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1. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer

Author

Salcher, Stefan, Sturm, Gregor, Horvath, Lena, Untergasser, Gerold, Kuempers, Christiane, Fotakis, Georgios, Panizzolo, Elisa, Martowicz, Agnieszka, Trebo, Manuel, Pall, Georg, Gamerith, Gabriele, Sykora, Martina, Augustin, Florian, Schmitz, Katja, Finotello, Francesca, Rieder, Dietmar, Perner, Sven, Sopper, Sieghart, Wolf, Dominik, Pircher, Andreas, and Trajanoski, Zlatko

Published
2022
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2. Hepatobiliary Adverse Drug Reactions Associated With Remdesivir: The WHO International Pharmacovigilance Study

Author

Kim, Min Seo, Jung, Se Yong, Lee, Seung Won, Li, Han, Koyanagi, Ai, Kronbichler, Andreas, Dragioti, Elena, Tizaoui, Kalthoum, Wasuwanich, Paul, Hong, Sung Hwi, Ghayda, Ramy Abou, Yoo, Hae Won, Kim, Hanna, Jacob, Louis, Salem, Joe-Elie, Kostev, Karel, Shin, Youn Ho, Kim, So Young, Gamerith, Gabriele, Yon, Dong Keon, Shin, Jae Il, and Smith, Lee

Published
2021
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3. Tea Consumption and Risk of Cancer: An Umbrella Review and Meta-Analysis of Observational Studies

Author

Kim, Tai Lim, Jeong, Gwang Hun, Yang, Jae Won, Lee, Keum Hwa, Kronbichler, Andreas, van der Vliet, Hans J, Grosso, Giuseppe, Galvano, Fabio, Aune, Dagfinn, Kim, Jong Yeob, Veronese, Nicola, Stubbs, Brendon, Solmi, Marco, Koyanagi, Ai, Hong, Sung Hwi, Dragioti, Elena, Cho, Eunyoung, de Rezende, Leandro F M, Giovannucci, Edward L, Shin, Jae Il, and Gamerith, Gabriele

Published
2020
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4. Consumption of Fish and ω-3 Fatty Acids and Cancer Risk: An Umbrella Review of Meta-Analyses of Observational Studies

Author

Lee, Keum Hwa, Seong, Hyo Jin, Kim, Gaeun, Jeong, Gwang Hun, Kim, Jong Yeob, Park, Hyunbong, Jung, Eunyoung, Kronbichler, Andreas, Eisenhut, Michael, Stubbs, Brendon, Solmi, Marco, Koyanagi, Ai, Hong, Sung Hwi, Dragioti, Elena, de Rezende, Leandro Fórnias Machado, Jacob, Louis, Keum, NaNa, van der Vliet, Hans J, Cho, Eunyoung, Veronese, Nicola, Grosso, Giuseppe, Ogino, Shuji, Song, Mingyang, Radua, Joaquim, Jung, Sun Jae, Thompson, Trevor, Jackson, Sarah E, Smith, Lee, Yang, Lin, Oh, Hans, Choi, Eun Kyoung, Shin, Jae Il, Giovannucci, Edward L, and Gamerith, Gabriele

Published
2020
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6. Whole stromal fibroblast signature is linked to specific chemokine and immune infiltration patterns and to improved survival in NSCLC

Author

Koeck, Stefan, primary, Amann, Arno, additional, Kern, Johan, additional, Zwierzina, Marit, additional, Lorenz, Edith, additional, Sopper, Sieghart, additional, Zwierzina, Heinz, additional, Mildner, Finn, additional, Sykora, Martina, additional, Sprung, Susanne, additional, Hackl, Hubert, additional, Augustin, Florian, additional, Maier, Hubert T., additional, Pircher, Andreas, additional, Pall, Georg, additional, Wolf, Dominik, additional, and Gamerith, Gabriele, additional

