101
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Manoharan M, Mandloi N, Priyadarshini S, Patil A, Gupta R, Iyer L, Gupta R, Chaudhuri A. A Computational Approach Identifies Immunogenic Features of Prognosis in Human Cancers. Front Immunol 2018; 9:3017. [PMID: 30622534 PMCID: PMC6308325 DOI: 10.3389/fimmu.2018.03017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/06/2018] [Indexed: 12/25/2022] Open
Abstract
A large number of tumor intrinsic and extrinsic factors determine long-term survival in human cancers. In this study, we stratified 9120 tumors from 33 cancers with respect to their immune cell content and identified immunogenomic features associated with long-term survival. Our analysis demonstrates that tumors infiltrated by CD8+ T cells expressing higher levels of activation marker (PD1hi) along with TCR signaling genes and cytolytic T cell markers (IL2hi/TNF-αhi/IFN-γhi/GZMA-Bhi) extend survival, whereas survival benefit was absent for tumors infiltrated by anergic and hyperexhausted CD8+ T cells characterized by high expression of CTLA-4, TIM3, LAG3, and genes linked to PI3K signaling pathway. The computational approach of using robust and highly specific gene expression signatures to deconvolute the tumor microenvironment has important clinical applications, such as selecting patients who will benefit from checkpoint inhibitor treatment.
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102
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OhAinle M, Helms L, Vermeire J, Roesch F, Humes D, Basom R, Delrow JJ, Overbaugh J, Emerman M. A virus-packageable CRISPR screen identifies host factors mediating interferon inhibition of HIV. eLife 2018; 7:e39823. [PMID: 30520725 PMCID: PMC6286125 DOI: 10.7554/elife.39823] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/13/2018] [Indexed: 12/14/2022] Open
Abstract
Interferon (IFN) inhibits HIV replication by inducing antiviral effectors. To comprehensively identify IFN-induced HIV restriction factors, we assembled a CRISPR sgRNA library of Interferon Stimulated Genes (ISGs) into a modified lentiviral vector that allows for packaging of sgRNA-encoding genomes in trans into budding HIV-1 particles. We observed that knockout of Zinc Antiviral Protein (ZAP) improved the performance of the screen due to ZAP-mediated inhibition of the vector. A small panel of IFN-induced HIV restriction factors, including MxB, IFITM1, Tetherin/BST2 and TRIM5alpha together explain the inhibitory effects of IFN on the CXCR4-tropic HIV-1 strain, HIV-1LAI, in THP-1 cells. A second screen with a CCR5-tropic primary strain, HIV-1Q23.BG505, described an overlapping, but non-identical, panel of restriction factors. Further, this screen also identifies HIV dependency factors. The ability of IFN-induced restriction factors to inhibit HIV strains to replicate in human cells suggests that these human restriction factors are incompletely antagonized. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Molly OhAinle
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Louisa Helms
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Jolien Vermeire
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Ferdinand Roesch
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Daryl Humes
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Ryan Basom
- Genomics and Bioinformatics Shared ResourceFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared ResourceFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Julie Overbaugh
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Michael Emerman
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
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103
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Kuri-Magaña H, Collado-Torres L, Jaffe AE, Valdovinos-Torres H, Ovilla-Muñoz M, Téllez-Sosa J, Bonifaz LC, Martínez-Barnetche J. Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses. Front Immunol 2018; 9:2679. [PMID: 30519242 PMCID: PMC6260145 DOI: 10.3389/fimmu.2018.02679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 10/30/2018] [Indexed: 12/22/2022] Open
Abstract
Antibody class switch recombination (CSR) to IgG, IgA, or IgE is a hallmark of adaptive immunity, allowing antibody function diversification beyond IgM. CSR involves a deletion of the IgM/IgD constant region genes placing a new acceptor Constant gene, downstream of the VDJH exon. CSR depends on non-coding (CSRnc) transcription of donor Iμ and acceptor IH exons, located 5′ upstream of each CH coding gene. Although, our knowledge of the role of CSRnc transcription has advanced greatly, its extension and importance in healthy and diseased humans is scarce. We analyzed CSRnc transcription in 70,603 publicly available RNA-seq samples, including GTEx, TCGA, and the Sequence Read Archive using recount2, an online resource consisting of normalized RNA-seq gene and exon counts, as well as, coverage BigWig files that can be programmatically accessed through R. CSRnc transcription was validated with a qRT-PCR assay for Iμ, Iγ3, and Iγ1 in humans in response to vaccination. We mapped IH transcription for the human IGH locus, including the less understood IGHD gene. CSRnc transcription was restricted to B cells and is widely distributed in normal adult tissues, but predominant in blood, spleen, MALT-containing tissues, visceral adipose tissue and some so-called “immune privileged” tissues. However, significant Iγ4 expression was found even in non-lymphoid fetal tissues. CSRnc expression in cancer tissues mimicked the expression of their normal counterparts, with notable pattern changes in some common cancer subsets. CSRnc transcription in tumors appears to result from tumor infiltration by B cells, since CSRnc transcription was not detected in corresponding tumor-derived immortal cell lines. Additionally, significantly increased Iδ transcription in ileal mucosa in Crohn's disease with ulceration was found. In conclusion, CSRnc transcription occurs in multiple anatomical locations beyond classical secondary lymphoid organs, representing a potentially useful marker of effector B cell responses in normal and pathological immune responses. The pattern of IH exon expression may reveal clues of the local immune response (i.e., cytokine milieu) in health and disease. This is a great example of how the public recount2 data can be used to further our understanding of transcription, including regions outside the known transcriptome.
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Affiliation(s)
- Helena Kuri-Magaña
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, United States.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, MD, United States.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Humberto Valdovinos-Torres
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Marbella Ovilla-Muñoz
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Laura C Bonifaz
- Unidad de Investigación Medica en Inmunoquímica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jesús Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
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104
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Tuccitto A, Shahaj E, Vergani E, Ferro S, Huber V, Rodolfo M, Castelli C, Rivoltini L, Vallacchi V. Immunosuppressive circuits in tumor microenvironment and their influence on cancer treatment efficacy. Virchows Arch 2018; 474:407-420. [PMID: 30374798 DOI: 10.1007/s00428-018-2477-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/10/2018] [Accepted: 10/14/2018] [Indexed: 01/05/2023]
Abstract
It has been for long conceived that hallmarks of cancer were intrinsic genetic features driving tumor development, proliferation, and progression, and that targeting such cell-autonomous pathways could be sufficient to achieve therapeutic cancer control. Clinical ex vivo data demonstrated that treatment efficacy often relied on the contribution of host immune responses, hence introducing the concept of tumor microenvironment (TME), namely the existence, along with tumor cells, of non-tumor components that could significantly influence tumor growth and survival. Among the complex network of TME-driving forces, immunity plays a key role and the balance between antitumor and protumor immune responses is a major driver in contrasting or promoting cancer spreading. TME is usually a very immunosuppressed milieu because of a vast array of local alterations contrasting antitumor adaptive immunity, where metabolic changes contribute to cancer dissemination by impairing T cell infiltration and favoring the accrual and activation of regulatory cells. Subcellular structures known as extracellular vesicles then help spreading immunosuppression at systemic levels by distributing genetic and protein tumor repertoire in distant tissues. A major improvement in the knowledge of TME is now pointing the attention back to tumor cells; indeed, recent findings are showing how oncogenic pathways and specific mutations in tumor cells can actually dictate the nature and the function of immune infiltrate. As our information on the reciprocal interactions regulating TME increases, finding a strategy to interfere with TME crosstalk becomes more complex and challenging. Nevertheless, TME interactions represent a promising field for the discovery of novel biomarkers and therapeutic targets for improving treatment efficacy in cancer.
