47 results on '"Chen, William S."'
Search Results
2. Predicting cancer drug TARGETS - TreAtment Response Generalized Elastic-neT Signatures
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Rydzewski, Nicholas R., Peterson, Erik, Lang, Joshua M., Yu, Menggang, Laura Chang, S., Sjöström, Martin, Bakhtiar, Hamza, Song, Gefei, Helzer, Kyle T., Bootsma, Matthew L., Chen, William S., Shrestha, Raunak M., Zhang, Meng, Quigley, David A., Aggarwal, Rahul, Small, Eric J., Wahl, Daniel R., Feng, Felix Y., and Zhao, Shuang G.
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- 2021
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3. An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer
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Das, Rajdeep, Sjöström, Martin, Shrestha, Raunak, Yogodzinski, Christopher, Egusa, Emily A., Chesner, Lisa N., Chen, William S., Chou, Jonathan, Dang, Donna K., Swinderman, Jason T., Ge, Alex, Hua, Junjie T., Kabir, Shaheen, Quigley, David A., Small, Eric J., Ashworth, Alan, Feng, Felix Y., and Gilbert, Luke A.
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- 2021
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4. The DNA methylation landscape of advanced prostate cancer
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Zhao, Shuang G., Chen, William S., Li, Haolong, Foye, Adam, Zhang, Meng, Sjöström, Martin, Aggarwal, Rahul, Playdle, Denise, Liao, Arnold, Alumkal, Joshi J., Das, Rajdeep, Chou, Jonathan, Hua, Junjie T., Barnard, Travis J., Bailey, Adina M., Chow, Eric D., Perry, Marc D., Dang, Ha X., Yang, Rendong, Moussavi-Baygi, Ruhollah, Zhang, Li, Alshalalfa, Mohammed, Laura Chang, S., Houlahan, Kathleen E., Shiah, Yu-Jia, Beer, Tomasz M., Thomas, George, Chi, Kim N., Gleave, Martin, Zoubeidi, Amina, Reiter, Robert E., Rettig, Matthew B., Witte, Owen, Yvonne Kim, M., Fong, Lawrence, Spratt, Daniel E., Morgan, Todd M., Bose, Rohit, Huang, Franklin W., Li, Hui, Chesner, Lisa, Shenoy, Tanushree, Goodarzi, Hani, Asangani, Irfan A., Sandhu, Shahneen, Lang, Joshua M., Mahajan, Nupam P., Lara, Primo N., Evans, Christopher P., Febbo, Phillip, Batzoglou, Serafim, Knudsen, Karen E., He, Housheng H., Huang, Jiaoti, Zwart, Wilbert, Costello, Joseph F., Luo, Jianhua, Tomlins, Scott A., Wyatt, Alexander W., Dehm, Scott M., Ashworth, Alan, Gilbert, Luke A., Boutros, Paul C., Farh, Kyle, Chinnaiyan, Arul M., Maher, Christopher A., Small, Eric J., Quigley, David A., and Feng, Felix Y.
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- 2020
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5. Germline polymorphisms associated with impaired survival outcomes and somatic tumor alterations in advanced prostate cancer
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Chen, William S., Feng, Eric L., Aggarwal, Rahul, Foye, Adam, Beer, Tomasz M., Alumkal, Joshi J., Gleave, Martin, Chi, Kim N., Reiter, Robert E., Rettig, Matthew B., Evans, Christopher P., Small, Eric J., Sharifi, Nima, and Zhao, Shuang G.
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- 2020
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6. Uncovering axes of variation among single-cell cancer specimens
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Chen, William S., Zivanovic, Nevena, van Dijk, David, Wolf, Guy, Bodenmiller, Bernd, and Krishnaswamy, Smita
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- 2020
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7. Visualizing structure and transitions in high-dimensional biological data
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Moon, Kevin R., van Dijk, David, Wang, Zheng, Gigante, Scott, Burkhardt, Daniel B., Chen, William S., Yim, Kristina, Elzen, Antonia van den, Hirn, Matthew J., Coifman, Ronald R., Ivanova, Natalia B., Wolf, Guy, and Krishnaswamy, Smita
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- 2019
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8. Transcriptomic and Clinical Characterization of Neuropeptide Y Expression in Localized and Metastatic Prostate Cancer: Identification of Novel Prostate Cancer Subtype with Clinical Implications
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Alshalalfa, Mohammed, Nguyen, Paul L., Beltran, Himisha, Chen, William S., Davicioni, Elai, Zhao, Shuang G., Rebbeck, Timothy R., Schaeffer, Edward M., Lotan, Tamara L., Feng, Felix Y., and Mahal, Brandon A.
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- 2019
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9. Exploring single-cell data with deep multitasking neural networks
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Amodio, Matthew, van Dijk, David, Srinivasan, Krishnan, Chen, William S., Mohsen, Hussein, Moon, Kevin R., Campbell, Allison, Zhao, Yujiao, Wang, Xiaomei, Venkataswamy, Manjunatha, Desai, Anita, Ravi, V., Kumar, Priti, Montgomery, Ruth, Wolf, Guy, and Krishnaswamy, Smita
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- 2019
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10. Author Correction: Visualizing structure and transitions in high-dimensional biological data
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Moon, Kevin R., van Dijk, David, Wang, Zheng, Gigante, Scott, Burkhardt, Daniel B., Chen, William S., Yim, Kristina, van den Elzen, Antonia, Hirn, Matthew J., Coifman, Ronald R., Ivanova, Natalia B., Wolf, Guy, and Krishnaswamy, Smita
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- 2020
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11. Akt1 Governs Breast Cancer Progression in vivo
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Ju, Xiaoming, Katiyar, Sanjay, Wang, Chenguang, Liu, Manran, Jiao, Xuanmao, Li, Shengwen, Zhou, Jie, Turner, Jacob, Lisanti, Michael P., Russell, Robert G., Mueller, Susette C., Ojeifo, John, Chen, William S., Hay, Nissim, and Pestell, Richard G.
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- 2007
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12. Publisher Correction: Global absence and targeting of protective immune states in severe COVID-19
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Combes, Alexis J., Courau, Tristan, Kuhn, Nicholas F., Hu, Kenneth H., Ray, Arja, Chen, William S., and Chew, Nayvin W.
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Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Alexis J. Combes [sup.1] [sup.2] [sup.3] , Tristan Courau [sup.1] [sup.2] [sup.3] , Nicholas F. Kuhn [sup.1] [sup.2] , Kenneth H. Hu [sup.1] [sup.2] , Arja Ray [sup.1] [sup.2] [...]
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- 2021
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13. Expression Cloning of Human EGF Receptor Complementary DNA: Gene Amplification and Three Related Messenger RNA Products in A431 Cells
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Lin, Chijen R., Chen, William S., Kruiger, Wiebe, Stolarsky, Lana S., Weber, Wolfgang, Evans, Ronald M., Verma, Inder M., Gill, Gordon N., and Rosenfeld, Michael G.
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- 1984
14. Genomic Characterization and Clinical Implications of Genomic Stromal Infiltration Markers in Prostate Cancer
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Mahal, Brandon A., Alshalalfa, Mohammed, Zhao, Shuang G., Beltran, Himisha, Chen, William S., Chipidza, Fallon, Davicioni, Elai, Karnes, R.Jeffrey, Ku, Sheng-Yu, Lotan, Tamara L., Muralidhar, Vinayak, Rebbeck, Timothy R., Schaeffer, Edward M., Spratt, Daniel E., Feng, Felix Y., and Nguyen, Paul L.
