51
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Duong E, Fessenden TB, Lutz E, Dinter T, Yim L, Blatt S, Bhutkar A, Wittrup KD, Spranger S. Type I interferon activates MHC class I-dressed CD11b + conventional dendritic cells to promote protective anti-tumor CD8 + T cell immunity. Immunity 2022; 55:308-323.e9. [PMID: 34800368 PMCID: PMC10827482 DOI: 10.1016/j.immuni.2021.10.020] [Citation(s) in RCA: 140] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/31/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022]
Abstract
Tumor-infiltrating dendritic cells (DCs) assume varied functional states that impact anti-tumor immunity. To delineate the DC states associated with productive anti-tumor T cell immunity, we compared spontaneously regressing and progressing tumors. Tumor-reactive CD8+ T cell responses in Batf3-/- mice lacking type 1 DCs (DC1s) were lost in progressor tumors but preserved in regressor tumors. Transcriptional profiling of intra-tumoral DCs within regressor tumors revealed an activation state of CD11b+ conventional DCs (DC2s) characterized by expression of interferon (IFN)-stimulated genes (ISGs) (ISG+ DCs). ISG+ DC-activated CD8+ T cells ex vivo comparably to DC1. Unlike cross-presenting DC1, ISG+ DCs acquired and presented intact tumor-derived peptide-major histocompatibility complex class I (MHC class I) complexes. Constitutive type I IFN production by regressor tumors drove the ISG+ DC state, and activation of MHC class I-dressed ISG+ DCs by exogenous IFN-β rescued anti-tumor immunity against progressor tumors in Batf3-/- mice. The ISG+ DC gene signature is detectable in human tumors. Engaging this functional DC state may present an approach for the treatment of human disease.
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Affiliation(s)
- Ellen Duong
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA; Department of Biology, MIT, Cambridge, MA, USA
| | - Tim B Fessenden
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Emi Lutz
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Teresa Dinter
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA; Department of Biology, MIT, Cambridge, MA, USA
| | - Leon Yim
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Sarah Blatt
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Arjun Bhutkar
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Karl Dane Wittrup
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Stefani Spranger
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA; Department of Biology, MIT, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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52
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Rangel R, Pickering CR, Sikora AG, Spiotto MT. Genetic Changes Driving Immunosuppressive Microenvironments in Oral Premalignancy. Front Immunol 2022; 13:840923. [PMID: 35154165 PMCID: PMC8829003 DOI: 10.3389/fimmu.2022.840923] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 12/25/2022] Open
Abstract
Oral premalignant lesions (OPLs) are the precursors to oral cavity cancers, and have variable rates of progression to invasive disease. As an intermediate state, OPLs have acquired a subset of the genomic alterations while arising in an oral inflammatory environment. These specific genomic changes may facilitate the transition to an immune microenvironment that permits malignant transformation. Here, we will discuss mechanisms by which OPLs develop an immunosuppressive microenvironment that facilitates progression to invasive cancer. We will describe how genomic alterations and immune microenvironmental changes co-evolve and cooperate to promote OSCC progression. Finally, we will describe how these immune microenvironmental changes provide specific and unique evolutionary vulnerabilities for targeted therapies. Therefore, understanding the genomic changes that drive immunosuppressive microenvironments may eventually translate into novel biomarker and/or therapeutic approaches to limit the progression of OPLs to potential lethal oral cancers.
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Affiliation(s)
- Roberto Rangel
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Curtis R. Pickering
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Andrew G. Sikora
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Michael T. Spiotto
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
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53
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Au L, Hatipoglu E, Robert de Massy M, Litchfield K, Beattie G, Rowan A, Schnidrig D, Thompson R, Byrne F, Horswell S, Fotiadis N, Hazell S, Nicol D, Shepherd STC, Fendler A, Mason R, Del Rosario L, Edmonds K, Lingard K, Sarker S, Mangwende M, Carlyle E, Attig J, Joshi K, Uddin I, Becker PD, Sunderland MW, Akarca A, Puccio I, Yang WW, Lund T, Dhillon K, Vasquez MD, Ghorani E, Xu H, Spencer C, López JI, Green A, Mahadeva U, Borg E, Mitchison M, Moore DA, Proctor I, Falzon M, Pickering L, Furness AJS, Reading JL, Salgado R, Marafioti T, Jamal-Hanjani M, Kassiotis G, Chain B, Larkin J, Swanton C, Quezada SA, Turajlic S. Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma. Cancer Cell 2021; 39:1497-1518.e11. [PMID: 34715028 PMCID: PMC8599450 DOI: 10.1016/j.ccell.2021.10.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 10/06/2021] [Indexed: 02/08/2023]
Abstract
ADAPTeR is a prospective, phase II study of nivolumab (anti-PD-1) in 15 treatment-naive patients (115 multiregion tumor samples) with metastatic clear cell renal cell carcinoma (ccRCC) aiming to understand the mechanism underpinning therapeutic response. Genomic analyses show no correlation between tumor molecular features and response, whereas ccRCC-specific human endogenous retrovirus expression indirectly correlates with clinical response. T cell receptor (TCR) analysis reveals a significantly higher number of expanded TCR clones pre-treatment in responders suggesting pre-existing immunity. Maintenance of highly similar clusters of TCRs post-treatment predict response, suggesting ongoing antigen engagement and survival of families of T cells likely recognizing the same antigens. In responders, nivolumab-bound CD8+ T cells are expanded and express GZMK/B. Our data suggest nivolumab drives both maintenance and replacement of previously expanded T cell clones, but only maintenance correlates with response. We hypothesize that maintenance and boosting of a pre-existing response is a key element of anti-PD-1 mode of action.
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Affiliation(s)
- Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Emine Hatipoglu
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Gordon Beattie
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Desiree Schnidrig
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicos Fotiadis
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London SW3 6JJ, UK
| | - Steve Hazell
- Department of Pathology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - David Nicol
- Department of Urology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Robert Mason
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lyra Del Rosario
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kim Edmonds
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Karla Lingard
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Sarah Sarker
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Mary Mangwende
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Eleanor Carlyle
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Jan Attig
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Kroopa Joshi
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Imran Uddin
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Pablo D Becker
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK
| | - Ayse Akarca
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Ignazio Puccio
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - William W Yang
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Tom Lund
- Translational Immune Oncology Lab, Centre for Molecular Pathology, The Royal Marsden Hospital, Sutton SM2 5PT, UK
| | - Kim Dhillon
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Marcos Duran Vasquez
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Hang Xu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charlotte Spencer
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - José I López
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Institute, 48903 Barakaldo, Bizkaia, Spain
| | - Anna Green
- Department of Cellular Pathology, Guy's & St Thomas' NHS Foundation Trust, St Thomas' Hospital, London SE1 7EH, UK
| | - Ula Mahadeva
- Department of Cellular Pathology, Guy's & St Thomas' NHS Foundation Trust, St Thomas' Hospital, London SE1 7EH, UK
| | - Elaine Borg
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Miriam Mitchison
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Ian Proctor
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Mary Falzon
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Lisa Pickering
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Andrew J S Furness
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne VIC 300, Australia; Department of Pathology, GZA-ZNA Hospitals, Wilrijk, Antwerp, Belgium
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London WC1E 6DD, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - James Larkin
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK.
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
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54
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Aldea M, Benitez JC, Chaput N, Besse B. New Immunotherapy Combinations Enter the Battlefield of Malignant Mesothelioma. Cancer Discov 2021; 11:2674-2676. [PMID: 34725087 DOI: 10.1158/2159-8290.cd-21-1046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chimeric antigen receptor (CAR) T cells targeting mesothelin plus pembrolizumab, and atezolizumab plus bevacizumab, have recently shown clinical efficacy in phase I trials in malignant pleural and peritoneal mesothelioma. Despite being tested in a highly selected patient population and requiring a complex engineering that can hardly be upscaled, CAR T cells combined with pembrolizumab bring the first proof of efficacy in cold solid tumors with low genomic heterogeneity, while atezolizumab-bevacizumab offers an easy-to-use combination of antiangiogenics and immunotherapy in an orphan disease.See related article by Raghav et al., p. 2738.See related article by Adusumilli et al., p. 2748.
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Affiliation(s)
- Mihaela Aldea
- School of Medicine, Paris-Saclay University, Paris, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | - Jose Carlos Benitez
- School of Medicine, Paris-Saclay University, Paris, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | - Nathalie Chaput
- Laboratory of Immunomonitoring in Oncology, Gustave Roussy, Villejuif, France.,School of Pharmacy, Paris-Saclay University, Chatenay-Malabry, France
| | - Benjamin Besse
- School of Medicine, Paris-Saclay University, Paris, France. .,Cancer Medicine Department, Gustave Roussy, Villejuif, France
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55
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Jaakkola MK, Elo LL. Estimating cell type-specific differential expression using deconvolution. Brief Bioinform 2021; 23:6396788. [PMID: 34651640 PMCID: PMC8769698 DOI: 10.1093/bib/bbab433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 12/02/2022] Open
Affiliation(s)
- Maria K Jaakkola
- Department of Mathematics and Statistics, University of Turku, Yliopistonmäki, 20014, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520, Turku, Finland.,Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FI-20520, Turku, Finland
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56
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STING protects breast cancer cells from intrinsic and genotoxic-induced DNA instability via a non-canonical, cell-autonomous pathway. Oncogene 2021; 40:6627-6640. [PMID: 34625708 DOI: 10.1038/s41388-021-02037-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 09/13/2021] [Accepted: 09/23/2021] [Indexed: 01/13/2023]
Abstract
STING (Stimulator of Interferon Genes) is an endoplasmic reticulum-anchored adaptor of the innate immunity best known to trigger pro-inflammatory cytokine expression in response to pathogen infection. In cancer, this canonical pathway can be activated by intrinsic or drug-induced genomic instability, potentiating antitumor immune responses. Here we report that STING downregulation decreases cell survival and increases sensitivity to genotoxic treatment in a panel of breast cancer cell lines in a cell-autonomous manner. STING silencing impaired DNA Damage Response (53BP1) foci formation and increased DNA break accumulation. These newly identified properties were found to be independent of STING partner cGAS and of its canonical pro-inflammatory pathway. STING was shown to partially localize at the inner nuclear membrane in a variety of breast cancer cell models and clinical tumor samples. Interactomics analysis of nuclear STING identified several proteins of the DNA Damage Response, including the three proteins of the DNA-PK complex, further supporting a role of STING in the regulation of genomic stability. In breast and ovarian cancer patients that received adjuvant chemotherapy, high STING expression is associated with increased risk of relapse. In summary, this study highlights an alternative, non-canonical tumor-promoting role of STING that opposes its well-documented function in tumor immunosurveillance.
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57
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Winkler C, King M, Berthe J, Ferraioli D, Garuti A, Grillo F, Rodriguez-Canales J, Ferrando L, Chopin N, Ray-Coquard I, Delpuech O, Rinchai D, Bedognetti D, Ballestrero A, Leo E, Zoppoli G. SLFN11 captures cancer-immunity interactions associated with platinum sensitivity in high-grade serous ovarian cancer. JCI Insight 2021; 6:146098. [PMID: 34549724 PMCID: PMC8492341 DOI: 10.1172/jci.insight.146098] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/28/2021] [Indexed: 01/30/2023] Open
Abstract
Large independent analyses on cancer cell lines followed by functional studies have identified Schlafen 11 (SLFN11), a putative helicase, as the strongest predictor of sensitivity to DNA-damaging agents (DDAs), including platinum. However, its role as a prognostic biomarker is undefined, partially due to the lack of validated methods to score SLFN11 in human tissues. Here, we implemented a pipeline to quantify SLFN11 in human cancer samples. By analyzing a cohort of high-grade serous ovarian carcinoma (HGSOC) specimens before platinum-based chemotherapy treatment, we show, for the first time to our knowledge, that SLFN11 density in both the neoplastic and microenvironmental components was independently associated with favorable outcome. We observed SLFN11 expression in both infiltrating innate and adaptive immune cells, and analyses in a second, independent, cohort revealed that SLFN11 was associated with immune activation in HGSOC. We found that platinum treatments activated immune-related pathways in ovarian cancer cells in an SLFN11-dependent manner, representative of tumor-immune transactivation. Moreover, SLFN11 expression was induced in activated, isolated immune cell subpopulations, hinting that SLFN11 in the immune compartment may be an indicator of immune transactivation. In summary, we propose SLFN11 is a dual biomarker capturing simultaneously interconnected immunological and cancer cell–intrinsic functional dispositions associated with sensitivity to DDA treatment.
