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Pan L, Parini P, Tremmel R, Loscalzo J, Lauschke VM, Maron BA, Paci P, Ernberg I, Tan NS, Liao Z, Yin W, Rengarajan S, Li X. Single Cell Atlas: a single-cell multi-omics human cell encyclopedia. Genome Biol 2024; 25:104. [PMID: 38641842 PMCID: PMC11027364 DOI: 10.1186/s13059-024-03246-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/12/2024] [Indexed: 04/21/2024] Open
Abstract
Single-cell sequencing datasets are key in biology and medicine for unraveling insights into heterogeneous cell populations with unprecedented resolution. Here, we construct a single-cell multi-omics map of human tissues through in-depth characterizations of datasets from five single-cell omics, spatial transcriptomics, and two bulk omics across 125 healthy adult and fetal tissues. We construct its complement web-based platform, the Single Cell Atlas (SCA, www.singlecellatlas.org ), to enable vast interactive data exploration of deep multi-omics signatures across human fetal and adult tissues. The atlas resources and database queries aspire to serve as a one-stop, comprehensive, and time-effective resource for various omics studies.
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Affiliation(s)
- Lu Pan
- Institute of Environmental Medicine, Karolinska Institutet, 171 65, Solna, Sweden
| | - Paolo Parini
- Cardio Metabolic Unit, Department of Medicine, and, Department of Laboratory Medicine , Karolinska Institutet, 141 86, Stockholm, Sweden
- Theme Inflammation and Ageing, Medicine Unit, Karolinska University Hospital, 141 86, Stockholm, Sweden
| | - Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
- University of Tuebingen, 72076, Tuebingen, Germany
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Volker M Lauschke
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
- University of Tuebingen, 72076, Tuebingen, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65, Solna, Sweden
| | - Bradley A Maron
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185, Rome, Italy
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Solna, Sweden
| | - Nguan Soon Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, 308232, Singapore
| | - Zehuan Liao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Solna, Sweden
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Weiyao Yin
- Institute of Environmental Medicine, Karolinska Institutet, 171 65, Solna, Sweden
| | - Sundararaman Rengarajan
- Department of Physical Therapy, Movement & Rehabilitation Sciences, Northeastern University, Boston, MA, 02115, USA
| | - Xuexin Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Solna, Sweden.
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2
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Proppe L, Jagomast T, Beume S, Klapper L, Gitas G, Köster F, Perner S, Rody A, Ribbat-Idel J, Hanker LC. Overexpression of the orphan nuclear receptor NR2F6 is associated with improved survival across molecular subgroups in endometrial cancer patients. J Cancer Res Clin Oncol 2023; 149:7155-7164. [PMID: 36884115 PMCID: PMC10374721 DOI: 10.1007/s00432-023-04632-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/02/2023] [Indexed: 03/09/2023]
Abstract
INTRODUCTION NR2F6 (nuclear receptor subfamily 2 group F member 6, also called Ear-2) is known to be an orphan nuclear receptor that has been characterized as an intracellular immune checkpoint in effector T cells and, therefore, may control tumor development and growth. The prognostic impact of NR2F6 in endometrial cancers is evaluated in this study. MATERIALS AND METHODS Expression analysis of NR2F6 in 142 endometrial cancer patients was performed by immunohistochemistry of primary paraffin‑embedded tumor samples. Staining intensity of positive tumor cells was automatically assessed semi-quantitatively, and results were correlated with clinicopathological characteristics and survival. RESULTS Forty five of 116 evaluable samples (38.8%) showed an overexpression of NR2F6. This leads to an improvement of the overall survival (OS) and progression-free survival (PFS). In NR2F6-positive patients, the estimated mean OS was 156.9 months (95% confidence interval (CI) 143.1-170.7) compared to 106.2 months in NR2F6-negative patients (95% CI 86.2-126.3; p = 0.022). The estimated PFS differed by 63 months (152 months (95% CI 135.7-168.4) vs. 88.3 months (95% CI 68.5-108.0), p = 0.002). Furthermore, we found significant associations between NR2F6 positivity, MMR status, and PD1 status. A multivariate analysis suggests NR2F6 to be an independent factor influencing the OS (p = 0.03). CONCLUSION In this study, we could demonstrate that there is a longer progression-free and overall survival for NR2F6-positive patients with endometrial cancer. We conclude that NR2F6 might play an essential role in endometrial cancers. Further studies are required to validate its prognostic impact.
