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Hornsteiner F, Vierthaler J, Strandt H, Resag A, Fu Z, Ausserhofer M, Tripp CH, Dieckmann S, Kanduth M, Farrand K, Bregar S, Nemati N, Hermann-Kleiter N, Seretis A, Morla S, Mullins D, Finotello F, Trajanoski Z, Wollmann G, Ronchese F, Schmitz M, Hermans IF, Stoitzner P. Tumor-targeted therapy with BRAF-inhibitor recruits activated dendritic cells to promote tumor immunity in melanoma. J Immunother Cancer 2024; 12:e008606. [PMID: 38631706 PMCID: PMC11029477 DOI: 10.1136/jitc-2023-008606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Tumor-targeted therapy causes impressive tumor regression, but the emergence of resistance limits long-term survival benefits in patients. Little information is available on the role of the myeloid cell network, especially dendritic cells (DC) during tumor-targeted therapy. METHODS Here, we investigated therapy-mediated immunological alterations in the tumor microenvironment (TME) and tumor-draining lymph nodes (LN) in the D4M.3A preclinical melanoma mouse model (harboring the V-Raf murine sarcoma viral oncogene homolog B (BRAF)V600E mutation) by using high-dimensional multicolor flow cytometry in combination with multiplex immunohistochemistry. This was complemented with RNA sequencing and cytokine quantification to characterize the immune status of the tumors. The importance of T cells during tumor-targeted therapy was investigated by depleting CD4+ or CD8+ T cells in tumor-bearing mice. Tumor antigen-specific T-cell responses were characterized by performing in vivo T-cell proliferation assays and the contribution of conventional type 1 DC (cDC1) to T-cell immunity during tumor-targeted therapy was assessed using Batf3-/- mice lacking cDC1. RESULTS Our findings reveal that BRAF-inhibitor therapy increased tumor immunogenicity, reflected by an upregulation of genes associated with immune activation. The T cell-inflamed TME contained higher numbers of activated cDC1 and cDC2 but also inflammatory CCR2-expressing monocytes. At the same time, tumor-targeted therapy enhanced the frequency of migratory, activated DC subsets in tumor-draining LN. Even more, we identified a cDC2 population expressing the Fc gamma receptor I (FcγRI)/CD64 in tumors and LN that displayed high levels of CD40 and CCR7 indicating involvement in T cell-mediated tumor immunity. The importance of cDC2 is underlined by just a partial loss of therapy response in a cDC1-deficient mouse model. Both CD4+ and CD8+ T cells were essential for therapy response as their respective depletion impaired therapy success. On resistance development, the tumors reverted to an immunologically inert state with a loss of DC and inflammatory monocytes together with the accumulation of regulatory T cells. Moreover, tumor antigen-specific CD8+ T cells were compromised in proliferation and interferon-γ-production. CONCLUSION Our results give novel insights into the remodeling of the myeloid landscape by tumor-targeted therapy. We demonstrate that the transient immunogenic tumor milieu contains more activated DC. This knowledge has important implications for the development of future combinatorial therapies.
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Affiliation(s)
- Florian Hornsteiner
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Janine Vierthaler
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Helen Strandt
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Antonia Resag
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Zhe Fu
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Markus Ausserhofer
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Christoph H Tripp
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sophie Dieckmann
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Kanduth
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Kathryn Farrand
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Sarah Bregar
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Niloofar Nemati
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Natascha Hermann-Kleiter
- Institute of Cell Genetics, Department for Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Athanasios Seretis
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Sudhir Morla
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - David Mullins
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Francesca Finotello
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Guido Wollmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Franca Ronchese
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Marc Schmitz
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Ian F Hermans
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Patrizia Stoitzner
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
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Nemati N, Boeck N, Lamberti G, Lisandrelli R, Trajanoski Z. Protocol for functional profiling of patient-derived organoids for precision oncology. STAR Protoc 2024; 5:102887. [PMID: 38367233 PMCID: PMC10879781 DOI: 10.1016/j.xpro.2024.102887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/19/2024] Open
Abstract
Functional precision oncology-a strategy based on perturbing primary tumor cells from cancer patients-could provide a road forward for personalized treatment. Here, we present a comprehensive protocol covering generation and culture of patient-derived colorectal organoids, isolation and expansion of tumor-infiltrating lymphocytes (TILs), and isolation and culture of peripheral blood mononuclear cells (PBMCs). With this protocol, samples fulfilling the demands for performing multi-omics analysis, e.g., RNA sequencing (RNA-seq), whole-exome sequencing (WES), single-cell RNA sequencing (scRNA-seq), and (phospho-)proteomics, can be generated. For complete details on the use and execution of this protocol, please refer to Plattner et al. (2023).1.
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Affiliation(s)
- Niloofar Nemati
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Boeck
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Giorgia Lamberti
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Rebecca Lisandrelli
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria.
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Horvath L, Puschmann C, Scheiber A, Martowicz A, Sturm G, Trajanoski Z, Wolf D, Pircher A, Salcher S. Beyond binary: bridging neutrophil diversity to new therapeutic approaches in NSCLC. Trends Cancer 2024:S2405-8033(24)00010-4. [PMID: 38360439 DOI: 10.1016/j.trecan.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Neutrophils represent the most abundant myeloid cell subtype in the non-small-cell lung cancer (NSCLC) tumor microenvironment (TME). By anti- or protumor polarization, they impact multiple aspects of tumor biology and affect sensitivity to conventional therapies and immunotherapies. Single-cell RNA sequencing (scRNA-seq) analyses have unraveled an extensive neutrophil heterogeneity, helping our understanding of their pleiotropic role. In this review we summarize recent data and models on tumor-associated neutrophil (TAN) biology, focusing on the diversity that evolves in response to tumor-intrinsic cues. We categorize available transcriptomic profiles from different cancer entities into a defined set of neutrophil subclusters with distinct phenotypic properties, to step beyond the traditional binary N1/2 classification. Finally, we discuss potential ways to exploit these neutrophil states in the setting of anticancer therapy.
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Affiliation(s)
- Lena Horvath
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Constanze Puschmann
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Alexandra Scheiber
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Agnieszka Martowicz
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria; Boehringer Ingelheim International Pharma GmbH & Co KG, Biberach, Germany
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Wolf
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Andreas Pircher
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Stefan Salcher
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria.
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Chiriac MT, Hracsko Z, Günther C, Gonzalez-Acera M, Atreya R, Stolzer I, Wittner L, Dressel A, Schickedanz L, Gamez-Belmonte R, Erkert L, Hundorfean G, Zundler S, Rath T, Vetrano S, Danese S, Sturm G, Trajanoski Z, Kühl AA, Siegmund B, Hartmann A, Wirtz S, Siebler J, Finotto S, Becker C, Neurath MF. IL-20 controls resolution of experimental colitis by regulating epithelial IFN/STAT2 signalling. Gut 2024; 73:282-297. [PMID: 37884352 PMCID: PMC10850655 DOI: 10.1136/gutjnl-2023-329628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 09/10/2023] [Indexed: 10/28/2023]
Abstract
OBJECTIVE We sought to investigate the role of interleukin (IL)-20 in IBD and experimental colitis. DESIGN Experimental colitis was induced in mice deficient in components of the IL-20 and signal transducer and activator of transcription (STAT)2 signalling pathways. In vivo imaging, high-resolution mini-endoscopy and histology were used to assess intestinal inflammation. We further used RNA-sequencing (RNA-Seq), RNAScope and Gene Ontology analysis, western blot analysis and co-immunoprecipitation, confocal microscopy and intestinal epithelial cell (IEC)-derived three-dimensional organoids to investigate the underlying molecular mechanisms. Results were validated using samples from patients with IBD and non-IBD control subjects by a combination of RNA-Seq, organoids and immunostainings. RESULTS In IBD, IL20 levels were induced during remission and were significantly higher in antitumour necrosis factor responders versus non-responders. IL-20RA and IL-20RB were present on IECs from patients with IBD and IL-20-induced STAT3 and suppressed interferon (IFN)-STAT2 signalling in these cells. In IBD, experimental dextran sulfate sodium (DSS)-induced colitis and mucosal healing, IECs were the main producers of IL-20. Compared with wildtype controls, Il20-/-, Il20ra-/- and Il20rb-/- mice were more susceptible to experimental DSS-induced colitis. IL-20 deficiency was associated with increased IFN/STAT2 activity in mice and IFN/STAT2-induced necroptotic cell death in IEC-derived organoids could be markedly blocked by IL-20. Moreover, newly generated Stat2ΔIEC mice, lacking STAT2 in IECs, were less susceptible to experimental colitis compared with wildtype controls and the administration of IL-20 suppressed colitis activity in wildtype animals. CONCLUSION IL-20 controls colitis and mucosal healing by interfering with the IFN/STAT2 death signalling pathway in IECs. These results indicate new directions for suppressing gut inflammation by modulating IL-20-controlled STAT2 signals.
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Affiliation(s)
- Mircea Teodor Chiriac
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
| | - Zsuzsanna Hracsko
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Claudia Günther
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
| | - Miguel Gonzalez-Acera
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Raja Atreya
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, and the Ludwig Demling Endoscopy Center of Excellence, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Iris Stolzer
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Leonie Wittner
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Anja Dressel
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Laura Schickedanz
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Reyes Gamez-Belmonte
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Lena Erkert
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Gheorghe Hundorfean
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, and the Ludwig Demling Endoscopy Center of Excellence, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Sebastian Zundler
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
| | - Timo Rath
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, and the Ludwig Demling Endoscopy Center of Excellence, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Stefania Vetrano
- IBD Center, Department of Gastroenterology, IRCCS Humanitas Research Hospital, Rozzano, Italy
- Pieve Emanuele, Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Silvio Danese
- Department of Gastroenterology and Digestive Endoscopy & Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milano, Italy
- Faculty of Medicine, Universita Vita Salute San Raffaele, Milano, Italy
| | - Gregor Sturm
- Medical University of Innsbruck, Biocenter, Institute of Bioinformatics, Innsbruck, Austria
| | - Zlatko Trajanoski
- Medical University of Innsbruck, Biocenter, Institute of Bioinformatics, Innsbruck, Austria
| | - Anja A Kühl
- iPATH.Berlin, Core Unit of Charité, Campus Benjamin Franklin, Charite Universitatsmedizin Berlin, Berlin, Germany
| | - Britta Siegmund
- Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Medical Department, Division of Gastroenterology, Infectious Diseases and Rheumatology, Campus Benjamin Franklin, Charite Universitatsmedizin Berlin, Berlin, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Stefan Wirtz
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
| | - Jürgen Siebler
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, and the Ludwig Demling Endoscopy Center of Excellence, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Susetta Finotto
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
- Department of Molecular Pneumology, University Hospital Erlangen, Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany
| | - Christoph Becker
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
| | - Markus F Neurath
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, and the Ludwig Demling Endoscopy Center of Excellence, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
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Plattner C, Lamberti G, Blattmann P, Kirchmair A, Rieder D, Loncova Z, Sturm G, Scheidl S, Ijsselsteijn M, Fotakis G, Noureen A, Lisandrelli R, Böck N, Nemati N, Krogsdam A, Daum S, Finotello F, Somarakis A, Schäfer A, Wilflingseder D, Gonzalez Acera M, Öfner D, Huber LA, Clevers H, Becker C, Farin HF, Greten FR, Aebersold R, de Miranda NF, Trajanoski Z. Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer. iScience 2023; 26:108399. [PMID: 38047086 PMCID: PMC10692669 DOI: 10.1016/j.isci.2023.108399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/21/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Precision oncology approaches for patients with colorectal cancer (CRC) continue to lag behind other solid cancers. Functional precision oncology-a strategy that is based on perturbing primary tumor cells from cancer patients-could provide a road forward to personalize treatment. We extend this paradigm to measuring proteome activity landscapes by acquiring quantitative phosphoproteomic data from patient-derived organoids (PDOs). We show that kinase inhibitors induce inhibitor- and patient-specific off-target effects and pathway crosstalk. Reconstruction of the kinase networks revealed that the signaling rewiring is modestly affected by mutations. We show non-genetic heterogeneity of the PDOs and upregulation of stemness and differentiation genes by kinase inhibitors. Using imaging mass-cytometry-based profiling of the primary tumors, we characterize the tumor microenvironment (TME) and determine spatial heterocellular crosstalk and tumor-immune cell interactions. Collectively, we provide a framework for inferring tumor cell intrinsic signaling and external signaling from the TME to inform precision (immuno-) oncology in CRC.
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Affiliation(s)
- Christina Plattner
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Giorgia Lamberti
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Peter Blattmann
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Alexander Kirchmair
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Zuzana Loncova
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Scheidl
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Marieke Ijsselsteijn
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Georgios Fotakis
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Asma Noureen
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Rebecca Lisandrelli
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Böck
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Niloofar Nemati
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Anne Krogsdam
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Sophia Daum
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Antonios Somarakis
- Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Alexander Schäfer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Miguel Gonzalez Acera
- Department of Medicine 1, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Dietmar Öfner
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas A. Huber
- Biocenter, Institute of Cell Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Hans Clevers
- Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Christoph Becker
- Department of Medicine 1, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Henner F. Farin
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, a partnership with DKFZ Heidelberg, Frankfurt/Mainz, Germany
| | - Florian R. Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, a partnership with DKFZ Heidelberg, Frankfurt/Mainz, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Noel F.C.C. de Miranda
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
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6
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Boeck N, Trajanoski Z, Galluzzi L. Bacterial antigens unleash tumor-targeting immunity. Cell Host Microbe 2023; 31:1945-1947. [PMID: 38096784 DOI: 10.1016/j.chom.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023]
Abstract
The composition of the gut microbiome has been shown to influence disease outcome in patients with colorectal cancer (CRC). In a recent Nature Biotechnology article, Wang et al. demonstrate that killing CRC-associated bacteria with a liposomal antibiotic elicits CRC-targeting immune responses of therapeutic relevance as a consequence of epitope mimicry.
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Affiliation(s)
- Nina Boeck
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
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7
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Sahanic S, Hilbe R, Dünser C, Tymoszuk P, Löffler-Ragg J, Rieder D, Trajanoski Z, Krogsdam A, Demetz E, Yurchenko M, Fischer C, Schirmer M, Theurl M, Lener D, Hirsch J, Holfeld J, Gollmann-Tepeköylü C, Zinner CP, Tzankov A, Zhang SY, Casanova JL, Posch W, Wilflingseder D, Weiss G, Tancevski I. SARS-CoV-2 activates the TLR4/MyD88 pathway in human macrophages: A possible correlation with strong pro-inflammatory responses in severe COVID-19. Heliyon 2023; 9:e21893. [PMID: 38034686 PMCID: PMC10686889 DOI: 10.1016/j.heliyon.2023.e21893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 09/26/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Background Toll-like receptors (TLRs) play a pivotal role in the immunologic response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Exaggerated inflammatory response of innate immune cells, however, may drive morbidity and death in Coronavirus disease 19 (COVID-19). Objective We investigated the engagement of SARS-CoV-2 with TLR4 in order to better understand how to tackle hyperinflammation in COVID-19. Methods We combined RNA-sequencing data of human lung tissue and of bronchoalveolar lavage fluid cells derived from COVID-19 patients with functional studies in human macrophages using SARS-CoV-2 spike proteins and viable SARS-CoV-2. Pharmacological inhibitors as well as gene editing with CRISPR/Cas9 were used to delineate the signalling pathways involved. Results We found TLR4 to be the most abundantly upregulated TLR in human lung tissue irrespective of the underlying pathology. Accordingly, bronchoalveolar lavage fluid cells from patients with severe COVID-19 showed an NF-κB-pathway dominated immune response, whereas they were mostly defined by type I interferon signalling in moderate COVID-19. Mechanistically, we found the Spike ectodomain, but not receptor binding domain monomer to induce TLR4-dependent inflammation in human macrophages. By using pharmacological inhibitors as well as CRISPR/Cas9 deleted macrophages, we identify SARS-CoV-2 to engage canonical TLR4-MyD88 signalling. Importantly, we demonstrate that TLR4 blockage prevents exaggerated inflammatory responses in human macrophages infected with different SARS-CoV-2 variants, including immune escape variants B.1.1.7.-E484K and B.1.1.529 (omicron). Conclusion Our study critically extends the current knowledge on TLR-mediated hyperinflammatory responses to SARS-CoV-2 in human macrophages, paving the way for novel approaches to tackle severe COVID-19. Take-home message Our study combining human lung transcriptomics with functional studies in human macrophages clearly supports the design and development of TLR4 - directed therapeutics to mitigate hyperinflammation in severe COVID-19.
