375 results on '"Lynda Chin"'
Search Results
2. Global impact of somatic structural variation on the DNA methylome of human cancers
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Yiqun Zhang, Lixing Yang, Melanie Kucherlapati, Angela Hadjipanayis, Angeliki Pantazi, Christopher A. Bristow, Eunjung Alice Lee, Harshad S. Mahadeshwar, Jiabin Tang, Jianhua Zhang, Sahil Seth, Semin Lee, Xiaojia Ren, Xingzhi Song, Huandong Sun, Jonathan Seidman, Lovelace J. Luquette, Ruibin Xi, Lynda Chin, Alexei Protopopov, Peter J. Park, Raju Kucherlapati, and Chad J. Creighton
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Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Background Genomic rearrangements exert a heavy influence on the molecular landscape of cancer. New analytical approaches integrating somatic structural variants (SSVs) with altered gene features represent a framework by which we can assign global significance to a core set of genes, analogous to established methods that identify genes non-randomly targeted by somatic mutation or copy number alteration. While recent studies have defined broad patterns of association involving gene transcription and nearby SSV breakpoints, global alterations in DNA methylation in the context of SSVs remain largely unexplored. Results By data integration of whole genome sequencing, RNA sequencing, and DNA methylation arrays from more than 1400 human cancers, we identify hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of a somatic structural variant (SSV) breakpoint is recurrently associated with altered expression or DNA methylation, respectively, independently of copy number alterations. CGIs with SSV-associated increased methylation are predominantly promoter-associated, while CGIs with SSV-associated decreased methylation are enriched for gene body CGIs. Rearrangement of genomic regions normally having higher or lower methylation is often involved in SSV-associated CGI methylation alterations. Across cancers, the overall structural variation burden is associated with a global decrease in methylation, increased expression in methyltransferase genes and DNA damage response genes, and decreased immune cell infiltration. Conclusion Genomic rearrangement appears to have a major role in shaping the cancer DNA methylome, to be considered alongside commonly accepted mechanisms including histone modifications and disruption of DNA methyltransferases.
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- 2019
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3. A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases
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Yiqun Zhang, Lixing Yang, Melanie Kucherlapati, Fengju Chen, Angela Hadjipanayis, Angeliki Pantazi, Christopher A. Bristow, Eunjung A. Lee, Harshad S. Mahadeshwar, Jiabin Tang, Jianhua Zhang, Sahil Seth, Semin Lee, Xiaojia Ren, Xingzhi Song, Huandong Sun, Jonathan Seidman, Lovelace J. Luquette, Ruibin Xi, Lynda Chin, Alexei Protopopov, Wei Li, Peter J. Park, Raju Kucherlapati, and Chad J. Creighton
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Biology (General) ,QH301-705.5 - Abstract
Summary: A systematic cataloging of genes affected by genomic rearrangement, using multiple patient cohorts and cancer types, can provide insight into cancer-relevant alterations outside of exomes. By integrative analysis of whole-genome sequencing (predominantly low pass) and gene expression data from 1,448 cancers involving 18 histopathological types in The Cancer Genome Atlas, we identified hundreds of genes for which the nearby presence (within 100 kb) of a somatic structural variant (SV) breakpoint is associated with altered expression. While genomic rearrangements are associated with widespread copy-number alteration (CNA) patterns, approximately 1,100 genes—including overexpressed cancer driver genes (e.g., TERT, ERBB2, CDK12, CDK4) and underexpressed tumor suppressors (e.g., TP53, RB1, PTEN, STK11)—show SV-associated deregulation independent of CNA. SVs associated with the disruption of topologically associated domains, enhancer hijacking, or fusion transcripts are implicated in gene upregulation. For cancer-relevant pathways, SVs considerably expand our understanding of how genes are affected beyond point mutation or CNA. : Zhang et al. analyzed over 1,400 cancers by high- or low-pass whole-genome sequencing, focusing on patterns of structural variation. They saw a widespread impact of somatic structural variants on gene expression patterns, independent of copy-number alterations, involving key oncogenes and tumor suppressor genes. Keywords: cancer, structural variation, genomic rearrangement, whole genome sequencing, pan-cancer, TCGA
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- 2018
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4. Integrated Molecular Characterization of Testicular Germ Cell Tumors
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Hui Shen, Juliann Shih, Daniel P. Hollern, Linghua Wang, Reanne Bowlby, Satish K. Tickoo, Vésteinn Thorsson, Andrew J. Mungall, Yulia Newton, Apurva M. Hegde, Joshua Armenia, Francisco Sánchez-Vega, John Pluta, Louise C. Pyle, Rohit Mehra, Victor E. Reuter, Guilherme Godoy, Jeffrey Jones, Carl S. Shelley, Darren R. Feldman, Daniel O. Vidal, Davor Lessel, Tomislav Kulis, Flavio M. Cárcano, Kristen M. Leraas, Tara M. Lichtenberg, Denise Brooks, Andrew D. Cherniack, Juok Cho, David I. Heiman, Katayoon Kasaian, Minwei Liu, Michael S. Noble, Liu Xi, Hailei Zhang, Wanding Zhou, Jean C. ZenKlusen, Carolyn M. Hutter, Ina Felau, Jiashan Zhang, Nikolaus Schultz, Gad Getz, Matthew Meyerson, Joshua M. Stuart, Rehan Akbani, David A. Wheeler, Peter W. Laird, Katherine L. Nathanson, Victoria K. Cortessis, Katherine A. Hoadley, David Wheeler, Daniel Hughes, Kyle Covington, Joy C. Jayaseelan, Viktoriya Korchina, Lora Lewis, Jianhong Hu, HarshaVardhan Doddapaneni, Donna Muzny, Richard Gibbs, Daniel Hollern, Benjamin G. Vincent, Shengjie Chai, Christof C. Smith, J. Todd Auman, Yan Shi, Shaowu Meng, Tara Skelly, Donghui Tan, Umadevi Veluvolu, Piotr A. Mieczkowski, Corbin D. Jones, Matthew D. Wilkerson, Saianand Balu, Tom Bodenheimer, Alan P. Hoyle, Stuart R. Jefferys, Lisle E. Mose, Janae V. Simons, Matthew G. Soloway, Jeffrey Roach, Joel S. Parker, D. Neil Hayes, Charles M. Perou, Gordon Saksena, Carrie Cibulskis, Steven E. Schumacher, Rameen Beroukhim, Stacey B. Gabriel, Adrian Ally, Miruna Balasundaram, Rebecca Carlsen, Dorothy Cheung, Eric Chuah, Noreen Dhalla, Robert A. Holt, Steven J.M. Jones, Yussanne Ma, Michael Mayo, Richard A. Moore, A. Gordon Robertson, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Tina Wong, Marco A. Marra, Daniel J. Weisenberger, David J. Van Den Berg, Phillip H. Lai, Mario Berrios, Andrea Holbrook, Moiz S. Bootwalla, Dennis T. Maglinte, Debyani Chakravarty, Jianjiong Gao, Zachary Heins, Ritika Kundra, Angelica Ochoa, Chris Sander, Marc Ladanyi, Vesteinn Thorsson, Amie J. Radenbaugh, Nils Gehlenborg, Doug Voet, Pei Lin, Scott Frazer, Jaegil Kim, Michael S. Lawrence, Sam Meier, Timothy Defreitas, Lynda Chin, John N. Weinstein, Wenbin Liu, Gordon B. Mills, Yiling Lu, Leendert Looijenga, Alan H. Bryce, André L. Carvalho, Darren Feldman, Michael Ittmann, Seth Lerner, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Carmen Helsel, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Sandra Cottingham, David Chesla, Charles Saller, Katherine Tarvin, Luiz Fernando Lopes, Cristovam Scapulatempo-Neto, Natália D.A. Aredes, Wolter Oosterhuis, Ad Gillis, Hans Stoop, Wil Eijkenboom, George Sandusky, Sue Ellen Martin, Manju Aron, Siamak Daneshmand, Hooman Djaladat, David Quinn, Tanya Dorff, Jochen K. Lennerz, Leigh B. Thorne, Marija Gamulin, Zeljko Kastelan, Tvrtko Hudolin, Christian Kubisch, Lori Boice, Mei Huang, Amy H. Perou, W. Kimryn Rathmell, Todd Pihl, Yunhu Wan, Qiang Sun, Rashi Naresh, Sudha Chudamani, Jia Liu, Laxmi Lolla, Ye Wu, Martin L. Ferguson, Jean C. Zenklusen, Jiashan (Julia) Zhang, Margi Sheth, John A. Demchok, Liming Yang, Zhining Wang, Roy Tarnuzzer, Heidi J. Sofia, and Tanja M. Davidsen
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Biology (General) ,QH301-705.5 - Abstract
Summary: We studied 137 primary testicular germ cell tumors (TGCTs) using high-dimensional assays of genomic, epigenomic, transcriptomic, and proteomic features. These tumors exhibited high aneuploidy and a paucity of somatic mutations. Somatic mutation of only three genes achieved significance—KIT, KRAS, and NRAS—exclusively in samples with seminoma components. Integrated analyses identified distinct molecular patterns that characterized the major recognized histologic subtypes of TGCT: seminoma, embryonal carcinoma, yolk sac tumor, and teratoma. Striking differences in global DNA methylation and microRNA expression between histology subtypes highlight a likely role of epigenomic processes in determining histologic fates in TGCTs. We also identified a subset of pure seminomas defined by KIT mutations, increased immune infiltration, globally demethylated DNA, and decreased KRAS copy number. We report potential biomarkers for risk stratification, such as miRNA specifically expressed in teratoma, and others with molecular diagnostic potential, such as CpH (CpA/CpC/CpT) methylation identifying embryonal carcinomas. : Shen et al. identify molecular characteristics that classify testicular germ cell tumor types, including a separate subset of seminomas defined by KIT mutations. This provides a set of candidate biomarkers for risk stratification and potential therapeutic targeting. Keywords: The Cancer Genome Atlas, testicular germ cell tumors, seminoma, nonseminoma, DNA methylation, exome sequencing, KIT, copy number, miR-375
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- 2018
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5. Modeling Genomic Instability and Selection Pressure in a Mouse Model of Melanoma
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Lawrence N. Kwong, Lihua Zou, Sharmeen Chagani, Chandra Sekhar Pedamallu, Mingguang Liu, Shan Jiang, Alexei Protopopov, Jianhua Zhang, Gad Getz, and Lynda Chin
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mouse models ,genomic instability ,selection pressure ,tumor evolution ,tumor genomics ,melanoma ,drug resistance ,telomere dysfunction ,evolution bottlenecks ,copy number aberrations ,Biology (General) ,QH301-705.5 - Abstract
Tumor evolution is an iterative process of selection for pro-oncogenic aberrations. This process can be accelerated by genomic instability, but how it interacts with different selection bottlenecks to shape the evolving genomic landscape remains understudied. Here, we assessed tumor initiation and therapy resistance bottlenecks in mouse models of melanoma, with or without genomic instability. At the initiation bottleneck, whole-exome sequencing revealed that drug-naive tumors were genomically silent, and this was surprisingly unaffected when genomic instability was introduced via telomerase inactivation. We hypothesize that the strong engineered alleles created low selection pressure. At the therapy resistance bottleneck, strong selective pressure was applied using a BRAF inhibitor. In the absence of genomic instability, tumors acquired a non-genomic drug resistance mechanism. By contrast, telomerase-deficient, drug-resistant melanomas acquired highly recurrent copy number gains. These proof-of-principle experiments demonstrate how different selection pressures can interact with genomic instability to impact tumor evolution.
