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Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry.

Cell systems

Schulz D, Zanotelli VRT, Fischer JR, Schapiro D, Engler S, Lun XK, Jackson HW, Bodenmiller B.
PMID: 29698648
Cell Syst. 2018 Apr 25;6(4):531. doi: 10.1016/j.cels.2018.04.004.

No abstract available.

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Schulz D, Zanotelli VRT, Fischer JR, et al. Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry. Cell Syst. 2018;6(4):531doi: 10.1016/j.cels.2018.04.004.
Schulz, D., Zanotelli, V. R. T., Fischer, J. R., Schapiro, D., Engler, S., Lun, X. K., Jackson, H. W., & Bodenmiller, B. (2018). Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry. Cell systems, 6(4), 531. https://doi.org/10.1016/j.cels.2018.04.004
Schulz, Daniel, et al. "Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry." Cell systems vol. 6,4 (2018): 531. doi: https://doi.org/10.1016/j.cels.2018.04.004
Schulz D, Zanotelli VRT, Fischer JR, Schapiro D, Engler S, Lun XK, Jackson HW, Bodenmiller B. Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry. Cell Syst. 2018 Apr 25;6(4):531. doi: 10.1016/j.cels.2018.04.004. PMID: 29698648; PMCID: PMC5929910.
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Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data.

Bioinformatics (Oxford, England)

Eling N, Damond N, Hoch T, Bodenmiller B.
PMID: 33367748
Bioinformatics. 2020 Dec 26; doi: 10.1093/bioinformatics/btaa1061. Epub 2020 Dec 26.

SUMMARY: Highly multiplexed imaging technologies enable spatial profiling of dozens of biomarkers in situ. Here we describe cytomapper, a computational tool written in R, that enables visualisation of pixel- and cell-level information obtained by multiplexed imaging. To illustrate its...

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Eling N, Damond N, Hoch T, et al. Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data. Bioinformatics. 2020;doi: 10.1093/bioinformatics/btaa1061.
Eling, N., Damond, N., Hoch, T., & Bodenmiller, B. (2020). Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data. Bioinformatics (Oxford, England), . https://doi.org/10.1093/bioinformatics/btaa1061
Eling, Nils, et al. "Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data." Bioinformatics (Oxford, England) vol. (2020). doi: https://doi.org/10.1093/bioinformatics/btaa1061
Eling N, Damond N, Hoch T, Bodenmiller B. Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data. Bioinformatics. 2020 Dec 26; doi: 10.1093/bioinformatics/btaa1061. Epub 2020 Dec 26. PMID: 33367748; PMCID: PMC8023672.
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A distinct innate immune signature marks progression from mild to severe COVID-19.

Cell reports. Medicine

Chevrier S, Zurbuchen Y, Cervia C, Adamo S, Raeber ME, de Souza N, Sivapatham S, Jacobs A, Bachli E, Rudiger A, Stüssi-Helbling M, Huber LC, Schaer DJ, Nilsson J, Boyman O, Bodenmiller B.
PMID: 33521697
Cell Rep Med. 2020 Dec 26;2(1):100166. doi: 10.1016/j.xcrm.2020.100166. eCollection 2021 Jan 19.

Coronavirus disease 2019 (COVID-19) manifests with a range of severities, but immune signatures of mild and severe disease are still not fully understood. Here, we use mass cytometry and targeted proteomics to profile the innate immune response of patients...

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Chevrier S, Zurbuchen Y, Cervia C, et al. A distinct innate immune signature marks progression from mild to severe COVID-19. Cell Rep Med. 2020;2(1):100166doi: 10.1016/j.xcrm.2020.100166.
Chevrier, S., Zurbuchen, Y., Cervia, C., Adamo, S., Raeber, M. E., de Souza, N., Sivapatham, S., Jacobs, A., Bachli, E., Rudiger, A., Stüssi-Helbling, M., Huber, L. C., Schaer, D. J., Nilsson, J., Boyman, O., & Bodenmiller, B. (2021). A distinct innate immune signature marks progression from mild to severe COVID-19. Cell reports. Medicine, 2(1), 100166. https://doi.org/10.1016/j.xcrm.2020.100166
Chevrier, Stéphane, et al. "A distinct innate immune signature marks progression from mild to severe COVID-19." Cell reports. Medicine vol. 2,1 (2021): 100166. doi: https://doi.org/10.1016/j.xcrm.2020.100166
Chevrier S, Zurbuchen Y, Cervia C, Adamo S, Raeber ME, de Souza N, Sivapatham S, Jacobs A, Bachli E, Rudiger A, Stüssi-Helbling M, Huber LC, Schaer DJ, Nilsson J, Boyman O, Bodenmiller B. A distinct innate immune signature marks progression from mild to severe COVID-19. Cell Rep Med. 2020 Dec 26;2(1):100166. doi: 10.1016/j.xcrm.2020.100166. eCollection 2021 Jan 19. PMID: 33521697; PMCID: PMC7817872.
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Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

