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1. A gene-protein assay for human epidermal growth factor receptor 2 (HER2): brightfield tricolor visualization of HER2 protein, the HER2 gene, and chromosome 17 centromere (CEN17) in formalin-fixed, paraffin-embedded breast cancer tissue sections

Author

Nitta Hiroaki, Kelly Brian D, Padilla Mary, Wick Nikolaus, Brunhoeber Patrick, Bai Isaac, Singh Shalini, Ranger-Moore Jim, Bieniarz Chris, Tsuda Hitoshi, and Grogan Thomas M

Subjects
Gene-protein assay, Dual color in situ hybridization, Immunohistochemistry, HER2, Breast cancer, Pathology, RB1-214
Abstract

Abstract Background The eligibility of breast cancer patients for human epidermal growth factor receptor 2 (HER2)-directed therapies is determined by the HER2 gene amplification and/or HER2 protein overexpression status of the breast tumor as determined by in situ hybridization (ISH) or immunohistochemistry (IHC), respectively. Our objective was to combine the US Food and Drug Administration (FDA)-approved HER2 & chromosome 17 centromere (CEN17) brightfield ISH (BISH) and HER2 IHC assays into a single automated HER2 gene-protein assay allowing simultaneous detection of all three targets in a single tissue section. Methods The HER2 gene-protein assay was optimized using formalin-fixed, paraffin-embedded (FFPE) samples of the xenograft tumors MCF7 [HER2 negative (non-amplified gene, protein negative)] and Calu-3 [HER2 positive (amplified gene, protein positive)]. HER2 IHC was performed using a rabbit monoclonal anti-HER2 antibody (clone 4B5) and a conventional 3,3'-diaminobenzidine IHC detection. The HER2 & CEN17 BISH signals were visualized using horseradish peroxidase-based silver and alkaline phosphatase-based red detection systems, respectively with a cocktail of 2,4-dinitrophenyl-labeled HER2 and digoxigenin-labeled CEN17 probes. The performance of the gene-protein assay on tissue microarray slides containing 189 randomly selected FFPE clinical breast cancer tissue cores was compared to that of the separate HER2 IHC and HER2 & CEN17 BISH assays. Results HER2 protein detection was optimal when the HER2 IHC protocol was used before (rather than after) the BISH protocol. The sequential use of HER2 IHC and HER2 & CEN17 BISH detection steps on FFPE xenograft tumor sections appropriately co-localized the HER2 protein, HER2 gene, and CEN17 signals after mitigating the silver background staining by using a naphthol phosphate-containing hybridization buffer for the hybridization step. The HER2 protein and HER2 gene status obtained using the multiplex HER2 gene-protein assay demonstrated high concordance with those obtained using the separate HER2 IHC and HER2 & CEN17 BISH assays, respectively. Conclusions We have developed a protocol that allows simultaneous visualization of the HER2 IHC and HER2 & CEN17 BISH targets. This automated protocol facilitated the determination of HER2 protein and HER2 gene status in randomly selected breast cancer samples, particularly in cases that were equivocal or exhibited tumor heterogeneity. The HER2 gene-protein assay produced results virtually equivalent to those of the single FDA-approved HER2 IHC and HER2 & CEN17 BISH assays. Virtual slides The virtual slides for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2041964038705297

Published
2012
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5. Evaluation of CD3 and CD8 T-Cell Immunohistochemistry for Prognostication and Prediction of Benefit From Adjuvant Chemotherapy in Early-Stage Colorectal Cancer Within the QUASAR Trial.

Author

Williams, Christopher J.M., Gray, Richard, Hills, Robert K., Shires, Michael, Zhang, Liping, Zhao, Zuo, Gardner, Tracie, Sapanara, Nancy, Xu, Xiao-Meng, Bai, Isaac, Yan, Dongyao, Muranyi, Andrea, Dance, Sarah, Aghaei, Faranak, Hemmings, Gemma, Hale, Michael, Kurkure, Uday, Guetter, Christoph, Richman, Susan D., and Hutchins, Gordon

Published
2024
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9. Supplementary Figure S2 from Associations between AI-Assisted Tumor Amphiregulin and Epiregulin IHC and Outcomes from Anti-EGFR Therapy in the Routine Management of Metastatic Colorectal Cancer

