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1,092 results on '"Koomen, John"'

8. Pathogenic Roles for RNASET2 in Clear Cell Renal Cell Carcinoma

Author

Peak, Taylor, Tian, Yijun, Patel, Aman, Shaw, Tim, Obermayer, Alyssa, Laborde, Jose, Kim, Youngchul, Johnson, Joseph, Stewart, Paul, Fang, Bin, Teer, Jamie K., Koomen, John, Berglund, Anders, Marchion, Doug, Francis, Natasha, Echevarria, Paola Ramos, Dhillon, Jasreman, Clark, Noel, Chang, Andrew, Sexton, Wade, Zemp, Logan, Chahoud, Jad, Wang, Liang, and Manley, Brandon

Published
2024
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9. Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell MigrationSystems Analysis of AXL Signaling in Lung Cancers

Author

Majumder, Anurima, Hosseinian, Sina, Stroud, Mia, Adhikari, Emma, Saller, James J, Smith, Matthew A, Zhang, Guolin, Agarwal, Shruti, Creixell, Marc, Meyer, Benjamin S, Kinose, Fumi, Bowers, Kiah, Fang, Bin, Stewart, Paul A, Welsh, Eric A, Boyle, Theresa A, Meyer, Aaron S, Koomen, John M, and Haura, Eric B

Subjects
Biochemistry and Cell Biology, Biological Sciences, Cancer, Lung Cancer, Lung, Prevention, Development of treatments and therapeutic interventions, 2.1 Biological and endogenous factors, 5.1 Pharmaceuticals, Aetiology, Cell Line, Tumor, Cell Movement, Drug Resistance, Neoplasm, ErbB Receptors, Humans, Lung Neoplasms, Protein Kinase Inhibitors, Proteomics, Signal Transduction, Oncology and Carcinogenesis, Developmental Biology, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

To better understand the signaling complexity of AXL, a member of the tumor-associated macrophage (TAM) receptor tyrosine kinase family, we created a physical and functional map of AXL signaling interactions, phosphorylation events, and target-engagement of three AXL tyrosine kinase inhibitors (TKI). We assessed AXL protein complexes using proximity-dependent biotinylation (BioID), effects of AXL TKI on global phosphoproteins using mass spectrometry, and target engagement of AXL TKI using activity-based protein profiling. BioID identifies AXL-interacting proteins that are mostly involved in cell adhesion/migration. Global phosphoproteomics show that AXL inhibition decreases phosphorylation of peptides involved in phosphatidylinositol-mediated signaling and cell adhesion/migration. Comparison of three AXL inhibitors reveals that TKI RXDX-106 inhibits pAXL, pAKT, and migration/invasion of these cells without reducing their viability, while bemcentinib exerts AXL-independent phenotypic effects on viability. Proteomic characterization of these TKIs demonstrates that they inhibit diverse targets in addition to AXL, with bemcentinib having the most off-targets. AXL and EGFR TKI cotreatment did not reverse resistance in cell line models of erlotinib resistance. However, a unique vulnerability was identified in one resistant clone, wherein combination of bemcentinib and erlotinib inhibited cell viability and signaling. We also show that AXL is overexpressed in approximately 30% to 40% of nonsmall but rarely in small cell lung cancer. Cell lines have a wide range of AXL expression, with basal activation detected rarely. Our study defines mechanisms of action of AXL in lung cancers which can be used to establish assays to measure drug targetable active AXL complexes in patient tissues and inform the strategy for targeting it's signaling as an anticancer therapy.

Published
2022

15. Tumor burden quantified by soluble B-cell maturation antigen and metabolic tumor volume determine myeloma CAR-T outcomes

Author

Freeman, Ciara L., Noble, Jerald, Menges, Meghan, Villanueva, Ricardo, Nakashima, Justyn Y., Figura, Nicholas B., Tonseth, Rolf Petter, Idiaquez, Dietrich Werner, Skelson, Lawrence, Smith, Eric, Abraham-Miranda, Julieta, Corallo, Salvatore, de Avila, Gabe, Castaneda Puglianini, Omar A., Liu, Hien, Alsina, Melissa, Nishihori, Taiga, Shain, Kenneth H., Baz, Rachid, Blue, Brandon, Cruz, Ariel Grajales, Koomen, John M., Atkins, Reginald M., Hansen, Doris K., Silva, Ariosto, Kim, Jongphil, Balagurunathan, Yoganand, and Locke, Frederick L.

