Browsing by Author "Bueno, Raphael"

Now showing items 1-18 of 18

    • Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context 

      Christensen, Brock C.; Marsit, Carmen J.; Zheng, Shichun; Wrensch, Margaret R.; Wiemels, Joseph L.; Nelson, Heather H.; Karagas, Margaret R.; Padbury, James F.; Yeh, Ru-Fang; Wiencke, John K.; Kelsey, Karl T.; Houseman, Eugene Andres; Bueno, Raphael; Sugarbaker, David John (Public Library of Science, 2009)
      Epigenetic control of gene transcription is critical for normal human development and cellular differentiation. While alterations of epigenetic marks such as DNA methylation have been linked to cancers and many other human ...

    • Asbestos Burden Predicts Survival in Pleural Mesothelioma 

      Christensen, Brock C.; Godleski, John Joseph; Roelofs, Cora R.; Longacker, Jennifer L.; Bueno, Raphael; Sugarbaker, David John; Marsit, Carmen J.; Nelson, Heather H.; Kelsey, Karl T. (National Institute of Environmental Health Sciences, 2008)
      Background: Malignant pleural mesothelioma (MPM) is a rapidly fatal asbestos-associated malignancy with a median survival time of < 1 year following diagnosis. Treatment strategy is determined in part using known ...

    • Asbestos exposure predicts cell cycle control gene promoter methylation in pleural mesothelioma 

      Christensen, Brock C.; Godleski, John Joseph; Marsit, Carmen J.; Houseman, Eugene Andres; Lopez-Fagundo, Cristina Y.; Longacker, Jennifer L.; Bueno, Raphael; Sugarbaker, David John; Nelson, Heather H.; Kelsey, Karl T. (Oxford University Press, 2008)
      Malignant pleural mesothelioma (MPM) is a rapidly fatal tumor with increasing incidence worldwide responsible for many thousands of deaths annually. Although there is a clear link between exposure to asbestos and mesothelioma, ...

    • Autophagy Correlates with the Therapeutic Responsiveness of Malignant Pleural Mesothelioma in 3D Models 

      Barbone, Dario; Follo, Carlo; Echeverry, Nohemy; Gerbaudo, Victor H.; Klabatsa, Astero; Bueno, Raphael; Felley-Bosco, Emanuela; Broaddus, V. Courtney (Public Library of Science, 2015)
      Malignant pleural mesothelioma is a highly chemoresistant solid tumor. We have studied this apoptotic resistance using in vitro and ex vivo three-dimensional models, which acquire a high level of chemoresistance that can ...

    • Differentially Expressed Alternatively Spliced Genes in Malignant Pleural Mesothelioma Identified Using Massively Parallel Transcriptome Sequencing 

      Dong, Lingsheng; Jensen, Roderick V; De Rienzo, Assunta; Gordon, Gavin J.; Xu, Yanlong; Sugarbaker, David John; Bueno, Raphael (BioMed Central, 2009)
      Background: Analyses of Expressed Sequence Tags (ESTs) databases suggest that most human genes have multiple alternative splice variants. The alternative splicing of pre-mRNA is tightly regulated during development and in ...

    • Fine needle aspirate flow cytometric phenotyping characterizes immunosuppressive nature of the mesothelioma microenvironment 

      Lizotte, Patrick H.; Jones, Robert E.; Keogh, Lauren; Ivanova, Elena; Liu, Hongye; Awad, Mark M.; Hammerman, Peter S.; Gill, Ritu R.; Richards, William G.; Barbie, David A.; Bass, Adam J.; Bueno, Raphael; English, Jessie M.; Bittinger, Mark; Wong, Kwok-Kin (Nature Publishing Group, 2016)
      With the emergence of checkpoint blockade and other immunotherapeutic drugs, and the growing adoption of smaller, more flexible adaptive clinical trial designs, there is an unmet need to develop diagnostics that can rapidly ...