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Affiliation(s)
| | | | - Julie Berthe
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Anna Garuti
- Department of Internal Medicine and Medical Specialties and
| | - Federica Grillo
- Department of Integrated Surgical and Diagnostic Sciences, University of Genova, Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | | | | | | | | | | | - Davide Bedognetti
- Department of Internal Medicine and Medical Specialties and.,Cancer Research Department, Sidra Medicine, Doha, Qatar.,Hamad Bin Khalifa University, Doha, Qatar
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties and.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties and.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
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58
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Razaghi A, Brusselaers N, Björnstedt M, Durand-Dubief M. Copy number alteration of the interferon gene cluster in cancer: Individual patient data meta-analysis prospects to personalized immunotherapy. Neoplasia 2021; 23:1059-1068. [PMID: 34555656 PMCID: PMC8458777 DOI: 10.1016/j.neo.2021.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 01/14/2023]
Abstract
Interferon (IFN) therapy has been the standard of care for a variety of cancers for decades due to the pleiotropic actions of IFNs against malignancies. However, little is known about the role of copy number alteration (CNA) of the IFN gene cluster, located at the 9p21.3, in cancer. This large individual patient data meta-analysis using 9937 patients obtained from cBioportal indicates that CNA of the IFN gene cluster is prevalent among 24 cancer types. Two statistical approaches showed that notably deletion of this cluster is significantly associated with increased mortality in many cancer types particularly uterus (OR = 2.71), kidney (OR = 2.26), and brain (OR = 2.08) cancers. The Cancer Genome Atlas PanCancer analysis also showed that CNA of the IFN gene cluster is significantly associated with decreased overall survival. For instance, the overall survival of patients with brain glioma reduced from 93m (diploidy) to 24m (with the CNA of the IFN gene). In conclusion, the CNA of the IFN gene cluster is associated with increased mortality and decreased overall survival in cancer. Thus, in the prospect of immunotherapy, CNA of IFN gene may be a useful biomarker to predict the prognosis of patients and also as a potential companion diagnostic test to prescribe IFN α/β therapy.
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Affiliation(s)
- Ali Razaghi
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University-Hospital, Stockholm, Sweden
| | - Nele Brusselaers
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Karolinska Hospital, Stockholm, Sweden; Global Health Institute, Antwerp University, Belgium; Department of Head and Skin, Ghent University, Belgium
| | - Mikael Björnstedt
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University-Hospital, Stockholm, Sweden.
| | - Mickael Durand-Dubief
- Department of Biosciences and Nutrition, Neo, Karolinska Institute, Huddinge, Sweden.
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59
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Musella M, Galassi C, Manduca N, Sistigu A. The Yin and Yang of Type I IFNs in Cancer Promotion and Immune Activation. BIOLOGY 2021; 10:856. [PMID: 34571733 PMCID: PMC8467547 DOI: 10.3390/biology10090856] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/22/2022]
Abstract
Type I Interferons (IFNs) are key regulators of natural and therapy-induced host defense against viral infection and cancer. Several years of remarkable progress in the field of oncoimmunology have revealed the dual nature of these cytokines. Hence, Type I IFNs may trigger anti-tumoral responses, while leading immune dysfunction and disease progression. This dichotomy relies on the duration and intensity of the transduced signaling, the nature of the unleashed IFN stimulated genes, and the subset of responding cells. Here, we discuss the role of Type I IFNs in the evolving relationship between the host immune system and cancer, as we offer a view of the therapeutic strategies that exploit and require an intact Type I IFN signaling, and the role of these cytokines in inducing adaptive resistance. A deep understanding of the complex, yet highly regulated, network of Type I IFN triggered molecular pathways will help find a timely and immune"logical" way to exploit these cytokines for anticancer therapy.
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Affiliation(s)
- Martina Musella
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (C.G.); (N.M.)
| | - Claudia Galassi
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (C.G.); (N.M.)
| | - Nicoletta Manduca
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (C.G.); (N.M.)
| | - Antonella Sistigu
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (C.G.); (N.M.)
- Tumor Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
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60
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Lapuente-Santana Ó, van Genderen M, Hilbers PA, Finotello F, Eduati F. Interpretable systems biomarkers predict response to immune-checkpoint inhibitors. PATTERNS (NEW YORK, N.Y.) 2021; 2:100293. [PMID: 34430923 PMCID: PMC8369166 DOI: 10.1016/j.patter.2021.100293] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
Cancer cells can leverage several cell-intrinsic and -extrinsic mechanisms to escape immune system recognition. The inherent complexity of the tumor microenvironment, with its multicellular and dynamic nature, poses great challenges for the extraction of biomarkers of immune response and immunotherapy efficacy. Here, we use RNA-sequencing (RNA-seq) data combined with different sources of prior knowledge to derive system-based signatures of the tumor microenvironment, quantifying immune-cell composition and intra- and intercellular communications. We applied multi-task learning to these signatures to predict different hallmarks of immune responses and derive cancer-type-specific models based on interpretable systems biomarkers. By applying our models to independent RNA-seq data from cancer patients treated with PD-1/PD-L1 inhibitors, we demonstrated that our method to Estimate Systems Immune Response (EaSIeR) accurately predicts therapeutic outcome. We anticipate that EaSIeR will be a valuable tool to provide a holistic description of immune responses in complex and dynamic systems such as tumors using available RNA-seq data.
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Affiliation(s)
- Óscar Lapuente-Santana
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Maisa van Genderen
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Peter A.J. Hilbers
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
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61
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Huang SSY, Toufiq M, Saraiva LR, Van Panhuys N, Chaussabel D, Garand M. Transcriptome and Literature Mining Highlight the Differential Expression of ERLIN1 in Immune Cells during Sepsis. BIOLOGY 2021; 10:755. [PMID: 34439987 PMCID: PMC8389572 DOI: 10.3390/biology10080755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/20/2022]
Abstract
Sepsis results from the dysregulation of the host immune system. This highly variable disease affects 19 million people globally, and accounts for 5 million deaths annually. In transcriptomic datasets curated from public repositories, we observed a consistent upregulation (3.26-5.29 fold) of ERLIN1-a gene coding for an ER membrane prohibitin and a regulator of inositol 1, 4, 5-trisphosphate receptors and sterol regulatory element-binding proteins-under septic conditions in healthy neutrophils, monocytes, and whole blood. In vitro expression of the ERLIN1 gene and proteins was measured by stimulating the whole blood of healthy volunteers to a combination of lipopolysaccharide and peptidoglycan. Septic stimulation induced a significant increase in ERLIN1 expression; however, ERLIN1 was differentially expressed among the immune blood cell subsets. ERLIN1 was uniquely increased in whole blood neutrophils, and confirmed in the differentiated HL60 cell line. The scarcity of ERLIN1 in sepsis literature indicates a knowledge gap between the functions of ERLIN1, calcium homeostasis, and cholesterol and fatty acid biosynthesis, and sepsis. In combination with experimental data, we bring forth the hypothesis that ERLIN1 is variably modulated among immune cells in response to cellular perturbations, and has implications for ER functions and/or ER membrane protein components during sepsis.
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Affiliation(s)
- Susie S. Y. Huang
- Research Department, Sidra Medicine, Doha 26999, Qatar; (M.T.); (L.R.S.); (N.V.P.); (D.C.)
| | - Mohammed Toufiq
- Research Department, Sidra Medicine, Doha 26999, Qatar; (M.T.); (L.R.S.); (N.V.P.); (D.C.)
| | - Luis R. Saraiva
- Research Department, Sidra Medicine, Doha 26999, Qatar; (M.T.); (L.R.S.); (N.V.P.); (D.C.)
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
| | - Nicholas Van Panhuys
- Research Department, Sidra Medicine, Doha 26999, Qatar; (M.T.); (L.R.S.); (N.V.P.); (D.C.)
| | - Damien Chaussabel
- Research Department, Sidra Medicine, Doha 26999, Qatar; (M.T.); (L.R.S.); (N.V.P.); (D.C.)
| | - Mathieu Garand
- Research Department, Sidra Medicine, Doha 26999, Qatar; (M.T.); (L.R.S.); (N.V.P.); (D.C.)
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62
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Altman MC, Rinchai D, Baldwin N, Toufiq M, Whalen E, Garand M, Syed Ahamed Kabeer B, Alfaki M, Presnell SR, Khaenam P, Ayllón-Benítez A, Mougin F, Thébault P, Chiche L, Jourde-Chiche N, Phillips JT, Klintmalm G, O'Garra A, Berry M, Bloom C, Wilkinson RJ, Graham CM, Lipman M, Lertmemongkolchai G, Bedognetti D, Thiebaut R, Kheradmand F, Mejias A, Ramilo O, Palucka K, Pascual V, Banchereau J, Chaussabel D. Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data. Nat Commun 2021; 12:4385. [PMID: 34282143 PMCID: PMC8289976 DOI: 10.1038/s41467-021-24584-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 06/21/2021] [Indexed: 01/21/2023] Open
Abstract
As the capacity for generating large-scale molecular profiling data continues to grow, the ability to extract meaningful biological knowledge from it remains a limitation. Here, we describe the development of a new fixed repertoire of transcriptional modules, BloodGen3, that is designed to serve as a stable reusable framework for the analysis and interpretation of blood transcriptome data. The construction of this repertoire is based on co-clustering patterns observed across sixteen immunological and physiological states encompassing 985 blood transcriptome profiles. Interpretation is supported by customized resources, including module-level analysis workflows, fingerprint grid plot visualizations, interactive web applications and an extensive annotation framework comprising functional profiling reports and reference transcriptional profiles. Taken together, this well-characterized and well-supported transcriptional module repertoire can be employed for the interpretation and benchmarking of blood transcriptome profiles within and across patient cohorts. Blood transcriptome fingerprints for the 16 reference cohorts can be accessed interactively via: https://drinchai.shinyapps.io/BloodGen3Module/ .
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Affiliation(s)
- Matthew C Altman
- Systems Immunology, Benaroya Research Institute, Seattle, WA, USA.
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA.
| | | | - Nicole Baldwin
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX, USA
| | | | - Elizabeth Whalen
- Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | | | | | | | - Scott R Presnell
- Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Prasong Khaenam
- Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Aaron Ayllón-Benítez
- Inserm U1219 Bordeaux Population Health Research Center, Bordeaux University, Bordeaux, France
| | - Fleur Mougin
- Inserm U1219 Bordeaux Population Health Research Center, Bordeaux University, Bordeaux, France
| | | | - Laurent Chiche
- Department of Internal Medicine, Hopital Européen, Marseille, France
| | | | - J Theodore Phillips
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX, USA
| | - Goran Klintmalm
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX, USA
| | - Anne O'Garra
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Chloe Bloom
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Robert J Wilkinson
- The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College, London, UK
- Wellcome Center for Infectious Diseases Research in Africa and Department of Medicine, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Observatory, 7925, Cape Town, Republic of South Africa
| | - Christine M Graham
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK
| | - Marc Lipman
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Ganjana Lertmemongkolchai
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | | | - Rodolphe Thiebaut
- Inserm U1219 Bordeaux Population Health Research Center, Bordeaux University, Bordeaux, France
| | - Farrah Kheradmand
- Baylor College of Medicine & Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey VAMC, Houston, TX, USA
| | - Asuncion Mejias
- Abigail Wexner Research Institute at Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH, USA
| | - Octavio Ramilo
- Abigail Wexner Research Institute at Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH, USA
| | - Karolina Palucka
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Virginia Pascual
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Jacques Banchereau
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Damien Chaussabel
- Systems Immunology, Benaroya Research Institute, Seattle, WA, USA.