Published
2024
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17. Targeted mass-spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP kinase, and AKT signaling

Author

Whiteaker, Jeffrey R, Sharma, Kanika, Hoffman, Melissa A, Kuhn, Eric, Zhao, Lei, Cocco, Alexandra R, Schoenherr, Regine M, Kennedy, Jacob J, Voytovich, Ulianna, Lin, Chenwei, Fang, Bin, Bowers, Kiah, Whiteley, Gordon, Colantonio, Simona, Bocik, William, Roberts, Rhonda, Hiltke, Tara, Boja, Emily, Rodriguez, Henry, McCormick, Frank, Holderfield, Matthew, Carr, Steven A, Koomen, John M, and Paulovich, Amanda G

Subjects
Biotechnology, Colo-Rectal Cancer, Bioengineering, Cancer, Digestive Diseases, AKT, Cancer signaling, MAP kinase, RAS, RTK, assay resource, immuno-MRM, pharmacodynamics, quantitative proteomics, targeted therapy
Abstract

SummaryA primary goal of the US National Cancer Institute's Ras initiative at the Frederick National Laboratory for Cancer Research is to develop methods to quantify RAS signaling to facilitate development of novel cancer therapeutics. We use targeted proteomics technologies to develop a community resource consisting of 256 validated multiple reaction monitoring (MRM)-based, multiplexed assays for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. As proof of concept, we quantify the response of melanoma (A375 and SK-MEL-2) and colorectal cancer (HCT-116 and HT-29) cell lines to BRAF inhibition by PLX-4720. These assays replace over 60 Western blots with quantitative mass spectrometry-based assays of high molecular specificity and quantitative precision, showing the value of these methods for pharmacodynamic measurements and mechanism of action studies. Methods, fit-for-purpose validation, and results are publicly available as a resource for the community at assays.cancer.gov.MotivationA lack of quantitative, multiplexable assays for phosphosignaling limits comprehensive investigation of aberrant signaling in cancer and evaluation of novel treatments. To alleviate this limitation, we sought to develop assays using targeted mass spectrometry for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. The resulting assays provide a resource for replacing over 60 Western blots in examining cancer signaling and tumor biology with high molecular specificity and quantitative rigor.

Published
2021

19. Fucosylation of HLA-DRB1 regulates CD4+ T cell-mediated anti-melanoma immunity and enhances immunotherapy efficacy

Author

Lester, Daniel K., Burton, Chase, Gardner, Alycia, Innamarato, Patrick, Kodumudi, Krithika, Liu, Qian, Adhikari, Emma, Ming, Qianqian, Williamson, Daniel B., Frederick, Dennie T., Sharova, Tatyana, White, Michael G., Markowitz, Joseph, Cao, Biwei, Nguyen, Jonathan, Johnson, Joseph, Beatty, Matthew, Mockabee-Macias, Andrea, Mercurio, Matthew, Watson, Gregory, Chen, Pei-Ling, McCarthy, Susan, MoranSegura, Carlos, Messina, Jane, Thomas, Kerry L., Darville, Lancia, Izumi, Victoria, Koomen, John M., Pilon-Thomas, Shari A., Ruffell, Brian, Luca, Vincent C., Haltiwanger, Robert S., Wang, Xuefeng, Wargo, Jennifer A., Boland, Genevieve M., and Lau, Eric K.

Published
2023
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22. Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma

Author

Chang, Andrew, Chakiryan, Nicholas H., Du, Dongliang, Stewart, Paul A., Zhang, Yonghong, Tian, Yijun, Soupir, Alex C., Bowers, Kiah, Fang, Bin, Morganti, Ashley, Teer, Jamie K., Kim, Youngchul, Spiess, Philippe E., Chahoud, Jad, Noble, Jerald D., Putney, Ryan M., Berglund, Anders E., Robinson, Timothy J., Koomen, John M., Wang, Liang, and Manley, Brandon J.

Published
2022
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26. Tumor-infiltrating lymphocyte treatment for anti-PD-1-resistant metastatic lung cancer: a phase 1 trial

Author

Creelan, Benjamin C., Wang, Chao, Teer, Jamie K., Toloza, Eric M., Yao, Jiqiang, Kim, Sungjune, Landin, Ana M., Mullinax, John E., Saller, James J., Saltos, Andreas N., Noyes, David R., Montoya, Leighann B., Curry, Wesley, Pilon-Thomas, Shari A., Chiappori, Alberto A., Tanvetyanon, Tawee, Kaye, Frederic J., Thompson, Zachary J., Yoder, Sean J., Fang, Bin, Koomen, John M., Sarnaik, Amod A., Chen, Dung-Tsa, Conejo-Garcia, Jose R., Haura, Eric B., and Antonia, Scott J.

