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1. AHRR and SFRP2 in primary versus recurrent high-grade serous ovarian carcinoma and their prognostic implication

Author

Monjé, Nanna, Dragomir, Mihnea P., Sinn, Bruno V., Hoffmann, Inga, Makhmut, Anuar, Simon, Tincy, Kunze, Catarina A., Ihlow, Jana, Schmitt, Wolfgang D., Pohl, Jonathan, Piwonski, Iris, Marchenko, Sofya, Keunecke, Carlotta, Calina, Teodor G., Tiso, Francesca, Kulbe, Hagen, Kreuzinger, Caroline, Cacsire Castillo-Tong, Dan, Sehouli, Jalid, Braicu, Elena I., Denkert, Carsten, Darb-Esfahani, Silvia, Kübler, Kirsten, Capper, David, Coscia, Fabian, Morkel, Markus, Horst, David, Sers, Christine, and Taube, Eliane T.

Published
2024
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2. Predictive Markers of Response to Neoadjuvant Durvalumab with Nab-Paclitaxel and Dose-Dense Doxorubicin/Cyclophosphamide in Basal-Like Triple-Negative Breast Cancer.

Author

Blenman, Kim RM, Marczyk, Michal, Karn, Thomas, Qing, Tao, Li, Xiaotong, Gunasekharan, Vignesh, Yaghoobi, Vesal, Bai, Yalai, Ibrahim, Eiman Y, Park, Tristen, Silber, Andrea, Wolf, Denise M, Reisenbichler, Emily, Denkert, Carsten, Sinn, Bruno V, Rozenblit, Mariya, Foldi, Julia, Rimm, David L, Loibl, Sibylle, and Pusztai, Lajos

Subjects
Genetics, Clinical Research, Cancer, Breast Cancer, 2.1 Biological and endogenous factors, Aetiology, Albumins, Antibodies, Monoclonal, Antineoplastic Combined Chemotherapy Protocols, Biomarkers, Tumor, Breast Neoplasms, Cyclophosphamide, Doxorubicin, Female, Humans, Neoadjuvant Therapy, Paclitaxel, Transforming Growth Factor beta, Triple Negative Breast Neoplasms, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

PurposeWe examined gene expression, germline variant, and somatic mutation features associated with pathologic response to neoadjuvant durvalumab plus chemotherapy in basal-like triple-negative breast cancer (bTNBC).Experimental designGermline and somatic whole-exome DNA and RNA sequencing, programmed death ligand 1 (PD-L1) IHC, and stromal tumor-infiltrating lymphocyte scoring were performed on 57 patients. We validated our results using 162 patients from the GeparNuevo randomized trial.ResultsGene set enrichment analysis showed that pathways involved in immunity (adaptive, humoral, innate), JAK-STAT signaling, cancer drivers, cell cycle, apoptosis, and DNA repair were enriched in cases with pathologic complete response (pCR), whereas epithelial-mesenchymal transition, extracellular matrix, and TGFβ pathways were enriched in cases with residual disease (RD). Immune-rich bTNBC with RD was enriched in CCL-3, -4, -5, -8, -23, CXCL-1, -3, -6, -10, and IL1, -23, -27, -34, and had higher expression of macrophage markers compared with immune-rich cancers with pCR that were enriched in IFNγ, IL2, -12, -21, chemokines CXCL-9, -13, CXCR5, and activated T- and B-cell markers (GZMB, CD79A). In the validation cohort, an immune-rich five-gene signature showed higher expression in pCR cases in the durvalumab arm (P = 0.040) but not in the placebo arm (P = 0.923) or in immune-poor cancers. Independent of immune markers, tumor mutation burden was higher, and PI3K, DNA damage repair, MAPK, and WNT/β-catenin signaling pathways were enriched in germline and somatic mutations in cases with pCR.ConclusionsThe TGFβ pathway is associated with immune-poor phenotype and RD in bTNBC. Among immune-rich bTNBC RD, macrophage/neutrophil chemoattractants dominate the cytokine milieu, and IFNγ and activated B cells and T cells dominate immune-rich cancers with pCR.

Published
2022

3. LRP1B—a prognostic marker in tubo-ovarian high-grade serous carcinoma

Author

Kolb, Svenja, Hoffmann, Inga, Monjé, Nanna, Dragomir, Mihnea P., Jank, Paul, Bischoff, Philip, Keunecke, Carlotta, Pohl, Jonathan, Kunze, Catarina Alisa, Marchenko, Sofya, Schmitt, Wolfgang D., Kulbe, Hagen, Sers, Christine, Sehouli, Jalid, Braicu, Elena Ioana, Denkert, Carsten, Darb-Esfahani, Silvia, Horst, David, Sinn, Bruno V., and Taube, Eliane T.

Published
2023
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4. Increased expression of IDO1 is associated with improved survival and increased number of TILs in patients with high-grade serous ovarian cancer

Author

Hoffmann, Inga, Dragomir, Mihnea P., Monjé, Nanna, Keunecke, Carlotta, Kunze, Catarina Alisa, Schallenberg, Simon, Marchenko, Sofya, Schmitt, Wolfgang D., Kulbe, Hagen, Sehouli, Jalid, Braicu, Ioana Elena, Jank, Paul, Denkert, Carsten, Darb-Esfahani, Silvia, Horst, David, Sinn, Bruno V., Sers, Christine, Bischoff, Philip, and Taube, Eliane T.

