Search

Your search keyword '"Casanova, Ruben"' showing total 110 results
Start Over Author "Casanova, Ruben"
110 results on '"Casanova, Ruben"'

1. Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia

Author

Wegmann, Rebekka, Bonilla, Ximena, Casanova, Ruben, Chevrier, Stéphane, Coelho, Ricardo, Esposito, Cinzia, Ficek-Pascual, Joanna, Goetze, Sandra, Gut, Gabriele, Jacob, Francis, Jacobs, Andrea, Kuipers, Jack, Lischetti, Ulrike, Mena, Julien, Milani, Emanuela S., Prummer, Michael, Del Castillo, Jacobo Sarabia, Singer, Franziska, Sivapatham, Sujana, Toussaint, Nora C., Vilinovszki, Oliver, Wildschut, Mattheus H. E., Thavayogarajah, Tharshika, Malani, Disha, Aebersold, Rudolf, Bacac, Marina, Beerenwinkel, Niko, Beisel, Christian, Bodenmiller, Bernd, Heinzelmann-Schwarz, Viola, Koelzer, Viktor H., Levesque, Mitchell P., Moch, Holger, Pelkmans, Lucas, Rätsch, Gunnar, Tolnay, Markus, Wicki, Andreas, Wollscheid, Bernd, Manz, Markus G., Snijder, Berend, and Theocharides, Alexandre P. A.

Published
2024
Full Text
View/download PDF

3. Establishing standardized immune phenotyping of metastatic melanoma by digital pathology

Author

Sobottka, Bettina, Nowak, Marta, Frei, Anja Laura, Haberecker, Martina, Merki, Samuel, Levesque, Mitchell P., Dummer, Reinhard, Moch, Holger, Koelzer, Viktor Hendrik, Aebersold, Rudolf, Ak, Melike, Al-Quaddoomi, Faisal S., Albinus, Jonas, Alborelli, Ilaria, Andani, Sonali, Attinger, Per-Olof, Bacac, Marina, Baumhoer, Daniel, Beck-Schimmer, Beatrice, Beerenwinkel, Niko, Beisel, Christian, Bernasconi, Lara, Bertolini, Anne, Bodenmiller, Bernd, Bonilla, Ximena, Casanova, Ruben, Chevrier, Stéphane, Chicherova, Natalia, D'Costa, Maya, Danenberg, Esther, Davidson, Natalie, Drăganmoch, Monica-Andreea, Engler, Stefanie, Erkens, Martin, Eschbach, Katja, Esposito, Cinzia, Fedier, André, Ferreira, Pedro, Ficek, Joanna, Frey, Bruno, Goetze, Sandra, Grob, Linda, Gut, Gabriele, Günther, Detlef, Haeuptle, Pirmin, Heinzelmann-Schwarz, Viola, Herter, Sylvia, Holtackers, Rene, Huesser, Tamara, Irmisch, Anja, Jacob, Francis, Jacobs, Andrea, Jaeger, Tim M., Jahn, Katharina, James, Alva R., Jermann, Philip M., Kahles, André, Kahraman, Abdullah, Kuebler, Werner, Kuipers, Jack, Kunze, Christian P., Kurzeder, Christian, Lehmann, Kjong-Van, Lugert, Sebastian, Maass, Gerd, Manz, Markus G., Markolin, Philipp, Mena, Julien, Menzel, Ulrike, Metzler, Julian M., Miglino, Nicola, Milani, Emanuela S., Muenst, Simone, Murri, Riccardo, Ng, Charlotte K.Y., Nicolet, Stefan, Pedrioli, Patrick G.A., Pelkmans, Lucas, Piscuoglio, Salvatore, Prummer, Michael, Ritter, Mathilde, Rommel, Christian, Rosano-González, María L., Rätsch, Gunnar, Santacroce, Natascha, del Castillo, Jacobo Sarabia, Schlenker, Ramona, Schwalie, Petra C., Schwan, Severin, Schär, Tobias, Senti, Gabriela, Singer, Franziska, Sivapatham, Sujana, Snijder, Berend, Sreedharan, Vipin T., Stark, Stefan, Stekhoven, Daniel J., Theocharides, Alexandre P.A., Thomas, Tinu M., Tolnay, Markus, Tosevski, Vinko, Toussaint, Nora C., Tuncel, Mustafa A., Tusup, Marina, Van Drogen, Audrey, Vetter, Marcus, Vlajnic, Tatjana, Weber, Sandra, Weber, Walter P., Wegmann, Rebekka, Weller, Michael, Wendt, Fabian, Wey, Norbert, Wicki, Andreas, Wildschut, Mattheus HE, Wollscheid, Bernd, Yu, Shuqing, Ziegler, Johanna, Zimmermann, Marc, Zoche, Martin, and Zuend, Gregor