Published
2021
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30. Cereblon harnesses Myc-dependent bioenergetics and activity of CD8+ T lymphocytes

Author

Hesterberg, Rebecca S., Beatty, Matthew S., Han, Ying, Fernandez, Mario R., Akuffo, Afua A., Goodheart, William E., Yang, Chunying, Chang, Shiun, Colin, Christelle M., Alontaga, Aileen Y., McDaniel, Jessica M., Mailloux, Adam W., Billington, Julia M.R., Yue, Lanzhu, Russell, Shonagh, Gillies, Robert J., Yun, Sang Y., Ayaz, Muhammad, Lawrence, Nicholas J., Lawrence, Harshani R., Yu, Xue-Zhong, Fu, Jianing, Darville, Lancia N., Koomen, John M., Ren, Xiubao, Messina, Jane, Jiang, Kun, Garrett, Timothy J., Rajadhyaksha, Anjali M., Cleveland, John L., and Epling-Burnette, Pearlie K.

Published
2020
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33. #1. Acid ceramidase (ASAH1) is a key mediator of drug resistance in relapsed/refractory multiple myeloma

Author

Bishop, Ryan T., primary, Li, Tao, additional, Alugubelli, Raghunandan R., additional, Nasr, Mostafa, additional, Nyman, Karl J., additional, Sudalagunta, Praneeth, additional, Meads, Mark, additional, Frieling, Jeremy, additional, Nerlakanti, Niveditha, additional, Tauro, Marilena, additional, Hampton, Oliver, additional, Fang, Bin, additional, Grant, Steven, additional, Koomen, John, additional, Siqueira Silva, Ariosto, additional, Shain, Kenneth H., additional, and Lynch, Conor C., additional

Published
2024
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34. Androgen drives melanoma invasiveness and metastatic spread by inducing tumorigenic fucosylation

Author

Liu, Qian, primary, Adhikari, Emma, additional, Lester, Daniel K., additional, Fang, Bin, additional, Johnson, Joseph O., additional, Tian, Yijun, additional, Mockabee-Macias, Andrea T., additional, Izumi, Victoria, additional, Guzman, Kelly M., additional, White, Michael G., additional, Koomen, John M., additional, Wargo, Jennifer A., additional, Messina, Jane L., additional, Qi, Jianfei, additional, and Lau, Eric K., additional

Published
2024
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35. Proteome-wide Profiling of Clinical PARP Inhibitors Reveals Compound-Specific Secondary Targets

Author

Knezevic, Claire E, Wright, Gabriela, Rix, Lily L Remsing, Kim, Woosuk, Kuenzi, Brent M, Luo, Yunting, Watters, January M, Koomen, John M, Haura, Eric B, Monteiro, Alvaro N, Radu, Caius, Lawrence, Harshani R, and Rix, Uwe

Subjects
Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, Cancer, 2.1 Biological and endogenous factors, 5.1 Pharmaceuticals, Good Health and Well Being, H6PD, PARP inhibitor, chemical proteomics, polypharmacology, target identification, target selectivity
Abstract

Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are a promising class of targeted cancer drugs, but their individual target profiles beyond the PARP family, which could result in differential clinical use or toxicity, are unknown. Using an unbiased, mass spectrometry-based chemical proteomics approach, we generated a comparative proteome-wide target map of the four clinical PARPi, olaparib, veliparib, niraparib, and rucaparib. PARPi as a class displayed high target selectivity. However, in addition to the canonical targets PARP1, PARP2, and several of their binding partners, we also identified hexose-6-phosphate dehydrogenase (H6PD) and deoxycytidine kinase (DCK) as previously unrecognized targets of rucaparib and niraparib, respectively. Subsequent functional validation suggested that inhibition of DCK by niraparib could have detrimental effects when combined with nucleoside analog pro-drugs. H6PD silencing can cause apoptosis and further sensitize cells to PARPi, suggesting that H6PD may be, in addition to its established role in metabolic disorders, a new anticancer target.