Published
2023
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5. Clinical and molecular characteristics of HER2-low-positive breast cancer: pooled analysis of individual patient data from four prospective, neoadjuvant clinical trials

Author

Denkert, Carsten, Seither, Fenja, Schneeweiss, Andreas, Link, Theresa, Blohmer, Jens-Uwe, Just, Marianne, Wimberger, Pauline, Forberger, Almuth, Tesch, Hans, Jackisch, Christian, Schmatloch, Sabine, Reinisch, Mattea, Solomayer, Erich F, Schmitt, Wolfgang D, Hanusch, Claus, Fasching, Peter A, Lübbe, Kristina, Solbach, Christine, Huober, Jens, Rhiem, Kerstin, Marmé, Frederik, Reimer, Toralf, Schmidt, Marcus, Sinn, Bruno V, Janni, Wolfgang, Stickeler, Elmar, Michel, Laura, Stötzer, Oliver, Hahnen, Eric, Furlanetto, Jenny, Seiler, Sabine, Nekljudova, Valentina, Untch, Michael, and Loibl, Sibylle

Published
2021
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6. Supplementary Table 1 from RANK Expression as an Independent Predictor for Response to Neoadjuvant Chemotherapy in Luminal-Like Breast Cancer: A Translational Insight from the GeparX Trial

Author

Link, Theresa, primary, Blohmer, Jens-Uwe, primary, Schmitt, Wolfgang D., primary, Kuhlmann, Jan Dominik, primary, Just, Marianne, primary, Untch, Michael, primary, Stotzer, Oliver, primary, Fasching, Peter A., primary, Thill, Marc, primary, Reinisch, Mattea, primary, Schneeweiss, Andreas, primary, Wimberger, Pauline, primary, Seiler, Sabine, primary, Huober, Jens, primary, Jackisch, Christian, primary, Rhiem, Kerstin, primary, Hanusch, Claus, primary, Sinn, Bruno V., primary, Nekljudova, Valentina, primary, Loibl, Sibylle, primary, and Denkert, Carsten, primary

Published
2023
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7. Data from RANK Expression as an Independent Predictor for Response to Neoadjuvant Chemotherapy in Luminal-Like Breast Cancer: A Translational Insight from the GeparX Trial

Author

Link, Theresa, primary, Blohmer, Jens-Uwe, primary, Schmitt, Wolfgang D., primary, Kuhlmann, Jan Dominik, primary, Just, Marianne, primary, Untch, Michael, primary, Stotzer, Oliver, primary, Fasching, Peter A., primary, Thill, Marc, primary, Reinisch, Mattea, primary, Schneeweiss, Andreas, primary, Wimberger, Pauline, primary, Seiler, Sabine, primary, Huober, Jens, primary, Jackisch, Christian, primary, Rhiem, Kerstin, primary, Hanusch, Claus, primary, Sinn, Bruno V., primary, Nekljudova, Valentina, primary, Loibl, Sibylle, primary, and Denkert, Carsten, primary

Published
2023
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9. DNA methylation profiling identifies two distinct subgroups in breast cancers with low hormone receptor expression, mainly associated with HER2 amplification status

Author

Jurmeister, Philipp, Weber, Karsten, Villegas, Sonia, Karn, Thomas, Untch, Michael, Thieme, Anne, Müller, Volkmar, Taube, Eliane, Fasching, Peter, Schmitt, Wolfgang D., Marmé, Frederik, Stickeler, Elmar, Sinn, Bruno V., Jank, Paul, Schem, Christian, Klauschen, Frederick, van Mackelenbergh, Marion, Denkert, Carsten, Loibl, Sibylle, and Capper, David

Published
2021
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10. RANK expression as an independent predictor for response to neoadjuvant chemotherapy in luminal-like breast cancer - a translational insight from the GeparX trial

Author

Link, Theresa, primary, Blohmer, Jens-Uwe, additional, Schmitt, Wolfgang D., additional, Kuhlmann, Jan Dominik., additional, Just, Marianne, additional, Untch, Michael, additional, Stotzer, Oliver, additional, Fasching, Peter A., additional, Thill, Marc, additional, Reinisch, Mattea, additional, Schneeweiss, Andreas, additional, Wimberger, Pauline, additional, Seiler, Sabine, additional, Huober, Jens, additional, Jackisch, Christian, additional, Rhiem, Kerstin, additional, Hanusch, Claus, additional, Sinn, Bruno V., additional, Nekljudova, Valentina, additional, Loibl, Sibylle, additional, and Denkert, Carsten, additional

Published
2023
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11. Clinical relevance and concordance of HER2 status in local and central testing—an analysis of 1581 HER2-positive breast carcinomas over 12 years

Author

Pfitzner, Berit M, Lederer, Bianca, Lindner, Judith, Solbach, Christine, Engels, Knut, Rezai, Mahdi, Dohnal, Karel, Tesch, Hans, Hansmann, Martin L, Salat, Christoph, Beer, Michaela, Schneeweiss, Andreas, Sinn, Peter, Bankfalvi, Agnes, Darb-Esfahani, Silvia, von Minckwitz, Gunter, Sinn, Bruno V, Kronenwett, Ralf, Weber, Karsten, Denkert, Carsten, and Loibl, Sibylle