- Research Branch, Sidra Medicine, Doha, Qatar.
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63
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Nalamalapu RR, Yue M, Stone AR, Murphy S, Saha MS. The tweety Gene Family: From Embryo to Disease. Front Mol Neurosci 2021; 14:672511. [PMID: 34262434 PMCID: PMC8273234 DOI: 10.3389/fnmol.2021.672511] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/18/2021] [Indexed: 12/31/2022] Open
Abstract
The tweety genes encode gated chloride channels that are found in animals, plants, and even simple eukaryotes, signifying their deep evolutionary origin. In vertebrates, the tweety gene family is highly conserved and consists of three members—ttyh1, ttyh2, and ttyh3—that are important for the regulation of cell volume. While research has elucidated potential physiological functions of ttyh1 in neural stem cell maintenance, proliferation, and filopodia formation during neural development, the roles of ttyh2 and ttyh3 are less characterized, though their expression patterns during embryonic and fetal development suggest potential roles in the development of a wide range of tissues including a role in the immune system in response to pathogen-associated molecules. Additionally, members of the tweety gene family have been implicated in various pathologies including cancers, particularly pediatric brain tumors, and neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease. Here, we review the current state of research using information from published articles and open-source databases on the tweety gene family with regard to its structure, evolution, expression during development and adulthood, biochemical and cellular functions, and role in human disease. We also identify promising areas for further research to advance our understanding of this important, yet still understudied, family of genes.
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Affiliation(s)
- Rithvik R Nalamalapu
- Department of Biology, College of William and Mary, Williamsburg, VA, United States
| | - Michelle Yue
- Department of Biology, College of William and Mary, Williamsburg, VA, United States
| | - Aaron R Stone
- Department of Biology, College of William and Mary, Williamsburg, VA, United States
| | - Samantha Murphy
- Department of Biology, College of William and Mary, Williamsburg, VA, United States
| | - Margaret S Saha
- Department of Biology, College of William and Mary, Williamsburg, VA, United States
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64
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Doostparast Torshizi A, Duan J, Wang K. A computational method for direct imputation of cell type-specific expression profiles and cellular compositions from bulk-tissue RNA-Seq in brain disorders. NAR Genom Bioinform 2021; 3:lqab056. [PMID: 34169279 PMCID: PMC8219045 DOI: 10.1093/nargab/lqab056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/24/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
The importance of cell type-specific gene expression in disease-relevant tissues is increasingly recognized in genetic studies of complex diseases. However, most gene expression studies are conducted on bulk tissues, without examining cell type-specific expression profiles. Several computational methods are available for cell type deconvolution (i.e. inference of cellular composition) from bulk RNA-Seq data, but few of them impute cell type-specific expression profiles. We hypothesize that with external prior information such as single cell RNA-seq and population-wide expression profiles, it can be computationally tractable to estimate both cellular composition and cell type-specific expression from bulk RNA-Seq data. Here we introduce CellR, which addresses cross-individual gene expression variations to adjust the weights of cell-specific gene markers. It then transforms the deconvolution problem into a linear programming model while taking into account inter/intra cellular correlations and uses a multi-variate stochastic search algorithm to estimate the cell type-specific expression profiles. Analyses on several complex diseases such as schizophrenia, Alzheimer’s disease, Huntington’s disease and type 2 diabetes validated the efficiency of CellR, while revealing how specific cell types contribute to different diseases. In summary, CellR compares favorably against competing approaches, enabling cell type-specific re-analysis of gene expression data on bulk tissues in complex diseases.
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Affiliation(s)
- Abolfazl Doostparast Torshizi
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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65
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Nicholls K, Wallace C. Comparison of sparse biclustering algorithms for gene expression datasets. Brief Bioinform 2021; 22:6265183. [PMID: 33951731 PMCID: PMC8574648 DOI: 10.1093/bib/bbab140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/08/2021] [Accepted: 03/25/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Gene clustering and sample clustering are commonly used to find patterns in gene expression datasets. However, genes may cluster differently in heterogeneous samples (e.g. different tissues or disease states), whilst traditional methods assume that clusters are consistent across samples. Biclustering algorithms aim to solve this issue by performing sample clustering and gene clustering simultaneously. Existing reviews of biclustering algorithms have yet to include a number of more recent algorithms and have based comparisons on simplistic simulated datasets without specific evaluation of biclusters in real datasets, using less robust metrics. RESULTS We compared four classes of sparse biclustering algorithms on a range of simulated and real datasets. All algorithms generally struggled on simulated datasets with a large number of genes or implanted biclusters. We found that Bayesian algorithms with strict sparsity constraints had high accuracy on the simulated datasets and did not require any post-processing, but were considerably slower than other algorithm classes. We found that non-negative matrix factorisation algorithms performed poorly, but could be re-purposed for biclustering through a sparsity-inducing post-processing procedure we introduce; one such algorithm was one of the most highly ranked on real datasets. In a multi-tissue knockout mouse RNA-seq dataset, the algorithms rarely returned clusters containing samples from multiple different tissues, whilst such clusters were identified in a human dataset of more closely related cell types (sorted blood cell subsets). This highlights the need for further thought in the design and analysis of multi-tissue studies to avoid differences between tissues dominating the analysis. AVAILABILITY Code to run the analysis is available at https://github.com/nichollskc/biclust_comp, including wrappers for each algorithm, implementations of evaluation metrics, and code to simulate datasets and perform pre- and post-processing. The full tables of results are available at https://doi.org/10.5281/zenodo.4581206.
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Affiliation(s)
- Kath Nicholls
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Chris Wallace
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK.,MRC Biostatistics Unit, Cambridge Biomedical Campus, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
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66
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Melnick M, Gonzales P, LaRocca TJ, Song Y, Wuu J, Benatar M, Oskarsson B, Petrucelli L, Dowell RD, Link CD, Prudencio M. Application of a bioinformatic pipeline to RNA-seq data identifies novel viruslike sequence in human blood. G3-GENES GENOMES GENETICS 2021; 11:6259144. [PMID: 33914880 PMCID: PMC8661426 DOI: 10.1093/g3journal/jkab141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022]
Abstract
Numerous reports have suggested that infectious agents could play a role in neurodegenerative diseases, but specific etiological agents have not been convincingly demonstrated. To search for candidate agents in an unbiased fashion, we have developed a bioinformatic pipeline that identifies microbial sequences in mammalian RNA-seq data, including sequences with no significant nucleotide similarity hits in GenBank. Effectiveness of the pipeline was tested using publicly available RNA-seq data and in a reconstruction experiment using synthetic data. We then applied this pipeline to a novel RNA-seq dataset generated from a cohort of 120 samples from amyotrophic lateral sclerosis patients and controls, and identified sequences corresponding to known bacteria and viruses, as well as novel virus-like sequences. The presence of these novel virus-like sequences, which were identified in subsets of both patients and controls, were confirmed by quantitative RT-PCR. We believe this pipeline will be a useful tool for the identification of potential etiological agents in the many RNA-seq datasets currently being generated.
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Affiliation(s)
- Marko Melnick
- Integrative Physiology, University of Colorado, Boulder, Colorado, 80303, USA
| | - Patrick Gonzales
- Integrative Physiology, University of Colorado, Boulder, Colorado, 80303, USA
| | - Thomas J LaRocca
- Department of Health and Exercise Science, Center for Healthy Aging, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Yuping Song
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida, 32224, USA
| | - Joanne Wuu
- Department of Neurology, University of Miami, Miami, Florida, 33136, USA
| | - Michael Benatar
- Department of Neurology, University of Miami, Miami, Florida, 33136, USA
| | - Björn Oskarsson
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville FL, 32224, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida, 32224, USA.,Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida, 32224, USA
| | - Robin D Dowell
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, 80303, USA
| | - Christopher D Link
- Integrative Physiology, University of Colorado, Boulder, Colorado, 80303, USA.,Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, 80303, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida, 32224, USA.,Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida, 32224, USA
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67
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Jin H, Liu Z. A benchmark for RNA-seq deconvolution analysis under dynamic testing environments. Genome Biol 2021; 22:102. [PMID: 33845875 PMCID: PMC8042713 DOI: 10.1186/s13059-021-02290-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/09/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Deconvolution analyses have been widely used to track compositional alterations of cell types in gene expression data. Although a large number of novel methods have been developed, due to a lack of understanding of the effects of modeling assumptions and tuning parameters, it is challenging for researchers to select an optimal deconvolution method suitable for the targeted biological conditions. RESULTS To systematically reveal the pitfalls and challenges of deconvolution analyses, we investigate the impact of several technical and biological factors including simulation model, quantification unit, component number, weight matrix, and unknown content by constructing three benchmarking frameworks. These frameworks cover comparative analysis of 11 popular deconvolution methods under 1766 conditions. CONCLUSIONS We provide new insights to researchers for future application, standardization, and development of deconvolution tools on RNA-seq data.
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Affiliation(s)
- Haijing Jin
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, USA.
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68
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Leon KE, Tangudu NK, Aird KM, Buj R. Loss of p16: A Bouncer of the Immunological Surveillance? Life (Basel) 2021; 11:309. [PMID: 33918220 PMCID: PMC8065641 DOI: 10.3390/life11040309] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
p16INK4A (hereafter called p16) is an important tumor suppressor protein frequently suppressed in human cancer and highly upregulated in many types of senescence. Although its role as a cell cycle regulator is very well delineated, little is known about its other non-cell cycle-related roles. Importantly, recent correlative studies suggest that p16 may be a regulator of tissue immunological surveillance through the transcriptional regulation of different chemokines, interleukins and other factors secreted as part of the senescence-associated secretory phenotype (SASP). Here, we summarize the current evidence supporting the hypothesis that p16 is a regulator of tumor immunity.
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Affiliation(s)
- Kelly E. Leon
- UPMC Hillman Cancer Center, Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; (K.E.L.); (N.K.T.); (K.M.A.)
- Biomedical Sciences Graduate Program, Penn State College of Medicine, Hershey, PA 15213, USA
| | - Naveen Kumar Tangudu
- UPMC Hillman Cancer Center, Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; (K.E.L.); (N.K.T.); (K.M.A.)
| | - Katherine M. Aird
- UPMC Hillman Cancer Center, Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; (K.E.L.); (N.K.T.); (K.M.A.)
| | - Raquel Buj
- UPMC Hillman Cancer Center, Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; (K.E.L.); (N.K.T.); (K.M.A.)