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Affiliation(s)
- Sabina Sahanic
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Richard Hilbe
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Christina Dünser
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Piotr Tymoszuk
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Judith Löffler-Ragg
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Anne Krogsdam
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Egon Demetz
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Maria Yurchenko
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
- The Central Norway Regional Health Authority, St. Olavs Hospital HF, Trondheim, Norway
| | - Christine Fischer
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Schirmer
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Theurl
- Department of Internal Medicine III, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniela Lener
- Department of Internal Medicine III, Medical University of Innsbruck, Innsbruck, Austria
| | - Jakob Hirsch
- Department of Cardiac Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Holfeld
- Department of Cardiac Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Carl P. Zinner
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, 10065, USA
| | - Wilfried Posch
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Austria
| | - Doris Wilflingseder
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Austria
| | - Guenter Weiss
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Ivan Tancevski
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
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8
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García-Mulero S, Fornelino R, Punta M, Lise S, Varela M, del Carpio LP, Moreno R, Costa-García M, Rieder D, Trajanoski Z, Gros A, Alemany R, Piulats JM, Sanz-Pamplona R. Driver mutations in GNAQ and GNA11 genes as potential targets for precision immunotherapy in uveal melanoma patients. Oncoimmunology 2023; 12:2261278. [PMID: 38126027 PMCID: PMC10732647 DOI: 10.1080/2162402x.2023.2261278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/17/2023] [Indexed: 12/23/2023] Open
Abstract
Uveal melanoma (UM) is the most common ocular malignancy in adults. Nearly 95% of UM patients carry the mutually exclusive mutations in the homologous genes GNAQ (amino acid change Q209L/Q209P) and GNA11 (aminoacid change Q209L). UM is located in an immunosuppressed organ and does not suffer immunoediting. Therefore, we hypothesize that driver mutations in GNAQ/11 genes could be recognized by the immune system. Genomic and transcriptomic data from primary uveal tumors were collected from the TCGA-UM dataset (n = 80) and used to assess the immunogenic potential for GNAQ/GNA11 Q209L/Q209P mutations using a variety of tools and HLA type information. All prediction tools showed stronger GNAQ/11 Q209L binding to HLA than GNAQ/11 Q209P. The immunogenicity analysis revealed that Q209L is likely to be presented by more than 73% of individuals in 1000 G databases whereas Q209P is only predicted to be presented in 24% of individuals. GNAQ/11 Q209L showed a higher likelihood to be presented by HLA-I molecules than almost all driver mutations analyzed. Finally, samples carrying Q209L had a higher immune-reactive phenotype. Regarding cancer risk, seven HLA genotypes with low Q209L affinity show higher frequency in uveal melanoma patients than in the general population. However, no clear association was found between any HLA genotype and survival. Results suggest a high potential immunogenicity of the GNAQ/11 Q209L variant that could allow the generation of novel therapeutic tools to treat UM like neoantigen vaccinations.
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Affiliation(s)
- Sandra García-Mulero
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, Barcelona, Spain
- Anatomy Unit, Department of Pathology and Experimental Therapy, and Department of Clinical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Roberto Fornelino
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, Barcelona, Spain
| | - Marco Punta
- Bioinformatics Core, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Stefano Lise
- Bioinformatics Core, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Mar Varela
- Department of Pathology, Bellvitge University Hospital, Barcelona, Spain
| | - Luis P. del Carpio
- Procure Program, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Rafael Moreno
- Procure Program, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Marcel Costa-García
- Procure Program, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Alena Gros
- Tumor Immunology and Immunotherapy, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ramón Alemany
- Procure Program, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | | | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, Barcelona, Spain
- Institute for Health Research Aragon (IISA), ARAID Foundation, Aragon Government, University Hospital Lozano Blesa, Zaragoza, Spain
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9
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Kirchmair A, Nemati N, Lamberti G, Trefny M, Krogsdam A, Siller A, Hörtnagl P, Schumacher P, Sopper S, Sandbichler A, Zippelius A, Ghesquière B, Trajanoski Z. 13C tracer analysis reveals the landscape of metabolic checkpoints in human CD8 + T cell differentiation and exhaustion. Front Immunol 2023; 14:1267816. [PMID: 37928527 PMCID: PMC10620935 DOI: 10.3389/fimmu.2023.1267816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Naïve T cells remain in an actively maintained state of quiescence until activation by antigenic signals, upon which they start to proliferate and generate effector cells to initiate a functional immune response. Metabolic reprogramming is essential to meet the biosynthetic demands of the differentiation process, and failure to do so can promote the development of hypofunctional exhausted T cells. Methods Here we used 13C metabolomics and transcriptomics to study the metabolism of CD8+ T cells in their complete course of differentiation from naïve over stem-like memory to effector cells and in exhaustion-inducing conditions. Results The quiescence of naïve T cells was evident in a profound suppression of glucose oxidation and a decreased expression of ENO1, downstream of which no glycolytic flux was detectable. Moreover, TCA cycle activity was low in naïve T cells and associated with a downregulation of SDH subunits. Upon stimulation and exit from quiescence, the initiation of cell growth and proliferation was accompanied by differential expression of metabolic enzymes and metabolic reprogramming towards aerobic glycolysis with high rates of nutrient uptake, respiration and lactate production. High flux in anabolic pathways imposed a strain on NADH homeostasis, which coincided with engagement of the proline cycle for mitochondrial redox shuttling. With acquisition of effector functions, cells increasingly relied on glycolysis as opposed to oxidative phosphorylation, which was, however, not linked to changes in mitochondrial abundance. In exhaustion, decreased effector function concurred with a reduction in mitochondrial metabolism, glycolysis and amino acid import, and an upregulation of quiescence-associated genes, TXNIP and KLF2, and the T cell suppressive metabolites succinate and itaconate. Discussion Overall, these results identify multiple metabolic features that regulate quiescence, proliferation and effector function, but also exhaustion of CD8+ T cells during differentiation. Thus, targeting these metabolic checkpoints may be a promising therapeutic strategy for both prevention of exhaustion and promotion of stemness of anti-tumor T cells.
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Affiliation(s)
- Alexander Kirchmair
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Niloofar Nemati
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Giorgia Lamberti
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Marcel Trefny
- Department of Biomedicine, Cancer Immunology, University and University Hospital of Basel, Basel, Switzerland
| | - Anne Krogsdam
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
- NGS Core Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Anita Siller
- Central Institute for Blood Transfusion and Immunology, Tirol Kliniken GmbH, Innsbruck, Austria
| | - Paul Hörtnagl
- Central Institute for Blood Transfusion and Immunology, Tirol Kliniken GmbH, Innsbruck, Austria
| | - Petra Schumacher
- Core Facility FACS Sorting, University Clinic for Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Sieghart Sopper
- Core Facility FACS Sorting, University Clinic for Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Alfred Zippelius
- Department of Biomedicine, Cancer Immunology, University and University Hospital of Basel, Basel, Switzerland
| | - Bart Ghesquière
- Laboratory of Applied Mass Spectrometry, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Metabolomics Core Facility Leuven, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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10
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Farin HF, Mosa MH, Ndreshkjana B, Grebbin BM, Ritter B, Menche C, Kennel KB, Ziegler PK, Szabó L, Bollrath J, Rieder D, Michels BE, Kress A, Bozlar M, Darvishi T, Stier S, Kur IM, Bankov K, Kesselring R, Fichtner-Feigl S, Brüne B, Goetze TO, Al-Batran SE, Brandts CH, Bechstein WO, Wild PJ, Weigert A, Müller S, Knapp S, Trajanoski Z, Greten FR. Colorectal Cancer Organoid-Stroma Biobank Allows Subtype-Specific Assessment of Individualized Therapy Responses. Cancer Discov 2023; 13:2192-2211. [PMID: 37489084 PMCID: PMC10551667 DOI: 10.1158/2159-8290.cd-23-0050] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/05/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
In colorectal cancers, the tumor microenvironment plays a key role in prognosis and therapy efficacy. Patient-derived tumor organoids (PDTO) show enormous potential for preclinical testing; however, cultured tumor cells lose important characteristics, including the consensus molecular subtypes (CMS). To better reflect the cellular heterogeneity, we established the colorectal cancer organoid-stroma biobank of matched PDTOs and cancer-associated fibroblasts (CAF) from 30 patients. Context-specific phenotyping showed that xenotransplantation or coculture with CAFs improves the transcriptomic fidelity and instructs subtype-specific stromal gene expression. Furthermore, functional profiling in coculture exposed CMS4-specific therapeutic resistance to gefitinib and SN-38 and prognostic expression signatures. Chemogenomic library screening identified patient- and therapy-dependent mechanisms of stromal resistance including MET as a common target. Our results demonstrate that colorectal cancer phenotypes are encrypted in the cancer epithelium in a plastic fashion that strongly depends on the context. Consequently, CAFs are essential for a faithful representation of molecular subtypes and therapy responses ex vivo. SIGNIFICANCE Systematic characterization of the organoid-stroma biobank provides a resource for context dependency in colorectal cancer. We demonstrate a colorectal cancer subtype memory of PDTOs that is independent of specific driver mutations. Our data underscore the importance of functional profiling in cocultures for improved preclinical testing and identification of stromal resistance mechanisms. This article is featured in Selected Articles from This Issue, p. 2109.
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Affiliation(s)
- Henner F. Farin
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mohammed H. Mosa
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Benardina Ndreshkjana
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Britta M. Grebbin
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Birgit Ritter
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Constantin Menche
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Kilian B. Kennel
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Paul K. Ziegler
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Lili Szabó
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Julia Bollrath
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Dietmar Rieder
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Birgitta E. Michels
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Alena Kress
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Müge Bozlar
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Tahmineh Darvishi
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Sara Stier
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Ivan-Maximilano Kur
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- Institute of Biochemistry I, Goethe University, Frankfurt am Main, Germany
| | - Katrin Bankov
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Rebecca Kesselring
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of General and Visceral Surgery, University of Freiburg, Freiburg, Germany
| | - Stefan Fichtner-Feigl
- Department of General and Visceral Surgery, University of Freiburg, Freiburg, Germany
| | - Bernhard Brüne
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Biochemistry I, Goethe University, Frankfurt am Main, Germany
| | | | | | - Christian H. Brandts
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Wolf O. Bechstein
- Department of General and Visceral Surgery, Goethe University, Frankfurt am Main, Germany
| | - Peter J. Wild
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies (FIAS), Frankfurt am Main, Germany
| | - Andreas Weigert
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Biochemistry I, Goethe University, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe University, Frankfurt am Main, Germany
| | - Stefan Knapp
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe University, Frankfurt am Main, Germany
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian R. Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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11
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Effenberger M, Waschina S, Bronowski C, Sturm G, Tassiello O, Sommer F, Zollner A, Watschinger C, Grabherr F, Gstir R, Grander C, Enrich B, Bale R, Putzer D, Djanani A, Moschen AR, Zoller H, Rupp J, Schreiber S, Burcelin R, Lass-Flörl C, Trajanoski Z, Oberhuber G, Rosenstiel P, Adolph TE, Aden K, Tilg H. A gut bacterial signature in blood and liver tissue characterizes cirrhosis and hepatocellular carcinoma. Hepatol Commun 2023; 7:e00182. [PMID: 37314752 DOI: 10.1097/hc9.0000000000000182] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/18/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND HCC is the leading cause of cancer in chronic liver disease. A growing body of experimental mouse models supports the notion that gut-resident and liver-resident microbes control hepatic immune responses and, thereby, crucially contribute to liver tumorigenesis. However, a comprehensive characterization of the intestinal microbiome in fueling the transition from chronic liver disease to HCC in humans is currently missing. METHODS Here, we profiled the fecal, blood, and liver tissue microbiome of patients with HCC by 16S rRNA sequencing and compared profiles to nonmalignant cirrhotic and noncirrhotic NAFLD patients. RESULTS We report a distinct bacterial profile, defined from 16S rRNA gene sequences, with reduced α-and β-diversity in the feces of patients with HCC and cirrhosis compared to NAFLD. Patients with HCC and cirrhosis exhibited an increased proportion of fecal bacterial gene signatures in the blood and liver compared to NAFLD. Differential analysis of the relative abundance of bacterial genera identified an increased abundance of Ruminococcaceae and Bacteroidaceae in blood and liver tissue from both HCC and cirrhosis patients compared to NAFLD. Fecal samples from cirrhosis and HCC patients both showed a reduced abundance for several taxa, including short-chain fatty acid-producing genera, such as Blautia and Agathobacter. Using paired 16S rRNA and transcriptome sequencing, we identified a direct association between gut bacterial genus abundance and host transcriptome response within the liver tissue. CONCLUSIONS Our study indicates perturbations of the intestinal and liver-resident microbiome as a critical determinant of patients with cirrhosis and HCC.
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Affiliation(s)
- Maria Effenberger
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Silvio Waschina
- Institute for Human Nutrition and Food Science, Division of Nutriinformatics, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christina Bronowski
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Oronzo Tassiello
- Institute for Human Nutrition and Food Science, Division of Nutriinformatics, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Andreas Zollner
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Christina Watschinger
- Department of Internal Medicine I, Gastroenterology, Nephrology, Metabolism & Endocrinology, Johannes Kepler University, Linz, Austria
| | - Felix Grabherr
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Ronald Gstir
- Institute of Hygiene and Medical Microbiology, ECMM, Medical University of Innsbruck, Innsbruck, Austria
| | - Christoph Grander
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Barbara Enrich
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Reto Bale
- Department of Radiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniel Putzer
- Department of Radiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Angela Djanani
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander R Moschen
- Department of Internal Medicine I, Gastroenterology, Nephrology, Metabolism & Endocrinology, Johannes Kepler University, Linz, Austria
- Christian Doppler Laboratory for Mucosal Immunology, Johannes Kepler University, Linz, Austria
| | - Heinz Zoller
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Luebeck, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Remy Burcelin
- INSERM 1297 and University Paul Sabatier: Institut des Maladies Métaboliques et Cardiovasculaires, France and Université Paul Sabatier, Toulouse, France
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, ECMM, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Georg Oberhuber
- INNPATH, Institute of Pathology, University Hospital of Innsbruck, Innsbruck, Austria
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Timon E Adolph
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
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12
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Rieder D, Trajanoski Z. Checking immunotoxicity risks of checkpoint blockade. Nat Cancer 2023; 4:779-780. [PMID: 37308677 DOI: 10.1038/s43018-023-00561-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria.
