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1. Author Correction: Evasion of immunosurveillance by genomic alterations of PPARγ/RXRα in bladder cancer

Author

Korpal, Manav, Puyang, Xiaoling, Wu, Zhenhua Jeremy, Seiler, Roland, Furman, Craig, Oo, Htoo Zarni, Seiler, Michael, Irwin, Sean, Subramanian, Vanitha, Joshi, Jaya Julie, Wang, Chris K., Rimkunas, Victoria, Tortora, Davide, Yang, Hua, Kumar, Namita, Kuznetsov, Galina, Matijevic, Mark, Chow, Jesse, Kumar, Pavan, Zou, Jian, Feala, Jacob, Corson, Laura, Henry, Ryan, Selvaraj, Anand, Davis, Allison, Bloudoff, Kristjan, Douglas, James, Kiss, Bernhard, Roberts, Morgan, Fazli, Ladan, Black, Peter C., Fekkes, Peter, Smith, Peter G., Warmuth, Markus, Yu, Lihua, Hao, Ming-Hong, Larsen, Nicholas, Daugaard, Mads, and Zhu, Ping

Published
2019
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2. Figures S1-S6 from Discovery of Selective Estrogen Receptor Covalent Antagonists for the Treatment of ERαWT and ERαMUT Breast Cancer

Author

Puyang, Xiaoling, primary, Furman, Craig, primary, Zheng, Guo Zhu, primary, Wu, Zhenhua J., primary, Banka, Deepti, primary, Aithal, Kiran, primary, Agoulnik, Sergei, primary, Bolduc, David M., primary, Buonamici, Silvia, primary, Caleb, Benjamin, primary, Das, Subhasree, primary, Eckley, Sean, primary, Fekkes, Peter, primary, Hao, Ming-Hong, primary, Hart, Andrew, primary, Houtman, René, primary, Irwin, Sean, primary, Joshi, Jaya J., primary, Karr, Craig, primary, Kim, Amy, primary, Kumar, Namita, primary, Kumar, Pavan, primary, Kuznetsov, Galina, primary, Lai, Weidong G., primary, Larsen, Nicholas, primary, Mackenzie, Crystal, primary, Martin, Lesley-Ann, primary, Melchers, Diana, primary, Moriarty, Alyssa, primary, Nguyen, Tuong-Vi, primary, Norris, John, primary, O'Shea, Morgan, primary, Pancholi, Sunil, primary, Prajapati, Sudeep, primary, Rajagopalan, Sujatha, primary, Reynolds, Dominic J., primary, Rimkunas, Victoria, primary, Rioux, Nathalie, primary, Ribas, Ricardo, primary, Siu, Amy, primary, Sivakumar, Sasirekha, primary, Subramanian, Vanitha, primary, Thomas, Michael, primary, Vaillancourt, Frédéric H., primary, Wang, John, primary, Wardell, Suzanne, primary, Wick, Michael J., primary, Yao, Shihua, primary, Yu, Lihua, primary, Warmuth, Markus, primary, Smith, Peter G., primary, Zhu, Ping, primary, and Korpal, Manav, primary

Published
2023
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3. Data from Covalent ERα Antagonist H3B-6545 Demonstrates Encouraging Preclinical Activity in Therapy-Resistant Breast Cancer

Author

Furman, Craig, primary, Puyang, Xiaoling, primary, Zhang, Zhaojie, primary, Wu, Zhenhua J., primary, Banka, Deepti, primary, Aithal, Kiran B., primary, Albacker, Lee A., primary, Hao, Ming-Hong, primary, Irwin, Sean, primary, Kim, Amy, primary, Montesion, Meagan, primary, Moriarty, Alyssa D., primary, Murugesan, Karthikeyan, primary, Nguyen, Tuong-Vi, primary, Rimkunas, Victoria, primary, Sahmoud, Tarek, primary, Wick, Michael J., primary, Yao, Shihua, primary, Zhang, Xun, primary, Zeng, Hao, primary, Vaillancourt, Frédéric H., primary, Bolduc, David M., primary, Larsen, Nicholas, primary, Zheng, Guo Zhu, primary, Prajapati, Sudeep, primary, Zhu, Ping, primary, and Korpal, Manav, primary

Published
2023
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4. Data from Discovery of Selective Estrogen Receptor Covalent Antagonists for the Treatment of ERαWT and ERαMUT Breast Cancer

Author

Puyang, Xiaoling, primary, Furman, Craig, primary, Zheng, Guo Zhu, primary, Wu, Zhenhua J., primary, Banka, Deepti, primary, Aithal, Kiran, primary, Agoulnik, Sergei, primary, Bolduc, David M., primary, Buonamici, Silvia, primary, Caleb, Benjamin, primary, Das, Subhasree, primary, Eckley, Sean, primary, Fekkes, Peter, primary, Hao, Ming-Hong, primary, Hart, Andrew, primary, Houtman, René, primary, Irwin, Sean, primary, Joshi, Jaya J., primary, Karr, Craig, primary, Kim, Amy, primary, Kumar, Namita, primary, Kumar, Pavan, primary, Kuznetsov, Galina, primary, Lai, Weidong G., primary, Larsen, Nicholas, primary, Mackenzie, Crystal, primary, Martin, Lesley-Ann, primary, Melchers, Diana, primary, Moriarty, Alyssa, primary, Nguyen, Tuong-Vi, primary, Norris, John, primary, O'Shea, Morgan, primary, Pancholi, Sunil, primary, Prajapati, Sudeep, primary, Rajagopalan, Sujatha, primary, Reynolds, Dominic J., primary, Rimkunas, Victoria, primary, Rioux, Nathalie, primary, Ribas, Ricardo, primary, Siu, Amy, primary, Sivakumar, Sasirekha, primary, Subramanian, Vanitha, primary, Thomas, Michael, primary, Vaillancourt, Frédéric H., primary, Wang, John, primary, Wardell, Suzanne, primary, Wick, Michael J., primary, Yao, Shihua, primary, Yu, Lihua, primary, Warmuth, Markus, primary, Smith, Peter G., primary, Zhu, Ping, primary, and Korpal, Manav, primary

