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Abstract
Cytometry technologies are able to profile immune cells at single-cell resolution. They are widely used for both clinical diagnosis and biological research. We developed a deep learning model for analyzing cytometry data. We demonstrated that the deep learning model accurately diagnoses the latent cytomegalovirus (CMV) in healthy individuals. In addition, we developed a method for interpreting the deep learning model, allowing us to identify biomarkers associated with latent CMV infection. The deep learning model is widely applicable to other cytometry data related to human diseases. Cytometry technologies are essential tools for immunology research, providing high-throughput measurements of the immune cells at the single-cell level. Existing approaches in interpreting and using cytometry measurements include manual or automated gating to identify cell subsets from the cytometry data, providing highly intuitive results but may lead to significant information loss, in that additional details in measured or correlated cell signals might be missed. In this study, we propose and test a deep convolutional neural network for analyzing cytometry data in an end-to-end fashion, allowing a direct association between raw cytometry data and the clinical outcome of interest. Using nine large cytometry by time-of-flight mass spectrometry or mass cytometry (CyTOF) studies from the open-access ImmPort database, we demonstrated that the deep convolutional neural network model can accurately diagnose the latent cytomegalovirus (CMV) in healthy individuals, even when using highly heterogeneous data from different studies. In addition, we developed a permutation-based method for interpreting the deep convolutional neural network model. We were able to identify a CD27- CD94+ CD8+ T cell population significantly associated with latent CMV infection, confirming the findings in previous studies. Finally, we provide a tutorial for creating, training, and interpreting the tailored deep learning model for cytometry data using Keras and TensorFlow (https://github.com/hzc363/DeepLearningCyTOF).
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402
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Establishment and validation of an immune-associated signature in lung adenocarcinoma. Int Immunopharmacol 2020; 88:106867. [PMID: 32799112 DOI: 10.1016/j.intimp.2020.106867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/18/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022]
Abstract
Recent studies demonstrated that immune associated genes (IAGs) played an important role in the treatment of lung adenocarcinoma (LUAD). In the research, we established an IAGs signature and validated its prognostic value in LUAD by using bioinformatic methods and public databases. Based on the RNA-Seq samples from The Cancer Genome Atlas (TCGA), 576 differentially expressed IAGs were firstly identified. The R package coxph was used to select significant prognostic IAGs using both univariate and multivariate analyses. As a result, four IAGs (SCG2, CCL20, CAT, S100P) were finally screened in an IAGs signature. Based on these four IAGs, LASSO (least absolute shrinkage and selection operator) Cox regression analysis was used to construct a Risk score prognostic model and survival analysis revealed that high risk score was significantly associated with poor survival outcomes, which was validated in the external datasets GSE68465 and GSE31210. In addition, Risk score was found to be significantly associated with stage, lymphatic involvement, tumor metastasis and immune cells (B cells and dendritic cells) infiltration. Moreover, it was found that TP53 and EGFR had a higher mutation frequency in high risk group. Then a nomogram with clinical characteristics was established to superiorly predict prognosis of LUAD patients, and calibration plots and ROC analysis proved its accuracy. We believe that our findings can be conveniently used for individualized prediction of the clinical prognosis for LUAD patients, but further clinical trials and experimental exploration are needed to validate our observations.
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403
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Quan J, Zhang W, Yu C, Bai Y, Cui J, Lv J, Zhang Q. Bioinformatic identification of prognostic indicators in bladder cancer. Biomark Med 2020; 14:1243-1254. [PMID: 32749145 DOI: 10.2217/bmm-2020-0316] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aim: Bladder cancer (BC) is one of the most common malignancies with poor prognosis. We aimed to identify a genetic signature for predicting the prognosis of BC. Materials & methods: Kaplan-Meier survival and Cox regression analyses were used to construct a prognostic signature using data from The Cancer Genome Atlas. Results: Fifty four upregulated and 47 downregulated immune-related genes (IRGs) were identified in BC. A prognostic signature based on the expression of five IRGs was determined, which was moderately accurate in the prognosis of tumors. The prognostic signature was correlated with tumor stage, tumor burden and lymph node metastasis. The expression of IRGs were associated with immune infiltration. Conclusion: We determined a five gene signature, which correlates with the prognosis of BC patients, providing additional information for effective treatment.
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Affiliation(s)
- Jing Quan
- Department of Urology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Weiyi Zhang
- The First People's Hospital of Foshan, Foshan 528000, China
| | - Chong Yu
- Department of Urology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Yuchen Bai
- Department of Urology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Jianxin Cui
- Department of Urology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Jia Lv
- Department of Urology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Qi Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China
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404
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Xu H, Wang G, Zhu L, Liu H, Li B. Eight immune-related genes predict survival outcomes and immune characteristics in breast cancer. Aging (Albany NY) 2020; 12:16491-16513. [PMID: 32756008 PMCID: PMC7485735 DOI: 10.18632/aging.103753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/06/2020] [Indexed: 12/27/2022]
Abstract
Advancements in immunotherapy have improved our understanding of the immune characteristics of breast cancer. Here, we analyzed gene expression profiles and clinical data obtained from The Cancer Genome Atlas database to identify genes that were differentially expressed between breast tumor tissues and normal breast tissues. Comparisons with the Immunology Database and Analysis Portal (ImmPort) indicated that many of the identified differentially expressed genes were immune-related. Risk scores calculated based on an eight-gene signature constructed from these immune-related genes predicted both overall survival and relapse-free survival outcomes in breast cancer patients. The predictive value of the eight-gene signature was validated in different breast cancer subtypes using external datasets. Associations between risk score and breast cancer immune characteristics were also identified; in vitro experiments using breast cancer cell lines confirmed those associations. Thus, the novel eight-gene signature described here accurately predicts breast cancer survival outcomes as well as immune checkpoint expression and immune cell infiltration processes.
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Affiliation(s)
- Han Xu
- The Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Gangjian Wang
- The Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lili Zhu
- The Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hong Liu
- The Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Bingjie Li
- The Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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405
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Li B, Gould J, Yang Y, Sarkizova S, Tabaka M, Ashenberg O, Rosen Y, Slyper M, Kowalczyk MS, Villani AC, Tickle T, Hacohen N, Rozenblatt-Rosen O, Regev A. Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq. Nat Methods 2020; 17:793-798. [PMID: 32719530 PMCID: PMC7437817 DOI: 10.1038/s41592-020-0905-x] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 06/18/2020] [Indexed: 11/10/2022]
Abstract
Massively parallel single-cell and single-nucleus RNA sequencing has opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so is the need for computational pipelines for scaled analysis. Here we developed Cumulus-a cloud-based framework for analyzing large-scale single-cell and single-nucleus RNA sequencing datasets. Cumulus combines the power of cloud computing with improvements in algorithm and implementation to achieve high scalability, low cost, user-friendliness and integrated support for a comprehensive set of features. We benchmark Cumulus on the Human Cell Atlas Census of Immune Cells dataset of bone marrow cells and show that it substantially improves efficiency over conventional frameworks, while maintaining or improving the quality of results, enabling large-scale studies.
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Affiliation(s)
- Bo Li
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Division of Rheumatology, Allergy, and Immunology, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Rheumatology, Allergy, and Immunology, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yanay Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Monika S Kowalczyk
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Alexandra-Chloé Villani
- Division of Rheumatology, Allergy, and Immunology, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Timothy Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nir Hacohen
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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406
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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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407
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Dhillon BK, Smith M, Baghela A, Lee AHY, Hancock REW. Systems Biology Approaches to Understanding the Human Immune System. Front Immunol 2020; 11:1683. [PMID: 32849587 PMCID: PMC7406790 DOI: 10.3389/fimmu.2020.01683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/24/2020] [Indexed: 12/18/2022] Open
Abstract
Systems biology is an approach to interrogate complex biological systems through large-scale quantification of numerous biomolecules. The immune system involves >1,500 genes/proteins in many interconnected pathways and processes, and a systems-level approach is critical in broadening our understanding of the immune response to vaccination. Changes in molecular pathways can be detected using high-throughput omics datasets (e.g., transcriptomics, proteomics, and metabolomics) by using methods such as pathway enrichment, network analysis, machine learning, etc. Importantly, integration of multiple omic datasets is becoming key to revealing novel biological insights. In this perspective article, we highlight the use of protein-protein interaction (PPI) networks as a multi-omics integration approach to unravel information flow and mechanisms during complex biological events, with a focus on the immune system. This involves a combination of tools, including: InnateDB, a database of curated interactions between genes and protein products involved in the innate immunity; NetworkAnalyst, a visualization and analysis platform for InnateDB interactions; and MetaBridge, a tool to integrate metabolite data into PPI networks. The application of these systems techniques is demonstrated for a variety of biological questions, including: the developmental trajectory of neonates during the first week of life, mechanisms in host-pathogen interaction, disease prognosis, biomarker discovery, and drug discovery and repurposing. Overall, systems biology analyses of omics data have been applied to a variety of immunology-related questions, and here we demonstrate the numerous ways in which PPI network analysis can be a powerful tool in contributing to our understanding of the immune system and the study of vaccines.
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Affiliation(s)
- Bhavjinder K. Dhillon
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Maren Smith
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Arjun Baghela
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Amy H. Y. Lee
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
- Molecular Biology & Biochemistry Department, Simon Fraser University, Burnaby, BC, Canada
| | - Robert E. W. Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
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408
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Guo L, Li X, Liu R, Chen Y, Ren C, Du S. TOX correlates with prognosis, immune infiltration, and T cells exhaustion in lung adenocarcinoma. Cancer Med 2020; 9:6694-6709. [PMID: 32700817 PMCID: PMC7520261 DOI: 10.1002/cam4.3324] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/30/2020] [Accepted: 07/05/2020] [Indexed: 12/31/2022] Open
Abstract
Background Thymocyte selection‐associated high mobility group box (TOX) plays a crucial role on the development of innate immunity and tumor microenvironment. This study aims to explore the prognostic potential of TOX and comprehensively analyze the correlations between TOX, immune infiltration, and T cells function in diverse cancers particularly lung adenocarcinoma (LUAD). Methods TIMER was used to analyze TOX expression in different cancers. Potential prognostic value of TOX was evaluated by the PrognoScan, Kaplan‐Meier Plotter, and GEPIA2. The relationships between TOX, immune infiltration, and related gene marker sets were analyzed by TIMER and GEPIA2. Single‐cell RNA‐seq for T cells in LUAD was analyzed to further investigate the correlations between TOX expression and different T cells populations. Results TOX downregulates in most of the cancer types and correlates with poor prognosis in LUAD. TOX shows significant impacts on survival of LUAD with early stage, ever‐smoking, or low‐TMB status. Increased TOX expression positively correlates with high immune infiltration levels in most of the immune cells and functional T cells including exhausted T cells. Moreover, multiple key genes of exhausted T cells comprising PD‐1, TIM‐3, TIGHT, and CXCL13 have remarkable interaction with TOX. Specifically, TOX is observed with high enrichment in exhausted CD4+ and CD8+ T cells populations in single‐cell RNA‐seq analysis for LUAD. Conclusion TOX is a prognosis‐related biomarker for multiple cancer types especially LUAD. Increased TOX expression significantly increase immune infiltration levels in most of the immune cells comprising CD8+ T cells, CD4+ T cells, mast cells, and functional T cells. Moreover, we verified that TOX highly correlates with exhausted T cells and is probable a critical regulator promoted T cells exhaustion in LUAD. Detection of TOX expression could help to predict prognosis and regulating TOX expression in exhausted T cells may offer a novel strategy in maximizing immunotherapy efficacy for LUAD.