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Affiliation(s)
- Alessandra Tuccitto
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G. Venezian 1, 20133, Milan, Italy
| | - Eriomina Shahaj
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G. Venezian 1, 20133, Milan, Italy.
| | - Elisabetta Vergani
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G. Venezian 1, 20133, Milan, Italy
| | - Simona Ferro
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G. Venezian 1, 20133, Milan, Italy
| | - Veronica Huber
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G. Venezian 1, 20133, Milan, Italy
| | - Monica Rodolfo
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G. Venezian 1, 20133, Milan, Italy
| | - Chiara Castelli
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G. Venezian 1, 20133, Milan, Italy
| | - Licia Rivoltini
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G. Venezian 1, 20133, Milan, Italy
| | - Viviana Vallacchi
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G. Venezian 1, 20133, Milan, Italy
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105
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Quaas A, Heydt C, Gebauer F, Alakus H, Loeser H, Buettner R, Hillmer A, Bruns C, Merkelbach-Bruse S, Zander T, Frommolt P. Genomic Characterization of TP53-Wild-Type Esophageal Carcinoma. Transl Oncol 2018; 12:154-161. [PMID: 30317074 PMCID: PMC6187090 DOI: 10.1016/j.tranon.2018.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/09/2018] [Accepted: 09/10/2018] [Indexed: 12/28/2022] Open
Affiliation(s)
| | - Carina Heydt
- Institute of Pathology, University of Cologne, Germany
| | - Florian Gebauer
- Department of General, Visceral and Cancer Surgery, University of Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral and Cancer Surgery, University of Cologne, Germany
| | - Heike Loeser
- Institute of Pathology, University of Cologne, Germany
| | | | - Axel Hillmer
- Institute of Pathology, University of Cologne, Germany
| | - Christiane Bruns
- Department of General, Visceral and Cancer Surgery, University of Cologne, Germany
| | | | - Thomas Zander
- Department I of Internal Medicine, Center for Integrated Oncology (CIO), University of Cologne, Germany
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106
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Bakhoum SF, Cantley LC. The Multifaceted Role of Chromosomal Instability in Cancer and Its Microenvironment. Cell 2018; 174:1347-1360. [PMID: 30193109 PMCID: PMC6136429 DOI: 10.1016/j.cell.2018.08.027] [Citation(s) in RCA: 377] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/03/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
Abstract
Chromosomal instability (CIN) is a hallmark of human cancer, and it is associated with poor prognosis, metastasis, and therapeutic resistance. CIN results from errors in chromosome segregation during mitosis, leading to structural and numerical chromosomal abnormalities. In addition to generating genomic heterogeneity that acts as a substrate for natural selection, CIN promotes inflammatory signaling by introducing double-stranded DNA into the cytosol, engaging the cGAS-STING anti-viral pathway. These multipronged effects distinguish CIN as a central driver of tumor evolution and as a genomic source for the crosstalk between the tumor and its microenvironment, in the course of immune editing and evasion.
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Affiliation(s)
- Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Lewis C Cantley
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
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107
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Chakravarthy A, Furness A, Joshi K, Ghorani E, Ford K, Ward MJ, King EV, Lechner M, Marafioti T, Quezada SA, Thomas GJ, Feber A, Fenton TR. Pan-cancer deconvolution of tumour composition using DNA methylation. Nat Commun 2018; 9:3220. [PMID: 30104673 PMCID: PMC6089972 DOI: 10.1038/s41467-018-05570-1] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/10/2018] [Indexed: 12/17/2022] Open
Abstract
The nature and extent of immune cell infiltration into solid tumours are key determinants of therapeutic response. Here, using a DNA methylation-based approach to tumour cell fraction deconvolution, we report the integrated analysis of tumour composition and genomics across a wide spectrum of solid cancers. Initially studying head and neck squamous cell carcinoma, we identify two distinct tumour subgroups: 'immune hot' and 'immune cold', which display differing prognosis, mutation burden, cytokine signalling, cytolytic activity and oncogenic driver events. We demonstrate the existence of such tumour subgroups pan-cancer, link clonal-neoantigen burden to cytotoxic T-lymphocyte infiltration, and show that transcriptional signatures of hot tumours are selectively engaged in immunotherapy responders. We also find that treatment-naive hot tumours are markedly enriched for known immune-resistance genomic alterations, potentially explaining the heterogeneity of immunotherapy response and prognosis seen within this group. Finally, we define a catalogue of mediators of active antitumour immunity, deriving candidate biomarkers and potential targets for precision immunotherapy.
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Affiliation(s)
- Ankur Chakravarthy
- Department of Oncology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
- Princess Margaret Cancer Centre, Toronto, ON, M5G 2C4, Canada
| | - Andrew Furness
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Kroopa Joshi
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Ehsan Ghorani
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Kirsty Ford
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Matthew J Ward
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Emma V King
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Matt Lechner
- Department of Oncology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Teresa Marafioti
- Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Sergio A Quezada
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Gareth J Thomas
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Andrew Feber
- Division of Surgery and Interventional Science, University College London, London, WC1E 6BT, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
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108
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Guittard G, Pontarotti P, Granjeaud S, Rodrigues M, Abi-Rached L, Nunès JA. Evolutionary and expression analyses reveal a pattern of ancient duplications and functional specializations in the diversification of the Downstream of Kinase (DOK) genes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 84:193-198. [PMID: 29453999 DOI: 10.1016/j.dci.2018.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/10/2018] [Accepted: 02/10/2018] [Indexed: 06/08/2023]
Abstract
Downstream of Kinase (DOK) proteins represent a multigenic family of adaptors that includes negative regulators of immune cell signaling. Using phylogenetics and intron/exon structure data, we show here that the seven human DOK genes (DOK1 to DOK7) form three highly divergent groups that emerged before the protostome-deuterostome split: DOK1/2/3, DOK4/5/6, and DOK7. For two of these three groups (DOK1/2/3 and DOK4/5/6), further gene duplications occurred in vertebrates and so while chordates only have three DOK genes, vertebrates have seven DOK genes over the three groups. From our expression analysis in humans, we show that each group of DOK genes has a distinct pattern of expression. The DOK1/2/3 group is immune specific, yet each of the three genes in the group has a distinct pattern of expression in immune cells. This immune specificity could thus be ancestral, with the DOK1/2/3 gene also being immune-related in protostomes. The DOK4/5/6 and DOK7 groups represent genes that are much less expressed in immune system than the DOK1/2/3 group. Interestingly, we identify a novel tyrosine based motif that is specific to the vertebrate DOK4/5/6 sequences. The evolution of the DOK genes is thus marked by a pattern of ancient duplications and functional specializations.