Author

Williams, Christopher J.M., primary, Elliott, Faye, primary, Sapanara, Nancy, primary, Aghaei, Faranak, primary, Zhang, Liping, primary, Muranyi, Andrea, primary, Yan, Dongyao, primary, Bai, Isaac, primary, Zhao, Zuo, primary, Shires, Michael, primary, Wood, Henry M., primary, Richman, Susan D., primary, Hemmings, Gemma, primary, Hale, Michael, primary, Bottomley, Daniel, primary, Galvin, Leanne, primary, Cartlidge, Caroline, primary, Dance, Sarah, primary, Bacon, Chris M., primary, Mansfield, Laura, primary, Young-Zvandasara, Kathe, primary, Sudan, Ajay, primary, Lambert, Katy, primary, Bibby, Irena, primary, Coupland, Sarah E., primary, Montazeri, Amir, primary, Kipling, Natalie, primary, Hughes, Kathryn, primary, Cross, Simon S., primary, Dewdney, Alice, primary, Pheasey, Leanne, primary, Leng, Cathryn, primary, Gochera, Tatenda, primary, Mangham, D. Chas, primary, Saunders, Mark, primary, Pritchard, Martin, primary, Stott, Helen, primary, Mukherjee, Abhik, primary, Ilyas, Mohammad, primary, Silverman, Rafael, primary, Hyland, Georgina, primary, Sculthorpe, Declan, primary, Thornton, Kirsty, primary, Gould, Imogen, primary, O'Callaghan, Ann, primary, Brown, Nicholas, primary, Turnbull, Samantha, primary, Shaw, Lisa, primary, Seymour, Matthew T., primary, West, Nicholas P., primary, Seligmann, Jenny F., primary, Singh, Shalini, primary, Shanmugam, Kandavel, primary, and Quirke, Philip, primary

Published
2023
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10. Supplementary Table S3 from Associations between AI-Assisted Tumor Amphiregulin and Epiregulin IHC and Outcomes from Anti-EGFR Therapy in the Routine Management of Metastatic Colorectal Cancer

Author

Williams, Christopher J.M., primary, Elliott, Faye, primary, Sapanara, Nancy, primary, Aghaei, Faranak, primary, Zhang, Liping, primary, Muranyi, Andrea, primary, Yan, Dongyao, primary, Bai, Isaac, primary, Zhao, Zuo, primary, Shires, Michael, primary, Wood, Henry M., primary, Richman, Susan D., primary, Hemmings, Gemma, primary, Hale, Michael, primary, Bottomley, Daniel, primary, Galvin, Leanne, primary, Cartlidge, Caroline, primary, Dance, Sarah, primary, Bacon, Chris M., primary, Mansfield, Laura, primary, Young-Zvandasara, Kathe, primary, Sudan, Ajay, primary, Lambert, Katy, primary, Bibby, Irena, primary, Coupland, Sarah E., primary, Montazeri, Amir, primary, Kipling, Natalie, primary, Hughes, Kathryn, primary, Cross, Simon S., primary, Dewdney, Alice, primary, Pheasey, Leanne, primary, Leng, Cathryn, primary, Gochera, Tatenda, primary, Mangham, D. Chas, primary, Saunders, Mark, primary, Pritchard, Martin, primary, Stott, Helen, primary, Mukherjee, Abhik, primary, Ilyas, Mohammad, primary, Silverman, Rafael, primary, Hyland, Georgina, primary, Sculthorpe, Declan, primary, Thornton, Kirsty, primary, Gould, Imogen, primary, O'Callaghan, Ann, primary, Brown, Nicholas, primary, Turnbull, Samantha, primary, Shaw, Lisa, primary, Seymour, Matthew T., primary, West, Nicholas P., primary, Seligmann, Jenny F., primary, Singh, Shalini, primary, Shanmugam, Kandavel, primary, and Quirke, Philip, primary

Published
2023
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11. Data from Associations between AI-Assisted Tumor Amphiregulin and Epiregulin IHC and Outcomes from Anti-EGFR Therapy in the Routine Management of Metastatic Colorectal Cancer

Author

Williams, Christopher J.M., primary, Elliott, Faye, primary, Sapanara, Nancy, primary, Aghaei, Faranak, primary, Zhang, Liping, primary, Muranyi, Andrea, primary, Yan, Dongyao, primary, Bai, Isaac, primary, Zhao, Zuo, primary, Shires, Michael, primary, Wood, Henry M., primary, Richman, Susan D., primary, Hemmings, Gemma, primary, Hale, Michael, primary, Bottomley, Daniel, primary, Galvin, Leanne, primary, Cartlidge, Caroline, primary, Dance, Sarah, primary, Bacon, Chris M., primary, Mansfield, Laura, primary, Young-Zvandasara, Kathe, primary, Sudan, Ajay, primary, Lambert, Katy, primary, Bibby, Irena, primary, Coupland, Sarah E., primary, Montazeri, Amir, primary, Kipling, Natalie, primary, Hughes, Kathryn, primary, Cross, Simon S., primary, Dewdney, Alice, primary, Pheasey, Leanne, primary, Leng, Cathryn, primary, Gochera, Tatenda, primary, Mangham, D. Chas, primary, Saunders, Mark, primary, Pritchard, Martin, primary, Stott, Helen, primary, Mukherjee, Abhik, primary, Ilyas, Mohammad, primary, Silverman, Rafael, primary, Hyland, Georgina, primary, Sculthorpe, Declan, primary, Thornton, Kirsty, primary, Gould, Imogen, primary, O'Callaghan, Ann, primary, Brown, Nicholas, primary, Turnbull, Samantha, primary, Shaw, Lisa, primary, Seymour, Matthew T., primary, West, Nicholas P., primary, Seligmann, Jenny F., primary, Singh, Shalini, primary, Shanmugam, Kandavel, primary, and Quirke, Philip, primary