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69
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Nguyen TT, Ramsay L, Ahanfeshar-Adams M, Lajoie M, Schadendorf D, Alain T, Watson IR. Mutations in the IFNγ-JAK-STAT Pathway Causing Resistance to Immune Checkpoint Inhibitors in Melanoma Increase Sensitivity to Oncolytic Virus Treatment. Clin Cancer Res 2021; 27:3432-3442. [PMID: 33593882 DOI: 10.1158/1078-0432.ccr-20-3365] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/15/2021] [Accepted: 02/09/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Next-generation sequencing studies and CRISPR-Cas9 screens have established mutations in the IFNγ-JAK-STAT pathway as an immune checkpoint inhibitor (ICI) resistance mechanism in a subset of patients with melanoma. We hypothesized ICI resistance mutations in the IFNγ pathway would simultaneously render melanomas susceptible to oncolytic virus (OV) therapy. EXPERIMENTAL DESIGN Cytotoxicity experiments were performed with a number of OVs on a matched melanoma cell line pair generated from a baseline biopsy and a progressing lesion with complete JAK2 loss from a patient that relapsed on anti-PD-1 therapy, in melanoma lines following JAK1/2 RNA interference (RNAi) and pharmacologic inhibition and in Jak2 knockout (KO) B16-F10 mouse melanomas. Furthermore, we estimated the frequency of genetic alterations in the IFNγ-JAK-STAT pathway in human melanomas. RESULTS The melanoma line from an anti-PD-1 progressing lesion was 7- and 22-fold more sensitive to the modified OVs, herpes simplex virus 1 (HSV1-dICP0) and vesicular stomatitis virus (VSV-Δ51), respectively, compared with the line from the baseline biopsy. RNAi, JAK1/2 inhibitor studies, and in vivo studies of Jak2 KOs B16-F10 melanomas revealed a significant increase in VSV-Δ51 sensitivity with JAK/STAT pathway inhibition. Our analysis of The Cancer Genome Atlas data estimated that approximately 11% of ICI-naïve cutaneous melanomas have alterations in IFNγ pathway genes that may confer OV susceptibility. CONCLUSIONS We provide mechanistic support for the use of OVs as a precision medicine strategy for both salvage therapy in ICI-resistant and first-line treatment in melanomas with IFNγ-JAK-STAT pathway mutations. Our study also supports JAK inhibitor-OV combination therapy for treatment-naïve melanomas without IFN signaling defects.See related commentary by Kaufman, p. 3278.
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Affiliation(s)
- Tan-Trieu Nguyen
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada.,Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - LeeAnn Ramsay
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | | | - Mathieu Lajoie
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, University Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Essen, Germany
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Ian R Watson
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada. .,Department of Biochemistry, McGill University, Montréal, Québec, Canada.,Research Institute of the McGill University Health Centre, Montréal, Canada
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70
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Jaakkola MK, Elo LL. Computational deconvolution to estimate cell type-specific gene expression from bulk data. NAR Genom Bioinform 2021; 3:lqaa110. [PMID: 33575652 PMCID: PMC7803005 DOI: 10.1093/nargab/lqaa110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 12/24/2022] Open
Abstract
Computational deconvolution is a time and cost-efficient approach to obtain cell type-specific information from bulk gene expression of heterogeneous tissues like blood. Deconvolution can aim to either estimate cell type proportions or abundances in samples, or estimate how strongly each present cell type expresses different genes, or both tasks simultaneously. Among the two separate goals, the estimation of cell type proportions/abundances is widely studied, but less attention has been paid on defining the cell type-specific expression profiles. Here, we address this gap by introducing a novel method Rodeo and empirically evaluating it and the other available tools from multiple perspectives utilizing diverse datasets.
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Affiliation(s)
- Maria K Jaakkola
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland
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71
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Mo Q, Li R, Adeegbe DO, Peng G, Chan KS. Integrative multi-omics analysis of muscle-invasive bladder cancer identifies prognostic biomarkers for frontline chemotherapy and immunotherapy. Commun Biol 2020; 3:784. [PMID: 33335285 PMCID: PMC7746703 DOI: 10.1038/s42003-020-01491-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 11/13/2020] [Indexed: 12/24/2022] Open
Abstract
Only a subgroup of patients with muscle-invasive bladder cancer (MIBC) are responders toward cisplatin-based chemotherapy and PD-L1 blockade immunotherapy. There is a clinical need to identify MIBC molecular subtypes and biomarkers for patient stratification toward the therapies. Here, we performed an integrative clustering analysis of 388 MIBC samples with multi-omics data and identified basal and luminal/differentiated integrative subtypes and derived a 42 gene panel for classification of MIBC. Using nine additional gene expression data (n = 844), we demonstrated the prognostic value of the 42 basal-luminal genes. The basal subtype was associated with worse overall survival in patients receiving no neoadjuvant chemotherapy (NAC), but better overall survival in patients receiving NAC in two clinical trials. Each of the subtypes could be further divided into chr9 p21.3 normal or loss subgroup. The patients with low expression of MTAP/CDKN2A/2B (indicative of chr9 p21.3 loss) had a significantly lower response rate to anti-PD-L1 immunotherapy and worse survival than the patients with high expression of MTAP/CDKN2A/2B. This integrative analysis reveals intrinsic MIBC subtypes and biomarkers with prognostic value for the frontline therapies.
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Affiliation(s)
- Qianxing Mo
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA.
| | - Roger Li
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Dennis O Adeegbe
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Keith Syson Chan
- Department of Pathology and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
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72
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Lei H, Wang C, Wang Y, Wang C. Single-cell RNA-Seq revealed profound immune alteration in the peripheral blood of patients with bacterial infection. Int J Infect Dis 2020; 103:527-535. [PMID: 33278616 DOI: 10.1016/j.ijid.2020.11.205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/21/2020] [Accepted: 11/28/2020] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES Bacterial infection remains one of the greatest threats to human health. However, how human hosts respond to bacterial infection has not been thoroughly understood. Better understanding of this response will improve human health. METHODS Here, we conducted an investigation on host response to bacterial infection using unperturbed clinical samples and single-cell RNA-Seq (scRNA-Seq) technology. To evaluate immune alteration upon bacterial infection in scRNA-Seq data of peripheral blood mononuclear cells (PBMCs), we developed a barcode analytical framework named PBMCode. RESULTS Using this PBMCode framework, we revealed profound immune alteration in peripheral blood under bacterial infection, including the emergence of natural killer T (NKT) cell cluster, reduction of B cell population, and considerable changes in T cells and monocytes. In addition, we also observed a large quantity of low-density neutrophils. CONCLUSIONS Our investigation on single cells provided unprecedented details in the alteration of both cell population and cell state under bacterial infection. These findings may be relevant to clinical decisions. The complexity of host response to bacterial infection revealed by scRNA-Seq deserves further attention in future studies.
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Affiliation(s)
- Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China; Cunji Medical School, University of Chinese Academy of Sciences, Beijing, China; Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China.
| | - Chi Wang
- Department of Clinical Laboratory of Medicine, Chinese PLA General Hospital & Medical School of Chinese PLA, Beijing, China
| | - Yunlai Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
| | - Chengbin Wang
- Department of Clinical Laboratory of Medicine, Chinese PLA General Hospital & Medical School of Chinese PLA, Beijing, China.
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73
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Rinchai D, Altman MC, Konza O, Hässler S, Martina F, Toufiq M, Garand M, Kabeer BSA, Palucka K, Mejias A, Ramilo O, Bedognetti D, Mariotti‐Ferrandiz E, Klatzmann D, Chaussabel D. Definition of erythroid cell-positive blood transcriptome phenotypes associated with severe respiratory syncytial virus infection. Clin Transl Med 2020; 10:e244. [PMID: 33377660 PMCID: PMC7733317 DOI: 10.1002/ctm2.244] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/31/2022] Open
Abstract
Biomarkers to assess the risk of developing severe respiratory syncytial virus (RSV) infection are needed. We conducted a meta-analysis of 490 unique profiles from six public RSV blood transcriptome datasets. A repertoire of 382 well-characterized transcriptional modules was used to define dominant host responses to RSV infection. The consolidated RSV cohort was stratified according to four traits: "interferon response" (IFN), "neutrophil-driven inflammation" (Infl), "cell cycle" (CC), and "erythrocytes" (Ery). We identified eight prevalent blood transcriptome phenotypes, of which three Ery+ phenotypes comprised higher proportions of patients requiring intensive care. This finding confirms on a larger scale data from one of our earlier reports describing an association between an erythrocyte signature and RSV disease severity. Further contextual interpretation made it possible to associate this signature with immunosuppressive states (late stage cancer, pharmacological immunosuppression), and with a population of fetal glycophorin A+ erythroid precursors. Furthermore, we posit that this erythrocyte cell signature may be linked to a population of immunosuppressive erythroid cells previously described in the literature, and that overabundance of this cell population in RSV patients may underlie progression to severe disease. These findings outline potential priority areas for biomarker development and investigations into the immune biology of RSV infection. The approach that we developed and employed here should also permit to delineate prevalent blood transcriptome phenotypes in other settings.
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Affiliation(s)
| | - Matthew C. Altman
- Benaroya Research InstituteSeattleWashington
- University of WashingtonSeattleWashington
| | - Oceane Konza
- Biotherapy (CIC‐BTi) and Inflammation‐Immunopathology‐Biotherapy Department (i2B)AP‐HP, Hôpital Pitié‐SalpêtrièreParisFrance
| | - Signe Hässler
- Biotherapy (CIC‐BTi) and Inflammation‐Immunopathology‐Biotherapy Department (i2B)AP‐HP, Hôpital Pitié‐SalpêtrièreParisFrance
- Immunology‐Immunopathology‐Immunotherapy (i3)Sorbonne UniversitéINSERMParisFrance
| | - Federica Martina
- Biotherapy (CIC‐BTi) and Inflammation‐Immunopathology‐Biotherapy Department (i2B)AP‐HP, Hôpital Pitié‐SalpêtrièreParisFrance
| | | | | | | | | | - Asuncion Mejias
- Division of Infectious DiseasesNationwide Children's HospitalColumbusOhio
| | - Octavio Ramilo
- Division of Infectious DiseasesNationwide Children's HospitalColumbusOhio
| | - Davide Bedognetti
- Sidra MedicineDohaQatar
- Department of Internal Medicine and Medical SpecialtiesUniversity of GenoaGenoaItaly
| | | | - David Klatzmann
- Biotherapy (CIC‐BTi) and Inflammation‐Immunopathology‐Biotherapy Department (i2B)AP‐HP, Hôpital Pitié‐SalpêtrièreParisFrance
- Immunology‐Immunopathology‐Immunotherapy (i3)Sorbonne UniversitéINSERMParisFrance
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74
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Rawat A, Rinchai D, Toufiq M, Marr AK, Kino T, Garand M, Tatari-Calderone Z, Kabeer BSA, Krishnamoorthy N, Bedognetti D, Karim MY, Sastry KS, Chaussabel D. A Neutrophil-Driven Inflammatory Signature Characterizes the Blood Transcriptome Fingerprint of Psoriasis. Front Immunol 2020; 11:587946. [PMID: 33329570 PMCID: PMC7732684 DOI: 10.3389/fimmu.2020.587946] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022] Open
Abstract
Transcriptome profiling approaches have been widely used to investigate the mechanisms underlying psoriasis pathogenesis. Most researchers have measured changes in transcript abundance in skin biopsies; relatively few have examined transcriptome changes in the blood. Although less relevant to the study of psoriasis pathogenesis, blood transcriptome profiles can be readily compared across various diseases. Here, we used a pre-established set of 382 transcriptional modules as a common framework to compare changes in blood transcript abundance in two independent public psoriasis datasets. We then compared the resulting "transcriptional fingerprints" to those obtained for a reference set of 16 pathological or physiological states. The perturbations in blood transcript abundance in psoriasis were relatively subtle compared to the changes we observed in other autoimmune and auto-inflammatory diseases. However, we did observe a consistent pattern of changes for a set of modules associated with neutrophil activation and inflammation; interestingly, this pattern resembled that observed in patients with Kawasaki disease. This similarity between the blood-transcriptome signatures in psoriasis and Kawasaki disease suggests that the immune mechanisms driving their pathogenesis might be partially shared.