Published
2023
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5. Supplementary Figure from Covalent ERα Antagonist H3B-6545 Demonstrates Encouraging Preclinical Activity in Therapy-Resistant Breast Cancer

Author

Furman, Craig, primary, Puyang, Xiaoling, primary, Zhang, Zhaojie, primary, Wu, Zhenhua J., primary, Banka, Deepti, primary, Aithal, Kiran B., primary, Albacker, Lee A., primary, Hao, Ming-Hong, primary, Irwin, Sean, primary, Kim, Amy, primary, Montesion, Meagan, primary, Moriarty, Alyssa D., primary, Murugesan, Karthikeyan, primary, Nguyen, Tuong-Vi, primary, Rimkunas, Victoria, primary, Sahmoud, Tarek, primary, Wick, Michael J., primary, Yao, Shihua, primary, Zhang, Xun, primary, Zeng, Hao, primary, Vaillancourt, Frédéric H., primary, Bolduc, David M., primary, Larsen, Nicholas, primary, Zheng, Guo Zhu, primary, Prajapati, Sudeep, primary, Zhu, Ping, primary, and Korpal, Manav, primary

Published
2023
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6. Tables S3-S4 from Discovery of Selective Estrogen Receptor Covalent Antagonists for the Treatment of ERαWT and ERαMUT Breast Cancer

Author

Puyang, Xiaoling, primary, Furman, Craig, primary, Zheng, Guo Zhu, primary, Wu, Zhenhua J., primary, Banka, Deepti, primary, Aithal, Kiran, primary, Agoulnik, Sergei, primary, Bolduc, David M., primary, Buonamici, Silvia, primary, Caleb, Benjamin, primary, Das, Subhasree, primary, Eckley, Sean, primary, Fekkes, Peter, primary, Hao, Ming-Hong, primary, Hart, Andrew, primary, Houtman, René, primary, Irwin, Sean, primary, Joshi, Jaya J., primary, Karr, Craig, primary, Kim, Amy, primary, Kumar, Namita, primary, Kumar, Pavan, primary, Kuznetsov, Galina, primary, Lai, Weidong G., primary, Larsen, Nicholas, primary, Mackenzie, Crystal, primary, Martin, Lesley-Ann, primary, Melchers, Diana, primary, Moriarty, Alyssa, primary, Nguyen, Tuong-Vi, primary, Norris, John, primary, O'Shea, Morgan, primary, Pancholi, Sunil, primary, Prajapati, Sudeep, primary, Rajagopalan, Sujatha, primary, Reynolds, Dominic J., primary, Rimkunas, Victoria, primary, Rioux, Nathalie, primary, Ribas, Ricardo, primary, Siu, Amy, primary, Sivakumar, Sasirekha, primary, Subramanian, Vanitha, primary, Thomas, Michael, primary, Vaillancourt, Frédéric H., primary, Wang, John, primary, Wardell, Suzanne, primary, Wick, Michael J., primary, Yao, Shihua, primary, Yu, Lihua, primary, Warmuth, Markus, primary, Smith, Peter G., primary, Zhu, Ping, primary, and Korpal, Manav, primary

Published
2023
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7. Supplementary Data from Covalent ERα Antagonist H3B-6545 Demonstrates Encouraging Preclinical Activity in Therapy-Resistant Breast Cancer

Author

Furman, Craig, primary, Puyang, Xiaoling, primary, Zhang, Zhaojie, primary, Wu, Zhenhua J., primary, Banka, Deepti, primary, Aithal, Kiran B., primary, Albacker, Lee A., primary, Hao, Ming-Hong, primary, Irwin, Sean, primary, Kim, Amy, primary, Montesion, Meagan, primary, Moriarty, Alyssa D., primary, Murugesan, Karthikeyan, primary, Nguyen, Tuong-Vi, primary, Rimkunas, Victoria, primary, Sahmoud, Tarek, primary, Wick, Michael J., primary, Yao, Shihua, primary, Zhang, Xun, primary, Zeng, Hao, primary, Vaillancourt, Frédéric H., primary, Bolduc, David M., primary, Larsen, Nicholas, primary, Zheng, Guo Zhu, primary, Prajapati, Sudeep, primary, Zhu, Ping, primary, and Korpal, Manav, primary

Published
2023
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8. Supplementary Methods from Discovery of Selective Estrogen Receptor Covalent Antagonists for the Treatment of ERαWT and ERαMUT Breast Cancer

