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1. A Rigorous Multi-Laboratory Study of Known PDAC Biomarkers Identifies Increased Sensitivity and Specificity Over CA19-9 Alone

Author

Haab, Brian, primary, Qian, Lu, additional, Staal, Ben, additional, Jain, Maneesh, additional, Fahrmann, Johannes Francois, additional, Worthington, Christine, additional, Prosser, Denise, additional, Velikokhatnaya, Liudmilla, additional, Lopez, Camden, additional, Tang, Runlong, additional, Hurd, Mark, additional, Gopalakrishnan, Natarajan, additional, Kumar, Sushil, additional, Smith, Lynette, additional, Hanash, Samir, additional, Batra, Surinder K., additional, Maitra, Anirban, additional, Lokshin, Anna, additional, Huang, Ying, additional, and Brand, Randall, additional

Published
2024
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2. Abstract A014: Combinations of previously reported biomarkers achieve improved sensitivity and specificity of detection of early stage pancreatic ductal adenocarcinoma

Author

Haab, Brian, primary, Qian, Lu, additional, Staal, Ben, additional, Jain, Maneesh, additional, Fahrmann, Johannes, additional, Worthington, Christine, additional, Prosser, Denise, additional, Velokokhatnaya, Liudmila, additional, Lopez, Camden, additional, Tang, Runlong, additional, Hurd, Mark, additional, Natarajan, Gopalakrishnan, additional, Kumar, Sushil, additional, Smith, Lynette, additional, Hanash, Samir, additional, Batra, Surinder, additional, Maitra, Anirban, additional, Lokshin, Anna, additional, Huang, Ying, additional, and Brand, Randall E., additional

Published
2024
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5. Supplementary Table 2 from Detection of Chemotherapy-resistant Pancreatic Cancer Using a Glycan Biomarker, sTRA

Author

Gao, ChongFeng, primary, Wisniewski, Luke, primary, Liu, Ying, primary, Staal, Ben, primary, Beddows, Ian, primary, Plenker, Dennis, primary, Aldakkak, Mohammed, primary, Hall, Johnathan, primary, Barnett, Daniel, primary, Gouda, Mirna Kheir, primary, Allen, Peter, primary, Drake, Richard, primary, Zureikat, Amer, primary, Huang, Ying, primary, Evans, Douglas, primary, Singhi, Aatur, primary, Brand, Randall E., primary, Tuveson, David A., primary, Tsai, Susan, primary, and Haab, Brian B., primary

Published
2023
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6. Supplemental Data from Detection of Chemotherapy-resistant Pancreatic Cancer Using a Glycan Biomarker, sTRA

Author

Gao, ChongFeng, primary, Wisniewski, Luke, primary, Liu, Ying, primary, Staal, Ben, primary, Beddows, Ian, primary, Plenker, Dennis, primary, Aldakkak, Mohammed, primary, Hall, Johnathan, primary, Barnett, Daniel, primary, Gouda, Mirna Kheir, primary, Allen, Peter, primary, Drake, Richard, primary, Zureikat, Amer, primary, Huang, Ying, primary, Evans, Douglas, primary, Singhi, Aatur, primary, Brand, Randall E., primary, Tuveson, David A., primary, Tsai, Susan, primary, and Haab, Brian B., primary

Published
2023
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7. Supplementary Data from The sTRA Plasma Biomarker: Blinded Validation of Improved Accuracy Over CA19-9 in Pancreatic Cancer Diagnosis

Author

Staal, Ben, primary, Liu, Ying, primary, Barnett, Daniel, primary, Hsueh, Peter, primary, He, Zonglin, primary, Gao, ChongFeng, primary, Partyka, Katie, primary, Hurd, Mark W., primary, Singhi, Aatur D., primary, Drake, Richard R., primary, Huang, Ying, primary, Maitra, Anirban, primary, Brand, Randall E., primary, and Haab, Brian B., primary

Published
2023
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8. Supplementary Table 1 from Detection of Chemotherapy-resistant Pancreatic Cancer Using a Glycan Biomarker, sTRA