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Affiliation(s)
- Longbin Guo
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuanzi Li
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rongping Liu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yulei Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chen Ren
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shasha Du
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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409
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Abstract
Over the last several years, next-generation sequencing and its recent push toward single-cell resolution have transformed the landscape of immunology research by revealing novel complexities about all components of the immune system. With the vast amounts of diverse data currently being generated, and with the methods of analyzing and combining diverse data improving as well, integrative systems approaches are becoming more powerful. Previous integrative approaches have combined multiple data types and revealed ways that the immune system, both as a whole and as individual parts, is affected by genetics, the microbiome, and other factors. In this review, we explore the data types that are available for studying immunology with an integrative systems approach, as well as the current strategies and challenges for conducting such analyses.
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Affiliation(s)
- Silvia Pineda
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, 28029 Madrid, Spain
| | - Daniel G. Bunis
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
| | - Idit Kosti
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
- Department of Pediatrics, University of California, San Francisco, California 94143, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
- Department of Pediatrics, University of California, San Francisco, California 94143, USA
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410
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Bras AE, van der Velden VHJ. Robust FCS Parsing: Exploring 211,359 Public Files. Cytometry A 2020; 97:1180-1186. [PMID: 32633075 PMCID: PMC7754493 DOI: 10.1002/cyto.a.24187] [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: 01/24/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 01/02/2023]
Abstract
When it comes to data storage, the field of flow cytometry is fairly standardized, thanks to the flow cytometry standard (FCS) file format. The structure of FCS files is described in the FCS specification. Software that strictly complies with the FCS specification is guaranteed to be interoperable (in terms of exchange via FCS files). Nowadays, software interoperability is crucial for eco system, as FCS files are frequently shared, and workflows rely on more than one piece of software (e.g., acquisition and analysis software). Ideally, software developers strictly follow the FCS specification. Unfortunately, this is not always the case, which resulted in various nonconformant FCS files being generated over time. Therefore, robust FCS parsers must be developed, which can handle a wide variety of nonconformant FCS files, from different resources. Development of robust FCS parsers would greatly benefit from a fully fledged set of testing files. In this study, readability of 211,359 public FCS files was evaluated. Each FCS file was checked for conformance with the FCS specification. For each data set, within each FCS file, validated parse results were obtained for the TEXT segment. Highly space efficient testing files were generated. FlowCore was benchmarked in depth, by using the validated parse results, the generated testing files, and the original FCS files. Robustness of FlowCore (as measured by testing against 211,359 files) was improved by re‐implementing the TEXT segment parser. Altogether, this study provides a comprehensive resource for FCS parser development, an in‐depth benchmark of FlowCore, and a concrete proposal for improving FlowCore. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Anne E Bras
- Laboratory Medical immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Vincent H J van der Velden
- Laboratory Medical immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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411
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Bellomo A, Mondor I, Spinelli L, Lagueyrie M, Stewart BJ, Brouilly N, Malissen B, Clatworthy MR, Bajénoff M. Reticular Fibroblasts Expressing the Transcription Factor WT1 Define a Stromal Niche that Maintains and Replenishes Splenic Red Pulp Macrophages. Immunity 2020; 53:127-142.e7. [PMID: 32562599 DOI: 10.1016/j.immuni.2020.06.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/20/2020] [Accepted: 06/04/2020] [Indexed: 12/21/2022]
Abstract
Located within red pulp cords, splenic red pulp macrophages (RPMs) are constantly exposed to the blood flow, clearing senescent red blood cells (RBCs) and recycling iron from hemoglobin. Here, we studied the mechanisms underlying RPM homeostasis, focusing on the involvement of stromal cells as these cells perform anchoring and nurturing macrophage niche functions in lymph nodes and liver. Microscopy revealed that RPMs are embedded in a reticular meshwork of red pulp fibroblasts characterized by the expression of the transcription factor Wilms' Tumor 1 (WT1) and colony stimulating factor 1 (CSF1). Conditional deletion of Csf1 in WT1+ red pulp fibroblasts, but not white pulp fibroblasts, drastically altered the RPM network without altering circulating CSF1 levels. Upon RPM depletion, red pulp fibroblasts transiently produced the monocyte chemoattractants CCL2 and CCL7, thereby contributing to the replenishment of the RPM network. Thus, red pulp fibroblasts anchor and nurture RPM, a function likely conserved in humans.
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Affiliation(s)
- Alicia Bellomo
- Aix Marseille Univ, CNRS, INSERM, CIML, Marseille, France
| | | | | | | | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nicolas Brouilly
- Aix-Marseille Université, Centre National de la Recherche Scientifique, Institut de Biologie du Développement de Marseille, Marseille, France
| | | | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Marc Bajénoff
- Aix Marseille Univ, CNRS, INSERM, CIML, Marseille, France.
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412
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Integrative Approaches to Cancer Immunotherapy. Trends Cancer 2020; 5:400-410. [PMID: 31311655 DOI: 10.1016/j.trecan.2019.05.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/17/2019] [Accepted: 05/30/2019] [Indexed: 12/11/2022]
Abstract
Cancer immunotherapy aims to arm patients with cancer-fighting immunity. Many new cancer-specific immunotherapeutic drugs have gained approval in the past several years, demonstrating immunotherapy's efficacy and promise as an anticancer modality. Despite these successes, several outstanding questions remain for cancer immunotherapy, including how to make immunotherapy more efficacious in a broader range of cancer types and patients, and how to predict which patients will respond or not respond to therapy. We present a case for integrative systems approaches that will answer these questions. This involves applying mechanistic and statistical modeling, establishing consistent and widely adopted experimental tools to generate systems-level data, and creating sustained mechanisms of support. If implemented, these approaches will lead to major advances in cancer treatment.
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413
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Chen S, Cao GD, Wei W, Yida L, Xiaobo H, Lei Y, Ke C, Chen B, Xiong MM. Prediction and identification of immune genes related to the prognosis of patients with colon adenocarcinoma and its mechanisms. World J Surg Oncol 2020; 18:146. [PMID: 32600423 PMCID: PMC7325073 DOI: 10.1186/s12957-020-01921-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Background Colon adenocarcinoma (COAD) is a gastrointestinal tumor with a high degree of malignancy. Its deterioration process is closely related to the tumor microenvironment, and transcription factors (TF) play a regulatory role in this process. Currently, there is a lack of exploration between the genes related to the COAD tumor microenvironment and the survival prognosis of patients. Models composed of multiple genes usually predict the survival prognosis of patients more accurately than single genes. We can analyze the multigene models that can predict the prognosis of COAD from the current database. Methods The limma package of the R programming language is used for gene differential expression analysis. Kaplan-Meier curve is used to analyze the relationship between the patient risk score model and survival data. The hazard model is used to analyze the relationship between the risk score and the clinical data of COAD patients. The information of immune genes and immune cells is obtained from IMMPORT database and TIMER database. Receiver operating characteristic (ROC) curve is used to judge the stability of the model. Results We found 7 immune genes, which can built a risk score model to predict the survival prognosis of COAD. According to univariate and multivariate analysis, the risk score can be used as an independent predictor. The content of some immune microenvironment cells will also increase as the risk score increases. Conclusions We found 7 immune genes, such as SLC10A2 (solute carrier family 10 member 2), CXCL3 (C-X-C motif chemokine ligand 3), IGHV5-51 (immunoglobulin heavy variable 5-51), INHBA (inhibin subunit beta A), STC1 (stanniocalcin 1), UCN (urocortin), and OXTR (oxytocin receptor), can constitute a model for predicting the prognosis of COAD. They may provide potential therapeutic targets for clinical treatment of COAD.
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Affiliation(s)
- Sihan Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Aahui, China
| | - G D Cao
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Aahui, China
| | - Wu Wei
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Aahui, China
| | - Lu Yida
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Aahui, China
| | - He Xiaobo
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Aahui, China
| | - Yang Lei
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Aahui, China
| | - Chen Ke
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Aahui, China
| | - Bo Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Aahui, China.
| | - Mao Ming Xiong
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Aahui, China.
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414
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Kennedy RB, Ovsyannikova IG, Palese P, Poland GA. Current Challenges in Vaccinology. Front Immunol 2020; 11:1181. [PMID: 32670279 PMCID: PMC7329983 DOI: 10.3389/fimmu.2020.01181] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022] Open
Abstract
The development of vaccines, which prime the immune system to respond to future infections, has led to global declines in morbidity and mortality from dreadful infectious communicable diseases. However, many pathogens of public health importance are highly complex and/or rapidly evolving, posing unique challenges to vaccine development. Several of these challenges include an incomplete understanding of how immunity develops, host and pathogen genetic variability, and an increased societal skepticism regarding vaccine safety. In particular, new high-dimensional omics technologies, aided by bioinformatics, are driving new vaccine development (vaccinomics). Informed by recent insights into pathogen biology, host genetic diversity, and immunology, the increasing use of genomic approaches is leading to new models and understanding of host immune system responses that may provide solutions in the rapid development of novel vaccine candidates.
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Affiliation(s)
- Richard B Kennedy
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, United States
| | - Inna G Ovsyannikova
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, United States
| | - Peter Palese
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Gregory A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, United States
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415
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Freeze B, Pandya S, Zeighami Y, Raj A. Regional transcriptional architecture of Parkinson's disease pathogenesis and network spread. Brain 2020; 142:3072-3085. [PMID: 31359041 DOI: 10.1093/brain/awz223] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/04/2019] [Accepted: 05/28/2019] [Indexed: 11/13/2022] Open
Abstract
Although a significant genetic contribution to the risk of developing sporadic Parkinson's disease has been well described, the relationship between local genetic factors, pathogenesis, and subsequent spread of pathology throughout the brain has been largely unexplained in humans. To address this question, we use network diffusion modelling to infer probable pathology seed regions and patterns of disease spread from MRI atrophy maps derived from 232 de novo subjects in the Parkinson's Progression Markers Initiative study. Allen Brain Atlas regional transcriptional profiles of 67 Parkinson's disease risk factor genes were mapped to the inferred seed regions to determine the local influence of genetic risk factors. We used hierarchical clustering and L1 regularized regression analysis to show that transcriptional profiles of immune-related and lysosomal risk factor genes predict seed region location and the pattern of disease propagation from the most likely seed region, substantia nigra. By leveraging recent advances in transcriptomics, we show that regional microglial abundance quantified by high fidelity gene expression also predicts seed region location. These findings suggest that early disease sites are genetically susceptible to dysfunctional lysosomal α-synuclein processing and microglia-mediated neuroinflammation, which may initiate the disease process and contribute to spread of pathology along neural connectivity pathways.
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Affiliation(s)
- Benjamin Freeze
- Department of Radiology, NewYork-Presbyterian Hospital/Weill Cornell Medicine, New York, USA
| | - Sneha Pandya
- Department of Radiology, NewYork-Presbyterian Hospital/Weill Cornell Medicine, New York, USA
| | - Yashar Zeighami
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Ashish Raj
- Department of Radiology, NewYork-Presbyterian Hospital/Weill Cornell Medicine, New York, USA.,Department of Radiology and Biomedical Imaging, University of California, San Francisco, USA
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416
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Maia PD, Pandya S, Freeze B, Torok J, Gupta A, Zeighami Y, Raj A. Origins of atrophy in Parkinson linked to early onset and local transcription patterns. Brain Commun 2020; 2:fcaa065. [PMID: 32954322 PMCID: PMC7472895 DOI: 10.1093/braincomms/fcaa065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/20/2020] [Accepted: 04/15/2020] [Indexed: 12/17/2022] Open
Abstract
There is enormous clinical value in inferring the brain regions initially atrophied in Parkinson disease for individual patients and understanding its relationship with clinical and genetic risk factors. The aim of this study is to leverage a new seed-inference algorithm demonstrated for Alzheimer's disease to the Parkinsonian context and to cluster patients in meaningful subgroups based on these incipient atrophy patterns. Instead of testing brain regions separately as the likely initiation site for each patient, we solve an L1-penalized optimization problem that can return a more predictive heterogeneous, multi-locus seed patterns. A cluster analysis of the individual seed patterns reveals two distinct subgroups (S1 versus S2). The S1 subgroup is characterized by the involvement of the brainstem and ventral nuclei, and S2 by cortex and striatum. Post hoc analysis in features not included in the clustering shows significant differences between subgroups regarding age of onset and local transcriptional patterns of Parkinson-related genes. Top genes associated with regional microglial abundance are strongly associated with subgroup S1 but not with S2. Our results suggest two distinct aetiological mechanisms operative in Parkinson disease. The interplay between immune-related genes, lysosomal genes, microglial abundance and atrophy initiation sites may explain why the age of onset for patients in S1 is on average 4.5 years later than for those in S2. We highlight and compare the most prominently affected brain regions for both subgroups. Altogether, our findings may improve current screening strategies for early Parkinson onsetters.