Published
2021
Full Text
View/download PDF

4. Computer-Based Intensity Measurement Assists Pathologists in Scoring Phosphatase and Tensin Homolog Immunohistochemistry — Clinical Associations in NSCLC Patients of the European Thoracic Oncology Platform Lungscape Cohort

Author

Rulle, Undine, Tsourti, Zoi, Casanova, Ruben, Deml, Karl-Friedrich, Verbeken, Eric, Thunnissen, Erik, Warth, Arne, Cheney, Richard, Sejda, Aleksandra, Speel, Ernst Jan, Madsen, Line Bille, Nonaka, Daisuke, Navarro, Atilio, Sansano, Irene, Marchetti, Antonio, Finn, Stephen P., Monkhorst, Kim, Kerr, Keith M., Haberecker, Martina, Wu, Chengguang, Zygoura, Panagiota, Kammler, Roswitha, Geiger, Thomas, Gendreau, Steven, Schulze, Katja, Vrugt, Bart, Wild, Peter, Moch, Holger, Weder, Walter, Ciftlik, Ata Tuna, Dafni, Urania, Peters, Solange, Bubendorf, Lukas, Stahel, Rolf A., and Soltermann, Alex

Published
2018
Full Text
View/download PDF

6. Figure S2. Threshold analysis of tumor fragmentation in correlation with RFS and OS. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
Full Text
View/download PDF

7. Figure S3. Biological processes associated with TF morphotypes from TCGA mRNAseq and WS Mass Spectrometry data. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
Full Text
View/download PDF

8. Table S1. Complete list of proteins identifications. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
Full Text
View/download PDF

9. Table S3. Association of TF scores with relapse-free survival. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
Full Text
View/download PDF

10. Table S4. Association of human-based TF scores with OS and RFS. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
Full Text
View/download PDF

11. Supplementary Figure 2 from Germinal Centers Determine the Prognostic Relevance of Tertiary Lymphoid Structures and Are Impaired by Corticosteroids in Lung Squamous Cell Carcinoma

Author

Siliņa, Karīna, primary, Soltermann, Alex, primary, Attar, Farkhondeh Movahedian, primary, Casanova, Ruben, primary, Uckeley, Zina M., primary, Thut, Helen, primary, Wandres, Muriel, primary, Isajevs, Sergejs, primary, Cheng, Phil, primary, Curioni-Fontecedro, Alessandra, primary, Foukas, Periklis, primary, Levesque, Mitchell P., primary, Moch, Holger, primary, Linē, Aija, primary, and van den Broek, Maries, primary

Published
2023
Full Text
View/download PDF

12. Supplementary Figure S4 from Germinal Centers Determine the Prognostic Relevance of Tertiary Lymphoid Structures and Are Impaired by Corticosteroids in Lung Squamous Cell Carcinoma

Author

Siliņa, Karīna, primary, Soltermann, Alex, primary, Attar, Farkhondeh Movahedian, primary, Casanova, Ruben, primary, Uckeley, Zina M., primary, Thut, Helen, primary, Wandres, Muriel, primary, Isajevs, Sergejs, primary, Cheng, Phil, primary, Curioni-Fontecedro, Alessandra, primary, Foukas, Periklis, primary, Levesque, Mitchell P., primary, Moch, Holger, primary, Linē, Aija, primary, and van den Broek, Maries, primary

Published
2023
Full Text
View/download PDF

13. PRoteomics IDEntifications database from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
Full Text
View/download PDF

14. Data from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
Full Text
View/download PDF

15. Table S2. Association of tumor fragmentation with clinico-pathological parameters. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
Full Text
View/download PDF

16. Table S5. List of proteins associated with tumor fragmentation. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
Full Text
View/download PDF

17. Supplementary Figure 3 from Germinal Centers Determine the Prognostic Relevance of Tertiary Lymphoid Structures and Are Impaired by Corticosteroids in Lung Squamous Cell Carcinoma

Author

Siliņa, Karīna, primary, Soltermann, Alex, primary, Attar, Farkhondeh Movahedian, primary, Casanova, Ruben, primary, Uckeley, Zina M., primary, Thut, Helen, primary, Wandres, Muriel, primary, Isajevs, Sergejs, primary, Cheng, Phil, primary, Curioni-Fontecedro, Alessandra, primary, Foukas, Periklis, primary, Levesque, Mitchell P., primary, Moch, Holger, primary, Linē, Aija, primary, and van den Broek, Maries, primary

Published
2023
Full Text
View/download PDF

18. Data from Germinal Centers Determine the Prognostic Relevance of Tertiary Lymphoid Structures and Are Impaired by Corticosteroids in Lung Squamous Cell Carcinoma

Author

Siliņa, Karīna, primary, Soltermann, Alex, primary, Attar, Farkhondeh Movahedian, primary, Casanova, Ruben, primary, Uckeley, Zina M., primary, Thut, Helen, primary, Wandres, Muriel, primary, Isajevs, Sergejs, primary, Cheng, Phil, primary, Curioni-Fontecedro, Alessandra, primary, Foukas, Periklis, primary, Levesque, Mitchell P., primary, Moch, Holger, primary, Linē, Aija, primary, and van den Broek, Maries, primary