Author

Gao, ChongFeng, primary, Wisniewski, Luke, primary, Liu, Ying, primary, Staal, Ben, primary, Beddows, Ian, primary, Plenker, Dennis, primary, Aldakkak, Mohammed, primary, Hall, Johnathan, primary, Barnett, Daniel, primary, Gouda, Mirna Kheir, primary, Allen, Peter, primary, Drake, Richard, primary, Zureikat, Amer, primary, Huang, Ying, primary, Evans, Douglas, primary, Singhi, Aatur, primary, Brand, Randall E., primary, Tuveson, David A., primary, Tsai, Susan, primary, and Haab, Brian B., primary

Published
2023
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9. Supplementary Table 3 from Detection of Chemotherapy-resistant Pancreatic Cancer Using a Glycan Biomarker, sTRA

Author

Gao, ChongFeng, primary, Wisniewski, Luke, primary, Liu, Ying, primary, Staal, Ben, primary, Beddows, Ian, primary, Plenker, Dennis, primary, Aldakkak, Mohammed, primary, Hall, Johnathan, primary, Barnett, Daniel, primary, Gouda, Mirna Kheir, primary, Allen, Peter, primary, Drake, Richard, primary, Zureikat, Amer, primary, Huang, Ying, primary, Evans, Douglas, primary, Singhi, Aatur, primary, Brand, Randall E., primary, Tuveson, David A., primary, Tsai, Susan, primary, and Haab, Brian B., primary

Published
2023
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10. Data from MET Kinase Inhibitor SGX523 Synergizes with Epidermal Growth Factor Receptor Inhibitor Erlotinib in a Hepatocyte Growth Factor–Dependent Fashion to Suppress Carcinoma Growth

Author

Zhang, Yu-Wen, primary, Staal, Ben, primary, Essenburg, Curt, primary, Su, Yanli, primary, Kang, Liang, primary, West, Rich, primary, Kaufman, Dafna, primary, DeKoning, Tom, primary, Eagleson, Bryn, primary, Buchanan, Sean G., primary, and Vande Woude, George F., primary

Published
2023
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11. Supplementary Methods, Figures 1-4 from MET Kinase Inhibitor SGX523 Synergizes with Epidermal Growth Factor Receptor Inhibitor Erlotinib in a Hepatocyte Growth Factor–Dependent Fashion to Suppress Carcinoma Growth

Author

Zhang, Yu-Wen, primary, Staal, Ben, primary, Essenburg, Curt, primary, Su, Yanli, primary, Kang, Liang, primary, West, Rich, primary, Kaufman, Dafna, primary, DeKoning, Tom, primary, Eagleson, Bryn, primary, Buchanan, Sean G., primary, and Vande Woude, George F., primary

Published
2023
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14. The Framing Preference for Large and Increasing Components in Static and Dynamic Descriptions

Author

Pander Maat, Henk, Staal, Ben, Holleman, Bregje, LS taalbeheersing van het Nederlands, ILS L&C, LS communicatie- en informatiewetenschap, LS taalbeheersing van het Nederlands, ILS L&C, and LS communicatie- en informatiewetenschap

Subjects
media_common.quotation_subject, Frame (networking), Context (language use), attribute framing, Relative strength, Preference, Task (project management), BF1-990, Variable (computer science), markedness, Framing (construction), task effect, Psychology, profiling, Function (engineering), Psychology(all), General Psychology, reference point, Original Research, media_common, Cognitive psychology
Abstract

Describing sets in terms of a two-valued variable, either value can be chosen: exam results may be referred to by pass rates or fail rates. What determines such framing choices? Building on work by McKenzie and colleagues on reference points in the production and interpretation of framed information, we investigate two determinants of frame choice. One is that speakers tend to focus on the component that has increased vis-à-vis a previous state, the other is the tendency to choose the component larger than 50%. We propose to view reference points as pointing to different kinds of communicative relevance. Hence the use of the previous state and the 50% reference points by speakers is not just a function of the information, but is co-determined by a communicative cue in the context: the question being asked about this information. This line of thought is supported by two experiments containing items offering two-sided distribution information at two points in time. Our first experiment employs a static task, requiring a description of the most recent situation. The second experiment uses a dynamic task, asking participants to describe the development between the two time points. We hypothesize that in static tasks the component size is the strongest frame choice determinant, while in dynamic tasks frame choice is mainly driven by whether a component has increased. The experiments consist of 16 different scenarios, both with symmetrical contrasts (i.e., dogs vs. cats) and with asymmetrical ones (i.e., winning vs. losing). Both experiments support the hypotheses. In the static task, the size effect is the only consistent effect; in the dynamic task, the effect of direction of change is much larger than that of size. This pattern of differences between size and change effects applies across symmetrical and asymmetrical contrasts. Our experiments shed light on cognitive and communicative regularities involved in the production of framed messages: people do tend to prefer larger and increasing components when choosing a frame, but the relative strength of both these preferences depends on the communicative task.