Published
2023
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10. Abstract 6668: Immune infiltrate co-occurrence and neoantigen similarity are prognostic factors in early stage NSCLC

Author

Sykora, Martina M., primary, Pugh, Jason, additional, Li, Bailiang, additional, Mildner, Finn O., additional, Hackl, Hubert, additional, Amann, Arno, additional, Nocera, Fabienne I., additional, Pyke, Rachel M., additional, McDaniel, Lee, additional, Abbott, Charles W., additional, Boyle, Sean M., additional, Chen, Richard O., additional, Wolf, Dominik, additional, Sopper, Sieghart, additional, and Gamerith, Gabriele, additional

Published
2023
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11. Real-world Data of Palliative First-line Checkpoint Inhibitor Therapy for Head and Neck Cancer

Author

WAGNER, SANDRO M., primary, MAGNES, TERESA, additional, MELCHARDT, THOMAS, additional, KIEM, DOMINIK, additional, WEISS, LUKAS, additional, NEUREITER, DANIEL, additional, WAGNER, CHRISTINA, additional, ARETIN, MARIE-BERNADETTE, additional, NEMEC, STEFAN, additional, GAMERITH, GABRIELE, additional, PALL, GEORG, additional, GREIL, RICHARD, additional, and FUEREDER, THORSTEN, additional

Published
2023
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14. High-resolution single-cell atlas reveals diversity and plasticity of tumor-associated neutrophils in non-small cell lung cancer

Author

Salcher, Stefan, Sturm, Gregor, Horvath, Lena, Untergasser, Gerold, Kuempers, Christiane, Fotakis, Georgios, Panizzolo, Elisa, Martowicz, Agnieszka, Trebo, Manuel, Pall, Georg, Gamerith, Gabriele, Sykora, Martina, Augustin, Florian, Schmitz, Katja, Finotello, Francesca, Rieder, Dietmar, Perner, Sven, Sopper, Sieghart, Wolf, Dominik, Pircher, Andreas, and Trajanoski, Zlatko

Subjects
Neutrophils, single-cell, NSCLC, data integration
Abstract

This archive contains all data required to reproduce the single-cell data integration and analysis for the paper High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer (https://doi.org/10.1101/2022.05.09.491204 ) In particular, it contains the following files: build_atlas_results.tar.xz contains all intermediate result of the first part of the workflow (data integration and annotation). It is also required to run the second part of the workflow without re-running the data integration steps. containers.tar.xz contains singularity containers that package all software dependencies required to reproduce the analyses core_atlas_scanvi_model.tar.gz contains a scArches model and the corresponding h5ad file (with only highly variable genes). You can use this to project your own data onto the atlas with scArches downstream_anslysis_results.tar.xz contains the results from the second part of the workflow, including an executed HTML version of all jupyter and rmarkdown notebooks that were used to derive the figures from the paper input_data.tar.xz contains the preprocessed input data (e.g. h5ad files for each individual dataset). It is required to run the first part of the analysis workflow. If you want to download the atlas to perform you own analyses, please refer to the CZI Cell-x-gene portal. From there, you can download h5ad (scverse) and rds (Seurat) files with standardized metadata.

Published
2022
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17. Association of baseline soluble immune checkpoints with the risk of relapse in PR3-ANCA vasculitis following induction of remission

Author

Gamerith, Gabriele, primary, Mildner, Finn, additional, Merkel, Peter A, additional, Harris, Kristina, additional, Cooney, Laura, additional, Lim, Noha, additional, Spiera, Robert, additional, Seo, Philip, additional, Langford, Carol A, additional, Hoffman, Gary S, additional, St Clair, E William, additional, Fervenza, Fernando C, additional, Monach, Paul, additional, Ytterberg, Steven R, additional, Geetha, Duvuru, additional, Amann, Arno, additional, Wolf, Dominik, additional, Specks, Ulrich, additional, Stone, John H, additional, and Kronbichler, Andreas, additional

Published
2022
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20. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer