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Affiliation(s)
- Geoffrey Guittard
- Centre de Recherche en Cancérologie de Marseille, Immunity and Cancer Team, Institut Paoli-Calmettes, Inserm, U1068, CNRS, UMR7258, Aix-Marseille Université UM 105, Marseille, France
| | - Pierre Pontarotti
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, équipe évolution Biologique Modélisation, Marseille, France
| | - Samuel Granjeaud
- Centre de Recherche en Cancérologie de Marseille, CiBi Platform, Institut Paoli-Calmettes, Inserm, U1068, CNRS, UMR7258, Aix-Marseille Université UM 105, Marseille, France
| | - Magda Rodrigues
- Centre de Recherche en Cancérologie de Marseille, Immunity and Cancer Team, Institut Paoli-Calmettes, Inserm, U1068, CNRS, UMR7258, Aix-Marseille Université UM 105, Marseille, France
| | - Laurent Abi-Rached
- Equipe ATIP, Aix Marseille Université, CNRS, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.
| | - Jacques A Nunès
- Centre de Recherche en Cancérologie de Marseille, Immunity and Cancer Team, Institut Paoli-Calmettes, Inserm, U1068, CNRS, UMR7258, Aix-Marseille Université UM 105, Marseille, France.
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109
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Osumi-Sutherland DJ, Ponta E, Courtot M, Parkinson H, Badi L. Using OWL reasoning to support the generation of novel gene sets for enrichment analysis. J Biomed Semantics 2018; 9:10. [PMID: 29444698 PMCID: PMC5813370 DOI: 10.1186/s13326-018-0175-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 01/03/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The Gene Ontology (GO) consists of over 40,000 terms for biological processes, cell components and gene product activities linked into a graph structure by over 90,000 relationships. It has been used to annotate the functions and cellular locations of several million gene products. The graph structure is used by a variety of tools to group annotated genes into sets whose products share function or location. These gene sets are widely used to interpret the results of genomics experiments by assessing which sets are significantly over- or under-represented in results lists. F Hoffmann-La Roche Ltd. has developed a bespoke, manually maintained controlled vocabulary (RCV) for use in over-representation analysis. Many terms in this vocabulary group GO terms in novel ways that cannot easily be derived using the graph structure of the GO. For example, some RCV terms group GO terms by the cell, chemical or tissue type they refer to. Recent improvements in the content and formal structure of the GO make it possible to use logical queries in Web Ontology Language (OWL) to automatically map these cross-cutting classifications to sets of GO terms. We used this approach to automate mapping between RCV and GO, largely replacing the increasingly unsustainable manual mapping process. We then tested the utility of the resulting groupings for over-representation analysis. RESULTS We successfully mapped 85% of RCV terms to logical OWL definitions and showed that these could be used to recapitulate and extend manual mappings between RCV terms and the sets of GO terms subsumed by them. We also show that gene sets derived from the resulting GO terms sets can be used to detect the signatures of cell and tissue types in whole genome expression data. CONCLUSIONS The rich formal structure of the GO makes it possible to use reasoning to dynamically generate novel, biologically relevant groupings of GO terms. GO term groupings generated with this approach can be used in. over-representation analysis to detect cell and tissue type signatures in whole genome expression data.
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Affiliation(s)
- David J Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK.
| | - Enrico Ponta
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, -4070, Basel, CH, Switzerland
| | - Melanie Courtot
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
| | - Laura Badi
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, -4070, Basel, CH, Switzerland
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110
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Tarbell KV, Egen JG. Breaking self-tolerance during autoimmunity and cancer immunity: Myeloid cells and type I IFN response regulation. J Leukoc Biol 2018; 103:1117-1129. [PMID: 29393979 DOI: 10.1002/jlb.3mir1017-400r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/18/2017] [Accepted: 12/21/2017] [Indexed: 02/28/2024] Open
Abstract
The generation and regulation of innate immune signals are key determinants of autoimmune pathogenesis. Emerging evidence suggests that parallel processes operating in the setting of solid tumors can similarly determine the balance between tolerance and immunity and ultimately the effectiveness of the antitumor immune response. In both contexts, self-specific responses start with innate immune cell activation that leads to the initial break in self-tolerance, which can be followed by immune response amplification and maturation through innate-adaptive crosstalk, and finally immune-mediated tissue/tumor destruction that can further potentiate inflammation. Of particular importance for these processes is type I IFN, which is induced in response to endogenous ligands, such as self-nucleic acids, and acts on myeloid cells to promote the expansion of autoreactive or tumor-specific T cells and their influx into the target tissue. Evidence from the study of human disease pathophysiology and genetics and mouse models of disease has revealed an extensive and complex network of negative regulatory pathways that has evolved to restrain type I IFN production and activity. Here, we review the overlapping features of self- and tumor-specific immune responses, including the central role that regulators of the type I IFN response and innate immune cell activation play in maintaining tolerance, and discuss how a better understanding of the pathophysiology of autoimmunity can help to identify new approaches to promote immune-mediated tumor destruction.
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Affiliation(s)
- Kristin V Tarbell
- Department of Oncology, Amgen, Inc., South San Francisco, California, USA
| | - Jackson G Egen
- Department of Oncology, Amgen, Inc., South San Francisco, California, USA
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111
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Chen B, Khodadoust MS, Liu CL, Newman AM, Alizadeh AA. Profiling Tumor Infiltrating Immune Cells with CIBERSORT. Methods Mol Biol 2018; 1711:243-259. [PMID: 29344893 DOI: 10.1007/978-1-4939-7493-1_12] [Citation(s) in RCA: 1778] [Impact Index Per Article: 296.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tumor infiltrating leukocytes (TILs) are an integral component of the tumor microenvironment and have been found to correlate with prognosis and response to therapy. Methods to enumerate immune subsets such as immunohistochemistry or flow cytometry suffer from limitations in phenotypic markers and can be challenging to practically implement and standardize. An alternative approach is to acquire aggregative high dimensional data from cellular mixtures and to subsequently infer the cellular components computationally. We recently described CIBERSORT, a versatile computational method for quantifying cell fractions from bulk tissue gene expression profiles (GEPs). Combining support vector regression with prior knowledge of expression profiles from purified leukocyte subsets, CIBERSORT can accurately estimate the immune composition of a tumor biopsy. In this chapter, we provide a primer on the CIBERSORT method and illustrate its use for characterizing TILs in tumor samples profiled by microarray or RNA-Seq.