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Affiliation(s)
- L Proppe
- Department of Gynecology and Obstetrics, University Hospital Schleswig-Holstein, Campus-Lübeck, Ratzeburger Allee 160, 23562, Luebeck, Germany.
| | - T Jagomast
- Department of Pathology, University Medical Center Schleswig-Holstein, Campus-Lübeck, Lübeck, Germany
| | - S Beume
- Department of Gynecology and Obstetrics, University Hospital Schleswig-Holstein, Campus-Lübeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
| | - L Klapper
- Department of Pathology, University Medical Center Schleswig-Holstein, Campus-Lübeck, Lübeck, Germany
| | - G Gitas
- Department of Gynecology and Obstetrics, University Hospital Schleswig-Holstein, Campus-Lübeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
- Department of Gynecology and Obstetrics, University Medical Center Charité Berlin, Berlin, Germany
| | - F Köster
- Department of Gynecology and Obstetrics, University Hospital Schleswig-Holstein, Campus-Lübeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
| | - S Perner
- Department of Pathology, University Medical Center Schleswig-Holstein, Campus-Lübeck, Lübeck, Germany
| | - A Rody
- Department of Gynecology and Obstetrics, University Hospital Schleswig-Holstein, Campus-Lübeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
| | - J Ribbat-Idel
- Department of Pathology, University Medical Center Schleswig-Holstein, Campus-Lübeck, Lübeck, Germany
| | - L C Hanker
- Department of Gynecology and Obstetrics, University Hospital Schleswig-Holstein, Campus-Lübeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
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3
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Kim H, Feng Y, Murad R, Pozniak J, Pelz C, Chen Y, Dalal B, Sears R, Sergienko E, Jackson M, Ruppin E, Herlyn M, Harris C, Marine JC, Klepsch V, Baier G, Ronai ZA. Melanoma-intrinsic NR2F6 activity regulates antitumor immunity. SCIENCE ADVANCES 2023; 9:eadf6621. [PMID: 37406115 DOI: 10.1126/sciadv.adf6621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 05/30/2023] [Indexed: 07/07/2023]
Abstract
Nuclear receptors (NRs) are implicated in the regulation of tumors and immune cells. We identify a tumor-intrinsic function of the orphan NR, NR2F6, regulating antitumor immunity. NR2F6 was selected from 48 candidate NRs based on an expression pattern in melanoma patient specimens (i.e., IFN-γ signature) associated with positive responses to immunotherapy and favorable patient outcomes. Correspondingly, genetic ablation of NR2F6 in a mouse melanoma model conferred a more effective response to PD-1 therapy. NR2F6 loss in B16F10 and YUMM1.7 melanoma cells attenuated tumor development in immune-competent but not -incompetent mice via the increased abundance of effector and progenitor-exhausted CD8+ T cells. Inhibition of NACC1 and FKBP10, identified as NR2F6 effectors, phenocopied NR2F6 loss. Inoculation of NR2F6 KO mice with NR2F6 KD melanoma cells further decreased tumor growth compared with NR2F6 WT mice. Tumor-intrinsic NR2F6 function complements its tumor-extrinsic role and justifies the development of effective anticancer therapies.