Published
2021

15. Detection of Chemotherapy-resistant Pancreatic Cancer Using a Glycan Biomarker, sTRA

Author

Gao, ChongFeng, primary, Wisniewski, Luke, additional, Liu, Ying, additional, Staal, Ben, additional, Beddows, Ian, additional, Plenker, Dennis, additional, Aldakkak, Mohammed, additional, Hall, Johnathan, additional, Barnett, Daniel, additional, Gouda, Mirna Kheir, additional, Allen, Peter, additional, Drake, Richard, additional, Zureikat, Amer, additional, Huang, Ying, additional, Evans, Douglas, additional, Singhi, Aatur, additional, Brand, Randall E., additional, Tuveson, David A., additional, Tsai, Susan, additional, and Haab, Brian B., additional

Published
2021
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16. Abstract PR-010: Blinded and meta-analysis validation of an improved serological test for PDAC using the combination of CA19-9 and the sTRA glycan

Author

Liu, Ying, primary, Staal, Ben, additional, Barnett, Daniel, additional, He, Zonglin, additional, Gao, Chongfeng, additional, Hurd, Mark, additional, Bartlett, Pamela, additional, Singhi, Aatur, additional, Morrow, J. Bradley, additional, Cote, Gregory, additional, Maitra, Anirban, additional, Huang, Ying, additional, Brand, Randall, additional, and Haab, Brian, additional

Published
2020
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17. Abstract PO-002: Detection of chemotherapy-resistant pancreatic cancer using a glycan Biomarker

Author

Gao, ChongFeng, primary, Wisniewski, Luke, additional, Liu, Ying, additional, Staal, Ben, additional, Beddows, Ian, additional, Plenker, Dennis, additional, Aldakkak, Mohammed, additional, Hall, Johnathan, additional, Barnett, Daniel, additional, Gouda, Mirna Kheir, additional, Allen, Peter, additional, Drake, Richard, additional, Zureikat, Amer, additional, Huang, Ying, additional, Evans, Douglas, additional, Singhi, Aatur, additional, Brand, Randall, additional, Tuveson, David, additional, Tsai, Susan, additional, and Haab, Brian, additional

Published
2020
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18. Detection of Chemotherapy-Resistant Pancreatic Cancer Using a Glycan Biomarker

Author

Gao, ChongFeng, primary, Wisniewski, Luke, additional, Liu, Ying, additional, Staal, Ben, additional, Beddows, Ian, additional, Plenker, Dennis, additional, Aldakkak, Mohammed, additional, Hall, Johnathan, additional, Barnett, Daniel, additional, Gouda, Mirna Kheir, additional, Allen, Peter, additional, Drake, Richard, additional, Zureikat, Amer, additional, Huang, Ying, additional, Evans, Douglas, additional, Singhi, Aatur, additional, Brand, Randall E., additional, Tuveson, David A., additional, Tsai, Susan, additional, and Haab, Brian B., additional

Published
2020
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20. MOESM1 of Differential responses of MET activations to MET kinase inhibitor and neutralizing antibody

Author

Jianqun Kou, Musich, Phillip, Staal, Ben, Kang, Liang, Qin, Yuan, Yao, Zhi, Boheng Zhang, Weizhong Wu, Tam, Angela, Huang, Alan, Huai-Xiang Hao, Woude, George Vande, and Xie, Qian

Subjects
digestive system diseases
Abstract

Additional file 1: Figure S1. INC280 alone is sufficient in inhibiting MKN45 proliferation. (A) INC280 (0.1, 1 µM) treatment for 72 hrs potently inhibited MKN45 proliferation as measured by the CellTiter-Glo assay. Further combination with ATM inhibitor Ku60019 did not improve efficacy. Data represents for Mean ± SD. Vertical bar represents the standard deviation. (B) INC280 mediated ATM signaling pathway activity in MKN45 cells.