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- 2017
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6. Genomic and immune heterogeneity are associated with differential responses to therapy in melanoma
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Alexandre Reuben, Christine N. Spencer, Peter A. Prieto, Vancheswaran Gopalakrishnan, Sangeetha M. Reddy, John P. Miller, Xizeng Mao, Mariana Petaccia De Macedo, Jiong Chen, Xingzhi Song, Hong Jiang, Pei-Ling Chen, Hannah C. Beird, Haven R. Garber, Whijae Roh, Khalida Wani, Eveline Chen, Cara Haymaker, Marie-Andrée Forget, Latasha D. Little, Curtis Gumbs, Rebecca L. Thornton, Courtney W. Hudgens, Wei-Shen Chen, Jacob Austin-Breneman, Robert Szczepaniak Sloane, Luigi Nezi, Alexandria P. Cogdill, Chantale Bernatchez, Jason Roszik, Patrick Hwu, Scott E. Woodman, Lynda Chin, Hussein Tawbi, Michael A. Davies, Jeffrey E. Gershenwald, Rodabe N. Amaria, Isabella C. Glitza, Adi Diab, Sapna P. Patel, Jianhua Hu, Jeffrey E. Lee, Elizabeth A. Grimm, Michael T. Tetzlaff, Alexander J. Lazar, Ignacio I. Wistuba, Karen Clise-Dwyer, Brett W. Carter, Jianhua Zhang, P. Andrew Futreal, Padmanee Sharma, James P. Allison, Zachary A. Cooper, and Jennifer A. Wargo
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Medicine ,Genetics ,QH426-470 - Abstract
Melanoma: Tumor differences within a patient may explain heterogeneous responses Patients with metastatic melanoma display molecular and immune differences across tumor sites associated with differential drug responses. A team led by Jennifer Wargo from the University of Texas MD Anderson Cancer Center, Houston, USA, studied the radiological responses of 60 patients with metastatic melanoma, half of whom received targeted drug therapy and half of whom received an immune checkpoint inhibitor. The majority (83%) showed differences in responses across metastases. The group then profiled tumors in a subset, and found molecular and immune heterogeneity in different tumors within the same patient. Heterogeneity in mutational and immune profiles within tumors from individual patients could explain differences in treatment response. Knowing this, the authors emphasize the importance of acquiring biopsies from more than one tumor site in order to best tailor therapies to the features of metastatic cancer.
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- 2017
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7. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression
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Petko Fiziev, Kadir C. Akdemir, John P. Miller, Emily Z. Keung, Neha S. Samant, Sneha Sharma, Christopher A. Natale, Christopher J. Terranova, Mayinuer Maitituoheti, Samirkumar B. Amin, Emmanuel Martinez-Ledesma, Mayura Dhamdhere, Jacob B. Axelrad, Amiksha Shah, Christine S. Cheng, Harshad Mahadeshwar, Sahil Seth, Michelle C. Barton, Alexei Protopopov, Kenneth Y. Tsai, Michael A. Davies, Benjamin A. Garcia, Ido Amit, Lynda Chin, Jason Ernst, and Kunal Rai
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chromatin state ,melanoma ,HDAC ,CBP ,epigenome ,ChIP-seq ,histone modifications ,DUSP5 ,Biology (General) ,QH301-705.5 - Abstract
The extent and nature of epigenomic changes associated with melanoma progression is poorly understood. Through systematic epigenomic profiling of 35 epigenetic modifications and transcriptomic analysis, we define chromatin state changes associated with melanomagenesis by using a cell phenotypic model of non-tumorigenic and tumorigenic states. Computation of specific chromatin state transitions showed loss of histone acetylations and H3K4me2/3 on regulatory regions proximal to specific cancer-regulatory genes in important melanoma-driving cell signaling pathways. Importantly, such acetylation changes were also observed between benign nevi and malignant melanoma human tissues. Intriguingly, only a small fraction of chromatin state transitions correlated with expected changes in gene expression patterns. Restoration of acetylation levels on deacetylated loci by histone deacetylase (HDAC) inhibitors selectively blocked excessive proliferation in tumorigenic cells and human melanoma cells, suggesting functional roles of observed chromatin state transitions in driving hyperproliferative phenotype. Through these results, we define functionally relevant chromatin states associated with melanoma progression.
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- 2017
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8. In Vivo Functional Platform Targeting Patient-Derived Xenografts Identifies WDR5-Myc Association as a Critical Determinant of Pancreatic Cancer
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Alessandro Carugo, Giannicola Genovese, Sahil Seth, Luigi Nezi, Johnathon Lynn Rose, Daniela Bossi, Angelo Cicalese, Parantu Krushnakant Shah, Andrea Viale, Piergiorgio Francesco Pettazzoni, Kadir Caner Akdemir, Christopher Aaron Bristow, Frederick Scott Robinson, James Tepper, Nora Sanchez, Sonal Gupta, Marcos Roberto Estecio, Virginia Giuliani, Gaetano Ivan Dellino, Laura Riva, Wantong Yao, Maria Emilia Di Francesco, Tessa Green, Carolina D’Alesio, Denise Corti, Ya’an Kang, Philip Jones, Huamin Wang, Jason Bates Fleming, Anirban Maitra, Pier Giuseppe Pelicci, Lynda Chin, Ronald Anthony DePinho, Luisa Lanfrancone, Timothy Paul Heffernan, and Giulio Francesco Draetta
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Biology (General) ,QH301-705.5 - Abstract
Current treatment regimens for pancreatic ductal adenocarcinoma (PDAC) yield poor 5-year survival, emphasizing the critical need to identify druggable targets essential for PDAC maintenance. We developed an unbiased and in vivo target discovery approach to identify molecular vulnerabilities in low-passage and patient-derived PDAC xenografts or genetically engineered mouse model-derived allografts. Focusing on epigenetic regulators, we identified WDR5, a core member of the COMPASS histone H3 Lys4 (H3K4) MLL (1–4) methyltransferase complex, as a top tumor maintenance hit required across multiple human and mouse tumors. Mechanistically, WDR5 functions to sustain proper execution of DNA replication in PDAC cells, as previously suggested by replication stress studies involving MLL1, and c-Myc, also found to interact with WDR5. We indeed demonstrate that interaction with c-Myc is critical for this function. By showing that ATR inhibition mimicked the effects of WDR5 suppression, these data provide rationale to test ATR and WDR5 inhibitors for activity in this disease.