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Cohort Studies ,Male ,Biomarkers, Tumor ,Tumor Microenvironment ,Humans ,Prostatic Neoplasms ,Middle Aged ,Transcriptome ,Article ,Aged - Abstract
PURPOSE: Progression of prostate cancer is a complex multistep process that involves molecular alterations in cells of the tumor and microenvironment with associated interactions between the stroma and epithelium. We performed genomic expression analyses of stromal infiltration markers to determine the prognostic significance thereof in prostate cancer. MATERIALS AND METHODS: Genome-wide expression profiles of formalin-fixed paraffin-embedded radical prostatectomy samples were evaluated from a prospective registry cohort (n=5,239) and three retrospective institutional cohorts (n=1,135). Two independent stromal gene expression signatures inferred stromal infiltration. Cox proportional hazards regression defined the association between stromal infiltration expression and metastasis-free survival. Cox proportional hazards regression defined the association between stromal infiltration expression and metastasis-free survival. RESULTS: Stromal expression scores were correlated with each other and with key stromal markers (CAV1, VIM, TAGLN), basal activity, and CD3 and CD4 immune biomarkers (r>0.5 for all). The top decile of stromal expression was associated with higher genomic-risk score, high CAPRA-S, Gleason 9–10 disease, and a higher risk for metastasis (HR:2.35[1.35–4.08],p=0.002). Higher stromal infiltration score was also associated with decreased expression of DNA repair genes and higher radiation sensitivity genomic scores. Post-operative radiation therapy (RT) was associated with a metastasis-free survival (MFS) benefit for patients with high stromal scores, but not for patients with low stromal scores (P(interaction)=0.02). CONCLUSTIONS: Expression of stromal infiltration markers is correlated with prostate cancer aggressiveness/progression and may be predictive of response to radiation therapy. Stromal infiltration markers should be studied and considered for incorporation into clinical prognostication and decision-making.
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- 2020
15. Akt1 regulates pathological angiogenesis, vascular maturation and permeability in vivo
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Chen, Juhua, Somanath, Payaningal R, Razorenova, Olga, Chen, William S, Hay, Nissim, Bornstein, Paul, and Byzova, Tatiana V
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Akt kinases control essential cellular functions, including proliferation, apoptosis, metabolism and transcription, and have been proposed as promising targets for treatment of angiogenesis-dependent pathologies, such as cancer and ischemic injury. But their precise roles in neovascularization remain elusive. Here we show that Akt1 is the predominant isoform in vascular cells and describe the unexpected consequences of Akt1 knockout on vascular integrity and pathological angiogenesis. Angiogenic responses in three distinct in vivo models were enhanced in Akt1[sup.-/-] mice; these enhanced responses were associated with impairment of blood vessel maturation and increased vascular permeability. Although impaired vascular maturation in Akt1[sup.-/-] mice may be attributed to reduced activation of endothelial nitric oxide synthase (eNOS), the major phenotypic changes in vascular permeability and angiogenesis were linked to reduced expression of two endogenous vascular regulators, thrombospondins 1 (TSP-1) and 2 (TSP-2). Re-expression of TSP-1 and TSP-2 in mice transplanted with wild-type bone marrow corrected the angiogenic abnormalities in Akt1[sup.-/-] mice. These findings establish a crucial role of an Akt-thrombospondin axis in angiogenesis., Author(s): Juhua Chen [1, 4]; Payaningal R Somanath [1, 4]; Olga Razorenova [1]; William S Chen [2]; Nissim Hay [2]; Paul Bornstein [3]; Tatiana V Byzova (corresponding author) [1] The [...]
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- 2005
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16. Epidemiology of Nonfatal Bicycle Injuries Presenting to United States Emergency Departments, 2001–2008
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Chen, William S., Dunn, Roger Y., Chen, Allison J., Linakis, James G., and Wilber, Scott T.
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- 2013
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17. Biological ion exchange shows promise to deliver safe water for island community.
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Chen, William S., Wright, Jaycee, and Mohseni, Madjid
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WATER purification ,BIOLOGICAL ion transport inhibition ,CARBON content of water ,ACTIVATED carbon - Abstract
The article informs that Gillies Bay, a community on Texada Island in British Columbia, has struggled with unstable access to clean water, leading to frequent boil water advisories. The study focused on biological ion exchange (BIEX) filtration, a method that sustains natural organic matter removal over time. The pilot system, consisting of BIEX and activated carbon filtration, demonstrated the feasibility of BIEX filtration as a long-term solution for Gillies Bay's water treatment needs.
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- 2023
18. Akt deficiency impairs normal cell proliferation and suppresses oncogenesis in a p53-independent and mTORC1-dependent manner
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Skeen, Jennifer E., Bhaskar, Prashanth T., Chen, Chia-Chen, Chen, William S., Peng, Xiao-ding, Nogueira, Veronique, Hahn-Windgassen, Annett, Kiyokawa, Hiroaki, and Hay, Nissim
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- 2006
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19. Large-scale assessment of needs in low vision individuals using the Aira assistive technology
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Nguyen,Brian J, Chen,William S, Chen,Allison J, Utt,Andrew, Hill,Emily, Apgar,Ryan, and Chao,Daniel L
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Clinical Ophthalmology - Abstract
Brian J Nguyen,1,2 William S Chen,3 Allison J Chen,1 Andrew Utt,4 Emily Hill,4 Ryan Apgar,5 Daniel L Chao1,2 1Shiley Eye Institute, University of California San Diego, La Jolla, CA, USA; 2University of California San Diego, School of Medicine, La Jolla, CA, USA; 3Yale School of Medicine, New Haven, CT, USA; 4Aira Tech Corp, La Jolla, CA, USA; 5University of New England, College of Osteopathic Medicine, Biddeford, ME, USACorrespondence: Daniel L ChaoShiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, La Jolla, CA 92093, USATel +1 858 534 6290Fax +1 619 543 1975Email d6chao@ucsd.eduPurpose: To systematically evaluate the needs of low vision individuals through call data obtained through the Aira assistive technology system.Patients and methods: Aira (Aira Tech Corporation, La Jolla, CA, USA) is an on-demand assistive wearable technology designed for individuals with low vision. The user wears glasses with an integrated front-facing video camera that connects with a remote human agent who assists the user with the specified task. Call types, temporal characteristics, and duration of call were compared by gender and vision status (low vision, light perception, and blind). Chi-square tests, t-tests, ANOVA, linear regression and Poisson regression analyses were performed.Results: 878 subscribers placed 10,022 total calls (4759 female, 5263 male) over 3 months. The most common categories were reading (35%), navigation (33%), and home management (16%). The distribution of categories (χ2=49.3, p
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- 2019
20. Impaired platelet responses to thrombin and collagen in AKT-1–deficient mice
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Chen, Juhua, De, Sarmishtha, Damron, Derek S., Chen, William S., Hay, Nissim, and Byzova, Tatiana V.
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- 2004
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21. Global absence and targeting of protective immune states in severe COVID-19.