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Affiliation(s)
- Binbin Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael S Khodadoust
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, 875 Blake Wilbur Drive, Stanford, CA, 94305, USA.,Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, 875 Blake Wilbur Drive, Stanford, CA, 94305, USA
| | - Aaron M Newman
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, 875 Blake Wilbur Drive, Stanford, CA, 94305, USA. .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, 875 Blake Wilbur Drive, Stanford, CA, 94305, USA. .,Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA. .,Stanford Cancer Institute, Stanford University, Stanford, CA, USA. .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
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112
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Attig J, Young GR, Stoye JP, Kassiotis G. Physiological and Pathological Transcriptional Activation of Endogenous Retroelements Assessed by RNA-Sequencing of B Lymphocytes. Front Microbiol 2017; 8:2489. [PMID: 29312197 PMCID: PMC5733090 DOI: 10.3389/fmicb.2017.02489] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/29/2017] [Indexed: 12/20/2022] Open
Abstract
In addition to evolutionarily-accrued sequence mutation or deletion, endogenous retroelements (EREs) in eukaryotic genomes are subject to epigenetic silencing, preventing or reducing their transcription, particularly in the germplasm. Nevertheless, transcriptional activation of EREs, including endogenous retroviruses (ERVs) and long interspersed nuclear elements (LINEs), is observed in somatic cells, variably upon cellular differentiation and frequently upon cellular transformation. ERE transcription is modulated during physiological and pathological immune cell activation, as well as in immune cell cancers. However, our understanding of the potential consequences of such modulation remains incomplete, partly due to the relative scarcity of information regarding genome-wide ERE transcriptional patterns in immune cells. Here, we describe a methodology that allows probing RNA-sequencing (RNA-seq) data for genome-wide expression of EREs in murine and human cells. Our analysis of B cells reveals that their transcriptional response during immune activation is dominated by induction of gene transcription, and that EREs respond to a much lesser extent. The transcriptional activity of the majority of EREs is either unaffected or reduced by B cell activation both in mice and humans, albeit LINEs appear considerably more responsive in the latter host. Nevertheless, a small number of highly distinct ERVs are strongly and consistently induced during B cell activation. Importantly, this pattern contrasts starkly with B cell transformation, which exhibits widespread induction of EREs, including ERVs that minimally overlap with those responsive to immune stimulation. The distinctive patterns of ERE induction suggest different underlying mechanisms and will help separate physiological from pathological expression.
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Affiliation(s)
- Jan Attig
- Retroviral Immunology, The Francis Crick Institute, London, United Kingdom
| | - George R Young
- Retrovirus-Host Interactions, The Francis Crick Institute, London, United Kingdom
| | - Jonathan P Stoye
- Retrovirus-Host Interactions, The Francis Crick Institute, London, United Kingdom.,Department of Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London, United Kingdom.,Department of Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
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113
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Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol 2017; 18:220. [PMID: 29141660 PMCID: PMC5688663 DOI: 10.1186/s13059-017-1349-1] [Citation(s) in RCA: 2346] [Impact Index Per Article: 335.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 10/10/2017] [Indexed: 12/12/2022] Open
Abstract
Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene signature-based method, and use it to infer 64 immune and stromal cell types. We harmonized 1822 pure human cell type transcriptomes from various sources and employed a curve fitting approach for linear comparison of cell types and introduced a novel spillover compensation technique for separating them. Using extensive in silico analyses and comparison to cytometry immunophenotyping, we show that xCell outperforms other methods. xCell is available at http://xCell.ucsf.edu/.
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Affiliation(s)
- Dvir Aran
- Institute for Computational Health Sciences, University of California, San Francisco, California, 94158, USA.
| | - Zicheng Hu
- Institute for Computational Health Sciences, University of California, San Francisco, California, 94158, USA
| | - Atul J Butte
- Institute for Computational Health Sciences, University of California, San Francisco, California, 94158, USA.
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114
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Racle J, de Jonge K, Baumgaertner P, Speiser DE, Gfeller D. Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. eLife 2017; 6:26476. [PMID: 29130882 PMCID: PMC5718706 DOI: 10.7554/elife.26476] [Citation(s) in RCA: 708] [Impact Index Per Article: 101.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 11/10/2017] [Indexed: 12/12/2022] Open
Abstract
Immune cells infiltrating tumors can have important impact on tumor progression and response to therapy. We present an efficient algorithm to simultaneously estimate the fraction of cancer and immune cell types from bulk tumor gene expression data. Our method integrates novel gene expression profiles from each major non-malignant cell type found in tumors, renormalization based on cell-type-specific mRNA content, and the ability to consider uncharacterized and possibly highly variable cell types. Feasibility is demonstrated by validation with flow cytometry, immunohistochemistry and single-cell RNA-Seq analyses of human melanoma and colorectal tumor specimens. Altogether, our work not only improves accuracy but also broadens the scope of absolute cell fraction predictions from tumor gene expression data, and provides a unique novel experimental benchmark for immunogenomics analyses in cancer research (http://epic.gfellerlab.org).
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Affiliation(s)
- Julien Racle
- Ludwig Centre for Cancer Research, Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kaat de Jonge
- Department of Fundamental Oncology, Lausanne University Hospital (CHUV), Epalinges, Switzerland
| | - Petra Baumgaertner
- Department of Fundamental Oncology, Lausanne University Hospital (CHUV), Epalinges, Switzerland
| | - Daniel E Speiser
- Department of Fundamental Oncology, Lausanne University Hospital (CHUV), Epalinges, Switzerland
| | - David Gfeller
- Ludwig Centre for Cancer Research, Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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115
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Genome-wide association analysis identifies genetic correlates of immune infiltrates in solid tumors. PLoS One 2017; 12:e0179726. [PMID: 28749946 PMCID: PMC5531551 DOI: 10.1371/journal.pone.0179726] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 06/02/2017] [Indexed: 12/27/2022] Open
Abstract
Therapeutic options for the treatment of an increasing variety of cancers have been expanded by the introduction of a new class of drugs, commonly referred to as checkpoint blocking agents, that target the host immune system to positively modulate anti-tumor immune response. Although efficacy of these agents has been linked to a pre-existing level of tumor immune infiltrate, it remains unclear why some patients exhibit deep and durable responses to these agents while others do not benefit. To examine the influence of tumor genetics on tumor immune state, we interrogated the relationship between somatic mutation and copy number alteration with infiltration levels of 7 immune cell types across 40 tumor cohorts in The Cancer Genome Atlas. Levels of cytotoxic T, regulatory T, total T, natural killer, and B cells, as well as monocytes and M2 macrophages, were estimated using a novel set of transcriptional signatures that were designed to resist interference from the cellular heterogeneity of tumors. Tumor mutational load and estimates of tumor purity were included in our association models to adjust for biases in multi-modal genomic data. Copy number alterations, mutations summarized at the gene level, and position-specific mutations were evaluated for association with tumor immune infiltration. We observed a strong relationship between copy number loss of a large region of chromosome 9p and decreased lymphocyte estimates in melanoma, pancreatic, and head/neck cancers. Mutations in the oncogenes PIK3CA, FGFR3, and RAS/RAF family members, as well as the tumor suppressor TP53, were linked to changes in immune infiltration, usually in restricted tumor types. Associations of specific WNT/beta-catenin pathway genetic changes with immune state were limited, but we noted a link between 9p loss and the expression of the WNT receptor FZD3, suggesting that there are interactions between 9p alteration and WNT pathways. Finally, two different cell death regulators, CASP8 and DIDO1, were often mutated in head/neck tumors that had higher lymphocyte infiltrates. In summary, our study supports the relevance of tumor genetics to questions of efficacy and resistance in checkpoint blockade therapies. It also highlights the need to assess genome-wide influences during exploration of any specific tumor pathway hypothesized to be relevant to therapeutic response. Some of the observed genetic links to immune state, like 9p loss, may influence response to cancer immune therapies. Others, like mutations in cell death pathways, may help guide combination therapeutic approaches.