Published
2023
Full Text
View/download PDF

19. Supplementary Figure Legends from Germinal Centers Determine the Prognostic Relevance of Tertiary Lymphoid Structures and Are Impaired by Corticosteroids in Lung Squamous Cell Carcinoma

Author

Siliņa, Karīna, primary, Soltermann, Alex, primary, Attar, Farkhondeh Movahedian, primary, Casanova, Ruben, primary, Uckeley, Zina M., primary, Thut, Helen, primary, Wandres, Muriel, primary, Isajevs, Sergejs, primary, Cheng, Phil, primary, Curioni-Fontecedro, Alessandra, primary, Foukas, Periklis, primary, Levesque, Mitchell P., primary, Moch, Holger, primary, Linē, Aija, primary, and van den Broek, Maries, primary

Published
2023
Full Text
View/download PDF

20. Supplementary Tables from Germinal Centers Determine the Prognostic Relevance of Tertiary Lymphoid Structures and Are Impaired by Corticosteroids in Lung Squamous Cell Carcinoma

Author

Siliņa, Karīna, primary, Soltermann, Alex, primary, Attar, Farkhondeh Movahedian, primary, Casanova, Ruben, primary, Uckeley, Zina M., primary, Thut, Helen, primary, Wandres, Muriel, primary, Isajevs, Sergejs, primary, Cheng, Phil, primary, Curioni-Fontecedro, Alessandra, primary, Foukas, Periklis, primary, Levesque, Mitchell P., primary, Moch, Holger, primary, Linē, Aija, primary, and van den Broek, Maries, primary

Published
2023
Full Text
View/download PDF

21. Supplementary Methods from Germinal Centers Determine the Prognostic Relevance of Tertiary Lymphoid Structures and Are Impaired by Corticosteroids in Lung Squamous Cell Carcinoma

Author

Siliņa, Karīna, primary, Soltermann, Alex, primary, Attar, Farkhondeh Movahedian, primary, Casanova, Ruben, primary, Uckeley, Zina M., primary, Thut, Helen, primary, Wandres, Muriel, primary, Isajevs, Sergejs, primary, Cheng, Phil, primary, Curioni-Fontecedro, Alessandra, primary, Foukas, Periklis, primary, Levesque, Mitchell P., primary, Moch, Holger, primary, Linē, Aija, primary, and van den Broek, Maries, primary

Published
2023
Full Text
View/download PDF

22. Figure S1. Frequency distributions, intra-tumor heterogeneity and inter-observer variability for TF scores. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
Full Text
View/download PDF

26. Lung Adenocarcinoma Patients with Malignant Pleural Effusions in Hot Adaptive Immunity Status Have a Longer Overall Survival

Author

Wu, Cheng-Guang, Casanova, Ruben, Mairinger, Fabian, and Soltermann, Alex

Subjects
Cancer Research, History, Oncology, Polymers and Plastics, Medizin, Business and International Management, Industrial and Manufacturing Engineering
Abstract

Malignant pleural effusion (MPE) is a common complication of lung adenocarcinoma (LADC) which is associated with a dismal prognosis. We investigated the prognostic role of PD-L1 and other immunomodulators expression in the immune compartment of MPE immune composition. MPE cytologic cell blocks of 83 LADC patients were analysed for the mRNA expression of 770 cancer-immune genes by the NanoString nCounter platform. The expression of relevant immune cell lineage markers was validated by immunohistochemistry (IHC) using quantitative pathology. The mRNA immune profiling identified four MPE patient clusters (C). C1/2 (adaptive+, hot) showed better overall survival (OS) than C3/4 (adaptive-, cold). Additionally, cold immunity profiles (adaptive-), C4 (innate+) were associated with worse OS than C3 (innate-). High PD-L1 expression was linked to the regulation of T cell activation and interferon signalling pathways. Genes of pattern recognition receptor and type I interferon signalling pathways were specifically upregulated in the long-survival (≥90 days) patient group. Moreover, immunomodulators were co-activated and highly expressed in hot adaptive immunity patient clusters, whereas CD274 (PD-L1), TNFRSF9 (4-1BB), VEGFA (VEGF-A) and CD276 (B7-H3) were upregulated in the groups referred as cold. The patient cluster, age and PD-L1 expression were independent prognosticators for LADC MPE patients (p-value < 0.05). Our study sheds light on the variances of immune contexture regarding different PD-L1 expression and survival conditions. It revealed four distinct prognostic patient clusters with specific immune cell components and immunomodulator expression profiles, which, collectively, is supportive for future therapeutic and prognosis for cancer management.

Published
2022

27. Lung adenocarcinoma patients with malignant pleural effusions in hot adaptive immunity status have a longer overall survival.