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Combes, Alexis J., Courau, Tristan, Kuhn, Nicholas F., Hu, Kenneth H., Ray, Arja, Chen, William S., Chew, Nayvin W., Cleary, Simon J., Kushnoor, Divyashree, Reeder, Gabriella C., Shen, Alan, Tsui, Jessica, Hiam-Galvez, Kamir J., Muñoz-Sandoval, Priscila, Zhu, Wandi S., Lee, David S., Sun, Yang, You, Ran, Magnen, Mélia, and Rodriguez, Lauren
- Abstract
Although infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has pleiotropic and systemic effects in some individuals1–3, many others experience milder symptoms. Here, to gain a more comprehensive understanding of the distinction between severe and mild phenotypes in the pathology of coronavirus disease 2019 (COVID-19) and its origins, we performed a whole-blood-preserving single-cell analysis protocol to integrate contributions from all major immune cell types of the blood—including neutrophils, monocytes, platelets, lymphocytes and the contents of the serum. Patients with mild COVID-19 exhibit a coordinated pattern of expression of interferon-stimulated genes (ISGs)3 across every cell population, whereas these ISG-expressing cells are systemically absent in patients with severe disease. Paradoxically, individuals with severe COVID-19 produce very high titres of anti-SARS-CoV-2 antibodies and have a lower viral load compared to individuals with mild disease. Examination of the serum from patients with severe COVID-19 shows that these patients uniquely produce antibodies that functionally block the production of the ISG-expressing cells associated with mild disease, by activating conserved signalling circuits that dampen cellular responses to interferons. Overzealous antibody responses pit the immune system against itself in many patients with COVID-19, and perhaps also in individuals with other viral infections. Our findings reveal potential targets for immunotherapies in patients with severe COVID-19 to re-engage viral defence.Patients with mild COVID-19 show a pattern of interferon-stimulated gene (ISG) expression across all major cell types, but in patients with severe disease, antibodies block the production of these ISG-expressing cells. [ABSTRACT FROM AUTHOR]
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- 2021
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22. Radiation-Specific Clinical Data Should Be Included in Existing Large-Scale Genomic Datasets
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Chen, William S., Townsend, Jeffrey P., and Yu, James B.
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- 2017
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23. Genomic and clinical characterization of stromal infiltration markers in prostate cancer.
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Mahal, Brandon A., Alshalalfa, Mohammed, Zhao, Shuang G., Beltran, Himisha, Chen, William S., Chipidza, Fallon, Davicioni, Elai, Karnes, R. Jeffrey, Ku, Sheng‐Yu, Lotan, Tamara L., Muralidhar, Vinayak, Rebbeck, Timothy R., Schaeffer, Edward M., Spratt, Daniel E., Feng, Felix Y., Nguyen, Paul L., and Ku, Sheng-Yu
- Subjects
TUMOR markers ,DNA repair ,TUMOR microenvironment ,GENE expression ,GLEASON grading system ,PROSTATE diseases ,RESEARCH ,RESEARCH methodology ,CELL physiology ,EVALUATION research ,MEDICAL cooperation ,COMPARATIVE studies ,GENE expression profiling ,RESEARCH funding ,PROSTATE tumors ,LONGITUDINAL method - Abstract
Background: The progression of prostate cancer is a complex, multistep process that involves molecular alterations in cells of the tumor and the microenvironment, with associated interactions between the stroma and epithelium. Genomic expression analyses of stromal infiltration markers were performed to determine the significance thereof in prostate cancer.Methods: Genome-wide expression profiles of formalin-fixed, paraffin-embedded radical prostatectomy samples were evaluated from a prospective registry cohort (n = 5239) and 3 retrospective institutional cohorts (n = 1135). Two independent stromal gene expression signatures implied stromal infiltration. Cox proportional hazards regression defined the association between stromal infiltration expression and metastasis-free survival (MFS).Results: Stromal expression scores were correlated with stromal signature genes and with other key stromal markers (CAV1, VIM, and TAGLN), basal activity, and CD3 and CD4 immune biomarkers (r > 0.5 for all). The top decile of stromal expression was associated with high genomic risk scores (Decipher ≥ 0.6) , high Cancer of the Prostate Risk Assessment-Postsurgical scores, Gleason 9 to 10 disease, and a higher risk for metastasis (hazard ratio, 2.35; 95% CI, 1.37-4.02; P = .001). A higher stromal infiltration score was also associated with decreased expression of DNA repair genes and higher radiation sensitivity genomic scores. Postoperative radiation therapy (RT) was associated with an MFS benefit for patients with high stromal scores, but not for patients with low stromal scores (Pinteraction = .02).Conclusions: Expression of stromal infiltration markers is correlated with prostate cancer aggressiveness/progression and may be predictive of a response to RT. Stromal infiltration markers should be studied and considered for incorporation into clinical prognostication and decision making. [ABSTRACT FROM AUTHOR]- Published
- 2020
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24. The deficiency of Akt1 is sufficient to suppress tumor development in [Pten.sup.?-] mice
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Mei-Ling Chen, Pei-Zhang Xu, Xiao-ding Peng, Hay, Nissim, Chen, William S., Pandolfi, Pier Paolo, Guzman, Grace, and Ximing Yang
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Intestinal polyps -- Genetic aspects ,Cancer -- Research ,Tumor suppressor genes -- Research ,Tumor suppressor genes -- Structure ,Biological sciences - Abstract
An attempt is made to show the deficiency of Akt1 activity, which is sufficient to dramatically inhibit tumor development in [Pten.sup.?-] mice. It is suggested that even haplodeficiency of Akt1 is sufficient to markedly attenuate the development of high-grade prostrate intraepithelial neoplasia (PIN) and endo metrial carcinoma and also, the findings have vital implications for cancer therapy.
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- 2006
25. Dwarfism, impaired skin development, skeletal muscle atrophy, delayed bone development, and impeded adipogenesis in mice lacking Akt1 and Akt2
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Peng, Xiao-ding, Xu, Pei-Zhang, Chen, Mei-Ling, Hahn-Windgassen, Annett, Skeen, Jennifer, Jacobs, Joel, Sundararajan, Deepa, Chen, William S., Crawford, Susan E., Coleman, Kevin G., and Hay, Nissim
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Genetic research -- Analysis ,Genetic regulation -- Analysis ,Adipose tissues -- Genetic aspects ,Skin -- Genetic aspects ,Developmental genetics -- Research ,Atrophy, Muscular -- Causes of ,Dwarfism -- Causes of ,Biological sciences - Abstract
Research has been conducted on Akt1 and Akt2 double-knockout mice which exhibit growth deficiency, impaired skin development and severe muscle atrophy. The authors suggest that Akt may be the most critical downstream effector of the IGF-1 receptor during development.