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Affiliation(s)
- Hyungsoo Kim
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Yongmei Feng
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Rabi Murad
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Carl Pelz
- Department of Molecular and Medical Genetics, Brenden Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
| | - Yeqing Chen
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Bhavik Dalal
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Rosalie Sears
- Department of Molecular and Medical Genetics, Brenden Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
| | - Eduard Sergienko
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael Jackson
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Curtis Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Victoria Klepsch
- Division of Translational Cell Genetics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Gottfried Baier
- Division of Translational Cell Genetics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Ze'ev A Ronai
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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Datta RR, Schran S, Persa OD, Aguilar C, Thelen M, Lehmann J, Garcia-Marquez MA, Wennhold K, Preugszat E, Zentis P, von Bergwelt-Baildon MS, Quaas A, Bruns CJ, Kurschat C, Mauch C, Löser H, Stippel DL, Schlößer HA. Post-transplant Malignancies Show Reduced T-cell Abundance and Tertiary Lymphoid Structures as Correlates of Impaired Cancer Immunosurveillance. Clin Cancer Res 2022; 28:1712-1723. [PMID: 35191474 DOI: 10.1158/1078-0432.ccr-21-3746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/11/2021] [Accepted: 02/03/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE An increased risk to develop cancer is one of the most challenging negative side effects of long-term immunosuppression in organ transplant recipients and impaired cancer immunosurveillance is assumed as underlying mechanism. This study aims to elucidate transplant-related changes in the tumor immune microenvironment (TME) of cancer. EXPERIMENTAL DESIGN Data from 123 organ transplant recipients (kidney, heart, lung, and liver) were compared with historic data from non-immunosuppressed patients. Digital image analysis of whole-section slides was used to assess abundance and spatial distribution of T cells and tertiary lymphoid structures (TLS) in the TME of 117 tumor samples. Expression of programmed cell death 1 ligand 1 (PD-L1) and human-leucocyte-antigen class I (HLA-I) was assessed on tissue microarrays. RESULTS We found a remarkably reduced immune infiltrate in the center tumor (CT) regions as well as the invasive margins (IM) of post-transplant cancers. These differences were more pronounced in the IM than in the CT and larger for CD8+ T cells than for CD3+ T cells. The Immune-score integrating results from CT and IM was also lower in transplant recipients. Density of TLS was lower in cancer samples of transplant recipients. The fraction of samples with PD-L1 expression was higher in controls whereas decreased expression of HLA-I was more common in transplant recipients. CONCLUSIONS Our study demonstrates the impact of immunosuppression on the TME and supports impaired cancer immunosurveillance as important cause of post-transplant cancer. Modern immunosuppressive protocols and cancer therapies should consider the distinct immune microenvironment of post-transplant malignancies.
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Affiliation(s)
- Rabi R Datta
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Simon Schran
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Oana-Diana Persa
- Department of Dermatology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Center for Integrated Oncology, CIO ABCD Aachen, Bonn, Cologne, Düsseldorf
| | - Claire Aguilar
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Martin Thelen
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jonas Lehmann
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Maria A Garcia-Marquez
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kerstin Wennhold
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Ella Preugszat
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Peter Zentis
- Cluster of Excellence for Aging-Associated Diseases, CECAD Imaging Facility Cologne, University of Cologne, Cologne, Germany
| | | | - Alexander Quaas
- Center for Integrated Oncology, CIO ABCD Aachen, Bonn, Cologne, Düsseldorf
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christiane J Bruns
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology, CIO ABCD Aachen, Bonn, Cologne, Düsseldorf
| | - Christine Kurschat
- Center for Integrated Oncology, CIO ABCD Aachen, Bonn, Cologne, Düsseldorf
- Department of Internal Medicine II, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Cornelia Mauch
- Department of Dermatology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Center for Integrated Oncology, CIO ABCD Aachen, Bonn, Cologne, Düsseldorf
| | - Heike Löser
- Center for Integrated Oncology, CIO ABCD Aachen, Bonn, Cologne, Düsseldorf
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Dirk L Stippel
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology, CIO ABCD Aachen, Bonn, Cologne, Düsseldorf
| | - Hans A Schlößer
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology, CIO ABCD Aachen, Bonn, Cologne, Düsseldorf