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Affiliation(s)
- Pedro D Maia
- Department of Radiology and Biomedical Imaging, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sneha Pandya
- Department of Radiology, Weill Cornell Medical College, New York, NY, USA
| | - Benjamin Freeze
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Radiology, Harvard Medical School, Boston, MA 02115, USA
| | - Justin Torok
- Department of Radiology, Weill Cornell Medical College, New York, NY, USA
| | - Ajay Gupta
- Department of Radiology, Weill Cornell Medical College, New York, NY, USA
| | - Yashar Zeighami
- Brain Imaging Center, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Ashish Raj
- Department of Radiology and Biomedical Imaging, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
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417
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Huang M, He M, Guo Y, Li H, Shen S, Xie Y, Li X, Xiao H, Fang L, Li D, Peng B, Liang L, Yu J, Kuang M, Xu L, Peng S. The Influence of Immune Heterogeneity on the Effectiveness of Immune Checkpoint Inhibitors in Multifocal Hepatocellular Carcinomas. Clin Cancer Res 2020; 26:4947-4957. [PMID: 32527942 DOI: 10.1158/1078-0432.ccr-19-3840] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 03/17/2020] [Accepted: 06/04/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Immune checkpoint inhibitor therapy is emerging as the promising option for patients with advanced hepatocellular carcinoma. We aimed to investigate the heterogeneity of different tumor nodules of the same patient with multifocal hepatocellular carcinomas in response to immunotherapy and its molecular mechanisms. EXPERIMENTAL DESIGN We attained 45 surgical tumor samples including 33 small and 12 large nodules from 12 patients with multifocal hepatocellular carcinoma and evaluated genomic and immune heterogeneity among tumors through whole-genome sequencing and RNA sequencing. IHC was performed to validate the expression of immune markers. The responses to anti-programmed cell death protein-1 (PD-1) therapy in patients with multifocal hepatocellular carcinoma were evaluated. RESULTS The small and large tumors within the same patient presented with similar genomic characteristics, indicating their same genomic origin. We further found the small tumors had higher immune cell infiltration including more CD8+ T cells, M1 macrophages, and monocytes as compared with large tumors. Besides, the expression of interferon signature predictive of response to anti-PD-1 therapy was significantly upregulated in the small tumors. Moreover, the immune pathways were more vigorous along with less active proliferation pathways in the small tumors. In keeping with this, we found that small nodules were more sensitive to anti-PD-1 therapy than large nodules in patients with multifocal hepatocellular carcinoma. CONCLUSIONS The small tumors in patients with multifocal hepatocellular carcinoma had higher immune cell infiltration and upregulation of immune pathways as compared with the large tumors, which can partially explain the different responses of small and large tumors in the same case to anti-PD-1 therapy.
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Affiliation(s)
- Manling Huang
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minghui He
- Department of Liver Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yu Guo
- Department of Liver Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Heping Li
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shunli Shen
- Department of Liver Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yubin Xie
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoxing Li
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Han Xiao
- Division of Interventional Ultrasound, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lujing Fang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dongming Li
- Department of Liver Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Baogang Peng
- Department of Liver Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lijian Liang
- Department of Liver Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jun Yu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ming Kuang
- Department of Liver Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Division of Interventional Ultrasound, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lixia Xu
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China. .,Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sui Peng
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China. .,Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Clinical Trial Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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418
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Andronis C, Silva JP, Lekka E, Virvilis V, Carmo H, Bampali K, Ernst M, Hu Y, Loryan I, Richard J, Carvalho F, Savić MM. Molecular basis of mood and cognitive adverse events elucidated via a combination of pharmacovigilance data mining and functional enrichment analysis. Arch Toxicol 2020; 94:2829-2845. [PMID: 32504122 PMCID: PMC7395038 DOI: 10.1007/s00204-020-02788-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 05/20/2020] [Indexed: 01/04/2023]
Abstract
Drug-induced Mood- and Cognition-related adverse events (MCAEs) are often only detected during the clinical trial phases of drug development, or even after marketing, thus posing a major safety concern and a challenge for both pharmaceutical companies and clinicians. To fill some gaps in the understanding and elucidate potential biological mechanisms of action frequently associated with MCAEs, we present a unique workflow linking observational population data with the available knowledge at molecular, cellular, and psychopharmacology levels. It is based on statistical analysis of pharmacovigilance reports and subsequent signaling pathway analyses, followed by evidence-based expert manual curation of the outcomes. Our analysis: (a) ranked pharmaceuticals with high occurrence of such adverse events (AEs), based on disproportionality analysis of the FDA Adverse Event Reporting System (FAERS) database, and (b) identified 120 associated genes and common pathway nodes possibly underlying MCAEs. Nearly two-thirds of the identified genes were related to immune modulation, which supports the critical involvement of immune cells and their responses in the regulation of the central nervous system function. This finding also means that pharmaceuticals with a negligible central nervous system exposure may induce MCAEs through dysregulation of the peripheral immune system. Knowledge gained through this workflow unravels putative hallmark biological targets and mediators of drug-induced mood and cognitive disorders that need to be further assessed and validated in experimental models. Thereafter, they can be used to substantially improve in silico/in vitro/in vivo tools for predicting these adversities at a preclinical stage.
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Affiliation(s)
| | - João Pedro Silva
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | | | | | - Helena Carmo
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Konstantina Bampali
- Department of Molecular Neurosciences, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Margot Ernst
- Department of Molecular Neurosciences, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Yang Hu
- Translational PKPD Group, Department of Pharmaceutical Biosciences, Associate Member of SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Irena Loryan
- Translational PKPD Group, Department of Pharmaceutical Biosciences, Associate Member of SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Jacques Richard
- Sanofi R&D, 371 avenue Professeur Blayac, 34000, Montpellier, France
| | - Félix Carvalho
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal.
| | - Miroslav M Savić
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000, Belgrade, Serbia.
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419
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Zhang Z, Bao S, Yan C, Hou P, Zhou M, Sun J. Computational principles and practice for decoding immune contexture in the tumor microenvironment. Brief Bioinform 2020; 22:5850909. [PMID: 32496512 DOI: 10.1093/bib/bbaa075] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
Tumor-infiltrating immune cells (TIICs) have been recognized as crucial components of the tumor microenvironment (TME) and induced both beneficial and adverse consequences for tumorigenesis as well as outcome and therapy (particularly immunotherapy). Computer-aided investigation of immune cell components in the TME has become a promising avenue to better understand the interplay between the immune system and tumors. In this study, we presented an overview of data sources, computational methods and software tools, as well as their application in inferring the composition of tumor-infiltrating immune cells in the TME. In parallel, we explored the future perspectives and challenges that may be faced with more accurate quantitative infiltration of immune cells in the future. Together, our study provides a little guide for scientists in the field of clinical and experimental immunology to look for dedicated resources and more competent tools for accelerating the unraveling of tumor-immune interactions with the implication in precision immunotherapy.
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Affiliation(s)
- Zicheng Zhang
- School of Biomedical Engineering, Wenzhou Medical University
| | - Siqi Bao
- School of Biomedical Engineering, Wenzhou Medical University
| | - Congcong Yan
- School of Biomedical Engineering, Wenzhou Medical University
| | - Ping Hou
- School of Biomedical Engineering, Wenzhou Medical University
| | - Meng Zhou
- School of Biomedical Engineering, Wenzhou Medical University
| | - Jie Sun
- School of Biomedical Engineering, Wenzhou Medical University
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420
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Lecchi C, Zamarian V, Borriello G, Galiero G, Grilli G, Caniatti M, D'Urso ES, Roccabianca P, Perego R, Minero M, Legnani S, Calogero R, Arigoni M, Ceciliani F. Identification of Altered miRNAs in Cerumen of Dogs Affected by Otitis Externa. Front Immunol 2020; 11:914. [PMID: 32547539 PMCID: PMC7273745 DOI: 10.3389/fimmu.2020.00914] [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: 10/14/2019] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Otitis externa is one of the most common diseases in dogs. It is associated with bacteria and yeast, which are regarded as secondary causes. Cerumen is a biological substance playing an important role in the protection of ear skin. The involvement of cerumen in immune defense is poorly understood. MicroRNAs can modulate the host immune response and can provide promising biomarkers for several inflammatory and infectious disorder diagnosis. The aims of this study were to profile the cerumen miRNA signature associated with otitis externa in dogs, integrate miRNAs to their target genes related to immune functions, and investigate their potential use as biomarkers. Cerumen was collected from healthy and otitis affected dogs and the expression of miRNAs was profiled by Next Generation Sequencing; the validation of the altered miRNAs was performed using RT-qPCR. The potential ability of miRNAs to modulate immune-related genes was investigated using bioinformatics tools. The results pointed out that 32 miRNAs, of which 14 were up- and 18 down-regulated, were differentially expressed in healthy vs. otitis-affected dogs. These results were verified by RT-qPCR. To assess the diagnostic value of miRNAs, ROC analysis was carried out, highlighting that 4 miRNAs are potential biomarkers to discriminate otitis-affected dogs. Bioinformatics showed that cerumen miRNAs may be involved in the modulation of host immune response. In conclusion, we have demonstrated for the first time that miRNAs can be efficiently extracted and quantified from cerumen, that their profile changes between healthy and otitis affected dogs, and that they may serve as potential biomarkers. Further studies are necessary to confirm their diagnostic value and to investigate their interaction with immune-related genes.
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Affiliation(s)
- Cristina Lecchi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Valentina Zamarian
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Giorgia Borriello
- Dipartimento di Sanità Animale, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Giorgio Galiero
- Dipartimento di Sanità Animale, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Guido Grilli
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Mario Caniatti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Elisa Silvia D'Urso
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Paola Roccabianca
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Roberta Perego
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Michela Minero
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Sara Legnani
- Department of Small Animal Clinical Science, Institute of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| | - Raffaele Calogero
- Department of Biotechnology and Health Sciences, Molecular Biotechnology Center, Università di Torino, Turin, Italy
| | - Maddalena Arigoni
- Department of Biotechnology and Health Sciences, Molecular Biotechnology Center, Università di Torino, Turin, Italy
| | - Fabrizio Ceciliani
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
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421
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Gao X, Yang J, Chen Y. Identification of a four immune-related genes signature based on an immunogenomic landscape analysis of clear cell renal cell carcinoma. J Cell Physiol 2020; 235:9834-9850. [PMID: 32452055 DOI: 10.1002/jcp.29796] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/06/2020] [Indexed: 12/13/2022]
Abstract
Renal clear cell carcinoma (ccRCC) is the most common type of renal cell carcinoma, which has strong immunogenicity. A comprehensive study of the role of immune-related genes (IRGs) in ccRCC is of great significance in finding ccRCC treatment targets and improving patient prognosis. In this study, we comprehensively analyzed the expression of IRGs in ccRCC based on The Cancer Genome Atlas datasets. The mechanism of differentially expressed IRGs in ccRCC was analyzed by bioinformatics. In addition, Cox regression analysis was used to screen prognostic related IRGs from differentially expressed IRGs. We also identified a four IRGs signature consisting of four IRGs (CXCL2, SEMA3G, PDGFD, and UCN) through lasso regression and multivariate Cox regression analysis. Further analysis results showed that the four IRGs signature could effectively predict the prognosis of patients with ccRCC, and its predictive power is independent of other clinical factors. In addition, the correlation analysis of immune cell infiltration showed that this four IRGs signature could effectively reflect the level of immune cell infiltration of ccRCC. We also found that the expression of immune checkpoint genes CTLA-4, LAG3, and PD-1 in the high-risk group was higher than that in the low-risk group. Our research revealed the role of IRGs in ccRCC, and developed a four IRGs signature that could be used to evaluate the prognosis of patients with ccRCC, which will help to develop personalized treatment strategies for patients with ccRCC and improve their prognosis. In addition, these four IRGs may be effective therapeutic targets for ccRCC.