- Published
- 2003
26. Genomic Drivers of Poor Prognosis and Enzalutamide Resistance in Metastatic Castration-resistant Prostate Cancer.
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Chen, William S., Aggarwal, Rahul, Zhang, Li, Zhao, Shuang G., Thomas, George V., Beer, Tomasz M., Quigley, David A., Foye, Adam, Playdle, Denise, Huang, Jiaoti, Lloyd, Paul, Lu, Eric, Sun, Duanchen, Guan, Xiangnan, Rettig, Matthew, Gleave, Martin, Evans, Christopher P., Youngren, Jack, True, Lawrence, and Lara, Primo
- Subjects
- *
CASTRATION-resistant prostate cancer , *FISHER exact test , *NUCLEOTIDE sequence - Abstract
Metastatic castration-resistant prostate cancer (mCRPC) is the lethal form of the disease. Several recent studies have identified genomic alterations in mCRPC, but the clinical implications of these genomic alterations have not been fully elucidated. To use whole-genome sequencing (WGS) to assess the association between key driver gene alterations and overall survival (OS), and to use whole-transcriptome RNA sequencing to identify genomic drivers of enzalutamide resistance. We performed survival analyses and gene set enrichment analysis (GSEA) on WGS and RNA sequencing results for a cohort of 101 mCRPC patients. OS was the clinical endpoint for all univariate and multivariable survival analyses. Candidate drivers of enzalutamide resistance were identified in an unbiased manner, and mutations of the top candidate were further assessed for enrichment among enzalutamide-resistant patients using Fisher's exact test. Harboring two DNA alterations in RB1 was independently predictive of poor OS (median 14.1 vs 42.0 mo; p = 0.007) for men with mCRPC. GSEA identified the Wnt/β-catenin pathway as the top differentially modulated pathway among enzalutamide-resistant patients. Furthermore, β-catenin mutations were exclusive to enzalutamide-resistant patients (p = 0.01) and independently predictive of poor OS (median 13.6 vs 41.7 mo; p = 0.025). The presence of two RB1 DNA alterations identified in our WGS analysis was independently associated with poor OS among men with mCRPC. The Wnt/β-catenin pathway plays an important role in enzalutamide resistance, with differential pathway expression and enrichment of β-catenin mutations in enzalutamide-resistant patients. Moreover, β-catenin mutations were predictive of poor OS in our cohort. We observed a correlation between genomic findings for biopsy samples from metastases from men with metastatic castration-resistant prostate cancer (mCRPC) and clinical outcomes. This work sheds new light on clinically relevant genomic alterations in mCRPC and provides a roadmap for the development of new personalized treatment regimens in mCRPC. The presence of two DNA alterations in RB1 is associated with poor overall survival independently of other clinicopathologic factors in metastatic castration-resistant prostate cancer. In addition, Wnt/β-catenin pathway activation and β-catenin mutations are associated with enzalutamide resistance and poor overall survival. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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27. CDKN2A Copy Number Loss Is an Independent Prognostic Factor in HPV-Negative Head and Neck Squamous Cell Carcinoma.
- Author
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Chen, William S., Bindra, Ranjit S., Mo, Allen, Hayman, Thomas, Husain, Zain, Contessa, Joseph N., Gaffney, Stephen G., Townsend, Jeffrey P., and Yu, James B.
- Subjects
SQUAMOUS cell carcinoma ,PAPILLOMAVIRUSES - Abstract
Background: HPV infection is associated with high p16 expression and good prognosis in head and neck squamous cell carcinomas (HNSCCs). Analysis of CDKN2A, the gene encoding p16, may further elucidate the association between p16 expression and prognosis. We sought to determine whether CDKN2A copy number loss was associated with poor survival in HPV-negative HNSCCs. Methods: The Cancer Genome Atlas HNSCC clinical and genomic data were obtained and integrated. Patients <80 years old with a primary tumor in the oral cavity, oropharynx, hypopharynx, or larynx were included. Stratifying by copy number loss status, CDKN2A mRNA and p16 protein expression levels were examined and overall survival (OS) and disease-free survival (DFS) were evaluated. results: 401 patients with HPV-negative HNSCC were identified. 146 patients demonstrated CDKN2A copy number loss. The CDKN2A copy number loss group expressed significantly lower levels of CDKN2A mRNA and p16 protein than did the non-copy number loss group. Median OS for patients with and without CDKN2A copy number loss was 16.5 and 46.6 months, respectively (p = 0.007). Median DFS for both groups was 11.6 and 19.2 months, respectively (p = 0.03). In both univariate and multivariable analyses, stage IV designation, receipt of chemotherapy and CDKN2A copy number loss were predictive of OS. conclusion: CDKN2A copy number loss predicted poor survival independently of other patient and treatment factors and may be a clinically useful prognostic factor. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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28. (S032) Investigating CDKN2A Copy Number Loss in HPV- and HPV+ Head and Neck Cancer: A Demonstration of Integrated Genomic and Clinical Analyses Using TCGA
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Chen, William S., Bindra, Ranjit S., Mo, Allen, Hayman, Thomas, Husain, Zain, Contessa, Joseph N., and Yu, James B.
- Published
- 2017
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29. EDITORIAL COMMENT.
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Chen, William S. and Roach III, Mack
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PROSTATE cancer ,EDITORIAL writing ,CHEMORADIOTHERAPY ,PROSTATECTOMY ,CANCER patients ,CLINICAL trials - Published
- 2022
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30. Automated Detection of Off-Label Drug Use.
- Author
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Jung, Kenneth, LePendu, Paea, Chen, William S., Iyer, Srinivasan V., Readhead, Ben, Dudley, Joel T., and Shah, Nigam H.
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DRUG utilization ,ESTIMATION theory ,PREDICTION models ,MEDICATION safety ,EPIDEMIOLOGY ,PHARMACOEPIDEMIOLOGY ,PHARMACY information services - Abstract
Off-label drug use, defined as use of a drug in a manner that deviates from its approved use defined by the drug's FDA label, is problematic because such uses have not been evaluated for safety and efficacy. Studies estimate that 21% of prescriptions are off-label, and only 27% of those have evidence of safety and efficacy. We describe a data-mining approach for systematically identifying off-label usages using features derived from free text clinical notes and features extracted from two databases on known usage (Medi-Span and DrugBank). We trained a highly accurate predictive model that detects novel off-label uses among 1,602 unique drugs and 1,472 unique indications. We validated 403 predicted uses across independent data sources. Finally, we prioritize well-supported novel usages for further investigation on the basis of drug safety and cost. [ABSTRACT FROM AUTHOR]
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- 2014
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31. Aktl governs breast cancer progression in vivo.
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Xiaoming Ju, Sanjay Katiyar, Chenguang Wang, Manran Liu, Xuanmao Jiao, Shengwen Li, Jie Zhou, Turner, Jacob, Lisanti, Michael P., Russell, Robert G., Mueller, Susette C., Ojeifo, John, Chen, William S., Hays, Nissim, and Pestell, Richard G.