Published
2023
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12. Supplementary Methods S1 from Associations between AI-Assisted Tumor Amphiregulin and Epiregulin IHC and Outcomes from Anti-EGFR Therapy in the Routine Management of Metastatic Colorectal Cancer

Author

Williams, Christopher J.M., primary, Elliott, Faye, primary, Sapanara, Nancy, primary, Aghaei, Faranak, primary, Zhang, Liping, primary, Muranyi, Andrea, primary, Yan, Dongyao, primary, Bai, Isaac, primary, Zhao, Zuo, primary, Shires, Michael, primary, Wood, Henry M., primary, Richman, Susan D., primary, Hemmings, Gemma, primary, Hale, Michael, primary, Bottomley, Daniel, primary, Galvin, Leanne, primary, Cartlidge, Caroline, primary, Dance, Sarah, primary, Bacon, Chris M., primary, Mansfield, Laura, primary, Young-Zvandasara, Kathe, primary, Sudan, Ajay, primary, Lambert, Katy, primary, Bibby, Irena, primary, Coupland, Sarah E., primary, Montazeri, Amir, primary, Kipling, Natalie, primary, Hughes, Kathryn, primary, Cross, Simon S., primary, Dewdney, Alice, primary, Pheasey, Leanne, primary, Leng, Cathryn, primary, Gochera, Tatenda, primary, Mangham, D. Chas, primary, Saunders, Mark, primary, Pritchard, Martin, primary, Stott, Helen, primary, Mukherjee, Abhik, primary, Ilyas, Mohammad, primary, Silverman, Rafael, primary, Hyland, Georgina, primary, Sculthorpe, Declan, primary, Thornton, Kirsty, primary, Gould, Imogen, primary, O'Callaghan, Ann, primary, Brown, Nicholas, primary, Turnbull, Samantha, primary, Shaw, Lisa, primary, Seymour, Matthew T., primary, West, Nicholas P., primary, Seligmann, Jenny F., primary, Singh, Shalini, primary, Shanmugam, Kandavel, primary, and Quirke, Philip, primary

Published
2023
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14. Associations between AI-Assisted Tumor Amphiregulin and Epiregulin IHC and Outcomes from Anti-EGFR Therapy in the Routine Management of Metastatic Colorectal Cancer

Author

Williams, Christopher J.M., primary, Elliott, Faye, additional, Sapanara, Nancy, additional, Aghaei, Faranak, additional, Zhang, Liping, additional, Muranyi, Andrea, additional, Yan, Dongyao, additional, Bai, Isaac, additional, Zhao, Zuo, additional, Shires, Michael, additional, Wood, Henry M., additional, Richman, Susan D., additional, Hemmings, Gemma, additional, Hale, Michael, additional, Bottomley, Daniel, additional, Galvin, Leanne, additional, Cartlidge, Caroline, additional, Dance, Sarah, additional, Bacon, Chris M., additional, Mansfield, Laura, additional, Young-Zvandasara, Kathe, additional, Sudan, Ajay, additional, Lambert, Katy, additional, Bibby, Irena, additional, Coupland, Sarah E., additional, Montazeri, Amir, additional, Kipling, Natalie, additional, Hughes, Kathryn, additional, Cross, Simon S., additional, Dewdney, Alice, additional, Pheasey, Leanne, additional, Leng, Cathryn, additional, Gochera, Tatenda, additional, Mangham, D. Chas, additional, Saunders, Mark, additional, Pritchard, Martin, additional, Stott, Helen, additional, Mukherjee, Abhik, additional, Ilyas, Mohammad, additional, Silverman, Rafael, additional, Hyland, Georgina, additional, Sculthorpe, Declan, additional, Thornton, Kirsty, additional, Gould, Imogen, additional, O'Callaghan, Ann, additional, Brown, Nicholas, additional, Turnbull, Samantha, additional, Shaw, Lisa, additional, Seymour, Matthew T., additional, West, Nicholas P., additional, Seligmann, Jenny F., additional, Singh, Shalini, additional, Shanmugam, Kandavel, additional, and Quirke, Philip, additional