Author

Cheng-Guang Wu, Casanova, Ruben, Mairinger, Fabian, and Soltermann, Alex

Subjects
PLEURAL effusions, OVERALL survival, TYPE I interferons, PATTERN perception receptors, LUNGS
Abstract

Malignant pleural effusion (MPE) is a common complication of lung adenocarcinoma (LADC) which is associated with a dismal prognosis. We investigated the prognostic role of PD-L1 and other immunomodulators expression in the immune compartment of MPE immune composition. MPE cytologic cell blocks of 83 LADC patients were analysed for the mRNA expression of 770 cancer-immune genes by the NanoString nCounter platform. The expression of relevant immune cell lineage markers was validated by immunohistochemistry (IHC) using quantitative pathology. The mRNA immune profiling identified four MPE patient clusters (C). C1/2 (adaptive+, hot) showed better overall survival (OS) than C3/4 (adaptive-, cold). Additionally, cold immunity profiles (adaptive-), C4 (innate+) were associated with worse OS than C3 (innate-). High PD-L1 expression was linked to the regulation of T cell activation and interferon signalling pathways. Genes of pattern recognition receptor and type I interferon signalling pathways were specifically upregulated in the long-survival (=90 days) patient group. Moreover, immunomodulators were co-activated and highly expressed in hot adaptive immunity patient clusters, whereas CD274 (PD-L1), TNFRSF9 (4-1BB), VEGFA (VEGF-A) and CD276 (B7-H3) were upregulated in the groups referred as cold. The patient cluster, age and PD-L1 expression were independent prognosticators for LADC MPE patients (p-value < 0.05). Our study sheds light on the variances of immune contexture regarding different PD-L1 expression and survival conditions. It revealed four distinct prognostic patient clusters with specific immune cell components and immunomodulator expression profiles, which, collectively, is supportive for future therapeutic and prognosis for cancer management. [ABSTRACT FROM AUTHOR]

Published
2022
Full Text
View/download PDF

28. SCIM: universal single-cell matching with unpaired feature sets

Author

Stark, Stefan G, Ficek, Joanna, Locatello, Francesco, Bonilla, Ximena, Chevrier, Stéphane, Singer, Franziska, Aebersold, Rudolf, Al-Quaddoomi, Faisal S, Albinus, Jonas, Alborelli, Ilaria, Andani, Sonali, Attinger, Per-Olof, Bacac, Marina, Baumhoer, Daniel, Beck-Schimmer, Beatrice, Beerenwinkel, Niko, Beisel, Christian, Bernasconi, Lara, Bertolini, Anne, Bodenmiller, Bernd, Casanova, Ruben, Chicherova, Natalia, D'Costa, Maya, Danenberg, Esther, Davidson, Natalie, gan, Monica-Andreea Dră, Dummer, Reinhard, Engler, Stefanie, Erkens, Martin, Eschbach, Katja, Esposito, Cinzia, Fedier, André, Ferreira, Pedro, Frei, Anja L, Frey, Bruno, Goetze, Sandra, Grob, Linda, Gut, Gabriele, Günther, Detlef, Haberecker, Martina, Haeuptle, Pirmin, Heinzelmann-Schwarz, Viola, Herter, Sylvia, Holtackers, Rene, Huesser, Tamara, Irmisch, Anja, Jacob, Francis, Jacobs, Andrea, Jaeger, Tim M, Jahn, Katharina, James, Alva R, Jermann, Philip M, Kahles, André, Kahraman, Abdullah, Koelzer, Viktor H, Kuebler, Werner, Kuipers, Jack, Kunze, Christian P, Kurzeder, Christian, Lehmann, Kjong-Van, Levesque, Mitchell, Lugert, Sebastian, Maass, Gerd, Manz, Markus, Markolin, Philipp, Mena, Julien, Menzel, Ulrike, Metzler, Julian M, Miglino, Nicola, Milani, Emanuela S, Moch, Holger, Muenst, Simone, Murri, Riccardo, Ng, Charlotte KY, Nicolet, Stefan, Nowak, Marta, Pedrioli, Patrick GA, Pelkmans, Lucas, Piscuoglio, Salvatore, Prummer, Michael, Ritter, Mathilde, Rommel, Christian, Rosano-González, María L, Rätsch, Gunnar, Santacroce, Natascha, Castillo, Jacobo Sarabia del, Schlenker, Ramona, Schwalie, Petra C, Schwan, Severin, Schär, Tobias, Senti, Gabriela, Sivapatham, Sujana, Snijder, Berend, Sobottka, Bettina, Sreedharan, Vipin T, Stark, Stefan, Stekhoven, Daniel J, Theocharides, Alexandre PA, Thomas, Tinu M, Tolnay, Markus, Tosevski, Vinko, Toussaint, Nora C, Tuncel, Mustafa A, Tusup, Marina, Drogen, Audrey Van, Vetter, Marcus, Vlajnic, Tatjana, Weber, Sandra, Weber, Walter P, Wegmann, Rebekka, Weller, Michael, Wendt, Fabian, Wey, Norbert, Wicki, Andreas, Wollscheid, Bernd, Yu, Shuqing, Ziegler, Johanna, Zimmermann, Marc, Zoche, Martin, Zuend, Gregor, and University of Zurich