Author

Puyang, Xiaoling, primary, Furman, Craig, primary, Zheng, Guo Zhu, primary, Wu, Zhenhua J., primary, Banka, Deepti, primary, Aithal, Kiran, primary, Agoulnik, Sergei, primary, Bolduc, David M., primary, Buonamici, Silvia, primary, Caleb, Benjamin, primary, Das, Subhasree, primary, Eckley, Sean, primary, Fekkes, Peter, primary, Hao, Ming-Hong, primary, Hart, Andrew, primary, Houtman, René, primary, Irwin, Sean, primary, Joshi, Jaya J., primary, Karr, Craig, primary, Kim, Amy, primary, Kumar, Namita, primary, Kumar, Pavan, primary, Kuznetsov, Galina, primary, Lai, Weidong G., primary, Larsen, Nicholas, primary, Mackenzie, Crystal, primary, Martin, Lesley-Ann, primary, Melchers, Diana, primary, Moriarty, Alyssa, primary, Nguyen, Tuong-Vi, primary, Norris, John, primary, O'Shea, Morgan, primary, Pancholi, Sunil, primary, Prajapati, Sudeep, primary, Rajagopalan, Sujatha, primary, Reynolds, Dominic J., primary, Rimkunas, Victoria, primary, Rioux, Nathalie, primary, Ribas, Ricardo, primary, Siu, Amy, primary, Sivakumar, Sasirekha, primary, Subramanian, Vanitha, primary, Thomas, Michael, primary, Vaillancourt, Frédéric H., primary, Wang, John, primary, Wardell, Suzanne, primary, Wick, Michael J., primary, Yao, Shihua, primary, Yu, Lihua, primary, Warmuth, Markus, primary, Smith, Peter G., primary, Zhu, Ping, primary, and Korpal, Manav, primary

Published
2023
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9. Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3′ Splice Site Selection through Use of a Different Branch Point

Author

Darman, Rachel B., Seiler, Michael, Agrawal, Anant A., Lim, Kian H., Peng, Shouyong, Aird, Daniel, Bailey, Suzanna L., Bhavsar, Erica B., Chan, Betty, Colla, Simona, Corson, Laura, Feala, Jacob, Fekkes, Peter, Ichikawa, Kana, Keaney, Gregg F., Lee, Linda, Kumar, Pavan, Kunii, Kaiko, MacKenzie, Crystal, Matijevic, Mark, Mizui, Yoshiharu, Myint, Khin, Park, Eun Sun, Puyang, Xiaoling, Selvaraj, Anand, Thomas, Michael P., Tsai, Jennifer, Wang, John Y., Warmuth, Markus, Yang, Hui, Zhu, Ping, Garcia-Manero, Guillermo, Furman, Richard R., Yu, Lihua, Smith, Peter G., and Buonamici, Silvia

Published
2015
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10. Evasion of immunosurveillance by genomic alterations of PPARγ/RXRα in bladder cancer

Author

Korpal, Manav, Puyang, Xiaoling, Jeremy Wu, Zhenhua, Seiler, Roland, Furman, Craig, Oo, Htoo Zarni, Seiler, Michael, Irwin, Sean, Subramanian, Vanitha, Julie Joshi, Jaya, Wang, Chris K., Rimkunas, Victoria, Tortora, Davide, Yang, Hua, Kumar, Namita, Kuznetsov, Galina, Matijevic, Mark, Chow, Jesse, Kumar, Pavan, Zou, Jian, Feala, Jacob, Corson, Laura, Henry, Ryan, Selvaraj, Anand, Davis, Allison, Bloudoff, Kristjan, Douglas, James, Kiss, Bernhard, Roberts, Morgan, Fazli, Ladan, Black, Peter C., Fekkes, Peter, Smith, Peter G., Warmuth, Markus, Yu, Lihua, Hao, Ming-Hong, Larsen, Nicholas, Daugaard, Mads, and Zhu, Ping

Published
2017
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11. Covalent ERα Antagonist H3B-6545 Demonstrates Encouraging Preclinical Activity in Therapy-Resistant Breast Cancer

Author

Furman, Craig, primary, Puyang, Xiaoling, additional, Zhang, Zhaojie, additional, Wu, Zhenhua J., additional, Banka, Deepti, additional, Aithal, Kiran B., additional, Albacker, Lee A., additional, Hao, Ming-Hong, additional, Irwin, Sean, additional, Kim, Amy, additional, Montesion, Meagan, additional, Moriarty, Alyssa D., additional, Murugesan, Karthikeyan, additional, Nguyen, Tuong-Vi, additional, Rimkunas, Victoria, additional, Sahmoud, Tarek, additional, Wick, Michael J., additional, Yao, Shihua, additional, Zhang, Xun, additional, Zeng, Hao, additional, Vaillancourt, Frédéric H., additional, Bolduc, David M., additional, Larsen, Nicholas, additional, Zheng, Guo Zhu, additional, Prajapati, Sudeep, additional, Zhu, Ping, additional, and Korpal, Manav, additional

Published
2022
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12. Identification of 2-Sulfonyl/Sulfonamide Pyrimidines as Covalent Inhibitors of WRN Using a Multiplexed High-Throughput Screening Assay

Author

Parker, Mackenzie J., Lee, Hyelee, Yao, Shihua, Irwin, Sean, Hwang, Sunil, Belanger, Kylie, de Mare, Sofia Woo, Surgenor, Richard, Yan, Lu, Gee, Patricia, Morla, Shravan, Puyang, Xiaoling, Hsiao, Peng, Zeng, Hao, Zhu, Ping, Korpal, Manav, Dransfield, Paul, Bolduc, David M., and Larsen, Nicholas A.

