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  • 1
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. NG03-NG03
    Abstract: Chromosomal instability (CIN) is a hallmark of cancer and it results from ongoing errors in chromosome segregation during mitosis. While CIN is a major driver of tumor evolution, its role in metastasis has not been established. Here we show that CIN promotes metastasis by sustaining a tumor-cell autonomous response to cytosolic DNA. Errors in chromosome segregation create a preponderance of micronuclei whose rupture spills genomic DNA into the cytosol. This leads to the activation of the cGAS-STING cytosolic DNA-sensing pathway and downstream noncanonical NF-κB signaling. Genetic suppression of CIN significantly delays metastasis even in highly aneuploid tumor models, whereas inducing continuous chromosome segregation errors promotes cellular invasion and metastasis in a STING-dependent manner. Using single-cell RNA sequencing, we uncover a CIN-induced transcriptional switch from a proliferative and metabolically active state to a mesenchymal phenotype associated with inflammatory pathways, offering an opportunity to target chromosome segregation errors for therapeutic benefit. Our work reveals an unexpected link between CIN, cytosolic DNA sensing pathways, and metastasis. The use of an isogenic system has enabled us to dissect the role of CIN from that of aneuploidy. Importantly, while we do not discount the role of CIN in generating karyotypic heterogeneity that can serve as the substrate for natural selection, our work demonstrates that continuous chromosome missegregation is also required to replenish cytosolic DNA pools leading to chronic upregulation of inflammatory pathways. In non-transformed settings, cytosolic DNA sensing is incompatible with viability. Unlike normal cells, chromosomally unstable cells are awash with cytosolic DNA and have adapted to coexist with a chronically active cGAS-STING pathway by suppressing downstream type I interferon signaling and instead upregulating the alternative NF-κB pathway. Persistent STING activation mediates carcinogen-induced tumor formation and we now show that tumor cells co-opt this otherwise lethal program to spread to distant organs. The evolutionary benefit of the noncanonical pathway might justify the scarcity of inactivating mutations in cGAS and STING among human cancers. The emergence, and subsequent tolerance, of CIN represents an important bottleneck during tumor evolution. Our single-cell analysis revealed that CIN induces a transcriptional switch whereby cells shift from a proliferative and highly metabolic state, ideally suited for primary tumor growth, to a chromosomally unstable and mesenchymal state associated with upregulation of inflammatory pathways. These two largely mutually exclusive states likely account for the reversibility in chromosome missegregation rates seen in primary tumors and metastases, and provide an explanation for the negative effect of aneuploidy during early tumorigenesis. Interestingly, this mutual exclusivity was recently observed in a pan-cancer genomic analysis of metastatic tumors, and it leads us to suggest that CIN underlies the subset of metastases that are characterized by EMT and inflammation. By providing a mechanistic link between CIN and metastasis, our work opens new avenues to target chromosomally unstable tumors for therapeutic benefit. Citation Format: Samuel F. Bakhoum, Bryon Ngo, Ashley L. Bakhoum, Julie-Ann Cavallo, Charles J. Murphy, Peter Ly, Pragya Shah, Roshan K. Sriram, Thomas B.k. Watkins, Neil K. Taunk, Mercedes Duran, Chantal Pauli, Christine Shaw, Kalyani Chadalavada, Vinagolu K. Rajasekhar, Giulio Genovese, Subramanian Venkatesan, Nicolai J. Birkbak, Nicholas McGranahan, Mark Lundquist, Quincy LaPlant, John H. Healey, Olivier Elemento, Christine H. Chung, Nancy Y. Lee, Marcin Imielinski, Gouri Nanjangud, Dana Pe'er, Don W. Cleveland, Simon N. Powell, Jan Lammerding, Charles Swanton, Lewis C. Cantley. Chromosomal instability promotes metastasis through a cytosolic DNA response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr NG03.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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  • 2
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 76, No. 14_Supplement ( 2016-07-15), p. 4368-4368
    Abstract: Recent cancer genome sequencing and analysis has identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood, limiting the use of this genetic knowledge for clinical decision-making. Here we describe a new high-throughput approach, expression-based variant impact phenotyping (eVIP), which uses gene expression changes to infer somatic mutation impact. We generated a lentiviral expression library representing 53 genes and 194 somatic mutations identified in primary lung adenocarcinomas. Next, we introduced this library into A549 lung adenocarcinoma cells and 96 hours later performed gene expression profiling using Luminex-based L1000 profiling. We built a computational pipeline, eVIP, to compare mutant and wild-type expression signatures to infer whether variants were gain-of-function, change-of-function, loss-of-function, or neutral. Overall, eVIP identified 69% of mutations as impactful whereas 31% appeared functionally neutral. A very high rate, 92%, of missense mutations in the KEAP1 and STK11 tumor suppressor genes were found to inactivate or diminish protein function. As a complementary approach, we assessed which mutations are epistatic to EGFR or capable of initiating xenograft tumor formation in vivo. A subset of the impactful mutations identified by eVIP could induce xenograft tumor formation in mice and/or confer resistance to cellular EGFR inhibition. Among these mutations were 20 rare or non-canonical somatic variants in clinically-actionable or -relevant oncogenes including EGFR S645C, ARAF S214C and S214F, ERBB2 S418T, and PIK3CA E600K. eVIP can, in principle, characterize any genetic variant, independent of prior knowledge of gene function. Further application of eVIP should significantly advance the pace of functional characterization of mutations identified from genome sequencing. Citation Format: Alice H. Berger, Angela N. Brooks, Xiaoyun Wu, Yashaswi Shrestha, Candace Chouinard, Federica Piccioni, Mukta Bagul, Atanas Kamburov, Marcin Imielinski, Larson Hogstrom, Cong Zhu, Xiaoping Yang, Sasha Pantel, Ryo Sakai, Nathan Kaplan, David Root, Rajiv Narayan, Ted Natoli, David Lahr, Itay Tirosh, Pablo Tamayo, Gad Getz, Bang Wong, John Doench, Aravind Subramanian, Todd R. Golub, Matthew Meyerson, Jesse S. Boehm. High-throughput phenotyping of lung cancer somatic mutations. [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 4368.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2016