Published
2018
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14. Standardized evaluation of tumor-infiltrating lymphocytes in breast cancer: results of the ring studies of the international immuno-oncology biomarker working group

Author

Denkert, Carsten, Wienert, Stephan, Poterie, Audrey, Loibl, Sibylle, Budczies, Jan, Badve, Sunil, Bago-Horvath, Zsuzsanna, Bane, Anita, Bedri, Shahinaz, Brock, Jane, Chmielik, Ewa, Christgen, Matthias, Colpaert, Cecile, Demaria, Sandra, Van den Eynden, Gert, Floris, Giuseppe, Fox, Stephen B, Gao, Dongxia, Ingold Heppner, Barbara, Kim, S Rim, Kos, Zuzana, Kreipe, Hans H, Lakhani, Sunil R, Penault-Llorca, Frederique, Pruneri, Giancarlo, Radosevic-Robin, Nina, Rimm, David L, Schnitt, Stuart J, Sinn, Bruno V, Sinn, Peter, Sirtaine, Nicolas, O'Toole, Sandra A, Viale, Giuseppe, Van de Vijver, Koen, de Wind, Roland, von Minckwitz, Gunter, Klauschen, Frederick, Untch, Michael, Fasching, Peter A, Reimer, Toralf, Willard-Gallo, Karen, Michiels, Stefan, Loi, Sherene, and Salgado, Roberto

Published
2016
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16. Figure S4 from A Small Hypoxia Signature Predicted pCR Response to Bevacizumab in the Neoadjuvant GeparQuinto Breast Cancer Trial

Author

Karn, Thomas, primary, Meissner, Tobias, primary, Weber, Karsten E., primary, Solbach, Christine, primary, Denkert, Carsten, primary, Engels, Knut, primary, Fasching, Peter A., primary, Sinn, Bruno V., primary, Schrader, Iris, primary, Budczies, Jan, primary, Marmé, Frederik, primary, Müller, Volkmar, primary, Holtrich, Uwe, primary, Gerber, Bernd, primary, Schem, Christian, primary, Young, Brandon M., primary, Hanusch, Claus, primary, Stickeler, Elmar, primary, Huober, Jens, primary, van Mackelenbergh, Marion, primary, Leyland-Jones, Brian, primary, Fehm, Tanja, primary, Nekljudova, Valentina, primary, Untch, Michael, primary, and Loibl, Sibylle, primary

Published
2023
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17. Figure S1 from Immune-related Gene Expression Predicts Response to Neoadjuvant Chemotherapy but not Additional Benefit from PD-L1 Inhibition in Women with Early Triple-negative Breast Cancer

Author

Sinn, Bruno V., primary, Loibl, Sibylle, primary, Hanusch, Claus A., primary, Zahm, Dirk-Michael, primary, Sinn, Hans-Peter, primary, Untch, Michael, primary, Weber, Karsten, primary, Karn, Thomas, primary, Becker, Clemens, primary, Marmé, Frederik, primary, Schmitt, Wolfgang D., primary, Müller, Volkmar, primary, Schem, Christian, primary, Treue, Denise, primary, Stickeler, Elmar, primary, Klauschen, Frederik, primary, Burchardi, Nicole, primary, Furlanetto, Jenny, primary, van Mackelenbergh, Marion, primary, Fasching, Peter A., primary, Schneeweiss, Andreas, primary, and Denkert, Carsten, primary

Published
2023
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18. Supplementary Figure Legend from Ki67 Measured after Neoadjuvant Chemotherapy for Primary Breast Cancer

Author

von Minckwitz, Gunter, primary, Schmitt, Wolfgang D., primary, Loibl, Sibylle, primary, Müller, Berit M., primary, Blohmer, Jens U., primary, Sinn, Bruno V., primary, Eidtmann, Holger, primary, Eiermann, Wolfgang, primary, Gerber, Bernd, primary, Tesch, Hans, primary, Hilfrich, Jörn, primary, Huober, Jens, primary, Fehm, Tanja, primary, Barinoff, Jana, primary, Rüdiger, Thomas, primary, Erbstoesser, Erhard, primary, Fasching, Peter A., primary, Karn, Thomas, primary, Müller, Volkmar, primary, Jackisch, Christian, primary, and Denkert, Carsten, primary

Published
2023
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19. Table S1 from Immune-related Gene Expression Predicts Response to Neoadjuvant Chemotherapy but not Additional Benefit from PD-L1 Inhibition in Women with Early Triple-negative Breast Cancer

Author

Sinn, Bruno V., primary, Loibl, Sibylle, primary, Hanusch, Claus A., primary, Zahm, Dirk-Michael, primary, Sinn, Hans-Peter, primary, Untch, Michael, primary, Weber, Karsten, primary, Karn, Thomas, primary, Becker, Clemens, primary, Marmé, Frederik, primary, Schmitt, Wolfgang D., primary, Müller, Volkmar, primary, Schem, Christian, primary, Treue, Denise, primary, Stickeler, Elmar, primary, Klauschen, Frederik, primary, Burchardi, Nicole, primary, Furlanetto, Jenny, primary, van Mackelenbergh, Marion, primary, Fasching, Peter A., primary, Schneeweiss, Andreas, primary, and Denkert, Carsten, primary