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BREAST cancer ,CELL metabolism ,MAMMARY glands ,CANCER cells ,CARCINOGENESIS ,TUMOR growth ,PHOSPHORYLATION - Abstract
The serine threonine kinase Akt1 has been implicated in the control of cellular metabolism, survival and growth. Here, disruption of the ubiquitously expressed member of the Akt family of genes, Akt1, in the mouse demonstrates a requirement for Akt1 in ErbB2-induced mammary tumorigenesis. Akt1 deficiency delayed tumor growth and reduced lung metastases, correlating with a reduction in phosphorylation of the Akt1 target, tuberous sclerosis 2 (TSC2) at Sero939. Akt1-deficient mammary epithelial tumor cells (MEC) were reduced in size and proliferative capacity, with reduced cyclin D1 and p27
KIP1 abundance. Akt1 deficiency abrogated the oncogene-induced changes in polarization of MEC in three-dimensional culture and reverted oncogene-induced relocalization of the phosphorylated ezrin-radixin-moesin proteins. Akt1 increased MEC migration across an endothelial cell barrier, enhancing the persistence of migratory directionality. An unbiased proteomic analysis demonstrated Akt1 mediated MEC migration through paracrine signaling via induction of expression and secretion of CXCL16 and MIP1γ. Akt1 governs MEC polarity, migratory directionality and breast cancer onset induced by ErbB2 in vivo. [ABSTRACT FROM AUTHOR]- Published
- 2007
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32. Akt1 regulates pathological angiogenesis, vascular maturation and permeability in vivo.
- Author
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Juhua Chen, Somanath, Payaningal R., Razorenova, Olga, Chen, William S., Hay, Nissim, Bornstein, Paul, and Byzova, Tatiana V.
- Subjects
NEOVASCULARIZATION ,PROTEIN kinases ,APOPTOSIS ,BLOOD-vessel development ,CELL proliferation - Abstract
Akt kinases control essential cellular functions, including proliferation, apoptosis, metabolism and transcription, and have been proposed as promising targets for treatment of angiogenesis-dependent pathologies, such as cancer and ischemic injury. But their precise roles in neovascularization remain elusive. Here we show that Akt1 is the predominant isoform in vascular cells and describe the unexpected consequences of Akt1 knockout on vascular integrity and pathological angiogenesis. Angiogenic responses in three distinct in vivo models were enhanced in Akt1
−/− mice; these enhanced responses were associated with impairment of blood vessel maturation and increased vascular permeability. Although impaired vascular maturation in Akt1−/− mice may be attributed to reduced activation of endothelial nitric oxide synthase (eNOS), the major phenotypic changes in vascular permeability and angiogenesis were linked to reduced expression of two endogenous vascular regulators, thrombospondins 1 (TSP-1) and 2 (TSP-2). Re-expression of TSP-1 and TSP-2 in mice transplanted with wild-type bone marrow corrected the angiogenic abnormalities in Akt1−/− mice. These findings establish a crucial role of an Akt-thrombospondin axis in angiogenesis. [ABSTRACT FROM AUTHOR]- Published
- 2005
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- View/download PDF
33. Requirement for intrinsic protein tyrosine kinase in the immediate and late actions of the EGF receptor.
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Chen, William S., Lazar, Cheri S., Poenie, Martin, Tsien, Roger Y., Gill, Gordon N., and Rosenfeld, Michael G.
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- 1987
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34. Apoptosis in mouse embryos: Elevated levels in pregastrulae and in the distal anterior region of gastrulae of normal and mutant mice.
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Manova, Katia, Tomihara-Newberger, Carol, Wang, Shasha, Godelman, Alla, Kalantry, Sundeep, Witty-Blease, Karen, De Leon, Victor, Chen, William S., Lacy, Elizabeth, and Bachvarova, Rosemary F.
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- 1998
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35. Measurements of aerodynamic noise on a flat plate in supersonic flow
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Chen, William S.
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Physics::Fluid Dynamics ,Aeronautics - Abstract
NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. Measurements of aerodynamic noise, in the form of pressure fluctuations in a turbulent boundary layer, were made on a smooth flat plate in the 12- and 20-in. supersonic wind tunnels at the Jet Propulsion Laboratory. The noise was measured with small piezoelectric pressure transducers (0.015-0.03 in. diameter) constructed of barium titanate crystals which were flush-mounted in the flat plate. Spectral-energy distributions of the pressure fluctuations are obtained up to a frequency of 0.5 mc at freestream Mach numbers from 2.0 to 5.0, and Reynolds numbers based an bound layer-displacement thickness from 5 x 10(3) to 5 x 10(4). By grouping the test variables into the proper nondimensional forms and correcting for the finite transducer size, the energy spectra are found to be similar and uniquely related to both Mach number and Reynolds number. The total, or integrated, level of noise at the plate surface, in terms of root-mean-square values of the pressure fluctuations, is a constant equal to about 10 times the shear stress [...] the wall. The intensity, [...], is directly proportional to the fourth power of the freestream Mach number. Correlation measurements in time and in the streamwise direction in space show that the noise at the plate surface to convected downstream with a characteristic velocity equal to 75% of the freestream velocity. The correlation dies off rapidly with spacing between pickup points, and the convection velocity shows no dependence on either Mach number or Reynolds number.
- Published
- 1961
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36. Dwarfism, impaired skin development, skeletal muscle atrophy, delayed bone development, and impeded adipogenesis in mice lacking Akt1 and Akt2.
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Xiao-ding Peng, Pei-Zhang Xu, Mei-Ling Chen, Hahn-Windgassen, Annett, Skeen, Jennifer, Jacobs, Joel, Sundararajan, Deepa, Chen, William S., Crawford, Susan E., Coleman, Kevin G., and Hay, Nissim
- Subjects
- *
SERINE , *GENETICS , *AMINO acids , *MICE , *BIOLOGY - Abstract
Presents a study which examined the function of serine/threonine kinase akt1 and akt2 in mice. Growth deficiency and diseases observed in mice without akt1 and akt 2; Characterization of the three isoforms of akt; Genotype distribution of newborn mice derived from akt1 and akt2 double-heterozygous mating.
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- 2003
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37. Down-regulation of ADRB2 expression is associated with small cell neuroendocrine prostate cancer and adverse clinical outcomes in castration-resistant prostate cancer.
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Kwon, Daniel H., Zhang, Li, Quigley, David A., Foye, Adam, Chen, William S., Wong, Christopher K., Feng, Felix Y., Bailey, Adina, Huang, Jiaoti, Stuart, Joshua M., Friedl, Verena, Weinstein, Alana S., Beer, Tomasz M., Alumkal, Joshi J., Rettig, Matthew, Gleave, Martin, Lara, Primo N., Thomas, George V., Li, Patricia, and Lui, Austin
- Subjects
- *
CASTRATION-resistant prostate cancer , *ADRENERGIC receptors , *PROSTATE cancer , *NEUROENDOCRINE cells , *PROPORTIONAL hazards models , *BETA adrenoceptors , *SYMPATHOMIMETIC agents - Abstract
Objectives: The net oncogenic effect of β2-adrenergic receptor ADRB2, whose downstream elements induce neuroendocrine differentiation and whose expression is regulated by EZH2, is unclear. ADRB2 expression and associated clinical outcomes in metastatic castration-resistant prostate cancer (mCRPC) are unknown.Methods and Materials: This was a retrospective analysis of a multi-center, prospectively enrolled cohort of mCRPC patients. Metastatic biopsies were obtained at progression, and specimens underwent laser capture microdissection and RNA-seq. ADRB2 expression was stratified by histology and clustering based on unsupervised hierarchical transcriptome analysis and correlated with EZH2 expression; an external dataset was used for validation. The association between ADRB2 expression and overall survival (OS) was assessed by log-rank test and a multivariable Cox proportional hazard model.Results: One hundred and twenty-seven patients with progressive mCRPC had sufficient metastatic tumor for RNA-seq. ADRB2 expression was lowest in the small cell-enriched transcriptional cluster (P < 0.01) and correlated inversely with EZH2 expression (r = -0.28, P < 0.01). These findings were validated in an external cohort enriched for neuroendocrine differentiation. Patients with tumors harboring low ADRB2 expression (lowest quartile) had a shorter median OS than those with higher (9.5 vs. 20.5 months, P = 0.02). In multivariable analysis, low ADRB2 expression was associated with a trend toward shorter OS (HR for death = 1.54, 95%CI 0.98-2.44). Conversely, higher expression of upstream transcriptional regulator EZH2 was associated with shortened OS (HR for death = 3.01, 95%CI 1.12-8.09).Conclusions: Low ADRB2 expression is associated with neuroendocrine differentiation and is associated with shortened survival. EZH2 is a potential therapeutic target for preventing neuroendocrine transdifferentiation and improving outcomes in mCRPC. Further studies of agents targeting β-adrenergic signaling are warranted. [ABSTRACT FROM AUTHOR]- Published
- 2020
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38. The deficiency of Akt1 is sufficient to suppress tumor development in Pten+/- mice.