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  • 3
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2017
    In:  Journal of the American Medical Informatics Association Vol. 24, No. 3 ( 2017-05-01), p. 513-519
    In: Journal of the American Medical Informatics Association, Oxford University Press (OUP), Vol. 24, No. 3 ( 2017-05-01), p. 513-519
    Abstract: Objective: This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations. Materials and Methods: PMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as the Human Genome Variation Society variant description format, we implemented a data model that links variants to tumor-specific and tissue-specific interpretations. Key features of PMKB include support for all major variant types, standardized authentication, distinct user roles including high-level approvers, and detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically. Results: At the time of writing, PMKB contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. PMKB’s interpretations have been used in over 1500 AmpliSeq tests and 750 whole-exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existing API. Discussion: An accurate and up-to-date knowledge base of genomic alterations of clinical significance is critical to the success of precision medicine programs. The open-access, programmatically accessible PMKB represents an important attempt at creating such a resource in the field of oncology. Conclusion: The PMKB was designed to help collect and maintain clinical-grade mutation interpretations and facilitate reporting for clinical cancer genomic testing. The PMKB was also designed to enable the creation of clinical cancer genomics automated reporting pipelines via an API.
    Type of Medium: Online Resource
    ISSN: 1067-5027 , 1527-974X
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2017
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  • 4
    In: Nature Genetics, Springer Science and Business Media LLC, Vol. 48, No. 6 ( 2016-6), p. 607-616
    Type of Medium: Online Resource
    ISSN: 1061-4036 , 1546-1718
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
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  • 5
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2016
    In:  Nature Genetics Vol. 48, No. 2 ( 2016-2), p. 176-182
    In: Nature Genetics, Springer Science and Business Media LLC, Vol. 48, No. 2 ( 2016-2), p. 176-182
    Type of Medium: Online Resource
    ISSN: 1061-4036 , 1546-1718
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
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  • 6
    In: Nature, Springer Science and Business Media LLC, Vol. 569, No. 7757 ( 2019-5), p. 503-508
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
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  • 7
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2018-06-21)
    Abstract: GWAS have identified 〉 200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis -eQTL. We show that these are determined by ∼9720 regulatory modules, of which ∼3000 operate in multiple tissues and ∼970 on multiple genes. We identify regulatory modules that drive the disease association for 63 of the 200 risk loci, and show that these are enriched in multigenic modules. Based on these analyses, we resequence 45 of the corresponding 100 candidate genes in 6600 Crohn disease (CD) cases and 5500 controls, and show with burden tests that they include likely causative genes. Our analyses indicate that ≥10-fold larger sample sizes will be required to demonstrate the causality of individual genes using this approach.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
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  • 8
    Online Resource
    Online Resource
    Elsevier BV ; 2017
    In:  Current Opinion in Systems Biology Vol. 1 ( 2017-02), p. 54-61
    In: Current Opinion in Systems Biology, Elsevier BV, Vol. 1 ( 2017-02), p. 54-61
    Type of Medium: Online Resource
    ISSN: 2452-3100
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2017
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  • 9
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 2018
    In:  Science Vol. 361, No. 6405 ( 2018-08-31), p. 848-849
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 361, No. 6405 ( 2018-08-31), p. 848-849
    Abstract: The cytogenetic definitions of many cancers predate the genome sequencing era. Indeed, some classes of cancers (largely subtypes of sarcomas, lymphomas, and leukemias) have long been defined by simple and distinct patterns of chromosomal changes, or karyotypes, that, in many cases, feature a single pathognomonic somatic translocation of two genomic regions that creates a fusion oncogene (for example, the Philadelphia chromosome translocation in chronic myelogenous leukemia results in the BCR-ABL1 fusion oncogene) ( 1 ). Whereas many common cancers display genomic complexity consistent with multistep oncogenesis, such as carcinomas of breast and lung, cancers that are defined by translocations typically display simple karyotypes, suggesting that they were shaped by a single translocation. However, the cytogenetic simplicity of these cancers may mask more complex genomic events. On page 891 of this issue, Anderson et al. ( 2 ) report whole-genome sequencing (WGS) of 50 Ewing sarcomas (EWSs), an aggressive sarcoma that is defined by fusion between the EWS RNA binding protein 1 ( EWSR1 ) gene on chromosome 22 and an E26 transformation-specific (ETS) family transcription factor gene, either FLI1 at 11q24 or ERG at 21q11 ( 3 ). Anderson et al. show that ∼40% of EWSR1-FLI1 fusions and all EWSR1-ERG fusions arise via a complex rearrangement pattern called chromoplexy, which was first identified in prostate cancer ( 4 ). They suggest that chromoplexy “bursts” may be early initiating events in Ewing sarcomagenesis and mark a more aggressive form of the disease.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2018
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  • 10
    In: Cancer Cell, Elsevier BV, Vol. 32, No. 6 ( 2017-12), p. 884-
    Type of Medium: Online Resource
    ISSN: 1535-6108
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2017
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