Published
2023
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20. Supplementary Tables S1-S8 from A Small Hypoxia Signature Predicted pCR Response to Bevacizumab in the Neoadjuvant GeparQuinto Breast Cancer Trial

Author

Karn, Thomas, primary, Meissner, Tobias, primary, Weber, Karsten E., primary, Solbach, Christine, primary, Denkert, Carsten, primary, Engels, Knut, primary, Fasching, Peter A., primary, Sinn, Bruno V., primary, Schrader, Iris, primary, Budczies, Jan, primary, Marmé, Frederik, primary, Müller, Volkmar, primary, Holtrich, Uwe, primary, Gerber, Bernd, primary, Schem, Christian, primary, Young, Brandon M., primary, Hanusch, Claus, primary, Stickeler, Elmar, primary, Huober, Jens, primary, van Mackelenbergh, Marion, primary, Leyland-Jones, Brian, primary, Fehm, Tanja, primary, Nekljudova, Valentina, primary, Untch, Michael, primary, and Loibl, Sibylle, primary

Published
2023
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21. Supplementary Figure from Ki67 Measured after Neoadjuvant Chemotherapy for Primary Breast Cancer

Author

von Minckwitz, Gunter, primary, Schmitt, Wolfgang D., primary, Loibl, Sibylle, primary, Müller, Berit M., primary, Blohmer, Jens U., primary, Sinn, Bruno V., primary, Eidtmann, Holger, primary, Eiermann, Wolfgang, primary, Gerber, Bernd, primary, Tesch, Hans, primary, Hilfrich, Jörn, primary, Huober, Jens, primary, Fehm, Tanja, primary, Barinoff, Jana, primary, Rüdiger, Thomas, primary, Erbstoesser, Erhard, primary, Fasching, Peter A., primary, Karn, Thomas, primary, Müller, Volkmar, primary, Jackisch, Christian, primary, and Denkert, Carsten, primary

Published
2023
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22. Abstract PD17-06: Immunohistochemical markers and determinants of clinical response in the Penelope-B trial

Author

Knudsen, Erik S., primary, Rachakonda, Sivaramakrishna, additional, Marmé, Frederik, additional, Martín, Miguel, additional, Untch, Michael, additional, Bonnefoi, Hervé R., additional, Schmitt, Wolfgang D., additional, Kim, Sung-Bae, additional, Bear, Harry D., additional, Witkiewicz, Agnieszka, additional, Im, Seock-Ah, additional, DeMichele, Angela, additional, Van’t Veer, Laura, additional, McCarthy, Nicole, additional, Sinn, Bruno V., additional, Gelmon, Karen, additional, García-Sáenz, José Ángel, additional, Kelly, Catherine M., additional, Reimer, Toralf, additional, Turner, Nicholas, additional, Rojo, Federico, additional, Filipits, Martin, additional, Fasching, Peter A., additional, Schem, Christian, additional, Martin, Lesley-Ann, additional, Liu, Yuan, additional, Toi, Masakazu, additional, Rugo, Hope, additional, Gnant, Michael, additional, Makris, Andreas, additional, Furlanetto, Jenny, additional, Weber, Karsten, additional, Denkert, Carsten, additional, and Loibl, Sibylle, additional

Published
2023
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23. Abstract PD4-02: PD4-02 Spatial and temporal heterogeneity of predictive and prognostic signatures in triple-negative breast cancer treated with neoadjuvant combination immune-chemotherapy

Author

Denkert, Carsten, primary, Schneeweiss, Andreas, additional, Rey, Julia, additional, Hattesohl, Akira, additional, Karn, Thomas, additional, Braun, Michael, additional, Jank, Paul, additional, Huober, Jens, additional, Sinn, Hans-Peter, additional, Zahm, Dirk-Michael, additional, Hanusch, Claus, additional, Marmé, Frederik, additional, Furlanetto, Jenny, additional, Thomalla, Jörg, additional, Blohmer, Jens-Uwe, additional, van Mackelenbergh, Marion, additional, Stiewe, Thorsten, additional, Staib, Peter, additional, Jackisch, Christian, additional, Teply-Szymanski, Julia, additional, Fasching, Peter A., additional, Sinn, Bruno V., additional, Untch, Michael, additional, Weber, Karsten, additional, and Loibl, Sibylle, additional

Published
2023
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25. SETER/PR: a robust 18-gene predictor for sensitivity to endocrine therapy for metastatic breast cancer

Author

Sinn, Bruno V., Fu, Chunxiao, Lau, Rosanna, Litton, Jennifer, Tsai, Tsung-Heng, Murthy, Rashmi, Tam, Alda, Andreopoulou, Eleni, Gong, Yun, Murthy, Ravi, Gould, Rebekah, Zhang, Ya, King, Tari A., Viale, Agnes, Andrade, Victor, Giri, Dilip, Salgado, Roberto, Laios, Ioanna, Sotiriou, Christos, Marginean, Esmeralda C., Kwiatkowski, Danielle N., Layman, Rachel M., Booser, Daniel, Hatzis, Christos, Vicente Valero, V., and Fraser Symmans, W.