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116
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Balli D, Rech AJ, Stanger BZ, Vonderheide RH. Immune Cytolytic Activity Stratifies Molecular Subsets of Human Pancreatic Cancer. Clin Cancer Res 2017; 23:3129-3138. [PMID: 28007776 DOI: 10.1158/1078-0432.ccr-16-2128] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/04/2016] [Accepted: 12/07/2016] [Indexed: 01/13/2023]
Abstract
Purpose: Immunotherapy has the potential to improve the dismal prognosis in pancreatic ductal adenocarcinoma (PDA), but clinical trials, including those with single-agent PD-1 or PD-L1 inhibition, have been disappointing. Our aim was to examine the immune landscape of PDA as it relates to aspects of tumor biology, including neoepitope burden.Experimental Design: We used publicly available expression data from 134 primary resection PDA samples from The Cancer Genome Atlas to stratify patients according to a cytolytic T-cell activity expression index. We correlated cytolytic immune activity with mutational, structural, and neoepitope features of the tumor.Results: Human PDA displays a range of intratumoral cytolytic T-cell activity. PDA tumors with low cytolytic activity exhibited significantly increased copy number alterations, including recurrent amplifications of MYC and NOTCH2 and recurrent deletions and mutations of CDKN2A/B In sharp contrast to other tumor types, high cytolytic activity in PDA did not correlate with increased mutational burden or neoepitope load (MHC class I and class II). Cytolytic-high tumors exhibited increased expression of multiple immune checkpoint genes compared to cytolytic-low tumors, except for PD-L1 expression, which was uniformly low.Conclusions: These data identify a subset of human PDA with high cytolytic T-cell activity. Rather than being linked to mutation burden or neoepitope load, immune activation indices in PDA were inversely linked to genomic alterations, suggesting that intrinsic oncogenic processes drive immune inactivity in human PDA. Furthermore, these data highlight the potential importance of immune checkpoints other than PD-L1/PD-1 as therapeutic targets in this lethal disease. Clin Cancer Res; 23(12); 3129-38. ©2016 AACR.
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Affiliation(s)
- David Balli
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew J Rech
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ben Z Stanger
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robert H Vonderheide
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
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117
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Role of carbonic anhydrases in skin wound healing. Exp Mol Med 2017; 49:e334. [PMID: 28524177 PMCID: PMC5454449 DOI: 10.1038/emm.2017.60] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 02/08/2023] Open
Abstract
Skin wound closure occurs when keratinocytes migrate from the edge of the wound and re-epithelialize the epidermis. Their migration takes place primarily before any vascularization is established, that is, under hypoxia, but relatively little is known regarding the factors that stimulate this migration. Hypoxia and an acidic environment are well-established stimuli for cancer cell migration. The carbonic anhydrases (CAs) contribute to tumor cell migration by generating an acidic environment through the conversion of carbon dioxide to bicarbonate and a proton. On this basis, we explored the possible role of CAs in tissue regeneration using mouse skin wound models. We show that the expression of mRNAs encoding CA isoforms IV and IX are increased (~25 × and 4 ×, respectively) during the wound hypoxic period (days 2-5) and that cells expressing CAs form a band-like structure beneath the migrating epidermis. RNA-Seq analysis suggested that the CA IV-specific signal in the wound is mainly derived from neutrophils. Due to the high level of induction of CA IV in the wound, we treated skin wounds locally with recombinant human CA IV enzyme. Recombinant CA IV significantly accelerated wound re-epithelialization. Thus, CA IV could contribute to wound healing by providing an acidic environment in which the migrating epidermis and neutrophils can survive and may offer novel opportunities to accelerate wound healing under compromised conditions.
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118
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Long SA, Thorpe J, DeBerg HA, Gersuk V, Eddy J, Harris KM, Ehlers M, Herold KC, Nepom GT, Linsley PS. Partial exhaustion of CD8 T cells and clinical response to teplizumab in new-onset type 1 diabetes. Sci Immunol 2016; 1:eaai7793. [PMID: 28664195 PMCID: PMC5486405 DOI: 10.1126/sciimmunol.aai7793] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Biologic treatment of T1D typically results in transient stabilization of C-peptide levels (a surrogate for endogenous insulin secretion) in some patients, followed by progression at the same rate as in untreated control groups. Here, we used integrated systems biology and flow cytometry approaches with clinical trial blood samples to elucidate pathways associated with C-peptide stabilization in T1D subjects treated with the anti-CD3 monoclonal antibody teplizumab. We identified a population of CD8 T cells that accumulated in subjects with the best response to treatment (responders) and showed that these cells phenotypically resembled exhausted T cells by expressing high levels of the transcription factor EOMES, effector molecules, and multiple inhibitory receptors (IRs), including TIGIT and KLRG1. These cells expanded after treatment, with levels peaking after 3-6 months. To functionally characterize these exhausted-like T cells, we isolated memory CD8 TIGIT+KLRG1+ T cells from responders and showed that they exhibited expanded TCR clonotypes, indicative of prior in vivo expansion; recognized a broad-based spectrum expressed of environmental and auto-antigens; and were hypo-proliferative during polyclonal stimulation, increasing expression of IR genes and decreasing cell cycle genes. Triggering these cells with a recombinant ligand for TIGIT during polyclonal stimulation further downregulated their activation, demonstrating their exhausted phenotype was not terminal. These findings identify and functionally characterize a partially exhausted cell type associated with response to teplizumab therapy and suggest that pathways regulating T cell exhaustion may play a role in successful immune interventions for T1D.
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Affiliation(s)
- S. Alice Long
- Translational Research Program, Benaroya Research Institute, Seattle, WA
| | - Jerill Thorpe
- Translational Research Program, Benaroya Research Institute, Seattle, WA
| | | | - Vivian Gersuk
- Systems Immunology, Benaroya Research Institute, Seattle, WA
| | - James Eddy
- Systems Immunology, Benaroya Research Institute, Seattle, WA
| | | | | | - Kevan C. Herold
- Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT
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119
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Abstract
PURPOSE OF REVIEW Here, we focus on molecular biomarkers derived from transcriptomic studies to summarize the recent advances in our understanding of the mechanisms associated with differential prognosis and treatment outcome in breast cancer. RECENT FINDINGS Breast cancer is certainly immunogenic; yet it has been historically resistant to immunotherapy. In the past few years, refined immunotherapeutic manipulations have been shown to be effective in a significant proportion of cancer patients. For example, drugs targeting the PD-1 immune checkpoint have been proven to be an effective therapeutic approach in several solid tumors including melanoma and lung cancer. Very recently, the activity of such therapeutics has also been demonstrated in breast cancer patients. Pari passu with the development of novel immune modulators, the transcriptomic analysis of human tumors unveiled unexpected and paradoxical relationships between cancer cells and immune cells. SUMMARY This review examines our understanding of the molecular pathways associated with intratumoral immune response, which represents a critical step for the implementation of stratification strategies toward the development of personalized immunotherapy of breast cancer.