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13
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Hautz T, Salcher S, Fodor M, Sturm G, Ebner S, Mair A, Trebo M, Untergasser G, Sopper S, Cardini B, Martowicz A, Hofmann J, Daum S, Kalb M, Resch T, Krendl F, Weissenbacher A, Otarashvili G, Obrist P, Zelger B, Öfner D, Trajanoski Z, Troppmair J, Oberhuber R, Pircher A, Wolf D, Schneeberger S. Immune cell dynamics deconvoluted by single-cell RNA sequencing in normothermic machine perfusion of the liver. Nat Commun 2023; 14:2285. [PMID: 37085477 PMCID: PMC10121614 DOI: 10.1038/s41467-023-37674-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/27/2023] [Indexed: 04/23/2023] Open
Abstract
Normothermic machine perfusion (NMP) has emerged as an innovative organ preservation technique. Developing an understanding for the donor organ immune cell composition and its dynamic changes during NMP is essential. We aimed for a comprehensive characterization of immune cell (sub)populations, cell trafficking and cytokine release during liver NMP. Single-cell transcriptome profiling of human donor livers prior to, during NMP and after transplantation shows an abundance of CXC chemokine receptor 1+/2+ (CXCR1+/CXCR2+) neutrophils, which significantly decreased during NMP. This is paralleled by a large efflux of passenger leukocytes with neutrophil predominance in the perfusate. During NMP, neutrophils shift from a pro-inflammatory state towards an aged/chronically activated/exhausted phenotype, while anti-inflammatory/tolerogenic monocytes/macrophages are increased. We herein describe the dynamics of the immune cell repertoire, phenotypic immune cell shifts and a dominance of neutrophils during liver NMP, which potentially contribute to the inflammatory response. Our findings may serve as resource to initiate future immune-interventional studies.
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Affiliation(s)
- T Hautz
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - S Salcher
- Department of Internal Medicine V, Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - M Fodor
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - G Sturm
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - S Ebner
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - A Mair
- Department of Internal Medicine V, Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - M Trebo
- Department of Internal Medicine V, Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - G Untergasser
- Department of Internal Medicine V, Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
- Tyrolpath Obrist Brunhuber GmbH, Zams, Austria
| | - S Sopper
- Department of Internal Medicine V, Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - B Cardini
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - A Martowicz
- Department of Internal Medicine V, Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
- Tyrolpath Obrist Brunhuber GmbH, Zams, Austria
| | - J Hofmann
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - S Daum
- Department of Internal Medicine V, Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - M Kalb
- Department of Internal Medicine V, Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - T Resch
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - F Krendl
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - A Weissenbacher
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - G Otarashvili
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - P Obrist
- Tyrolpath Obrist Brunhuber GmbH, Zams, Austria
| | - B Zelger
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - D Öfner
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - Z Trajanoski
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - J Troppmair
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - R Oberhuber
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - A Pircher
- Department of Internal Medicine V, Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - D Wolf
- Department of Internal Medicine V, Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria.
| | - S Schneeberger
- Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria.
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14
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Wittner L, Wagener L, Wiese JJ, Stolzer I, Krug SM, Naschberger E, Jackstadt R, Beyaert R, Atreya R, Kühl AA, Sturm G, Gonzalez-Acera M, Patankar JV, Becker C, Siegmund B, Trajanoski Z, Winner B, Neurath MF, Schumann M, Günther C. Proteolytic Activity of the Paracaspase MALT1 Is Involved in Epithelial Restitution and Mucosal Healing. Int J Mol Sci 2023; 24:ijms24087402. [PMID: 37108564 PMCID: PMC10138456 DOI: 10.3390/ijms24087402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/30/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The paracaspase MALT1 is a crucial regulator of immune responses in various cellular contexts. Recently, there is increasing evidence suggesting that MALT1 might represent a novel key player in mucosal inflammation. However, the molecular mechanisms underlying this process and the targeted cell population remain unclear. In this study, we investigate the role of MALT1 proteolytic activity in the context of mucosal inflammation. We demonstrate a significant enrichment of MALT1 gene and protein expression in colonic epithelial cells of UC patients, as well as in the context of experimental colitis. Mechanistically we demonstrate that MALT1 protease function inhibits ferroptosis, a form of iron-dependent cell death, upstream of NF-κB signaling, which can promote inflammation and tissue damage in IBD. We further show that MALT1 activity contributes to STAT3 signaling, which is essential for the regeneration of the intestinal epithelium after injury. In summary, our data strongly suggests that the protease function of MALT1 plays a critical role in the regulation of immune and inflammatory responses, as well as mucosal healing. Understanding the mechanisms by which MALT1 protease function regulates these processes may offer novel therapeutic targets for the treatment of IBD and other inflammatory diseases.
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Affiliation(s)
- Leonie Wittner
- Department of Medicine 1, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Lukas Wagener
- Department of Medicine 1, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Jakob J Wiese
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, 12203 Berlin, Germany
| | - Iris Stolzer
- Department of Medicine 1, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Susanne M Krug
- Clinical Physiology/Nutritional Medicine, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, 12203 Berlin, Germany
| | - Elisabeth Naschberger
- Division Molecular and Experimental Surgery, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Rene Jackstadt
- Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rudi Beyaert
- VIB-UGent Center for Inflammation Research, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Raja Atreya
- Department of Medicine 1, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
- IBDome Consortium, 91054 Erlangen, Germany
- IBDome Consortium, 12203 Berlin, Germany
| | - Anja A Kühl
- IBDome Consortium, 91054 Erlangen, Germany
- IBDome Consortium, 12203 Berlin, Germany
- iPATH.Berlin-Core Unit, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, 12203 Berlin, Germany
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Miguel Gonzalez-Acera
- Department of Medicine 1, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Jay V Patankar
- Department of Medicine 1, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
- IBDome Consortium, 91054 Erlangen, Germany
- IBDome Consortium, 12203 Berlin, Germany
| | - Christoph Becker
- Department of Medicine 1, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
- IBDome Consortium, 91054 Erlangen, Germany
- IBDome Consortium, 12203 Berlin, Germany
| | - Britta Siegmund
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, 12203 Berlin, Germany
- IBDome Consortium, 91054 Erlangen, Germany
- IBDome Consortium, 12203 Berlin, Germany
| | - Zlatko Trajanoski
- IBDome Consortium, 91054 Erlangen, Germany
- IBDome Consortium, 12203 Berlin, Germany
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Beate Winner
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
- Department of Stem Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
- Center of Rare Diseases (ZSEER), University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
- VIB-UGent Center for Inflammation Research, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
- IBDome Consortium, 91054 Erlangen, Germany
- IBDome Consortium, 12203 Berlin, Germany
| | - Michael Schumann
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, 12203 Berlin, Germany
- IBDome Consortium, 91054 Erlangen, Germany
- IBDome Consortium, 12203 Berlin, Germany
| | - Claudia Günther
- Department of Medicine 1, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
- IBDome Consortium, 91054 Erlangen, Germany
- IBDome Consortium, 12203 Berlin, Germany
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15
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Indelicato E, Kirchmair A, Amprosi M, Steixner S, Nachbauer W, Eigentler A, Wahl N, Apostolova G, Krogsdam A, Schneider R, Wanschitz J, Trajanoski Z, Boesch S. Skeletal muscle transcriptomics dissects the pathogenesis of Friedreich's Ataxia. Hum Mol Genet 2023:7110888. [PMID: 37027192 DOI: 10.1093/hmg/ddad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
OBJECTIVE In Friedreich ́s Ataxia (FRDA), the most affected tissues are not accessible to sampling and available transcriptomic findings originate from blood-derived cells and animal models. Herein, we aimed at dissecting for the first time the pathophysiology of FRDA by means of RNA-sequencing in an affected tissue sampled in vivo. METHODS Skeletal muscle biopsies were collected from seven FRDA patients before and after treatment with recombinant human Erythropoietin (rhuEPO) within a clinical trial. Total RNA extraction, 3'-mRNA library preparation and sequencing were performed according to standard procedures. We tested for differential gene expression with DESeq2 and performed gene set enrichment analysis with respect to control subjects. RESULTS FRDA transcriptomes showed 1873 genes differentially expressed from controls. Two main signatures emerged: 1) a global downregulation of the mitochondrial transcriptome as well as of ribosome/translational machinery and 2) an upregulation of genes related to transcription and chromatin regulation, especially of repressor terms. Downregulation of the mitochondrial transcriptome was more profound than previously shown in other cellular systems. Furthermore, we observed in FRDA patients a marked upregulation of leptin, the master regulator of energy homeostasis. RhuEPO treatment further enhanced leptin expression. INTERPRETATION Our findings reflect a double hit in the pathophysiology of FRDA: a transcriptional/translational issue, and a profound mitochondrial failure downstream. Leptin upregulation in the skeletal muscle in FRDA may represent a compensatory mechanism of mitochondrial dysfunction, which is amenable to pharmacological boosting. Skeletal muscle transcriptomics is a valuable biomarker to monitor therapeutic interventions in FRDA.
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Affiliation(s)
- Elisabetta Indelicato
- Center for Rare Movement Disorders Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander Kirchmair
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Matthias Amprosi
- Center for Rare Movement Disorders Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stephan Steixner
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Wolfgang Nachbauer
- Center for Rare Movement Disorders Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Eigentler
- Center for Rare Movement Disorders Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Nico Wahl
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck, Austria
| | - Galina Apostolova
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck, Austria
| | - Anne Krogsdam
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Rainer Schneider
- Institute of Biochemistry, Leopold Franzens University, Innsbruck, and Center of Molecular Biosciences Innsbruck (CMBI), Innsbruck, Austria
| | - Julia Wanschitz
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Sylvia Boesch
- Center for Rare Movement Disorders Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
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16
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Koop K, Enderle K, Hillmann M, Ruspeckhofer L, Vieth M, Sturm G, Trajanoski Z, Kühl AA, Atreya R, Leppkes M, Baum P, Roy J, Martin A, Neurath MF, Neufert C. Interleukin 36 receptor-inducible matrix metalloproteinase 13 mediates intestinal fibrosis. Front Immunol 2023; 14:1163198. [PMID: 37207229 PMCID: PMC10189878 DOI: 10.3389/fimmu.2023.1163198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
Background Fibrostenotic disease is a common complication in Crohn's disease (CD) patients hallmarked by transmural extracellular matrix (ECM) accumulation in the intestinal wall. The prevention and medical therapy of fibrostenotic CD is an unmet high clinical need. Although targeting IL36R signaling is a promising therapy option, downstream mediators of IL36 during inflammation and fibrosis have been incompletely understood. Candidate molecules include matrix metalloproteinases which mediate ECM turnover and are thereby potential targets for anti-fibrotic treatment. Here, we have focused on understanding the role of MMP13 during intestinal fibrosis. Methods We performed bulk RNA sequencing of paired colon biopsies taken from non-stenotic and stenotic areas of patients with CD. Corresponding tissue samples from healthy controls and CD patients with stenosis were used for immunofluorescent (IF) staining. MMP13 gene expression was analyzed in cDNA of intestinal biopsies from healthy controls and in subpopulations of patients with CD in the IBDome cohort. In addition, gene regulation on RNA and protein level was studied in colon tissue and primary intestinal fibroblasts from mice upon IL36R activation or blockade. Finally, in vivo studies were performed with MMP13 deficient mice and littermate controls in an experimental model of intestinal fibrosis. Ex vivo tissue analysis included Masson's Trichrome and Sirius Red staining as well as evaluation of immune cells, fibroblasts and collagen VI by IF analysis. Results Bulk RNA sequencing revealed high upregulation of MMP13 in colon biopsies from stenotic areas, as compared to non-stenotic regions of patients with CD. IF analysis confirmed higher levels of MMP13 in stenotic tissue sections of CD patients and demonstrated αSMA+ and Pdpn+ fibroblasts as a major source. Mechanistic experiments demonstrated that MMP13 expression was regulated by IL36R signaling. Finally, MMP13 deficient mice, as compared to littermate controls, developed less fibrosis in the chronic DSS model and showed reduced numbers of αSMA+ fibroblasts. These findings are consistent with a model suggesting a molecular axis involving IL36R activation in gut resident fibroblasts and MMP13 expression during the pathogenesis of intestinal fibrosis. Conclusion Targeting IL36R-inducible MMP13 could evolve as a promising approach to interfere with the development and progression of intestinal fibrosis.
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Affiliation(s)
- Kristina Koop
- First Department of Medicine, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- *Correspondence: Kristina Koop,
| | - Karin Enderle
- First Department of Medicine, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Miriam Hillmann
- First Department of Medicine, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Laura Ruspeckhofer
- First Department of Medicine, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Vieth
- Institute of Pathology, Klinikum Bayreuth, Friedrich-Alexander-Universität Erlangen-Nürnberg, Bayreuth, Germany
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University Innsbruck, Innsbruck, Austria
- The Transregio 241 IBDome Consortium, Erlangen, Germany
| | - Anja A. Kühl
- The Transregio 241 IBDome Consortium, Erlangen, Germany
- iPATH.Berlin, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Raja Atreya
- First Department of Medicine, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- The Transregio 241 IBDome Consortium, Erlangen, Germany
| | - Moritz Leppkes
- First Department of Medicine, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Patrick Baum
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany
| | | | - Andrea Martin
- Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States
| | - Markus F. Neurath
- First Department of Medicine, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Clemens Neufert
- First Department of Medicine, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie, Erlangen, Germany
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17
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Effenberger M, Widjaja AA, Grabherr F, Schaefer B, Grander C, Mayr L, Schwaerzler J, Enrich B, Moser P, Fink J, Pedrini A, Jaschke N, Kirchmair A, Pfister A, Hausmann B, Bale R, Putzer D, Zoller H, Schafer S, Pjevac P, Trajanoski Z, Oberhuber G, Adolph T, Cook S, Tilg H. Interleukin-11 drives human and mouse alcohol-related liver disease. Gut 2023; 72:168-179. [PMID: 35365572 DOI: 10.1136/gutjnl-2021-326076] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/18/2022] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Alcoholic hepatitis (AH) reflects acute exacerbation of alcoholic liver disease (ALD) and is a growing healthcare burden worldwide. Interleukin-11 (IL-11) is a profibrotic, proinflammatory cytokine with increasingly recognised toxicities in parenchymal and epithelial cells. We explored IL-11 serum levels and their prognostic value in patients suffering from AH and cirrhosis of various aetiology and experimental ALD. DESIGN IL-11 serum concentration and tissue expression was determined in a cohort comprising 50 patients with AH, 110 patients with cirrhosis and 19 healthy volunteers. Findings were replicated in an independent patient cohort (n=186). Primary human hepatocytes exposed to ethanol were studied in vitro. Ethanol-fed wildtype mice were treated with a neutralising murine IL-11 receptor-antibody (anti-IL11RA) and examined for severity signs and markers of ALD. RESULTS IL-11 serum concentration and hepatic expression increased with severity of liver disease, mostly pronounced in AH. In a multivariate Cox-regression, a serum level above 6.4 pg/mL was a model of end-stage liver disease independent risk factor for transplant-free survival in patients with compensated and decompensated cirrhosis. In mice, severity of alcohol-induced liver inflammation correlated with enhanced hepatic IL-11 and IL11RA expression. In vitro and in vivo, anti-IL11RA reduced pathogenic signalling pathways (extracellular signal-regulated kinases, c-Jun N-terminal kinase, NADPH oxidase 4) and protected hepatocytes and murine livers from ethanol-induced inflammation and injury. CONCLUSION Pathogenic IL-11 signalling in hepatocytes plays a crucial role in the pathogenesis of ALD and could serve as an independent prognostic factor for transplant-free survival. Blocking IL-11 signalling might be a therapeutic option in human ALD, particularly AH.