Subjects
Statistics and Probability, 1303 Biochemistry, AcademicSubjects/SCI01060, Computer science, 610 Medicine & health, computer.software_genre, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, Text mining, 1312 Molecular Biology, 1706 Computer Science Applications, Humans, Profiling (information science), 2613 Statistics and Probability, Molecular Biology, 030304 developmental biology, Data, 0303 health sciences, Sequence Analysis, RNA, business.industry, Gene Expression Profiling, Autoencoder, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, 10032 Clinic for Oncology and Hematology, Bipartite graph, Data mining, Single-Cell Analysis, business, computer, 2605 Computational Mathematics, Algorithms, Software, 030217 neurology & neurosurgery, Data integration, 1703 Computational Theory and Mathematics
Abstract

Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed. Results: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively., Bioinformatics, 36 (S2), ISSN:1367-4803, ISSN:1460-2059

Published
2020

29. The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support

Author

Irmisch, Anja, primary, Bonilla, Ximena, additional, Chevrier, Stéphane, additional, Lehmann, Kjong-Van, additional, Singer, Franziska, additional, Toussaint, Nora C., additional, Esposito, Cinzia, additional, Mena, Julien, additional, Milani, Emanuela S., additional, Casanova, Ruben, additional, Stekhoven, Daniel J., additional, Wegmann, Rebekka, additional, Jacob, Francis, additional, Sobottka, Bettina, additional, Goetze, Sandra, additional, Kuipers, Jack, additional, Sarabia del Castillo, Jacobo, additional, Prummer, Michael, additional, Tuncel, Mustafa A., additional, Menzel, Ulrike, additional, Jacobs, Andrea, additional, Engler, Stefanie, additional, Sivapatham, Sujana, additional, Frei, Anja L., additional, Gut, Gabriele, additional, Ficek, Joanna, additional, Miglino, Nicola, additional, Aebersold, Rudolf, additional, Bacac, Marina, additional, Beerenwinkel, Niko, additional, Beisel, Christian, additional, Bodenmiller, Bernd, additional, Dummer, Reinhard, additional, Heinzelmann-Schwarz, Viola, additional, Koelzer, Viktor H., additional, Manz, Markus G., additional, Moch, Holger, additional, Pelkmans, Lucas, additional, Snijder, Berend, additional, Theocharides, Alexandre P.A., additional, Tolnay, Markus, additional, Wicki, Andreas, additional, Wollscheid, Bernd, additional, Rätsch, Gunnar, additional, Levesque, Mitchell P., additional, Ak, Melike, additional, Al-Quaddoomi, Faisal S., additional, Albinus, Jonas, additional, Alborelli, Ilaria, additional, Andani, Sonali, additional, Attinger, Per-Olof, additional, Baumhoer, Daniel, additional, Beck-Schimmer, Beatrice, additional, Bernasconi, Lara, additional, Bertolini, Anne, additional, Chicherova, Natalia, additional, D'Costa, Maya, additional, Danenberg, Esther, additional, Davidson, Natalie, additional, Drăgan, Monica-Andreea, additional, Erkens, Martin, additional, Eschbach, Katja, additional, Fedier, André, additional, Ferreira, Pedro, additional, Frey, Bruno, additional, Grob, Linda, additional, Günther, Detlef, additional, Haberecker, Martina, additional, Haeuptle, Pirmin, additional, Herter, Sylvia, additional, Holtackers, Rene, additional, Huesser, Tamara, additional, Jaeger, Tim M., additional, Jahn, Katharina, additional, James, Alva R., additional, Jermann, Philip M., additional, Kahles, André, additional, Kahraman, Abdullah, additional, Kuebler, Werner, additional, Kunze, Christian P., additional, Kurzeder, Christian, additional, Lugert, Sebastian, additional, Maass, Gerd, additional, Markolin, Philipp, additional, Metzler, Julian M., additional, Muenst, Simone, additional, Murri, Riccardo, additional, Ng, Charlotte K.Y., additional, Nicolet, Stefan, additional, Nowak, Marta, additional, Pedrioli, Patrick G.A., additional, Piscuoglio, Salvatore, additional, Ritter, Mathilde, additional, Rommel, Christian, additional, Rosano-González, María L., additional, Santacroce, Natascha, additional, Schlenker, Ramona, additional, Schwalie, Petra C., additional, Schwan, Severin, additional, Schär, Tobias, additional, Senti, Gabriela, additional, Sreedharan, Vipin T., additional, Stark, Stefan, additional, Thomas, Tinu M., additional, Tosevski, Vinko, additional, Tusup, Marina, additional, Van Drogen, Audrey, additional, Vetter, Marcus, additional, Vlajnic, Tatjana, additional, Weber, Sandra, additional, Weber, Walter P., additional, Weller, Michael, additional, Wendt, Fabian, additional, Wey, Norbert, additional, Wildschut, Mattheus H.E., additional, Yu, Shuqing, additional, Ziegler, Johanna, additional, Zimmermann, Marc, additional, Zoche, Martin, additional, and Zuend, Gregor, additional