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- 2016
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9. Post-translational Regulation of Cas9 during G1 Enhances Homology-Directed Repair
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Tony Gutschner, Monika Haemmerle, Giannicola Genovese, Giulio F. Draetta, and Lynda Chin
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CRISPR ,cell cycle ,genome editing ,MALAT1 ,homologous recombination ,proteolysis ,synthetic biology ,Biology (General) ,QH301-705.5 - Abstract
CRISPR/Cas9 induces DNA double-strand breaks that are repaired by cell-autonomous repair pathways, namely, non-homologous end-joining (NHEJ), or homology-directed repair (HDR). While HDR is absent in G1, NHEJ is active throughout the cell cycle and, thus, is largely favored over HDR. We devised a strategy to increase HDR by directly synchronizing the expression of Cas9 with cell-cycle progression. Fusion of Cas9 to the N-terminal region of human Geminin converted this gene-editing protein into a substrate for the E3 ubiquitin ligase complex APC/Cdh1, resulting in a cell-cycle-tailored expression with low levels in G1 but high expression in S/G2/M. Importantly, Cas9-hGem(1/110) increased the rate of HDR by up to 87% compared to wild-type Cas9. Future developments may enable high-resolution expression of genome engineering proteins, which might increase HDR rates further, and may contribute to a better understanding of DNA repair pathways due to spatiotemporal control of DNA damage induction.
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- 2016
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10. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles
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Farshad Farshidfar, Siyuan Zheng, Marie-Claude Gingras, Yulia Newton, Juliann Shih, A. Gordon Robertson, Toshinori Hinoue, Katherine A. Hoadley, Ewan A. Gibb, Jason Roszik, Kyle R. Covington, Chia-Chin Wu, Eve Shinbrot, Nicolas Stransky, Apurva Hegde, Ju Dong Yang, Ed Reznik, Sara Sadeghi, Chandra Sekhar Pedamallu, Akinyemi I. Ojesina, Julian M. Hess, J. Todd Auman, Suhn K. Rhie, Reanne Bowlby, Mitesh J. Borad, Rehan Akbani, Loretta K. Allotey, Adrian Ally, Domenico Alvaro, Jesper B. Andersen, Elizabeth L. Appelbaum, Arshi Arora, Miruna Balasundaram, Saianand Balu, Nabeel Bardeesy, Oliver F. Bathe, Stephen B. Baylin, Rameen Beroukhim, Mario Berrios, Tom Bodenheimer, Lori Boice, Moiz S. Bootwalla, Jay Bowen, Maria Consiglia Bragazzi, Denise Brooks, Vincenzo Cardinale, Rebecca Carlsen, Guido Carpino, Andre L. Carvalho, Roongruedee Chaiteerakij, Vishal C. Chandan, Andrew D. Cherniack, Lynda Chin, Juok Cho, Gina Choe, Eric Chuah, Sudha Chudamani, Carrie Cibulskis, Matthew G. Cordes, Daniel Crain, Erin Curley, Agostino Maria De Rose, Timothy Defreitas, John A. Demchok, Vikram Deshpande, Noreen Dhalla, Li Ding, Kimberley Evason, Ina Felau, Martin L. Ferguson, Wai Chin Foo, Antonio Franchitto, Scott Frazer, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Stacey B. Gabriel, Johanna Gardner, Julie M. Gastier-Foster, Eugenio Gaudio, Nils Gehlenborg, Giannicola Genovese, Mark Gerken, Gad Getz, Nasra H. Giama, Richard A. Gibbs, Felice Giuliante, Gian Luca Grazi, D. Neil Hayes, Apurva M. Hegde, David I. Heiman, Andrea Holbrook, Robert A. Holt, Alan P. Hoyle, Mei Huang, Carolyn M. Hutter, Stuart R. Jefferys, Steven J.M. Jones, Corbin D. Jones, Katayoon Kasaian, Robin K. Kelley, Jaegil Kim, David E. Kleiner, Jean-Pierre A. Kocher, Lawrence N. Kwong, Phillip H. Lai, Peter W. Laird, Michael S. Lawrence, Kristen M. Leraas, Tara M. Lichtenberg, Pei Lin, Wenbin Liu, Jia Liu, Laxmi Lolla, Yiling Lu, Yussanne Ma, David Mallery, Elaine R. Mardis, Marco A. Marra, Marcus M. Matsushita, Michael Mayo, Michael D. McLellan, Autumn J. McRee, Sam Meier, Shaowu Meng, Matthew Meyerson, Piotr A. Mieczkowski, Christopher A. Miller, Gordon B. Mills, Richard A. Moore, Scott Morris, Lisle E. Mose, Catherine D. Moser, Taofic Mounajjed, Andrew J. Mungall, Karen Mungall, Bradley A. Murray, Rashi Naresh, Michael S. Noble, Daniel R. O’Brien, Joel S. Parker, Tushar C. Patel, Joseph Paulauskis, Robert Penny, Charles M. Perou, Amy H. Perou, Todd Pihl, Amie J. Radenbaugh, Nilsa C. Ramirez, W. Kimryn Rathmell, Jeffrey Roach, Lewis R. Roberts, Gordon Saksena, Chris Sander, Jacqueline E. Schein, Heather K. Schmidt, Steven E. Schumacher, Candace Shelton, Troy Shelton, Ronglai Shen, Margi Sheth, Yan Shi, Rachna Shroff, Janae V. Simons, Payal Sipahimalani, Tara Skelly, Heidi J. Sofia, Matthew G. Soloway, Hubert Stoppler, Josh Stuart, Qiang Sun, Angela Tam, Donghui Tan, Roy Tarnuzzer, Nina Thiessen, Leigh B. Thorne, Michael S. Torbenson, David J. Van Den Berg, Umadevi Veluvolu, Roel G.W. Verhaak, Doug Voet, Yunhu Wan, Zhining Wang, John N. Weinstein, Daniel J. Weisenberger, David A. Wheeler, Richard K. Wilson, Lisa Wise, Tina Wong, Ye Wu, Liu Xi, Liming Yang, Jean C. Zenklusen, Hailei Zhang, Jiashan (Julia) Zhang, and Erik Zmuda
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Biology (General) ,QH301-705.5 - Published
- 2017
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11. Somatic mutations of PIK3R1 promote gliomagenesis.
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Steven N Quayle, Jennifer Y Lee, Lydia W T Cheung, Li Ding, Ruprecht Wiedemeyer, Robert W Dewan, Emmet Huang-Hobbs, Li Zhuang, Richard K Wilson, Keith L Ligon, Gordon B Mills, Lewis C Cantley, and Lynda Chin
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Medicine ,Science - Abstract
The phosphoinositide 3-kinase (PI3K) pathway is targeted for frequent alteration in glioblastoma (GBM) and is one of the core GBM pathways defined by The Cancer Genome Atlas. Somatic mutations of PIK3R1 are observed in multiple tumor types, but the tumorigenic activity of these mutations has not been demonstrated in GBM. We show here that somatic mutations in the iSH2 domain of PIK3R1 act as oncogenic driver events. Specifically, introduction of a subset of the mutations identified in human GBM, in the nSH2 and iSH2 domains, increases signaling through the PI3K pathway and promotes tumorigenesis of primary normal human astrocytes in an orthotopic xenograft model. Furthermore, we show that cells that are dependent on mutant P85α-mediated PI3K signaling exhibit increased sensitivity to a small molecule inhibitor of AKT. Together, these results suggest that GBM patients whose tumors carry mutant PIK3R1 alleles may benefit from treatment with inhibitors of AKT.
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- 2012
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12. Correction: Targeting EGFR Induced Oxidative Stress by PARP1 Inhibition in Glioblastoma Therapy.
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Masayuki Nitta, David Kozono, Richard Kennedy, Jayne Stommel, Kimberly Ng, Pascal O. Zinn, Deepa Kushwaha, Santosh Kesari, Frank Furnari, Katherine A. Hoadley, Lynda Chin, Ronald A. DePinho, Webster K. Cavenee, Alan D'Andrea, and Clark C. Chen
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Medicine ,Science - Published
- 2011
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13. A role for ATF2 in regulating MITF and melanoma development.
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Meera Shah, Anindita Bhoumik, Vikas Goel, Antimone Dewing, Wolfgang Breitwieser, Harriet Kluger, Stan Krajewski, Maryla Krajewska, Jason Dehart, Eric Lau, David M Kallenberg, Hyeongnam Jeong, Alexey Eroshkin, Dorothy C Bennett, Lynda Chin, Marcus Bosenberg, Nic Jones, and Ze'ev A Ronai
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Genetics ,QH426-470 - Abstract
The transcription factor ATF2 has been shown to attenuate melanoma susceptibility to apoptosis and to promote its ability to form tumors in xenograft models. To directly assess ATF2's role in melanoma development, we crossed a mouse melanoma model (Nras(Q61K)::Ink4a⁻/⁻) with mice expressing a transcriptionally inactive form of ATF2 in melanocytes. In contrast to 7/21 of the Nras(Q61K)::Ink4a⁻/⁻ mice, only 1/21 mice expressing mutant ATF2 in melanocytes developed melanoma. Gene expression profiling identified higher MITF expression in primary melanocytes expressing transcriptionally inactive ATF2. MITF downregulation by ATF2 was confirmed in the skin of Atf2⁻/⁻ mice, in primary human melanocytes, and in 50% of human melanoma cell lines. Inhibition of MITF transcription by MITF was shown to be mediated by ATF2-JunB-dependent suppression of SOX10 transcription. Remarkably, oncogenic BRAF (V600E)-dependent focus formation of melanocytes on soft agar was inhibited by ATF2 knockdown and partially rescued upon shMITF co-expression. On melanoma tissue microarrays, a high nuclear ATF2 to MITF ratio in primary specimens was associated with metastatic disease and poor prognosis. Our findings establish the importance of transcriptionally active ATF2 in melanoma development through fine-tuning of MITF expression.