Author

Salcher, Stefan, primary, Sturm, Gregor, additional, Horvath, Lena, additional, Untergasser, Gerold, additional, Fotakis, Georgios, additional, Panizzolo, Elisa, additional, Martowicz, Agnieszka, additional, Pall, Georg, additional, Gamerith, Gabriele, additional, Sykora, Martina, additional, Augustin, Florian, additional, Schmitz, Katja, additional, Finotello, Francesca, additional, Rieder, Dietmar, additional, Sopper, Sieghart, additional, Wolf, Dominik, additional, Pircher, Andreas, additional, and Trajanoski, Zlatko, additional

Published
2022
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22. Molecular Characteristics of Radon Associated Lung Cancer Highlights MET Alterations

Author

Gamerith, Gabriele, Kloppenburg, Marcel, Mildner, Finn, Amann, Arno, Merkelbach-Bruse, Sabine, Heydt, Carina, Siemanowski, Janna, Buettner, Reinhard, Fiegl, Michael, Manzl, Claudia, Pall, Georg, Gamerith, Gabriele, Kloppenburg, Marcel, Mildner, Finn, Amann, Arno, Merkelbach-Bruse, Sabine, Heydt, Carina, Siemanowski, Janna, Buettner, Reinhard, Fiegl, Michael, Manzl, Claudia, and Pall, Georg

Abstract

Simple Summary Lung cancer (LC) is the leading cause of cancer death worldwide. After smoking, one of the most prominent risk factors for LC development is radon (Rn) exposure. In our study we analysed and compared the genetic landscape of LC patients from a Rn exposed village with local matched non-exposed patients. Within the concordant genetic landscape, an increase in genetic MET proto-oncogene, receptor tyrosine kinase (MET) alteration in the Rn-exposed cohort was monitored, underlining the importance of routine MET testing and potential to enable a more effective treatment for this specific subgroup. Effective targeted treatment strategies resulted from molecular profiling of lung cancer with distinct prevalent mutation profiles in smokers and non-smokers. Although Rn is the second most important risk factor, data for Rn-dependent driver events are limited. Therefore, a Rn-exposed cohort of lung cancer patients was screened for oncogenic drivers and their survival and genetic profiles were compared with data of the average regional population. Genetic alterations were analysed in 20 Rn-exposed and 22 histologically matched non-Rn exposed LC patients using targeted Next generation sequencing (NGS) and Fluorescence In Situ Hybridization (FISH). Sufficient material and sample quality could be obtained in 14/27 non-exposed versus 17/22 Rn-exposed LC samples. Survival was analysed in comparison to a histologically and stage-matched regional non-exposed lung cancer cohort (n = 51) for hypothesis generating. Median overall survivals were 83.02 months in the Rn-exposed and 38.7 months in the non-exposed lung cancer cohort (p = 0.22). Genetic alterations of both patient cohorts were in high concordance, except for an increase in MET alterations and a decrease in TP53 mutations in the Rn-exposed patients in this small hypothesis generating study.

Published
2022

23. Functional Outcomes in Head and Neck Cancer Patients

Author

Riechelmann, Herbert, primary, Dejaco, Daniel, additional, Steinbichler, Teresa Bernadette, additional, Lettenbichler-Haug, Anna, additional, Anegg, Maria, additional, Ganswindt, Ute, additional, Gamerith, Gabriele, additional, and Riedl, David, additional

Published
2022
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24. Association of baseline soluble immune checkpoints with the risk of relapse in PR3-ANCA vasculitis following induction of remission.