Abstract

Werner syndrome protein (WRN) is a multifunctional enzyme with helicase, ATPase, and exonuclease activities that are necessary for numerous DNA-related transactions in the human cell. Recent studies identified WRN as a synthetic lethal target in cancers characterized by genomic microsatellite instability resulting from defects in DNA mismatch repair pathways. WRN’s helicase activity is essential for the viability of these high microsatellite instability (MSI-H) cancers and thus presents a therapeutic opportunity. To this end, we developed a multiplexed high-throughput screening assay that monitors exonuclease, ATPase, and helicase activities of full-length WRN. This screening campaign led to the discovery of 2-sulfonyl/sulfonamide pyrimidine derivatives as novel covalent inhibitors of WRN helicase activity. The compounds are specific for WRN versus other human RecQ family members and show competitive behavior with ATP. Examination of these novel chemical probes established the sulfonamide NH group as a key driver of compound potency. One of the leading compounds, H3B-960, showed consistent activities in a range of assays (IC50= 22 nM, KD= 40 nM, KI= 32 nM), and the most potent compound identified, H3B-968, has inhibitory activity IC50∼ 10 nM. These kinetic properties trend toward other known covalent druglike molecules. Our work provides a new avenue for screening WRN for inhibitors that may be adaptable to different therapeutic modalities such as targeted protein degradation, as well as a proof of concept for the inhibition of WRN helicase activity by covalent molecules.

Published
2023
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13. Mycobacterium tuberculosis SigM positively regulates Esx secreted protein and nonribosomal peptide synthetase genes and down regulates virulence-associated surface lipid synthesis

Author

Raman, Sahadevan, Puyang, Xiaoling, Cheng, Tan-Yun, Young, David C., Moody, D. Branch, and Husson, Robert N.

Subjects
Mycobacterium tuberculosis -- Genetic aspects, Mycobacterium tuberculosis -- Physiological aspects, Lipids -- Synthesis, Lipids -- Research, Genetic research, Biological sciences
Abstract

The Mycobacterium tuberculosis genome encodes 12 alternative sigma factors, several of which regulate stress responses and are required for virulence in animal models of acute infection. In this work we investigated M. tuberculosis SigM, a member of the extracytoplasmic function subfamily of alternative sigma factors. This sigma factor is expressed at low levels in vitro and does not appear to function in stress response regulation. Instead, SigM positively regulates genes required for the synthesis of surface or secreted molecules. Among these are genes encoding two pairs of Esx secreted proteins, a multisubunit nonribosomal peptide synthetase operon, and genes encoding two members of the proline-proline-glutamate (PPE) family of proteins. Genes up regulated in a sigM mutant strain include a different PPE gene, as well as several genes involved in surface lipid synthesis. Among these are genes involved in synthesis of phthiocerol dimycocerosate (PDIM), a surface lipid critical for virulence during acute infection, and the kasA-kasB operon, which is required for mycolic acid synthesis. Analysis of surface lipids showed that PDIM synthesis is increased in a sigM-disrupted strain and is undetectable in a sigM overexpression strain. These findings demonstrate that SigM positively and negatively regulates cell surface and secreted molecules that are likely to function in host-pathogen interactions.

Published
2006

14. Abstract PS12-23: Development of H3B-6545, a first-in-class oral selective ER covalent antagonist (SERCA), for the treatment of ERaWTand ERaMUTbreast cancer

Author

Korpal, Manav, primary, Furman, Craig, additional, Puyang, Xiaoling, additional, Zhang, Zhaojie, additional, Wu, Zhenhua, additional, Banka, Deepti, additional, Das, Subhasree, additional, Destenaves, Benoit, additional, Gao, Lei, additional, Hamilton, Erika, additional, Hao, Ming-Hong, additional, Irwin, Sean, additional, Johnston, Stephen, additional, Joshi, Jaya J, additional, Juric, Dejan, additional, Kim, Amy, additional, Nguyen, Tuong-Vi, additional, Pipas, Marc, additional, Pluard, Timothy, additional, Rimkunas, Victoria, additional, Rioux, Nathalie, additional, Schindler, Joanne, additional, Smith, Peter, additional, Thomas, Michael, additional, Wang, John, additional, Wang, Judy S, additional, Warmuth, Markus, additional, Yao, Huilan, additional, Yao, Shihua, additional, Yu, Lihua, additional, Vaillancourt, Frédéric H, additional, Bolduc, David M, additional, Larsen, Nicholas A, additional, Zheng, GuoZhu, additional, Prajapati, Sudeep, additional, Sahmoud, Tarek, additional, Gualberto, Antonio, additional, and Zhu, Ping, additional

Published
2021
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15. The alternative sigma factor SigH regulates major components of oxidative and heat stress responses in Mycobacterium tuberculosis

Author

Raman, Sahadevan, Song, Taeksun, Puyang, Xiaoling, Bardarov, Stoyan, Jacobs, William R., Jr., and Husson, Robert N.