Published
2019
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26. Neoadjuvant carboplatin in patients with triple-negative and HER2-positive early breast cancer (GeparSixto; GBG 66): a randomised phase 2 trial

Author

von Minckwitz, Gunter, Schneeweiss, Andreas, Loibl, Sibylle, Salat, Christoph, Denkert, Carsten, Rezai, Mahdi, Blohmer, Jens U, Jackisch, Christian, Paepke, Stefan, Gerber, Bernd, Zahm, Dirk M, Kümmel, Sherko, Eidtmann, Holger, Klare, Peter, Huober, Jens, Costa, Serban, Tesch, Hans, Hanusch, Claus, Hilfrich, Jörn, Khandan, Fariba, Fasching, Peter A, Sinn, Bruno V, Engels, Knut, Mehta, Keyur, Nekljudova, Valentina, and Untch, Michael

Published
2014
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27. CYP3A5 mediates basal and acquired therapy resistance in different subtypes of pancreatic ductal adenocarcinoma

Author

Noll, Elisa M., Eisen, Christian, Stenzinger, Albrecht, Espinet, Elisa, Muckenhuber, Alexander, Klein, Corinna, Vogel, Vanessa, Klaus, Bernd, Nadler, Wiebke, Rosli, Christoph, Lutz, Christian, Kulke, Michael, Engelhardt, Jan, Zickgraf, Franziska M., Espinosa, Octavio, Schlesner, Matthias, Jiang, Xiaoqi, Kopp-Schneider, Annette, Neuhaus, Peter, Bahra, Marcus, Sinn, Bruno V., Eils, Roland, Giese, Nathalia A., Hackert, Thilo, Strobel, Oliver, Werner, Jens, Buchler, Markus W., Weichert, Wilko, Trumpp, Andreas, and Sprick, Martin R.

Subjects
Adenocarcinoma -- Genetic aspects -- Drug therapy -- Research, Drug resistance -- Risk factors -- Genetic aspects -- Research, Cytochrome P-450 -- Physiological aspects -- Genetic aspects -- Research, Pancreatic cancer -- Genetic aspects -- Drug therapy -- Research, Biological sciences, Health
Abstract

Although subtypes of pancreatic ductal adenocarcinoma (PDAC) have been described, this malignancy is clinically still treated as a single disease. Here we present patient-derived models representing the full spectrum of previously identified quasimesenchymal (QM-PDA), classical and exocrine-like PDAC subtypes, and identify two markers--HNF1A and KRT81--that enable stratification of tumors into different subtypes by using immunohistochemistry. Individuals with tumors of these subtypes showed substantial differences in overall survival, and their tumors differed in drug sensitivity, with the exocrine-like subtype being resistant to tyrosine kinase inhibitors and paclitaxel. Cytochrome P450 3A5 (CYP3A5) metabolizes these compounds in tumors of the exocrine-like subtype, and pharmacological or short hairpin RNA (shRNA)-mediated CYP3A5 inhibition sensitizes tumor cells to these drugs. Whereas hepatocyte nuclear factor 4, alpha (HNF4A) controls basal expression of CYP3A5, drug-induced CYP3A5 upregulation is mediated by the nuclear receptor NR1I2. CYP3A5 also contributes to acquired drug resistance in QM-PDA and classical PDAC, and it is highly expressed in several additional malignancies. These findings designate CYP3A5 as a predictor of therapy response and as a tumor cell-autonomous detoxification mechanism that must be overcome to prevent drug resistance., PDAC is a very aggressive disease with poor prognosis (1). In both Europe and the USA, pancreatic cancer is the fourth leading cause of cancer deaths (2,3). Treatment with gemcitabine [...]

Published
2016
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28. Correction to “Integration of Metabolomics and Expression of Glycerol-3-phosphate Acyltransferase (GPAM) in Breast Cancer─Link to Patient Survival, Hormone Receptor Status, and Metabolic Profiling”

Author

Brockmöller, Scarlet F., primary, Bucher, Elmar, additional, Müller, Berit M., additional, Budczies, Jan, additional, Hilvo, Mika, additional, Griffin, Julian L., additional, Orešič, Matej, additional, Kallioniemi, Olli, additional, Iljin, Kristiina, additional, Loibl, Sibylle, additional, Darb-Esfahani, Silvia, additional, Sinn, Bruno V., additional, Klauschen, Frederick, additional, Prinzler, Judith, additional, Bangemann, Nikola, additional, Ismaeel, Fakher, additional, Fiehn, Oliver, additional, Dietel, Manfred, additional, and Denkert, Carsten, additional

Published
2022
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29. Phase III randomised trial comparing intense dose-dense chemotherapy to tailored dose-dense chemotherapy in high-risk early breast cancer (GAIN-2)

Author

Möbus, Volker, primary, Lück, Hans-Joachim, additional, Ladda, Ekkehart, additional, Klare, Peter, additional, Schmidt, Marcus, additional, Schneeweiss, Andreas, additional, Grischke, Eva-Maria, additional, Wachsmann, Grischa, additional, Forstbauer, Helmut, additional, Untch, Michael, additional, Marmé, Frederik, additional, Blohmer, Jens-Uwe, additional, Jackisch, Christian, additional, Huober, Jens, additional, Stickeler, Elmar, additional, Reinisch, Mattea, additional, Link, Theresa, additional, Sinn, Bruno V., additional, Janni, Wolfgang, additional, Denkert, Carsten, additional, Furlanetto, Jenny, additional, Engels, Knut, additional, Solbach, Christine, additional, Schmatloch, Sabine, additional, Rey, Julia, additional, Burchardi, Nicole, additional, and Loibl, Sibylle, additional