Published
2023
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16. Determining PD-L1 Status in Patients With Triple-Negative Breast Cancer: Lessons Learned From IMpassion130

Author

Jary, Marine, Liu, Wen-Wei, Yan, Dongyao, Bai, Isaac, Muranyi, Andrea, Colle, Elise, Brocheriou, Isabelle, Turpin, Anthony, Radosevic-Robin, Nina, Bourgoin, Pierre, Penault-Llorca, Frédérique, Cohen, Romain, Vernerey, Dewi, André, Thierry, Borg, Christophe, Shanmugam, Kandavel, Svrcek, Magali, Liu, Wen‐wei, Cooperator Multidisciplinary Oncology Group (GERCOR), CHU Clermont-Ferrand, Ventana Medical Systems, Hôpital Beaujon [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service d'oncologie médicale (CHRU Lille), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), CHU Saint-Antoine [AP-HP], Service d'Oncologie Médicale [CHRU Besançon], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Interactions hôte-greffon-tumeur, ingénierie cellulaire et génique - UFC (UMR INSERM 1098) (RIGHT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS BFC)-Université de Franche-Comté (UFC), Breast Cancer Translational Research Laboratory, Institut Jules Bordet [Bruxelles], Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB)-Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), Translational Cancer Research Unit [Antwerp], Philipps Universität Marburg = Philipps University of Marburg, Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, Division of Pathology and Laboratory Medicine, Università degli Studi di Milano = University of Milan (UNIMI)-European Institute of Oncology [Milan] (ESMO), University of the Sunshine Coast (USC), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Department of Pathology, Aberdeen University Medical School, Hospital Universitario Ramón y Cajal [Madrid], Universidad de Alcalá - University of Alcalá (UAH), VU Medical Center, Cell Biology and Biotherapy Unit, INT-Fondazione Pascale, Department of Oncology and Metabolism [Sheffield, UK], The University of Sheffield [Sheffield, U.K.], Institute for Surgical Pathology, University hospital of Zurich [Zurich], Service de pathologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de Pathologie [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Service d'Oncologie Médicale [CHU Saint -Antoine], Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté])-Université de Franche-Comté (UFC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté]), Service d'Anatomie et cytologie pathologiques = Service de Pathologie [CHU Pitié-Salpêtrière] (ACP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service d'Oncologie Médicale [CHU Saint-Antoine], HAL-SU, Gestionnaire, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre de Recherche Saint-Antoine (CRSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), and Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)

Subjects
Cancer Research, Biopsy, Best practice, BluePrint 80-gene signature, Predictive, DNA Mismatch Repair, pMMR, B7-H1 Antigen, Cohort Studies, Breast cancer, MESH: Tumor Microenvironment, Tumor Microenvironment, MESH: B7-H1 Antigen, Prospective Studies, MESH: Lymphocytes, Tumor-Infiltrating, MESH: Cohort Studies, Oligometastatic colorectal cancer, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, high/low risk, immune profile, General Medicine, Immunohistochemistry, External quality assessment, 3. Good health, MESH: DNA Mismatch Repair, Oncology, Cytological techniques, Colonic Neoplasms, Molecular Medicine, HER2-low, Colorectal Neoplasms, PD-L1, Histology, Serum proteins, T lymphocytes, [SDV.CAN]Life Sciences [q-bio]/Cancer, Prognostic, Non-small cell lung carcinoma, Lymphocytes, Tumor-Infiltrating, Molecular diagnostics, Genetics, Humans, early breast cancer, MESH: Colonic Neoplasms, MESH: Humans, Liquid biopsy, gene expression profiles, MammaPrint 70-gene signature, Plasma proteins, Biomarker, MESH: Prospective Studies, digestive system diseases, Next-generation sequencing, Trastuzumab-deruxtecan, MESH: Tissue Fixation, hallmarks of cancer, MESH: Colorectal Neoplasms, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; In the era of immune checkpoint inhibitors, understanding the metastatic microenvironment of proficient mismatch repair/microsatellite stable (pMMR/MSS) colorectal cancer (CRC) is of paramount importance to both prognostication and the development of more effective novel therapies. In this study, primary and paired metastasis tissue samples were collected from patients with resectable metastatic CRC treated with adjuvant FOLFOX or peri-operative chemotherapy in the MIROX phase III prospective study. In total, 74 cancer tissues were stained for CD3, CD8, Forkhead box protein 3 (FOXP3), programmed cell death protein-1 (PD-1, invasive front, stromal, intra-epithelial compartments), and programmed death-ligand 1 (PD-L1, tumor, immune cells). The immune profiling of primary CRC had a limited value to predict the immune context of paired metastases for all markers but CD3+. The expression of CD8 and PD-L1 was higher in metastases after neoadjuvant FOLFOX. In metastases, both CD3 T cells at the invasive front and PD-L1 expressions on immune cells were predictive of better disease-free survival. These results show that the effect of FOLFOX on modifying the immune microenvironment in resected CRC metastases and measurement of PD-L1 expression and tumor-infiltrating CD8 T cells in pMMR/MSS metastatic tissue samples could improve treatment strategies of metastatic CRC patients.