    • Gender-Specific Molecular and Clinical Features Underlie Malignant Pleural Mesothelioma 

      De Rienzo, Assunta; Archer, Michael A.; Yeap, Beow; Dao, Nhien; Sciaranghella, Daniele; Sideris, Antonios C.; Zheng, Yifan; Holman, Alexander G.; Wang, Yaoyu E.; Dal Cin, Paola; Fletcher, Jonathan; Rubio, Renee; Croft, Larry; Quackenbush, John; Sugarbaker, Peter E.; Munir, Kiara J.; Battilana, Jesse R.; Gustafson, Corinne; Chirieac, Lucian; Ching, Soo Meng; Wong, James; Tay, Liang Chung; Rudd, Stephen; Hercus, Robert; Sugarbaker, David J.; Richards, William; Bueno, Raphael (American Association for Cancer Research (AACR), 2016-01-15)
      Malignant pleural mesothelioma (MPM) is an aggressive cancer that occurs more frequently in men, but is associated with longer survival in women. Insight into the survival advantage of female patients may advance the ...

    • Genes Associated with Prognosis after Surgery for Malignant Pleural Mesothelioma Promote Tumor Cell Survival In Vitro 

      Gordon, Gavin J.; Bueno, Raphael; Sugarbaker, David John (BioMed Central, 2011)
      Background: Mesothelioma is an aggressive neoplasm with few effective treatments, one being cytoreductive surgery. We previously described a test, based on differential expression levels of four genes, to predict clinical ...

    • MET and PI3K/mTOR as a Potential Combinatorial Therapeutic Target in Malignant Pleural Mesothelioma 

      Kanteti, Rajani; Dhanasingh, Immanuel; Kawada, Ichiro; Lennon, Frances E.; Arif, Qudsia; Bueno, Raphael; Hasina, Rifat; Husain, Aliya N.; Vigneswaran, Wickii; Seiwert, Tanguy; Kindler, Hedy L.; Salgia, Ravi (Public Library of Science, 2014)
      Malignant pleural mesothelioma (MPM) is an aggressive disease with a poor prognosis. Studies have shown that both MET and its key downstream intracellular signaling partners, PI3K and mTOR, are overexpressed in MPM. Here ...

    • Molecular pathways and therapeutic targets in lung cancer 

      Shtivelman, Emma; Hensing, Thomas; Simon, George R.; Dennis, Phillip A.; Otterson, Gregory A.; Bueno, Raphael; Salgia, Ravi (Impact Journals LLC, 2014)
      Lung cancer is still the leading cause of cancer death worldwide. Both histologically and molecularly lung cancer is heterogeneous. This review summarizes the current knowledge of the pathways involved in the various types ...

    • Neoadjuvant irinotecan, cisplatin, and concurrent radiation therapy with celecoxib for patients with locally advanced esophageal cancer 

      Cleary, James M.; Mamon, Harvey J.; Szymonifka, Jackie; Bueno, Raphael; Choi, Noah; Donahue, Dean M.; Fidias, Panos M.; Gaissert, Henning A.; Jaklitsch, Michael T.; Kulke, Matthew H.; Lynch, Thomas P.; Mentzer, Steven J.; Meyerhardt, Jeffrey A.; Swanson, Richard S.; Wain, John; Fuchs, Charles S.; Enzinger, Peter C. (BioMed Central, 2016)
      Background: Patients with locally advanced esophageal cancer who are treated with trimodality therapy have a high recurrence rate. Preclinical evidence suggests that inhibition of cyclooxygenase 2 (COX2) increases the ...

    • Second Generation Sequencing of the Mesothelioma Tumor Genome 

      Bueno, Raphael; De Rienzo, Assunta; Dong, Lingsheng; Gordon, Gavin J.; Hercus, Colin F.; Richards, William; Jensen, Roderick V.; Anwar, Arif; Maulik, Gautam; Chirieac, Lucian; Ho, Kim-Fong; Taillon, Bruce E.; Turcotte, Cynthia L.; Hercus, Robert G.; Gullans, Steven R.; Sugarbaker, David J. (Public Library of Science (PLoS), 2010-05-13)
      The current paradigm for elucidating the molecular etiology of cancers relies on the interrogation of small numbers of genes, which limits the scope of investigation. Emerging second-generation massively parallel DNA ...

    • Sequential Binary Gene-Ratio Tests Define a Novel Molecular Diagnostic Strategy for Malignant Pleural Mesothelioma 

      De Rienzo, Assunta; Richards, William; Yeap, Beow; Coleman, Melissa H.; Sugarbaker, Peter E.; Chirieac, Lucian; Wang, Yaoyu E.; Quackenbush, John; Jensen, Roderick V.; Bueno, Raphael (American Association for Cancer Research, 2013-05-01)
      Purpose To develop a standardized approach for molecular diagnostics, we used the gene-expression ratio bioinformatic technique to design a molecular signature to diagnose MPM from among other potentially confounding ...