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Affiliation(s)
- Xin Gao
- Clinical Laboratory, The First People's Hospital of Huaihua, Huaihua, Hunan, China
| | - Jinlian Yang
- Clinical Laboratory, The First People's Hospital of Huaihua, Huaihua, Hunan, China
| | - Yinyi Chen
- Clinical Laboratory, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
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422
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Zhang H, Qin C, Gan H, Guo X, Zhang L. Construction of an Immunogenomic Risk Score for Prognostication in Colon Cancer. Front Genet 2020; 11:499. [PMID: 32508884 PMCID: PMC7253627 DOI: 10.3389/fgene.2020.00499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/22/2020] [Indexed: 01/18/2023] Open
Abstract
Immune-related genes (IRGs) play regulatory roles in the immune system and are involved in the initiation and progression of colon cancer. This study aimed to develop an immunogenomic risk score for predicting survival outcomes among colon cancer patients. We analyzed the expressions of IRGs in colon specimens and discovered 484 differentially expressed IRGs when we compared specimens from colon cancer and adjacent normal tissue. Univariate Cox regression analyses were performed to identify 26 IRGs that were associated with survival. A Cox proportional hazards model with a lasso penalty identified five optimal IRGs for constructing the immunogenomic risk score (CD1B, XCL1, PLCG2, NGF, and OXTR). The risk score had good performance in predicting overall survival among patients with colon cancer and was correlated with the amount of tumor-infiltrating immune cells. Our findings suggest that the immunogenomic risk score may be useful for prognostication in colon cancer cases. Furthermore, the five IRGs included in the risk score might be useful targets for investigating the initiation of colon cancer and designing personalized treatments.
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Affiliation(s)
- Han Zhang
- First Clinical Medical College, Chongqing Medical University, Chongqing, China.,Department of Digestive Oncology, Three Gorges Hospital, Chongqing University, Chongqing, China
| | - Chuan Qin
- Department of Gastrointestinal Surgery, Three Gorges Hospital, Chongqing University, Chongqing, China
| | - Hua Gan
- First Clinical Medical College, Chongqing Medical University, Chongqing, China
| | - Xiong Guo
- First Clinical Medical College, Chongqing Medical University, Chongqing, China
| | - Li Zhang
- Department of Digestive Oncology, Three Gorges Hospital, Chongqing University, Chongqing, China
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423
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Resolving Clinical Phenotypes into Endotypes in Allergy: Molecular and Omics Approaches. Clin Rev Allergy Immunol 2020; 60:200-219. [PMID: 32378146 DOI: 10.1007/s12016-020-08787-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allergic diseases are highly complex with respect to pathogenesis, inflammation, and response to treatment. Current efforts for allergic disease diagnosis have focused on clinical evidence as a binary outcome. Although outcome status based on clinical phenotypes (observable characteristics) is convenient and inexpensive to measure in large studies, it does not adequately provide insight into the complex molecular determinants of allergic disease. Individuals with similar clinical diagnoses do not necessarily have similar disease etiologies, natural histories, or responses to treatment. This heterogeneity contributes to the ineffective response to treatment leading to an annual estimated cost of $350 billion in the USA alone. There has been a recent focus to deconvolute the clinical heterogeneity of allergic diseases into specific endotypes using molecular and omics approaches. Endotypes are a means to classify patients based on the underlying pathophysiological mechanisms involving distinct functions or treatment response. The advent of high-throughput molecular omics, immunophenotyping, and bioinformatics methods including machine learning algorithms is facilitating the development of endotype-based diagnosis. As we move to the next decade, we should truly start treating clinical endotypes not clinical phenotype. This review highlights current efforts taking place to improve allergic disease endotyping via molecular omics profiling, immunophenotyping, and machine learning approaches in the context of precision diagnostics in allergic diseases. Graphical Abstract.
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424
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van de Veen W, Globinska A, Jansen K, Straumann A, Kubo T, Verschoor D, Wirz OF, Castro-Giner F, Tan G, Rückert B, Ochsner U, Herrmann M, Stanić B, van Splunter M, Huntjens D, Wallimann A, Fonseca Guevara RJ, Spits H, Ignatova D, Chang YT, Fassnacht C, Guenova E, Flatz L, Akdis CA, Akdis M. A novel proangiogenic B cell subset is increased in cancer and chronic inflammation. SCIENCE ADVANCES 2020; 6:eaaz3559. [PMID: 32426497 PMCID: PMC7220305 DOI: 10.1126/sciadv.aaz3559] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 03/06/2020] [Indexed: 05/17/2023]
Abstract
B cells contribute to immune responses through the production of immunoglobulins, antigen presentation, and cytokine production. Several B cell subsets with distinct functions and polarized cytokine profiles have been reported. In this study, we used transcriptomics analysis of immortalized B cell clones to identify an IgG4+ B cell subset with a unique function. These B cells are characterized by simultaneous expression of proangiogenic cytokines including VEGF, CYR61, ADM, FGF2, PDGFA, and MDK. Consequently, supernatants from these clones efficiently promote endothelial cell tube formation. We identified CD49b and CD73 as surface markers identifying proangiogenic B cells. Circulating CD49b+CD73+ B cells showed significantly increased frequency in patients with melanoma and eosinophilic esophagitis (EoE), two diseases associated with angiogenesis. In addition, tissue-infiltrating IgG4+CD49b+CD73+ B cells expressing proangiogenic cytokines were detected in patients with EoE and melanoma. Our results demonstrate a previously unidentified proangiogenic B cell subset characterized by expression of CD49b, CD73, and proangiogenic cytokines.
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Affiliation(s)
- Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Anna Globinska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Kirstin Jansen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Alex Straumann
- Swiss EoE Clinic and EoE Research Network, Olten, Switzerland
| | - Terufumi Kubo
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Daniëlle Verschoor
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Oliver F. Wirz
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Francesc Castro-Giner
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Ge Tan
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Beate Rückert
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Urs Ochsner
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Marietta Herrmann
- AO Research Institute Davos, Davos, Switzerland
- IZKF Group Tissue Regeneration in Musculoskeletal Diseases, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Barbara Stanić
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Marloes van Splunter
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Daan Huntjens
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Alexandra Wallimann
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
- AO Research Institute Davos, Davos, Switzerland
| | | | - Hergen Spits
- AIMM Therapeutics, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Medical Centers, Amsterdam, Netherlands
| | - Desislava Ignatova
- Department of Dermatology, University Hospital Zurich, University of Zurich, Switzerland
| | - Yun-Tsan Chang
- Department of Dermatology, University Hospital Zurich, University of Zurich, Switzerland
| | - Christina Fassnacht
- Department of Dermatology, University Hospital Zurich, University of Zurich, Switzerland
| | - Emmanuella Guenova
- Department of Dermatology, University Hospital Zurich, University of Zurich, Switzerland
- University Hospital of Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Lukas Flatz
- Institute of Immunobiology, Kantonsspital St. Gallen, Switzerland
- Department of Oncology and Haematology, Kantonsspital St. Gallen, Switzerland
- Department of Dermatology and Allergology, Kantonsspital St. Gallen, Switzerland
| | - Cezmi A. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
- Corresponding author.
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425
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Lu Y, Zhou X, Liu Z, Wang B, Wang W, Fu W. Assessment for Risk Status of Colorectal Cancer Patients: A Novel Prediction Model Based on Immune-Related Genes. DNA Cell Biol 2020; 39:958-964. [PMID: 32243216 DOI: 10.1089/dna.2019.5195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Heterogeneity in patients with colorectal cancer (CRC) leads to different strategies in clinical decision making. Identifying distinctive subgroups in patients contributes to develop more individualized treatments. This study constructed a novel prediction model for the prognosis of CRC patients based on the value of risk score combining the expression status of immune-related genes and coefficients. In this study, we built an interactive network of prognosis-related immune genes and transcription factors and adopted several methods to verify the accuracy of model. Moreover, we assessed the correlation between risk score and immune infiltration. The results suggested that the model was well fit and the risk score could be an independent predictive factor for CRC patients. This model has high application value in the clinic.
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Affiliation(s)
- Yongqu Lu
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Xin Zhou
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Zhenzhen Liu
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Bingyan Wang
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Wendong Wang
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Wei Fu
- Department of General Surgery, Peking University Third Hospital, Beijing, China
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426
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Lin K, Huang J, Luo H, Luo C, Zhu X, Bu F, Xiao H, Xiao L, Zhu Z. Development of a prognostic index and screening of potential biomarkers based on immunogenomic landscape analysis of colorectal cancer. Aging (Albany NY) 2020; 12:5832-5857. [PMID: 32235004 PMCID: PMC7185108 DOI: 10.18632/aging.102979] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/03/2020] [Indexed: 12/26/2022]
Abstract
Background: Colorectal cancer (CRC) accounts for the highest fatality rate among all malignant tumors. Immunotherapy has shown great promise in management of many malignant tumors, necessitating the need to explore its role in CRC. Results: Our analysis revealed a total of 71 differentially expressed IRGs, that were associated with prognosis of CRC patients. Ten IRGs (FABP4, IGKV1-33, IGKV2D-40, IGLV6-57, NGF, RETNLB, UCN, VIP, NGFR, and OXTR) showed high prognostic performance in predicting CRC outcomes, and were further associated with tumor burden, metastasis, tumor TNM stage, gender, age, and pathological stage. Interestingly, the IRG-based prognostic index (IRGPI) reflected infiltration of multiple immune cell types. Conclusions: This model provides an effective approach for stratification and characterization of patients using IRG-based immunolabeling tools to monitor prognosis of CRC. Methods: We performed a comprehensive analysis of expression profiles for immune-related genes (IRGs) and overall survival time in 437 CRC patients from the TCGA database. We employed computational algorithms and Cox regression analysis to estimate the relationship between differentially expressed IRGs and survival rates in CRC patients. Furthermore, we investigated the mechanisms of action of the IRGs involved in CRC, and established a novel prognostic index based on multivariate Cox models.
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Affiliation(s)
- Kang Lin
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Jun Huang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Hongliang Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Chen Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Xiaojian Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Fanqin Bu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Han Xiao
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Li Xiao
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Zhengming Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
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427
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Sjöstedt E, Zhong W, Fagerberg L, Karlsson M, Mitsios N, Adori C, Oksvold P, Edfors F, Limiszewska A, Hikmet F, Huang J, Du Y, Lin L, Dong Z, Yang L, Liu X, Jiang H, Xu X, Wang J, Yang H, Bolund L, Mardinoglu A, Zhang C, von Feilitzen K, Lindskog C, Pontén F, Luo Y, Hökfelt T, Uhlén M, Mulder J. An atlas of the protein-coding genes in the human, pig, and mouse brain. Science 2020; 367:367/6482/eaay5947. [PMID: 32139519 DOI: 10.1126/science.aay5947] [Citation(s) in RCA: 512] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 02/06/2020] [Indexed: 12/12/2022]
Abstract
The brain, with its diverse physiology and intricate cellular organization, is the most complex organ of the mammalian body. To expand our basic understanding of the neurobiology of the brain and its diseases, we performed a comprehensive molecular dissection of 10 major brain regions and multiple subregions using a variety of transcriptomics methods and antibody-based mapping. This analysis was carried out in the human, pig, and mouse brain to allow the identification of regional expression profiles, as well as to study similarities and differences in expression levels between the three species. The resulting data have been made available in an open-access Brain Atlas resource, part of the Human Protein Atlas, to allow exploration and comparison of the expression of individual protein-coding genes in various parts of the mammalian brain.