Published
2016

36. HDAC11 deficiency disrupts oncogene-induced hematopoiesis in myeloproliferative neoplasms

Author

Yue, Lanzhu, Sharma, Vasundhara, Horvat, Nathan P., Akuffo, Afua A., Beatty, Matthew S., Murdun, Cem, Colin, Christelle, Billington, Julia M.R., Goodheart, William E., Sahakian, Eva, Zhang, Ling, Powers, John J., Amin, Narmin E., Lambert-Showers, Que T., Darville, Lancia N., Pinilla-Ibarz, Javier, Reuther, Gary W., Wright, Kenneth L., Conti, Chiara, Lee, Jennifer Y., Zheng, Xiaozhang, Ng, Pui Yee, Martin, Matthew W., Marshall, C. Gary, Koomen, John M., Levine, Ross L., Verma, Amit, Grimes, H. Leighton, Sotomayor, Eduardo M., Shao, Zonghong, and Epling-Burnette, Pearlie K.

Published
2020
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39. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.

Author

Carr, Steven A, Abbatiello, Susan E, Ackermann, Bradley L, Borchers, Christoph, Domon, Bruno, Deutsch, Eric W, Grant, Russell P, Hoofnagle, Andrew N, Hüttenhain, Ruth, Koomen, John M, Liebler, Daniel C, Liu, Tao, MacLean, Brendan, Mani, DR, Mansfield, Elizabeth, Neubert, Hendrik, Paulovich, Amanda G, Reiter, Lukas, Vitek, Olga, Aebersold, Ruedi, Anderson, Leigh, Bethem, Robert, Blonder, Josip, Boja, Emily, Botelho, Julianne, Boyne, Michael, Bradshaw, Ralph A, Burlingame, Alma L, Chan, Daniel, Keshishian, Hasmik, Kuhn, Eric, Kinsinger, Christopher, Lee, Jerry SH, Lee, Sang-Won, Moritz, Robert, Oses-Prieto, Juan, Rifai, Nader, Ritchie, James, Rodriguez, Henry, Srinivas, Pothur R, Townsend, R Reid, Van Eyk, Jennifer, Whiteley, Gordon, Wiita, Arun, and Weintraub, Susan

Subjects
Animals, Humans, Peptides, Biological Assay, Isotope Labeling, Proteomics, Biology, Medicine, Reference Standards, Software, Mass Spectrometry, Guidelines as Topic, Biochemistry & Molecular Biology
Abstract

Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this "fit-for-purpose" approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and recommendations.

Published
2014

40. Branched-chain keto acids promote an immune-suppressive and neurodegenerative microenvironment in leptomeningeal disease

Author

Khaled, Mariam Lotfy, primary, Ren, Yuan, additional, Kundalia, Ronak, additional, Alhaddad, Hasan, additional, Chen, Zhihua, additional, Wallace, Gerald C., additional, Evernden, Brittany, additional, Ospina, Oscar E., additional, Hall, MacLean, additional, Liu, Min, additional, Darville, Lancia N.F., additional, Izumi, Victoria, additional, Chen, Y. Ann, additional, Pilon-Thomas, Shari, additional, Stewart, Paul Ann, additional, Koomen, John M., additional, Corallo, Salvatore A., additional, Jain, Michael D., additional, Robinson, Timothy J., additional, Locke, Fredrick L., additional, Forsyth, Peter A., additional, and Smalley, Inna, additional

Published
2023
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42. Figure S7 Part 2 from CK1δ and CK1ε Signaling Sustains Mitochondrial Metabolism and Cell Survival in Multiple Myeloma

Author

Burger, Karen L., primary, Fernandez, Mario R., primary, Meads, Mark B., primary, Sudalagunta, Praneeth, primary, Oliveira, Paula S., primary, Renatino Canevarolo, Rafael, primary, Alugubelli, Raghunandan Reddy, primary, Tungsevik, Alexandre, primary, De Avila, Gabe, primary, Silva, Maria, primary, Graeter, Allison I., primary, Dai, Hongyue A., primary, Vincelette, Nicole D., primary, Prabhu, Antony, primary, Magaletti, Dario, primary, Yang, Chunying, primary, Li, Weimin, primary, Kulkarni, Amit, primary, Hampton, Oliver, primary, Koomen, John M., primary, Roush, William R., primary, Monastyrskyi, Andrii, primary, Berglund, Anders E., primary, Silva, Ariosto S., primary, Cleveland, John L., primary, and Shain, Kenneth H., primary

Published
2023
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44. Managing a Large-Scale Multiomics Project: A Team Science Case Study in Proteogenomics