Published
2022
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17. Artificial intelligence-assisted evaluation of tumor infiltrating CD3+ and CD8+ T cells for prognostication and prediction of benefit from adjuvant chemotherapy in early stage colorectal cancer (CRC): A retrospective analysis of the QUASAR trial.

Author

Williams, Christopher, primary, Gray, Richard G, additional, Shires, Mike, additional, Zhang, Liping, additional, Zhao, Zuo, additional, Bai, Isaac, additional, Yan, Dongyao, additional, Dance, Sarah, additional, Aghaei, Faranak, additional, Hemmings, Gemma, additional, Hale, Michael, additional, Kurkure, Uday, additional, Guetter, Christoph, additional, Richman, Susan D, additional, Hutchins, Gordon, additional, Seligmann, Jenny F., additional, West, Nicholas, additional, Singh, Shalini, additional, Shanmugam, Kandavel, additional, and Quirke, Philip, additional

Published
2023
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18. Association between artificial intelligence (AI) -assisted tumor AREG and EREG immunohistochemistry (IHC) and outcomes from anti-EGFR therapy during the routine management of metastatic colorectal cancer (mCRC): An observational cohort study.

Author

Williams, Christopher, primary, Elliott, Faye, additional, Shires, Mike, additional, Wood, Henry, additional, Zhang, Liping, additional, Zhao, Zuo, additional, Bai, Isaac, additional, Yan, Dongyao, additional, Aghaei, Faranak, additional, Kurkure, Uday, additional, Bacon, Chris, additional, Coupland, Sarah E, additional, Cross, Simon, additional, Mangham, D Chas, additional, Mukherjee, Abhik, additional, Seligmann, Jenny F., additional, West, Nicholas, additional, Singh, Shalini, additional, Shanmugam, Kandavel, additional, and Quirke, Philip, additional

Published
2023
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19. How to use the regulatory data from Health Canada for secondary analyses on new drugs, biologics and vaccines

Author

Bai, Isaac, Doshi, Peter, and Herder, Matthew

Abstract

Incorporating clinical data held by national health product regulatory authorities into secondary analyses such as systematic reviews can help combat publication bias and selective outcome reporting, in turn, supporting more evidence-based decisions regarding the prescribing of drugs, biologics and vaccines. Owing to recent changes in Canadian law, Health Canada has begun to make clinical information—whether it has been previously published or not—publicly available through its ‘Public Release of Clinical Information’ (PRCI) online database. We provide guidance about how to access and use regulatory data obtained through the PRCI database for the purpose of conducting drug and biologic secondary analyses.

Published
2024
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22. Abstract P1-02-17: Artificial intelligence-based whole slide scoring of nuclear breast cancer IHC markers Ki67, ER, and PR matches performance of manual clinical scoring

Author

Kapadia, Monesh, primary, Khojasteh, Mehrnoush, additional, Kouzova, Margarita, additional, Jones, Carol, additional, Xu, Xiao-Meng, additional, Olson, Matthew T., additional, Gladden, Sarah, additional, Sapanara, Nancy, additional, Singh, Shalini, additional, Chen, Chen Chun, additional, Bai, Isaac, additional, Ranger-Moore, Jim, additional, Inge, Landon J., additional, Kurkure, Uday, additional, Bhattacharya, Ipshita, additional, Zhao, Margaret, additional, Zuiderveld, Karel, additional, Chintakindi, Chandana, additional, Lopez, Bryan, additional, and Guetter, Christoph, additional

Published
2022
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23. Immune microenvironment in patients with mismatch‐repair‐proficient oligometastatic colorectal cancer exposed to chemotherapy: the randomized MIROX GERCOR cohort study

Author

Jary, Marine, primary, Liu, Wen‐Wei, additional, Yan, Dongyao, additional, Bai, Isaac, additional, Muranyi, Andrea, additional, Colle, Elise, additional, Brocheriou, Isabelle, additional, Turpin, Anthony, additional, Radosevic‐Robin, Nina, additional, Bourgoin, Pierre, additional, Penault‐Llorca, Frédérique, additional, Cohen, Romain, additional, Vernerey, Dewi, additional, André, Thierry, additional, Borg, Christophe, additional, Shanmugam, Kandavel, additional, and Svrcek, Magali, additional