BMC bioinformatics

Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD.
PMID: 19087345
BMC Bioinformatics. 2008 Dec 16;9:542. doi: 10.1186/1471-2105-9-542.

BACKGROUND: Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry...

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Brusniak MY, Bodenmiller B, Campbell D, et al. Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics. 2008;9:542doi: 10.1186/1471-2105-9-542.
Brusniak, M. Y., Bodenmiller, B., Campbell, D., Cooke, K., Eddes, J., Garbutt, A., Lau, H., Letarte, S., Mueller, L. N., Sharma, V., Vitek, O., Zhang, N., Aebersold, R., & Watts, J. D. (2008). Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC bioinformatics, 9542. https://doi.org/10.1186/1471-2105-9-542
Brusniak, Mi-Youn, et al. "Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics." BMC bioinformatics vol. 9 (2008): 542. doi: https://doi.org/10.1186/1471-2105-9-542
Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD. Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics. 2008 Dec 16;9:542. doi: 10.1186/1471-2105-9-542. PMID: 19087345; PMCID: PMC2651178.
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Towards a comprehensive proteome of normal and malignant human colon tissue by 2-D-LC-ESI-MS and 2-DE proteomics and identification of S100A12 as potential cancer biomarker.

Proteomics. Clinical applications

Thierolf M, Hagmann ML, Pfeffer M, Berntenis N, Wild N, Roeßler M, Palme S, Karl J, Bodenmüller H, Rüschoff J, Rossol S, Rohr G, Rösch W, Friess H, Eickhoff A, Jauch KW, Langen H, Zolg W, Tacke M.
PMID: 21136775
Proteomics Clin Appl. 2008 Jan;2(1):11-22. doi: 10.1002/prca.200780046. Epub 2007 Dec 11.

No abstract available.

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Thierolf M, Hagmann ML, Pfeffer M, et al. Towards a comprehensive proteome of normal and malignant human colon tissue by 2-D-LC-ESI-MS and 2-DE proteomics and identification of S100A12 as potential cancer biomarker. Proteomics Clin Appl. 2007;2(1):11-22doi: 10.1002/prca.200780046.
Thierolf, M., Hagmann, M. L., Pfeffer, M., Berntenis, N., Wild, N., Roeßler, M., Palme, S., Karl, J., Bodenmüller, H., Rüschoff, J., Rossol, S., Rohr, G., Rösch, W., Friess, H., Eickhoff, A., Jauch, K. W., Langen, H., Zolg, W., & Tacke, M. (2008). Towards a comprehensive proteome of normal and malignant human colon tissue by 2-D-LC-ESI-MS and 2-DE proteomics and identification of S100A12 as potential cancer biomarker. Proteomics. Clinical applications, 2(1), 11-22. https://doi.org/10.1002/prca.200780046
Thierolf, Michael, et al. "Towards a comprehensive proteome of normal and malignant human colon tissue by 2-D-LC-ESI-MS and 2-DE proteomics and identification of S100A12 as potential cancer biomarker." Proteomics. Clinical applications vol. 2,1 (2008): 11-22. doi: https://doi.org/10.1002/prca.200780046
Thierolf M, Hagmann ML, Pfeffer M, Berntenis N, Wild N, Roeßler M, Palme S, Karl J, Bodenmüller H, Rüschoff J, Rossol S, Rohr G, Rösch W, Friess H, Eickhoff A, Jauch KW, Langen H, Zolg W, Tacke M. Towards a comprehensive proteome of normal and malignant human colon tissue by 2-D-LC-ESI-MS and 2-DE proteomics and identification of S100A12 as potential cancer biomarker. Proteomics Clin Appl. 2008 Jan;2(1):11-22. doi: 10.1002/prca.200780046. Epub 2007 Dec 11. PMID: 21136775.
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Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia.