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Mei-Ling Chen, Pei-Zhang Xu, Xiao Peng, Chen, William S., Guzman, Grace, Ximing Yang, Di Cristofano, Antonio, Pandolfi, Pier Paolo, and Hay, Nissim
- Subjects
- *
TUMOR suppressor genes , *TUMOR suppressor proteins , *ONCOGENES , *PROTEINS , *CARCINOGENESIS - Abstract
The tumor suppressor PTEN is frequently inactivated in human cancers. A major downstream effector of PTEN is Akt, which is hyperactivated via PTEN inactivation. It is not known, however, whether diminished Akt activity is sufficient to inhibit tumorigenesis initiated by Pten deficiency. Here we showed that the deficiency of Akt1 is sufficient to dramatically inhibit tumor development in Pten+/- mice. Akt1 deficiency had a profound effect on endometrium and prostate neoplasia, two types of human cancer, in which PTEN is frequently mutated, and also affected thyroid and adrenal medulla tumors and intestinal polyps. Even haplodeficiency of Akt1 was sufficient to markedly attenuate the development of high-grade prostate intraepithelial neoplasia (PIN) and endometrial carcinoma. These results have significant implications for cancer therapy. [ABSTRACT FROM AUTHOR]
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- 2006
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39. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.
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Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, and Feng FY
- Subjects
- Male, Humans, Prostate, Biopsy, 5-Methylcytosine, Prostatic Neoplasms
- Abstract
Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease., Significance: In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880., (©2022 The Authors; Published by the American Association for Cancer Research.)
- Published
- 2022
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40. Autoantibody Landscape in Patients with Advanced Prostate Cancer.
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Chen WS, Haynes WA, Waitz R, Kamath K, Vega-Crespo A, Shrestha R, Zhang M, Foye A, Baselga Carretero I, Perez Garcilazo I, Zhang M, Zhao SG, Sjöström M, Quigley DA, Chou J, Beer TM, Rettig M, Gleave M, Evans CP, Lara P, Chi KN, Reiter RE, Alumkal JJ, Ashworth A, Aggarwal R, Small EJ, Daugherty PS, Ribas A, Oh DY, Shon JC, and Feng FY
- Subjects
- Aged, Autoantibodies blood, Biomarkers, Tumor genetics, Biomarkers, Tumor immunology, Case-Control Studies, Follow-Up Studies, Humans, Male, Mutation, Prognosis, Prospective Studies, Prostatic Neoplasms blood, Prostatic Neoplasms pathology, Antigens, Neoplasm immunology, Autoantibodies immunology, Biomarkers, Tumor blood, Epitopes immunology, Prostatic Neoplasms immunology
- Abstract
Purpose: Autoantibody responses in cancer are of great interest, as they may be concordant with T-cell responses to cancer antigens or predictive of response to cancer immunotherapies. Thus, we sought to characterize the antibody landscape of metastatic castration-resistant prostate cancer (mCRPC)., Experimental Design: Serum antibody epitope repertoire analysis (SERA) was performed on patient serum to identify tumor-specific neoepitopes. Somatic mutation-specific neoepitopes were investigated by associating serum epitope enrichment scores with whole-genome sequencing results from paired solid tumor metastasis biopsies and germline blood samples. A protein-based immunome-wide association study (PIWAS) was performed to identify significantly enriched epitopes, and candidate serum antibodies enriched in select patients were validated by ELISA profiling. A distinct cohort of patients with melanoma was evaluated to validate the top cancer-specific epitopes., Results: SERA was performed on 1,229 serum samples obtained from 72 men with mCRPC and 1,157 healthy control patients. Twenty-nine of 6,636 somatic mutations (0.44%) were associated with an antibody response specific to the mutated peptide. PIWAS analyses identified motifs in 11 proteins, including NY-ESO-1 and HERVK-113, as immunogenic in mCRPC, and ELISA confirmed serum antibody enrichment in candidate patients. Confirmatory PIWAS, Identifying Motifs Using Next-generation sequencing Experiments (IMUNE), and ELISA analyses performed on serum samples from 106 patients with melanoma similarly revealed enriched cancer-specific antibody responses to NY-ESO-1., Conclusions: We present the first large-scale profiling of autoantibodies in advanced prostate cancer, utilizing a new antibody profiling approach to reveal novel cancer-specific antigens and epitopes. Our study recovers antigens of known importance and identifies novel tumor-specific epitopes of translational interest., (©2020 American Association for Cancer Research.)
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- 2020
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41. Global Absence and Targeting of Protective Immune States in Severe COVID-19.
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Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, and Krummel MF
- Abstract
While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holistic understanding of the severe/mild distinction in COVID-19 pathology, and its origins. We performed a whole-blood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum. Patients with mild COVID-19 disease display a coordinated pattern of interferon-stimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease. Examination of the serum from severe patients demonstrates that they uniquely produce antibodies with multiple patterns of specificity against interferon-stimulated cells and that those antibodies functionally block the production of the mild disease-associated ISG-expressing cells. Overzealous and auto-directed antibody responses pit the immune system against itself in many COVID-19 patients and this defines targets for immunotherapies to allow immune systems to provide viral defense., One Sentence Summary: In severe COVID-19 patients, the immune system fails to generate cells that define mild disease; antibodies in their serum actively prevents the successful production of those cells.
- Published
- 2020
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42. Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer.