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- 2010
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14. Integrative genome comparison of primary and metastatic melanomas.
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Omar Kabbarah, Cristina Nogueira, Bin Feng, Rosalynn M Nazarian, Marcus Bosenberg, Min Wu, Kenneth L Scott, Lawrence N Kwong, Yonghong Xiao, Carlos Cordon-Cardo, Scott R Granter, Sridhar Ramaswamy, Todd Golub, Lyn M Duncan, Stephan N Wagner, Cameron Brennan, and Lynda Chin
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Medicine ,Science - Abstract
A cardinal feature of malignant melanoma is its metastatic propensity. An incomplete view of the genetic events driving metastatic progression has been a major barrier to rational development of effective therapeutics and prognostic diagnostics for melanoma patients. In this study, we conducted global genomic characterization of primary and metastatic melanomas to examine the genomic landscape associated with metastatic progression. In addition to uncovering three genomic subclasses of metastastic melanomas, we delineated 39 focal and recurrent regions of amplification and deletions, many of which encompassed resident genes that have not been implicated in cancer or metastasis. To identify progression-associated metastasis gene candidates, we applied a statistical approach, Integrative Genome Comparison (IGC), to define 32 genomic regions of interest that were significantly altered in metastatic relative to primary melanomas, encompassing 30 resident genes with statistically significant expression deregulation. Functional assays on a subset of these candidates, including MET, ASPM, AKAP9, IMP3, PRKCA, RPA3, and SCAP2, validated their pro-invasion activities in human melanoma cells. Validity of the IGC approach was further reinforced by tissue microarray analysis of Survivin showing significant increased protein expression in thick versus thin primary cutaneous melanomas, and a progression correlation with lymph node metastases. Together, these functional validation results and correlative analysis of human tissues support the thesis that integrated genomic and pathological analyses of staged melanomas provide a productive entry point for discovery of melanoma metastases genes.
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- 2010
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15. Targeting EGFR induced oxidative stress by PARP1 inhibition in glioblastoma therapy.
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Masayuki Nitta, David Kozono, Richard Kennedy, Jayne Stommel, Kimberly Ng, Pascal O Zinn, Deepa Kushwaha, Santosh Kesari, Maria-del-Mar Inda, Jill Wykosky, Frank Furnari, Katherine A Hoadley, Lynda Chin, Ronald A DePinho, Webster K Cavenee, Alan D'Andrea, and Clark C Chen
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Medicine ,Science - Abstract
Despite the critical role of Epidermal Growth Factor Receptor (EGFR) in glioblastoma pathogenesis, EGFR targeted therapies have achieved limited clinical efficacy. Here we propose an alternate therapeutic strategy based on the conceptual framework of non-oncogene addiction. A directed RNAi screen revealed that glioblastoma cells over-expressing EGFRvIII, an oncogenic variant of EGFR, become hyper-dependent on a variety of DNA repair genes. Among these, there was an enrichment of Base Excision Repair (BER) genes required for the repair of Reactive Oxygen Species (ROS)-induced DNA damage, including poly-ADP ribose polymerase 1 (PARP1). Subsequent studies revealed that EGFRvIII over-expression in glioblastoma cells caused increased levels of ROS, DNA strand break accumulation, and genome instability. In a panel of primary glioblastoma lines, sensitivity to PARP1 inhibition correlated with the levels of EGFR activation and oxidative stress. Gene expression analysis indicated that reduced expression of BER genes in glioblastomas with high EGFR expression correlated with improved patient survival. These observations suggest that oxidative stress secondary to EGFR hyper-activation necessitates increased cellular reliance on PARP1 mediated BER, and offer critical insights into clinical trial design.
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- 2010
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16. BRAF activation initiates but does not maintain invasive prostate adenocarcinoma.
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Joseph H Jeong, Zhenxiong Wang, Alexander S Guimaraes, Xuesong Ouyang, Jose L Figueiredo, Zhihu Ding, Shan Jiang, Isil Guney, Gyeong Hoon Kang, Eyoung Shin, William C Hahn, Massimo F Loda, Cory Abate-Shen, Ralph Weissleder, and Lynda Chin
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Medicine ,Science - Abstract
Prostate cancer is the second leading cause of cancer-related deaths in men. Activation of MAP kinase signaling pathway has been implicated in advanced and androgen-independent prostate cancers, although formal genetic proof has been lacking. In the course of modeling malignant melanoma in a tyrosinase promoter transgenic system, we developed a genetically-engineered mouse (GEM) model of invasive prostate cancers, whereby an activating mutation of BRAF(V600E)--a mutation found in approximately 10% of human prostate tumors--was targeted to the epithelial compartment of the prostate gland on the background of Ink4a/Arf deficiency. These GEM mice developed prostate gland hyperplasia with progression to rapidly growing invasive adenocarcinoma without evidence of AKT activation, providing genetic proof that activation of MAP kinase signaling is sufficient to drive prostate tumorigenesis. Importantly, genetic extinction of BRAF(V600E) in established prostate tumors did not lead to tumor regression, indicating that while sufficient to initiate development of invasive prostate adenocarcinoma, BRAF(V600E) is not required for its maintenance.
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- 2008
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17. Supplementary Table S5 from Targeting YAP-Dependent MDSC Infiltration Impairs Tumor Progression
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Ronald A. DePinho, Y. Alan Wang, Lynda Chin, Mark J. McArthur, Christopher J. Logothetis, Patricia Troncoso, Qing Chang, Liren Li, Yanxia Shi, Zhihu Ding, Xiaolu Pan, Wantong Yao, Eun-Jung Jin, Baoli Hu, Pingping Hou, Sunada Khadka, Xiaoying Shang, Di Zhao, Tim Heffernan, Trang N. Tieu, Vandhana Ramamoorthy, Zhenglin Guo, Neelay Bhaskar Patel, Chang-Jiun Wu, Avnish Kapoor, Elsa M. Li-Ning-Tapia, Jianhua Zhang, Sujun Hua, Ramakrishna Konaparthi, Kun Zhao, Zhuangna Fang, Shan Jiang, Chia Chin Wu, Pingna Deng, Prasenjit Dey, Xin Lu, and Guocan Wang
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Overlapped genes between Genes upregulated in Ptenpc-/-Smad4pc-/- tumors as compared to Ptenpc-/- tumors ({greater than or equal to}2 fold) and genes upregulated in GFP+ tumors cells from Ptenpc-/-Smad4pc-/- mice as compared to Tomato+ cells ({greater than or equal to}4 fold).
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- 2023
18. Supplementary Methods, Figure Legends, Table Legends from Dual Roles of RNF2 in Melanoma Progression
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Lynda Chin, Jason Ernst, Alexander J. Lazar, Suhendan Ekmekcioglu, James W. Horner, Timothy P. Heffernan, Denai R. Milton, Michelle C. Barton, Elizabeth A. Grimm, Dong Yang, Amiksha Shah, Jacob B. Axelrad, Maura Williams, Neha S. Samant, Sneha Sharma, Emily Z. Keung, Chang-Jiun Wu, Petko Fiziev, Lawrence N. Kwong, Kadir C. Akdemir, and Kunal Rai
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This file contains supplementary methods, supplementary figure legends, supplementary table legends and supplementary references.
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- 2023
19. Supplementary Figures 1 - 5 from Dual Roles of RNF2 in Melanoma Progression
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Lynda Chin, Jason Ernst, Alexander J. Lazar, Suhendan Ekmekcioglu, James W. Horner, Timothy P. Heffernan, Denai R. Milton, Michelle C. Barton, Elizabeth A. Grimm, Dong Yang, Amiksha Shah, Jacob B. Axelrad, Maura Williams, Neha S. Samant, Sneha Sharma, Emily Z. Keung, Chang-Jiun Wu, Petko Fiziev, Lawrence N. Kwong, Kadir C. Akdemir, and Kunal Rai
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Supplementary Figure 1. Western blots. Supplementary Figure 2. Graphs showing tumor volume from mice following intradermal injection of (A) HMEL-BRAF^V600E cells, (B) WM115 cells, (C) 1205 Lu cells, and (D) pMEL-NRAS^G12D overexpressing GFP, RNF2 wild-type or catalytic mutant derivatives (R70C or I53S). Supplementary Figure 3. (A) RNF expression in the melanoma expression data for normal skin, nevi, and primary tumors. Supplementary Figure 4. (A) Heat map showing clustering of top 10 percent deregulated genes in duplicates of expression data from RNF2^WT overexpressing compared to GFP overexpressing HMEL-BRAF^V600E cells. Supplementary Figure 5. Chromatin state analysis on HMEL-BRAF^V600E cells.