Nature cancer

Lu J, Cannizzaro E, Meier-Abt F, Scheinost S, Bruch PM, Giles HA, Lütge A, Hüllein J, Wagner L, Giacopelli B, Nadeu F, Delgado J, Campo E, Mangolini M, Ringshausen I, Böttcher M, Mougiakakos D, Jacobs A, Bodenmiller B, Dietrich S, Oakes CC, Zenz T, Huber W.
PMID: 34423310
Nat Cancer. 2021 Aug;2(8):853-864. doi: 10.1038/s43018-021-00216-6. Epub 2021 Jul 01.

Chronic Lymphocytic Leukemia (CLL) has a complex pattern of driver mutations and much of its clinical diversity remains unexplained. We devised a method for simultaneous subgroup discovery across multiple data types and applied it to genomic, transcriptomic, DNA methylation...

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Lu J, Cannizzaro E, Meier-Abt F, et al. Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia. Nat Cancer. 2021;2(8):853-864doi: 10.1038/s43018-021-00216-6.
Lu, J., Cannizzaro, E., Meier-Abt, F., Scheinost, S., Bruch, P. M., Giles, H. A., Lütge, A., Hüllein, J., Wagner, L., Giacopelli, B., Nadeu, F., Delgado, J., Campo, E., Mangolini, M., Ringshausen, I., Böttcher, M., Mougiakakos, D., Jacobs, A., Bodenmiller, B., Dietrich, S., Oakes, C. C., Zenz, T., & Huber, W. (2021). Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia. Nature cancer, 2(8), 853-864. https://doi.org/10.1038/s43018-021-00216-6
Lu, Junyan, et al. "Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia." Nature cancer vol. 2,8 (2021): 853-864. doi: https://doi.org/10.1038/s43018-021-00216-6
Lu J, Cannizzaro E, Meier-Abt F, Scheinost S, Bruch PM, Giles HA, Lütge A, Hüllein J, Wagner L, Giacopelli B, Nadeu F, Delgado J, Campo E, Mangolini M, Ringshausen I, Böttcher M, Mougiakakos D, Jacobs A, Bodenmiller B, Dietrich S, Oakes CC, Zenz T, Huber W. Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia. Nat Cancer. 2021 Aug;2(8):853-864. doi: 10.1038/s43018-021-00216-6. Epub 2021 Jul 01. PMID: 34423310; PMCID: PMC7611543.
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Cutaneous and systemic hyperinflammation drives maculopapular drug exanthema in severely ill COVID-19 patients.

Allergy

Mitamura Y, Schulz D, Oro S, Li N, Kolm I, Lang C, Ziadlou R, Tan G, Bodenmiller B, Steiger P, Marzano A, de Prost N, Caudin O, Levesque M, Stoffel C, Schmid-Grendelmeier P, Maverakis E, Akdis CA, Brüggen MC.
PMID: 34157151
Allergy. 2021 Jun 22; doi: 10.1111/all.14983. Epub 2021 Jun 22.

BACKGROUND: Coronavirus disease-2019 (COVID-19) has been associated with cutaneous findings, some being the result of drug hypersensitivity reactions such as maculopapular drug rashes (MDR). The aim of this study was to investigate whether COVID-19 may impact the development of...

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Mitamura Y, Schulz D, Oro S, et al. Cutaneous and systemic hyperinflammation drives maculopapular drug exanthema in severely ill COVID-19 patients. Allergy. 2021;doi: 10.1111/all.14983.
Mitamura, Y., Schulz, D., Oro, S., Li, N., Kolm, I., Lang, C., Ziadlou, R., Tan, G., Bodenmiller, B., Steiger, P., Marzano, A., de Prost, N., Caudin, O., Levesque, M., Stoffel, C., Schmid-Grendelmeier, P., Maverakis, E., Akdis, C. A., & Brüggen, M. C. (2021). Cutaneous and systemic hyperinflammation drives maculopapular drug exanthema in severely ill COVID-19 patients. Allergy, . https://doi.org/10.1111/all.14983
Mitamura, Yasutaka, et al. "Cutaneous and systemic hyperinflammation drives maculopapular drug exanthema in severely ill COVID-19 patients." Allergy vol. (2021). doi: https://doi.org/10.1111/all.14983
Mitamura Y, Schulz D, Oro S, Li N, Kolm I, Lang C, Ziadlou R, Tan G, Bodenmiller B, Steiger P, Marzano A, de Prost N, Caudin O, Levesque M, Stoffel C, Schmid-Grendelmeier P, Maverakis E, Akdis CA, Brüggen MC. Cutaneous and systemic hyperinflammation drives maculopapular drug exanthema in severely ill COVID-19 patients. Allergy. 2021 Jun 22; doi: 10.1111/all.14983. Epub 2021 Jun 22. PMID: 34157151; PMCID: PMC8441838.
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Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd.

