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  1. AU="Zlatko Trajanoski"
  2. AU="Hopke, Philip K"
  3. AU="Kothandaraman, Venkatraman"
  4. AU="Wiencek, Joesph R"
  5. AU="Gachon, Philippe"
  6. AU="Tsuboi, Yoshio"
  7. AU=Woolard Stacie N AU=Woolard Stacie N
  8. AU="Rowland, Jonathan"
  9. AU="Chloe C. Y. Wong"

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  1. Artikel ; Online: Advancing cancer immunotherapy

    Noel F. C. C. de Miranda / Zlatko Trajanoski

    Genome Medicine, Vol 11, Iss 1, Pp 1-

    a vision for the field

    2019  Band 3

    Schlagwörter Medicine ; R ; Genetics ; QH426-470
    Sprache Englisch
    Erscheinungsdatum 2019-07-01T00:00:00Z
    Verlag BMC
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Dynamic, Transient, and Robust Increase in the Innervation of the Inflamed Mucosa in Inflammatory Bowel Diseases

    Miguel Gonzalez Acera / Marvin Bubeck / Fabrizio Mascia / Leonard Diemand / Gregor Sturm / Anja A. Kühl / Raja Atreya / Dieter Chichung Lie / Markus F. Neurath / Michael Schumann / Christoph S.N. Klose / Zlatko Trajanoski / Christoph Becker / Jay V. Patankar

    Cells, Vol 10, Iss 2253, p

    2021  Band 2253

    Abstract: Inflammatory bowel diseases (IBD) are characterized by chronic dysregulation of immune homeostasis, epithelial demise, immune cell activation, and microbial translocation. Each of these processes leads to proinflammatory changes via the release of ... ...

    Abstract Inflammatory bowel diseases (IBD) are characterized by chronic dysregulation of immune homeostasis, epithelial demise, immune cell activation, and microbial translocation. Each of these processes leads to proinflammatory changes via the release of cytokines, damage-associated molecular patterns (DAMPs), and pathogen-associated molecular patterns (PAMPs), respectively. The impact of these noxious agents on the survival and function of the enteric nervous system (ENS) is poorly understood. Here, we show that in contrast to an expected decrease, experimental as well as clinical colitis causes an increase in the transcript levels of enteric neuronal and glial genes. Immunostaining revealed an elevated neuronal innervation of the inflamed regions of the gut mucosa. The increase was seen in models with overt damage to epithelial cells and models of T cell-induced colitis. Transcriptomic data from treatment naïve pediatric IBD patients also confirmed the increase in the neuroglial genes and were replicated on an independent adult IBD dataset. This induction in the neuroglial genes was transient as levels returned to normal upon the induction of remission in both mouse models as well as colitis patients. Our data highlight the dynamic and robust nature of the enteric nervous system in colitis and open novel questions on its regulation.
    Schlagwörter enteric nervous system ; neurogenesis ; inflammatory bowel diseases ; ulcerative colitis ; Crohn’s disease ; Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 610
    Sprache Englisch
    Erscheinungsdatum 2021-08-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer

    Christina Plattner / Giorgia Lamberti / Peter Blattmann / Alexander Kirchmair / Dietmar Rieder / Zuzana Loncova / Gregor Sturm / Stefan Scheidl / Marieke Ijsselsteijn / Georgios Fotakis / Asma Noureen / Rebecca Lisandrelli / Nina Böck / Niloofar Nemati / Anne Krogsdam / Sophia Daum / Francesca Finotello / Antonios Somarakis / Alexander Schäfer /
    Doris Wilflingseder / Miguel Gonzalez Acera / Dietmar Öfner / Lukas A. Huber / Hans Clevers / Christoph Becker / Henner F. Farin / Florian R. Greten / Ruedi Aebersold / Noel F.C.C. de Miranda / Zlatko Trajanoski

    iScience, Vol 26, Iss 12, Pp 108399- (2023)

    2023  

    Abstract: Summary: 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 ... ...