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120
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Clancy T, Hovig E. Profiling networks of distinct immune-cells in tumors. BMC Bioinformatics 2016; 17:263. [PMID: 27377892 PMCID: PMC4932723 DOI: 10.1186/s12859-016-1141-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/20/2016] [Indexed: 11/16/2022] Open
Abstract
Background It is now clearly evident that cancer outcome and response to therapy is guided by diverse immune-cell activity in tumors. Presently, a key challenge is to comprehensively identify networks of distinct immune-cell signatures present in complex tissue, at higher-resolution and at various stages of differentiation, activation or function. This is particularly so for closely related immune-cells with diminutive, yet critical, differences. Results To predict networks of infiltrated distinct immune-cell phenotypes at higher resolution, we explored an integrated knowledge-based approach to select immune-cell signature genes integrating not only expression enrichment across immune-cells, but also an automatic capture of relevant immune-cell signature genes from the literature. This knowledge-based approach was integrated with resources of immune-cell specific protein networks, to define signature genes of distinct immune-cell phenotypes. We demonstrate the utility of this approach by profiling signatures of distinct immune-cells, and networks of immune-cells, from metastatic melanoma patients who had undergone chemotherapy. The resultant bioinformatics strategy complements immunohistochemistry from these tumors, and predicts both tumor-killing and immunosuppressive networks of distinct immune-cells in responders and non-responders, respectively. The approach is also shown to capture differences in the immune-cell networks of BRAF versus NRAS mutated metastatic melanomas, and the dynamic changes in resistance to targeted kinase inhibitors in MAPK signalling. Conclusions This integrative bioinformatics approach demonstrates that capturing the protein network signatures and ratios of distinct immune-cell in the tumor microenvironment maybe an important factor in predicting response to therapy. This may serve as a computational strategy to define network signatures of distinct immune-cells to guide immuno-pathological discovery. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1141-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Trevor Clancy
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway. .,Department of Cancer Immunology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Biomedical Research Group, Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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121
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Lasfar A, Gogas H, Zloza A, Kaufman HL, Kirkwood JM. IFN-λ cancer immunotherapy: new kid on the block. Immunotherapy 2016; 8:877-88. [PMID: 27381684 PMCID: PMC5619162 DOI: 10.2217/imt-2015-0021] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/21/2016] [Indexed: 02/08/2023] Open
Abstract
Interferon-lambda (IFN-λ) is a new IFN type, related to IFN-α, that is commonly used in the clinic. However, significant side effects accompanying IFN-α treatment limit enthusiasm for IFN-α. In this review, we discuss the current landscape of IFN-α use in oncology and describe the biologic characteristics of IFN-λ. IFN-λ offers unique advantages, including a more tumor cell selective targeting, lower off-target binding and an ability to generate both innate and adaptive immune responses. IFN-λ has also demonstrated therapeutic benefit in murine cancer models. IFN-λ may be used in clinic as a single agent or in combination with other immunotherapy agents, such as immune checkpoint inhibitors. Further clinical trials will be needed to fully elucidate the potential of this novel agent in oncology.
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Affiliation(s)
- Ahmed Lasfar
- Department of Pharmacology & Toxicology, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Helen Gogas
- First Department of Medicine, Medical School, University of Athens, Athens, Greece
| | - Andrew Zloza
- Department of Surgery, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, NJ, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Howard L Kaufman
- Department of Surgery, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, NJ, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - John M Kirkwood
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh Medical Center, PA, USA
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122
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Rinchai D, Anguiano E, Nguyen P, Chaussabel D. Finger stick blood collection for gene expression profiling and storage of tempus blood RNA tubes. F1000Res 2016; 5:1385. [PMID: 28357036 PMCID: PMC5357033 DOI: 10.12688/f1000research.8841.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/27/2017] [Indexed: 12/20/2022] Open
Abstract
With this report we aim to make available a standard operating procedure (SOP) developed for RNA stabilization of small blood volumes collected via a finger stick. The anticipation that this procedure may be improved through peer-review and/or readers public comments is another element motivating the publication of this SOP. Procuring blood samples from human subjects can, among other uses, enable assessment of the immune status of an individual subject via the profiling of RNA abundance using technologies such as real time PCR, NanoString, microarrays or RNA-sequencing. It is often desirable to minimize blood volumes and employ methods that are the least invasive and can be practically implemented outside of clinical settings. Finger stick blood samples are increasingly used for measurement of levels of pharmacological drugs and biological analytes. It is a simple and convenient procedure amenable for instance to field use or self-collection at home using a blood sample collection kit. Such methodologies should also enable the procurement of blood samples at high frequency for health or disease monitoring applications.
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Affiliation(s)
- Darawan Rinchai
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | | | | | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
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123
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Szegezdi E, Leverkus M. Guiding the Killer and Bringing in Accomplices: Bispecific Antibody Treatment for Malignant Melanoma. J Invest Dermatol 2016; 136:362-364. [PMID: 26802233 DOI: 10.1016/j.jid.2015.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Discovery of oncogene and immune checkpoint targeting has transformed melanoma therapy in the last 5 years. However, treatment of primary or secondary drug-resistant melanoma remains a challenge. Agents designed to activate the cell death machinery directly, for example by activating the death receptors expressed by melanoma cells, could break drug resistance, and they may achieve long-lasting therapeutic success. He et al. report their studies of an MCSPxDR5 bispecific, tetravalent antibody that can simultaneously target death receptor 5 (DR5, TRAIL-R2) and melanoma-associated chondroitin sulfate proteoglycan (MCSP). This antibody can exert strong and selective DR5-dependent cytotoxic activity against MCSP-expressing melanoma cells. Crosslinking of the antibody with Fcγ-receptors increased the cytotoxic potential further, without compromising its selectivity. This approach offers a novel immunotherapeutic tool via coupling of three cooperating processes: delivering the death receptor agonist to the malignant cell population, potent activation of DR5-mediated cell death signaling, and recruitment of Fcγ-receptor-carrying immune cells that can mount an immune response against the tumor cells.
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Affiliation(s)
- Eva Szegezdi
- Apoptosis Research Centre (ARC), School of Natural Sciences, National University of Ireland, Galway, Biosciences, Dangan, Galway, Ireland.
| | - Martin Leverkus
- Department of Dermatology and Allergology, Medical Faculty of the RWTH Aachen, Aachen, Germany.
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124
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Reinartz S, Finkernagel F, Adhikary T, Rohnalter V, Schumann T, Schober Y, Nockher WA, Nist A, Stiewe T, Jansen JM, Wagner U, Müller-Brüsselbach S, Müller R. A transcriptome-based global map of signaling pathways in the ovarian cancer microenvironment associated with clinical outcome. Genome Biol 2016; 17:108. [PMID: 27215396 PMCID: PMC4877997 DOI: 10.1186/s13059-016-0956-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/15/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Soluble protein and lipid mediators play essential roles in the tumor environment, but their cellular origins, targets, and clinical relevance are only partially known. We have addressed this question for the most abundant cell types in human ovarian carcinoma ascites, namely tumor cells and tumor-associated macrophages. RESULTS Transcriptome-derived datasets were adjusted for errors caused by contaminating cell types by an algorithm using expression data derived from pure cell types as references. These data were utilized to construct a network of autocrine and paracrine signaling pathways comprising 358 common and 58 patient-specific signaling mediators and their receptors. RNA sequencing based predictions were confirmed for several proteins and lipid mediators. Published expression microarray results for 1018 patients were used to establish clinical correlations for a number of components with distinct cellular origins and target cells. Clear associations with early relapse were found for STAT3-inducing cytokines, specific components of WNT and fibroblast growth factor signaling, ephrin and semaphorin axon guidance molecules, and TGFβ/BMP-triggered pathways. An association with early relapse was also observed for secretory macrophage-derived phospholipase PLA2G7, its product arachidonic acid (AA) and signaling pathways controlled by the AA metabolites PGE2, PGI2, and LTB4. By contrast, the genes encoding norrin and its receptor frizzled 4, both selectively expressed by cancer cells and previously not linked to tumor suppression, show a striking association with a favorable clinical course. CONCLUSIONS We have established a signaling network operating in the ovarian cancer microenvironment with previously unidentified pathways and have defined clinically relevant components within this network.