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5
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Alemohammad H, Najafzadeh B, Asadzadeh Z, Baghbanzadeh A, Ghorbaninezhad F, Najafzadeh A, Safarpour H, Bernardini R, Brunetti O, Sonnessa M, Fasano R, Silvestris N, Baradaran B. The importance of immune checkpoints in immune monitoring: A future paradigm shift in the treatment of cancer. Biomed Pharmacother 2021; 146:112516. [PMID: 34906767 DOI: 10.1016/j.biopha.2021.112516] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 12/20/2022] Open
Abstract
The growth and development of cancer are directly correlated to the suppression of the immune system. A major breakthrough in cancer immunotherapy depends on various mechanisms to detect immunosuppressive factors that inhibit anti-tumor immune responses. Immune checkpoints are expressed on many immune cells such as T-cells, regulatory B cells (Bregs), dendritic cells (DCs), natural killer cells (NKs), regulatory T (Tregs), M2-type macrophages, and myeloid-derived suppressor cells (MDSCs). Immune inhibitory molecules, including CTLA-4, TIM-3, TIGIT, PD-1, and LAG-3, normally inhibit immune responses via negatively regulating immune cell signaling pathways to prevent immune injury. However, the up-regulation of inhibitory immune checkpoints during tumor progression on immune cells suppresses anti-tumor immune responses and promotes immune escape in cancer. It has recently been indicated that cancer cells can up-regulate various pathways of the immune checkpoints. Therefore, targeting immune inhibitory molecules through antibodies or miRNAs is a promising therapeutic strategy and shows favorable results. Immune checkpoint inhibitors (ICIs) are introduced as a new immunotherapy strategy that enhance immune cell-induced antitumor responses in many patients. In this review, we highlighted the function of each immune checkpoint on different immune cells and therapeutic strategies aimed at using monoclonal antibodies and miRNAs against inhibitory receptors. We also discussed current challenges and future strategies for maximizing these FDA-approved immunosuppressants' effectiveness and clinical success in cancer treatment.
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Affiliation(s)
- Hajar Alemohammad
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Basira Najafzadeh
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Zahra Asadzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Baghbanzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Arezoo Najafzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Safarpour
- Cellular & Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Renato Bernardini
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 97, Catania, Italy
| | - Oronzo Brunetti
- Medical Oncological Unite, IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Margherita Sonnessa
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Rossella Fasano
- Medical Oncological Unite, IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Nicola Silvestris
- Medical Oncological Unite, IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy; Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari, Bari, Italy.
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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6
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Immune Regulatory Processes of the Tumor Microenvironment under Malignant Conditions. Int J Mol Sci 2021; 22:ijms222413311. [PMID: 34948104 PMCID: PMC8706102 DOI: 10.3390/ijms222413311] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 02/07/2023] Open
Abstract
The tumor microenvironment (TME) is a critical regulator of tumor growth, progression, and metastasis. Since immune cells represent a large fraction of the TME, they play a key role in mediating pro- and anti-tumor immune responses. Immune escape, which suppresses anti-tumor immunity, enables tumor cells to maintain their proliferation and growth. Numerous mechanisms, which have been intensively studied in recent years, are involved in this process and based on these findings, novel immunotherapies have been successfully developed. Here, we review the composition of the TME and the mechanisms by which immune evasive processes are regulated. In detail, we describe membrane-bound and soluble factors, their regulation, and their impact on immune cell activation in the TME. Furthermore, we give an overview of the tumor/antigen presentation and how it is influenced under malignant conditions. Finally, we summarize novel TME-targeting agents, which are already in clinical trials for different tumor entities.
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7
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Thuille N, Sajinovic T, Siegmund K, Baier G. Chemically modified mRNA nucleofection of primary human T cells. J Immunol Methods 2020; 487:112878. [PMID: 33031795 DOI: 10.1016/j.jim.2020.112878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
Here we show that an approach of in-vitro transcribed mRNA nucleofection expands the range of transfection of primary human T cells. It represents a reproducible and time-efficient technology, and is thus an ideal tool in basic research involving highly controlled in-vitro experiments with a gene of interest aiming at identifying its biological human T cell function.