Author

Gamerith, Gabriele, Mildner, Finn, Merkel, Peter A., Harris, Kristina, Cooney, Laura, Lim, Noha, Spiera, Robert, Seo, Philip, Langford, Carol A., Hoffman, Gary S., St Clair, E. William, Fervenza, Fernando C., Monach, Paul, Ytterberg, Steven R., Geetha, Duvuru, Amann, Arno, Wolf, Dominik, Specks, Ulrich, Stone, John H., and Kronbichler, Andreas

Published
2023
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26. Consumption of fish and omega-3 fatty acids and cancer risk: an umbrella review of meta-analyses of observational studies

Author

Lee, Keum Hwa, Seong, Hyo Jin, Kim, Gaeun, Jeong, Gwang Hun, Kim, Jong Yeob, Park, Hyunbong, Jung, Eunyoung, Kronbichler, Andreas, Eisenhut, Michael, Stubbs, Brendon, Solmi, Marco, Koyanagi, Ai, Hong, Sung Hwi, Dragioti, Elena, de Rezende, Leandro F. M., Jacob, Louis, Keum, NaNa, van der Vliet, Hans J., Cho, Eunyoung, Veronese, Nicola, Grosso, Giuseppe, Ogino, Shuji, Song, Mingyang, Radua, Joaquim, Jung, Sun Jae, Thompson, Trevor, Jackson, Sarah E., Smith, Lee, Yang, Lin, Oh, Hans, Choi, Eun Kyoung, Shin, Jae Il, Giovannucci, Edward L., and Gamerith, Gabriele

Abstract

Multiple studies have suggested that ω-3 fatty acid intake may have a protective effect on cancer risk; however, its true association with cancer risk remains controversial. We performed an umbrella review of meta-analyses to summarize and evaluate the evidence for the association between ω-3 fatty acid intake and cancer outcomes. We searched PubMed, Embase, and the Cochrane Database of Systematic Reviews from inception to December 1, 2018. We included meta-analyses of observational studies that examined associations between intake of fish or ω-3 fatty acid and cancer risk (gastrointestinal, liver, breast, gynecologic, prostate, brain, lung, and skin) and determined the level of evidence of associations. In addition, we appraised the quality of the evidence of significant meta-analyses by using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) system. We initially screened 598 articles, and 15 articles, including 57 meta-analyses, were eligible. Among 57 meta-analyses, 15 reported statistically significant results. We found that 12 meta-analyses showed weak evidence of an association between ω-3 fatty acid intake and risk of the following types of cancer: liver cancer (n = 4 of 6), breast cancer (n = 3 of 14), prostate cancer (n = 3 of 11), and brain tumor (n = 2 of 2). In the other 3 meta-analyses, studies of endometrial cancer and skin cancer, there were no assessable data for determining the evidence levels. No meta-analysis showed convincing, highly suggestive, or suggestive evidence of an association. In the sensitivity analysis of meta-analyses by study design, we found weak associations between ω-3 fatty acid intake and breast cancer risk in cohort studies, but no statistically significant association in case-control studies. However, the opposite results were found in case of brain tumor risk. Although ω-3 fatty acids have been studied in several meta-analyses with regard to a wide range of cancer outcomes, only weak associations were identified in some cancer types, with several limitations. Considering the nonsignificant or weak evidence level, clinicians and researchers should cautiously interpret reported associations between ω-3 fatty acid consumption and cancer risks.

Published
2020

30. Genetic variations in MicroRNA genes and cancer risk: A field synopsis and meta‐analysis

Author

Park, Jae Hyon, primary, Jeong, Gwang Hun, additional, Lee, Kwang Seob, additional, Lee, Keum Hwa, additional, Suh, Jin‐Soon, additional, Eisenhut, Michael, additional, Vliet, Hans J., additional, Kronbichler, Andreas, additional, Stubbs, Brendon, additional, Solmi, Marco, additional, Dragioti, Elena, additional, Koyanagi, Ai, additional, Shin, Jae Il, additional, and Gamerith, Gabriele, additional

Published
2020
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31. Genetic variations in MicroRNA genes and cancer risk: A field synopsis and meta-analysis