Published
2021
Full Text
View/download PDF

30. Additional file 1 of In vitro cell culture of patient derived malignant pleural and peritoneal effusions for personalised drug screening

Author

Cheng-Guang Wu, Chiovaro, Francesca, Curioni-Fontecedro, Alessandra, Casanova, Ruben, and Soltermann, Alex

Abstract

Additional file 1: Fig. S1. Digital image analysis of IHC staining of S100 and ER. (A) S100 staining of the showcase (P6) sample after 3D hanging drop culture. (B) ER staining of the showcase (P5) sample after 3D hanging drop culture. Positive staining area (brown) was recognised by colour thresholding using the “Lab” colour space and was annotated in yellow; non-staining area (blue/grey) was annotated into purple, scale bar = 200 µm.

Published
2020
Full Text
View/download PDF

31. Enhanced prognostic stratification of neoadjuvant treated lung squamous cell carcinoma by computationally-guided tumor regression scoring

Author

Casanova, Ruben, Leblond, Anne-Laure, Wu, Chengguang, Haberecker, Martina, Burger, Irene A, Soltermann, Alex, Casanova, Ruben, Leblond, Anne-Laure, Wu, Chengguang, Haberecker, Martina, Burger, Irene A, and Soltermann, Alex

Abstract

INTRODUCTION The amount of residual tumor burden after neoadjuvant chemotherapy is an important prognosticator, but for non-small cell lung carcinoma (NSCLC), no official regression scoring system is yet established. Computationally derived histological regression scores could provide unbiased and quantitative readouts to complement the clinical assessment of treatment response. METHODS Histopathologic tumor regression was microscopically assessed on whole cases in a neoadjuvant chemotherapy-treated cohort (NAC, n = 55 patients) of lung squamous cell carcinomas (LSCC). For each patient, the slide showing the least pathologic regression was selected for subsequent computational analysis and histological features were quantified: percentage of vital tumor cells (cTu.Percentage), total surface covered by vital tumor cells (cTu.Area), area of the largest vital tumor fragment (cTu.Size.max), and total number of vital tumor fragments (cTu.Fragments). A chemo-naïve LSCC cohort (CN, n = 104) was used for reference. For 23 of the 55 patients [$^{18}$F]-Fluorodeoxyglucose (FDG) PET/CT measurements of maximum standard uptake value (SUV$_{max}$), background subtracted lesion activity (BSL) and background subtracted volume (BSV) were correlated with pathologic regression. Survival analysis was carried out using Cox regression and receiver operating characteristic (ROC) curve analysis using a 3-years cutoff. RESULTS All computational regression parameters significantly correlated with relative changes of BSV FDG PET/CT values after neoadjuvant chemotherapy. ROC curve analysis of histological parameters of NAC patients showed that cTu.Percentage was the most accurate prognosticator of overall survival (ROC curve AUC = 0.77, p-value = 0.001, Cox regression HR = 3.6, p = 0.001, variable cutoff < = 30 %). CONCLUSIONS This study demonstrates the prognostic relevance of computer-derived histopathologic scores. Additionally, the analysis carried out on slides displaying the least pathol

Published
2020

35. Computer-based intensity measurement assists pathologists in scoring PTEN immunohistochemistry - Clinical associations in NSCLC patients of the ETOP Lungscape cohort

Author

Rulle, Undine, Tsourti, Zoi, Casanova, Ruben, Deml, Karl-Friedrich, Verbeken, Eric, Thunnissen, Erik, Warth, Arne, Cheney, Richard, Sejda, Aleksandra, Speel, Ernst Jan, Madsen, Line Bille, Nonaka, Daisuke, Navarro, Atilio, Sansano, Irene, Marchetti, Antonio, Finn, Stephen P, Monkhorst, Kim, Kerr, Keith M, Haberecker, Martina, Wu, Chengguang, Zygoura, Panagiota, Kammler, Roswitha, Geiger, Thomas, Gendreau, Steven, Schulze, Katja, Vrugt, Bart, Wild, Peter, Moch, Holger, Weder, Walter, Ciftlik, Ata Tuna, Dafni, Urania, Peters, Solange, Bubendorf, Lukas, Stahel, Rolf A, Soltermann, Alex, University of Zurich, and Soltermann, Alex

Subjects
10255 Clinic for Thoracic Surgery, 2740 Pulmonary and Respiratory Medicine, 10049 Institute of Pathology and Molecular Pathology, 10032 Clinic for Oncology and Hematology, 610 Medicine & health, 2730 Oncology
Published
2018