- Author
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Guan X, Sun D, Lu E, Urrutia JA, Reiter RE, Rettig M, Evans CP, Lara P Jr, Gleave M, Beer TM, Thomas GV, Huang J, Aggarwal RR, Quigley DA, Foye A, Chen WS, Youngren J, Weinstein AS, Stuart JM, Feng FY, Small EJ, Xia Z, and Alumkal JJ
- Subjects
- Benzamides therapeutic use, Biopsy, DNA Copy Number Variations, Disease-Free Survival, Humans, Male, Nitriles therapeutic use, Phenylthiohydantoin therapeutic use, Prostate pathology, Prostatic Neoplasms, Castration-Resistant drug therapy, Prostatic Neoplasms, Castration-Resistant mortality, Prostatic Neoplasms, Castration-Resistant pathology, RNA-Seq, Survival Analysis, Benzamides pharmacology, Biomarkers, Tumor genetics, Chromosomes, Human, Pair 17 genetics, Drug Resistance, Neoplasm genetics, Nitriles pharmacology, Phenylthiohydantoin pharmacology, Prostatic Neoplasms, Castration-Resistant genetics
- Abstract
Purpose: The purpose of this study was to measure genomic changes that emerge with enzalutamide treatment using analyses of whole-genome sequencing and RNA sequencing., Experimental Design: One hundred and one tumors from men with metastatic castration-resistant prostate cancer (mCRPC) who had not been treated with enzalutamide ( n = 64) or who had enzalutamide-resistant mCRPC ( n = 37) underwent whole genome sequencing. Ninety-nine of these tumors also underwent RNA sequencing. We analyzed the genomes and transcriptomes of these mCRPC tumors., Results: Copy number loss was more common than gain in enzalutamide-resistant tumors. Specially, we identified 124 protein-coding genes that were more commonly lost in enzalutamide-resistant samples. These 124 genes included eight putative tumor suppressors located at nine distinct genomic regions. We demonstrated that focal deletion of the 17q22 locus that includes RNF43 and SRSF1 was not present in any patient with enzalutamide-naïve mCRPC but was present in 16% (6/37) of patients with enzalutamide-resistant mCRPC. 17q22 loss was associated with lower RNF43 and SRSF1 expression and poor overall survival from time of biopsy [median overall survival of 19.3 months in 17q22 intact vs. 8.9 months in 17q22 loss, HR, 3.44 95% confidence interval (CI), 1.338-8.867, log-rank P = 0.006]. Finally, 17q22 loss was linked with activation of several targetable factors, including CDK1/2, Akt, and PLK1, demonstrating the potential therapeutic relevance of 17q22 loss in mCRPC., Conclusions: Copy number loss is common in enzalutamide-resistant tumors. Focal deletion of chromosome 17q22 defines a previously unappreciated molecular subset of enzalutamide-resistant mCRPC associated with poor clinical outcome., (©2020 American Association for Cancer Research.)
- Published
- 2020
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43. Novel RB1-Loss Transcriptomic Signature Is Associated with Poor Clinical Outcomes across Cancer Types.
- Author
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Chen WS, Alshalalfa M, Zhao SG, Liu Y, Mahal BA, Quigley DA, Wei T, Davicioni E, Rebbeck TR, Kantoff PW, Maher CA, Knudsen KE, Small EJ, Nguyen PL, and Feng FY
- Subjects
- Biomarkers, Tumor, Disease Progression, Humans, Male, Prognosis, Neoplasms, Transcriptome
- Abstract
Purpose: Rb-pathway disruption is of great clinical interest, as it has been shown to predict outcomes in multiple cancers. We sought to develop a transcriptomic signature for detecting biallelic RB1 loss (RBS) that could be used to assess the clinical implications of RB1 loss on a pan-cancer scale., Experimental Design: We utilized data from the Cancer Cell Line Encyclopedia ( N = 995) to develop the first pan-cancer transcriptomic signature for predicting biallelic RB1 loss (RBS). Model accuracy was validated using The Cancer Genome Atlas (TCGA) Pan-Cancer dataset ( N = 11,007). RBS was then used to assess the clinical relevance of biallelic RB1 loss in TCGA Pan-Cancer and in an additional metastatic castration-resistant prostate cancer (mCRPC) cohort., Results: RBS outperformed the leading existing signature for detecting RB1 biallelic loss across all cancer types in TCGA Pan-Cancer (AUC, 0.89 vs. 0.66). High RBS ( RB1 biallelic loss) was associated with promoter hypermethylation ( P = 0.008) and gene body hypomethylation ( P = 0.002), suggesting RBS could detect epigenetic gene silencing. TCGA Pan-Cancer clinical analyses revealed that high RBS was associated with short progression-free ( P < 0.00001), overall ( P = 0.0004), and disease-specific ( P < 0.00001) survival. On multivariable analyses, high RBS was predictive of shorter progression-free survival in TCGA Pan-Cancer ( P = 0.03) and of shorter overall survival in mCRPC ( P = 0.004) independently of the number of DNA alterations in RB1 ., Conclusions: Our study provides the first validated tool to assess RB1 biallelic loss across cancer types based on gene expression. RBS can be useful for analyzing datasets with or without DNA-sequencing results to investigate the emerging prognostic and treatment implications of Rb-pathway disruption. See related commentary by Choudhury and Beltran, p. 4199 ., (©2019 American Association for Cancer Research.)
- Published
- 2019
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44. Clinical and Genomic Implications of Luminal and Basal Subtypes Across Carcinomas.
- Author
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Zhao SG, Chen WS, Das R, Chang SL, Tomlins SA, Chou J, Quigley DA, Dang HX, Barnard TJ, Mahal BA, Gibb EA, Liu Y, Davicioni E, Duska LR, Posadas EM, Jolly S, Spratt DE, Nguyen PL, Maher CA, Small EJ, and Feng FY
- Subjects
- Antineoplastic Agents pharmacology, Antineoplastic Agents therapeutic use, Biomarkers, Tumor, Carcinoma drug therapy, Carcinoma, Basal Cell drug therapy, Cell Line, Tumor, Computational Biology methods, Drug Resistance, Neoplasm genetics, Gene Expression Profiling, Gene Expression Regulation, Neoplastic drug effects, Humans, Kaplan-Meier Estimate, Mutation, Prognosis, Transcriptome, Carcinoma diagnosis, Carcinoma genetics, Carcinoma, Basal Cell diagnosis, Carcinoma, Basal Cell genetics, Genetic Association Studies methods, Genetic Predisposition to Disease, Genomics methods
- Abstract
Purpose: Carcinomas originate from epithelial tissues, which have apical (luminal) and basal orientations. The degree of luminal versus basal differentiation in cancer has been shown to be biologically important in some carcinomas and impacts treatment response., Experimental Design: Although prior studies have focused on individual cancer types, we used a modified clinical-grade classifier (PAM50) to subtype 8,764 tumors across 22 different carcinomas into luminal A, luminal B, and basal-like tumors., Results: We found that all epithelial tumors demonstrated similar gene expression-based luminal/basal subtypes. As expected, basal-like tumors were associated with increased expression of the basal markers KRT5/6 and KRT14, and luminal-like tumors were associated with increased expression of the luminal markers KRT20. Luminal A tumors consistently had improved outcomes compared with basal across many tumor types, with luminal B tumors falling between the two. Basal tumors had the highest rates of TP53 and RB1 mutations and copy number loss. Luminal breast, cervical, ovarian, and endometrial tumors had increased ESR1 expression, and luminal prostate, breast, cervical, and bladder tumors had increased androgen receptor (AR) expression. Furthermore, luminal B tumors had the highest rates of AR and ESR1 mutations and had increased sensitivity in vitro to bicalutamide and tamoxifen. Luminal B tumors were more sensitive to gemcitabine, and basal tumors were more sensitive to docetaxel., Conclusions: This first pan-carcinoma luminal/basal subtyping across epithelial tumors reveals global similarities across carcinomas in the transcriptome, genome, clinical outcomes, and drug sensitivity, emphasizing the biological and translational importance of these luminal versus basal subtypes., (©2018 American Association for Cancer Research.)