Author

Park, Jae Hyon, Jeong, Gwang Hun, Lee, Kwang Seob, Lee, Keum Hwa, Suh, Jin-Soon, Eisenhut, Michael, Vliet, Hans J. van der, Kronbichler, Andreas, Stubbs, Brendon, Solmi, Marco, Dragioti, Elena, Koyanagi, Ai, Shin, Jae Il, Gamerith, Gabriele, Park, Jae Hyon, Jeong, Gwang Hun, Lee, Kwang Seob, Lee, Keum Hwa, Suh, Jin-Soon, Eisenhut, Michael, Vliet, Hans J. van der, Kronbichler, Andreas, Stubbs, Brendon, Solmi, Marco, Dragioti, Elena, Koyanagi, Ai, Shin, Jae Il, and Gamerith, Gabriele

Abstract

Background Cancer risk has been associated with certain gene variations in microRNA (miRNA), but conflicting evidence warrants re-assessing of significant results in meta-analyses. We summarized published meta-analyses that assess the associations between miRNA polymorphism and cancers to show the validity of the findings. Method We searched PubMed and investigated the results of meta-analyses published through November 2018. We re-assessed the results based on false-positive report probability (FPRP) to test the noteworthiness of the associations. Results Sixty-eight miRNA polymorphisms in 45 meta-analyses associated with cancer were included. Four (7.4%) and sixteen (25.0%) single nucleotide polymorphisms (SNPs) were noteworthy (FPRP < 0.2) at a prior probability of 0.001 for interesting candidate genes and a statistical power to detect an odds ratio (OR) of 1.1 and 1.5, respectively. The four miRNA SNPs noteworthy at an OR of 1.1 were as follows: miR-146a/rs2910164 Cvs.G; miR-27a/rs895819 Cvs.T; miR-423/rs6505162 Cvs.A; and miR-605/rs2043556 Cvs.T. The 16 SNPs noteworthy at an OR of 1.5 include the four genotype comparisons at an OR of 1.1, and the additional 12 genotype comparisons were as follows: miR-196a2/rs11614913 Tvs.C; miR-27a/rs895819 GGvs.AA + AG; miR-196a2/rs11614913 C vs.T; miR-146a/rs2910164 Gvs.C; miR-196a2/rs11614913 Tvs.C; miR-146a/rs2910164 Cvs.G; miR-499/rs3746444 homozygous model; miR-146a/rs2910164 CCvs.GG + GC; miR-499/rs3746444 TCvs.TT; miR-499/rs3746444 GAvs.AA; miR-146a/rs2910164 CCvs.GG; and miR-499/rs3746444 Gvs.A. No association was noteworthy at a prior probability of 0.000001. Conclusion Out of 68 published associations of miRNA polymorphisms with cancer, sixteen have shown noteworthiness in our re-assessing meta-analysis. Our findings summarize the results of meta-analyses on the association of cancer with SNPs and underline the importance of interpreting results with caution.

Published
2020
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34. Hyperprogressive Disease during Anti-PD-1 (PDCD1) / PD-L1 (CD274) Therapy: A Systematic Review and Meta-Analysis

Author

Kim, Jong Yeob, primary, Lee, Keum Hwa, additional, Kang, Jeonghyun, additional, Borcoman, Edith, additional, Saada-Bouzid, Esma, additional, Kronbichler, Andreas, additional, Hong, Sung Hwi, additional, de Rezende, Leandro Fórnias Machado, additional, Ogino, Shuji, additional, Keum, Nana, additional, Song, Mingyang, additional, Luchini, Claudio, additional, van der Vliet, Hans J., additional, Shin, Jae Il, additional, and Gamerith, Gabriele, additional

Published
2019
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36. Nuclear receptor NR2F6 inhibition potentiates responses to PD-L1/PD-1 cancer immune checkpoint blockade