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20. Supplementary Table 3 from Dual Roles of RNF2 in Melanoma Progression
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Lynda Chin, Jason Ernst, Alexander J. Lazar, Suhendan Ekmekcioglu, James W. Horner, Timothy P. Heffernan, Denai R. Milton, Michelle C. Barton, Elizabeth A. Grimm, Dong Yang, Amiksha Shah, Jacob B. Axelrad, Maura Williams, Neha S. Samant, Sneha Sharma, Emily Z. Keung, Chang-Jiun Wu, Petko Fiziev, Lawrence N. Kwong, Kadir C. Akdemir, and Kunal Rai
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Description of states in 45-state chromatin state model.This table describes the biological annotation of each chromatin state in 50-state chromatin model from HMEL-BRAFV600E cells from ChromHMM program.
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- 2023
21. Supplementary Figures 1 - 13 from Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade
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Jennifer A. Wargo, Lynda Chin, James P. Allison, Padmanee Sharma, Jorge Blando, P. Andrew Futreal, Jianhua Hu, Arlene H. Sharpe, Willem W. Overwijk, Wencai Ma, R. Eric Davis, Victor Prieto, Lawrence N. Kwong, Rodabe N. Amaria, Ignacio I. Wistuba, Luis M. Vence, Scott E. Woodman, Isabella C. Glitza, Adi Diab, Wen-Jen Hwu, Patrick Hwu, Sapna P. Patel, Alexander J. Lazar, Lauren Haydu, Jeffrey E. Gershenwald, Michael A. Davies, Russell J. Broaddus, Michael T. Tetzlaff, Wei-Shen Chen, Sangeetha M. Reddy, Qing Chang, Hong Jiang, Jacob L. Austin-Breneman, Mariana Petaccia De Macedo, Khalida Wani, Vancheswaran Gopalakrishnan, Roland L. Bassett, John P. Miller, Peter A. Prieto, Christine N. Spencer, Zachary A. Cooper, Alexandre Reuben, Whijae Roh, and Pei-Ling Chen
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Supplementary Figure 1. Immune profiling of pre-treatment, on-treatment and progression CTLA-4 blockade samples by immunohistochemistry. Supplementary Figure 2. Myeloid cell profiling of pre-treatment, on-treatment and progression CTLA-4 blockade samples by immunohistochemistry. Supplementary Figure 3. Increased contact between CD8 T cells and CD68 myeloid cells in non-responding patients to anti-CTLA-4 and anti-PD-1 therapy at pre-treatment CTLA-4 blockade, pre-treatment PD-1 blockade, and on-treatment PD-1 blockade time points. Supplementary Figure 4. Immune profiling of pre anti-PD-1, on-treatment anti-PD-1 and progression anti-PD-1 samples by immunohistochemistry. Supplementary Figure 5. Longitudinal increase in CD8, PD-1, and PD-L1 expression in responders to anti-PD-1 therapy. Supplementary Figure 6. Relative increase in CD8 T cell infiltrate at tumor center in responders to anti-PD-1 on treatment. Supplementary Figure 7. Significant increase in immune infiltrate between responders and non-responders to PD-1 blockade in absence of prior anti-CTLA-4 therapy. Supplementary Figure 8. Immune profiling of myeloid cells atpre-treatment and on-treatment PD-1 blockade time pointsby immunohistochemistry. Supplementary Figure 9. Heatmap of 54 NanoString samples. Supplementary Figure 10. Gene-specific NanoString concordance with immune profiling by IHC in pre-treatment, on-treatment and progression CTLA-4 blockade samples. Supplementary Figure 11. Gene-specific NanoString concordance with immune profiling by IHC in pre-treatment, on-treatment and progression PD-1 blockade samples. Supplementary Figure 12. Prior CTLA-4 blockade is not required for PD-1 early on-treatment profile. Supplementary Figure 13. Hierarchical clustering of gene expression across 54 samples confirms lack of batch effect.
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22. Supplementary Tables 1-10 from microRNA Regulatory Network Inference Identifies miR-34a as a Novel Regulator of TGF-β Signaling in Glioblastoma
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Lynda Chin, James J. Collins, David L. Rimm, Hongwu Zheng, Cameron Brennan, Wolf Ruprecht Wiedemeyer, Katherine Dunn, Lawrence Kwong, Hailei Zhang, Jianhua Zhang, Yonghong Xiao, Sharmistha Sarkar, Chang-Jiun Wu, Haoqiang Ying, Simona Colla, Kunal Rai, Steven N. Quayle, Papia Ghosh, Jason Hanna, Benito Campos, Sachet A. Shukla, Ayla Ergun, and Giannicola Genovese
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PDF file - 1.1MB, Supplementary Table 1: list of 290 TCGA samples used in the study. Supplementary Table 2: list of miR-mRNA edges identified by CLR. Supplementary Table 3: list of putative direct miR-mRNA edges in the network. Supplementary Table 4: miR-mRNA edges identified as unique to each of the 4 molecular subtypes. (A) Classical (B) Neural (C) Proneural (D) Mesenchymal. Supplementary Table 5: miR and mRNA nodes in regions of copy number aberration in the sub-network corresponding to the 8 discriminatory miRs. Supplementary Table 6: survival analysis results for the 8 discriminatory miRs. Supplementary Table 7: multivariate Cox regression analysis in the TCGA dataset and in the 4 molecular subclasses. Supplementary Table 8: patients' characteristics (validation cohort, n=220). Supplementary Table 9: AQUA values (raw data) for miR-34a expression in Glioblastoma TMAs (validation cohort). Supplementary Table 10: list of transcription factors enriched in the PN subtype
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23. Supplementary Figure Legends from Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade
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Jennifer A. Wargo, Lynda Chin, James P. Allison, Padmanee Sharma, Jorge Blando, P. Andrew Futreal, Jianhua Hu, Arlene H. Sharpe, Willem W. Overwijk, Wencai Ma, R. Eric Davis, Victor Prieto, Lawrence N. Kwong, Rodabe N. Amaria, Ignacio I. Wistuba, Luis M. Vence, Scott E. Woodman, Isabella C. Glitza, Adi Diab, Wen-Jen Hwu, Patrick Hwu, Sapna P. Patel, Alexander J. Lazar, Lauren Haydu, Jeffrey E. Gershenwald, Michael A. Davies, Russell J. Broaddus, Michael T. Tetzlaff, Wei-Shen Chen, Sangeetha M. Reddy, Qing Chang, Hong Jiang, Jacob L. Austin-Breneman, Mariana Petaccia De Macedo, Khalida Wani, Vancheswaran Gopalakrishnan, Roland L. Bassett, John P. Miller, Peter A. Prieto, Christine N. Spencer, Zachary A. Cooper, Alexandre Reuben, Whijae Roh, and Pei-Ling Chen
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Supplementary Figure Legends
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- 2023
24. Supplementary Methods from Biomarker Accessible and Chemically Addressable Mechanistic Subtypes of BRAF Melanoma
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Michael A. White, Ralf Kittler, Georgina V. Long, Helen Rizos, Lynda Chin, Noelle S. Williams, Jef K. De Brabander, Yonghao Yu, Jennifer A. Wargo, Michael A. Davies, Claudia Wellbrock, Ralph J. Deberardinis, Kakajan Komurov, Jessica Sudderth, Michael P. Smith, Ugur Eskiocak, Tracy I. Rosales, Aubhishek Zaman, Ming Ding, Jose Garcia-Rodriguez, Changguang Wang, Caroline G. Humphries, Hailei Zhang, Rahul K. Kollipara, Saurabh Mendiratta, Elizabeth A. McMillan, and Banu Eskiocak
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Extended Experimental Methods
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25. Supplementary Text, Figure Legends, Figures S1-S12 from Biomarker Accessible and Chemically Addressable Mechanistic Subtypes of BRAF Melanoma
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Michael A. White, Ralf Kittler, Georgina V. Long, Helen Rizos, Lynda Chin, Noelle S. Williams, Jef K. De Brabander, Yonghao Yu, Jennifer A. Wargo, Michael A. Davies, Claudia Wellbrock, Ralph J. Deberardinis, Kakajan Komurov, Jessica Sudderth, Michael P. Smith, Ugur Eskiocak, Tracy I. Rosales, Aubhishek Zaman, Ming Ding, Jose Garcia-Rodriguez, Changguang Wang, Caroline G. Humphries, Hailei Zhang, Rahul K. Kollipara, Saurabh Mendiratta, Elizabeth A. McMillan, and Banu Eskiocak
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Supplemental Figure S1. Integrative Analysis of Functional Genomics and Copy Number Variation in Melanoma Cells and Tissues, Supplemental Figure S2. Elastic Net Derived Biomarker Results for Melanoma Survival Genes and Detection of These Biomarkers in TCGA SKCM, Supplemental Figure S3. The SOX10 Regulatory Network Supporting Cell Autonomous Melanoma Cell Growth and Survival, Supplemental Figure S4. SOX10 Addiction Specifies Sensitivity of BRAF Mutant Melanomas to BRAF and MEK Inhibitors In Vitro, Related to Figure 1, Supplemental Figure S5. SOX10 Addiction Specifies Sensitivity of BRAF Mutant Melanomas to BRAF and MEK Inhibitors In Patients, Related to Figure 2, Supplemental Figure S6. Bicluster of melanoma cell lines and chemical compounds in McDermott/Benes GDSC dataset, Related to Figure 3, Supplemental Figure S7. Nomination of TBK1 as a Therapeutic Target for Drug-Resistant Melanoma, Related to Figure 3, Supplemental Figure S8. TBK1/IKKε-Addiction is Conserved In Vivo, Related to Figure 4, Supplemental Figure S9. TBK1/IKKε-Addiction Corresponds to a Cell Autonomous Innate Immune Melanoma Subtype, Related to Figure 5, Supplemental Figure S10. TBK1/IKKε Activate AKT and YAP to Support Survival of the Cell-autonomous Immune Melanoma Subtype, Related to Figure 6, Supplemental Figure S11. 13C glucose and 13C glutamine metabolism at 30m and 2h, Related to Figure 7 and Supplemental Fig. S7, Supplemental Figure S12. Distinct Epigenetic Cell Fate Programs Specify TBK1/IKKε Addiction, Related to Figure 7.