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Affiliation(s)
- Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden.,Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Wen Zhong
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Linn Fagerberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Max Karlsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Nicholas Mitsios
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Csaba Adori
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Per Oksvold
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Fredrik Edfors
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | | | - Feria Hikmet
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Jinrong Huang
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark.,Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Yutao Du
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Lin Lin
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark
| | - Zhanying Dong
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark
| | - Ling Yang
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark
| | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Hui Jiang
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark
| | - Adil Mardinoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Cheng Zhang
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Kalle von Feilitzen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark
| | - Tomas Hökfelt
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mathias Uhlén
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden. .,Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden.
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428
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Guo D, Wang M, Shen Z, Zhu J. A new immune signature for survival prediction and immune checkpoint molecules in lung adenocarcinoma. J Transl Med 2020; 18:123. [PMID: 32143735 PMCID: PMC7060601 DOI: 10.1186/s12967-020-02286-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the most frequent subtype of lung cancer. The prognostic signature could be reliable to stratify LUAD patients according to risk, which helps the management of the systematic treatments. In this study, a systematic and reliable immune signature was performed to estimate the prognostic stratification in LUAD. Methods The profiles of immune-related genes for patients with LUAD were used as one TCGA training set: n = 494, other validation set 1: n = 226 and validation set 2: n = 398. Univariate Cox survival analysis was used to identify the candidate immune-related genes from each cohort. Then, the immune signature was developed and validated in the training and validation sets. Results In this study, functional analysis showed that immune-related genes involved in immune regulation and MAPK signaling pathway. A prognostic signature based on 10 immune-related genes was established in the training set and patients were divided into high-risk and low-risk groups. Our 10 immune-related gene signature was significantly related to worse survival, especially during early-stage tumors. Further stratification analyses revealed that this 10 immune-related gene signature was still an effective tool for predicting prognosis in smoking or nonsmoking patients, patients with KRAS mutation or KRAS wild-type, and patients with EGFR mutation or EGFR wild-type. Our signature was negatively correlated with B cell, CD4+ T cell, CD8+ T cell, neutrophil, dendritic cell (DC), and macrophage immune infiltration, and immune checkpoint molecules PD-1 and CTLA-4 (P < 0.05). Conclusions These findings suggested that our signature was a promising biomarker for prognosis prediction and can facilitate the management of immunotherapy in LUAD.
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Affiliation(s)
- Dina Guo
- Department of Infectious Diseases, Ningbo Yinzhou No.2 Hospital, Ningbo, 315100, Zhejiang, China
| | - Mian Wang
- Department of Infectious Diseases, Ningbo Yinzhou No.2 Hospital, Ningbo, 315100, Zhejiang, China
| | - Zhihong Shen
- Department of Infectious Diseases, Ningbo Yinzhou No.2 Hospital, Ningbo, 315100, Zhejiang, China
| | - Jiaona Zhu
- Department of Infectious Diseases, Ningbo Yinzhou No.2 Hospital, Ningbo, 315100, Zhejiang, China.
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429
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Garg SK, Ott MJ, Mostofa AGM, Chen Z, Chen YA, Kroeger J, Cao B, Mailloux AW, Agrawal A, Schaible BJ, Sarnaik A, Weber JS, Berglund AE, Mulé JJ, Markowitz J. Multi-Dimensional Flow Cytometry Analyses Reveal a Dichotomous Role for Nitric Oxide in Melanoma Patients Receiving Immunotherapy. Front Immunol 2020; 11:164. [PMID: 32161584 PMCID: PMC7052497 DOI: 10.3389/fimmu.2020.00164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/21/2020] [Indexed: 11/13/2022] Open
Abstract
Phenotyping of immune cell subsets in clinical trials is limited to well-defined phenotypes, due to technological limitations of reporting flow cytometry multi-dimensional phenotyping data. We developed a multi-dimensional phenotyping analysis tool and applied it to detect nitric oxide (NO) levels in peripheral blood immune cells before and after adjuvant ipilimumab co-administration with a peptide vaccine in melanoma patients. We analyzed inhibitory and stimulatory markers for immune cell phenotypes that were felt to be important in the NO analysis. The pipeline allows visualization of immune cell phenotypes without knowledge of clustering techniques and to categorize cells by association with relapse-free survival (RFS). Using this analysis, we uncovered the potential for a dichotomous role of NO as a pro- and anti-melanoma factor. NO was found in subsets of immune-suppressor cells associated with shorter-term (≤ 1 year) RFS, whereas NO was also present in immune-stimulatory effector cells obtained from patients with significant longer-term (> 1 year) RFS. These studies provide insights into the cell-specific immunomodulatory role of NO. The methods presented herein can be applied to monitor the pro- and anti-tumor effects of a variety of immune-based therapeutics in cancer patients. Clinical Trial Registration Number: NCT00084656 (https://clinicaltrials.gov/ct2/show/NCT00084656).
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Affiliation(s)
- Saurabh K Garg
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Matthew J Ott
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - A G M Mostofa
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Zhihua Chen
- Cancer Informatics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Jodi Kroeger
- Flow Cytometry Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Biwei Cao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Adam W Mailloux
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Alisha Agrawal
- Department of Oncologic Sciences, USF Health Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Braydon J Schaible
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Amod Sarnaik
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States.,Department of Oncologic Sciences, USF Health Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Jeffrey S Weber
- Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, United States
| | - Anders E Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - James J Mulé
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Joseph Markowitz
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States.,Department of Oncologic Sciences, USF Health Morsani College of Medicine, University of South Florida, Tampa, FL, United States
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430
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Li Y, Jiang T, Zhou W, Li J, Li X, Wang Q, Jin X, Yin J, Chen L, Zhang Y, Xu J, Li X. Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers. Nat Commun 2020; 11:1000. [PMID: 32081859 PMCID: PMC7035327 DOI: 10.1038/s41467-020-14802-2] [Citation(s) in RCA: 270] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/03/2020] [Indexed: 12/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression and they play fundamental roles in immune regulation. Here we introduce an integrated algorithm, ImmLnc, for identifying lncRNA regulators of immune-related pathways. We comprehensively chart the landscape of lncRNA regulation in the immunome across 33 cancer types and show that cancers with similar tissue origin are likely to share lncRNA immune regulators. Moreover, the immune-related lncRNAs are likely to show expression perturbation in cancer and are significantly correlated with immune cell infiltration. ImmLnc can help prioritize cancer-related lncRNAs and further identify three molecular subtypes (proliferative, intermediate, and immunological) of non-small cell lung cancer. These subtypes are characterized by differences in mutation burden, immune cell infiltration, expression of immunomodulatory genes, response to chemotherapy, and prognosis. In summary, the ImmLnc pipeline and the resulting data serve as a valuable resource for understanding lncRNA function and to advance identification of immunotherapy targets.
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Affiliation(s)
- Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China. .,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 570100, China.
| | - Tiantongfei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Weiwei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Junyi Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Xinhui Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Qi Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Xiaoyan Jin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Jiaqi Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Liuxin Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China. .,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 570100, China.
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China. .,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 570100, China.
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431
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Hu Z, Glicksberg BS, Butte AJ. Robust prediction of clinical outcomes using cytometry data. Bioinformatics 2020; 35:1197-1203. [PMID: 30169745 PMCID: PMC6449751 DOI: 10.1093/bioinformatics/bty768] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/02/2018] [Accepted: 08/29/2018] [Indexed: 12/25/2022] Open
Abstract
Motivation Flow cytometry and mass cytometry are widely used to diagnose diseases and to predict clinical outcomes. When associating clinical features with cytometry data, traditional analysis methods require cell gating as an intermediate step, leading to information loss and susceptibility to batch effects. Here, we wish to explore an alternative approach that predicts clinical features from cytometry data without the cell-gating step. We also wish to test if such a gating-free approach increases the accuracy and robustness of the prediction. Results We propose a novel strategy (CytoDx) to predict clinical outcomes using cytometry data without cell gating. Applying CytoDx on real-world datasets allow us to predict multiple types of clinical features. In particular, CytoDx is able to predict the response to influenza vaccine using highly heterogeneous datasets, demonstrating that it is not only accurate but also robust to batch effects and cytometry platforms. Availability and implementation CytoDx is available as an R package on Bioconductor (bioconductor.org/packages/CytoDx). Data and scripts for reproducing the results are available on bitbucket.org/zichenghu_ucsf/cytodx_study_code/downloads. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zicheng Hu
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Benjamin S Glicksberg
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Atul J Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
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432
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M A, Chatterjee S, A P, S M, Davuluri S, Ar AK, T A, M P, Cs P, Sinha M, Chugani A, R VP, Kk A, R S J. Natural Killer cell transcriptome during primary EBV infection and EBV associated Hodgkin Lymphoma in children-A preliminary observation. Immunobiology 2020; 225:151907. [PMID: 32044149 DOI: 10.1016/j.imbio.2020.151907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/09/2020] [Accepted: 01/25/2020] [Indexed: 01/22/2023]
Abstract
Epstein Barr Viral infection is a common childhood infection in India and is also nearly 100 % etiologically associated with pediatric Hodgkin Lymphoma (HL). The main question in EBV immunobiology has been, why only a small subset of infected individuals develop EBV associated malignancies, while the vast majority carry this virus asymptomatically for life. Natural Killer (NK) cells, with a phenotype of CD56dim CD16+ exhibit potent cytotoxicity towards both virus infected cells and transformed cells and hence have been considered to be crucial in preventing the development of symptomatic EBV infection and lymphoma. In order to get an insight into the various possible molecular aspects of NK cells, in the pathogenesis of both these EBV mediated diseases in children we studied the whole transcriptome of MACS sorted CD56dim CD16 + NK cells from four patients from each of the three groups of children viz. Infectious Mononucleosis (IM), HL and age matched controls by using a massively parallel sequencing approach. NK cells from both IM and HL had down-regulated innate immunity and chemokine signaling genes. While down-regulation of genes responsible for polarization of the secretory apparatus, activated NK cell signaling and MAP kinase signaling were exclusive to NK cells in patients with IM, in NK cells of HL, specifically, genes involved in extracellular matrix (ECM) - receptor interaction, cytokine-cytokine receptor interaction, TNF signaling, Toll-like receptor signaling pathway and cytosolic DNA-sensing pathways were significantly down-regulated. Enrichment analysis showed STAT3 to be the most significant transcription factor (TF) for the down-regulated genes in IM, whereas, GATA1 was found to be the most significant TF for the genes down-regulated in HL. Analysis of protein interaction network identified functionally important protein clusters. Top clusters, comprised of down-regulated genes, involved in signaling and ubiquitin-related processes and pathways. These may perhaps be responsible for the hypo-responsiveness of NK cells in both diseases. These possibly point to different deficiencies in NK cell activation, loss of activating receptor signaling and degranulation in IM, versus loss of cytokine and chemokine signaling in HL, in the two EBV associated pathologies investigated. Various suppressed molecules and pathways were novel, which have not been reported earlier and could therefore be potential targets for immunotherapy of NK cell reactivation in both the diseases in future.