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Affiliation(s)
- Silke Reinartz
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Florian Finkernagel
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany
| | - Till Adhikary
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany
| | - Verena Rohnalter
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany
| | - Tim Schumann
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany
| | - Yvonne Schober
- Metabolomics Core Facility and Institute of Laboratory Medicine and Pathobiochemistry, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - W Andreas Nockher
- Metabolomics Core Facility and Institute of Laboratory Medicine and Pathobiochemistry, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Julia M Jansen
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Uwe Wagner
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Sabine Müller-Brüsselbach
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany
| | - Rolf Müller
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany.
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125
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Bedognetti D, Hendrickx W, Ceccarelli M, Miller LD, Seliger B. Disentangling the relationship between tumor genetic programs and immune responsiveness. Curr Opin Immunol 2016; 39:150-8. [PMID: 26967649 DOI: 10.1016/j.coi.2016.02.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 12/13/2022]
Abstract
Correlative studies in humans have demonstrated that an active immune microenvironment characterized by the presence of a T-helper 1 immune response typifies a tumor phenotype associated with better outcome and increased responsiveness to immune manipulation. This phenotype also signifies the counter activation of immune-regulatory mechanisms. Variables modulating the development of an effective anti-tumor immune response are increasingly scrutinized as potential therapeutic targets. Genetic alterations of cancer cells that functionally influence intratumoral immune response include mutational load, specific mutations of genes involved in oncogenic pathways and copy number aberrations involving chemokine and cytokine genes. Inhibiting oncogenic pathways that prevent the development of the immune-favorable cancer phenotype may complement modern immunotherapeutic approaches.
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Affiliation(s)
- Davide Bedognetti
- Tumor Biology, Immunology and Therapy Section, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, Doha, Qatar.
| | - Wouter Hendrickx
- Tumor Biology, Immunology and Therapy Section, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, Doha, Qatar
| | - Michele Ceccarelli
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
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Baker MJ, Goldstein AM, Gordon PL, Harbaugh KS, Mackley HB, Glantz MJ, Drabick JJ. An interstitial deletion within 9p21.3 and extending beyond CDKN2A predisposes to melanoma, neural system tumours and possible haematological malignancies. J Med Genet 2016; 53:721-727. [PMID: 26794401 DOI: 10.1136/jmedgenet-2015-103446] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/25/2015] [Accepted: 12/22/2015] [Indexed: 11/04/2022]
Abstract
Familial atypical multiple mole melanoma syndrome (FAMMM) is characterised by dysplastic naevi, malignant melanoma and pancreatic cancer. Given that large deletions involving CDKN2A (cyclin-dependent kinase inhibitor 2A) account for only 2% of cases, we describe a family that highlights the co-occurrence of both melanoma and neural system tumours to aid clinical recognition and propose a management strategy. A patient with multiple neurofibromas was referred with a provisional diagnosis of neurofibromatosis type 1 (NF1). Prior molecular testing, though, had failed to identify an NF1 mutation by sequencing and multiplex ligation-dependent probe amplification. His family history was significant for multiple in situ/malignant melanomas at young ages and several different cancers reminiscent of an underlying syndrome. A search of the Familial Cancer Database, FaCD Online, highlighted several families with cutaneous melanoma and nervous system tumours who were subsequently identified to have large deletions spanning CDKN2A Although sequencing of CDKN2A and TP53 failed to identify a mutation, a heterozygous CDKN2A deletion was identified by targeted array comparative genomic hybridisation (CGH). Whole-genome oligonucleotide array CGH and SNP analysis identified an interstitial deletion of at least 1.5 Mb within 9p21.3 and spanning approximately 25 genes. Identification of the underlying molecular abnormality permits predictive testing for at-risk relatives. Given the young cancer diagnoses, a surveillance regimen was developed and a clinical team organised for ongoing management so that genetic testing could be offered to both adults and minor children. Surveillance recommendations addressed cancer risks associated with FAMMM, and other cancers exhibited by this family with a large contiguous gene deletion.
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Affiliation(s)
- Maria J Baker
- Department of Medicine, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, Genetic Epidemiology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Patricia L Gordon
- Department of Pediatrics, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
| | - Kimberly S Harbaugh
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
| | - Heath B Mackley
- Department of Radiation Oncology, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
| | - Michael J Glantz
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
| | - Joseph J Drabick
- Department of Medicine, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
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Satoh JI, Takitani M, Miyoshi J, Kino Y. RNA-Seq data analysis identifies the comprehensive profile ofin vivointerferon-β-stimulated genes in multiple sclerosis. ACTA ACUST UNITED AC 2015. [DOI: 10.1111/cen3.12268] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun-ichi Satoh
- Department of Bioinformatics and Molecular Neuropathology; Meiji Pharmaceutical University; Tokyo Japan
| | - Mika Takitani
- Department of Bioinformatics and Molecular Neuropathology; Meiji Pharmaceutical University; Tokyo Japan
| | - Junko Miyoshi
- Department of Bioinformatics and Molecular Neuropathology; Meiji Pharmaceutical University; Tokyo Japan
| | - Yoshihiro Kino
- Department of Bioinformatics and Molecular Neuropathology; Meiji Pharmaceutical University; Tokyo Japan
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128
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Linsley PS, Chaussabel D, Speake C. The Relationship of Immune Cell Signatures to Patient Survival Varies within and between Tumor Types. PLoS One 2015; 10:e0138726. [PMID: 26398410 PMCID: PMC4580625 DOI: 10.1371/journal.pone.0138726] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/02/2015] [Indexed: 12/27/2022] Open
Abstract
Enhancing pre-existing anti-tumor immunity leads to therapeutic benefit for some patients, but why some tumors are more immunogenic than others remains unresolved. We took a unique systems approach to relate patient survival to immune gene expression in >3,500 tumor RNAseq profiles from a dozen tumor types. We found significant links between immune gene expression and patient survival in 8/12 tumor types, with tumors partitioned by gene expression comprising distinct molecular subtypes. T/NK cell genes were most clearly survival-related for melanoma, head and neck, and bladder tumors, whereas myeloid cell genes were most clearly survival-related with kidney and breast tumors. T/NK or myeloid cell gene expression was linked to poor prognosis in bladder and kidney tumors, respectively, suggesting tumor-specific immunosuppressive checkpoints. Our results suggest new biomarkers for existing cancer immunotherapies and identify targets for new immunotherapies.