Subjects
Bacteriology -- Research, Mycobacterium tuberculosis -- Genetic aspects, Oxidation-reduction reaction -- Physiological aspects, Heat -- Physiological aspects, Gene mutations -- Physiological aspects, Biological sciences
Abstract

Research has been conducted on the regulation by Mycobacterium tuberculosis of the gene expression in overcoming stresses during infection. The role of sigH in the M. tuberculosis response to heat and oxidative stress has been examined and the results indicate that sigH mutant is more susceptible to the oxidative stress.

Published
2001

16. Is1626, a new IS900-related Mycobacterium avium insertion sequence

Author

Puyang, Xiaoling, Lee, Karen, Pawlichuk, Corey, and Kunimoto, Dennis Y.

Subjects
Insertion elements, DNA -- Research, Translocation (Genetics) -- Analysis, Microorganisms -- Evolution, DNA probes -- Usage, Biological sciences
Abstract

Research was conducted to characterize the chromosomal insertion sequence IS1626 from a bacterial species. Results show that IS1626 is a 1418 base pair long with 65 mol% of G+C content and without terminal inverted or flanking direct repeats.

Published
1999

17. A mycobacterial extracytoplasmic sigma factor involved in survival following heat shock and oxidative stress

Author

Fernandes, Norvin D., Wu, Qi-Long, Kong, Dequan, Puyang, Xiaoling, Garg, Sumeet, and Husson, Robert N.

Subjects
Mycobacterium -- Research, Bacterial proteins -- Research, Biological sciences
Abstract

Extracytoplasmic function (ECF) sigma factors are a heterologous group of alternative sigma factors that control gene expression in response to various conditions including stress. A gene encoding the sigma factor, sigH, was cloned from Mycobacterium tuberculosis and M. smegmatis. A single copy of this gene is present in these and other fast- and slow-growing mycobacteria, including M. fortuitum and M. avium. While the M. tuberculosis and M. smegmatis sigH genes encode highly similar proteins, there are several differences in adjacent genes.

Published
1999

18. Discovery of Selective Estrogen Receptor Covalent Antagonists for the Treatment of ERαWT and ERαMUT Breast Cancer

Author

Puyang, Xiaoling, primary, Furman, Craig, additional, Zheng, Guo Zhu, additional, Wu, Zhenhua J., additional, Banka, Deepti, additional, Aithal, Kiran, additional, Agoulnik, Sergei, additional, Bolduc, David M., additional, Buonamici, Silvia, additional, Caleb, Benjamin, additional, Das, Subhasree, additional, Eckley, Sean, additional, Fekkes, Peter, additional, Hao, Ming-Hong, additional, Hart, Andrew, additional, Houtman, René, additional, Irwin, Sean, additional, Joshi, Jaya J., additional, Karr, Craig, additional, Kim, Amy, additional, Kumar, Namita, additional, Kumar, Pavan, additional, Kuznetsov, Galina, additional, Lai, Weidong G., additional, Larsen, Nicholas, additional, Mackenzie, Crystal, additional, Martin, Lesley-Ann, additional, Melchers, Diana, additional, Moriarty, Alyssa, additional, Nguyen, Tuong-Vi, additional, Norris, John, additional, O'Shea, Morgan, additional, Pancholi, Sunil, additional, Prajapati, Sudeep, additional, Rajagopalan, Sujatha, additional, Reynolds, Dominic J., additional, Rimkunas, Victoria, additional, Rioux, Nathalie, additional, Ribas, Ricardo, additional, Siu, Amy, additional, Sivakumar, Sasirekha, additional, Subramanian, Vanitha, additional, Thomas, Michael, additional, Vaillancourt, Frédéric H., additional, Wang, John, additional, Wardell, Suzanne, additional, Wick, Michael J., additional, Yao, Shihua, additional, Yu, Lihua, additional, Warmuth, Markus, additional, Smith, Peter G., additional, Zhu, Ping, additional, and Korpal, Manav, additional

Published
2018
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19. Abstract 126: A chemogenomic approach reveals the action of splicing modulators at the branch point adenosine binding pocket defined by the PHF5A/SF3b complex

Author

Teng, Teng, primary, Tsai, Jennifer, additional, Puyang, Xiaoling, additional, Seiler, Michael, additional, Peng, Shouyong, additional, Aird, Daniel, additional, Buonamici, Silvia, additional, Caleb, Benjamin, additional, Chan, Betty, additional, Corson, Laura, additional, Feala, Jacob, additional, Fekkes, Peter, additional, Karr, Craig, additional, Korpal, Manav, additional, Mizui, Yoshiharu, additional, Park, Eunice, additional, Palacino, James, additional, Smith, Peter, additional, Subramanian, Vanitha, additional, Wu, Jeremy, additional, Yu, Lihua, additional, Chicas, Agustin, additional, Warmuth, Markus, additional, Larsen, Nicholas, additional, and Zhu, Ping, additional

Published
2017
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20. Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A–SF3b complex

Author

Teng, Teng, primary, Tsai, Jennifer HC, additional, Puyang, Xiaoling, additional, Seiler, Michael, additional, Peng, Shouyong, additional, Prajapati, Sudeep, additional, Aird, Daniel, additional, Buonamici, Silvia, additional, Caleb, Benjamin, additional, Chan, Betty, additional, Corson, Laura, additional, Feala, Jacob, additional, Fekkes, Peter, additional, Gerard, Baudouin, additional, Karr, Craig, additional, Korpal, Manav, additional, Liu, Xiang, additional, T. Lowe, Jason, additional, Mizui, Yoshiharu, additional, Palacino, James, additional, Park, Eunice, additional, Smith, Peter G., additional, Subramanian, Vanitha, additional, Wu, Zhenhua Jeremy, additional, Zou, Jian, additional, Yu, Lihua, additional, Chicas, Agustin, additional, Warmuth, Markus, additional, Larsen, Nicholas, additional, and Zhu, Ping, additional

Published
2017
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21. Two-Dimensional Direct-Reading Fluorescence Spectrograph for DNA Sequencing by Capillary Array Electrophoresis

Author

Zhang, Jianzhong, Yang, Minjian, Puyang, Xiaoling, Fang, Yu, Cook, Lillian M., and Dovichi, Norman J.