Published
2022
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24. Artificial Intelligence–Assisted Amphiregulin and Epiregulin IHC Predicts Panitumumab Benefit in RAS Wild-Type Metastatic Colorectal Cancer

Author

Williams, Christopher J.M., primary, Seligmann, Jenny F., additional, Elliott, Faye, additional, Shires, Michael, additional, Richman, Susan D., additional, Brown, Sarah, additional, Zhang, Liping, additional, Singh, Shalini, additional, Pugh, Judith, additional, Xu, Xiao-Meng, additional, Muranyi, Andrea, additional, Guetter, Christoph, additional, Lorsakul, Auranuch, additional, Kurkure, Uday, additional, Zhao, Zuo, additional, Martin, Jim, additional, Wang, Xingwei, additional, Nguyen, Kien, additional, Liu, Wen-Wei, additional, Yan, Dongyao, additional, West, Nicholas P., additional, Barrett, Jennifer H., additional, Barnes, Michael, additional, Bai, Isaac, additional, Seymour, Matthew T., additional, Quirke, Philip, additional, and Shanmugam, Kandavel, additional

Published
2021
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26. Artificial intelligence-assisted immunohistochemical (IHC) evaluation of tumor amphiregulin (AREG) and epiregulin (EREG) expression as a combined predictive biomarker for panitumumab (Pan) therapy benefit in RAS wild-type (wt) metastatic colorectal cancer (mCRC): Analysis within the phase III PICCOLO trial.

Author

Williams, Christopher, primary, Seligmann, Jenny F., additional, Guetter, Christoph, additional, Zhang, Liping, additional, Yan, Dongyao, additional, Muranyi, Andrea, additional, Bai, Isaac, additional, Singh, Shalini, additional, Elliott, Faye, additional, Shires, Mike, additional, Richman, Susan, additional, West, Nicholas, additional, Barrett, Jenny, additional, Seymour, Matthew T., additional, Quirke, Philip, additional, and Shanmugam, Kandavel, additional

Published
2021
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27. P2.01-043 Pathologist Agreement Rates of PD-L1 Tumor and Immune Cell Quantitation Using Digital Read, Field-Of-View, and Whole Tumor Image Analysis

Author

Barnes, Michael, primary, Bai, Isaac, additional, Nguyen, Kien, additional, Bredno, Joerg, additional, Vennapusa, Bharathi, additional, Fonstad, Rachel, additional, Agarwal, Suresh, additional, Patil, Suhas, additional, Little, Elizabeth, additional, Koeppen, Hartmut, additional, and Guetter, Christoph, additional

Published
2017
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28. FAST FASHION: the global implications of our clothes.

Author

BAI, ISAAC

Subjects
FAST fashion, CLOTHING & dress, SOCIAL media, POOR people, SYNTHETIC fibers industry
Abstract

The article discusses the global implications of fast fashion, including environmental degradation, labor exploitation, and social implications, and suggests actions that individuals can take to reduce the fashion industry's impact.

Published
2023

29. A gene-protein assay for human epidermal growth factor receptor 2 (HER2): brightfield tricolor visualization of HER2 protein, the HER2 gene, and chromosome 17 centromere (CEN17) in formalin-fixed, paraffin-embedded breast cancer tissue sections.

Author

Hiroaki Nitta, Kelly, Brian D., Padilla, Mary, Wick, Nikolaus, Brunhoeber, Patrick, Bai, Isaac, Singh, Shalini, Ranger-Moore, Jim, Bieniarz, Chris, Hitoshi Tsuda, and Grogan, Thomas M.

Subjects
HER2 protein, CANCER patients, VISUAL perception, CYTOKINES, CELL nuclei
Abstract