    Abstract Summary: 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.
    Schlagwörter Cancer systems biology ; Cancer ; Proteomics ; Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2023-12-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: Impact of the Chromatin Remodeling Factor CHD1 on Gut Microbiome Composition of Drosophila melanogaster.

    Johanna Sebald / Michaela Willi / Ines Schoberleitner / Anne Krogsdam / Dorothea Orth-Höller / Zlatko Trajanoski / Alexandra Lusser

    PLoS ONE, Vol 11, Iss 4, p e

    2016  Band 0153476

    Abstract: The composition of the intestinal microbiota of Drosophila has been studied in some detail in recent years. Environmental, developmental and host-specific genetic factors influence microbiome composition in the fly. Our previous work has indicated that ... ...

    Abstract The composition of the intestinal microbiota of Drosophila has been studied in some detail in recent years. Environmental, developmental and host-specific genetic factors influence microbiome composition in the fly. Our previous work has indicated that intestinal bacterial load can be affected by chromatin-targeted regulatory mechanisms. Here we studied a potential role of the conserved chromatin assembly and remodeling factor CHD1 in the shaping of the gut microbiome in Drosophila melanogaster. Using high-throughput sequencing of 16S rRNA gene amplicons, we found that Chd1 deletion mutant flies exhibit significantly reduced microbial diversity compared to rescued control strains. Specifically, although Acetobacteraceae dominated the microbiota of both Chd1 wild-type and mutant guts, Chd1 mutants were virtually monoassociated with this bacterial family, whereas in control flies other bacterial taxa constituted ~20% of the microbiome. We further show age-linked differences in microbial load and microbiota composition between Chd1 mutant and control flies. Finally, diet supplementation experiments with Lactobacillus plantarum revealed that, in contrast to wild-type flies, Chd1 mutant flies were unable to maintain higher L. plantarum titres over time. Collectively, these data provide evidence that loss of the chromatin remodeler CHD1 has a major impact on the gut microbiome of Drosophila melanogaster.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 590
    Sprache Englisch
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: Nuclear receptor NR2F6 inhibition potentiates responses to PD-L1/PD-1 cancer immune checkpoint blockade

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

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Band 13

    Abstract: Immune checkpoints blockade (ICB) is a viable anti-cancer strategy. Here the authors show that nuclear receptor NR2F6 acts as an immune checkpoint in T cells and, using mouse models and human T cells, they show NR2F6 inhibition might improve current ICB ... ...

    Abstract Immune checkpoints blockade (ICB) is a viable anti-cancer strategy. Here the authors show that nuclear receptor NR2F6 acts as an immune checkpoint in T cells and, using mouse models and human T cells, they show NR2F6 inhibition might improve current ICB therapy or work as an alternative therapeutic strategy.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2018-04-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution

    Mirjana Efremova / Dietmar Rieder / Victoria Klepsch / Pornpimol Charoentong / Francesca Finotello / Hubert Hackl / Natascha Hermann-Kleiter / Martin Löwer / Gottfried Baier / Anne Krogsdam / Zlatko Trajanoski

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Band 13

    Abstract: The cancer immunoediting hypothesis assumes the immune system sculpts the cancer genome. Here the authors show, in a mouse model, that neutral evolution outweighs the effects of immunoselection and that immune checkpoint blockade potentiates the ... ...

    Abstract The cancer immunoediting hypothesis assumes the immune system sculpts the cancer genome. Here the authors show, in a mouse model, that neutral evolution outweighs the effects of immunoselection and that immune checkpoint blockade potentiates the immunoediting, switching the system to non-neutral evolution.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2018-01-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution

    Mirjana Efremova / Dietmar Rieder / Victoria Klepsch / Pornpimol Charoentong / Francesca Finotello / Hubert Hackl / Natascha Hermann-Kleiter / Martin Löwer / Gottfried Baier / Anne Krogsdam / Zlatko Trajanoski

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Band 13

    Abstract: The cancer immunoediting hypothesis assumes the immune system sculpts the cancer genome. Here the authors show, in a mouse model, that neutral evolution outweighs the effects of immunoselection and that immune checkpoint blockade potentiates the ... ...