Subjects
DNA sequencers -- Research, Fluorescence spectroscopy -- Research, Electrophoresis -- Research, Chemistry
Abstract

We report a compact, two-dimensional direct-reading fluorescence spectrograph and demonstrate its application to DNA sequencing by capillary array electrophoresis. The detection cuvette is based on sheath flow, wherein the capillaries terminate in a two-dimensional array in a fluid-rifled chamber that is pressurized with buffer. A thin metal plate is located downstream from the capillaries. This barrier plate has an array of holes that precisely matches the location of the capillaries. Buffer flows through the holes, drawing analyte from the capillaries in a well-defined array of thin filaments. Fluorescence is excited in the upper chamber with an elliptically shaped laser beam. The bottom chamber is sealed with a glass window and drained from the side. Fluorescence is detected by imaging the illuminated sample streams through the holes in the barrier plate. A prism is used to disperse fluorescence from each sample across a CCD camera so that the emission spectrum is monitored simultaneously from each capillary. The instrument is demonstrated in a 32-capillary configuration but can be scaled to several thousand capillaries.

Published
2001

22. Abstract 3013: Identification of PHF5A as a common cellular target of splicing-modulating chemical probes

Author

Teng, Teng, primary, Puyang, Xiaoling, additional, Peng, Shouyong, additional, Feala, Jacob, additional, Chan, Betty, additional, Tsai, Jennifer, additional, Caleb, Benjamin, additional, Karr, Craig, additional, Park, Eunice, additional, Corson, Laura, additional, Mizui, Yoshiharu, additional, Smith, Peter, additional, Larsen, Nicholas, additional, Yu, Lihua, additional, Warmuth, Markus, additional, Zhu, Ping, additional, and Chicas, Agustin, additional

Published
2016
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24. Cancer-Associated Mutations in SF3B1 Exhibit Neomorphic Splicing Activity and Block Erythroid Differentiation

Author

Buonamici, Silvia, primary, Perino, Samantha, additional, Lim, Kian Huat, additional, Feala, Jacob, additional, Obeng, Esther A., additional, Aicher, Michelle, additional, Aird, Daniel, additional, Bailey, Suzanna, additional, Berkenblit, Anna, additional, Chan, Betty, additional, Erik, Corcoran, additional, Corson, Laura, additional, Darman, Rachel, additional, Fekkes, Peter, additional, Furman, Richard R., additional, Keaney, Gregg F, additional, Kumar, Pavan, additional, Kunii, Kaiko, additional, Lee, Linda, additional, Mackenzie, Crystal, additional, Park, Eunice, additional, Puyang, Xiaoling, additional, Selvaraj, Anand, additional, Thomas, Michael, additional, Wang, John, additional, Warmuth, Markus, additional, Yu, Lihua, additional, Zhu, Ping, additional, Mizui, Yoshiharu, additional, Ebert, Benjamin L., additional, and Smith, Peter G, additional

Published
2014
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25. Abstract 2932: SF3B1 mutations induce aberrant mRNA splicing in cancer and confer sensitivity to spliceosome inhibition

Author

Buonamici, Silvia, primary, Lim, Kian Huat, additional, Feala, Jacob, additional, Park, Eunice, additional, Corson, Laura, additional, Aicher, Michelle, additional, Aird, Daniel, additional, Chan, Betty, additional, Corcoran, Erik, additional, Darman, Rachel, additional, Fekkes, Peter, additional, Keaney, Gregg, additional, Kumar, Pavan, additional, Kunii, Kaiko, additional, Lee, Linda, additional, Puyang, Xiaoling, additional, Rodrigues, Jose, additional, Selvaraj, Anand, additional, Thomas, Michael, additional, Wang, John, additional, Warmuth, Markus, additional, Yu, Lihua, additional, Zhu, Ping, additional, Smith, Peter, additional, and Mizui, Yoshiharu, additional

Published
2014
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26. NAMPT Is the Cellular Target of STF-31-Like Small-Molecule Probes

Author

Adams, Drew J., primary, Ito, Daisuke, additional, Rees, Matthew G., additional, Seashore-Ludlow, Brinton, additional, Puyang, Xiaoling, additional, Ramos, Alex H., additional, Cheah, Jaime H., additional, Clemons, Paul A., additional, Warmuth, Markus, additional, Zhu, Ping, additional, Shamji, Alykhan F., additional, and Schreiber, Stuart L., additional

Published
2014
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29. Class III Phosphatidylinositol 4-Kinase Alpha and Beta Are Novel Host Factor Regulators of Hepatitis C Virus Replication