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Affiliation(s)
- Maria Effenberger
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Anissa A Widjaja
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore
| | - Felix Grabherr
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Benedikt Schaefer
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Christoph Grander
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Lisa Mayr
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Julian Schwaerzler
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Barbara Enrich
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Patrizia Moser
- INNPATH, Innsbruck Medical University Hospital, Innsbruck, Austria
| | - Julia Fink
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Alisa Pedrini
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Nikolai Jaschke
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander Kirchmair
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexandra Pfister
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Reto Bale
- Department of Radiology, Section of Interventional Oncology-Microinvasive Therapy (SIP), Medical University of Innsbruck, Innsbruck, Austria
| | - Daniel Putzer
- Department of Radiology, Section of Interventional Oncology-Microinvasive Therapy (SIP), Medical University of Innsbruck, Innsbruck, Austria
| | - Heinz Zoller
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schafer
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Georg Oberhuber
- INNPATH, Innsbruck Medical University Hospital, Innsbruck, Austria
| | - Timon Adolph
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Stuart Cook
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore
- MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London, UK
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
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Salcher S, Sturm G, Horvath L, Untergasser G, Kuempers C, Fotakis G, Panizzolo E, Martowicz A, Trebo M, Pall G, Gamerith G, Sykora M, Augustin F, Schmitz K, Finotello F, Rieder D, Perner S, Sopper S, Wolf D, Pircher A, Trajanoski Z. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell 2022; 40:1503-1520.e8. [PMID: 36368318 PMCID: PMC9767679 DOI: 10.1016/j.ccell.2022.10.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/26/2022] [Accepted: 10/06/2022] [Indexed: 11/12/2022]
Abstract
Non-small cell lung cancer (NSCLC) is characterized by molecular heterogeneity with diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and resistance. However, full understanding of how immune cell phenotypes vary across different patient subgroups is lacking. Here, we dissect the NSCLC tumor microenvironment at high resolution by integrating 1,283,972 single cells from 556 samples and 318 patients across 29 datasets, including our dataset capturing cells with low mRNA content. We stratify patients into immune-deserted, B cell, T cell, and myeloid cell subtypes. Using bulk samples with genomic and clinical information, we identify cellular components associated with tumor histology and genotypes. We then focus on the analysis of tissue-resident neutrophils (TRNs) and uncover distinct subpopulations that acquire new functional properties in the tissue microenvironment, providing evidence for the plasticity of TRNs. Finally, we show that a TRN-derived gene signature is associated with anti-programmed cell death ligand 1 (PD-L1) treatment failure.
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Affiliation(s)
- Stefan Salcher
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Lena Horvath
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Gerold Untergasser
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Christiane Kuempers
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Georgios Fotakis
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Elisa Panizzolo
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Agnieszka Martowicz
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria; Tyrolpath Obrist Brunhuber GmbH, Zams, Austria
| | - Manuel Trebo
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Georg Pall
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriele Gamerith
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Martina Sykora
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Augustin
- Department of Visceral, Transplant and Thoracic Surgery, Medical University Innsbruck, Innsbruck, Austria
| | - Katja Schmitz
- Tyrolpath Obrist Brunhuber GmbH, Zams, Austria; INNPATH GmbH, Institute of Pathology, Innsbruck, Austria
| | - Francesca Finotello
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria; Digital Science Center, University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Sven Perner
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany; Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Lung Research (DZL), Luebeck and Borstel, Germany
| | - Sieghart Sopper
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Wolf
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Pircher
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria.
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria.
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19
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Cesaro G, Milia M, Baruzzo G, Finco G, Morandini F, Lazzarini A, Alotto P, da Cunha Carvalho de Miranda NF, Trajanoski Z, Finotello F, Di Camillo B. MAST: a hybrid Multi-Agent Spatio-Temporal model of tumor microenvironment informed using a data-driven approach. Bioinform Adv 2022; 2:vbac092. [PMID: 36699399 PMCID: PMC9744439 DOI: 10.1093/bioadv/vbac092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/03/2022] [Indexed: 12/10/2022]
Abstract
Motivation Recently, several computational modeling approaches, such as agent-based models, have been applied to study the interaction dynamics between immune and tumor cells in human cancer. However, each tumor is characterized by a specific and unique tumor microenvironment, emphasizing the need for specialized and personalized studies of each cancer scenario. Results We present MAST, a hybrid Multi-Agent Spatio-Temporal model which can be informed using a data-driven approach to simulate unique tumor subtypes and tumor-immune dynamics starting from high-throughput sequencing data. It captures essential components of the tumor microenvironment by coupling a discrete agent-based model with a continuous partial differential equations-based model.The application to real data of human colorectal cancer tissue investigating the spatio-temporal evolution and emergent properties of four simulated human colorectal cancer subtypes, along with their agreement with current biological knowledge of tumors and clinical outcome endpoints in a patient cohort, endorse the validity of our approach. Availability and implementation MAST, implemented in Python language, is freely available with an open-source license through GitLab (https://gitlab.com/sysbiobig/mast), and a Docker image is provided to ease its deployment. The submitted software version and test data are available in Zenodo at https://dx.doi.org/10.5281/zenodo.7267745. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | | | - Giacomo Baruzzo
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - Giovanni Finco
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - Francesco Morandini
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - Alessio Lazzarini
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - Piergiorgio Alotto
- Department of Industrial Engineering, University of Padova, 35131 Padova, Italy
| | | | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria,Institute of Molecular Biology, University Innsbruck, 6020 Innsbruck, Austria,Digital Science Center (DiSC), University Innsbruck, 6020 Innsbruck, Austria
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20
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Ingruber J, Dudás J, Savic D, Schweigl G, Steinbichler TB, Greier MDC, Santer M, Carollo S, Trajanoski Z, Riechelmann H. Corrigendum to "EMT-related transcription factors and protein stabilization mechanisms involvement in cadherin switch of head and neck squamous cell carcinoma" [Exp. Cell Res. 414, 1 May 2022, 113084]. Exp Cell Res 2022; 416:113174. [PMID: 35525075 DOI: 10.1016/j.yexcr.2022.113174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Julia Ingruber
- Department of Otorhinolaryngology and Head and Neck Surgery, Medical University of Innsbruck, Innsbruck, Austria and University Hospital of Tyrol, Innsbruck, Austria.
| | - József Dudás
- Department of Otorhinolaryngology and Head and Neck Surgery, Medical University of Innsbruck, Innsbruck, Austria and University Hospital of Tyrol, Innsbruck, Austria.
| | - Dragana Savic
- Laboratory for Experimental and Translational Research on Radiation Oncology (EXTRO-Lab), Department of Therapeutic Radiology and Oncology, Medical University of Innsbruck, Austria; Tyrolean Cancer Research Institute, Innsbruck, Austria.
| | - Gabrielle Schweigl
- Department of Otorhinolaryngology and Head and Neck Surgery, Medical University of Innsbruck, Innsbruck, Austria and University Hospital of Tyrol, Innsbruck, Austria.
| | - Teresa Bernadette Steinbichler
- Department of Otorhinolaryngology and Head and Neck Surgery, Medical University of Innsbruck, Innsbruck, Austria and University Hospital of Tyrol, Innsbruck, Austria.
| | - Maria do Carmo Greier
- Department of Otorhinolaryngology and Head and Neck Surgery, Medical University of Innsbruck, Innsbruck, Austria and University Hospital of Tyrol, Innsbruck, Austria.
| | - Matthias Santer
- Department of Otorhinolaryngology and Head and Neck Surgery, Medical University of Innsbruck, Innsbruck, Austria and University Hospital of Tyrol, Innsbruck, Austria.
| | - Sandro Carollo
- Institute of Bioinformatics Medical University of Innsbruck, Austria.
| | - Zlatko Trajanoski
- Institute of Bioinformatics Medical University of Innsbruck, Austria.
| | - Herbert Riechelmann
- Department of Otorhinolaryngology and Head and Neck Surgery, Medical University of Innsbruck, Innsbruck, Austria and University Hospital of Tyrol, Innsbruck, Austria.
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21
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Seeber A, Battaglin F, Zimmer K, Kocher F, Baca Y, Xiu J, Spizzo G, Novotny-Diermayr V, Rieder D, Puccini A, Swensen J, Ellis M, Goldberg RM, Grothey A, Shields AF, Marshall JL, Weinberg BA, Sackstein PE, Hon Lim K, San Tan G, Nabhan C, Korn WM, Amann A, Trajanoski Z, Berger MD, Lou E, Wolf D, Lenz HJ. Comprehensive analysis of R-spondin fusions and RNF43 mutations implicate novel therapeutic options in colorectal cancer. Clin Cancer Res 2022; 28:1863-1870. [PMID: 35254413 DOI: 10.1158/1078-0432.ccr-21-3018] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/23/2021] [Accepted: 02/10/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Gene fusions involving R-spondin (RSPOfp) and RNF43 mutations have been shown to drive Wnt-dependent tumor initiation in colorectal cancer (CRC). Herein, we aimed to characterize the molecular features of RSPOfp/RNF43 mutated (mut) compared to wildtype CRCs to gain insights into potential rationales for therapeutic strategies. EXPERIMENTAL DESIGN A discovery cohort was classified for RSPOfp/RNF43 status using DNA/RNA sequencing and immunohistochemistry. An independent cohort was used to validate our findings. RESULTS The discovery cohort consisted of 7,245 CRC samples. RSPOfp and RNF43 mutations were detected in 1.3% (n=94) and 6.1% (n=443) of cases. We found 5 RSPO fusion events that had not previously been reported (e.g. IFNGR1-RSPO3). RNF43-mut tumors were associated with right-sided primary tumors. No RSPOfp tumors had RNF43 mutations. In comparison to wildtype CRCs, RSPOfp tumors were characterized by a higher frequency of BRAF, BMPR1A and SMAD4 mutations. APC mutations were observed in only a minority of RSPOfp-positive compared to wildtype cases (4.4 vs. 81.4%). Regarding RNF43 mutations, a higher rate of KMT2D and BRAF mutations were detectable compared to wildtype samples. While RNF43 mutations were associated with a microsatellite instability (MSI-H)/mismatch repair deficiency (dMMR) phenotype (64.3%), and a TMB {greater than or equal to}10 mt/Mb (65.8%), RSPOfp was not associated with MSI-H/dMMR. The validation cohort replicated our genetic findings. CONCLUSIONS This is the largest series of RSPOfp/RNF43-mut CRCs reported to date. Comprehensive molecular analyses asserted the unique molecular landscape associated with RSPO/RNF43 and suggested potential alternative strategies to overcome the low clinical impact of Wnt-targeted agents and immunotherapy.
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Affiliation(s)
| | - Francesca Battaglin
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Kai Zimmer
- Medical University of Innsbruck, Innsbruck, Austria
| | | | - Yasmine Baca
- Caris Life Sciences (United States), Phoenix, United States
| | - Joanne Xiu
- Caris Life Sciences (United States), Phoenix, AZ, United States
| | - Gilbert Spizzo
- Department of Internale Medicine, Oncologic Day Hospital, Bressanone-Brixen, South Tyrol, Italy
| | | | | | - Alberto Puccini
- IRCCS Ospedale Policlinico San Martino, Genova, Italy, Italy
| | | | - Michelle Ellis
- Caris Life Sciences (United States), Phoenix, United States
| | - Richard M Goldberg
- The West Virginia University Cancer Institute, Morgantown, WV, United States
| | - Axel Grothey
- West Cancer Center, Germantown, TN, Germantown, TN, United States
| | | | | | - Benjamin A Weinberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, United States
| | - Paul E Sackstein
- Ruesch Center for The Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, United States
| | - Kiat Hon Lim
- Translational Pathology centre, Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Gek San Tan
- Translational Pathology centre, Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Chadi Nabhan
- Caris Life Sciences and College of Pharmacy, University of South Carolina, Deerfield, United States
| | - W Michael Korn
- Caris Life Sciences (United States), Phoenix, AZ, United States
| | - Arno Amann
- Innsbruck Medical Universtiy, Innsbruck, Austria
| | | | | | - Emil Lou
- University of Minnesota, Minneapolis, MN, United States
| | - Dominik Wolf
- Innsbruck Medical University, Innsbruck, Tyrol, Austria
| | - Heinz-Josef Lenz
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
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22
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Atreya R, Bojarski C, Kühl AA, Trajanoski Z, Neurath MF, Siegmund B. Ileal and colonic Crohn'´s disease: Ddoes location makes a difference in therapy efficacy? Current Research in Pharmacology and Drug Discovery 2022; 3:100097. [PMID: 35345820 PMCID: PMC8956925 DOI: 10.1016/j.crphar.2022.100097] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 12/05/2022] Open
Abstract
Within the IBD entity of Crohn's disease, there is currently no differentiation between ileal and colonic manifestation for recruitment of patients in clinical trials, well-powered analysis of study results or therapeutic decisions in daily clinical practice. However, there is accumulating evidence from epidemiological, genetic, microbial, immunological, and clinical characteristics that clearly indicate that ileal Crohn's disease represents a distinct disease entity, which differentiates itself from colonic Crohn's disease. This is also reflected by lower efficacy of targeted therapies in isolated ileal compared to colonic Crohn's disease. The distinct site-specific mechanisms that drive heightened non-response in ileal disease need to be analysed in-depth in the future, to enable optimized therapy in the individual Crohn's disease patient.
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23
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Abdulrahman Z, Santegoets SJ, Sturm G, Charoentong P, Ijsselsteijn ME, Somarakis A, Höllt T, Finotello F, Trajanoski Z, van Egmond SL, Mustafa DAM, Welters MJP, de Miranda NFCC, van der Burg SH. Tumor-specific T cells support chemokine-driven spatial organization of intratumoral immune microaggregates needed for long survival. J Immunother Cancer 2022; 10:e004346. [PMID: 35217577 PMCID: PMC8883276 DOI: 10.1136/jitc-2021-004346] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The composition of the tumor immune microenvironment (TIME) associated with good prognosis generally also predicts the success of immunotherapy, and both entail the presence of pre-existing tumor-specific T cells. Here, the blueprint of the TIME associated with such an ongoing tumor-specific T-cell response was dissected in a unique prospective oropharyngeal squamous cell carcinoma (OPSCC) cohort, in which tumor-specific tumor-infiltrating T cells were detected (immune responsiveness (IR+)) or not (lack of immune responsiveness (IR-)). METHODS A comprehensive multimodal, high-dimensional strategy was applied to dissect the TIME of treatment-naive IR+ and IR- OPSCC tissue, including bulk RNA sequencing (NanoString), imaging mass cytometry (Hyperion) for phenotyping and spatial interaction analyses of immune cells, and combined single-cell gene expression profiling and T-cell receptor (TCR) sequencing (single-cell RNA sequencing (scRNAseq)) to characterize the transcriptional states of clonally expanded tumor-infiltrating T cells. RESULTS IR+ patients had an excellent survival during >10 years follow-up. The tumors of IR+ patients expressed higher levels of genes strongly related to interferon gamma signaling, T-cell activation, TCR signaling, and mononuclear cell differentiation, as well as genes involved in several immune signaling pathways, than IR- patients. The top differently overexpressed genes included CXCL12 and LTB, involved in ectopic lymphoid structure development. Moreover, scRNAseq not only revealed that CD4+ T cells were the main producers of LTB but also identified a subset of clonally expanded CD8+ T cells, dominantly present in IR+ tumors, which secreted the T cell and dendritic cell (DC) attracting chemokine CCL4. Indeed, immune cell infiltration in IR+ tumors is stronger, highly coordinated, and has a distinct spatial phenotypical signature characterized by intratumoral microaggregates of CD8+CD103+ and CD4+ T cells with DCs. In contrast, the IR- TIME comprised spatial interactions between lymphocytes and various immunosuppressive myeloid cell populations. The impact of these chemokines on local immunity and clinical outcome was confirmed in an independent The Cancer Genome Atlas OPSCC cohort. CONCLUSION The production of lymphoid cell attracting and organizing chemokines by tumor-specific T cells in IR+ tumors constitutes a positive feedback loop to sustain the formation of the DC-T-cell microaggregates and identifies patients with excellent survival after standard therapy.