Published
2018
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22. The sTRA Plasma Biomarker: Blinded Validation of Improved Accuracy Over CA19-9 in Pancreatic Cancer Diagnosis

Author

Staal, Ben, primary, Liu, Ying, additional, Barnett, Daniel, additional, Hsueh, Peter, additional, He, Zonglin, additional, Gao, ChongFeng, additional, Partyka, Katie, additional, Hurd, Mark W., additional, Singhi, Aatur D., additional, Drake, Richard R., additional, Huang, Ying, additional, Maitra, Anirban, additional, Brand, Randall E., additional, and Haab, Brian B., additional

Published
2019
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23. Mining High-Complexity Motifs in Glycans: A New Language To Uncover the Fine Specificities of Lectins and Glycosidases

Author

Klamer, Zachary, Staal, Ben, Prudden, Anthony R, Liu, Lin, Smith, David F, Boons, Geert-Jan, Haab, Brian, Afd Chemical Biology and Drug Discovery, Sub Algemeen Scheikunde, Chemical Biology and Drug Discovery, Afd Chemical Biology and Drug Discovery, Sub Algemeen Scheikunde, and Chemical Biology and Drug Discovery

Subjects
0301 basic medicine, Glycan, Glycoside Hydrolases, Fucose, Article, Analytical Chemistry, Substrate Specificity, 03 medical and health sciences, chemistry.chemical_compound, Polysaccharides, Lectins, Humans, Fucosidase, Binding site, Binding Sites, biology, Milk, Human, Glycobiology, Lectin, Microarray Analysis, Sialic acid, 030104 developmental biology, chemistry, Biochemistry, biology.protein, Neuraminidase, Algorithms
Abstract

Knowledge of lectin and glycosidase specificities is fundamental to the study of glycobiology. The primary specificities of such molecules can be uncovered using well-established tools, but the complex details of their specificities are difficult to determine and describe. Here we present a language and algorithm for the analysis and description of glycan motifs with high complexity. The language uses human-readable notation and wildcards, modifiers, and logical operators to define motifs of nearly any complexity. By applying the syntax to the analysis of glycan-array data, we found that the lectin AAL had higher binding where fucose groups are displayed on separate branches. The lectin SNA showed gradations in binding based on the length of the extension displaying sialic acid and on characteristics of the opposing branches. A new algorithm to evaluate changes in lectin binding upon treatment with exoglycosidases identified the primary specificities and potential fine specificities of an α1-2-fucosidase and an α2-3,6,8-neuraminidase. The fucosidase had significantly lower action where sialic acid neighbors the fucose, and the neuraminidase showed statistically lower action where α1-2 fucose neighbors the sialic acid or is on the opposing branch. The complex features identified here would have been inaccessible to analysis using previous methods. The new language and algorithms promise to facilitate the precise determination and description of lectin and glycosidase specificities.

Published
2017

24. Abstract LB-015: Differential therapeutic responses of MET oncogenic activations to Met kinase inhibitor and neutralizing antibody

Author

Kou, Jianqun, primary, Staal, Ben, additional, Musich, Phillip R., additional, Kang, Liang, additional, Qin, Yuan, additional, Yao, Zhi Q., additional, Zhang, Boheng, additional, Angela, Tam, additional, Huang, Alan, additional, Hao, Huaixiang, additional, Woude, George F. Vande, additional, and Xie, Qian, additional

Published
2018
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30. MET Kinase Inhibitor SGX523 Synergizes with Epidermal Growth Factor Receptor Inhibitor Erlotinib in a Hepatocyte Growth Factor–Dependent Fashion to Suppress Carcinoma Growth

Author

Zhang, Yu-Wen, primary, Staal, Ben, additional, Essenburg, Curt, additional, Su, Yanli, additional, Kang, Liang, additional, West, Rich, additional, Kaufman, Dafna, additional, DeKoning, Tom, additional, Eagleson, Bryn, additional, Buchanan, Sean G., additional, and Vande Woude, George F., additional

Published
2010
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31. Abstract LB-305: Why two are better than one: Suppression of carcinoma cell growth in vitro and in human HGF/SF transgenic SCID by inhibitors of MET (SGX523) and EGFR (erlotinib)

Author

Zhang, Yu-Wen, primary, Staal, Ben, additional, Essenburg, Curt, additional, Su, Yanli, additional, Kang, Liang, additional, West, Rich, additional, Kaufman, Dafna, additional, DeKoning, Tom, additional, Eagleson, Bryn, additional, Buchanan, Sean, additional, and Vande Woude, George, additional

Published
2010
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32. Cancer-Type Regulation of MIG-6 Expression by Inhibitors of Methylation and Histone Deacetylation.