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26. Supplementary Figures 1-13 from microRNA Regulatory Network Inference Identifies miR-34a as a Novel Regulator of TGF-β Signaling in Glioblastoma
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Lynda Chin, James J. Collins, David L. Rimm, Hongwu Zheng, Cameron Brennan, Wolf Ruprecht Wiedemeyer, Katherine Dunn, Lawrence Kwong, Hailei Zhang, Jianhua Zhang, Yonghong Xiao, Sharmistha Sarkar, Chang-Jiun Wu, Haoqiang Ying, Simona Colla, Kunal Rai, Steven N. Quayle, Papia Ghosh, Jason Hanna, Benito Campos, Sachet A. Shukla, Ayla Ergun, and Giannicola Genovese
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PDF file - 854K, Supplementary Figure 1: miR-mRNA relationship (miR-34a; PDGFRA) detected by CLR in all GBM samples. Supplementary Figure 2: loss of p53 and Pten in murine neural stem cells and progenitor cells promotes the formation of proneural malignant gliomas. Supplementary Figure 3: expression levels of the subtype-specific miRNAs in p53/Pten-/- E13 embryonic neural stem cells infected with lentiviral miRNA precursors. Supplementary Figure 4: miR-34a expression in an independent cohort of GBM by in situ hybridization. Supplementary Figure 5: miR-34a levels in human and mouse proneural GBM. Supplementary Figure 6: miR-34a impairs tumor formation in orthotopic transplants. Supplementary Figure 7: miR-34a impairs the self-renewal of human proneural malignant spheroids. Supplementary Figure 8: miR-34a loss induces the expression of its oncogenic targets. Supplementary Figure 9: validation of PDGFRA as a direct target of miR-34a. Supplementary Figure 10: PDGFRA rescue on the self-renewal phenotype caused by miR-34a over-expression. Supplementary Figure 11: inverse correlation between the expression levels of miR-34a, PDGFRA and Smad4 in the GBM TCGA dataset. Supplementary Figure 12: validation of Smad4 as a direct target of miR-34a. Supplementary Figure 13: Smad4 rescue on the self-renewal phenotype caused by miR-34a over-expression
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27. Supplementary Methods, Figure Legends, Figures S1 - S7 from Targeting YAP-Dependent MDSC Infiltration Impairs Tumor Progression
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Ronald A. DePinho, Y. Alan Wang, Lynda Chin, Mark J. McArthur, Christopher J. Logothetis, Patricia Troncoso, Qing Chang, Liren Li, Yanxia Shi, Zhihu Ding, Xiaolu Pan, Wantong Yao, Eun-Jung Jin, Baoli Hu, Pingping Hou, Sunada Khadka, Xiaoying Shang, Di Zhao, Tim Heffernan, Trang N. Tieu, Vandhana Ramamoorthy, Zhenglin Guo, Neelay Bhaskar Patel, Chang-Jiun Wu, Avnish Kapoor, Elsa M. Li-Ning-Tapia, Jianhua Zhang, Sujun Hua, Ramakrishna Konaparthi, Kun Zhao, Zhuangna Fang, Shan Jiang, Chia Chin Wu, Pingna Deng, Prasenjit Dey, Xin Lu, and Guocan Wang
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Supplementary Figure S1. CyTOF analysis of biological samples from Ptenpc-/-Smad4pc-/- mice (Related to Figure 2). Supplementary Figure S2. Strategy used for MDSCs Isolation (Related to Figure 3). Supplementary Figure S3. Treatment scheme for Gr-1 antibody, peptibody, and Cxcr2 inhibitor SB225002. Supplementary Figure S4. IHC staining of Ki67, CD45, Vimentin, Smooth muscle actin (SMA) and Trichrome staining of mouse prostate tissues treated with IgG control or Gr1 antibody. Supplementary Figure S5. The top 10 differentially expressed genes in Ptenpc-/-Smad4pc-/- tumors as compared to Ptenpc-/- tumors, identified by microarray analysis (n=5). Figure S6. Top 10 activated oncogenic signatures identified by GSEA analysis in Ptenpc-/- Smad4pc-/- tumors as compared to Ptenpc-/- tumors (n=5). Figure S7. Clustering of primary prostate tumors from Wallace et al into MDSC-high and MDSC-low subtypes.
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28. Supplementary Methods, Figure Legends 1-13, Table Legends 1-10 from microRNA Regulatory Network Inference Identifies miR-34a as a Novel Regulator of TGF-β Signaling in Glioblastoma
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Lynda Chin, James J. Collins, David L. Rimm, Hongwu Zheng, Cameron Brennan, Wolf Ruprecht Wiedemeyer, Katherine Dunn, Lawrence Kwong, Hailei Zhang, Jianhua Zhang, Yonghong Xiao, Sharmistha Sarkar, Chang-Jiun Wu, Haoqiang Ying, Simona Colla, Kunal Rai, Steven N. Quayle, Papia Ghosh, Jason Hanna, Benito Campos, Sachet A. Shukla, Ayla Ergun, and Giannicola Genovese
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PDF file - 198K
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- 2023
29. Supplementary Tables 1-2, Figures 1-8 from PTEN Is a Major Tumor Suppressor in Pancreatic Ductal Adenocarcinoma and Regulates an NF-κB–Cytokine Network
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Ronald A. DePinho, Sarah P. Thayer, Lynda Chin, Y. Alan Wang, Shannon J. Turley, Nabeel Bardeesy, Aram F. Hezel, Yonghong Xiao, Simona Colla, Alexei Protopopov, Brian Malinn, Shan Jiang, Samuel R. Perry, Carol Lim, Ji-hye Paik, Alec C. Kimmelman, Hongwu Zheng, Xiaojia Ren, Wei Wang, Yingchun Liu, Hailei Zhang, Eliot Fletcher-Sananikone, Haiyan Yan, Gerald C. Chu, Stephanie M. Zimmerman, Anant Vinjamoori, Kutlu G. Elpek, and Haoqiang Ying
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Supplementary Tables 1-2, Figures 1-8 from PTEN Is a Major Tumor Suppressor in Pancreatic Ductal Adenocarcinoma and Regulates an NF-κB–Cytokine Network
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- 2023
30. Supplementary Tables 1 - 11 from Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade
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Jennifer A. Wargo, Lynda Chin, James P. Allison, Padmanee Sharma, Jorge Blando, P. Andrew Futreal, Jianhua Hu, Arlene H. Sharpe, Willem W. Overwijk, Wencai Ma, R. Eric Davis, Victor Prieto, Lawrence N. Kwong, Rodabe N. Amaria, Ignacio I. Wistuba, Luis M. Vence, Scott E. Woodman, Isabella C. Glitza, Adi Diab, Wen-Jen Hwu, Patrick Hwu, Sapna P. Patel, Alexander J. Lazar, Lauren Haydu, Jeffrey E. Gershenwald, Michael A. Davies, Russell J. Broaddus, Michael T. Tetzlaff, Wei-Shen Chen, Sangeetha M. Reddy, Qing Chang, Hong Jiang, Jacob L. Austin-Breneman, Mariana Petaccia De Macedo, Khalida Wani, Vancheswaran Gopalakrishnan, Roland L. Bassett, John P. Miller, Peter A. Prieto, Christine N. Spencer, Zachary A. Cooper, Alexandre Reuben, Whijae Roh, and Pei-Ling Chen
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Supplementary Table S1a. Patient Cohort Clinical Summary. Supplementary Table S1b. Patient clinical characteristics. Supplementary Table S1c. Immune profiling by IHC sample log. Supplementary Table S1d. Nanostring 54 sample log. Supplementary Table S2. Summary of immune profiling by immunohistochemistry. Supplementary Table S3. Summary of immune profiling by 4 additional myeloid markers. Supplementary Table S4. Summary of immune profiling by IHC of additional CTLA-4 blockade-naïve samples. Supplementary Table S5. Nanostring Gene List. Supplementary Table S6a. Nanostring summary 54 samples. Supplementary Table S6b. Differentially upregulated and downregulated genes in pre-treatment anti-CTLA-4 samples. Supplementary Table S6c. Differentially upregulated and downregulated genes in on-treatment anti-CTLA-4 samples. Supplementary Table S6d. Differentially upregulated and downregulated genes in pre-treatment anti-PD-1 samples. Supplementary Table S6e. Differentially upregulated and downregulated genes in on-treatment anti-PD-1 samples. Supplementary Table S7. Differentially upregulated and downregulated genes from pre- to on-treatment anti-CTLA-4. Supplementary Table S8. Differentially upregulated and downregulated genes from pre- to on-treatment anti-PD-1. Supplementary Table S9a. Nanostring gene list - chip used for comparison of CTLA-4 blockade-experienced vs -naive anti-PD1 samples (28 samples). Supplementary Table S9b. NanoString additional 28 samples to compare CTLA-4 blockade-experienced vs -naive anti-PD1 samples. Supplementary Table S9c. NanoString normalized data of additional 28 samples to compare CTLA-4 blockade-experienced vs -naive anti-PD1 samples. Supplementary Table S10. Commonly differentially regulated genes between pre- to on-treatment CTLA-4 blockade and PD-1 blockade. Supplementary Table S11a. Fold changes of significant change by anti-PD-1 therapy for paired samples. Supplementary Table S11b. Frequency of significant change by anti-PD1 therapy for paired samples.