Author

Stewart, Paul A., primary, Welsh, Eric A., additional, Fang, Bin, additional, Izumi, Victoria, additional, Mesa, Tania, additional, Zhang, Chaomei, additional, Yoder, Sean, additional, Zhang, Guolin, additional, Cen, Ling, additional, Pettersson, Fredrik, additional, Zhang, Yonghong, additional, Chen, Zhihua, additional, Cheng, Chia-Ho, additional, Thapa, Ram, additional, Thompson, Zachary, additional, Avedon, Melissa, additional, Wloch, Marek, additional, Fournier, Michelle, additional, Fellows, Katherine M., additional, Francis, Jewel M., additional, Saller, James J., additional, Boyle, Theresa A., additional, Chen, Y. Ann, additional, Haura, Eric B., additional, Teer, Jamie K., additional, Eschrich, Steven A., additional, and Koomen, John M., additional

Published
2020
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47. Modulating the polyamine/hypusine axis controls generation of CD8+ tissue-resident memory T cells

Author

Elmarsafawi, Aya G., primary, Hesterberg, Rebecca S., additional, Fernandez, Mario R., additional, Yang, Chunying, additional, Darville, Lancia N.F., additional, Liu, Min, additional, Koomen, John M., additional, Phanstiel, Otto, additional, Atkins, Reginald, additional, Mullinax, John E., additional, Pilon-Thomas, Shari A., additional, Locke, Frederick L., additional, Epling-Burnette, Pearlie K., additional, and Cleveland, John L., additional

Published
2023
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48. CK1δ/CK1ε Signaling Sustains Mitochondrial Metabolism and Cell Survival in Multiple Myeloma

Author

Burger, Karen L., primary, Fernandez, Mario R., additional, Meads, Mark B., additional, Sudalagunta, Praneeth Reddy, additional, Oliveira, Paula S., additional, Renatino Canevarolo, Rafael, additional, Alugubelli, Raghunandan Reddy, additional, Tungsevik, Alexandre, additional, De Avila, Gabe, additional, Silva, Maria, additional, Graeter, Allison I., additional, Dai, Hongyue, additional, Vincelette, Nicole D., additional, Prabhu, Antony, additional, Magaletti, Dario, additional, Yang, Chunying, additional, Li, Weimin, additional, Kulkarni, Amit, additional, Hampton, Oliver Alexander., additional, Koomen, John M., additional, Roush, William R., additional, Monastyrskyi, Andrii, additional, Berglund, Anders E., additional, Silva, Ariosto S., additional, Cleveland, John L., additional, and Shain, Kenneth H., additional

Published
2023
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49. PLK1 stabilizes a MYC-dependent kinase network in aggressive B cell lymphomas

Author

Ren, Yuan, Bi, Chengfeng, Zhao, Xiaohong, Lwin, Tint, Wang, Cheng, Yuan, Ji, Silva, Ariosto S., Shah, Bijal D., Fang, Bin, Li, Tao, Koomen, John M., Jiang, Huijuan, Chavez, Julio C., Pham, Lan V., Sudalagunta, Praneeth R., Wan, Lixin, Wang, Xuefeng, Dalton, William S., Moscinski, Lynn C., Shain, Kenneth H., Vose, Julie, Cleveland, John L., Sotomayor, Eduardo M., Fu, Kai, and Tao, Jianguo

Subjects
Gene expression -- Research, Lymphocytic leukemia -- Care and treatment -- Genetic aspects -- Patient outcomes, Health care industry
Abstract

Concordant activation of MYC and BCL-2 oncoproteins in double-hit lymphoma (DHL) results in aggressive disease that is refractory to treatment. By integrating activity-based proteomic profiling and drug screens, polo-like kinase-1 (PLK1) was identified as an essential regulator of the MYC-dependent kinome in DHL. Notably, PLK1 was expressed at high levels in DHL, correlated with MYC expression, and connoted poor outcome. Further, PLK1 signaling augmented MYC protein stability, and in turn, MYC directly induced PLK1 transcription, establishing a feed-forward MYC-PLK1 circuit in DHL. Finally, inhibition of PLK1 triggered degradation of MYC and of the antiapoptotic protein MCL-1, and PLK1 inhibitors showed synergy with BCL-2 antagonists in blocking DHL cell growth, survival, and tumorigenicity, supporting clinical targeting of PLK1 in DHL., Introduction MYC is a transcription factor that promotes oncogenesis by activating and repressing target genes that control cell growth, metabolism, and division (1, 2). MYC is deregulated in a large [...]

Published
2018
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