Molecular systems biology

Gabor A, Tognetti M, Driessen A, Tanevski J, Guo B, Cao W, Shen H, Yu T, Chung V, Bodenmiller B, Saez-Rodriguez J.
PMID: 34661974
Mol Syst Biol. 2021 Oct;17(10):e10402. doi: 10.15252/msb.202110402.

Recent technological developments allow us to measure the status of dozens of proteins in individual cells. This opens the way to understand the heterogeneity of complex multi-signaling networks across cells and cell types, with important implications to understand and...

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Gabor A, Tognetti M, Driessen A, et al. Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd. Mol Syst Biol. 2021;17(10):e10402doi: 10.15252/msb.202110402.
Gabor, A., Tognetti, M., Driessen, A., Tanevski, J., Guo, B., Cao, W., Shen, H., Yu, T., Chung, V., Bodenmiller, B., & Saez-Rodriguez, J. (2021). Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd. Molecular systems biology, 17(10), e10402. https://doi.org/10.15252/msb.202110402
Gabor, Attila, et al. "Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd." Molecular systems biology vol. 17,10 (2021): e10402. doi: https://doi.org/10.15252/msb.202110402
Gabor A, Tognetti M, Driessen A, Tanevski J, Guo B, Cao W, Shen H, Yu T, Chung V, Bodenmiller B, Saez-Rodriguez J. Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd. Mol Syst Biol. 2021 Oct;17(10):e10402. doi: 10.15252/msb.202110402. PMID: 34661974; PMCID: PMC8522707.
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Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition.

Frontiers in physiology

Wade JD, Lun XK, Zivanovic N, Voit EO, Bodenmiller B.
PMID: 33329028
Front Physiol. 2020 Nov 30;11:579117. doi: 10.3389/fphys.2020.579117. eCollection 2020.

Intracellular signaling pathways are at the core of cellular information processing. The states of these pathways and their inputs determine signaling dynamics and drive cell function. Within a cancerous tumor, many combinations of cell states and microenvironments can lead...

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Wade JD, Lun XK, Zivanovic N, et al. Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition. Front Physiol. 2020;11:579117doi: 10.3389/fphys.2020.579117.
Wade, J. D., Lun, X. K., Zivanovic, N., Voit, E. O., & Bodenmiller, B. (2020). Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition. Frontiers in physiology, 11579117. https://doi.org/10.3389/fphys.2020.579117
Wade, James D, et al. "Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition." Frontiers in physiology vol. 11 (2020): 579117. doi: https://doi.org/10.3389/fphys.2020.579117
Wade JD, Lun XK, Zivanovic N, Voit EO, Bodenmiller B. Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition. Front Physiol. 2020 Nov 30;11:579117. doi: 10.3389/fphys.2020.579117. eCollection 2020. PMID: 33329028; PMCID: PMC7733964.
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Isolation and amino acid sequence of a morphogenetic peptide from hydra.

Proceedings of the National Academy of Sciences of the United States of America

Schaller HC, Bodenmüller H.
PMID: 16593123
Proc Natl Acad Sci U S A. 1981 Nov;78(11):7000-4. doi: 10.1073/pnas.78.11.7000.

From Anthopleura elegantissima and from Hydra attenuata, a morphogenetic peptide-the head activator-was isolated in pure form. The sequence of the head activator was established by enzymatic and by chemical degradation of the whole peptide or fragments thereof and subsequent...