Author

Borawski, Jason, primary, Troke, Philip, additional, Puyang, Xiaoling, additional, Gibaja, Veronica, additional, Zhao, ShanChaun, additional, Mickanin, Craig, additional, Leighton-Davies, Juliet, additional, Wilson, Christopher J., additional, Myer, Vic, additional, CornellaTaracido, Ivan, additional, Baryza, Jeremy, additional, Tallarico, John, additional, Joberty, Gerard, additional, Bantscheff, Marcus, additional, Schirle, Markus, additional, Bouwmeester, Tewis, additional, Mathy, Joanna E., additional, Lin, Kai, additional, Compton, Teresa, additional, Labow, Mark, additional, Wiedmann, Brigitte, additional, and Gaither, L. Alex, additional

Published
2009
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30. From proteomics to systems biology of bacterial pathogens: Approaches, tools, and applications

Author

Plikat, Uwe, primary, Voshol, Hans, additional, Dangendorf, Yvonne, additional, Wiedmann, Brigitte, additional, Devay, Piroska, additional, Müller, Dieter, additional, Wirth, Urs, additional, Szustakowski, Joseph, additional, Chirn, Gung-Wei, additional, Inverardi, Bruno, additional, Puyang, Xiaoling, additional, Brown, Kara, additional, Kamp, Heather, additional, Hoving, Sjouke, additional, Ruchti, Alexandra, additional, Brendlen, Nathalie, additional, Peterson, Ron, additional, Buco, Jennifer, additional, Oostrum, Jan van, additional, and Peitsch, Manuel C., additional

Published
2007
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31. Reduced Susceptibility of Haemophilus influenzae to the Peptide Deformylase Inhibitor LBM415 Can Result from Target Protein Overexpression Due to Amplified Chromosomal def Gene Copy Number

Author

Dean, Charles R., primary, Narayan, Shubha, additional, Richards, Joel, additional, Daigle, Denis M., additional, Esterow, Stacy, additional, Leeds, Jennifer A., additional, Kamp, Heather, additional, Puyang, Xiaoling, additional, Wiedmann, Brigitte, additional, Mueller, Dieter, additional, Voshol, Hans, additional, van Oostrum, Jan, additional, Wall, Daniel, additional, Koehn, James, additional, Dzink-Fox, JoAnn, additional, and Ryder, Neil S., additional

Published
2007
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32. Role of the AcrAB-TolC Efflux Pump in Determining Susceptibility of Haemophilus influenzae to the Novel Peptide Deformylase Inhibitor LBM415

Author

Dean, Charles R., primary, Narayan, Shubha, additional, Daigle, Denis M., additional, Dzink-Fox, JoAnn L., additional, Puyang, Xiaoling, additional, Bracken, Kathryn R., additional, Dean, Karl E., additional, Weidmann, Beat, additional, Yuan, Zhengyu, additional, Jain, Rakesh, additional, and Ryder, Neil S., additional

Published
2005
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33. Reduced Susceptibility of Haemophilus influenzaeto the Peptide Deformylase Inhibitor LBM415 Can Result from Target Protein Overexpression Due to Amplified Chromosomal defGene Copy Number

Author

Dean, Charles R., Narayan, Shubha, Richards, Joel, Daigle, Denis M., Esterow, Stacy, Leeds, Jennifer A., Kamp, Heather, Puyang, Xiaoling, Wiedmann, Brigitte, Mueller, Dieter, Voshol, Hans, van Oostrum, Jan, Wall, Daniel, Koehn, James, Dzink-Fox, JoAnn, and Ryder, Neil S.

Abstract

ABSTRACTPrevious genetic analysis of Haemophilus influenzaerevealed two mechanisms associated with decreased susceptibility to the novel peptide deformylase inhibitor LBM415: AcrAB-TolC-mediated efflux and Fmt bypass, resulting from mutations in the pump repressor gene acrRand in the fmtgene, respectively. We have isolated an additional mutant, CDS23 (LBM415 MIC, 64 μg/ml versus 4 μg/ml against the parent strain NB65044) that lacks mutations in the acrRor fmtstructural genes or in the gene encoding Def, the intracellular target of LBM415. Western immunoblot analysis, two-dimensional gel electrophoresis, and tryptic digestion combined with mass spectrometric identification showed that the Def protein was highly overexpressed in the mutant strain. Consistent with this, real-time reverse transcription-PCR revealed a significant increase in deftranscript titer. No mutations were found in the region upstream of defthat might account for altered expression; however, pulsed-field gel electrophoresis suggested that a genetic rearrangement of the region containing defhad occurred. Using a combination of PCR, sequencing, and Southern blot analyses, it was determined that the defgene had undergone copy number amplification, explaining the high level of target protein expression. Inactivation of the AcrAB-TolC efflux pump in this mutant increased susceptibility 16-fold, highlighting the role of efflux in exacerbating the overall reduced susceptibility resulting from target overexpression.

Published
2007
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34. Role of the AcrAB-TolC Efflux Pump in Determining Susceptibility of Haemophilus influenzaeto the Novel Peptide Deformylase Inhibitor LBM415

Author

Dean, Charles R., Narayan, Shubha, Daigle, Denis M., Dzink-Fox, JoAnn L., Puyang, Xiaoling, Bracken, Kathryn R., Dean, Karl E., Weidmann, Beat, Yuan, Zhengyu, Jain, Rakesh, and Ryder, Neil S.