Published
2021
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30. Additional file 1 of DNA methylation profiling identifies two distinct subgroups in breast cancers with low hormone receptor expression, mainly associated with HER2 amplification status

Author

Jurmeister, Philipp, Weber, Karsten, Villegas, Sonia, Karn, Thomas, Untch, Michael, Thieme, Anne, Müller, Volkmar, Taube, Eliane, Fasching, Peter, Schmitt, Wolfgang D., Marmé, Frederik, Stickeler, Elmar, Sinn, Bruno V., Jank, Paul, Schem, Christian, Klauschen, Frederick, van Mackelenbergh, Marion, Denkert, Carsten, Loibl, Sibylle, and Capper, David

Abstract

Additional file 1. Fig. S1: t-distributed stochastic neighbor embedding (t-SNE) plots showing the estimated tumor purity of The Cancer Genome Atlas samples based on manual estimation using light microscopy (a), RNAseq data (ESTIMATE; b), copy number variations (ABSOLUTE; c), DNA methylation (LUMP; d) and a combined score (CPE; e).

Published
2021
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31. Additional file 4 of Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Author

Chunxiao Fu, Marczyk, Michal, Samuels, Michael, Trevarton, Alexander J., Jiaxin Qu, Lau, Rosanna, Du, Lili, Pappas, Todd, Sinn, Bruno V., Gould, Rebekah E., Pusztai, Lajos, Hatzis, Christos, and Symmans, W. Fraser

Abstract

Additional File 4: Fig. S4. Concordance between wtRNAseq and targeted RNAseq of gene expression levels and transcriptional signature scores. Distribution of Pearson correlation (Rho), bias, scale and location coefficient (components of concordance correlation coefficient (CCC)) for all 28 targeted genes within each protocol. The green points represent the two transcriptional signatures.

Published
2021
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32. Additional file 2 of DNA methylation profiling identifies two distinct subgroups in breast cancers with low hormone receptor expression, mainly associated with HER2 amplification status

Author

Jurmeister, Philipp, Weber, Karsten, Villegas, Sonia, Karn, Thomas, Untch, Michael, Thieme, Anne, Müller, Volkmar, Taube, Eliane, Fasching, Peter, Schmitt, Wolfgang D., Marmé, Frederik, Stickeler, Elmar, Sinn, Bruno V., Jank, Paul, Schem, Christian, Klauschen, Frederick, van Mackelenbergh, Marion, Denkert, Carsten, Loibl, Sibylle, and Capper, David

Subjects
skin and connective tissue diseases
Abstract

Additional file 2. Fig. S2: Flowchart showing the composition of the study cohort with samples from the publicly available “The Cancer Genome Atlas” (TCGA) dataset as well as specimens from the clinical GeparSixto and GeparSepto trial. Abbreviations: BRCA = breast cancer; ER = estrogen receptor; PR = progesterone receptor; TNBC = triple negative breast cancer; t-SNE = t-distributed stochastic neighbor embedding.

Published
2021
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33. Additional file 1 of Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Author

Chunxiao Fu, Marczyk, Michal, Samuels, Michael, Trevarton, Alexander J., Jiaxin Qu, Lau, Rosanna, Du, Lili, Pappas, Todd, Sinn, Bruno V., Gould, Rebekah E., Pusztai, Lajos, Hatzis, Christos, and Symmans, W. Fraser

Abstract

Additional file 1: Fig. S1. Technical variance of expression measurements in targeted RNAseq data using FF samples. (A) Distribution of absolute difference in expression between replicates for 28 targeted genes within each protocol. (B) Distribution of absolute difference in molecular signature score between replicates for 2 signatures within each protocol.

Published
2021
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34. Additional file 3 of Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Author

Chunxiao Fu, Marczyk, Michal, Samuels, Michael, Trevarton, Alexander J., Jiaxin Qu, Lau, Rosanna, Du, Lili, Pappas, Todd, Sinn, Bruno V., Gould, Rebekah E., Pusztai, Lajos, Hatzis, Christos, and Symmans, W. Fraser

Abstract

Additional File 3: Fig. S3. Distribution of raw read depth across all gene targets in FFPE samples. Line type (solid or dashed) distinguishes two technical replicates, while color represents different protocol. Genes are sorted by average read depth in all samples.

Published
2021
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35. Additional file 2 of Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Author

Chunxiao Fu, Marczyk, Michal, Samuels, Michael, Trevarton, Alexander J., Jiaxin Qu, Lau, Rosanna, Du, Lili, Pappas, Todd, Sinn, Bruno V., Gould, Rebekah E., Pusztai, Lajos, Hatzis, Christos, and Symmans, W. Fraser

Abstract

Additional File 2: Fig. S2. Distribution of raw read depth across all gene targets in FF samples. Line type (solid or dashed) distinguishes two technical replicates (6 samples have only 1 replicate in FF), while color represents different protocol. Genes are sorted by average read depth in all samples.

