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8 results on '"Haeuptle, Pirmin"'

1. First-Line Chemo-Immunotherapy in SCLC: Outcomes of a Binational Real-World Study

Author

Moliner, Laura, Zellweger, Núria, Schmid, Sabine, Bertschinger, Martina, Waibel, Christine, Cerciello, Ferdinando, Froesch, Patrizia, Mark, Michael, Bettini, Adrienne, Häuptle, Pirmin, Blum, Veronika, Holer, Lisa, Hayoz, Stefanie, Früh, Martin, Ahmed, Samreen, Bhagani, Shradha, Steele, Nicoloa, Gray, Hannah L., Robinson, Stephen D., Davidson, Michael, Cox, Samantha, Khalid, Taha, Geldart, Tom R., Nolan, Luke, Scott, Deborah C., Hennah, Lindsay, Newsom-Davis, Tom, Rathbone, Emma, Handforth, Catherine, Denton, Arshi, Merchant, Shairoz, Blackhall, Fiona, Mauti, Laetitia A., Califano, Raffaele, and Rothschild, Sacha I.

Published
2024
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2. Precision Oncology in Older Cancer Patients: A Single-Center Experience.

Author

Petitat-Berli, Meret, Knufinke, Marie, Voegeli, Michèle, Sonderegger, Martina, Seifert, Bettina, Chiru, Elena Diana, Haeuptle, Pirmin, van't Walderveen, Lisanne, Rosenberg, Robert, Burri, Emanuel, Subotic, Svetozar, Schwab, Fabienne Dominique, Dougoud-Chauvin, Vérène, Unger, Heinz, Mertz, Kirsten, Tahan, Loay, and Vetter, Marcus

Subjects
NUCLEOTIDE sequencing, OLDER patients, CANCER patients, OVERALL survival, METASTASIS
Abstract

In the last two decades, next-generation sequencing (NGS) has facilitated enormous progress in cancer medicine, in both diagnosis and treatment. However, the usefulness of NGS in older cancer patients is unclear. To determine the role of NGS in older cancer patients, we retrospectively assessed demographic, clinicopathologic, and disease-specific data from 100 randomly selected cancer patients (any subtype/stage) who underwent NGS testing in 2020 at our institution and compared the treatment outcomes (progression-free survival [PFS] and overall survival [OS]) in the younger and older patient cohorts (A [n = 34] and B [n = 66]: age < 70 and ≥70 years, respectively). Overall, 27% had targetable mutations, and 8% received NGS-determined targeted therapy (45% and 19% of patients with a targetable mutation in cohorts A and B, respectively; p = 0.2), of whom 38% (3% of the whole cohort) benefited from the therapy (PFS > 6 months). The median OS (from diagnosis) was 192 and 197 weeks in cohorts A and B, respectively (p = 0.08). This pilot study revealed no significant age-stratified difference in the diagnostic approach and treatment strategy. A small, but relevant, proportion of the cohort (3%) benefited from NGS-determined treatment. Nevertheless, older cancer patients with targetable mutations less frequently received targetable therapies. [ABSTRACT FROM AUTHOR]

Published
2024
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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
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5. Integrated Analysis Of Immunotherapy Treated Clear Cell Renal Cell Carcinomas: An Exploratory Study

Author

Sobottka-Brillout, Bettina, Nienhold, Ronny, Nowak, Marta, Hench, Juergen, Haeuptle, Pirmin, Frank, Angela, Sachs, Melanie, Kahraman, Abdullah; https://orcid.org/0000-0003-3523-4467, Moch, Holger; https://orcid.org/0000-0002-7986-2839, Koelzer, Viktor H; https://orcid.org/0000-0001-9206-4885, Mertz, Kirsten D; https://orcid.org/0000-0002-3074-6925, Sobottka-Brillout, Bettina, Nienhold, Ronny, Nowak, Marta, Hench, Juergen, Haeuptle, Pirmin, Frank, Angela, Sachs, Melanie, Kahraman, Abdullah; https://orcid.org/0000-0003-3523-4467, Moch, Holger; https://orcid.org/0000-0002-7986-2839, Koelzer, Viktor H; https://orcid.org/0000-0001-9206-4885, and Mertz, Kirsten D; https://orcid.org/0000-0002-3074-6925

Abstract

Molecular or immunological differences between responders and nonresponders to immune checkpoint inhibitors (ICIs) of clear cell renal cell carcinomas (ccRCCs) remain incompletely understood. To address this question, we performed next-generation sequencing, methylation analysis, genome wide copy number analysis, targeted RNA sequencing and T-cell receptor sequencing, and we studied frequencies of tumor-infiltrating CD8+ T cells, presence of tertiary lymphoid structures (TLS) and PD-L1 expression in 8 treatment-naive ccRCC patients subsequently treated with ICI (3 responders, 5 nonresponders). Unexpectedly, we identified decreased frequencies of CD8+ tumor-infiltrating T cells and TLS, and a decreased expression of PD-L1 in ICI responders when compared with nonresponders. However, neither tumor-specific genetic alterations nor gene expression profiles correlated with response to ICI or the observed immune features. Our results underline the challenge to stratify ccRCC patients for immunotherapy based on routinely available pathologic primary tumor material, even with advanced technologies. Our findings emphasize the analysis of pretreated metastatic tissue in line with recent observations describing treatment effects on the tumor microenvironment. In addition, our data call for further investigation of additional parameters in a larger ccRCC cohort to understand the mechanistic implications of the observed differences in tumor-infiltrating CD8+ T cells, TLS, and PD-L1 expression.

Published
2022

7. 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

8. 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
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