36. Prognostic Immune Cell Profiling of Malignant Pleural Effusion Patients by Computerized Immunohistochemical and Transcriptional Analysis

Author

Wu, Chengguang, Mairinger, Fabian, Casanova, Ruben, Batavia, Aashil A, Leblond, Anne-Laure, Soltermann, Alex, Wu, Chengguang, Mairinger, Fabian, Casanova, Ruben, Batavia, Aashil A, Leblond, Anne-Laure, and Soltermann, Alex

Abstract

Malignant pleural effusion (MPE) is a severe condition of advanced tumors without effective therapy. We used digitalized immunohistochemical and transcriptional approaches to investigate the prognostic influence of immune cells and expression variance of associated immunomodulatory molecules in MPE. Cytology tissue microarrays were constructed from MPE cell blocks of 155 patients with five tumor entities. Immune cells lineage markers were quantified by computational cytopathology on immunohistochemistry. mRNA expression analysis of nine lineage markers and 17 immunomodulators was performed by NanoString. Immunohistochemically quantified high B cells to leukocytes ratio (hazard ratio (HR) = 0.70, p-value = 0.043) and low neutrophils to leukocytes ratio (HR = 1.78, p-value = 0.003) were favorable prognosticators for overall survival independent of tumor entity. Correspondingly, patients with high B cells but low neutrophils gene expression signature showed longer median overall survival of 500 days (HR = 2.29, p-value = 0.009). Regarding targetable molecule expressions, lung adenocarcinomas were characterized by high PD-L1, but mesothelioma by high LAG-3. Ovarian carcinoma was least immunogenic. Independent of tumor entity, the condition of the immune system in MPE liquids is able to provide additional prognostic cytologic information. Combined analysis of lineage specific markers and related immunomodulators may direct immune-based therapeutic decisions.

Published
2019

37. Morphoproteomic characterization of lung squamous cell carcinoma fragmentation, a histological marker of increased tumor invasiveness

Author

Casanova, Ruben, Xia, Daniel, Rulle, Undīne, Nanni, Paolo, Grossmann, Jonas, Vrugt, Bart, Wettstein, Reto, Ballester, Rafael, Astolfo, Alberto, Weder, Walter, Moch, Holger, Stampanoni, Marco, Beck, Andrew H, Soltermann, Alex, University of Zurich, and Casanova, Ruben

Subjects
10255 Clinic for Thoracic Surgery, 10049 Institute of Pathology and Molecular Pathology, 610 Medicine & health, 2730 Oncology, 1306 Cancer Research
Published
2017

38. Germinal centers determine the prognostic relevance of tertiary lymphoid structures and are impaired by corticosteroids in lung squamous cell carcinoma

Author

Silina, Karina, Soltermann, Alex, Movahedian Attar, Farkhondeh, Casanova, Ruben, Uckeley, Zina M, Thut, Helen, Wandres, Muriel, Isajevs, Sergejs, Cheng, Phil, Curioni Fontecedro, Alessandra, Foukas, Periklis, Levesque, Mitchell P, Moch, Holger, Linē, Aija, van den Broek, Maries, University of Zurich, and van den Broek, Maries

Subjects
10049 Institute of Pathology and Molecular Pathology, 10032 Clinic for Oncology and Hematology, 570 Life sciences, biology, 610 Medicine & health, 2730 Oncology, 1306 Cancer Research, 10263 Institute of Experimental Immunology
Published
2018

39. Abstract A113: Harnessing lymphoid organ neogenesis as a novel prognostic biomarker and therapeutic target

Author

Silina, Karina, primary, Soltermann, Alex, additional, Burkhardt, Chiara, additional, Attar, Farkhondeh Movahedian, additional, Casanova, Ruben, additional, Curioni-Fontecedro, Alessandra, additional, Moch, Holger, additional, Posch, Florian, additional, Winder, Thomas, additional, Dijk, Nick van, additional, Voskuilen, Charlotte, additional, Heijden, Michiel van der, additional, and Broek, Maries van den, additional

Published
2019
Full Text
View/download PDF

40. A Quantitative Pathology Approach to Analyze the Development of Human Cancer-Associated Tertiary Lymphoid Structures

Author

Dieu-Nosjean, Marie-Caroline, Dieu-Nosjean, M ( Marie-Caroline ), Siliņa, Karīna, Burkhardt, Chiara, Casanova, Ruben, Solterman, Alex, van den Broek, Maries; https://orcid.org/0000-0002-9489-3692, Dieu-Nosjean, Marie-Caroline, Dieu-Nosjean, M ( Marie-Caroline ), Siliņa, Karīna, Burkhardt, Chiara, Casanova, Ruben, Solterman, Alex, and van den Broek, Maries; https://orcid.org/0000-0002-9489-3692