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Affiliation(s)
- Arun Rawat
- Research Department, SIDRA Medicine, Doha, Qatar
| | | | | | | | | | | | | | | | | | - Davide Bedognetti
- Research Department, SIDRA Medicine, Doha, Qatar
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
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75
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Bhuva DD, Cursons J, Davis MJ. Stable gene expression for normalisation and single-sample scoring. Nucleic Acids Res 2020; 48:e113. [PMID: 32997146 PMCID: PMC7641762 DOI: 10.1093/nar/gkaa802] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/08/2020] [Accepted: 09/29/2020] [Indexed: 12/22/2022] Open
Abstract
Gene expression signatures have been critical in defining the molecular phenotypes of cells, tissues, and patient samples. Their most notable and widespread clinical application is stratification of breast cancer patients into molecular (PAM50) subtypes. The cost and relatively large amounts of fresh starting material required for whole-transcriptome sequencing has limited clinical application of thousands of existing gene signatures captured in repositories such as the Molecular Signature Database. We identified genes with stable expression across a range of abundances, and with a preserved relative ordering across thousands of samples, allowing signature scoring and supporting general data normalisation for transcriptomic data. Our new method, stingscore, quantifies and summarises relative expression levels of signature genes from individual samples through the inclusion of these ‘stably-expressed genes’. We show that our list of stable genes has better stability across cancer and normal tissue data than previously proposed gene sets. Additionally, we show that signature scores computed from targeted transcript measurements using stingscore can predict docetaxel response in breast cancer patients. This new approach to gene expression signature analysis will facilitate the development of panel-type tests for gene expression signatures, thus supporting clinical translation of the powerful insights gained from cancer transcriptomic studies.
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Affiliation(s)
- Dharmesh D Bhuva
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.,School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia
| | - Joseph Cursons
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Melissa J Davis
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
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76
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Sage AP, Ng KW, Marshall EA, Stewart GL, Minatel BC, Enfield KSS, Martin SD, Brown CJ, Abraham N, Lam WL. Assessment of long non-coding RNA expression reveals novel mediators of the lung tumour immune response. Sci Rep 2020; 10:16945. [PMID: 33037279 PMCID: PMC7547676 DOI: 10.1038/s41598-020-73787-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/21/2020] [Indexed: 12/31/2022] Open
Abstract
The tumour immune microenvironment is a crucial mediator of lung tumourigenesis, and characterizing the immune landscape of patient tumours may guide immunotherapy treatment regimens and uncover novel intervention points. We sought to identify the landscape of tumour-infiltrating immune cells in the context of long non-coding RNA (lncRNAs), known regulators of gene expression. We examined the lncRNA profiles of lung adenocarcinoma (LUAD) tumours by interrogating RNA sequencing data from microdissected and non-microdissected samples (BCCRC and TCGA). Subsequently, analysis of single-cell RNA sequencing data from lung tumours and flow-sorted healthy peripheral blood mononuclear cells identified lncRNAs in immune cells, highlighting their biological and prognostic relevance. We discovered lncRNA expression patterns indicative of regulatory relationships with immune-related protein-coding genes, including the relationship between AC008750.1 and NKG7 in NK cells. Activation of NK cells in vitro was sufficient to induce AC008750.1 expression. Finally, siRNA-mediated knockdown of AC008750.1 significantly impaired both the expression of NKG7 and the anti-tumour capacity of NK cells. We present an atlas of cancer-cell extrinsic immune cell-expressed lncRNAs, in vitro evidence for a functional role of lncRNAs in anti-tumour immune activity, which upon further exploration may reveal novel clinical utility as markers of immune infiltration.
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Affiliation(s)
- Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada.
| | - Greg L Stewart
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Brenda C Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Katey S S Enfield
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Spencer D Martin
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ninan Abraham
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
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77
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Li H, Sharma A, Ming W, Sun X, Liu H. A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples. BMC Genomics 2020; 21:652. [PMID: 32967610 PMCID: PMC7510109 DOI: 10.1186/s12864-020-06888-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/07/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of gene expression across multiple conditions. In addition, the knowledge about the identification of gene expression markers across multiple conditions is still paucity. RESULTS Herein, we developed a hybrid tool, LinDeconSeq, which consists of 1) identifying marker genes using specificity scoring and mutual linearity strategies across any number of cell types, and 2) predicting cellular fractions of bulk samples using weighted robust linear regression with the marker genes identified in the first stage. On multiple publicly available datasets, the marker genes identified by LinDeconSeq demonstrated better accuracy and reproducibility compared to MGFM and RNentropy. Among deconvolution methods, LinDeconSeq showed low average deviations (≤0.0958) and high average Pearson correlations (≥0.8792) between the predicted and actual fractions on the benchmark datasets. Importantly, the cellular fractions predicted by LinDeconSeq appear to be relevant in the diagnosis of acute myeloid leukemia (AML). The distinct cellular fractions in granulocyte-monocyte progenitor (GMP), lymphoid-primed multipotent progenitor (LMPP) and monocytes (MONO) were found to be closely associated with AML compared to the healthy samples. Moreover, the heterogeneity of cellular fractions in AML patients divided these patients into two subgroups, differing in both prognosis and mutation patterns. GMP fraction was the most pronounced between these two subgroups, particularly, in SubgroupA, which was strongly associated with the better AML prognosis and the younger population. Totally, the identification of marker genes by LinDeconSeq represents the improved feature for deconvolution. The data processing strategy with regard to the cellular fractions used in this study also showed potential for the diagnosis and prognosis of diseases. CONCLUSIONS Taken together, we developed a freely-available and open-source tool LinDeconSeq ( https://github.com/lihuamei/LinDeconSeq ), which includes marker identification and deconvolution procedures. LinDeconSeq is comparable to other current methods in terms of accuracy when applied to benchmark datasets and has broad application in clinical outcome and disease-specific molecular mechanisms.
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Affiliation(s)
- Huamei Li
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Amit Sharma
- Department of Ophthalmology, University Hospital Bonn, 53127, Bonn, Germany
| | - Wenglong Ming
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China.
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78
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Lee S, Zhang AY, Su S, Ng AP, Holik AZ, Asselin-Labat ML, Ritchie ME, Law CW. Covering all your bases: incorporating intron signal from RNA-seq data. NAR Genom Bioinform 2020; 2:lqaa073. [PMID: 33575621 PMCID: PMC7671406 DOI: 10.1093/nargab/lqaa073] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/31/2022] Open
Abstract
RNA-seq datasets can contain millions of intron reads per library that are typically removed from downstream analysis. Only reads overlapping annotated exons are considered to be informative since mature mRNA is assumed to be the major component sequenced, especially for poly(A) RNA libraries. In this study, we show that intron reads are informative, and through exploratory data analysis of read coverage that intron signal is representative of both pre-mRNAs and intron retention. We demonstrate how intron reads can be utilized in differential expression analysis using our index method where a unique set of differentially expressed genes can be detected using intron counts. In exploring read coverage, we also developed the superintronic software that quickly and robustly calculates user-defined summary statistics for exonic and intronic regions. Across multiple datasets, superintronic enabled us to identify several genes with distinctly retained introns that had similar coverage levels to that of neighbouring exons. The work and ideas presented in this paper is the first of its kind to consider multiple biological sources for intron reads through exploratory data analysis, minimizing bias in discovery and interpretation of results. Our findings open up possibilities for further methods development for intron reads and RNA-seq data in general.
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Affiliation(s)
- Stuart Lee
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Albert Y Zhang
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Shian Su
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Ashley P Ng
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aliaksei Z Holik
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Matthew E Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Charity W Law
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
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79
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Toufiq M, Roelands J, Alfaki M, Syed Ahamed Kabeer B, Saadaoui M, Lakshmanan AP, Bangarusamy DK, Murugesan S, Bedognetti D, Hendrickx W, Al Khodor S, Terranegra A, Rinchai D, Chaussabel D, Garand M. Annexin A3 in sepsis: novel perspectives from an exploration of public transcriptome data. Immunology 2020; 161:291-302. [PMID: 32682335 PMCID: PMC7692248 DOI: 10.1111/imm.13239] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022] Open
Abstract
According to publicly available transcriptome datasets, the abundance of Annexin A3 (ANXA3) is robustly increased during the course of sepsis; however, no studies have examined the biological significance or clinical relevance of ANXA3 in this pathology. Here we explored this interpretation gap and identified possible directions for future research. Based on reference transcriptome datasets, we found that ANXA3 expression is restricted to neutrophils, is upregulated in vitro after exposure to plasma obtained from septic patients, and is associated with adverse clinical outcomes. Secondly, an increase in ANXA3 transcript abundance was also observed in vivo, in the blood of septic patients in multiple independent studies. ANXA3 is known to mediate calcium-dependent granules-phagosome fusion in support of microbicidal activity in neutrophils. More recent work has also shown that ANXA3 enhances proliferation and survival of tumour cells via a Caspase-3-dependent mechanism. And this same molecule is also known to play a critical role in regulation of apoptotic events in neutrophils. Thus, we posit that during sepsis ANXA3 might either play a beneficial role, by facilitating microbial clearance and resolution of the infection; or a detrimental role, by prolonging neutrophil survival, which is known to contribute to sepsis-mediated organ damage.
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80
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Rinchai D, Syed Ahamed Kabeer B, Toufiq M, Tatari-Calderone Z, Deola S, Brummaier T, Garand M, Branco R, Baldwin N, Alfaki M, Altman MC, Ballestrero A, Bassetti M, Zoppoli G, De Maria A, Tang B, Bedognetti D, Chaussabel D. A modular framework for the development of targeted Covid-19 blood transcript profiling panels. J Transl Med 2020; 18:291. [PMID: 32736569 PMCID: PMC7393249 DOI: 10.1186/s12967-020-02456-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Covid-19 morbidity and mortality are associated with a dysregulated immune response. Tools are needed to enhance existing immune profiling capabilities in affected patients. Here we aimed to develop an approach to support the design of targeted blood transcriptome panels for profiling the immune response to SARS-CoV-2 infection. METHODS We designed a pool of candidates based on a pre-existing and well-characterized repertoire of blood transcriptional modules. Available Covid-19 blood transcriptome data was also used to guide this process. Further selection steps relied on expert curation. Additionally, we developed several custom web applications to support the evaluation of candidates. RESULTS As a proof of principle, we designed three targeted blood transcript panels, each with a different translational connotation: immunological relevance, therapeutic development relevance and SARS biology relevance. CONCLUSION Altogether the work presented here may contribute to the future expansion of immune profiling capabilities via targeted profiling of blood transcript abundance in Covid-19 patients.