Background: The eligibility of breast cancer patients for human epidermal growth factor receptor 2 (HER2)-directed therapies is determined by the HER2 gene amplification and/or HER2 protein overexpression status of the breast tumor as determined by in situ hybridization (ISH) or immunohistochemistry (IHC), respectively. Our objective was to combine the US Food and Drug Administration (FDA)-approved HER2 & chromosome 17 centromere (CEN17) brightfield ISH (BISH) and HER2 IHC assays into a single automated HER2 gene-protein assay allowing simultaneous detection of all three targets in a single tissue section. Methods: The HER2 gene-protein assay was optimized using formalin-fixed, paraffin-embedded (FFPE) samples of the xenograft tumors MCF7 [HER2 negative (non-amplified gene, protein negative)] and Calu-3 [HER2 positive (amplified gene, protein positive)]. HER2 IHC was performed using a rabbit monoclonal anti-HER2 antibody (clone 4B5) and a conventional 3,3'-diaminobenzidine IHC detection. The HER2 & CEN17 BISH signals were visualized using horseradish peroxidase-based silver and alkaline phosphatase-based red detection systems, respectively with a cocktail of 2,4-dinitrophenyl-labeled HER2 and digoxigenin-labeled CEN17 probes. The performance of the gene-protein assay on tissue microarray slides containing 189 randomly selected FFPE clinical breast cancer tissue cores was compared to that of the separate HER2 IHC and HER2 & CEN17 BISH assays. Results: HER2 protein detection was optimal when the HER2 IHC protocol was used before (rather than after) the BISH protocol. The sequential use of HER2 IHC and HER2 & CEN17 BISH detection steps on FFPE xenograft tumor sections appropriately co-localized the HER2 protein, HER2 gene, and CEN17 signals after mitigating the silver background staining by using a naphthol phosphate-containing hybridization buffer for the hybridization step. The HER2 protein and HER2 gene status obtained using the multiplex HER2 gene-protein assay demonstrated high concordance with those obtained using the separate HER2 IHC and HER2 & CEN17 BISH assays, respectively. Conclusions: We have developed a protocol that allows simultaneous visualization of the HER2 IHC and HER2 & CEN17 BISH targets. This automated protocol facilitated the determination of HER2 protein and HER2 gene status in randomly selected breast cancer samples, particularly in cases that were equivocal or exhibited tumor heterogeneity. The HER2 gene-protein assay produced results virtually equivalent to those of the single FDA-approved HER2 IHC and HER2 & CEN17 BISH assays. [ABSTRACT FROM AUTHOR]

Published
2012
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30. Use of a knowledge exchange event strategy to identify key priorities for implementing deprescribing in primary healthcare in Nova Scotia, Canada

Author

Isaac Bai, Olga Kits, Sarah Burgess, Anne Marie Whelan, Emily Reeve, Jennifer E. Isenor, Natalie Kennie-Kaulbach, Sarah Kehoe, Kennie-Kaulbach, Natalie, Kehoe, Sarah, Whelan, Anne Marie, Reeve, Emily, Bai, Isaac, Burgess, Sarah, Kits, Olga, and Isenor, Jennifer E

Subjects
Nova scotia, knowledge translation, History, Process management, deprescribing, Event (computing), Key (cryptography), Primary health care, knowledge exchange event, key priorities, Deprescribing, Social Sciences (miscellaneous)
Abstract

Background:Deprescribing, the process of dose reduction or stopping of medication(s) that may no longer be required, may improve medication use and patient outcomes. A collaborative interprofessional deprescribing research team was formed in 2017 in Nova Scotia (NS), Canada with the goal of investigating potential deprescribing initiatives which could be translated to primary healthcare in NS. The knowledge-to-action framework, which includes knowledge exchange, was used to guide the work of this team. Preliminary work involved knowledge inquiry and synthesis through a scoping review of deprescribing strategies in primary healthcare, a qualitative study to understand influences on deprescribing by local practitioners, and an analysis that combined the two. Aims and objectives:To describe and reflect on how an interactive knowledge exchange event strategy was used to (1) share the results, including knowledge tools, of previously conducted deprescribing research with stakeholders; (2) identify priorities for the development and implementation of collaborative deprescribing strategies in primary healthcare in NS. Key conclusions:The knowledge exchange event strategy utilised in this project achieved the planned objectives of sharing research results, raising awareness about deprescribing, and providing direction for future initiatives. The successful implementation of the knowledge exchange event hinged on many factors such as hiring a research coordinator; limiting the in-person event to one half-day; and using a variety of strategies for participant engagement both before and after the event. Other research teams could adopt a similar knowledge exchange event process as an approach for sharing research results and identifying future research and translation priorities.

Published
2022
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31. Using the behavior change wheel to link published deprescribing strategies to identified local primary healthcare needs

Author

Isaac Bai, Jennifer E. Isenor, Emily Reeve, Anne Marie Whelan, Ruth Martin-Misener, Sarah Burgess, Natalie Kennie-Kaulbach, Bai, Isaac, Isenor, Jennifer E., Reeve, Emily, Whelan, Anne Marie, Martin-Misener, Ruth, Burgess, Sarah, and Kennie-Kaulbach, Natalie

Subjects
primary health care, theoretical domains theory, Deprescriptions, deprescribing, Primary Health Care, behaviour change wheel, Pharmaceutical Science, Humans, Pharmacy, Focus Groups, Pharmacists, Qualitative Research
Abstract