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Affiliation(s)
- Alka M
- Departments of Microbiology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | | | - Parchure A
- Departments of Microbiology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Mahantesh S
- Departments of Microbiology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Sravanthi Davuluri
- Biological Data Analyzers' Association (BdataA), Electronic City, Phase I, Bangalore, India
| | - Arun Kumar Ar
- Departments of Pediatric Oncology, Kidwai Memorial Institute of Oncology, India
| | - Avinash T
- Departments of Pediatric Oncology, Kidwai Memorial Institute of Oncology, India
| | - Padma M
- Departments of Pediatric Oncology, Kidwai Memorial Institute of Oncology, India
| | - Premalata Cs
- Departments of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Mahua Sinha
- Departments of Microbiology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | | | | | - Acharya Kk
- Biological Data Analyzers' Association (BdataA), Electronic City, Phase I, Bangalore, India; Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Jayshree R S
- Departments of Microbiology, Kidwai Memorial Institute of Oncology, Bangalore, India.
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433
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Shahin MH, Bhattacharya S, Silva D, Kim S, Burton J, Podichetty J, Romero K, Conrado DJ. Open Data Revolution in Clinical Research: Opportunities and Challenges. Clin Transl Sci 2020; 13:665-674. [PMID: 32004409 PMCID: PMC7359943 DOI: 10.1111/cts.12756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/05/2019] [Indexed: 01/24/2023] Open
Abstract
Efforts for sharing individual clinical data are gaining momentum due to a heightened recognition that integrated data sets can catalyze biomedical discoveries and drug development. Among the benefits are the fact that data sharing can help generate and investigate new research hypothesis beyond those explored in the original study. Despite several accomplishments establishing public systems and guidance for data sharing in clinical trials, this practice is not the norm. Among the reasons are ethical challenges, such as privacy of individuals, data ownership, and control. This paper creates awareness of the potential benefits and challenges of sharing individual clinical data, how to overcome these challenges, and how as a clinical pharmacology community we can shape future directions in this field.
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Affiliation(s)
| | - Sanchita Bhattacharya
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, California, USA.,Department of Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Diego Silva
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada.,Sydney Health Ethics, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Sarah Kim
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, Florida, USA
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434
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Identification of Prognostic Immune Genes in Bladder Urothelial Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7510120. [PMID: 32420368 PMCID: PMC7201587 DOI: 10.1155/2020/7510120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/20/2019] [Accepted: 12/17/2019] [Indexed: 12/27/2022]
Abstract
Background The aim of this study is to identify possible prognostic-related immune genes in bladder urothelial carcinoma and to try to predict the prognosis of bladder urothelial carcinoma based on these genes. Methods The Cancer Genome Atlas (TCGA) expression profile data and corresponding clinical traits were obtained. Differential gene analysis was performed using R software. Reactome was used to analyze the pathway of immune gene participation. The differentially expressed transcription factors and differentially expressed immune-related genes were extracted from the obtained list of differentially expressed genes, and the transcription factor-immune gene network was constructed. To analyze the relationship between immune genes and clinical traits of bladder urothelial carcinoma, a multifactor Cox proportional hazards regression model based on the expression of immune genes was established and validated. Results Fifty-eight immune genes were identified to be associated with the prognosis of bladder urothelial carcinoma. These genes were enriched in Cytokine Signaling in Immune System, Signaling by Receptor Tyrosine Kinases, Interferon alpha/beta signaling, and other immune related pathways. Transcription factor-immune gene regulatory network was established, and EBF1, IRF4, SOX17, MEF2C, NFATC1, STAT1, ANXA6, SLIT2, and IGF1 were screened as hub genes in the network. The model calculated by the expression of 16 immune genes showed a good survival prediction ability (p < 0.05 and AUC = 0.778). Conclusion A transcription factor-immune gene regulatory network related to the prognosis of bladder urothelial carcinoma was established. EBF1, IRF4, SOX17, MEF2C, NFATC1, STAT1, ANXA6, SLIT2, and IGF1 were identified as hub genes in the network. The proportional hazards regression model constructed by 16 immune genes shows a good predictive ability for the prognosis of bladder urothelial carcinoma.
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435
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Zhou J, Li X, Zhang M, Gong J, Li Q, Shan B, Wang T, Zhang L, Zheng T, Li X. The aberrant expression of rhythm genes affects the genome instability and regulates the cancer immunity in pan-cancer. Cancer Med 2020; 9:1818-1829. [PMID: 31927791 PMCID: PMC7050078 DOI: 10.1002/cam4.2834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/18/2019] [Accepted: 12/27/2019] [Indexed: 12/17/2022] Open
Abstract
Although emerging studies showed that certain rhythm genes regulate cancer progression, the expression and roles of the vast majority of rhythm genes in human cancer are largely unknown, and the hallmarks of cancer regulated by rhythm genes have not been detected. In this study, we detected the expression changes of rhythm genes in pan-cancer and found that almost all rhythm genes mutated in all cancer types, and their expression level was significantly altered partially due to abnormal methylation, and several rhythm genes regulate the expression of other rhythm genes in various cancer types. Furthermore, we revealed that rhythm genes are significantly enriched in genome instability and the expression of certain rhythm genes is correlated with the tumor mutation burden, microsatellite instability, and the expression of DNA damage repair genes in most of the detected cancer types. Moreover, rhythm genes are associated with the infiltration of immune cells and the efficiency of immune blockade therapy. This study provides a comprehensive understanding of the roles of rhythm genes in cancer immunity, which may provide a novel method for the diagnosis and treatment of cancer.
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Affiliation(s)
- Jian Zhou
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Xinhui Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Minghui Zhang
- Department of Oncology, Chifeng City Hospital, Chifeng, China
| | - Ji'nan Gong
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Qi Li
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Baocong Shan
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Tianzhen Wang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Lei Zhang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Tongsen Zheng
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, China
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436
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Sun YL, Zhang Y, Guo YC, Yang ZH, Xu YC. A Prognostic Model Based on the Immune-related Genes in Colon Adenocarcinoma. Int J Med Sci 2020; 17:1879-1896. [PMID: 32788867 PMCID: PMC7415395 DOI: 10.7150/ijms.45813] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Immune-related genes (IRGs) are critically involved in the tumor microenvironment (TME) of colon adenocarcinoma (COAD). Here, the study was mainly designed to establish a prognostic model of IRGs to predict the survival of COAD patients. Methods: The Cancer Genome Atlas (TCGA), Immunology Database and Analysis Portal (ImmPort) database, and Cistrome database were utilized for extracting data regarding the expression of immune gene- and tumor-related transcription factors (TFs), aimed at the identification of differentially expressed genes (DEGs), differentially expressed IRGs (DEIRGs), and differentially expressed TFs (DETFs). Univariate Cox regression analysis was subsequently performed for the acquisition of prognosis-related IRGs, followed by establishment of TF regulatory network for uncovering the possible molecular regulatory association in COAD. Subsequently, multivariate Cox regression analysis was conducted to further determine the role of prognosis-related IRGs for prognostic prediction in COAD. Finally, the feasibility of a prognostic model with immunocytes was explored by immunocyte infiltration analysis. Results: A total of 2450 DEGs, 8 DETFs, and 79 DEIRGs were extracted from the corresponding databases. Univariate Cox regression analysis revealed 11 prognosis-related IRGs, followed by establishment of a regulatory network on prognosis-related IRGs at transcriptional levels. Functionally, IRG GLP2R was negatively modulated by TF MYH11, whereas IRG TDGF1 was positively modulated by TF TFAP2A. Multivariate Cox regression analysis was subsequently performed to establish a prognostic model on the basis of seven prognosis-related IRGs (GLP2R, ESM1, TDGF1, SLC10A2, INHBA, STC2, and CXCL1). Moreover, correlation analysis of immunocyte infiltration also revealed that the seven-IRG prognostic model was positively associated with five types of immunocytes (dendritic cell, macrophage, CD4 T cell, CD8 T cell, and neutrophil), which may directly reflect tumor immune state in COAD. Conclusions: Our present findings indicate that the prognostic model based on prognosis-related IRGs plays a crucial role in the clinical supervision and prognostic prediction of COAD patients at both molecular and cellular levels.
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Affiliation(s)
- Yuan-Lin Sun
- Department of Gastrointestinal Surgery, The First Hospital, Jilin University, Changchun 130021, Jilin Province, China
| | - Yang Zhang
- Department of Gastrointestinal Surgery, The First Hospital, Jilin University, Changchun 130021, Jilin Province, China
| | - Yu-Chen Guo
- Department of Gastrointestinal Surgery, The First Hospital, Jilin University, Changchun 130021, Jilin Province, China
| | - Zi-Hao Yang
- Department of Gastrointestinal Surgery, The First Hospital, Jilin University, Changchun 130021, Jilin Province, China
| | - Yue-Chao Xu
- Department of Gastrointestinal Surgery, The First Hospital, Jilin University, Changchun 130021, Jilin Province, China
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437
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Vita R, Overton JA, Dunn P, Cheung KH, Kleinstein SH, Sette A, Peters B. A structured model for immune exposures. Database (Oxford) 2020; 2020:5818925. [PMID: 32283555 PMCID: PMC7153954 DOI: 10.1093/database/baaa016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/10/2020] [Accepted: 02/06/2020] [Indexed: 11/13/2022]
Abstract
An Immune Exposure is the process by which components of the immune system first encounter a potential trigger. The ability to describe consistently the details of the Immune Exposure process was needed for data resources responsible for housing scientific data related to the immune response. This need was met through the development of a structured model for Immune Exposures. This model was created during curation of the immunology literature, resulting in a robust model capable of meeting the requirements of such data. We present this model with the hope that overlapping projects will adopt and or contribute to this work.
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Affiliation(s)
- Randi Vita
- Division for Vaccine Discovery, 9420 Athena Circle La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - James A Overton
- Knocean Inc., 2 - 107 Quebec Ave Toronto M6P 2T3, Ontario, Canada
| | - Patrick Dunn
- ImmPort Curation Team, NG Health Solutions, 2101 Gaither Road Rockville, MD 20850, USA
| | - Kei-Hoi Cheung
- 464 Congress Ave Department of Emergency Medicine, Yale University, New Haven, CT, 06519 USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 464 Congress Ave New Haven, CT, 06519 USA.,Department of Pathology, Yale School of Medicine, 464 Congress Ave New Haven, CT, 06519 USA
| | - Alessandro Sette
- Division for Vaccine Discovery, 9420 Athena Circle La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Department of Medicine, University of California San Diego, 9500 Gilman Dr La Jolla, CA, 92093 USA
| | - Bjoern Peters
- Division for Vaccine Discovery, 9420 Athena Circle La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Department of Medicine, University of California San Diego, 9500 Gilman Dr La Jolla, CA, 92093 USA
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438
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Jung JH, Hwang J, Kim JH, Sim DY, Im E, Park JE, Park WY, Shim BS, Kim B, Kim SH. Phyotochemical candidates repurposing for cancer therapy and their molecular mechanisms. Semin Cancer Biol 2019; 68:164-174. [PMID: 31883914 DOI: 10.1016/j.semcancer.2019.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/18/2019] [Accepted: 12/15/2019] [Indexed: 12/24/2022]
Abstract
Though limited success through chemotherapy, radiotherapy and surgery has been obtained for efficient cancer therapy for modern decades, cancers are still considered high burden to human health worldwide to date. Recently repurposing drugs are attractive with lower cost and shorter time compared to classical drug discovery, just as Metformin from Galega officinalis, originally approved for treating Type 2 diabetes by FDA, is globally valued at millions of US dollars for cancer therapy. As most previous reviews focused on FDA approved drugs and synthetic agents, current review discussed the anticancer potential of phytochemicals originally approved for treatment of cardiovascular diseases, diabetes, infectious diarrhea, depression and malaria with their molecular mechanisms and efficacies and suggested future research perspectives.