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Affiliation(s)
| | | | | | | | | | - Tobias Brummaier
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | - Nicole Baldwin
- Baylor Institute for Immunology Research and Baylor Research Institute, Dallas, TX, USA
| | | | - Matthew C Altman
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
- Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Alberto Ballestrero
- Department of Internal Medicine, Università degli Studi di Genova, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Matteo Bassetti
- Division of Infectious and Tropical Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine, Università degli Studi di Genova, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Andrea De Maria
- Division of Infectious and Tropical Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Benjamin Tang
- Nepean Clinical School, University of Sydney, Sydney, NSW, Australia
| | - Davide Bedognetti
- Sidra Medicine, Doha, Qatar
- Department of Internal Medicine, Università degli Studi di Genova, Genoa, Italy
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81
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Host and Parasite Transcriptomic Changes upon Successive Plasmodium falciparum Infections in Early Childhood. mSystems 2020; 5:5/4/e00116-20. [PMID: 32636334 PMCID: PMC7343306 DOI: 10.1128/msystems.00116-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We show that dual RNA-seq from patient blood samples allows characterization of host/parasite interactions during malaria infections and can provide a solid framework to study the acquisition of antimalarial immunity, as well as the adaptations of P. falciparum to malaria-experienced hosts. Children are highly susceptible to clinical malaria, and in regions where malaria is endemic, their immune systems must face successive encounters with Plasmodium falciparum parasites before they develop immunity, first against severe disease and later against uncomplicated malaria. Understanding cellular and molecular interactions between host and parasites during an infection could provide insights into the processes underlying this gradual acquisition of immunity, as well as to how parasites adapt to infect hosts that are successively more malaria experienced. Here, we describe methods to analyze the host and parasite gene expression profiles generated simultaneously from blood samples collected from five consecutive symptomatic P. falciparum infections in three Malian children. We show that the data generated enable statistical assessment of the proportions of (i) each white blood cell subset and (ii) the parasite developmental stages, as well as investigations of host-parasite gene coexpression. We also use the sequences generated to analyze allelic variations in transcribed regions and determine the complexity of each infection. While limited by the modest sample size, our analyses suggest that host gene expression profiles primarily clustered by individual, while the parasite gene expression profiles seemed to differentiate early from late infections. Overall, this study provides a solid framework to examine the mechanisms underlying acquisition of immunity to malaria infections using whole-blood transcriptome sequencing (RNA-seq). IMPORTANCE We show that dual RNA-seq from patient blood samples allows characterization of host/parasite interactions during malaria infections and can provide a solid framework to study the acquisition of antimalarial immunity, as well as the adaptations of P. falciparum to malaria-experienced hosts.
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82
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Niss K, Gomez-Casado C, Hjaltelin JX, Joeris T, Agace WW, Belling KG, Brunak S. Complete Topological Mapping of a Cellular Protein Interactome Reveals Bow-Tie Motifs as Ubiquitous Connectors of Protein Complexes. Cell Rep 2020; 31:107763. [PMID: 32553166 DOI: 10.1016/j.celrep.2020.107763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 02/03/2020] [Accepted: 05/21/2020] [Indexed: 11/18/2022] Open
Abstract
The network topology of a protein interactome is shaped by the function of each protein, making it a resource of functional knowledge in tissues and in single cells. Today, this resource is underused, as complete network topology characterization has proved difficult for large protein interactomes. We apply a matrix visualization and decoding approach to a physical protein interactome of a dendritic cell, thereby characterizing its topology with no prior assumptions of structure. We discover 294 proteins, each forming topological motifs called "bow-ties" that tie together the majority of observed protein complexes. The central proteins of these bow-ties have unique network properties, display multifunctional capabilities, are enriched for essential proteins, and are widely expressed in other cells and tissues. Collectively, the bow-tie motifs are a pervasive and previously unnoted topological trend in cellular interactomes. As such, these results provide fundamental knowledge on how intracellular protein connectivity is organized and operates.
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Affiliation(s)
- Kristoffer Niss
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Cristina Gomez-Casado
- Immunology Section, Lund University, BMC D14, 221-84 Lund, Sweden; Institute of Applied Molecular Medicine, Faculty of Medicine, San Pablo CEU University, 28925 Madrid, Spain
| | - Jessica X Hjaltelin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Thorsten Joeris
- Immunology Section, Lund University, BMC D14, 221-84 Lund, Sweden
| | - William W Agace
- Immunology Section, Lund University, BMC D14, 221-84 Lund, Sweden; Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Kirstine G Belling
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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83
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Choi J, Baldwin TM, Wong M, Bolden JE, Fairfax KA, Lucas EC, Cole R, Biben C, Morgan C, Ramsay KA, Ng AP, Kauppi M, Corcoran LM, Shi W, Wilson N, Wilson MJ, Alexander WS, Hilton DJ, de Graaf CA. Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans. Nucleic Acids Res 2020; 47:D780-D785. [PMID: 30395284 PMCID: PMC6324085 DOI: 10.1093/nar/gky1020] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/12/2018] [Indexed: 11/24/2022] Open
Abstract
During haematopoiesis, haematopoietic stem cells differentiate into restricted potential progenitors before maturing into the many lineages required for oxygen transport, wound healing and immune response. We have updated Haemopedia, a database of gene-expression profiles from a broad spectrum of haematopoietic cells, to include RNA-seq gene-expression data from both mice and humans. The Haemopedia RNA-seq data set covers a wide range of lineages and progenitors, with 57 mouse blood cell types (flow sorted populations from healthy mice) and 12 human blood cell types. This data set has been made accessible for exploration and analysis, to researchers and clinicians with limited bioinformatics experience, on our online portal Haemosphere: https://www.haemosphere.org. Haemosphere also includes nine other publicly available high-quality data sets relevant to haematopoiesis. We have added the ability to compare gene expression across data sets and species by curating data sets with shared lineage designations or to view expression gene vs gene, with all plots available for download by the user.
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Affiliation(s)
- Jarny Choi
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Centre for Stem Cell Systems, Anatomy and Neuroscience Department, The University of Melbourne, Parkville, Victoria, Australia
| | - Tracey M Baldwin
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Mae Wong
- CSL Limited, Parkville, Victoria, Australia
| | - Jessica E Bolden
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kirsten A Fairfax
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Erin C Lucas
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Rebecca Cole
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Christine Biben
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Clare Morgan
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kerry A Ramsay
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Ashley P Ng
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Maria Kauppi
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Lynn M Corcoran
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Wei Shi
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria, Australia
| | | | | | - Warren S Alexander
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Douglas J Hilton
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Carolyn A de Graaf
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
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84
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Smith MA, Chiang CC, Zerrouki K, Rahman S, White WI, Streicher K, Rees WA, Schiffenbauer A, Rider LG, Miller FW, Manna Z, Hasni S, Kaplan MJ, Siegel R, Sinibaldi D, Sanjuan MA, Casey KA. Using the circulating proteome to assess type I interferon activity in systemic lupus erythematosus. Sci Rep 2020; 10:4462. [PMID: 32157125 PMCID: PMC7064569 DOI: 10.1038/s41598-020-60563-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 02/13/2020] [Indexed: 12/27/2022] Open
Abstract
Type I interferon (IFN) drives pathology in systemic lupus erythematosus (SLE) and can be tracked via IFN-inducible transcripts in blood. Here, we examined whether measurement of circulating proteins, which enter the bloodstream from inflamed tissues, also offers insight into global IFN activity. Using a novel protocol we generated 1,132 aptamer-based protein measurements from anti-dsDNApos SLE blood samples and derived an IFN protein signature (IFNPS) that approximates the IFN 21-gene signature (IFNGS). Of 82 patients with SLE, IFNPS was elevated for 89% of IFNGS-high patients (49/55) and 26% of IFNGS-low patients (7/27). IFNGS-high/IFNPS-high patients exhibited activated NK, CD4, and CD8 T cells, while IFNPS-high only patients did not. IFNPS correlated with global disease activity in lymphopenic and non-lymphopenic patients and decreased following type I IFN neutralisation with anifrolumab in the SLE phase IIb study, MUSE. In summary, we developed a protein signature that reflects IFNGS and identifies a new subset of patients with SLE who have IFN activity.
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Affiliation(s)
| | | | | | | | | | | | | | - Adam Schiffenbauer
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Lisa G Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Frederick W Miller
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Zerai Manna
- Lupus Clinical Research Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarfaraz Hasni
- Lupus Clinical Research Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, MD, USA
| | - Richard Siegel
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
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85
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Speake C, Skinner SO, Berel D, Whalen E, Dufort MJ, Young WC, Odegard JM, Pesenacker AM, Gorus FK, James EA, Levings MK, Linsley PS, Akirav EM, Pugliese A, Hessner MJ, Nepom GT, Gottardo R, Long SA. A composite immune signature parallels disease progression across T1D subjects. JCI Insight 2019; 4:126917. [PMID: 31671072 PMCID: PMC6962023 DOI: 10.1172/jci.insight.126917] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 10/29/2019] [Indexed: 02/06/2023] Open
Abstract
At diagnosis, most people with type 1 diabetes (T1D) produce measurable levels of endogenous insulin, but the rate at which insulin secretion declines is heterogeneous. To explain this heterogeneity, we sought to identify a composite signature predictive of insulin secretion, using a collaborative assay evaluation and analysis pipeline that incorporated multiple cellular and serum measures reflecting β cell health and immune system activity. The ability to predict decline in insulin secretion would be useful for patient stratification for clinical trial enrollment or therapeutic selection. Analytes from 12 qualified assays were measured in shared samples from subjects newly diagnosed with T1D. We developed a computational tool (DIFAcTO, Data Integration Flexible to Account for different Types of data and Outcomes) to identify a composite panel associated with decline in insulin secretion over 2 years following diagnosis. DIFAcTO uses multiple filtering steps to reduce data dimensionality, incorporates error estimation techniques including cross-validation and sensitivity analysis, and is flexible to assay type, clinical outcome, and disease setting. Using this novel analytical tool, we identified a panel of immune markers that, in combination, are highly associated with loss of insulin secretion. The methods used here represent a potentially novel process for identifying combined immune signatures that predict outcomes relevant for complex and heterogeneous diseases like T1D.
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Affiliation(s)
- Cate Speake
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Samuel O. Skinner
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Dror Berel
- Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Elizabeth Whalen
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Matthew J. Dufort
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - William Chad Young
- Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jared M. Odegard
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Anne M. Pesenacker
- University of British Columbia BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Frans K. Gorus
- Diabetes Research Center, Medical School and University Hospital (UZ Brussel), Brussels Free University Vrije Universiteit Brussel, Brussels, Belgium
| | - Eddie A. James
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Megan K. Levings
- University of British Columbia BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Peter S. Linsley
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Eitan M. Akirav
- Research Institute, Islet Biology, New York University Winthrop Hospital, Mineola, New York, USA
- Stony Brook University School of Medicine, Stony Brook, New York, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Department of Medicine, Division of Diabetes Endocrinology and Metabolism, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | | | - Gerald T. Nepom
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
- Immune Tolerance Network, Bethesda, Maryland, USA
| | - Raphael Gottardo
- Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - S. Alice Long
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
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86
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Ng KW, Attig J, Young GR, Ottina E, Papamichos SI, Kotsianidis I, Kassiotis G. Soluble PD-L1 generated by endogenous retroelement exaptation is a receptor antagonist. eLife 2019; 8:e50256. [PMID: 31729316 PMCID: PMC6877088 DOI: 10.7554/elife.50256] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/13/2019] [Indexed: 12/27/2022] Open
Abstract
Immune regulation is a finely balanced process of positive and negative signals. PD-L1 and its receptor PD-1 are critical regulators of autoimmune, antiviral and antitumoural T cell responses. Although the function of its predominant membrane-bound form is well established, the source and biological activity of soluble PD-L1 (sPD-L1) remain incompletely understood. Here, we show that sPD-L1 in human healthy tissues and tumours is produced by exaptation of an intronic LINE-2A (L2A) endogenous retroelement in the CD274 gene, encoding PD-L1, which causes omission of the transmembrane domain and the regulatory sequence in the canonical 3' untranslated region. The alternatively spliced CD274-L2A transcript forms the major source of sPD-L1 and is highly conserved in hominids, but lost in mice and a few related species. Importantly, CD274-L2A-encoded sPD-L1 lacks measurable T cell inhibitory activity. Instead, it functions as a receptor antagonist, blocking the inhibitory activity of PD-L1 bound on cellular or exosomal membranes.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick InstituteLondonUnited Kingdom
| | - Jan Attig
- Retroviral Immunology, The Francis Crick InstituteLondonUnited Kingdom
| | - George R Young
- Retrovirus-Host Interactions, The Francis Crick InstituteLondonUnited Kingdom
| | - Eleonora Ottina
- Retroviral Immunology, The Francis Crick InstituteLondonUnited Kingdom
| | - Spyros I Papamichos
- Department of HaematologyDemocritus University of Thrace Medical SchoolAlexandroupolisGreece
| | - Ioannis Kotsianidis
- Department of HaematologyDemocritus University of Thrace Medical SchoolAlexandroupolisGreece
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick InstituteLondonUnited Kingdom
- Department of MedicineFaculty of Medicine, Imperial College LondonLondonUnited Kingdom
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87
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Bhuva DD, Cursons J, Smyth GK, Davis MJ. Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer. Genome Biol 2019; 20:236. [PMID: 31727119 PMCID: PMC6857226 DOI: 10.1186/s13059-019-1851-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/02/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Elucidation of regulatory networks, including identification of regulatory mechanisms specific to a given biological context, is a key aim in systems biology. This has motivated the move from co-expression to differential co-expression analysis and numerous methods have been developed subsequently to address this task; however, evaluation of methods and interpretation of the resulting networks has been hindered by the lack of known context-specific regulatory interactions. RESULTS In this study, we develop a simulator based on dynamical systems modelling capable of simulating differential co-expression patterns. With the simulator and an evaluation framework, we benchmark and characterise the performance of inference methods. Defining three different levels of "true" networks for each simulation, we show that accurate inference of causation is difficult for all methods, compared to inference of associations. We show that a z-score-based method has the best general performance. Further, analysis of simulation parameters reveals five network and simulation properties that explained the performance of methods. The evaluation framework and inference methods used in this study are available in the dcanr R/Bioconductor package. CONCLUSIONS Our analysis of networks inferred from simulated data show that hub nodes are more likely to be differentially regulated targets than transcription factors. Based on this observation, we propose an interpretation of the inferred differential network that can reconstruct a putative causal network.