    • A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors 

      Slyper, Michal; Porter, Caroline; Ashenberg, Orr; Waldman, Julia; Drokhlyansky, Eugene; Wakiro, Isaac; Smilie, Christopher; Smith-Rosario, Gabriela; Wu, Jingyi; Dionne, Danielle; Vigneau, Sebastien; Jane-Valbuena, Judit; Tickle, Timothy; Napolitano, Sara; Su, Mei-Ju; Patel, Anand; Karlstrom, Asa; Gristch, Simon; Nomura, Masashi; Waghray, Avinash; Gohil, Satyen; Tsankov, Alexander; Jerby-Arnon, Livnat; Cohen, Ofir; Klughammer, Johanna; Rosen, Yanay; Gould, Joshua; Nguyen, Lan; Hofree, Matan; Tramontozzi, Peter; Levy, Rachel; Li, Bo; Wu, Catherine; Izar, Benjamin; Haq, Rizwan; Hodi, Stephen; Yoon, Charles; Hata, Aaron; Baker, Suzanne; Suva, Mario; Bueno, Raphael; Stover, Elizabeth; Clay, Michael; Dyer, M Aiven; Collins, Natalie; Matulonis, Ursula; Wagle, Nikhil; Johnson, Bruce; Rotem, Asaf; Rozenblatt-Rosen, Orit; Regev, Aviv (Springer Science and Business Media LLC, 2020-05-01)
      Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen ...

    • Transcriptome Sequencing of Malignant Pleural Mesothelioma Tumors 

      Sugarbaker, David; Richards, William; Gordon, Gavin; Dong, Lingsheng; De Rienzo, Assunta; Maulik, Gautam; Glickman, Jonathan; Chirieac, Lucian; Hartman, Mor-li; Taillon, Bruce; Du, Lei; Bouffard, Pascal; Kingsmore, Stephen F.; Miller, Neil; Farmer, Andrew; Jensen, Roderick V.; Gullans, Steve R.; Bueno, Raphael (Proceedings of the National Academy of Sciences, 2008-02-26)
      Cancers arise by the gradual accumulation of mutations in multiple genes. We now use shotgun pyrosequencing to characterize RNA mutations and expression levels unique to malignant pleural mesotheliomas (MPMs) and not present ...

    • Tsc1-Tp53 loss induces mesothelioma in mice, and evidence for this mechanism in human mesothelioma 

      Guo, Yanan; Chirieac, Lucian R.; Bueno, Raphael; Pass, Harvey; Wu, Wenhao; Malinowska, Izabela A.; Kwiatkowski, David J. (2014)
      Mesothelioma is diagnosed in approximately 2,500 patients in the United States every year, most often arising in the pleural space, but also occurring as primary peritoneal mesothelioma. The vast majority of patients with ...

    • Validation of a Molecular and Pathological Model for Five-Year Mortality Risk in Patients with Early Stage Lung Adenocarcinoma 

      Bueno, Raphael; Hughes, Elisha; Wagner, Susanne; Gutin, Alexander S.; Lanchbury, Jerry S.; Zheng, Yifan; Archer, Michael A.; Gustafson, Corinne; Jones, Joshua T.; Rushton, Kristen; Saam, Jennifer; Kim, Edward; Barberis, Massimo; Wistuba, Ignacio; Wenstrup, Richard J.; Wallace, William A.; Hartman, Anne-Renee; Harrison, David J. (Lippincott Williams & Wilkins, 2014)
      Introduction: The aim of this study was to validate a molecular expression signature [cell cycle progression (CCP) score] that identifies patients with a higher risk of cancer-related death after surgical resection of early ...

    • Vorinostat Eliminates Multicellular Resistance of Mesothelioma 3D Spheroids via Restoration of Noxa Expression 

      Barbone, Dario; Cheung, Priscilla; Battula, Sailaja; Busacca, Sara; Gray, Steven G.; Longley, Daniel B.; Bueno, Raphael; Sugarbaker, David John; Bueno, Raphael; Broaddus, V. Courtney (Public Library of Science, 2012)
      When grown in 3D cultures as spheroids, mesothelioma cells acquire a multicellular resistance to apoptosis that resembles that of solid tumors. We have previously found that resistance to the proteasome inhibitor bortezomib ...