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Affiliation(s)
- Ziena Abdulrahman
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Saskia J Santegoets
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Pornpimol Charoentong
- Medical Oncology and National Center for Tumor diseases, University Hospital Heidelberg, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Thomas Höllt
- Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | | | | | - Dana A M Mustafa
- Pathology, Tumor Immuno-Pathology Laboratory, Leiden University Medical Center, Leiden, The Netherlands
| | - Marij J P Welters
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Sjoerd H van der Burg
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
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24
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Ingruber J, Dudás J, Savic D, Schweigl G, Steinbichler TB, Greier MDC, Santer M, Carollo S, Trajanoski Z, Riechelmann H. EMT-related transcription factors and protein stabilization mechanisms involvement in cadherin switch of head and neck squamous cell carcinoma. Exp Cell Res 2022; 414:113084. [DOI: 10.1016/j.yexcr.2022.113084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/03/2022] [Accepted: 02/22/2022] [Indexed: 12/16/2022]
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25
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Welz L, Kakavand N, Hang X, Laue G, Ito G, Silva MG, Plattner C, Mishra N, Tengen F, Ogris C, Jesinghaus M, Wottawa F, Arnold P, Kaikkonen L, Stengel S, Tran F, Das S, Kaser A, Trajanoski Z, Blumberg R, Roecken C, Saur D, Tschurtschenthaler M, Schreiber S, Rosenstiel P, Aden K. Epithelial X-Box Binding Protein 1 Coordinates Tumor Protein p53-Driven DNA Damage Responses and Suppression of Intestinal Carcinogenesis. Gastroenterology 2022; 162:223-237.e11. [PMID: 34599932 PMCID: PMC8678303 DOI: 10.1053/j.gastro.2021.09.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Throughout life, the intestinal epithelium undergoes constant self-renewal from intestinal stem cells. Together with genotoxic stressors and failing DNA repair, this self-renewal causes susceptibility toward malignant transformation. X-box binding protein 1 (XBP1) is a stress sensor involved in the unfolded protein response (UPR). We hypothesized that XBP1 acts as a signaling hub to regulate epithelial DNA damage responses. METHODS Data from The Cancer Genome Atlas were analyzed for association of XBP1 with colorectal cancer (CRC) survival and molecular interactions between XBP1 and p53 pathway activity. The role of XBP1 in orchestrating p53-driven DNA damage response was tested in vitro in mouse models of chronic intestinal epithelial cell (IEC) DNA damage (Xbp1/H2bfl/fl, Xbp1ΔIEC, H2bΔIEC, H2b/Xbp1ΔIEC) and via orthotopic tumor organoid transplantation. Transcriptome analysis of intestinal organoids was performed to identify molecular targets of Xbp1-mediated DNA damage response. RESULTS In The Cancer Genome Atlas data set of CRC, low XBP1 expression was significantly associated with poor overall survival and reduced p53 pathway activity. In vivo, H2b/Xbp1ΔIEC mice developed spontaneous intestinal carcinomas. Orthotopic tumor organoid transplantation revealed a metastatic potential of H2b/Xbp1ΔIEC-derived tumors. RNA sequencing of intestinal organoids (H2b/Xbp1fl/fl, H2bΔIEC, H2b/Xbp1ΔIEC, and H2b/p53ΔIEC) identified a transcriptional program downstream of p53, in which XBP1 directs DNA-damage-inducible transcript 4-like (Ddit4l) expression. DDIT4L inhibits mechanistic target of rapamycin-mediated phosphorylation of 4E-binding protein 1. Pharmacologic mechanistic target of rapamycin inhibition suppressed epithelial hyperproliferation via 4E-binding protein 1. CONCLUSIONS Our data suggest a crucial role for XBP1 in coordinating epithelial DNA damage responses and stem cell function via a p53-DDIT4L-dependent feedback mechanism.
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Affiliation(s)
- Lina Welz
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Nassim Kakavand
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Xiang Hang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Georg Laue
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Go Ito
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Miguel Gomes Silva
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
| | - Christina Plattner
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Felicitas Tengen
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Christoph Ogris
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Moritz Jesinghaus
- Institute of Pathology, University Hospital Marburg, Marburg, Germany
| | - Felix Wottawa
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philipp Arnold
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Leena Kaikkonen
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Stefanie Stengel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Arthur Kaser
- Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Richard Blumberg
- Gastroenterology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christoph Roecken
- Department of Pathology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
| | - Markus Tschurtschenthaler
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
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26
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Duurland CL, Santegoets SJ, Abdulrahman Z, Loof NM, Sturm G, Wesselink TH, Arens R, Boekestijn S, Ehsan I, van Poelgeest MIE, Finotello F, Hackl H, Trajanoski Z, Ten Dijke P, Braud VM, Welters MJP, van der Burg SH. CD161 expression and regulation defines rapidly responding effector CD4+ T cells associated with improved survival in HPV16-associated tumors. J Immunother Cancer 2022; 10:e003995. [PMID: 35039463 PMCID: PMC8765066 DOI: 10.1136/jitc-2021-003995] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Expression of killer cell lectin-like receptor B1 (KLRB1), the gene encoding the cell surface molecule CD161, is associated with favorable prognosis in many cancers. CD161 is expressed by several lymphocyte populations, but its role and regulation on tumor-specific CD4+ T cells is unknown. METHODS We examined the clinical impact of CD4+CD161+ T cells in human papillomavirus (HPV)16+ oropharyngeal squamous cell carcinoma (OPSCC), analyzed their contribution in a cohort of therapeutically vaccinated patients and used HPV16-specific CD4+CD161+ tumor-infiltrating lymphocytes and T cell clones for in-depth mechanistic studies. RESULTS Central and effector memory CD4+ T cells express CD161, but only CD4+CD161+ effector memory T cells (Tem) are associated with improved survival in OPSCC. Therapeutic vaccination activates and expands type 1 cytokine-producing CD4+CD161+ effector T cells. The expression of CD161 is dynamic and follows a pattern opposite of the checkpoint molecules PD1 and CD39. CD161 did not function as an immune checkpoint molecule as demonstrated using multiple experimental approaches using antibodies to block CD161 and gene editing to knockout CD161 expression. Single-cell transcriptomics revealed KLRB1 expression in many T cell clusters suggesting differences in their activation. Indeed, CD4+CD161+ effector cells specifically expressed the transcriptional transactivator SOX4, known to enhance T cell receptor (TCR) signaling via CD3ε. Consistent with this observation, CD4+CD161+ cells respond more vigorously to limiting amounts of cognate antigen in presence of interleukin (IL)-12 and IL-18 compared to their CD161- counterparts. The expression of CD161/KLRB1 and SOX4 was downregulated upon TCR stimulation and this effect was boosted by transforming growth factor (TGF)β1. CONCLUSION High levels of CD4+CD161+ Tem are associated with improved survival and our data show that CD161 is dynamically regulated by cell intrinsic and extrinsic factors. CD161 expressing CD4+ T cells rapidly respond to suboptimal antigen stimulation suggesting that CD161, similar to SOX4, is involved in the amplification of TCR signals in CD4+ T cells.
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Affiliation(s)
- Chantal L Duurland
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Saskia J Santegoets
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Ziena Abdulrahman
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Nikki M Loof
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Tom H Wesselink
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ramon Arens
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sanne Boekestijn
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Ilina Ehsan
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
- Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Hubert Hackl
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Ten Dijke
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Veronique M Braud
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Université Côte d'Azur, UMR7275, 06560 Valbonne, Sophia Antipolis, France
| | - Marij J P Welters
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
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27
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Abstract
Over the last few decades, immunotherapy has shown significant therapeutic efficacy in a broad range of cancer types. Antitumor immune responses are contingent on the recognition of tumor-specific antigens, which are termed neoantigens. Tumor neoantigens are ideal targets for immunotherapy since they can be recognized as non-self antigens by the host immune system and thus are able to elicit an antitumor T-cell response. There are an increasing number of studies that highlight the importance of tumor neoantigens in immunoediting and in the sensitivity to immune checkpoint blockade. Therefore, one of the most fundamental tasks in the field of immuno-oncology research is the identification of patient-specific neoantigens. To this end, a plethora of computational approaches have been developed in order to predict tumor-specific aberrant peptides and quantify their likelihood of binding to patients' human leukocyte antigen molecules in order to be recognized by T cells. In this review, we systematically summarize and present the most recent advances in computational neoantigen prediction, and discuss the challenges and novel methods that are being developed to resolve them. Tumors have the ability to acquire immune escape mechanisms. Tumor-specific aberrant peptides (neoantigens) can elicit an immune response by the host immune system. The identification of neoantigens is one of the most fundamental tasks in the field of immuno-oncology research. A plethora of computational approaches have been developed in order to predict patient-specificneoantigens.
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Affiliation(s)
- G Fotakis
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Z Trajanoski
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - D Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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28
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Rieder D, Fotakis G, Ausserhofer M, René G, Paster W, Trajanoski Z, Finotello F. nextNEOpi: a comprehensive pipeline for computational neoantigen prediction. Bioinformatics 2021; 38:1131-1132. [PMID: 34788790 PMCID: PMC8796378 DOI: 10.1093/bioinformatics/btab759] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/30/2021] [Accepted: 11/02/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY Somatic mutations and gene fusions can produce immunogenic neoantigens mediating anticancer immune responses. However, their computational prediction from sequencing data requires complex computational workflows to identify tumor-specific aberrations, derive the resulting peptides, infer patients' Human Leukocyte Antigen types and predict neoepitopes binding to them, together with a set of features underlying their immunogenicity. Here, we present nextNEOpi (nextflow NEOantigen prediction pipeline) a comprehensive and fully automated bioinformatic pipeline to predict tumor neoantigens from raw DNA and RNA sequencing data. In addition, nextNEOpi quantifies neoepitope- and patient-specific features associated with tumor immunogenicity and response to immunotherapy. AVAILABILITY AND IMPLEMENTATION nextNEOpi source code and documentation are available at https://github.com/icbi-lab/nextNEOpi. CONTACT dietmar.rieder@i-med.ac.at or francesca.finotello@uibk.ac.at. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Georgios Fotakis
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Markus Ausserhofer
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Geyeregger René
- St. Anna Children’s Cancer Research Institute, Vienna 1090, Austria
| | - Wolfgang Paster
- St. Anna Children’s Cancer Research Institute, Vienna 1090, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
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29
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Abdulrahman Z, Santegoets S, Sturm G, Charoentong P, Ijsselsteijn M, Somarakis A, Höllt T, Finotello F, Trajanoski Z, Egmond SV, Mustafa D, Welters M, Miranda ND, Burg SVD. 35 Chemokine-driven spatial organization of immune cell microaggregates marks oropharyngeal squamous cell carcinomas containing tumor-specific T cells. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BackgroundOropharyngeal squamous cell carcinoma (OPSCC) is the most prevalent type of head and neck cancer. The survival of patients with OPSCC is tightly linked to the intratumoral presence of tumor-specific CD4+ and CD8+ T cells. Yet, immunotherapy is currently far from effective in OPSCC partly due to our limited understanding of its immune microenvironment.MethodsHere a multi-modal, high-dimensional approach was used to dissect the immune landscape in a unique cohort of pre-therapy OPSCC patient samples (n=20) in which intratumoral tumor-specific T cells were either detected (immune response positive, IR+) or not (IR-). This included imaging mass cytometry (Hyperion) for high-dimensional phenotyping, spatial localization and interaction analyses of the cells in the tumor mircoenvironment with our newly developed imaging processing pipeline employing machine learning, Nanostring PanCancer IO360 panel analysis of immune signaling pathways, and combined single-cell gene expression profiling and T cell receptor sequencing (scRNAseq) to characterize the transcriptional states of clonally expanded tumor-infiltrating T cells.ResultsImmune cell infiltration in IR+ tumors is stronger and highly coordinated, with a distinct spatial phenotypic signature characterized by microaggregates of tumor-resident (CD103+) CD8+ and CD4+ T cells and dendritic cells within the tumor cell beds, which retained after permutation based correction for differences in cell frequencies. Furthermore, the increased expression of CXCL12 and LTB produced by CD4+ T cells, both involved in the spatial organization of immune cell infiltration, and the clonal expansion of CD8+ T cells producing the DC-attracting chemokines CCL4 or XCL1 in IR+ OPSCC, indicate that tumor-reactive T cells act as a positive feedback loop in the formation of these aggregates. The impact of these chemokines on local immunity and clinical outcome was confirmed in an independent TCGA OPSCC cohort. In contrast, the IR- OPSCC signature comprised spatial interactions between lymphocytes and different subpopulations of immunosuppressive myeloid cells.ConclusionsOur study reveals that the chemokine-driven spatial immune signature of OPSCC has strong potential as a prognostic and predictive biomarker. While the immune signature of IR+ OPSCC suggests potential benefit from neoadjuvant immunotherapeutic approaches to limit the side effects of current radio(chemo)therapy, that of IR- OPSCC calls for strategies focused on stimulating T cells and counteracting immune suppressive mechanisms.
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30
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Borst L, Sluijter M, Sturm G, Charoentong P, Santegoets SJ, van Gulijk M, van Elsas MJ, Groeneveldt C, van Montfoort N, Finotello F, Trajanoski Z, Kiełbasa SM, van der Burg SH, van Hall T. NKG2A is a late immune checkpoint on CD8 T cells and marks repeated stimulation and cell division. Int J Cancer 2021; 150:688-704. [PMID: 34716584 PMCID: PMC9299709 DOI: 10.1002/ijc.33859] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/08/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
The surface inhibitory receptor NKG2A forms heterodimers with the invariant CD94 chain and is expressed on a subset of activated CD8 T cells. As antibodies to block NKG2A are currently tested in several efficacy trials for different tumor indications, it is important to characterize the NKG2A+ CD8 T cell population in the context of other inhibitory receptors. Here we used a well‐controlled culture system to study the kinetics of inhibitory receptor expression. Naïve mouse CD8 T cells were synchronously and repeatedly activated by artificial antigen presenting cells in the presence of the homeostatic cytokine IL‐7. The results revealed NKG2A as a late inhibitory receptor, expressed after repeated cognate antigen stimulations. In contrast, the expression of PD‐1, TIGIT and LAG‐3 was rapidly induced, hours after first contact and subsequently down regulated during each resting phase. This late, but stable expression kinetics of NKG2A was most similar to that of TIM‐3 and CD39. Importantly, single‐cell transcriptomics of human tumor‐infiltrating lymphocytes (TILs) showed indeed that these receptors were often coexpressed by the same CD8 T cell cluster. Furthermore, NKG2A expression was associated with cell division and was promoted by TGF‐β in vitro, although TGF‐β signaling was not necessary in a mouse tumor model in vivo. In summary, our data show that PD‐1 reflects recent TCR triggering, but that NKG2A is induced after repeated antigen stimulations and represents a late inhibitory receptor. Together with TIM‐3 and CD39, NKG2A might thus mark actively dividing tumor‐specific TILs.
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Affiliation(s)
- Linda Borst
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Sluijter
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Gregor Sturm
- Institute of Bioinformatics, Innsbruck Medical University, Innsbruck, Austria
| | - Pornpimol Charoentong
- Department of Medical Oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Saskia J Santegoets
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Mandy van Gulijk
- Department of Pulmonology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marit J van Elsas
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Christianne Groeneveldt
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Nadine van Montfoort
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Francesca Finotello
- Institute of Bioinformatics, Innsbruck Medical University, Innsbruck, Austria
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Innsbruck Medical University, Innsbruck, Austria
| | - Szymon M Kiełbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Thorbald van Hall
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
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31
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Furlan T, Kirchmair A, Sampson N, Puhr M, Gruber M, Trajanoski Z, Santer FR, Parson W, Handle F, Culig Z. MYC-Mediated Ribosomal Gene Expression Sensitizes Enzalutamide-resistant Prostate Cancer Cells to EP300/CREBBP Inhibitors. Am J Pathol 2021; 191:1094-1107. [PMID: 33705753 DOI: 10.1016/j.ajpath.2021.02.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/22/2022]
Abstract
Patients with advanced prostate cancer are frequently treated with the antiandrogen enzalutamide. However, resistance eventually develops in virtually all patients, and various mechanisms have been associated with this process. The histone acetyltransferases EP300 and CREBBP are involved in regulation of cellular events in advanced prostate cancer. This study investigated the role of EP300/CREBBP inhibitors in enzalutamide-resistant prostate cancer. EP300/CREBBP inhibitors led to the same inhibition of androgen receptor activity in enzalutamide-resistant and -sensitive cells. However, enzalutamide-resistant cells were more sensitive to these inhibitors in viability assays. As indicated by the RNA-sequencing-based pathway analysis, genes related to the ribosome and MYC activity were significantly altered upon EP300/CREBBP inhibitor treatment. EP300/CREBBP inhibitors led to the down-regulation of ribosomal proteins RPL36 and RPL29. High-level ribosomal proteins amplifications and MYC amplifications were observed in castration-resistant prostate cancer samples of the publicly available Stand Up to Cancer data set. An inhibitor of RNA polymerase I-mediated transcription was used to evaluate the functional implications of these findings. The enzalutamide-resistant cell lines were more sensitive to this treatment. In addition, the migration rate of enzalutamide-resistant cells was strongly inhibited by this treatment. Taken together, the current data show that EP300/CREBBP inhibitors affect the MYC/ribosomal protein axis in enzalutamide-resistant cells and may have promising therapeutic implications.