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Affiliation(s)
- Peter S. Linsley
- Department of Systems Immunology, Benaroya Research Institute, 1201 Ninth Avenue, Seattle, WA 98101–2795, United States of America
- * E-mail:
| | - Damien Chaussabel
- Department of Systems Immunology, Benaroya Research Institute, 1201 Ninth Avenue, Seattle, WA 98101–2795, United States of America
| | - Cate Speake
- Department of Systems Immunology, Benaroya Research Institute, 1201 Ninth Avenue, Seattle, WA 98101–2795, United States of America
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129
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Palumbo A, Da Costa NDOM, Bonamino MH, Pinto LFR, Nasciutti LE. Genetic instability in the tumor microenvironment: a new look at an old neighbor. Mol Cancer 2015; 14:145. [PMID: 26227631 PMCID: PMC4521350 DOI: 10.1186/s12943-015-0409-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/08/2015] [Indexed: 12/19/2022] Open
Abstract
The recent exponential increase in our knowledge of cellular and molecular mechanisms involved in carcinogenesis has largely failed to translate into new therapies and clinical practices. This lack of success may result in part from the fact that most studies focus on tumor cells as potential therapeutic targets and neglect the complex microenvironment that undergoes profound changes during tumor development. Furthermore, an unfortunate association of factors such as tumor genetic complexity, overestimation of biomarker and drug potentials, as well as a poor understanding of tumor microenvironment in diagnosis and prognosis leads to the current levels of treatment failure regarding a vast majority of cancer types. A growing body of evidence points to the importance of the functional diversity of immune and structural cells during tumor development. In this sense, the lack of technologies that would allow for molecular screening of individual stromal cell types poses a major challenge for the development of therapies targeting the tumor microenvironment. Progress in microenvironment genetic studies represents a formidable opportunity for the development of new selective drugs because stromal cells have lower mutation rates than malignant cells, and should prove to be good targets for therapy.
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Affiliation(s)
- Antonio Palumbo
- Laboratório de Interações Celulares, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Prédio de Ciências da Saúde - Cidade Universitária, Ilha do Fundão, A. Carlos Chagas, 373 - bloco F, sala 26, 21941-902, Rio de Janeiro, RJ, Brasil. .,Programa de Carcinogênese Molecular, Instituto Nacional de Câncer José de Alencar Gomes da Silva, Rua André Cavalcanti, 37 - 6° andar - Centro, 20231-050, Rio de Janeiro, RJ, Brasil.
| | - Nathalia de Oliveira Meireles Da Costa
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer José de Alencar Gomes da Silva, Rua André Cavalcanti, 37 - 6° andar - Centro, 20231-050, Rio de Janeiro, RJ, Brasil.
| | - Martin Hernan Bonamino
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer José de Alencar Gomes da Silva, Rua André Cavalcanti, 37 - 6° andar - Centro, 20231-050, Rio de Janeiro, RJ, Brasil. .,Fundação Oswaldo Cruz, Vice-presidência de Pesquisa e Laboratórios de Referência, Rio de Janeiro, Brasil, Av. Brasil, 4365 - Pavilhão Mourisco - Manguinhos, 21040-900, Rio de Janeiro, RJ, Brasil.
| | - Luis Felipe Ribeiro Pinto
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer José de Alencar Gomes da Silva, Rua André Cavalcanti, 37 - 6° andar - Centro, 20231-050, Rio de Janeiro, RJ, Brasil.
| | - Luiz Eurico Nasciutti
- Laboratório de Interações Celulares, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Prédio de Ciências da Saúde - Cidade Universitária, Ilha do Fundão, A. Carlos Chagas, 373 - bloco F, sala 26, 21941-902, Rio de Janeiro, RJ, Brasil.
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Abstract
Type I interferons (IFNs) are known for their key role in antiviral immune responses. In this Review, we discuss accumulating evidence indicating that type I IFNs produced by malignant cells or tumour-infiltrating dendritic cells also control the autocrine or paracrine circuits that underlie cancer immunosurveillance. Many conventional chemotherapeutics, targeted anticancer agents, immunological adjuvants and oncolytic viruses are only fully efficient in the presence of intact type I IFN signalling. Moreover, the intratumoural expression levels of type I IFNs or of IFN-stimulated genes correlate with favourable disease outcome in several cohorts of patients with cancer. Finally, new anticancer immunotherapies are being developed that are based on recombinant type I IFNs, type I IFN-encoding vectors and type I IFN-expressing cells.
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131
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Rinchai D, Kewcharoenwong C, Kessler B, Lertmemongkolchai G, Chaussabel D. Increased abundance of ADAM9 transcripts in the blood is associated with tissue damage. F1000Res 2015; 4:89. [PMID: 27990250 PMCID: PMC5130078 DOI: 10.12688/f1000research.6241.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/17/2016] [Indexed: 02/10/2024] Open
Abstract
Background: Members of the ADAM (a disintegrin and metalloprotease domain) family have emerged as critical regulators of cell-cell signaling during development and homeostasis. ADAM9 is consistently overexpressed in various human cancers, and has been shown to play an important role in tumorigenesis. However, little is known about the involvement of ADAM9 during immune-mediated processes. Results: Mining of an extensive compendium of transcriptomic datasets identified important gaps in knowledge regarding the possible role of ADAM9 in immunological homeostasis and inflammation: 1) The abundance of ADAM9 transcripts in the blood was increased in patients with acute infection but, 2) changed very little after in vitro exposure to a wide range of pathogen-associated molecular patterns (PAMPs). 3) Furthermore it was found to increase significantly in subjects as a result of tissue injury or tissue remodeling, in absence of infectious processes. Conclusions: Our findings indicate that ADAM9 may constitute a valuable biomarker for the assessment of tissue damage, especially in clinical situations where other inflammatory markers are confounded by infectious processes.
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Affiliation(s)
- Darawan Rinchai
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Chidchamai Kewcharoenwong
- Cellular and Molecular Immunology Unit, The Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40000, Thailand
| | - Bianca Kessler
- Cellular and Molecular Immunology Unit, The Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40000, Thailand
| | - Ganjana Lertmemongkolchai
- Cellular and Molecular Immunology Unit, The Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40000, Thailand
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
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132
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Rinchai D, Kewcharoenwong C, Kessler B, Lertmemongkolchai G, Chaussabel D. Increased abundance of ADAM9 transcripts in the blood is associated with tissue damage. F1000Res 2015; 4:89. [PMID: 27990250 PMCID: PMC5130078 DOI: 10.12688/f1000research.6241.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/17/2016] [Indexed: 12/22/2022] Open
Abstract
Background: Members of the ADAM (a disintegrin and metalloprotease domain) family have emerged as critical regulators of cell-cell signaling during development and homeostasis. ADAM9 is consistently overexpressed in various human cancers, and has been shown to play an important role in tumorigenesis. However, little is known about the involvement of ADAM9 during immune-mediated processes. Results: Mining of an extensive compendium of transcriptomic datasets identified important gaps in knowledge regarding the possible role of ADAM9 in immunological homeostasis and inflammation: 1) The abundance of ADAM9 transcripts in the blood was increased in patients with acute infection but, 2) changed very little after
in vitro exposure to a wide range of pathogen-associated molecular patterns (PAMPs). 3) Furthermore it was found to increase significantly in subjects as a result of tissue injury or tissue remodeling, in absence of infectious processes. Conclusions: Our findings indicate that ADAM9 may constitute a valuable biomarker for the assessment of tissue damage, especially in clinical situations where other inflammatory markers are confounded by infectious processes.
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Affiliation(s)
- Darawan Rinchai
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Chidchamai Kewcharoenwong
- Cellular and Molecular Immunology Unit, The Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40000, Thailand
| | - Bianca Kessler
- Cellular and Molecular Immunology Unit, The Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40000, Thailand
| | - Ganjana Lertmemongkolchai
- Cellular and Molecular Immunology Unit, The Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40000, Thailand
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
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