Abstract

ABSTRACTHaemophilus influenzaeisolates vary widely in their susceptibilities to the peptide deformylase inhibitor LBM415 (MIC range, 0.06 to 32 μg/ml); however, on average, they are less susceptible than gram-positive organisms, such as Staphylococcus aureusand Streptococcus pneumoniae. Insertional inactivation of the H. influenzae acrBor tolCgene in strain NB65044 (Rd strain KW20) increased susceptibility to LBM415, confirming a role for the AcrAB-TolC pump in determining resistance. Consistent with this, sequencing of a PCR fragment generated with primers flanking the acrRAregion from an LBM415-hypersusceptible H. influenzaeclinical isolate revealed a genetic deletion of acrA. Inactivation of acrBor tolCin several clinical isolates with atypically reduced susceptibility to LBM415 (MIC of 16 μg/ml or greater) significantly increased susceptibility, confirming that the pump is also a determinant of decreased susceptibility in these clinical isolates. Examination of acrR, encoding the putative repressor of pump gene expression, from several of these strains revealed mutations introducing frameshifts, stop codons, and amino acid changes relative to the published sequence, suggesting that loss of pump repression leads to decreased susceptibility. Supporting this, NB65044 acrRmutants selected by exposure to LBM415 at 8 μg/ml had susceptibilities to LBM415 and other pump substrates comparable to the least sensitive clinical isolates and showed increased expression of pump genes.

Published
2005
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36. Discovery of Selective Estrogen Receptor Covalent Antagonists for the Treatment of ERα WT and ERα MUT Breast Cancer.

Author

Puyang X, Furman C, Zheng GZ, Wu ZJ, Banka D, Aithal K, Agoulnik S, Bolduc DM, Buonamici S, Caleb B, Das S, Eckley S, Fekkes P, Hao MH, Hart A, Houtman R, Irwin S, Joshi JJ, Karr C, Kim A, Kumar N, Kumar P, Kuznetsov G, Lai WG, Larsen N, Mackenzie C, Martin LA, Melchers D, Moriarty A, Nguyen TV, Norris J, O'Shea M, Pancholi S, Prajapati S, Rajagopalan S, Reynolds DJ, Rimkunas V, Rioux N, Ribas R, Siu A, Sivakumar S, Subramanian V, Thomas M, Vaillancourt FH, Wang J, Wardell S, Wick MJ, Yao S, Yu L, Warmuth M, Smith PG, Zhu P, and Korpal M

Subjects
Administration, Oral, Animals, Breast Neoplasms genetics, Cell Line, Tumor, Cell Proliferation drug effects, Cell Survival drug effects, Cysteine antagonists & inhibitors, Drug Screening Assays, Antitumor, Drug Synergism, Estrogen Receptor Antagonists chemistry, Estrogen Receptor Antagonists pharmacology, Estrogen Receptor alpha chemistry, Estrogen Receptor alpha genetics, Female, Humans, Indazoles chemistry, Indazoles pharmacology, MCF-7 Cells, Mice, Protein Conformation drug effects, Protein Kinase Inhibitors administration & dosage, Protein Kinase Inhibitors pharmacology, Xenograft Model Antitumor Assays, Breast Neoplasms drug therapy, Drug Resistance, Neoplasm drug effects, Estrogen Receptor Antagonists administration & dosage, Estrogen Receptor alpha antagonists & inhibitors, Indazoles administration & dosage, Mutation
Abstract

Mutations in estrogen receptor alpha (ERα) that confer resistance to existing classes of endocrine therapies are detected in up to 30% of patients who have relapsed during endocrine treatments. Because a significant proportion of therapy-resistant breast cancer metastases continue to be dependent on ERα signaling, there remains a critical need to develop the next generation of ERα antagonists that can overcome aberrant ERα activity. Through our drug-discovery efforts, we identified H3B-5942, which covalently inactivates both wild-type and mutant ERα by targeting Cys530 and enforcing a unique antagonist conformation. H3B-5942 belongs to a class of ERα antagonists referred to as selective estrogen receptor covalent antagonists (SERCA). In vitro comparisons of H3B-5942 with standard-of-care (SoC) and experimental agents confirmed increased antagonist activity across a panel of ERα WT and ERα MUT cell lines. In vivo , H3B-5942 demonstrated significant single-agent antitumor activity in xenograft models representing ERα WT and ERα Y537S breast cancer that was superior to fulvestrant. Lastly, H3B-5942 potency can be further improved in combination with CDK4/6 or mTOR inhibitors in both ERα WT and ERα MUT cell lines and/or tumor models. In summary, H3B-5942 belongs to a class of orally available ERα covalent antagonists with an improved profile over SoCs. Significance: Nearly 30% of endocrine therapy-resistant breast cancer metastases harbor constitutively activating mutations in ERα. SERCA H3B-5942 engages C530 of both ERα WT and ERα MUT , promotes a unique antagonist conformation, and demonstrates improved in vitro and in vivo activity over SoC agents. Importantly, single-agent efficacy can be further enhanced by combining with CDK4/6 or mTOR inhibitors. Cancer Discov; 8(9); 1176-93. ©2018 AACR. This article is highlighted in the In This Issue feature, p. 1047 ., (©2018 American Association for Cancer Research.)

Published
2018
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