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Affiliation(s)
- Ji Hoon Jung
- Cancer Molecular Target Herbal Research Laboratory, College of Korean Medicine, Seoul 02447, Republic of Korea
| | - Jisung Hwang
- Cancer Molecular Target Herbal Research Laboratory, College of Korean Medicine, Seoul 02447, Republic of Korea
| | - Ju-Ha Kim
- Cancer Molecular Target Herbal Research Laboratory, College of Korean Medicine, Seoul 02447, Republic of Korea
| | - Deok Yong Sim
- Cancer Molecular Target Herbal Research Laboratory, College of Korean Medicine, Seoul 02447, Republic of Korea
| | - Eunji Im
- Cancer Molecular Target Herbal Research Laboratory, College of Korean Medicine, Seoul 02447, Republic of Korea
| | - Ji Eon Park
- Cancer Molecular Target Herbal Research Laboratory, College of Korean Medicine, Seoul 02447, Republic of Korea
| | - Woon Yi Park
- Cancer Molecular Target Herbal Research Laboratory, College of Korean Medicine, Seoul 02447, Republic of Korea
| | - Bum-Sang Shim
- Cancer Molecular Target Herbal Research Laboratory, College of Korean Medicine, Seoul 02447, Republic of Korea
| | - Bonglee Kim
- Cancer Molecular Target Herbal Research Laboratory, College of Korean Medicine, Seoul 02447, Republic of Korea
| | - Sung-Hoon Kim
- Cancer Molecular Target Herbal Research Laboratory, College of Korean Medicine, Seoul 02447, Republic of Korea.
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439
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Uhlen M, Karlsson MJ, Zhong W, Tebani A, Pou C, Mikes J, Lakshmikanth T, Forsström B, Edfors F, Odeberg J, Mardinoglu A, Zhang C, von Feilitzen K, Mulder J, Sjöstedt E, Hober A, Oksvold P, Zwahlen M, Ponten F, Lindskog C, Sivertsson Å, Fagerberg L, Brodin P. A genome-wide transcriptomic analysis of protein-coding genes in human blood cells. Science 2019; 366:366/6472/eaax9198. [DOI: 10.1126/science.aax9198] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022]
Abstract
Blood is the predominant source for molecular analyses in humans, both in clinical and research settings. It is the target for many therapeutic strategies, emphasizing the need for comprehensive molecular maps of the cells constituting human blood. In this study, we performed a genome-wide transcriptomic analysis of protein-coding genes in sorted blood immune cell populations to characterize the expression levels of each individual gene across the blood cell types. All data are presented in an interactive, open-access Blood Atlas as part of the Human Protein Atlas and are integrated with expression profiles across all major tissues to provide spatial classification of all protein-coding genes. This allows for a genome-wide exploration of the expression profiles across human immune cell populations and all major human tissues and organs.
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Affiliation(s)
- Mathias Uhlen
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Max J. Karlsson
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Wen Zhong
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Abdellah Tebani
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Christian Pou
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Jaromir Mikes
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Tadepally Lakshmikanth
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Björn Forsström
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Jacob Odeberg
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
- Coagulation Unit, Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London, UK
| | - Cheng Zhang
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Andreas Hober
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Per Oksvold
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Petter Brodin
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
- Unit of Pediatric Rheumatology, Karolinska University Hospital, Stockholm, Sweden
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440
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Zhang M, Zhu K, Pu H, Wang Z, Zhao H, Zhang J, Wang Y. An Immune-Related Signature Predicts Survival in Patients With Lung Adenocarcinoma. Front Oncol 2019; 9:1314. [PMID: 31921619 PMCID: PMC6914845 DOI: 10.3389/fonc.2019.01314] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022] Open
Abstract
We investigated the local immune status and its prognostic value in lung adenocarcinoma. In total, 513 lung adenocarcinoma samples from TCGA and ImmPort databases were collected and analyzed. The R package coxph was employed to mine immune-related genes that were significant prognostic indicators using both univariate and multivariate analyses. The R software package glmnet was then used for Lasso Cox regression analysis, and a prognosis prediction model was constructed for lung adenocarcinoma; clusterProfiler was selected for functional gene annotations and KEGG enrichment analysis. Finally, correlations between the RiskScore and clinical features or signaling pathways were established. Sixty-four immune-related genes remarkably correlated with patient prognosis and were further applied. Samples were hierarchically clustered into two subgroups. Accordingly, the LASSO regression algorithm was employed to screen the 14 most representative immune-related genes (PSMD11, PPIA, MIF, BMP5, DKK1, PDGFB, ANGPTL4, IL1R2, THRB, LTBR, TNFRSF1, TNFRSF17, IL20RB, and MC1R) with respect to patient prognosis. Then, the prognosis prediction model for lung adenocarcinoma patients (namely, the RiskScore equation) was constructed, and the training set samples were incorporated to evaluate the efficiency of this model to predict and classify patient prognosis. Subsequently, based on functional annotations and KEGG pathway analysis, the 14 immune-related genes were mainly enriched in pathways closely associated with lung adenocarcinoma and its immune microenvironment, such as cytokine–cytokine receptor interaction and human T-cell leukemia virus 1 infection. Furthermore, correlations between the RiskScore and clinical features of the training set samples and signaling pathways (such as p53, cell cycle, and DNA repair) were also demonstrated. Finally, the test set sample data were employed for independent testing and verifying the model. We established a prognostic prediction RiskScore model based on the expression profiles of 14 immune-related genes, which shows high prediction accuracy and stability in identifying immune features. This could provide clinical guidance for the diagnosis and prognosis of different immunophenotypes, and suggest multiple targets for precise advanced lung adenocarcinoma therapy based on subtype-specific immune molecules.
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Affiliation(s)
- Minghui Zhang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Kaibin Zhu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Haihong Pu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Zhuozhong Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Hongli Zhao
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jinfeng Zhang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yan Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
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441
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Bongen E, Lucian H, Khatri A, Fragiadakis GK, Bjornson ZB, Nolan GP, Utz PJ, Khatri P. Sex Differences in the Blood Transcriptome Identify Robust Changes in Immune Cell Proportions with Aging and Influenza Infection. Cell Rep 2019; 29:1961-1973.e4. [PMID: 31722210 PMCID: PMC6856718 DOI: 10.1016/j.celrep.2019.10.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/12/2019] [Accepted: 10/03/2019] [Indexed: 02/09/2023] Open
Abstract
Sex differences in autoimmunity and infection suggest that a better understanding of molecular sex differences will improve the diagnosis and treatment of immune-related disease. We identified 144 differentially expressed genes, referred to as immune sex expression signature (iSEXS), between human males and females using an integrated multi-cohort analysis of blood transcriptome profiles from six discovery cohorts from five continents with 458 healthy individuals. We validated iSEXS in 11 additional cohorts of 524 peripheral blood samples. When we separated iSEXS into genes located on sex chromosomes (XY-iSEXS) or autosomes (autosomal-iSEXS), both modules distinguished males and females. iSEXS reflects sex differences in immune cell proportions, with female-associated genes showing higher expression by CD4+ T cells and male-associated genes showing higher expression by myeloid cells. Autosomal-iSEXS detected an increase in monocytes with age in females, reflected sex-differential immune cell dynamics during influenza infection, and predicted antibody response in males, but not females.
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Affiliation(s)
- Erika Bongen
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Haley Lucian
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Avani Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gabriela K Fragiadakis
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zachary B Bjornson
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
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442
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Rogers LRK, de Los Campos G, Mias GI. Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination. Front Immunol 2019; 10:2616. [PMID: 31787983 PMCID: PMC6854009 DOI: 10.3389/fimmu.2019.02616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/21/2019] [Indexed: 12/18/2022] Open
Abstract
Influenza, a communicable disease, affects thousands of people worldwide. Young children, elderly, immunocompromised individuals and pregnant women are at higher risk for being infected by the influenza virus. Our study aims to highlight differentially expressed genes in influenza disease compared to influenza vaccination, including variability due to age and sex. To accomplish our goals, we conducted a meta-analysis using publicly available microarray expression data. Our inclusion criteria included subjects with influenza, subjects who received the influenza vaccine and healthy controls. We curated 18 microarray datasets for a total of 3,481 samples (1,277 controls, 297 influenza infection, 1,907 influenza vaccination). We pre-processed the raw microarray expression data in R using packages available to pre-process Affymetrix and Illumina microarray platforms. We used a Box-Cox power transformation of the data prior to our down-stream analysis to identify differentially expressed genes. Statistical analyses were based on linear mixed effects model with all study factors and successive likelihood ratio tests (LRT) to identify differentially-expressed genes. We filtered LRT results by disease (Bonferroni adjusted p < 0.05) and used a two-tailed 10% quantile cutoff to identify biologically significant genes. Furthermore, we assessed age and sex effects on the disease genes by filtering for genes with a statistically significant (Bonferroni adjusted p < 0.05) interaction between disease and age, and disease and sex. We identified 4,889 statistically significant genes when we filtered the LRT results by disease factor, and gene enrichment analysis (gene ontology and pathways) included innate immune response, viral process, defense response to virus, Hematopoietic cell lineage and NF-kappa B signaling pathway. Our quantile filtered gene lists comprised of 978 genes each associated with influenza infection and vaccination. We also identified 907 and 48 genes with statistically significant (Bonferroni adjusted p < 0.05) disease-age and disease-sex interactions, respectively. Our meta-analysis approach highlights key gene signatures and their associated pathways for both influenza infection and vaccination. We also were able to identify genes with an age and sex effect. This gives potential for improving current vaccines and exploring genes that are expressed equally across ages when considering universal vaccinations for influenza.
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Affiliation(s)
- Lavida R K Rogers
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States
| | - Gustavo de Los Campos
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States.,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States.,Department of Statistics and Probability, Michigan State University, East Lansing, MI, United States
| | - George I Mias
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States.,Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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443
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Bukhari SAC, Mandell J, Kleinstein SH, Cheung KH. A linked data graph approach to integration of immunological data. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2019; 2019:1742-1749. [PMID: 34707915 DOI: 10.1109/bibm47256.2019.8982986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Systems biology involves the integration of multiple data types (across different data sources) to offer a more complete picture of the biological system being studied. While many existing biological databases are implemented using the traditional SQL (Structured Query Language) database technology, NoSQL database technologies have been explored as a more relationship-based, flexible and scalable method of data integration. In this paper, we describe how to use the Neo4J graph database to integrate a variety of types of data sets in the context of systems vaccinology. Specifically, we have converted into a common graph model diverse types of vaccine response measurement data from the NIH/NIAID ImmPort data repository, pathway data from Reactome, influenza virus strains from WHO, and taxonomic data from NCBI Taxon. While Neo4J provides a graph-based query language (Cypher) for data retrieval, we develop a web-based dashboard for users to easily browse and visualize data without the need to learn Cypher. In addition, we have prototyped a natural language query interface for users to interact with our system. In conclusion, we demonstrate the feasibility of using a graph-based database for storing and querying immunological data with complex biological relationships. Querying a graph database through such relationships has the potential to reveal novel relationships among heterogeneous biological data.