Abstract

Tertiary lymphoid structures (TLS) develop in the human tumor microenvironment and correlate with prolonged survival in most cancer types. We recently demonstrated that TLS development follows sequential maturation stages and culminates in the generation of a germinal center (GC) reaction. This maturation process is crucial for the prognostic relevance of TLS in lung and colorectal cancer patients. The mechanisms underlying TLS development in various inflammatory conditions or their functional relevance in tumor immunity are not fully understood. Investigating which cell types and soluble mediators orchestrate lymphoid neogenesis in human tissues requires a method that allows simultaneous detection of multiple markers. Here, we describe a quantitative pathology approach to identify and quantify different TLS maturation stages in combination with other parameters. This approach consists of seven-color immunofluorescence protocol using tyramide signal amplification combined with multispectral microscopy and quantitative data acquisition from histological images.

Published
2018

41. Computationally-Guided Development of a Stromal Inflammation Histologic Biomarker in Lung Squamous Cell Carcinoma

Author

Xia, Daniel, Casanova, Ruben, Machiraju, Devayani, McKee, Trevor D, Weder, Walter, Beck, Andrew H, Soltermann, Alex, Xia, Daniel, Casanova, Ruben, Machiraju, Devayani, McKee, Trevor D, Weder, Walter, Beck, Andrew H, and Soltermann, Alex

Abstract

The goal of this study is to use computational pathology to help guide the development of human-based prognostic H&E biomarker(s) suitable for research and potential clinical use in lung squamous cell carcinoma (SCC). We started with high-throughput computational image analysis with tissue microarrays (TMAs) to screen for histologic features associated with patient overall survival, and found that features related to stromal inflammation were the most strongly prognostic. Based on this, we developed an H&E stromal inflammation (SI) score. The prognostic value of the SI score was validated by two blinded human observers on two large cohorts from a single institution. The SI score was found to be reproducible on TMAs (Spearman rho = 0.88 between the two observers), and highly prognostic (e.g. hazard ratio = 0.32; 95% confidence interval: 0.19-0.54; p-value = 2.5 × 10 in multivariate analyses), particularly in comparison to established histologic biomarkers. Guided by downstream molecular/biomarker correlation studies starting with TCGA cases, we investigated the hypothesis that epithelial PD-L1 expression modified the prognostic value of SI. Our research demonstrates that computational pathology can be an efficient hypothesis generator for human pathology research, and support the histologic evaluation of SI as a prognostic biomarker in lung SCCs.

Published
2018

42. Non-internalizing antibody-drug conjugates and their anti-cancer activity

Author

Gébleux, Rémy, Stringhini, Marco, Casanova, Ruben, Soltermann, Alex, Neri, Dario, University of Zurich, and Neri, Dario

Subjects
Cancer Research, Oncology, 10049 Institute of Pathology and Molecular Pathology, 610 Medicine & health, 2730 Oncology, 1306 Cancer Research
Published
2017

45. Germinal Centers Determine the Prognostic Relevance of Tertiary Lymphoid Structures and Are Impaired by Corticosteroids in Lung Squamous Cell Carcinoma

Author

Siliņa, Karīna, primary, Soltermann, Alex, additional, Attar, Farkhondeh Movahedian, additional, Casanova, Ruben, additional, Uckeley, Zina M., additional, Thut, Helen, additional, Wandres, Muriel, additional, Isajevs, Sergejs, additional, Cheng, Phil, additional, Curioni-Fontecedro, Alessandra, additional, Foukas, Periklis, additional, Levesque, Mitchell P., additional, Moch, Holger, additional, Linē, Aija, additional, and van den Broek, Maries, additional

Published
2018
Full Text
View/download PDF

46. FDG-PET/CT of non-small cell lung carcinoma under neo-adjuvant chemotherapy: background based adaptive volume metrics outperform TLG and MTV in predicting histopathological response

Author

Burger, Irene A, Casanova, Ruben, Steiger, Seraina, Husmann, Lars, Stolzmann, Paul, Huellner, Martin W, Curioni, Alessandra, Hillinger, Sven, Schmidtlein, Charles Ross, Soltermann, Alex, University of Zurich, and Burger, Irene A

Subjects
10255 Clinic for Thoracic Surgery, 10049 Institute of Pathology and Molecular Pathology, 10032 Clinic for Oncology and Hematology, 2741 Radiology, Nuclear Medicine and Imaging, 610 Medicine & health, 10181 Clinic for Nuclear Medicine
Published
2016

48. Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, additional, Rulle, Undine, additional, Nanni, Paolo, additional, Grossmann, Jonas, additional, Vrugt, Bart, additional, Wettstein, Reto, additional, Ballester-Ripoll, Rafael, additional, Astolfo, Alberto, additional, Weder, Walter, additional, Moch, Holger, additional, Stampanoni, Marco, additional, Beck, Andrew H., additional, and Soltermann, Alex, additional

Published
2017
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results