Author

Klepsch, Victoria, primary, Hermann-Kleiter, Natascha, additional, Do-Dinh, Patricia, additional, Jakic, Bojana, additional, Offermann, Anne, additional, Efremova, Mirjana, additional, Sopper, Sieghart, additional, Rieder, Dietmar, additional, Krogsdam, Anne, additional, Gamerith, Gabriele, additional, Perner, Sven, additional, Tzankov, Alexandar, additional, Trajanoski, Zlatko, additional, Wolf, Dominik, additional, and Baier, Gottfried, additional

Published
2018
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37. 3D-cultivation of NSCLC cell lines induce gene expression alterations of key cancer-associated pathways and mimicin-vivoconditions

Author

Gamerith, Gabriele, primary, Rainer, Johannes, additional, Huber, Julia M., additional, Hackl, Hubert, additional, Trajanoski, Zlatko, additional, Koeck, Stefan, additional, Lorenz, Edith, additional, Kern, Johann, additional, Kofler, Reinhard, additional, Kelm, Jens M., additional, Zwierzina, Heinz, additional, and Amann, Arno, additional

Published
2017
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39. Development of a 3D angiogenesis model to study tumour – endothelial cell interactions and the effects of anti-angiogenic drugs

Author

Amann, Arno, primary, Zwierzina, Marit, additional, Koeck, Stefan, additional, Gamerith, Gabriele, additional, Pechriggl, Elisabeth, additional, Huber, Julia M., additional, Lorenz, Edith, additional, Kelm, Jens M., additional, Hilbe, Wolfgang, additional, Zwierzina, Heinz, additional, and Kern, Johann, additional

Published
2017
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47. Emergency diagnosis of lung cancer: An international problem.

Author

Newsom-Davis, Thomas, primary, Berardi, Rossana, additional, Cassidy, Norah, additional, Coate, Linda, additional, Figueiredo, Ana, additional, Gamerith, Gabriele, additional, Giblin, Gareth, additional, Jakopović, Marko, additional, Van Der Leest, Cor, additional, Pouessel, Damien, additional, Tiseo, Marcello, additional, Toffart, Anne Claire, additional, and Hughes, Cathy, additional

Published
2015
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48. ITOC2 – 034. Development of a 3D cell culture model for the investigation of cancer cell/immune cell interactions

Author

Amann Arno, Lorenz Edith, Britsche Mario, Gamerith Gabriele, Huber Julia, Knab Annabella, Köck Stefan, Zwierzina Heinz, and Zwierzina Marit

Subjects
Cancer Research, Cell, Biology, Peripheral blood mononuclear cell, Cell biology, 3D cell culture, medicine.anatomical_structure, Oncology, Cell culture, Cancer cell, medicine, Cytotoxic T cell, Viability assay, Cytometry
Abstract

Background Recent studies have shown the obvious interaction between cancer cells and immune cells. These effects can be hardly studied in conventional culture systems using cell monolayers. Therefore, alternative in vitro models are required. We describe a novel 3D cell culture model and a 3D migration assay for investigating cancer cell/immune cell interactions. Methods A multi-well hanging drops system was used to produce 3D tumour spheres. The human NSCLC cell lines A549, Calu-6 and Colo699 were incubated for 6 and 7 days in the hanging drops to form spheroids. On day 5, peripheral blood mononuclear cells (PBMC) were added either with or without interleukin-2 (IL-2). Viability was investigated via flowing cytometry. Invasion of PBMC into the tumour spheres was measured by performing immunohistochemistry. Results No effect on cell viability was observed in A549 and Colo699 spheroids. In Calu-6 spheroids, a significant PBMC induced cytotoxic effect was measured, what was even stronger under IL-2 stimulation. Immunohistochemical staining revealed PBMC infiltration in all three cell lines. Under IL-2 stimulation, infiltration of PBMC increased in Calu-6 and Colo699 spheroids. Conclusion This work provides evidence that our 3D co-culture model is a reliable and effective approach to study interactions between cancer cells and immune cells. Additionally, we were able to establish for the first time an innovative ex vivo infiltration assay based on 3D microtissues.

Published
2015
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