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Affiliation(s)
- Tobias Furlan
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander Kirchmair
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Natalie Sampson
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Puhr
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Martina Gruber
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Frédéric R Santer
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania
| | - Florian Handle
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zoran Culig
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria.
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32
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Sonnweber T, Sahanic S, Pizzini A, Luger A, Schwabl C, Sonnweber B, Kurz K, Koppelstätter S, Haschka D, Petzer V, Boehm A, Aichner M, Tymoszuk P, Lener D, Theurl M, Lorsbach-Köhler A, Tancevski A, Schapfl A, Schaber M, Hilbe R, Nairz M, Puchner B, Hüttenberger D, Tschurtschenthaler C, Aßhoff M, Peer A, Hartig F, Bellmann R, Joannidis M, Gollmann-Tepeköylü C, Holfeld J, Feuchtner G, Egger A, Hoermann G, Schroll A, Fritsche G, Wildner S, Bellmann-Weiler R, Kirchmair R, Helbok R, Prosch H, Rieder D, Trajanoski Z, Kronenberg F, Wöll E, Weiss G, Widmann G, Löffler-Ragg J, Tancevski I. Cardiopulmonary recovery after COVID-19: an observational prospective multicentre trial. Eur Respir J 2021; 57:13993003.03481-2020. [PMID: 33303539 PMCID: PMC7736754 DOI: 10.1183/13993003.03481-2020] [Citation(s) in RCA: 261] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND After the 2002/2003 severe acute respiratory syndrome outbreak, 30% of survivors exhibited persisting structural pulmonary abnormalities. The long-term pulmonary sequelae of coronavirus disease 2019 (COVID-19) are yet unknown, and comprehensive clinical follow-up data are lacking. METHODS In this prospective, multicentre, observational study, we systematically evaluated the cardiopulmonary damage in subjects recovering from COVID-19 at 60 and 100 days after confirmed diagnosis. We conducted a detailed questionnaire, clinical examination, laboratory testing, lung function analysis, echocardiography and thoracic low-dose computed tomography (CT). RESULTS Data from 145 COVID-19 patients were evaluated, and 41% of all subjects exhibited persistent symptoms 100 days after COVID-19 onset, with dyspnoea being most frequent (36%). Accordingly, patients still displayed an impaired lung function, with a reduced diffusing capacity in 21% of the cohort being the most prominent finding. Cardiac impairment, including a reduced left ventricular function or signs of pulmonary hypertension, was only present in a minority of subjects. CT scans unveiled persisting lung pathologies in 63% of patients, mainly consisting of bilateral ground-glass opacities and/or reticulation in the lower lung lobes, without radiological signs of pulmonary fibrosis. Sequential follow-up evaluations at 60 and 100 days after COVID-19 onset demonstrated a vast improvement of symptoms and CT abnormalities over time. CONCLUSION A relevant percentage of post-COVID-19 patients presented with persisting symptoms and lung function impairment along with radiological pulmonary abnormalities >100 days after the diagnosis of COVID-19. However, our results indicate a significant improvement in symptoms and cardiopulmonary status over time.
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Affiliation(s)
- Thomas Sonnweber
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria.,Contributed equally as first authors
| | - Sabina Sahanic
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria.,Contributed equally as first authors
| | - Alex Pizzini
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Anna Luger
- Dept of Radiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christoph Schwabl
- Dept of Radiology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Katharina Kurz
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Sabine Koppelstätter
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - David Haschka
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Verena Petzer
- Dept of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Anna Boehm
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Magdalena Aichner
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Piotr Tymoszuk
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniela Lener
- Dept of Internal Medicine III, Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Theurl
- Dept of Internal Medicine III, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Amra Tancevski
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Anna Schapfl
- Dept of Internal Medicine, St Vinzenz Hospital, Zams, Austria
| | - Marc Schaber
- Dept of Internal Medicine, St Vinzenz Hospital, Zams, Austria
| | - Richard Hilbe
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Manfred Nairz
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Bernhard Puchner
- The Karl Landsteiner Institute, Reha Zentrum Münster, Münster, Austria
| | - Doris Hüttenberger
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Malte Aßhoff
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Peer
- Division of Intensive Care and Emergency Medicine, Dept of Internal Medicine I, Medical University of Innsbruck, Innsbruck, Austria
| | - Frank Hartig
- Division of Intensive Care and Emergency Medicine, Dept of Internal Medicine I, Medical University of Innsbruck, Innsbruck, Austria
| | - Romuald Bellmann
- Division of Intensive Care and Emergency Medicine, Dept of Internal Medicine I, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Joannidis
- Division of Intensive Care and Emergency Medicine, Dept of Internal Medicine I, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Johannes Holfeld
- Dept of Cardiac Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Gudrun Feuchtner
- Dept of Radiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander Egger
- Central Institute of Medical and Chemical Laboratory Diagnostics, University Hospital Innsbruck, Innsbruck, Austria
| | - Gregor Hoermann
- Central Institute of Medical and Chemical Laboratory Diagnostics, University Hospital Innsbruck, Innsbruck, Austria.,Dept of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.,MLL Munich Leukemia Laboratory, Munich, Germany
| | - Andrea Schroll
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Gernot Fritsche
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Sophie Wildner
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Rosa Bellmann-Weiler
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Rudolf Kirchmair
- Dept of Internal Medicine III, Medical University of Innsbruck, Innsbruck, Austria.,The Karl Landsteiner Institute, Reha Zentrum Münster, Münster, Austria
| | - Raimund Helbok
- Dept of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Helmut Prosch
- Dept of Biomedical Imaging and Image-guided Therapy, Medical University Vienna, Vienna, Austria
| | - Dietmar Rieder
- Institute for Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Institute for Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ewald Wöll
- Dept of Internal Medicine, St Vinzenz Hospital, Zams, Austria
| | - Günter Weiss
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerlig Widmann
- Dept of Radiology, Medical University of Innsbruck, Innsbruck, Austria.,Contributed equally to this article as lead authors and supervised the work
| | - Judith Löffler-Ragg
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria.,Contributed equally to this article as lead authors and supervised the work
| | - Ivan Tancevski
- Dept of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria.,Contributed equally to this article as lead authors and supervised the work
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Sturm G, Szabo T, Fotakis G, Haider M, Rieder D, Trajanoski Z, Finotello F. Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data. Bioinformatics 2021; 36:4817-4818. [PMID: 32614448 PMCID: PMC7751015 DOI: 10.1093/bioinformatics/btaa611] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/08/2020] [Accepted: 06/24/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Advances in single-cell technologies have enabled the investigation of T-cell phenotypes and repertoires at unprecedented resolution and scale. Bioinformatic methods for the efficient analysis of these large-scale datasets are instrumental for advancing our understanding of adaptive immune responses. However, while well-established solutions are accessible for the processing of single-cell transcriptomes, no streamlined pipelines are available for the comprehensive characterization of T-cell receptors. Here, we propose single-cell immune repertoires in Python (Scirpy), a scalable Python toolkit that provides simplified access to the analysis and visualization of immune repertoires from single cells and seamless integration with transcriptomic data. AVAILABILITY AND IMPLEMENTATION Scirpy source code and documentation are available at https://github.com/icbi-lab/scirpy. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Tamas Szabo
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria.,Biocenter, Institute of Developmental Immunology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Georgios Fotakis
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Marlene Haider
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
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Prokopi A, Tripp CH, Tummers B, Hornsteiner F, Spoeck S, Crawford JC, Clements DR, Efremova M, Hutter K, Bellmann L, Cappellano G, Cadilha BL, Kobold S, Boon L, Ortner D, Trajanoski Z, Chen S, de Gruijl TD, Idoyaga J, Green DR, Stoitzner P. Skin dendritic cells in melanoma are key for successful checkpoint blockade therapy. J Immunother Cancer 2021; 9:jitc-2020-000832. [PMID: 33408092 PMCID: PMC7789456 DOI: 10.1136/jitc-2020-000832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Immunotherapy with checkpoint inhibitors has shown impressive results in patients with melanoma, but still many do not benefit from this line of treatment. A lack of tumor-infiltrating T cells is a common reason for therapy failure but also a loss of intratumoral dendritic cells (DCs) has been described. METHODS We used the transgenic tg(Grm1)EPv melanoma mouse strain that develops spontaneous, slow-growing tumors to perform immunological analysis during tumor progression. With flow cytometry, the frequencies of DCs and T cells at different tumor stages and the expression of the inhibitory molecules programmed cell death protein-1 (PD-1) and T-cell immunoglobulin and mucin-domain containing-3 (TIM-3) on T cells were analyzed. This was complemented with RNA-sequencing (RNA-seq) and real-time quantitative PCR (RT-qPCR) analysis to investigate the immune status of the tumors. To boost DC numbers and function, we administered Fms-related tyrosine 3 ligand (Flt3L) plus an adjuvant mix of polyI:C and anti-CD40. To enhance T cell function, we tested several checkpoint blockade antibodies. Immunological alterations were characterized in tumor and tumor-draining lymph nodes (LNs) by flow cytometry, CyTOF, microarray and RT-qPCR to understand how immune cells can control tumor growth. The specific role of migratory skin DCs was investigated by coculture of sorted DC subsets with melanoma-specific CD8+ T cells. RESULTS Our study revealed that tumor progression is characterized by upregulation of checkpoint molecules and a gradual loss of the dermal conventional DC (cDC) 2 subset. Monotherapy with checkpoint blockade could not restore antitumor immunity, whereas boosting DC numbers and activation increased tumor immunogenicity. This was reflected by higher numbers of activated cDC1 and cDC2 as well as CD4+ and CD8+ T cells in treated tumors. At the same time, the DC boost approach reinforced migratory dermal DC subsets to prime gp100-specific CD8+ T cells in tumor-draining LNs that expressed PD-1/TIM-3 and produced interferon γ (IFNγ)/tumor necrosis factor α (TNFα). As a consequence, the combination of the DC boost with antibodies against PD-1 and TIM-3 released the brake from T cells, leading to improved function within the tumors and delayed tumor growth. CONCLUSIONS Our results set forth the importance of skin DC in cancer immunotherapy, and demonstrates that restoring DC function is key to enhancing tumor immunogenicity and subsequently responsiveness to checkpoint blockade therapy.
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Affiliation(s)
- Anastasia Prokopi
- Department of Dermatology, Venereology & Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christoph H Tripp
- Department of Dermatology, Venereology & Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Bart Tummers
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Florian Hornsteiner
- Department of Dermatology, Venereology & Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sarah Spoeck
- Department of Dermatology, Venereology & Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Derek R Clements
- Department of Micobiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Mirjana Efremova
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Katharina Hutter
- Department of Dermatology, Venereology & Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lydia Bellmann
- Department of Dermatology, Venereology & Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Giuseppe Cappellano
- Department of Dermatology, Venereology & Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Bruno L Cadilha
- Center of Integrated Protein Science Munich (CIPS-M) and Division of Clinical Pharmacology, Department of Medicine IV, Klinikum der Universität München, LMU Munich, Germany.,Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sebastian Kobold
- Center of Integrated Protein Science Munich (CIPS-M) and Division of Clinical Pharmacology, Department of Medicine IV, Klinikum der Universität München, LMU Munich, Germany.,Member of the German Center for Lung Research (DZL), Munich, Germany.,German Center for Translational Cancer Research (DKTK), partner site Munich, Munich, Germany
| | | | - Daniela Ortner
- Department of Dermatology, Venereology & Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Suzie Chen
- Ernest Mario School of Pharmacy and Rutgers Cancer Institute, Rutgers University, New Brunswick, New Jersey, USA
| | - Tanja D de Gruijl
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Juliana Idoyaga
- Department of Micobiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Patrizia Stoitzner
- Department of Dermatology, Venereology & Allergology, Medical University of Innsbruck, Innsbruck, Austria
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Kortekaas KE, Santegoets SJ, Sturm G, Ehsan I, van Egmond SL, Finotello F, Trajanoski Z, Welters MJP, van Poelgeest MIE, van der Burg SH. CD39 Identifies the CD4 + Tumor-Specific T-cell Population in Human Cancer. Cancer Immunol Res 2020; 8:1311-1321. [PMID: 32759363 DOI: 10.1158/2326-6066.cir-20-0270] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/04/2020] [Accepted: 08/03/2020] [Indexed: 11/16/2022]
Abstract
The accumulation of tumor-specific CD4+ and CD8+ effector T cells is key to an effective antitumor response. Locally, CD4+ T cells promote the recruitment and effector function of tumor-specific CD8+ T cells and activate innate killer cells in the tumor. Here, we show that tumor-specific CD4+ T cells were predominantly present in the CD39+ subset of tumor-infiltrating lymphocytes (TIL). The CD39+ CD4+ and CD8+ TILs were detected in three different tumor types, and displayed an activated (PD-1+, HLA-DR+) effector memory phenotype. CD4+CD39+ single-cell RNA-sequenced TILs shared similar well-known activation, tissue residency, and effector cell-associated genes with CD8+CD39+CD103+ TILs. Finally, analysis of directly ex vivo cell-sorted and in vitro expanded pure populations of CD39-positive and negative CD4+ and CD8+ TILs revealed that tumor-specific antigen reactivity was almost exclusively detected among CD39+ cells. Immunotherapy of cancer is based on the activation of tumor-reactive CD4+ and CD8+ T cells. We show that the expression of CD39 can be used to identify, isolate, and expand tumor-reactive T-cell populations in cancers.
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Affiliation(s)
- Kim E Kortekaas
- Department of Gynecology, Leiden University Medical Center, Leiden, the Netherlands
| | - Saskia J Santegoets
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Gregor Sturm
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Ilina Ehsan
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Sylvia L van Egmond
- Department of Otolaryngology and Head and Neck Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Francesca Finotello
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Marij J P Welters
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands.
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36
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Yamazaki T, Kirchmair A, Sato A, Buqué A, Rybstein M, Petroni G, Bloy N, Finotello F, Stafford L, Navarro Manzano E, Ayala de la Peña F, García-Martínez E, Formenti SC, Trajanoski Z, Galluzzi L. Mitochondrial DNA drives abscopal responses to radiation that are inhibited by autophagy. Nat Immunol 2020; 21:1160-1171. [PMID: 32747819 DOI: 10.1038/s41590-020-0751-0] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 06/23/2020] [Indexed: 12/18/2022]
Abstract
Autophagy supports both cellular and organismal homeostasis. However, whether autophagy should be inhibited or activated for cancer therapy remains unclear. Deletion of essential autophagy genes increased the sensitivity of mouse mammary carcinoma cells to radiation therapy in vitro and in vivo (in immunocompetent syngeneic hosts). Autophagy-deficient cells secreted increased amounts of type I interferon (IFN), which could be limited by CGAS or STING knockdown, mitochondrial DNA depletion or mitochondrial outer membrane permeabilization blockage via BCL2 overexpression or BAX deletion. In vivo, irradiated autophagy-incompetent mammary tumors elicited robust immunity, leading to improved control of distant nonirradiated lesions via systemic type I IFN signaling. Finally, a genetic signature of autophagy had negative prognostic value in patients with breast cancer, inversely correlating with mitochondrial abundance, type I IFN signaling and effector immunity. As clinically useful autophagy inhibitors are elusive, our findings suggest that mitochondrial outer membrane permeabilization may represent a valid target for boosting radiation therapy immunogenicity in patients with breast cancer.