Published
2021
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36. Therapy response and prognosis of patients with early breast cancer with low positivity for hormone receptors – An analysis of 2765 patients from neoadjuvant clinical trials

Author

Villegas, Sonia L., primary, Nekljudova, Valentina, additional, Pfarr, Nicole, additional, Engel, Jutta, additional, Untch, Michael, additional, Schrodi, Simone, additional, Holms, Frank, additional, Ulmer, Hans U., additional, Fasching, Peter A., additional, Weber, Karsten E., additional, Albig, Christian, additional, Heinrichs, Clemens, additional, Marmé, Frederik, additional, Hartmann, Arndt, additional, Hanusch, Claus, additional, Schmitt, Wolfgang D., additional, Huober, Jens, additional, Lederer, Bianca, additional, van Mackelenbergh, Marion, additional, Tesch, Hans, additional, Jackisch, Christian, additional, Rezai, Mahdi, additional, Sinn, Peter, additional, Sinn, Bruno V., additional, Hackmann, John, additional, Kiechle, Marion, additional, Schneeweiss, Andreas, additional, Weichert, Wilko, additional, Denkert, Carsten, additional, and Loibl, Sibylle, additional

Published
2021
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38. Immune-related Gene Expression Predicts Response to Neoadjuvant Chemotherapy but not Additional Benefit from PD-L1 Inhibition in Women with Early Triple-negative Breast Cancer

Author

Sinn, Bruno V., primary, Loibl, Sibylle, additional, Hanusch, Claus A., additional, Zahm, Dirk-Michael, additional, Sinn, Hans-Peter, additional, Untch, Michael, additional, Weber, Karsten, additional, Karn, Thomas, additional, Becker, Clemens, additional, Marmé, Frederik, additional, Schmitt, Wolfgang D., additional, Müller, Volkmar, additional, Schem, Christian, additional, Treue, Denise, additional, Stickeler, Elmar, additional, Klauschen, Frederik, additional, Burchardi, Nicole, additional, Furlanetto, Jenny, additional, van Mackelenbergh, Marion, additional, Fasching, Peter A., additional, Schneeweiss, Andreas, additional, and Denkert, Carsten, additional

Published
2021
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42. TP53 Mutations Predict Sensitivity to Adjuvant Gemcitabine in Patients with Pancreatic Ductal Adenocarcinoma: Next-Generation Sequencing Results from the CONKO-001 Trial

Author

Sinn, Marianne, primary, Sinn, Bruno V., additional, Treue, Denise, additional, Keilholz, Ulrich, additional, Damm, Frederik, additional, Schmuck, Rosa, additional, Lohneis, Philipp, additional, Klauschen, Frederick, additional, Striefler, Jana K., additional, Bahra, Marcus, additional, Bläker, Hendrik, additional, Bischoff, Sven, additional, Pelzer, Uwe, additional, Oettle, Helmut, additional, Riess, Hanno, additional, Budczies, Jan, additional, and Denkert, Carsten, additional

Published
2020
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44. A Small Hypoxia Signature Predicted pCR Response to Bevacizumab in the Neoadjuvant GeparQuinto Breast Cancer Trial

Author

Karn, Thomas, primary, Meissner, Tobias, additional, Weber, Karsten E., additional, Solbach, Christine, additional, Denkert, Carsten, additional, Engels, Knut, additional, Fasching, Peter A., additional, Sinn, Bruno V., additional, Schrader, Iris, additional, Budczies, Jan, additional, Marmé, Frederik, additional, Müller, Volkmar, additional, Holtrich, Uwe, additional, Gerber, Bernd, additional, Schem, Christian, additional, Young, Brandon M., additional, Hanusch, Claus, additional, Stickeler, Elmar, additional, Huober, Jens, additional, van Mackelenbergh, Marion, additional, Leyland-Jones, Brian, additional, Fehm, Tanja, additional, Nekljudova, Valentina, additional, Untch, Michael, additional, and Loibl, Sibylle, additional

Published
2020
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46. Decentral gene expression analysis: analytical validation of the Endopredict genomic multianalyte breast cancer prognosis test

Author

Kronenwett Ralf, Bohmann Kerstin, Prinzler Judith, Sinn Bruno V, Haufe Franziska, Roth Claudia, Averdick Manuela, Ropers Tanja, Windbergs Claudia, Brase Jan C, Weber Karsten E, Fisch Karin, Müller Berit M, Schmidt Marcus, Filipits Martin, Dubsky Peter, Petry Christoph, Dietel Manfred, and Denkert Carsten