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Affiliation(s)
- Dharmesh D Bhuva
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Joseph Cursons
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gordon K Smyth
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia.
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88
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Abstract
Over the past decade, preclinical and clinical research have confirmed the essential role of interferons for effective host immunological responses to malignant cells. Type I interferons (IFNα and IFNβ) directly regulate transcription of >100 downstream genes, which results in a myriad of direct (on cancer cells) and indirect (through immune effector cells and vasculature) effects on the tumour. New insights into endogenous and exogenous activation of type I interferons in the tumour and its microenvironment have given impetus to drug discovery and patient evaluation of interferon-directed strategies. When combined with prior observations or with other effective modalities for cancer treatment, modulation of the interferon system could contribute to further reductions in cancer morbidity and mortality. This Review discusses new interferon-directed therapeutic opportunities, ranging from cyclic dinucleotides to genome methylation inhibitors, angiogenesis inhibitors, chemoradiation, complexes with neoantigen-targeted monoclonal antibodies, combinations with other emerging therapeutic interventions and associations of interferon-stimulated gene expression with patient prognosis - all of which are strategies that have or will soon enter translational clinical evaluation.
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89
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Johansson J, Kiffin R, Aydin E, Nilsson MS, Hellstrand K, Lindnér P, Naredi P, Olofsson Bagge R, Martner A. Isolated limb perfusion with melphalan activates interferon-stimulated genes to induce tumor regression in patients with melanoma in-transit metastasis. Oncoimmunology 2019; 9:1684126. [PMID: 32002296 PMCID: PMC6959433 DOI: 10.1080/2162402x.2019.1684126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 09/27/2019] [Accepted: 10/20/2019] [Indexed: 12/16/2022] Open
Abstract
Hyperthermic isolated limb perfusion (ILP) with high-dose melphalan is a treatment option for melanoma patients with metastasis confined to limbs (in-transit metastasis). The therapy entails a complete response (CR) rate of 50–70%. Cellular immunity is proposed to impact on the clinical efficacy of ILP, but the detailed aspects of ILP-induced immune activation remain to be explored. For this study, we explored the potential role of interferon-stimulated gene (ISG) products, including CXCL10, CCL2, PD-L2 and IFN-γ along with expression of their cognate receptors CXCR3, CCR4, CCR5 and PD-1 on lymphocytes, for the clinical efficacy of ILP. Patients with high serum levels of CXCL10, CCL2, PD-L2 and IFN-γ were more likely to achieve CR after ILP. Additionally, the expression of CXCR3, CCR4 and CCR5 on T cells and/or natural killer (NK) cells was enhanced by ILP. Peripheral blood mononuclear cells (PBMCs) secreted high levels of CXCL10, CCL2 and IFN-γ in response to co-culture with melphalan-exposed melanoma cells in vitro. Activated T cells migrated toward supernatants from these co-cultures. Furthermore, melphalan-exposed melanoma cells triggered upregulation of CXCR3, CCR4, CCR5 and PD-1 on co-cultured T cells and/or NK cells. Our results suggest that constituents released from melphalan-exposed melanoma cells stimulate the ISG axis with ensuing formation of chemokines and upregulation of chemokine receptor expression on anti-neoplastic immune cells, which may contribute in ILP-induced tumor regression.
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Affiliation(s)
- Junko Johansson
- TIMM Laboratory, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Roberta Kiffin
- TIMM Laboratory, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ebru Aydin
- TIMM Laboratory, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Malin S Nilsson
- TIMM Laboratory, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kristoffer Hellstrand
- TIMM Laboratory, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Per Lindnér
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Transplantation Centre, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Peter Naredi
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Roger Olofsson Bagge
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Anna Martner
- TIMM Laboratory, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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90
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Molecular profiling of rheumatoid arthritis patients reveals an association between innate and adaptive cell populations and response to anti-tumor necrosis factor. Arthritis Res Ther 2019; 21:216. [PMID: 31647025 PMCID: PMC6813112 DOI: 10.1186/s13075-019-1999-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/06/2019] [Indexed: 12/13/2022] Open
Abstract
Background The goal of this study is to use comprehensive molecular profiling to characterize clinical response to anti-TNF therapy in a real-world setting and identify reproducible markers differentiating good responders and non-responders in rheumatoid arthritis (RA). Methods Whole-blood mRNA, plasma proteins, and glycopeptides were measured in two cohorts of biologic-naïve RA patients (n = 40 and n = 36) from the Corrona CERTAIN (Comparative Effectiveness Registry to study Therapies for Arthritis and Inflammatory coNditions) registry at baseline and after 3 months of anti-TNF treatment. Response to treatment was categorized by EULAR criteria. A cell type-specific data analysis was conducted to evaluate the involvement of the most common immune cell sub-populations. Findings concordant between the two cohorts were further assessed for reproducibility using selected NCBI-GEO datasets and clinical laboratory measurements available in the CERTAIN database. Results A treatment-related signature suggesting a reduction in neutrophils, independent of the status of response, was indicated by a high level of correlation (ρ = 0.62; p < 0.01) between the two cohorts. A baseline, response signature of increased innate cell types in responders compared to increased adaptive cell types in non-responders was identified in both cohorts. This result was further assessed by applying the cell type-specific analysis to five other publicly available RA datasets. Evaluation of the neutrophil-to-lymphocyte ratio at baseline in the remaining patients (n = 1962) from the CERTAIN database confirmed the observation (odds ratio of good/moderate response = 1.20 [95% CI = 1.03–1.41, p = 0.02]). Conclusion Differences in innate/adaptive immune cell type composition at baseline may be a major contributor to response to anti-TNF treatment within the first 3 months of therapy.
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91
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Roelands J, Garand M, Hinchcliff E, Ma Y, Shah P, Toufiq M, Alfaki M, Hendrickx W, Boughorbel S, Rinchai D, Jazaeri A, Bedognetti D, Chaussabel D. Long-Chain Acyl-CoA Synthetase 1 Role in Sepsis and Immunity: Perspectives From a Parallel Review of Public Transcriptome Datasets and of the Literature. Front Immunol 2019; 10:2410. [PMID: 31681299 PMCID: PMC6813721 DOI: 10.3389/fimmu.2019.02410] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 09/26/2019] [Indexed: 12/21/2022] Open
Abstract
A potential role for the long-chain acyl-CoA synthetase family member 1 (ACSL1) in the immunobiology of sepsis was explored during a hands-on training workshop. Participants first assessed the robustness of the potential gap in biomedical knowledge identified via an initial screen of public transcriptome data and of the literature associated with ACSL1. Increase in ACSL1 transcript abundance during sepsis was confirmed in several independent datasets. Querying the ACSL1 literature also confirmed the absence of reports associating ACSL1 with sepsis. Inferences drawn from both the literature (via indirect associations) and public transcriptome data (via correlation) point to the likely participation of ACSL1 and ACSL4, another family member, in inflammasome activation in neutrophils during sepsis. Furthermore, available clinical data indicate that levels of ACSL1 and ACSL4 induction was significantly higher in fatal cases of sepsis. This denotes potential translational relevance and is consistent with involvement in pathways driving potentially deleterious systemic inflammation. Finally, while ACSL1 expression was induced in blood in vitro by a wide range of pathogen-derived factors as well as TNF, induction of ACSL4 appeared restricted to flagellated bacteria and pathogen-derived TLR5 agonists and IFNG. Taken together, this joint review of public literature and omics data records points to two members of the acyl-CoA synthetase family potentially playing a role in inflammasome activation in neutrophils. Translational relevance of these observations in the context of sepsis and other inflammatory conditions remain to be investigated.
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Affiliation(s)
- Jessica Roelands
- Sidra Medicine, Doha, Qatar.,Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | | | - Emily Hinchcliff
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ying Ma
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Parin Shah
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | | | | | | | | | - Amir Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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92
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Virotherapy as a Potential Therapeutic Approach for the Treatment of Aggressive Thyroid Cancer. Cancers (Basel) 2019; 11:cancers11101532. [PMID: 31636245 PMCID: PMC6826611 DOI: 10.3390/cancers11101532] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/13/2022] Open
Abstract
Virotherapy is a novel cancer treatment based on oncolytic viruses (OVs), which selectively infect and lyse cancer cells, without harming normal cells or tissues. Several viruses, either naturally occurring or developed through genetic engineering, are currently under investigation in clinical studies. Emerging reports suggesting the immune-stimulatory property of OVs against tumor cells further support the clinical use of OVs for the treatment of lesions lacking effective therapies. Poorly differentiated thyroid carcinoma (PDTC) and anaplastic thyroid carcinoma (ATC), have a poor prognosis and limited treatment options. Therefore, several groups investigated the therapeutic potential of OVs in PDTC/ATC models producing experimental data sustaining the potential clinical efficacy of OVs in these cancer models. Moreover, the presence of an immunosuppressive microenvironment further supports the potential use of OVs in ATC. In this review, we present the results of the studies evaluating the efficacy of OVs alone or in combination with other treatment options. In particular, their potential therapeutic combination with multiple kinases inhibitors (MKIs) or immune checkpoint inhibitors are discussed.
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93
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Wilson DR, Jin C, Ibrahim JG, Sun W. ICeD-T Provides Accurate Estimates of Immune Cell Abundance in Tumor Samples by Allowing for Aberrant Gene Expression Patterns. J Am Stat Assoc 2019; 115:1055-1065. [PMID: 33012900 DOI: 10.1080/01621459.2019.1654874] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Immunotherapies have attracted lots of research interests recently. The need to understand the underlying mechanisms of immunotherapies and to develop precision immunotherapy regimens has spurred great interest in characterizing immune cell composition within the tumor microenvironment. Several methods have been developed to estimate immune cell composition using gene expression data from bulk tumor samples. However, these methods are not flexible enough to handle aberrant patterns of gene expression data, e.g., inconsistent cell type-specific gene expression between purified reference samples and tumor samples. We propose a novel statistical method for expression deconvolution called ICeD-T (Immune Cell Deconvolution in Tumor tissues). ICeD-T automatically identifies aberrant genes whose expression are inconsistent with the deconvolution model and down-weights their contributions to cell type abundance estimates. We evaluated the performance of ICeD-T versus existing methods in simulation studies and several real data analyses. ICeD-T displayed comparable or superior performance to these competing methods. Applying these methods to assess the relationship between immunotherapy response and immune cell composition, ICeD-T is able to identify significant associations that are missed by its competitors.