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Affiliation(s)
- Takahiro Yamazaki
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Alexander Kirchmair
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Ai Sato
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Aitziber Buqué
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Marissa Rybstein
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Giulia Petroni
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Norma Bloy
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Lena Stafford
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Esther Navarro Manzano
- Hematology and Oncology Department, Hospital Universitario Morales Meseguer, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain.,Universidad de Murcia, Murcia, Spain
| | - Francisco Ayala de la Peña
- Hematology and Oncology Department, Hospital Universitario Morales Meseguer, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain.,Universidad de Murcia, Murcia, Spain
| | - Elena García-Martínez
- Hematology and Oncology Department, Hospital Universitario Morales Meseguer, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain.,Universidad Católica San Antonio de Murcia, Guadalupe, Spain
| | - Silvia C Formenti
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.,Sandra and Edward Meyer Cancer Center, New York, NY, USA
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA. .,Sandra and Edward Meyer Cancer Center, New York, NY, USA. .,Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA. .,Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA. .,Université Paris Descartes/Paris V, Paris, France.
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37
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Pflügler S, Svinka J, Scharf I, Crncec I, Filipits M, Charoentong P, Tschurtschenthaler M, Kenner L, Awad M, Stift J, Schernthanner M, Bischl R, Herndler-Brandstetter D, Glitzner E, Moll HP, Casanova E, Timelthaler G, Sibilia M, Gnant M, Lax S, Thaler J, Müller M, Strobl B, Mohr T, Kaser A, Trajanoski Z, Heller G, Eferl R. IDO1 + Paneth cells promote immune escape of colorectal cancer. Commun Biol 2020; 3:252. [PMID: 32444775 PMCID: PMC7244549 DOI: 10.1038/s42003-020-0989-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 04/10/2020] [Indexed: 02/07/2023] Open
Abstract
Tumors have evolved mechanisms to escape anti-tumor immunosurveillance. They limit humoral and cellular immune activities in the stroma and render tumors resistant to immunotherapy. Sensitizing tumor cells to immune attack is an important strategy to revert immunosuppression. However, the underlying mechanisms of immune escape are still poorly understood. Here we discover Indoleamine-2,3-dioxygenase-1 (IDO1)+ Paneth cells in the stem cell niche of intestinal crypts and tumors, which promoted immune escape of colorectal cancer (CRC). Ido1 expression in Paneth cells was strictly Stat1 dependent. Loss of IDO1+ Paneth cells in murine intestinal adenomas with tumor cell-specific Stat1 deletion had profound effects on the intratumoral immune cell composition. Patient samples and TCGA expression data suggested corresponding cells in human colorectal tumors. Thus, our data uncovered an immune escape mechanism of CRC and identify IDO1+ Paneth cells as a target for immunotherapy. Pflügler, Svinka et al. identify a subset of Paneth cells in mouse intestinal crypts and tumors, which express the immune checkpoint molecule Ido1 in a Stat1-dependent manner and promote tumor growth. Gene expression data from human colorectal cancer (CRC) suggest that a similar population is present in human cancer and opens the door for further studies of immune escape mechanisms in CRC.
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Affiliation(s)
- Sandra Pflügler
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Jasmin Svinka
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Irene Scharf
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Ilija Crncec
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Martin Filipits
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Pornpimol Charoentong
- Institute of Bioinformatics, Medical University Innsbruck, Biocenter, 6020, Innsbruck, Austria.,Department of Medical Oncology, National Center for Tumor diseases, University Hospital Heidelberg, 69120, Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Markus Tschurtschenthaler
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK.,Center for Translational Cancer Research (TranslaTUM), Technical University of Munich, 81675, Munich, Germany
| | - Lukas Kenner
- Ludwig Boltzmann Institute for Cancer Research LBICR, 1090, Vienna, Austria.,Institute of Clinical Pathology, Medical University of Vienna, 1090, Vienna, Austria.,Department of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Monira Awad
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Judith Stift
- Institute of Clinical Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Marina Schernthanner
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Romana Bischl
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | | | - Elisabeth Glitzner
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Herwig P Moll
- Department of Physiology, Center of Physiology and Pharmacology, Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090, Vienna, Austria
| | - Emilio Casanova
- Ludwig Boltzmann Institute for Cancer Research LBICR, 1090, Vienna, Austria.,Department of Physiology, Center of Physiology and Pharmacology, Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090, Vienna, Austria
| | - Gerald Timelthaler
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Maria Sibilia
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Michael Gnant
- Department of Surgery, Breast Health Center, Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
| | - Sigurd Lax
- Department of Pathology, Hospital Graz II, 8020, Graz, Austria.,Institute of Pathology and Molecular Pathology, Johannes Kepler University, 4040, Linz, Austria
| | - Josef Thaler
- Department of Internal Medicine IV, Klinikum Wels-Grieskirchen, 4600, Wels, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Birgit Strobl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Thomas Mohr
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Arthur Kaser
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Medical University Innsbruck, Biocenter, 6020, Innsbruck, Austria
| | - Gerwin Heller
- Division of Oncology, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria
| | - Robert Eferl
- Institute of Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, 1090, Vienna, Austria.
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Fotakis G, Rieder D, Haider M, Trajanoski Z, Finotello F. NeoFuse: predicting fusion neoantigens from RNA sequencing data. Bioinformatics 2020; 36:2260-2261. [PMID: 31755900 PMCID: PMC7141848 DOI: 10.1093/bioinformatics/btz879] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/29/2019] [Accepted: 11/21/2019] [Indexed: 12/30/2022] Open
Abstract
SUMMARY Gene fusions can generate immunogenic neoantigens that mediate anticancer immune responses. However, their computational prediction from RNA sequencing (RNA-seq) data requires deep bioinformatics expertise to assembly a computational workflow covering the prediction of: fusion transcripts, their translated proteins and peptides, Human Leukocyte Antigen (HLA) types, and peptide-HLA binding affinity. Here, we present NeoFuse, a computational pipeline for the prediction of fusion neoantigens from tumor RNA-seq data. NeoFuse can be applied to cancer patients' RNA-seq data to identify fusion neoantigens that might expand the repertoire of suitable targets for immunotherapy. AVAILABILITY AND IMPLEMENTATION NeoFuse source code and documentation are available under GPLv3 license at https://icbi.i-med.ac.at/NeoFuse/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Georgios Fotakis
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Marlene Haider
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria,To whom correspondence should be addressed. E-mail:
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39
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Lamberti G, Plattner C, Blattner P, Scheidl S, Finotello F, Rieder D, Krogsdam A, Farin H, Greten F, Öfner-Velano D, de Miranda N, Aebersold R, Huber L, Trajanoski Z. Abstract B60: Perturbation biology of colorectal cancer organoids reveals patient-specific signaling rewiring and interference with immunity. Cancer Immunol Res 2020. [DOI: 10.1158/2326-6074.tumimm19-b60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Colorectal cancer (CRC), a cancer with 1.4 million new cases diagnosed annually worldwide, is refractory to immunotherapy (with the exception of a minority of tumors with microsatellite instability). This is somehow paradoxical as CRC is a cancer which we have shown is under immunologic control and that tumor-infiltrating lymphocytes represent a strong independent predictor of survival (1). Based on our previous work showing that the immunophenotypes are determined by the genotypes (2), we hypothesized that mutations are rewiring signaling pathways and thereby modulate the recognition of tumor cells by T cells. In order to investigate rewiring of signaling networks and their interference with immunity for individual patients, we developed an experimental-computational concept using perturbation experiments with patient-derived tumor organoids. A biobank of CRC organoids was generated from histologically verified tumor samples, normal tissue, and liver metastases obtained from CRC patients (n=22). Comprehensive characterization of the organoids (exome sequencing, RNA sequencing, and proteomics) and of the tumors (multiplexed immunofluorescence for 6 immune cell types) was carried out and the resulting data were used to prioritize perturbation experiments. Patient-derived organoids were then perturbed with kinase inhibitors (MEKi, PI3Ki, mTORi, TBK1i, IKKi, BRAFi, and TAKi) and large-scale phosphoproteomic profiling using data-independent acquisition (SWATH-MS) was carried out. Deep phosphoproteomic profiling of perturbed organoids enabled reconstruction of patient-specific signaling networks and revealed profound rewiring by targeted drugs and interference with immune-related pathways, suggesting possible pharmacologic modulation by approved targeted agents to induce immunogenic effects. We show for the first time that systematic and comprehensive analysis of the signaling rewiring can provide a mechanistic rationale for immunotherapy-based combination regimens in CRC. This work is an important step towards the development of a precision immuno-oncology platform that integrates tumor organoids with high-throughput and high-content data for making therapeutic recommendations for individual patients.
References
1. Galon J, Costes A, Sanchez-Cabo F, Kirilovsky A, Mlecnik B, Lagorce-Pages C, Tosolini M, Camus M, Berger A, Wind P, et al. Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science 2006;313:1960-1964.
2. Angelova M, Charoentong P, Hackl H, Fischer ML, Snajder R, Krogsdam AM, Waldner MJ, Bindea G, Mlecnik B, Galon J, Trajanoski Z: Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. Genome Biol 2015;16:64.
Citation Format: Giorgia Lamberti, Christina Plattner, Peter Blattner, Stefan Scheidl, Francesca Finotello, Dietmar Rieder, Anne Krogsdam, Henner Farin, Florian Greten, Dietmar Öfner-Velano, Noel de Miranda, Ruedi Aebersold, Lukas Huber, Zlatko Trajanoski. Perturbation biology of colorectal cancer organoids reveals patient-specific signaling rewiring and interference with immunity [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr B60.
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Affiliation(s)
| | | | | | | | | | | | - Anne Krogsdam
- 1Medical University of Innsbruck, Innsbruck, Austria,
| | | | | | | | | | | | - Lukas Huber
- 1Medical University of Innsbruck, Innsbruck, Austria,
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de Boo L, Cimino-Mathews A, Lubeck Y, Daletzakis A, Opdam M, Sanders J, Hooijberg E, van Rossum A, Loncova Z, Rieder D, Trajanoski Z, Vollebergh M, Sobral-Leite M, van de Vijver K, Broeks A, van der Wiel R, van Tinteren H, Linn S, Horlings HM, Kok M. Tumour-infiltrating lymphocytes (TILs) and BRCA-like status in stage III breast cancer patients randomised to adjuvant intensified platinum-based chemotherapy versus conventional chemotherapy. Eur J Cancer 2020; 127:240-250. [PMID: 31956037 DOI: 10.1016/j.ejca.2019.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/26/2019] [Accepted: 12/05/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND The prognostic value of tumour-infiltrating lymphocytes (TILs) differs by breast cancer (BC) subtype. The aim of this study was to evaluate TILs in stage III BC in the context of BRCA1/2-like phenotypes and association with outcome and benefit of intensified platinum-based chemotherapy. PATIENTS AND METHODS Patients participated in a randomised controlled trial of adjuvant intensified platinum-based chemotherapy versus conventional anthracycline-based chemotherapy carried out between 1993 and 1999 in stage III BC. Stromal TILs were scored according to International guidelines in these human epidermal growth factor receptor 2 (HER2)-negative tumours. BRCA-profiles were determined using Comparative Genomic Hybridization. RESULTS TIL levels were evaluated in 248 BCs. High TILs were associated with Triple Negative BC (TNBC). BRCA-like tumours harboured higher TILs compared to non-BRCA-like tumours (median TILs of 20% versus 10%, p < 0.01). TIL levels in BRCA1-like tumours were higher compared to BRCA2-like tumours (median TILs of 20% versus 10%, p < 0.001). These correlations remained significant within the oestrogen (ER)-positive subgroup, however not within the TNBC subgroup. In this stage III BC cohort, high TIL level was associated with favourable outcome (TILs per 10% increment, recurrence-free survival (RFS): multivariate hazard ratio (HR) 0.82, 95% confidence interval (CI) 0.71-0.94, p = 0.01; overall survival (OS): multivariate HR 0.80, 95% CI 0.68-0.94, p = 0.01). There was no significant interaction between TILs and benefit of intensified platinum-based chemotherapy. CONCLUSION In this high-risk breast cancer cohort, high TILs were associated with TNBC and BRCA1-like status. Within the ER-positive subgroup, TIL levels were higher in BRCA1-like compared to BRCA2-like tumours. When adjusted for clinical characteristics, TILs were significantly associated with a more favourable outcome in stage III BC patients.
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MESH Headings
- Adult
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- BRCA1 Protein/genetics
- BRCA2 Protein/genetics
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carboplatin/administration & dosage
- Carcinoma, Ductal, Breast/drug therapy
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/immunology
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Lobular/drug therapy
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/immunology
- Carcinoma, Lobular/pathology
- Chemotherapy, Adjuvant
- Cyclophosphamide/administration & dosage
- Epirubicin/administration & dosage
- Female
- Fluorouracil/administration & dosage
- Follow-Up Studies
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Mutation
- Neoplasm Recurrence, Local/drug therapy
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/immunology
- Neoplasm Recurrence, Local/pathology
- Neoplasm Staging
- Receptor, ErbB-2/metabolism
- Receptors, Estrogen/metabolism
- Receptors, Progesterone/metabolism
- Retrospective Studies
- Survival Rate
- Thiotepa/administration & dosage
- Triple Negative Breast Neoplasms/drug therapy
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/immunology
- Triple Negative Breast Neoplasms/pathology
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Affiliation(s)
- Leonora de Boo
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Yoni Lubeck
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Antonios Daletzakis
- Biometrics Department, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mark Opdam
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joyce Sanders
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Erik Hooijberg
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Annelot van Rossum
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Zuzana Loncova
- Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Marieke Vollebergh
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marcelo Sobral-Leite
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Koen van de Vijver
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Annegien Broeks
- Core Facility Molecular Pathology and Biobanking, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rianne van der Wiel
- Core Facility Molecular Pathology and Biobanking, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Harm van Tinteren
- Biometrics Department, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sabine Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Pathology, University Medical Centre, Utrecht, the Netherlands
| | - Hugo Mark Horlings
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marleen Kok
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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42
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De Boo L, Cimino-Mathews A, Lubeck Y, Daletzakis A, Opdam M, Sanders J, Hooijberg E, van Rossum A, Loncova Z, Rieder D, Trajanoski Z, Vollebergh M, Sobral-Leite M, Van de Vijver K, Broeks A, van der Wiel R, van Tinteren H, Linn S, Horlings H, Kok M. Tumour-infiltrating lymphocytes and BRCA-like status in stage III breast cancer patients treated with intensified carboplatin-based chemotherapy. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz240.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Schmidt F, Dahlke K, Batra A, Keye J, Wu H, Friedrich M, Glauben R, Ring C, Loh G, Schaubeck M, Hackl H, Trajanoski Z, Schumann M, Kühl AA, Blaut M, Siegmund B. Microbial Colonization in Adulthood Shapes the Intestinal Macrophage Compartment. J Crohns Colitis 2019; 13:1173-1185. [PMID: 30938416 DOI: 10.1093/ecco-jcc/jjz036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Contact with distinct microbiota early in life has been shown to educate the mucosal immune system, hence providing protection against immune-mediated diseases. However, the impact of early versus late colonization with regard to the development of the intestinal macrophage compartment has not been studied so far. METHODS Germ-free mice were colonized with specific-pathogen-free [SPF] microbiota at the age of 5 weeks. The ileal and colonic macrophage compartment were analysed by immunohistochemistry, flow cytometry, and RNA sequencing 1 and 5 weeks after colonization and in age-matched SPF mice, which had had contact with microbiota since birth. To evaluate the functional differences, dextran sulfate sodium [DSS]-induced colitis was induced, and barrier function analyses were undertaken. RESULTS Germ-free mice were characterized by an atrophied intestinal wall and a profoundly reduced number of ileal macrophages. Strikingly, morphological restoration of the intestine occurred within the first week after colonization. In contrast, ileal macrophages required 5 weeks for complete restoration, whereas colonic macrophages were numerically unaffected. However, following DSS exposure, the presence of microbiota was a prerequisite for colonic macrophage infiltration. One week after colonization, mild colonic inflammation was observed, paralleled by a reduced inflammatory response after DSS treatment, in comparison with SPF mice. This attenuated inflammation was paralleled by a lack of TNFα production of LPS-stimulated colonic macrophages from SPF and colonized mice, suggesting desensitization of colonized mice by the colonization itself. CONCLUSIONS This study provides the first data indicating that after colonization of adult mice, the numeric, phenotypic, and functional restoration of the macrophage compartment requires the presence of intestinal microbiota and is time dependent.