    Abstract The cancer immunoediting hypothesis assumes the immune system sculpts the cancer genome. Here the authors show, in a mouse model, that neutral evolution outweighs the effects of immunoselection and that immune checkpoint blockade potentiates the immunoediting, switching the system to non-neutral evolution.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2018-01-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel ; Online: Nuclear receptor NR2F6 inhibition potentiates responses to PD-L1/PD-1 cancer immune checkpoint blockade

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

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Band 13

    Abstract: Immune checkpoints blockade (ICB) is a viable anti-cancer strategy. Here the authors show that nuclear receptor NR2F6 acts as an immune checkpoint in T cells and, using mouse models and human T cells, they show NR2F6 inhibition might improve current ICB ... ...

    Abstract Immune checkpoints blockade (ICB) is a viable anti-cancer strategy. Here the authors show that nuclear receptor NR2F6 acts as an immune checkpoint in T cells and, using mouse models and human T cells, they show NR2F6 inhibition might improve current ICB therapy or work as an alternative therapeutic strategy.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2018-04-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel ; Online: Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

    Francesca Finotello / Clemens Mayer / Christina Plattner / Gerhard Laschober / Dietmar Rieder / Hubert Hackl / Anne Krogsdam / Zuzana Loncova / Wilfried Posch / Doris Wilflingseder / Sieghart Sopper / Marieke Ijsselsteijn / Thomas P. Brouwer / Douglas Johnson / Yaomin Xu / Yu Wang / Melinda E. Sanders / Monica V. Estrada / Paula Ericsson-Gonzalez /
    Pornpimol Charoentong / Justin Balko / Noel Filipe da Cunha Carvalho de Miranda / Zlatko Trajanoski

    Genome Medicine, Vol 11, Iss 1, Pp 1-

    2019  Band 20

    Abstract: 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. ... ...

    Abstract 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.
    Schlagwörter Cancer immunology ; Immunotherapy ; Deconvolution ; RNA-seq ; Immune contexture ; Medicine ; R ; Genetics ; QH426-470
    Sprache Englisch
    Erscheinungsdatum 2019-05-01T00:00:00Z
    Verlag BMC
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel ; Online: Correction to

    Francesca Finotello / Clemens Mayer / Christina Plattner / Gerhard Laschober / Dietmar Rieder / Hubert Hackl / Anne Krogsdam / Zuzana Loncova / Wilfried Posch / Doris Wilflingseder / Sieghart Sopper / Marieke Ijsselsteijn / Thomas P. Brouwer / Douglas Johnson / Yaomin Xu / Yu Wang / Melinda E. Sanders / Monica V. Estrada / Paula Ericsson-Gonzalez /
    Pornpimol Charoentong / Justin Balko / Noel Filipe da Cunha Carvalho de Miranda / Zlatko Trajanoski

    Genome Medicine, Vol 11, Iss 1, Pp 1-

    Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

    2019  Band 3

    Abstract: It was highlighted that the original article [1] contained a typesetting mistake in the name of Noel Filipe da Cunha Carvalho de Miranda. This was incorrectly captured as Noel Filipe da Cunha Carvahlo de Miranda. It was also highlighted that in Fig. 3C ... ...

    Abstract It was highlighted that the original article [1] contained a typesetting mistake in the name of Noel Filipe da Cunha Carvalho de Miranda. This was incorrectly captured as Noel Filipe da Cunha Carvahlo de Miranda. It was also highlighted that in Fig. 3C the left panels Y-axis were cropped and in Fig. 5C, CD8 bar was cropped. This Correction article shows the correct Figs. 3 and 5. The original article has been updated.
    Schlagwörter Medicine ; R ; Genetics ; QH426-470
    Sprache Englisch
    Erscheinungsdatum 2019-07-01T00:00:00Z
    Verlag BMC
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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