Background: Polypharmacy is a major global problem. Evidence in primary care shows deprescribing can be beneficial. Behaviour change theories such as the Theoretical Domains Framework (TDF) and the Behaviour Change Wheel (BCW) can help develop successful implementation of deprescribing initiatives. Objectives: To link locally identified deprescribing influencers with components of successfully trialed deprescribing strategies, with the aim of informing the development of local deprescribing initiatives. Methods: Two background studies were completed. A qualitative study of interviews and focus groups identified influencers of deprescribing from local primary care physicians, nurse practitioners, and pharmacists. Transcripts were coded using the TDF and mapped to the Intervention Functions of the BCW. A scoping review identified studies that investigated primary care deprescribing strategies, which were mapped to the BCW Intervention Functions and the Behaviour Change Techniques (BCTs). For this analysis, six main TDF domains from the qualitative study were linked to the BCTs identified in the scoping review through the Intervention Functions of the BCW. Results: Within the BCW component Capability, one TDF domain identified in the qualitative study, Memory, Attention and Decision Process, was linked to strategies like academic detailing from the scoping review. For the Opportunity component, two TDF domains, Social Influences and Environmental Context and Resources, were linked to strategies such as pharmacist medication reviews, providing patient information leaflets, and evidence-based deprescribing tools. For the Motivation component, three TDF domains, Social/Professional Role and Identity, Intentions, and Beliefs about Consequences, were linked to strategies such as sending deprescribing information to prescribers, using tools to identify eligible patients, and having patients report adverse events of medications. Conclusions: This analysis identified deprescribing strategies that can be used to address influencers related to behaviour change from the perspective of primary care providers, and to assist with future deprescribing initiative development and implementation in the local context. Refereed/Peer-reviewed

Published
2021

32. Key priorities to implement deprescribing in primary health care in Nova Scotia: results from the deprescribing in primary health care in Nova Scotia knowledge exchange event (June 20, 2019)

Author

Isenor, Jennifer, Kennie-Kaulbach, Natalie, Kehoe, Sarah, Bai, Isaac, Reeve, Emily, Whelan, Anne Marie, Burgess, Sarah, Kits, Olga, Burge, Frederick, Martin-Misener, Ruth, Helwig, Melissa, and Sampalli, Tara

Subjects
deprescribing, drug reactions, polypharmacy, mortality, health care
Abstract

Inappropriate medication use and polypharmacy are associated with increased adverse drug reactions, hospitalizations and mortality. Deprescribing has been found to decrease the use of medications and medication costs and is expected to improve clinical outcomes. An interactive in-person knowledge exchange event using World Café and Nominal Group Technique was held with stakeholders including patient advisors, representatives from nursing, pharmacy, family medicine, and members of advocacy/regulatory bodies and government/policy representatives. Six themes were identified with accompanying key priorities that need to be addressed to implement deprescribing strategies in Nova Scotia. These included: Communication (including public awareness and communication between providers and patients, families and caregivers), Compensation (for all providers), Education (for the public and providers), Prompts (electronic and social), Resources (technology supports and resources) and Roles (providers, patients, families and caregivers). The key priorities will be shared with stakeholders to help inform future sustainable deprescribing strategies in Nova Scotia.

Published
2020

33. How to use the regulatory data from Health Canada for secondary analyses on new drugs, biologics and vaccines.

Author

Bai I, Doshi P, and Herder M

Subjects
Canada, Humans, Databases, Factual, Biological Products therapeutic use, Vaccines
Abstract

Incorporating clinical data held by national health product regulatory authorities into secondary analyses such as systematic reviews can help combat publication bias and selective outcome reporting, in turn, supporting more evidence-based decisions regarding the prescribing of drugs, biologics and vaccines. Owing to recent changes in Canadian law, Health Canada has begun to make clinical information-whether it has been previously published or not-publicly available through its 'Public Release of Clinical Information' (PRCI) online database. We provide guidance about how to access and use regulatory data obtained through the PRCI database for the purpose of conducting drug and biologic secondary analyses., Competing Interests: Competing interests: IB has no competing interest to disclose. PD reported running the RIAT Support Center, which was funded by Laura and John Arnold Foundation (2017–2022), and supported part of his university salary. He also reported receiving US FDA funds (via University of Maryland M-CERSI) for supporting graduate students (2020), being an unpaid IMEDS steering committee member (2016–2020), and is an editor at The BMJ (ongoing). In the past 36 months, MH reported being a member of the Patented Medicine Prices Review Board, Canada’s national drug price regulator, and receiving honoraria from the Board for his service, and received grants from CIHR (PJT 156256) as well as CIHR and the Public Health Agency of Canada., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Published
2024
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