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Affiliation(s)
- Franziska Schmidt
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Fachbereich Biologie, Chemie, Pharmazie, Freie Universität Berlin, Berlin, Germany
| | - Katja Dahlke
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Arvind Batra
- Neuroimmunology, Max-Planck-Institute of Neurobiology, Planegg-Martinsried, Germany
| | - Jacqueline Keye
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Fachbereich Biologie, Chemie, Pharmazie, Freie Universität Berlin, Berlin, Germany
| | - Hao Wu
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Fachbereich Biologie, Chemie, Pharmazie, Freie Universität Berlin, Berlin, Germany
| | - Marie Friedrich
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Fachbereich Biologie, Chemie, Pharmazie, Freie Universität Berlin, Berlin, Germany
| | - Rainer Glauben
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christiane Ring
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Gunnar Loh
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Monika Schaubeck
- Neuroimmunology, Max-Planck-Institute of Neurobiology, Planegg-Martinsried, Germany
| | - Hubert Hackl
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Schumann
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Anja A Kühl
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Britta Siegmund
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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Di Giacomo AM, Covre A, Finotello F, Rieder D, Danielli R, Sigalotti L, Giannarelli D, Petitprez F, Lacroix L, Valente M, Cutaia O, Fazio C, Amato G, Lazzeri A, Monterisi S, Miracco C, Coral S, Anichini A, Bock C, Nemc A, Oganesian A, Lowder J, Azab M, Fridman WH, Sautès-Fridman C, Trajanoski Z, Maio M. Guadecitabine Plus Ipilimumab in Unresectable Melanoma: The NIBIT-M4 Clinical Trial. Clin Cancer Res 2019; 25:7351-7362. [PMID: 31530631 DOI: 10.1158/1078-0432.ccr-19-1335] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/23/2019] [Accepted: 09/13/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE The immunomodulatory activity of DNA hypomethylating agents (DHAs) suggests they may improve the effectiveness of cancer immunotherapies. The phase Ib NIBIT-M4 trial tested this hypothesis using the next-generation DHA guadecitabine combined with ipilimumab. PATIENTS AND METHODS Patients with unresectable stage III/IV melanoma received escalating doses of guadecitabine 30, 45, or 60 mg/m2/day subcutaneously on days 1 to 5 every 3 weeks, and ipilimumab 3 mg/kg intravenously on day 1 every 3 weeks, starting 1 week after guadecitabine, for four cycles. Primary endpoints were safety, tolerability, and MTD of treatment; secondary were immune-related (ir) disease control rate (DCR) and objective response rate (ORR); and exploratory were changes in methylome, transcriptome, and immune contextures in sequential tumor biopsies, and pharmacokinetics. RESULTS Nineteen patients were treated; 84% had grade 3/4 adverse events, and neither dose-limiting toxicities per protocol nor overlapping toxicities were observed. Ir-DCR and ir-ORR were 42% and 26%, respectively. Median CpG site methylation of tumor samples (n = 8) at week 4 (74.5%) and week 12 (75.5%) was significantly (P < 0.05) lower than at baseline (80.3%), with a median of 2,454 (week 4) and 4,131 (week 12) differentially expressed genes. Among the 136 pathways significantly (P < 0.05; Z score >2 or ←2) modulated by treatment, the most frequently activated were immune-related. Tumor immune contexture analysis (n = 11) demonstrated upregulation of HLA class I on melanoma cells, an increase in CD8+, PD-1+ T cells and in CD20+ B cells in posttreatment tumor cores. CONCLUSIONS Treatment of guadecitabine combined with ipilimumab is safe and tolerable in advanced melanoma and has promising immunomodulatory and antitumor activity.
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Affiliation(s)
| | - Alessia Covre
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Francesca Finotello
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Riccardo Danielli
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Luca Sigalotti
- Oncogenetics and Functional Oncogenomics Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | | | - Florent Petitprez
- INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Team Cancer, Immune Control and Escape, Paris, France
- University Paris Descartes Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Programme Cartes d'Identitié des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Laetitia Lacroix
- INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Team Cancer, Immune Control and Escape, Paris, France
- University Paris Descartes Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Monica Valente
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Ornella Cutaia
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Carolina Fazio
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Giovanni Amato
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Andrea Lazzeri
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Santa Monterisi
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Clelia Miracco
- Pathology Unit, Department of Medical, Surgical and Neurological Science, University of Siena, S. Maria alle Scotte Hospital, Siena, Italy
| | - Sandra Coral
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Andrea Anichini
- HumanTumors Immunobiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Amelie Nemc
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - James Lowder
- Astex Pharmaceuticals Inc., Pleasanton, California
| | | | - Wolf H Fridman
- INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Team Cancer, Immune Control and Escape, Paris, France
- University Paris Descartes Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Catherine Sautès-Fridman
- INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Team Cancer, Immune Control and Escape, Paris, France
- University Paris Descartes Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Zlatko Trajanoski
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Michele Maio
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy.
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45
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Finotello F, Rieder D, Hackl H, Trajanoski Z. Next-generation computational tools for interrogating cancer immunity. Nat Rev Genet 2019; 20:724-746. [PMID: 31515541 DOI: 10.1038/s41576-019-0166-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2019] [Indexed: 12/17/2022]
Abstract
The remarkable success of cancer therapies with immune checkpoint blockers is revolutionizing oncology and has sparked intensive basic and translational research into the mechanisms of cancer-immune cell interactions. In parallel, numerous novel cutting-edge technologies for comprehensive molecular and cellular characterization of cancer immunity have been developed, including single-cell sequencing, mass cytometry and multiplexed spatial cellular phenotyping. In order to process, analyse and visualize multidimensional data sets generated by these technologies, computational methods and software tools are required. Here, we review computational tools for interrogating cancer immunity, discuss advantages and limitations of the various methods and provide guidelines to assist in method selection.
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Affiliation(s)
- Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Hubert Hackl
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria.
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46
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Lamberti G, De Smet CH, Angelova M, Kremser L, Taub N, Herrmann C, Hess MW, Rainer J, Tancevski I, Schweigreiter R, Kofler R, Schmiedinger T, Vietor I, Trajanoski Z, Ejsing CS, Lindner HH, Huber LA, Stasyk T. LAMTOR/Ragulator regulates lipid metabolism in macrophages and foam cell differentiation. FEBS Lett 2019; 594:31-42. [PMID: 31423582 PMCID: PMC7003824 DOI: 10.1002/1873-3468.13579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 11/08/2022]
Abstract
Late endosomal/lysosomal adaptor and MAPK and mTOR activator (LAMTOR/Ragulator) is a scaffold protein complex that anchors and regulates multiprotein signaling units on late endosomes/lysosomes. To identify LAMTOR‐modulated endolysosomal proteins, primary macrophages were derived from bone marrow of conditional knockout mice carrying a specific deletion of LAMTOR2 in the monocyte/macrophage cell lineage. Affymetrix‐based transcriptomic analysis and quantitative iTRAQ‐based organelle proteomic analysis of endosomes derived from macrophages were performed. Further analyses showed that LAMTOR could be a novel regulator of foam cell differentiation. The lipid droplet formation phenotype observed in macrophages was additionally confirmed in MEFs, where lipidomic analysis identified cholesterol esters as specifically downregulated in LAMTOR2 knockout cells. The data obtained indicate a function of LAMTOR2 in lipid metabolism.
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Affiliation(s)
- Giorgia Lamberti
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Austria
| | - Cedric H De Smet
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Austria
| | - Mihaela Angelova
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Austria
| | - Nicole Taub
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Austria
| | - Caroline Herrmann
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Austria
| | - Michael W Hess
- Division of Histology and Embryology, Medical University of Innsbruck, Austria
| | - Johannes Rainer
- Division of Molecular Pathophysiology, Biocenter, Medical University of Innsbruck, Austria
| | - Ivan Tancevski
- Department of Internal Medicine, Medical University of Innsbruck, Austria
| | | | - Reinhard Kofler
- Division of Molecular Pathophysiology, Biocenter, Medical University of Innsbruck, Austria
| | - Thomas Schmiedinger
- Department of Therapeutic Radiology and Oncology, Medical University of Innsbruck, Austria
| | - Ilja Vietor
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Austria
| | - Zlatko Trajanoski
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Austria
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Herbert H Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Austria
| | - Lukas A Huber
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Austria.,Austrian Drug Screening Institute, ADSI, Innsbruck, Austria
| | - Taras Stasyk
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Austria
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47
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Affiliation(s)
- Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Centre, Albinusdreef, 2333 ZA, Leiden, The Netherlands.
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innrain, 6020, Innsbruck, Austria.
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48
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Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H, Krogsdam A, Loncova Z, Posch W, Wilflingseder D, Sopper S, Ijsselsteijn M, Brouwer TP, Johnson D, Xu Y, Wang Y, Sanders ME, Estrada MV, Ericsson-Gonzalez P, Charoentong P, Balko J, da Cunha Carvalho de Miranda NF, Trajanoski Z. Correction to: Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Med 2019; 11:50. [PMID: 31358023 PMCID: PMC6661746 DOI: 10.1186/s13073-019-0655-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 11/30/2022] Open
Affiliation(s)
- Francesca Finotello
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Clemens Mayer
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Christina Plattner
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Gerhard Laschober
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Hubert Hackl
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Anne Krogsdam
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Zuzana Loncova
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Wilfried Posch
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sieghart Sopper
- Department of Haematology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Marieke Ijsselsteijn
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas P Brouwer
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Douglas Johnson
- Vanderbilt University, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yu Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melinda E Sanders
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Monica V Estrada
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paula Ericsson-Gonzalez
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pornpimol Charoentong
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Division of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Justin Balko
- Vanderbilt University, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Zlatko Trajanoski
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria. .,Austrian Drug Screening Institute, Innrain 66A, Innsbruck, Austria.
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49
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Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H, Krogsdam A, Loncova Z, Posch W, Wilflingseder D, Sopper S, Ijsselsteijn M, Brouwer TP, Johnson D, Xu Y, Wang Y, Sanders ME, Estrada MV, Ericsson-Gonzalez P, Charoentong P, Balko J, de Miranda NFDCC, Trajanoski Z. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Med 2019; 11:34. [PMID: 31126321 PMCID: PMC6534875 DOI: 10.1186/s13073-019-0638-6] [Citation(s) in RCA: 615] [Impact Index Per Article: 123.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/09/2019] [Indexed: 12/26/2022] Open
Abstract
We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry, and immunohistochemistry data.quanTIseq analysis of 8000 tumor samples revealed that cytotoxic T cell infiltration is more strongly associated with the activation of the CXCR3/CXCL9 axis than with mutational load and that deconvolution-based cell scores have prognostic value in several solid cancers. Finally, we used quanTIseq to show how kinase inhibitors modulate the immune contexture and to reveal immune-cell types that underlie differential patients' responses to checkpoint blockers.Availability: quanTIseq is available at http://icbi.at/quantiseq .
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Affiliation(s)
- Francesca Finotello
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Clemens Mayer
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Christina Plattner
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Gerhard Laschober
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Hubert Hackl
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Anne Krogsdam
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Zuzana Loncova
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Wilfried Posch
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sieghart Sopper
- Department of Haematology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Marieke Ijsselsteijn
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas P Brouwer
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Douglas Johnson
- Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yu Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melinda E Sanders
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Monica V Estrada
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paula Ericsson-Gonzalez
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pornpimol Charoentong
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Division of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Justin Balko
- Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Zlatko Trajanoski
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria.
- Austrian Drug Screening Institute, Innrain 66A, Innsbruck, Austria.
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50
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Di Giacomo AM, Covre A, Finotello F, Rieder D, Sigalotti L, Giannarelli D, Petitprez F, Lacroix L, Cutaia O, Fazio C, Coral S, Anichini A, Bock C, Lowder JN, Azab M, Fridman WH, Sautes-Fridman C, Trajanoski Z, Maio M. Safety and immunobiological activity of guadecitabine sequenced with ipilimumab in metastatic melanoma patients: The phase Ib NIBIT-M4 study. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.2549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2549 Background: DNA hypomethylating agents show broad immuno-modulatory activity in neoplastic cells, and may improve the effectiveness of cancer immunotherapies. The phase 1b NIBIT-M4 trial investigated a previously unexplored therapeutic strategy using the next-generation DNA hypomethylating agent guadecitabine sequenced with ipilimumab for the treatment of advanced melanoma. Methods: Patients with unresectable Stage III/IV melanoma received escalating doses of guadecitabine 30, 45 or 60 mg/m2 subcutaneously on Days 1–5 every three weeks, and ipilimumab 3 mg/kg intravenously on Day 1 every three weeks, starting one week after guadecitabine, for four cycles. Primary endpoints were the safety, tolerability and maximum tolerated dose of treatment; secondary endpoints included immune-related disease control and objective response. Genome-wide methylation, RNA sequencing, and immunohistochemistry analyses were performed on tumor samples collected at baseline, W4 and W12. (NCT02608437). Results: 19 patients were treated and evaluable for safety and efficacy. The most common treatment-related adverse events of any grade were myelotoxicity (n = 17; 89%) and immune-related adverse events (n = 12; 63%). Grade 3 or 4 myelotoxicity occurred in 15 (79%) patients. There were no dose limiting toxicities. Rates of immune-related disease control and objective response were 8/19 (42%) and 5/19 (26%), respectively. Exploratory analyses of tumour samples (n = 8) showed that median CpG site methylation at Week 4 (74.5%) and Week 12 (75.5%) was significantly lower (p < 0.05) than at baseline (80.3%), with a median of 2454 (Week 4) and 4131 (Week 12) differentially expressed genes identified compared to baseline; among the 136 pathways significantly modulated by treatment, the most frequently activated were immune-related. Tumour immune contexture analysis (n = 11) demonstrated up-regulation of Human Leukocyte Antigen (HLA) class I molecules on melanoma cells, and an increase in CD8+, PD-1+ T cells and in CD20+ B cells in post-treatment tumour core specimens. Conclusions: Sequential guadecitabine and ipilimumab is safe and tolerable in patients with metastatic melanoma, and has promising immunological and anti-tumour activity. Clinical trial information: NCT02608437.
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Affiliation(s)
| | - Alessia Covre
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Francesca Finotello
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Luca Sigalotti
- Oncogenetics and Functional Oncogenomics Unit, Centro di Riferimento Oncologico (CRO) di Aviano, Aviano, Italy
| | | | | | | | - Ornella Cutaia
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Carolina Fazio
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Sandra Coral
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | - Andrea Anichini
- Fondazione IRCCS-Istituto Nazionale dei Tumori, Milan, Italy
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | | | | | - Zlatko Trajanoski
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Michele Maio
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
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