- Published
- 2019
- Full Text
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45. Leptin deficiency and beta-cell dysfunction underlie type 2 diabetes in compound Akt knockout mice.
- Author
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Chen WS, Peng XD, Wang Y, Xu PZ, Chen ML, Luo Y, Jeon SM, Coleman K, Haschek WM, Bass J, Philipson LH, and Hay N
- Subjects
- Animals, Blood Glucose metabolism, Diabetes Mellitus, Type 2 blood, Feeding Behavior, Homeostasis, In Vitro Techniques, Insulin metabolism, Insulin Secretion, Insulin-Secreting Cells metabolism, Insulin-Secreting Cells pathology, Isoenzymes deficiency, Isoenzymes metabolism, Leptin blood, Mice, Mice, Knockout, Diabetes Mellitus, Type 2 enzymology, Diabetes Mellitus, Type 2 physiopathology, Insulin-Secreting Cells enzymology, Leptin deficiency, Proto-Oncogene Proteins c-akt deficiency, Proto-Oncogene Proteins c-akt metabolism
- Abstract
Phenotypic analyses of mice null for the individual Akt isoforms suggested that they are functionally distinct and that only Akt2 plays a role in diabetes. We show here that Akt isoforms play compensatory and complementary roles in glucose homeostasis and diabetes. Insulin resistance in Akt2(-/-) mice was inhibited by haplodeficiency of Pten, suggesting that other Akt isoforms can compensate for Akt2 function. Haplodeficiency of Akt1 in Akt2(-/-) mice, however, converts prediabetes to overt type 2 diabetes, which is also reversed by haplodeficiency of Pten. Akt3 does not appear to contribute significantly to diabetes. Overt type 2 diabetes in Akt1(+/-) Akt2(-/-) mice is manifested by hyperglycemia due to beta-cell dysfunction combined with impaired glucose homeostasis due to markedly decreased leptin levels. Restoring leptin levels was sufficient to restore normal blood glucose and insulin levels in Akt1(+/-) Akt2(-/-) and Akt2(-/-) mice, suggesting that leptin-deficiency is the predominant cause of diabetes in these mice. These results uncover a new mechanism linking Akt to diabetes, provide a therapeutic strategy, and show that diabetes induced as a consequence of cancer therapy, via Akt inhibition, could be reversed by leptin therapy.
- Published
- 2009
- Full Text
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46. Akt1 in osteoblasts and osteoclasts controls bone remodeling.
- Author
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Kawamura N, Kugimiya F, Oshima Y, Ohba S, Ikeda T, Saito T, Shinoda Y, Kawasaki Y, Ogata N, Hoshi K, Akiyama T, Chen WS, Hay N, Tobe K, Kadowaki T, Azuma Y, Tanaka S, Nakamura K, Chung UI, and Kawaguchi H
- Subjects
- Animals, Apoptosis Regulatory Proteins metabolism, Bcl-2-Like Protein 11, Cell Differentiation, Forkhead Box Protein O1, Forkhead Box Protein O3, Forkhead Transcription Factors chemistry, Forkhead Transcription Factors metabolism, Humans, Membrane Proteins metabolism, Mice, Mice, Inbred C57BL, Mice, Transgenic, Models, Biological, Osteoblasts metabolism, Proto-Oncogene Proteins metabolism, RANK Ligand metabolism, Bone Remodeling, Osteoblasts enzymology, Osteoclasts enzymology, Proto-Oncogene Proteins c-akt biosynthesis
- Abstract
Bone mass and turnover are maintained by the coordinated balance between bone formation by osteoblasts and bone resorption by osteoclasts, under regulation of many systemic and local factors. Phosphoinositide-dependent serine-threonine protein kinase Akt is one of the key players in the signaling of potent bone anabolic factors. This study initially showed that the disruption of Akt1, a major Akt in osteoblasts and osteoclasts, in mice led to low-turnover osteopenia through dysfunctions of both cells. Ex vivo cell culture analyses revealed that the osteoblast dysfunction was traced to the increased susceptibility to the mitochondria-dependent apoptosis and the decreased transcriptional activity of runt-related transcription factor 2 (Runx2), a master regulator of osteoblast differentiation. Notably, our findings revealed a novel role of Akt1/forkhead box class O (FoxO) 3a/Bim axis in the apoptosis of osteoblasts: Akt1 phosphorylates the transcription factor FoxO3a to prevent its nuclear localization, leading to impaired transactivation of its target gene Bim which was also shown to be a potent proapoptotic molecule in osteoblasts. The osteoclast dysfunction was attributed to the cell autonomous defects of differentiation and survival in osteoclasts and the decreased expression of receptor activator of nuclear factor-kappaB ligand (RANKL), a major determinant of osteoclastogenesis, in osteoblasts. Akt1 was established as a crucial regulator of osteoblasts and osteoclasts by promoting their differentiation and survival to maintain bone mass and turnover. The molecular network found in this study will provide a basis for rational therapeutic targets for bone disorders.
- Published
- 2007
- Full Text
- View/download PDF
47. The deficiency of Akt1 is sufficient to suppress tumor development in Pten+/- mice.
- Author
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Chen ML, Xu PZ, Peng XD, Chen WS, Guzman G, Yang X, Di Cristofano A, Pandolfi PP, and Hay N
- Subjects
- Adrenal Gland Neoplasms enzymology, Adrenal Gland Neoplasms genetics, Adrenal Gland Neoplasms pathology, Animals, Endometrial Neoplasms enzymology, Endometrial Neoplasms genetics, Endometrial Neoplasms pathology, Female, Heterozygote, Intestinal Polyps enzymology, Intestinal Polyps pathology, Male, Mice, Neoplasms genetics, Prostatic Intraepithelial Neoplasia enzymology, Prostatic Intraepithelial Neoplasia genetics, Prostatic Intraepithelial Neoplasia pathology, Prostatic Neoplasms enzymology, Prostatic Neoplasms genetics, Prostatic Neoplasms pathology, Proto-Oncogene Proteins c-akt genetics, Pseudolymphoma enzymology, Pseudolymphoma genetics, Pseudolymphoma pathology, Thyroid Neoplasms enzymology, Thyroid Neoplasms genetics, Thyroid Neoplasms pathology, Neoplasms enzymology, Neoplasms pathology, PTEN Phosphohydrolase genetics, PTEN Phosphohydrolase metabolism, Proto-Oncogene Proteins c-akt deficiency
- Abstract
The tumor suppressor PTEN is frequently inactivated in human cancers. A major downstream effector of PTEN is Akt, which is hyperactivated via PTEN inactivation. It is not known, however, whether diminished Akt activity is sufficient to inhibit tumorigenesis initiated by Pten deficiency. Here we showed that the deficiency of Akt1 is sufficient to dramatically inhibit tumor development in Pten+/- mice. Akt1 deficiency had a profound effect on endometrium and prostate neoplasia, two types of human cancer, in which PTEN is frequently mutated, and also affected thyroid and adrenal medulla tumors and intestinal polyps. Even haplodeficiency of Akt1 was sufficient to markedly attenuate the development of high-grade prostate intraepithelial neoplasia (PIN) and endometrial carcinoma. These results have significant implications for cancer therapy.
- Published
- 2006
- Full Text
- View/download PDF
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