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Affiliation(s)
- Syed Ahmad Chan Bukhari
- Division of Computer Science, Mathematics and Science Lesley H. & William L. Collins College of Professional Studies, St. John's University, New York, NY, USA
| | - Jeff Mandell
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Steven H Kleinstein
- Department of Pathology, Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Kei-Hoi Cheung
- Department of Emergency Medicine and Yale Center for Medical Informatics Computationa Biology and Bioinformaticcs, Yale University, New Haven, CT, USA
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444
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Rahman MM, Lai YC, Husna AA, Chen HW, Tanaka Y, Kawaguchi H, Hatai H, Miyoshi N, Nakagawa T, Fukushima R, Miura N. Transcriptome analysis of dog oral melanoma and its oncogenic analogy with human melanoma. Oncol Rep 2019; 43:16-30. [PMID: 31661138 PMCID: PMC6908934 DOI: 10.3892/or.2019.7391] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022] Open
Abstract
Dogs have been considered as an excellent immunocompetent model for human melanoma due to the same tumor location and the common clinical and pathological features with human melanoma. However, the differences in the melanoma transcriptome between the two species have not been yet fully determined. Considering the role of oncogenes in melanoma development, in this study, we first characterized the transcriptome in canine oral melanoma and then compared the transcriptome with that of human melanoma. The global transcriptome from 8 canine oral melanoma samples and 3 healthy oral tissues were compared by RNA-Seq followed by RT-qPCR validation. The results revealed 2,555 annotated differentially expressed genes, as well as 364 novel differentially expressed genes. Dog chromosomes 1 and 9 were enriched with downregulated and upregulated genes, respectively. Along with 10 significant transcription site binding motifs; the NF-κB and ATF1 binding motifs were the most significant and 4 significant unknown motifs were indentified among the upregulated differentially expressed genes. Moreover, it was found that canine oral melanoma shared >80% significant oncogenes (upregulated genes) with human melanoma, and JAK-STAT was the most common significant pathway between the species. The results identified a 429 gene signature in melanoma, which was up-regulated in both species; these genes may be good candidates for therapeutic development. Furthermore, this study demonstrates that as regards oncogene expression, human melanoma contains an oncogene group that bears similarities with dog oral melanoma, which supports the use of dogs as a model for the development of novel therapeutics and experimental trials before human application.
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Affiliation(s)
- Md Mahfuzur Rahman
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890‑0065, Japan
| | - Yu-Chang Lai
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890‑0065, Japan
| | - Al Asmaul Husna
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890‑0065, Japan
| | - Hui-Wen Chen
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Kagoshima 890‑0065, Japan
| | - Yuiko Tanaka
- Department of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113‑8657, Japan
| | - Hiroaki Kawaguchi
- Hygiene and Health Promotion Medicine, Kagoshima University Graduate School of Medicine and Dental Science, Kagoshima University, Kagoshima 890‑0065, Japan
| | - Hitoshi Hatai
- Department of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890‑0065, Japan
| | - Noriaki Miyoshi
- Department of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890‑0065, Japan
| | - Takayuki Nakagawa
- Department of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113‑8657, Japan
| | - Ryuji Fukushima
- Animal Medical Center, Tokyo University of Agriculture and Technology, Tokyo 183‑8538, Japan
| | - Naoki Miura
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890‑0065, Japan
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445
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Tomic A, Tomic I, Dekker CL, Maecker HT, Davis MM. The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system. Sci Data 2019; 6:214. [PMID: 31636302 PMCID: PMC6803714 DOI: 10.1038/s41597-019-0213-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 08/27/2019] [Indexed: 01/30/2023] Open
Abstract
Machine learning has the potential to identify novel biological factors underlying successful antibody responses to influenza vaccines. The first attempts have revealed a high level of complexity in establishing influenza immunity, and many different cellular and molecular components are involved. Of note is that the previously identified correlates of protection fail to account for the majority of individual responses across different age groups and influenza seasons. Challenges remain from the small sample sizes in most studies and from often limited data sets, such as transcriptomic data. Here we report the creation of a unified database, FluPRINT, to enable large-scale studies exploring the cellular and molecular underpinnings of successful antibody responses to influenza vaccines. Over 3,000 parameters were considered, including serological responses to influenza strains, serum cytokines, cell phenotypes, and cytokine stimulations. FluPRINT, facilitates the application of machine learning algorithms for data mining. The data are publicly available and represent a resource to uncover new markers and mechanisms that are important for influenza vaccine immunogenicity. Measurement(s) | immune response trait | Technology Type(s) | digital curation | Factor Type(s) | gender • race • visit_age • bmi • flu_vaccination_history • statin_use • influenza_infection_history • influenza_hospitalization • cmv_status • ebv_status | Sample Characteristic - Organism | Homo sapiens |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9902447
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Affiliation(s)
- Adriana Tomic
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94304, USA. .,Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, OX3 9DU, UK.
| | | | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Holden T Maecker
- Human Immune Monitoring Center, Stanford University, Stanford, CA, 94304, USA
| | - Mark M Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94304, USA. .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94304, USA. .,Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94304, USA.
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446
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Loiseau C, Cooper MM, Doolan DL. Deciphering host immunity to malaria using systems immunology. Immunol Rev 2019; 293:115-143. [PMID: 31608461 DOI: 10.1111/imr.12814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022]
Abstract
A century of conceptual and technological advances in infectious disease research has changed the face of medicine. However, there remains a lack of effective interventions and a poor understanding of host immunity to the most significant and complex pathogens, including malaria. The development of successful interventions against such intractable diseases requires a comprehensive understanding of host-pathogen immune responses. A major advance of the past decade has been a paradigm switch in thinking from the contemporary reductionist (gene-by-gene or protein-by-protein) view to a more holistic (whole organism) view. Also, a recognition that host-pathogen immunity is composed of complex, dynamic interactions of cellular and molecular components and networks that cannot be represented by any individual component in isolation. Systems immunology integrates the field of immunology with omics technologies and computational sciences to comprehensively interrogate the immune response at a systems level. Herein, we describe the system immunology toolkit and report recent studies deploying systems-level approaches in the context of natural exposure to malaria or controlled human malaria infection. We contribute our perspective on the potential of systems immunity for the rational design and development of effective interventions to improve global public health.
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Affiliation(s)
- Claire Loiseau
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Martha M Cooper
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
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447
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Liu CC, Steen CB, Newman AM. Computational approaches for characterizing the tumor immune microenvironment. Immunology 2019; 158:70-84. [PMID: 31347163 PMCID: PMC6742767 DOI: 10.1111/imm.13101] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 12/13/2022] Open
Abstract
Recent advances in high-throughput molecular profiling technologies and multiplexed imaging platforms have revolutionized our ability to characterize the tumor immune microenvironment. As a result, studies of tumor-associated immune cells increasingly involve complex data sets that require sophisticated methods of computational analysis. In this review, we present an overview of key assays and related bioinformatics tools for analyzing the tumor-associated immune system in bulk tissues and at the single-cell level. In parallel, we describe how data science strategies and novel technologies have advanced tumor immunology and opened the door for new opportunities to exploit host immunity to improve cancer clinical outcomes.
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Affiliation(s)
- Candace C. Liu
- Immunology Graduate ProgramSchool of MedicineStanford UniversityStanfordCAUSA
| | - Chloé B. Steen
- Division of OncologyDepartment of MedicineStanford Cancer InstituteStanford UniversityStanfordCAUSA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative MedicineStanford UniversityStanfordCAUSA
- Department of Biomedical Data ScienceStanford UniversityStanfordCAUSA
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448
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Bras AE, van der Velden VHJ. Lossless Compression of Cytometric Data. Cytometry A 2019; 95:1108-1112. [PMID: 31430053 DOI: 10.1002/cyto.a.23879] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/21/2019] [Accepted: 08/02/2019] [Indexed: 11/10/2022]
Abstract
Nowadays, most cytometrists apply lossless compression by storing their FCS files in ZIP archives. Unfortunately, ZIP only achieves modest space savings in cytometric data, due to DEFLATE being used as the underlying lossless compression algorithm (LCA). Presumably, other modern LCA can outperform DEFLATE, especially in terms of space savings. Twenty-one codecs (programs implementing LCA) were evaluated in 167,131 publicly available FCS files. Within floating-point data, as produced by modern instruments, most favorable compression ratios (CRs) were achieved by ZPAQ (median 0.469), BCM (median 0.523), and LZMA (median 0.545). In comparison, the DEFLATE-based codecs only achieved median CR of 0.728 under the most optimal conditions. By default, ZIP offers nine compression level (CL) settings, where lower ZIP-CL optimizes for time efficiency, while higher ZIP-CL optimizes for space efficiency. Interestingly, the third ZIP-CL already resulted in near optimal CR in 90% of the files with floating-point data, as produced by digital cytometers. LZMA is well established, widely supported, and actively maintained (in sharp contrast to ZPAQ and BCM) and therefore arguably the most attractive alternative for ZIP. Within floating-point data, by shifting from ZIP (under optimal conditions) to LZMA (at default settings), the median CR can be improved by 25%. Based on our results, cytometrists can benefit from state-of-the-art compression by choosing the appropriate codec for their situation. Our results are likely to speed-up the adaptation of modern codecs, as CR around 0.5 were beyond all expectations, and such space savings will benefit the field of cytometry. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- Anne E Bras
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Vincent H J van der Velden
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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449
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Papillary Thyroid Carcinoma Variants are Characterized by Co-dysregulation of Immune and Cancer Associated Genes. Cancers (Basel) 2019; 11:cancers11081179. [PMID: 31443155 PMCID: PMC6721495 DOI: 10.3390/cancers11081179] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) variants exhibit different prognosis, but critical characteristics of PTC variants that contribute to differences in pathogenesis are not well-known. This study aims to characterize dysregulated immune-associated and cancer-associated genes in three PTC subtypes to explore how the interplay between cancer and immune processes causes differential prognosis. RNA-sequencing data from The Cancer Genome Atlas (TCGA) were used to identify dysregulated genes in each variant. The dysregulation profiles of the subtypes were compared using functional pathways clustering and correlations to relevant clinical variables, genomic alterations, and microRNA regulation. We discovered that the dysregulation profiles of classical PTC (CPTC) and the tall cell variant (TCPTC) are similar and are distinct from that of the follicular variant (FVPTC). However, unique cancer or immune-associated genes are associated with clinical variables for each subtype. Cancer-related genes MUC1, FN1, and S100-family members were the most clinically relevant in CPTC, while APLN and IL16, both immune-related, were clinically relevant in FVPTC. RAET-family members, also immune-related, were clinically relevant in TCPTC. Collectively, our data suggest that dysregulation of both cancer and immune associated genes defines the gene expression landscapes of PTC variants, but different cancer or immune related genes may drive the phenotype of each variant.
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450
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Tomic A, Tomic I, Rosenberg-Hasson Y, Dekker CL, Maecker HT, Davis MM. SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 203:749-759. [PMID: 31201239 PMCID: PMC6643048 DOI: 10.4049/jimmunol.1900033] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/17/2019] [Indexed: 12/18/2022]
Abstract
Machine learning holds considerable promise for understanding complex biological processes such as vaccine responses. Capturing interindividual variability is essential to increase the statistical power necessary for building more accurate predictive models. However, available approaches have difficulty coping with incomplete datasets which is often the case when combining studies. Additionally, there are hundreds of algorithms available and no simple way to find the optimal one. In this study, we developed Sequential Iterative Modeling "OverNight" (SIMON), an automated machine learning system that compares results from 128 different algorithms and is particularly suitable for datasets containing many missing values. We applied SIMON to data from five clinical studies of seasonal influenza vaccination. The results reveal previously unrecognized CD4+ and CD8+ T cell subsets strongly associated with a robust Ab response to influenza Ags. These results demonstrate that SIMON can greatly speed up the choice of analysis modalities. Hence, it is a highly useful approach for data-driven hypothesis generation from disparate clinical datasets. Our strategy could be used to gain biological insight from ever-expanding heterogeneous datasets that are publicly available.
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Affiliation(s)
- Adriana Tomic
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304;
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Ivan Tomic
- Independent researcher, Palo Alto, CA 94303
| | | | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304
| | - Holden T Maecker
- Human Immune Monitoring Center, Stanford University, Stanford, CA 94304
| | - Mark M Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304; and
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94304
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