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31. Supplementary Table 1 from Dual Roles of RNF2 in Melanoma Progression
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Lynda Chin, Jason Ernst, Alexander J. Lazar, Suhendan Ekmekcioglu, James W. Horner, Timothy P. Heffernan, Denai R. Milton, Michelle C. Barton, Elizabeth A. Grimm, Dong Yang, Amiksha Shah, Jacob B. Axelrad, Maura Williams, Neha S. Samant, Sneha Sharma, Emily Z. Keung, Chang-Jiun Wu, Petko Fiziev, Lawrence N. Kwong, Kadir C. Akdemir, and Kunal Rai
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Binding sites for RNF2 in HMEL-RNF2WT cells. This file contains list of all chromosomal locations that show enrichment by MACS for RNF2 binding by V5 ChIP-Seq in HMEL-RNF2 cells.
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32. Supplementary Tables and Figures from MAPK Pathway Inhibitors Sensitize BRAF-Mutant Melanoma to an Antibody-Drug Conjugate Targeting GPNMB
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Peter M. Siegel, Keith T. Flaherty, Ian R. Watson, Thomas Hawthorne, Tibor Keler, Lynda Chin, Lawrence Kwong, Zhifeng Dong, Marco Biondini, Dennie T. Frederick, Matthew G. Annis, and April A.N. Rose
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Supplementary Fig. S1. Heatmap of mRNA expression for individual melanosomal differentiation antigens and a MITF transcriptional signature using a published dataset of melanoma samples (2). Supplementary Fig. S2. GPNMB expression is induced in multiple BRAF-mutant cells in response to MAPK pathway inhibition. Supplementary Fig. S3. Gene expression of MITF and GPNMB in melanoma cells following MAPK pathway inhibition. Supplementary Fig. S4. Dabrafenib and Trametinib stimulate MITF nuclear localization. Supplementary Fig. S5. Correlation of MITF and GPNMB mRNA expression in melanoma samples from patients that were on-treatment or that progressed on therapy with MAPK pathway 7 inhibitors. RT-qPCR data for MITF and GPNMB was expressed as the ratio relative to pretreatment levels. Supplementary Fig. S6. Correlation between the expression of individual melanosomal genes with MITF mRNA expression in melanoma samples from patients that were on-treatment or that progressed on therapy with MAPK pathway inhibitors. RT-qPCR data for each gene and MITF was normalized to GAPDH and expressed as the ratio relative to pre-treatment levels. Supplementary Fig. S7. MAPK pathway inhibition results in elevated levels of soluble GPNMB released from melanoma cells. Table S1: Clinical characteristics of patients biopsied for evaluation of MITF and GPNMB mRNA expression Table S2: Correlation coefficients between individual gene expression and MITF or a MITF Signature Table S3: Complete Responses Following Trametinib Treatment in Cohorts Injected with A375 or WM-2664 Melanoma Cells. Table S4: List of Primers for RT-qPCR Analyses
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33. Supplementary Material from MAPK Pathway Inhibitors Sensitize BRAF-Mutant Melanoma to an Antibody-Drug Conjugate Targeting GPNMB
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Peter M. Siegel, Keith T. Flaherty, Ian R. Watson, Thomas Hawthorne, Tibor Keler, Lynda Chin, Lawrence Kwong, Zhifeng Dong, Marco Biondini, Dennie T. Frederick, Matthew G. Annis, and April A.N. Rose
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Contains supplementary methods, references and figure legends.
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- 2023
34. Data from MAPK Pathway Inhibitors Sensitize BRAF-Mutant Melanoma to an Antibody-Drug Conjugate Targeting GPNMB
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Peter M. Siegel, Keith T. Flaherty, Ian R. Watson, Thomas Hawthorne, Tibor Keler, Lynda Chin, Lawrence Kwong, Zhifeng Dong, Marco Biondini, Dennie T. Frederick, Matthew G. Annis, and April A.N. Rose
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Purpose: To determine if BRAF and/or MEK inhibitor–induced GPNMB expression renders melanomas sensitive to CDX-011, an antibody-drug conjugate targeting GPNMB.Experimental Design: The Cancer Genome Atlas melanoma dataset was interrogated for a panel of MITF-regulated melanosomal differentiation antigens, including GPNMB. BRAF-mutant melanoma cell lines treated with BRAF or MEK inhibitors were assessed for GPNMB expression by RT-qPCR, immunoblot, and FACS analyses. Transient siRNA-mediated knockdown approaches were used to determine if MITF is requirement for treatment-induced GPNMB upregulation. GPNMB expression was analyzed in serial biopsies and serum samples from patients with melanoma taken before, during, and after disease progression on MAPK inhibitor treatment. Subcutaneous injections were performed to test the efficacy of MAPK inhibitors alone, CDX-011 alone, or their combination in suppressing melanoma growth.Results: A MITF-dependent melanosomal differentiation signature is associated with poor prognosis in patients with this disease. MITF is increased following BRAF and MEK inhibitor treatment and induces the expression of melanosomal differentiation genes, including GPNMB. GPNMB is expressed at the cell surface in MAPK inhibitor–treated melanoma cells and is also elevated in on-treatment versus pretreatment biopsies from melanoma patients receiving MAPK pathway inhibitors. Combining BRAF and/or MEK inhibitors with CDX-011, an antibody-drug conjugate targeting GPNMB, is effective in causing melanoma regression in preclinical animal models and delays the recurrent melanoma growth observed with MEK or BRAF/MEK inhibitor treatment alone.Conclusions: The combination of MAPK pathway inhibitors with an antibody-drug conjugate targeting GPNMB is an effective therapeutic option for patients with melanoma. Clin Cancer Res; 22(24); 6088–98. ©2016 AACR.
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35. Supplementary Figures 1-5 from A Genome-Wide Screen Reveals Functional Gene Clusters in the Cancer Genome and Identifies EphA2 as a Mitogen in Glioblastoma
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Mark D. Johnson, Peter M. Black, Rona S. Carroll, Isaac Kohane, Ronald A. DePinho, Cameron Brennan, Lynda Chin, Meredith Thomas, Amanda Brosius, Yi Yu, Xiuli Jiang, Laura Durso, Arnab Chakravarti, Elizabeth Maher, Weil Lai, Peter J. Park, and Fenghua Liu
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Supplementary Figures 1-5 from A Genome-Wide Screen Reveals Functional Gene Clusters in the Cancer Genome and Identifies EphA2 as a Mitogen in Glioblastoma
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36. Supplementary Methods from Double Minute Chromosomes in Glioblastoma Multiforme Are Revealed by Precise Reconstruction of Oncogenic Amplicons
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David Haussler, Lynda Chin, Sol Katzman, Suresh Jhanwar, Tom Mikkelsen, Cameron W. Brennan, Mia Grifford, Sofie R. Salama, and J. Zachary Sanborn
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PDF file, 260K.
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37. Supplementary Figure 2 from Mutations in BRAF and KRAS Converge on Activation of the Mitogen-Activated Protein Kinase Pathway in Lung Cancer Mouse Models
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Kwok-Kin Wong, Lynda Chin, Bruce E. Johnson, Pasi A. Jänne, Levi A. Garraway, Roman K. Thomas, Roderick T. Bronson, Robert Padera, Lucian R. Chirieac, Ruqayyah Al-Hashem, Yanping Sun, Mitchell Albert, Liang Chen, Kate McNamara, Sara Zaghlul, Mei-Chih Liang, Danan Li, Samanthi A. Perera, Zhenxiong Wang, and Hongbin Ji
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Supplementary Figure 2 from Mutations in BRAF and KRAS Converge on Activation of the Mitogen-Activated Protein Kinase Pathway in Lung Cancer Mouse Models
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38. Supplementary Figure 1 from Common and Distinct Genomic Events in Sporadic Colorectal Cancer and Diverse Cancer Types
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Ronald A. DePinho, Lynda Chin, Mark Redston, Gerald Bailey, Raju Kucherlapati, Kate Montgomery, Cameron Brennan, Elena Ivanova, Alexei Protopopov, Alec C. Kimmelman, Bin Feng, Yonghong Xiao, Raktim Sinha, Giovanni Tonon, and Eric S. Martin
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Supplementary Figure 1 from Common and Distinct Genomic Events in Sporadic Colorectal Cancer and Diverse Cancer Types
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39. Supplementary Figure 5 from Chromosome 10, Frequently Lost in Human Melanoma, Encodes Multiple Tumor-Suppressive Functions
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Lynda Chin and Lawrence N. Kwong
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PDF file - 59KB, RAS/RAF mutations correlate with chr 10 status.
