prrA had no effect on the expression of the gene encoding NnrR, a transcriptional activator required for the expression of nirK. Inactivation of ccoN, part of the cbb(3)-type cytochrome oxidase shown to regulate the kinase activity of PrrB, also caused a significant decrease in both nirK expression and Nir activity. This was unexpected, since PrrA-P accumulates in the ccoN strain. Together, these results demonstrate that PrrBA plays an essential role in the regulation of nirK.
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Affiliation(s)
- William P Laratta
- Department of Microbiology, Cornell University, Ithaca, New York 14853-8101, USA
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Basile Júnior R, Rosemberg LA, Pedrosa FM, Von Uhlendorff E, Matuoka CM, Choi PS. Vascular lesions of the lumbar epidural space: magnetic resonance imaging features of epidural cavernous hemangioma and epidural hematoma. Rev Hosp Clin Fac Med Sao Paulo 1999; 54:25-8. [PMID: 10488598 DOI: 10.1590/s0041-87811999000100006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The authors report the magnetic resonance imaging diagnostic features in two cases with respectively lumbar epidural hematoma and cavernous hemangioma of the lumbar epidural space. Enhanced MRI T1-weighted scans show a hyperintense signal rim surrounding the vascular lesion. Non-enhanced T2-weighted scnas showed hyperintense signal.
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Affiliation(s)
- R Basile Júnior
- Instituto de Ortopedia e Traumatologia do Hospital das Clínicas University of São Paulo
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Abstract
Emphysematous cystitis is characterized by gas collection within the bladder wall and lumen. We report two cases of emphysematous cystitis of the urinary bladder in a 67-year-old and a 63-year-old women. They presented with bladder irritation symptoms such as dysuria, hematuria and frequency. Urinalysis showed pyuria. Cystoscopic examination revealed that bladder mucosa was studded with vesicles varying in size and arranged in clumps. CT scans of the pelvis showed mottled gas bubbles within the bladder. They were treated with antibiotics. Four days after the treatment, the symptoms subsided and plain abdominal film showed no evidence of gas shadows in the pelvic cavity.
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Affiliation(s)
- G Lee
- Department of Urology, College of Medicine, Dankook University, Cheonan, Choongnam, Korea
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Paulsen IT, Park JH, Choi PS, Saier MH. A family of gram-negative bacterial outer membrane factors that function in the export of proteins, carbohydrates, drugs and heavy metals from gram-negative bacteria. FEMS Microbiol Lett 1997; 156:1-8. [PMID: 9368353 DOI: 10.1111/j.1574-6968.1997.tb12697.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.0] [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: 02/05/2023] Open
Abstract
Gram-negative bacteria have evolved transport complexes that export macromolecules and toxic substances across the two membranes of the cell envelope in a single energy coupled step. The process requires (1) a cytoplasmic membrane export system, (2) a membrane fusion protein (MFP), and (3) an outer membrane factor (OMF). Families comprising the former two constituents have been described previously. We here present an analysis of the phylogenetic and structural characteristics of the OMF family. Twenty-one members of this family have been identified, and based on available evidence, they function in conjunction with ABC, RND, MFS and/or other types of cytoplasmic transport systems. OMFs exhibit fairly uniform sizes (398-495 residues with two exceptions), and based on computational analyses, they may form beta-barrel structures consisting of up to 16 beta-strands. Phylogenetic analyses reveal that while the MFPs cluster in accordance with the type of cytoplasmic membrane transport systems with which they function, OMFs do not. We conclude that OMFs probably comprise a family of outer membrane porin-type proteins of uniform structure which did not coevolve with their cognate cytoplasmic membrane transport systems.
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Affiliation(s)
- I T Paulsen
- Department of Biology, University of California at San Diego, La Jolla 92093-0116, USA
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Choi PS, Soh WY, Kim YS, Yoo OJ, Liu JR. Genetic transformation and plant regeneration of watermelon using Agrobacterium tumefaciens. Plant Cell Rep 1994; 13:344-8. [PMID: 24193834 DOI: 10.1007/bf00232634] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/1993] [Revised: 12/16/1993] [Indexed: 05/09/2023]
Abstract
Adventitious shoots formed on the proximal cut edges of different cotyledonary explants of watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai; cvs. Sweet Gem and Gold Medal] cultured on Murashige and Skoog's (MS) medium with 1 mgl(-1) 6-benzyladenine (BA). Light (16-h photoperiod, about 7 Wm(-2) cool-white fluorescent lamps) was essential for shoot formation. To obtain transformed plants, cotyledonary explants of 'Sweet Gem' were cocultured with Agrobacterium tumefaciens LBA4404, a disarmed strain harboring a binary vector pBI121 carrying the CaMV 35S promoter-β-glucuronidase (GUS) gene fusion used as a reporter gene and NOS promoter-neomycin phosphotransferase gene as a positive selection marker, for 48 h on MS medium with 1 mgl(-1) BA and 200 μM β-hydroxyacetosyringone. After 48 h of culture, explants were transferred to medium with 1 mgl(-1) BA 250 mgl(-1) carbenicillin, and 100 mgl(-1) kanamycin and cultured in the light. Adventitious shoots formed on the explants after 4 weeks of culture. When subjected to GUS histochemical assay, young leaves obtained from the shoots showed a positive response at a frequency of up to 16%. Preculturing cotyledonary explants on MS medium with 1 mgl(-1) BA for 5 d enhanced the competence of the cells to be transformed by Agrobacterium. Southern blot analysis confirmed that the GUS gene was incorporated into the genomic DNA of the GUS-positive regenerants. The transformed plants were grown to maturity.
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Affiliation(s)
- P S Choi
- Plant Cell Biology Laboratory, Genetic Engineering Research Institute, KIST, Taejon, Korea
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Min SR, Yang SG, Liu JR, Choi PS, Soh WY. High frequency somatic embryogenesis and plant regeneration in tissue cultures of Codonopsis lanceolata. Plant Cell Rep 1992; 10:621-623. [PMID: 24212875 DOI: 10.1007/bf00232383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/1991] [Revised: 10/23/1991] [Indexed: 06/02/2023]
Abstract
Culture conditions for high frequency somatic embryogenesis and plant regeneration from cotyledonary explants of Codonopsis lanceolata are described. The maximum induction frequency of somatic embryos from cotyledonary explants was 80% on Murashige and Skoog (MS) medium containing 6% sucrose with 1 mg/l 2,4-dichlorophenoxyacetic acid and 10% coconut water. Upon transfer onto MS basal medium containing 3% sucrose, most somatic embryos developed into plantlets.
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Affiliation(s)
- S R Min
- Plant Cell Biology Laboratory, Genetic Engineering Research Institute, Korea Institute of Science and Technology, P.O. Box 17, 305-606, Taedok Science Town, Taejon, Korea
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Abstract
The authors present an experimental study of 30 rats, in which human dura mater preserved in glycerin was used to repair gaps in the Achilles tendon. The animals were killed 8 weeks after the surgery and evaluated by gross and microscopic examination. The results showed that the dura mater did not cause foreign-body reactions or adhesions and was surrounded by concentric layers of fibroblasts and collagen fibers, suggesting that it could be employed as a substitute for damaged tendons.
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