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Affiliation(s)
- Douglas R Wilson
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Chong Jin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Joseph G Ibrahim
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Wei Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA.,Department of Biostatistics, University of Washington, Seattle, WA
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94
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Li Z, Wu H. TOAST: improving reference-free cell composition estimation by cross-cell type differential analysis. Genome Biol 2019; 20:190. [PMID: 31484546 PMCID: PMC6727351 DOI: 10.1186/s13059-019-1778-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/30/2019] [Indexed: 02/07/2023] Open
Abstract
In the analysis of high-throughput data from complex samples, cell composition is an important factor that needs to be accounted for. Except for a limited number of tissues with known pure cell type profiles, a majority of genomics and epigenetics data relies on the "reference-free deconvolution" methods to estimate cell composition. We develop a novel computational method to improve reference-free deconvolution, which iteratively searches for cell type-specific features and performs composition estimation. Simulation studies and applications to six real datasets including both DNA methylation and gene expression data demonstrate favorable performance of the proposed method. TOAST is available at https://bioconductor.org/packages/TOAST .
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Affiliation(s)
- Ziyi Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, 30322, GA, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, 30322, GA, USA.
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95
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An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets. BMC Bioinformatics 2019; 20:433. [PMID: 31438843 PMCID: PMC6704630 DOI: 10.1186/s12859-019-2994-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/15/2019] [Indexed: 02/08/2023] Open
Abstract
Background Host immune response is coordinated by a variety of different specialized cell types that vary in time and location. While host immune response can be studied using conventional low-dimensional approaches, advances in transcriptomics analysis may provide a less biased view. Yet, leveraging transcriptomics data to identify immune cell subtypes presents challenges for extracting informative gene signatures hidden within a high dimensional transcriptomics space characterized by low sample numbers with noisy and missing values. To address these challenges, we explore using machine learning methods to select gene subsets and estimate gene coefficients simultaneously. Results Elastic-net logistic regression, a type of machine learning, was used to construct separate classifiers for ten different types of immune cell and for five T helper cell subsets. The resulting classifiers were then used to develop gene signatures that best discriminate among immune cell types and T helper cell subsets using RNA-seq datasets. We validated the approach using single-cell RNA-seq (scRNA-seq) datasets, which gave consistent results. In addition, we classified cell types that were previously unannotated. Finally, we benchmarked the proposed gene signatures against other existing gene signatures. Conclusions Developed classifiers can be used as priors in predicting the extent and functional orientation of the host immune response in diseases, such as cancer, where transcriptomic profiling of bulk tissue samples and single cells are routinely employed. Information that can provide insight into the mechanistic basis of disease and therapeutic response. The source code and documentation are available through GitHub: https://github.com/KlinkeLab/ImmClass2019. Electronic supplementary material The online version of this article (10.1186/s12859-019-2994-z) contains supplementary material, which is available to authorized users.
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96
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Cursons J, Souza-Fonseca-Guimaraes F, Foroutan M, Anderson A, Hollande F, Hediyeh-Zadeh S, Behren A, Huntington ND, Davis MJ. A Gene Signature Predicting Natural Killer Cell Infiltration and Improved Survival in Melanoma Patients. Cancer Immunol Res 2019; 7:1162-1174. [PMID: 31088844 DOI: 10.1158/2326-6066.cir-18-0500] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 01/31/2019] [Accepted: 05/07/2019] [Indexed: 12/14/2022]
Abstract
Natural killer (NK) cell activity is essential for initiating antitumor responses and may be linked to immunotherapy success. NK cells and other innate immune components could be exploitable for cancer treatment, which drives the need for tools and methods that identify therapeutic avenues. Here, we extend our gene-set scoring method singscore to investigate NK cell infiltration by applying RNA-seq analysis to samples from bulk tumors. Computational methods have been developed for the deconvolution of immune cell types within solid tumors. We have taken the NK cell gene signatures from several such tools, then curated the gene list using a comparative analysis of tumors and immune cell types. Using a gene-set scoring method to investigate RNA-seq data from The Cancer Genome Atlas (TCGA), we show that patients with metastatic cutaneous melanoma have an improved survival rate if their tumor shows evidence of NK cell infiltration. Furthermore, these survival effects are enhanced in tumors that show higher expression of genes that encode NK cell stimuli such as the cytokine IL15 Using this signature, we then examine transcriptomic data to identify tumor and stromal components that may influence the penetrance of NK cells into solid tumors. Our results provide evidence that NK cells play a role in the regulation of human tumors and highlight potential survival effects associated with increased NK cell activity. Our computational analysis identifies putative gene targets that may be of therapeutic value for boosting NK cell antitumor immunity.
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Affiliation(s)
- Joseph Cursons
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Fernando Souza-Fonseca-Guimaraes
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Momeneh Foroutan
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Ashley Anderson
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Frédéric Hollande
- Department of Clinical Pathology, The University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Andreas Behren
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - Nicholas D Huntington
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia.
- Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
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97
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Sprooten J, Agostinis P, Garg AD. Type I interferons and dendritic cells in cancer immunotherapy. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 348:217-262. [PMID: 31810554 DOI: 10.1016/bs.ircmb.2019.06.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Type I interferons (IFNs) facilitate cancer immunosurveillance, antitumor immunity and antitumor efficacy of conventional cell death-inducing therapies (chemotherapy/radiotherapy) as well as immunotherapy. Moreover, it is clear that dendritic cells (DCs) play a significant role in aiding type I IFN-driven immunity. Owing to these antitumor properties several immunotherapies involving, or inducing, type I IFNs have received considerable clinical attention, e.g., recombinant IFNα2 or agonists targeting pattern recognition receptor (PRR) pathways like Toll-like receptors (TLRs), cGAS-STING or RIG-I/MDA5/MAVS. A series of preclinical and clinical evidence concurs that the success of anticancer therapy hinges on responsiveness of both cancer cells and DCs to type I IFNs. In this article, we discuss this link between type I IFNs and DCs in the context of cancer biology, with particular attention to mechanisms behind type I IFN production, their impact on DC driven anticancer immunity, and the implications of this for cancer immunotherapy, including DC-based vaccines.
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Affiliation(s)
- Jenny Sprooten
- Cell Death Research & Therapy (CDRT) Unit, Department for Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Cell Death Research & Therapy (CDRT) Unit, Department for Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium; Center for Cancer Biology (CCB), VIB, Leuven, Belgium
| | - Abhishek D Garg
- Cell Death Research & Therapy (CDRT) Unit, Department for Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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98
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El Amrani K, Alanis-Lobato G, Mah N, Kurtz A, Andrade-Navarro MA. Detection of condition-specific marker genes from RNA-seq data with MGFR. PeerJ 2019; 7:e6970. [PMID: 31179178 PMCID: PMC6542349 DOI: 10.7717/peerj.6970] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/07/2019] [Indexed: 12/19/2022] Open
Abstract
The identification of condition-specific genes is key to advancing our understanding of cell fate decisions and disease development. Differential gene expression analysis (DGEA) has been the standard tool for this task. However, the amount of samples that modern transcriptomic technologies allow us to study, makes DGEA a daunting task. On the other hand, experiments with low numbers of replicates lack the statistical power to detect differentially expressed genes. We have previously developed MGFM, a tool for marker gene detection from microarrays, that is particularly useful in the latter case. Here, we have adapted the algorithm behind MGFM to detect markers in RNA-seq data. MGFR groups samples with similar gene expression levels and flags potential markers of a sample type if their highest expression values represent all replicates of this type. We have benchmarked MGFR against other methods and found that its proposed markers accurately characterize the functional identity of different tissues and cell types in standard and single cell RNA-seq datasets. Then, we performed a more detailed analysis for three of these datasets, which profile the transcriptomes of different human tissues, immune and human blastocyst cell types, respectively. MGFR’s predicted markers were compared to gold-standard lists for these datasets and outperformed the other marker detectors. Finally, we suggest novel candidate marker genes for the examined tissues and cell types. MGFR is implemented as a freely available Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.MGFR), which facilitates its use and integration with bioinformatics pipelines.
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Affiliation(s)
- Khadija El Amrani
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Nancy Mah
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Kurtz
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
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99
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Crupi MJF, Bell JC, Singaravelu R. Concise Review: Targeting Cancer Stem Cells and Their Supporting Niche Using Oncolytic Viruses. Stem Cells 2019; 37:716-723. [PMID: 30875126 DOI: 10.1002/stem.3004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 02/08/2019] [Accepted: 03/02/2019] [Indexed: 12/22/2022]
Abstract
Cancer stem cells (CSCs) have the capacity to self-renew and differentiate to give rise to heterogenous cancer cell lineages in solid tumors. These CSC populations are associated with metastasis, tumor relapse, and resistance to conventional anticancer therapies. Here, we focus on the use of oncolytic viruses (OVs) to target CSCs as well as the OV-driven interferon production in the tumor microenvironment (TME) that can repress CSC properties. We explore the ability of OVs to deliver combinations of immune-modulating therapeutic transgenes, such as immune checkpoint inhibitor antibodies. In particular, we highlight the advantages of virally encoded bi-specific T cell engagers (BiTEs) to not only target cell-surface markers on CSCs, but also tumor-associated antigens on contributing components of the surrounding TME and other cancer cells. We also highlight the crucial role of combination anticancer treatments, evidenced by synergy of OV-delivered BiTEs and chimeric-antigen receptor T cell therapy. Stem Cells 2019;37:716-723.
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Affiliation(s)
- Mathieu J F Crupi
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - John C Bell
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ragunath Singaravelu
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
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100
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Linsley PS, Greenbaum CJ, Rosasco M, Presnell S, Herold KC, Dufort MJ. Elevated T cell levels in peripheral blood predict poor clinical response following rituximab treatment in new-onset type 1 diabetes. Genes Immun 2019; 20:293-307. [PMID: 29925930 PMCID: PMC6477779 DOI: 10.1038/s41435-018-0032-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 12/11/2022]
Abstract
Biologic treatment of type 1 diabetes (T1D) with agents including anti-CD3 (otelixizumab and teplizumab), anti-CD20 (rituximab), LFA3Ig (alafacept), and CTLA4Ig (abatacept) results in transient stabilization of insulin C-peptide, a surrogate for endogenous insulin secretion. With the goal of inducing more robust immune tolerance, we used systems biology approaches to elucidate mechanisms associated with C-peptide stabilization in clinical trial blood samples from new-onset T1D subjects treated with the B cell-depleting drug, rituximab. RNA sequencing (RNA-seq) analysis of whole-blood samples from this trial revealed a transient increase in heterogeneous T cell populations, which were associated with decreased pharmacodynamic activity of rituximab, increased proliferative responses to islet antigens, and more rapid C-peptide loss. Our findings illustrate complexity in hematopoietic remodeling that accompanies B cell depletion by rituximab, which impacts and predicts therapeutic efficacy in T1D. Our data also suggest that a combination of rituximab with therapy targeting CD4 + T cells may be beneficial for T1D subjects.
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Affiliation(s)
- Peter S Linsley
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.
| | - Carla J Greenbaum
- Diabetes Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Mario Rosasco
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Scott Presnell
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Kevan C Herold
- Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT, 06520, USA
| | - Matthew J Dufort
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
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