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40. Supplementary Materials and Figure Legends 1-4 from Mutations in BRAF and KRAS Converge on Activation of the Mitogen-Activated Protein Kinase Pathway in Lung Cancer Mouse Models
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Kwok-Kin Wong, Lynda Chin, Bruce E. Johnson, Pasi A. Jänne, Levi A. Garraway, Roman K. Thomas, Roderick T. Bronson, Robert Padera, Lucian R. Chirieac, Ruqayyah Al-Hashem, Yanping Sun, Mitchell Albert, Liang Chen, Kate McNamara, Sara Zaghlul, Mei-Chih Liang, Danan Li, Samanthi A. Perera, Zhenxiong Wang, and Hongbin Ji
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Supplementary Materials and Figure Legends 1-4 from Mutations in BRAF and KRAS Converge on Activation of the Mitogen-Activated Protein Kinase Pathway in Lung Cancer Mouse Models
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- 2023
41. Supplementary Table 3 from Marked Genomic Differences Characterize Primary and Secondary Glioblastoma Subtypes and Identify Two Distinct Molecular and Clinical Secondary Glioblastoma Entities
- Author
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Ronald A. DePinho, Lynda Chin, Peter McL. Black, John Quackenbush, David N. Louis, Raktim Sinha, Bin Feng, Deepak Khatry, Aaron Richardson, Keith L. Ligon, Laura Durso, Patrick Y. Wen, Cameron Brennan, and Elizabeth A. Maher
- Abstract
Supplementary Table 3 from Marked Genomic Differences Characterize Primary and Secondary Glioblastoma Subtypes and Identify Two Distinct Molecular and Clinical Secondary Glioblastoma Entities
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- 2023
42. Supplementary Methods from Marked Genomic Differences Characterize Primary and Secondary Glioblastoma Subtypes and Identify Two Distinct Molecular and Clinical Secondary Glioblastoma Entities
- Author
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Ronald A. DePinho, Lynda Chin, Peter McL. Black, John Quackenbush, David N. Louis, Raktim Sinha, Bin Feng, Deepak Khatry, Aaron Richardson, Keith L. Ligon, Laura Durso, Patrick Y. Wen, Cameron Brennan, and Elizabeth A. Maher
- Abstract
Supplementary Methods from Marked Genomic Differences Characterize Primary and Secondary Glioblastoma Subtypes and Identify Two Distinct Molecular and Clinical Secondary Glioblastoma Entities
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- 2023
43. Supplementary Table 4 from Marked Genomic Differences Characterize Primary and Secondary Glioblastoma Subtypes and Identify Two Distinct Molecular and Clinical Secondary Glioblastoma Entities
- Author
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Ronald A. DePinho, Lynda Chin, Peter McL. Black, John Quackenbush, David N. Louis, Raktim Sinha, Bin Feng, Deepak Khatry, Aaron Richardson, Keith L. Ligon, Laura Durso, Patrick Y. Wen, Cameron Brennan, and Elizabeth A. Maher
- Abstract
Supplementary Table 4 from Marked Genomic Differences Characterize Primary and Secondary Glioblastoma Subtypes and Identify Two Distinct Molecular and Clinical Secondary Glioblastoma Entities
- Published
- 2023
44. Data from Common and Distinct Genomic Events in Sporadic Colorectal Cancer and Diverse Cancer Types
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Ronald A. DePinho, Lynda Chin, Mark Redston, Gerald Bailey, Raju Kucherlapati, Kate Montgomery, Cameron Brennan, Elena Ivanova, Alexei Protopopov, Alec C. Kimmelman, Bin Feng, Yonghong Xiao, Raktim Sinha, Giovanni Tonon, and Eric S. Martin
- Abstract
Colorectal cancer (CRC) is a major cause of cancer morbidity and mortality, and elucidation of its underlying genetics has advanced diagnostic screening, early detection, and treatment. Because CRC genomes are characterized by numerous non-random chromosomal structural alterations, we sought to delimit regions of recurrent amplifications and deletions in a collection of 42 primary specimens and 37 tumor cell lines derived from chromosomal instability neoplasia and microsatellite instability neoplasia CRC subtypes and to compare the pattern of genomic aberrations in CRC with those in other cancers. Application of oligomer-based array-comparative genome hybridization and custom analytic tools identified 50 minimal common regions (MCRs) of copy number alterations, 28 amplifications, and 22 deletions. Fifteen were highly recurrent and focal (EGFR and MYC with the remaining 10 containing a total of 65 resident genes with established links to cancer. Furthermore, comparisons of these delimited genomic profiles revealed that 22 of the 50 CRC MCRs are also present in lung cancer, glioblastoma, and/or multiple myeloma. Among 22 shared MCRs, nine do not contain genes previously shown genetically altered in cancer, whereas the remaining 13 harbor 35 known cancer genes, of which only 14 have been linked to CRC pathogenesis. Together, these observations point to the existence of many yet-to-be discovered cancer genes driving CRC development, as well as other human cancers, and show the utility of high-resolution copy number analysis in the identification of genetic events common and specific to the development of various tumor types. [Cancer Res 2007;67(22):10736–43]
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- 2023
45. Supplementary Material from High-Resolution Global Profiling of Genomic Alterations with Long Oligonucleotide Microarray
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Lynda Chin, Alexei Protopopov, Minjung Kim, Andrew J. Aguirre, Craig Cauwels, Bin Feng, Christopher Leo, Yunyu Zhang, and Cameron Brennan
- Abstract
Figures, Legends and Tables
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- 2023
46. Data Supplement from The RAC1 P29S Hotspot Mutation in Melanoma Confers Resistance to Pharmacological Inhibition of RAF
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Lynda Chin, Gordon B. Mills, Michael A. Davies, Kenneth Y. Tsai, Katherine Stemke-Hale, James M. Tepper, Zhuangna Fang, Guocan Wang, Giannicola Genovese, Tony Gutschner, Mozhdeh Mahdavi, Peter K. Cabeceiras, Liren Li, and Ian R. Watson
- Abstract
Supplementary Table 1. (Top) IC50 (nM), fold changes (FC) and (Bottom) % viability at 10uM drug treatment compared to DMSO control for BRAF mutant cell lines, A375, MALME-3M, 451Lu and IGR1 (expresses RAC1 P29S) are shown.
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- 2023
47. Supplementary Figure 1 from Chromosome 10, Frequently Lost in Human Melanoma, Encodes Multiple Tumor-Suppressive Functions
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Lynda Chin and Lawrence N. Kwong
- Abstract
PDF file - 328KB, Correlation of DNA copy number aberrations to survival statistics.
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- 2023
48. Data from High-Resolution Global Profiling of Genomic Alterations with Long Oligonucleotide Microarray
- Author
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Lynda Chin, Alexei Protopopov, Minjung Kim, Andrew J. Aguirre, Craig Cauwels, Bin Feng, Christopher Leo, Yunyu Zhang, and Cameron Brennan
- Abstract
Cancer represents the phenotypic end point of multiple genetic lesions that endow cells with a full range of biological properties required for tumorigenesis. Among the hallmark features of the cancer genome are recurrent regional gains and losses that, upon detailed characterization, have provided highly productive discovery paths for new oncogenes and tumor suppressor genes. In this study, we describe the use of an oligonucleotide-based microarray platform and development of requisite assay conditions and bioinformatic mining tools that permits high-resolution genome-wide array-comparative genome hybridization profiling of human and mouse tumors. Using a commercially available 60-mer oligonucleotide microarray, we demonstrate that this platform provides sufficient sensitivity to detect single-copy difference in gene dosage of full complexity genomic DNA while offering high resolution. The commercial availability of the microarrays and associated reagents, along with the technical protocols and analytical tools described in this report, should provide investigators with the immediate capacity to perform DNA analysis of normal and diseased genomes in a global and detailed manner.
- Published
- 2023
49. Supplementary Table 2 from Double Minute Chromosomes in Glioblastoma Multiforme Are Revealed by Precise Reconstruction of Oncogenic Amplicons
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David Haussler, Lynda Chin, Sol Katzman, Suresh Jhanwar, Tom Mikkelsen, Cameron W. Brennan, Mia Grifford, Sofie R. Salama, and J. Zachary Sanborn
- Abstract
PDF file, 634K, BamBam output of peaks and rearrangements for TCGA-GBM-0145, TCGA-GBM-0152 and TCGA-GBM-0648 (Whole Genome Sequence analysis).
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- 2023
50. Supplementary Table 2 from Chromosome 10, Frequently Lost in Human Melanoma, Encodes Multiple Tumor-Suppressive Functions
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Lynda Chin and Lawrence N. Kwong
- Abstract
XLSX file - 131KB, Genotypes and characteristics of human melanoma cell lines used in this study.
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- 2023
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