Subjects
Breast cancer, Prognostic multigene expression test, Analytical validation, PCR, Pathology, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background EndoPredict (EP) is a clinically validated multianalyte gene expression test to predict distant metastasis in ER-positive, HER2-negative breast cancer treated with endocrine therapy alone. The test is based on the combined analysis of 12 genes in formalin-fixed, paraffin-embedded (FFPE) tissue by reverse transcription-quantitative real-time PCR (RT-qPCR). Recently, it was shown that EP is feasible for reliable decentralized assessment of gene expression. The aim of this study was the analytical validation of the performance characteristics of the assay and its verification in a molecular-pathological routine laboratory. Methods Gene expression values to calculate the EP score were assayed by one-step RT-qPCR using RNA from FFPE tumor tissue. Limit of blank, limit of detection, linear range, and PCR efficiency were assessed for each of the 12 PCR assays using serial samples dilutions. Different breast cancer samples were used to evaluate RNA input range, precision and inter-laboratory variability. Results PCR assays were linear up to Cq values between 35.1 and 37.2. Amplification efficiencies ranged from 75% to 101%. The RNA input range without considerable change of the EP score was between 0.16 and 18.5 ng/μl. Analysis of precision (variation of day, day time, instrument, operator, reagent lots) resulted in a total noise (standard deviation) of 0.16 EP score units on a scale from 0 to 15. The major part of the total noise (SD 0.14) was caused by the replicate-to-replicate noise of the PCR assays (repeatability) and was not associated with different operating conditions (reproducibility). Performance characteristics established in the manufacturer’s laboratory were verified in a routine molecular pathology laboratory. Comparison of 10 tumor samples analyzed in two different laboratories showed a Pearson coefficient of 0.995 and a mean deviation of 0.15 score units. Conclusions The EP test showed reproducible performance characteristics with good precision and negligible laboratory-to-laboratory variation. This study provides further evidence that the EP test is suitable for decentralized testing in specialized molecular pathological laboratories instead of a reference laboratory. This is a unique feature and a technical advance in comparison with existing RNA-based prognostic multigene expression tests.

Published
2012
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47. Abstract B77: CYP3A5 mediates basal and acquired therapy resistance in different subtypes of pancreatic ductal adenocarcinoma

Author

Noll, Elisa M., primary, Eisen, Christian, additional, Stenzinger, Albrecht, additional, Espinet, Elisa, additional, Muckenhuber, Alexander, additional, Klein, Corinna, additional, Vogel, Vanessa, additional, Klaus, Bernd, additional, Nadler, Wiebke, additional, Rösli, Christoph, additional, Lutz, Christian, additional, Kulke, Michael, additional, Engelhardt, Jan, additional, Zickgraf, Franziska, additional, Espinosa, Octavio, additional, Schlesner, Matthias, additional, Jiang, Xiaoqi, additional, Kopp-Schneider, Annette, additional, Neuhaus, Peter, additional, Bahra, Marcus, additional, Sinn, Bruno V., additional, Eils, Roland, additional, Giese, Nathalia A., additional, Hackert, Thilo, additional, Strobel, Oliver, additional, Werner, Jens, additional, Büchler, Markus W., additional, Weichert, Wilko, additional, Trumpp, Andreas, additional, and Sprick, Martin R., additional

Published
2016
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48. P53 overexpression and Ki67-index are associated with outcome in ductal pancreatic adenocarcinoma with adjuvant gemcitabine treatment

Author

Striefler, Jana K., primary, Sinn, Marianne, additional, Pelzer, Uwe, additional, Jühling, Anja, additional, Wislocka, Lilianna, additional, Bahra, Marcus, additional, Sinn, Bruno V., additional, Denkert, Carsten, additional, Dörken, Bernd, additional, Oettle, Helmut, additional, Riess, Hanno, additional, Bläker, Hendrik, additional, and Lohneis, Philipp, additional

Published
2016
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49. Abstract A69: A novel mechanism mediates drug resistance in the exocrine-like pancreatic ductal adenocarcinoma (PDAC) subtype

Author

Noll, Elisa M., primary, Eisen, Christian, additional, Espinet, Elisa, additional, Vogel, Vanessa, additional, Klein, Corinna, additional, Stenzinger, Albrecht, additional, Zickgraf, Franziska, additional, Neuhaus, Peter, additional, Bahra, Marcus, additional, Sinn, Bruno V., additional, Lutz, Christian, additional, Kulke, Michael, additional, Pahl, Andreas, additional, Giese, Nathalia A., additional, Strobel, Oliver, additional, Werner, Jens, additional, Weichert, Wilko, additional, Trumpp, Andreas, additional, and Sprick, Martin R., additional

Published
2015
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50. Tumor-Infiltrating Lymphocytes and Response to Neoadjuvant Chemotherapy With or Without Carboplatin in Human Epidermal Growth Factor Receptor 2–Positive and Triple-Negative Primary Breast Cancers

Author

Denkert, Carsten, primary, von Minckwitz, Gunter, additional, Brase, Jan C., additional, Sinn, Bruno V., additional, Gade, Stephan, additional, Kronenwett, Ralf, additional, Pfitzner, Berit M., additional, Salat, Christoph, additional, Loi, Sherene, additional, Schmitt, Wolfgang D., additional, Schem, Christian, additional, Fisch, Karin, additional, Darb-Esfahani, Silvia, additional, Mehta, Keyur, additional, Sotiriou, Christos, additional, Wienert, Stephan, additional, Klare, Peter, additional, André, Fabrice, additional, Klauschen, Frederick, additional, Blohmer, Jens-Uwe, additional, Krappmann, Kristin, additional, Schmidt, Marcus, additional, Tesch, Hans, additional, Kümmel, Sherko, additional, Sinn, Peter, additional, Jackisch, Christian, additional, Dietel, Manfred, additional, Reimer, Toralf, additional, Untch, Michael, additional, and Loibl, Sibylle, additional

Published
2015
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