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Schaller HC, Bodenmüller H. Isolation and amino acid sequence of a morphogenetic peptide from hydra. Proc Natl Acad Sci U S A. 1981;78(11):7000-4doi: 10.1073/pnas.78.11.7000.
Schaller, H. C., & Bodenmüller, H. (1981). Isolation and amino acid sequence of a morphogenetic peptide from hydra. Proceedings of the National Academy of Sciences of the United States of America, 78(11), 7000-4. https://doi.org/10.1073/pnas.78.11.7000
Schaller, H C, and Bodenmüller, H. "Isolation and amino acid sequence of a morphogenetic peptide from hydra." Proceedings of the National Academy of Sciences of the United States of America vol. 78,11 (1981): 7000-4. doi: https://doi.org/10.1073/pnas.78.11.7000
Schaller HC, Bodenmüller H. Isolation and amino acid sequence of a morphogenetic peptide from hydra. Proc Natl Acad Sci U S A. 1981 Nov;78(11):7000-4. doi: 10.1073/pnas.78.11.7000. PMID: 16593123; PMCID: PMC349181.
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The head activator is released from regenerating Hydra bound to a carrier molecule.

The EMBO journal

Schaller HC, Roberge M, Zachmann B, Hoffmeister S, Schilling E, Bodenmüller H.
PMID: 16453697
EMBO J. 1986 Aug;5(8):1821-4.

Hydra forced to regenerate a head releases head activator and head inhibitor during the first hours after cutting to induce head-specific growth and differentiation processes. Analysis of the size distribution demonstrated that the head-activator peptide is co-released with (a)...

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Schaller HC, Roberge M, Zachmann B, et al. The head activator is released from regenerating Hydra bound to a carrier molecule. EMBO J. 1986;5(8):1821-4
Schaller, H. C., Roberge, M., Zachmann, B., Hoffmeister, S., Schilling, E., & Bodenmüller, H. (1986). The head activator is released from regenerating Hydra bound to a carrier molecule. The EMBO journal, 5(8), 1821-4.
Schaller, H C, et al. "The head activator is released from regenerating Hydra bound to a carrier molecule." The EMBO journal vol. 5,8 (1986): 1821-4.
Schaller HC, Roberge M, Zachmann B, Hoffmeister S, Schilling E, Bodenmüller H. The head activator is released from regenerating Hydra bound to a carrier molecule. EMBO J. 1986 Aug;5(8):1821-4. PMID: 16453697; PMCID: PMC1167046.
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Deciphering the signaling network of breast cancer improves drug sensitivity prediction.

Cell systems

Tognetti M, Gabor A, Yang M, Cappelletti V, Windhager J, Rueda OM, Charmpi K, Esmaeilishirazifard E, Bruna A, de Souza N, Caldas C, Beyer A, Picotti P, Saez-Rodriguez J, Bodenmiller B.
PMID: 33932331
Cell Syst. 2021 May 19;12(5):401-418.e12. doi: 10.1016/j.cels.2021.04.002. Epub 2021 Apr 30.

One goal of precision medicine is to tailor effective treatments to patients' specific molecular markers of disease. Here, we used mass cytometry to characterize the single-cell signaling landscapes of 62 breast cancer cell lines and five lines from healthy...

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Tognetti M, Gabor A, Yang M, et al. Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell Syst. 2021;12(5):401-418.e12doi: 10.1016/j.cels.2021.04.002.
Tognetti, M., Gabor, A., Yang, M., Cappelletti, V., Windhager, J., Rueda, O. M., Charmpi, K., Esmaeilishirazifard, E., Bruna, A., de Souza, N., Caldas, C., Beyer, A., Picotti, P., Saez-Rodriguez, J., & Bodenmiller, B. (2021). Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell systems, 12(5), 401-418.e12. https://doi.org/10.1016/j.cels.2021.04.002
Tognetti, Marco, et al. "Deciphering the signaling network of breast cancer improves drug sensitivity prediction." Cell systems vol. 12,5 (2021): 401-418.e12. doi: https://doi.org/10.1016/j.cels.2021.04.002
Tognetti M, Gabor A, Yang M, Cappelletti V, Windhager J, Rueda OM, Charmpi K, Esmaeilishirazifard E, Bruna A, de Souza N, Caldas C, Beyer A, Picotti P, Saez-Rodriguez J, Bodenmiller B. Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell Syst. 2021 May 19;12(5):401-418.e12. doi: 10.1016/j.cels.2021.04.002. Epub 2021 Apr 30. PMID: 33932331.
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