Author

Yu-Wen Zhang, Staal, Ben, Dykema, Karl J., Furge, Kyle A., and Vande Woude, George F.

Subjects
*CELLULAR mechanics, *LUNG cancer, *CANCER, *HEALTH risk assessment, *SMALL cell lung cancer
Abstract

Epigenetic silencing is one of the mechanisms leading to inactivation of a tumor suppressor gene, either by DNA methylation or histone modification in a promoter regulatory region. Mitogen inducible gene 6 (MIG-6), mainly known as a negative feedback inhibitor of the epidermal growth factor receptor (EGFR) family, is a tumor suppressor gene that is associated with many human cancers. To determine if MIG-6 is inactivated by epigenetic alteration, we identified a group of human lung cancer and melanoma cell lines in which its expression is either low or undetectable and studied the effects of methylation and of histone deacetylation on its expression. The DNA methyltransferase (DNMT) inhibitor 5-aza-2'- deoxycytidine (5-aza-dC) induced MIG-6 expression in melanoma cell lines but little in lung cancer lines. By contrast, the histone deacetylase (HDAC) inhibitor trichostatin A (TSA) induced MIG-6 expression in lung cancer lines but had little effect in melanoma lines. However, the MIG-6 promoter itself did not appear to be directly affected by either methylation or histone deacetylation, indicating an indirect regulatory mechanism. Luciferase reporter assays revealed that a short segment of exon 1 in the MIG-6 gene is responsible for TSA response in the lung cancer cells; thus, the MIG-6 gene can be epigenetically silenced through an indirect mechanism without having a physical alteration in its promoter. Furthermore, our data also suggest that MIG-6 gene expression is differentially regulated in lung cancer and melanoma. [ABSTRACT FROM AUTHOR]

Published
2012
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33. A Rigorous Multi-Laboratory Study of Known PDAC Biomarkers Identifies Increased Sensitivity and Specificity Over CA19-9 Alone.

Author

Haab B, Qian L, Staal B, Jain M, Fahrmann J, Worthington C, Prosser D, Velokokhatnaya L, Lopez C, Tang R, Hurd MW, Natarajan G, Kumar S, Smith L, Hanash S, Batra SK, Maitra A, Lokshin A, Huang Y, and Brand RE

Abstract

A blood test that enables surveillance for early-stage pancreatic ductal adenocarcinoma (PDAC) is an urgent need. Independent laboratories have reported PDAC biomarkers that could improve biomarker performance over CA19-9 alone, but the performance of the previously reported biomarkers in combination is not known. Therefore, we conducted a coordinated case/control study across multiple laboratories using common sets of blinded training and validation samples (132 and 295 plasma samples, respectively) from PDAC patients and non-PDAC control subjects representing conditions under which surveillance occurs. We analyzed the training set to identify candidate biomarker combination panels using biomarkers across laboratories, and we applied the fixed panels to the validation set. The panels identified in the training set, CA19-9 with CA199.STRA, LRG1, TIMP-1, TGM2, THSP2, ANG, and MUC16.STRA, achieved consistent performance in the validation set. The panel of CA19-9 with the glycan biomarker CA199.STRA improved sensitivity from 0.44 with 0.98 specificity for CA19-9 alone to 0.71 with 0.98 specificity (p < 0.001, 1000-fold bootstrap). Similarly, CA19-9 combined with the protein biomarker LRG1 and CA199.STRA improved specificity from 0.16 with 0.94 sensitivity for CA19-9 to 0.65 with 0.89 sensitivity (p < 0.001, 1000-fold bootstrap). We further validated significantly improved performance using biomarker panels that did not include CA19-9. This study establishes the effectiveness of a coordinated study of previously discovered biomarkers and identified panels of those biomarkers that significantly increased the sensitivity and specificity of early-stage PDAC detection in a rigorous validation trial.

Published
2024
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