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Affiliation(s)
- Nikolaus Thuille
- Department of Pharmacology and Genetics, Medical University of Innsbruck, Austria.
| | - Tajana Sajinovic
- Department of Pharmacology and Genetics, Medical University of Innsbruck, Austria
| | - Kerstin Siegmund
- Department of Pharmacology and Genetics, Medical University of Innsbruck, Austria
| | - Gottfried Baier
- Department of Pharmacology and Genetics, Medical University of Innsbruck, Austria
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8
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Routh ED, Pullikuth AK, Jin G, Chifman J, Chou JW, D'Agostino RB, Seino KI, Wada H, Print CG, Zhang W, Lu Y, Miller LD. Transcriptomic Features of T Cell-Barren Tumors Are Conserved Across Diverse Tumor Types. Front Immunol 2020; 11:57. [PMID: 32117236 PMCID: PMC7031496 DOI: 10.3389/fimmu.2020.00057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Understanding how tumors subvert immune destruction is essential to the development of cancer immunotherapies. New evidence suggests that tumors limit anti-tumor immunity by exploiting transcriptional programs that regulate intratumoral trafficking and accumulation of effector cells. Here, we investigated the gene expression profiles that distinguish immunologically “cold” and “hot” tumors across diverse tumor types. Methods: RNAseq profiles of tumors (n = 8,920) representing 23 solid tumor types were analyzed using immune gene signatures that quantify CD8+ T cell abundance. Genes and pathways associated with a low CD8+ T cell infiltration profile (CD8-Low) were identified by correlation, differential expression, and statistical ranking methods. Gene subsets were evaluated in immunotherapy treatment cohorts and functionally characterized in cell lines and mouse tumor models. Results: Among different cancer types, we observed highly significant overlap of genes enriched in CD8-Low tumors, which included known immunomodulatory genes (e.g., BMP7, CMTM4, KDM5B, RCOR2) and exhibited significant associations with Wnt signaling, neurogenesis, cell-cell junctions, lipid biosynthesis, epidermal development, and cancer-testis antigens. Analysis of mutually exclusive gene clusters demonstrated that different transcriptional programs may converge on the T cell-cold phenotype as well as predict for response and survival of patients to Nivo treatment. Furthermore, we confirmed that a top-ranking candidate belonging to the TGF-β superfamily, BMP7, negatively regulates CD8+ T cell abundance in immunocompetent murine tumor models, with and without anti-PD-L1 treatment. Conclusions: This study presents the first evidence that solid tumors of diverse anatomical origin acquire conserved transcriptional alterations that may be operative in the T cell-cold state. Our findings demonstrate the potential clinical utility of CD8-Low tumor-associated genes for predicting patient immunotherapy outcomes and point to novel mechanisms with potential for broad therapeutic exploitation.
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Affiliation(s)
- Eric D Routh
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Ashok K Pullikuth
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Guangxu Jin
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States.,Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, United States
| | - Julia Chifman
- Department of Mathematics and Statistics, American University, Washington, DC, United States
| | - Jeff W Chou
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Ralph B D'Agostino
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, United States.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Ken-Ichiro Seino
- Department of Immunobiology, Hokkaido University, Sapporo, Japan
| | - Haruka Wada
- Department of Immunobiology, Hokkaido University, Sapporo, Japan
| | - Cristin G Print
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Wei Zhang
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States.,Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, United States
| | - Yong Lu
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, United States.,Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States.,Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, United States
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9
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Klepsch V, Pommermayr M, Humer D, Brigo N, Hermann-Kleiter N, Baier G. Targeting the orphan nuclear receptor NR2F6 in T cells primes tumors for immune checkpoint therapy. Cell Commun Signal 2020; 18:8. [PMID: 31937317 PMCID: PMC6961368 DOI: 10.1186/s12964-019-0454-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/04/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND NR2F6 has been proposed as an alternative cancer immune checkpoint in the effector T cell compartment. However, a realistic assessment of the in vivo therapeutic potential of NR2F6 requires acute depletion. METHODS Employing primary T cells isolated from Cas9-transgenic mice for electroporation of chemically synthesized sgRNA, we established a CRISPR/Cas9-mediated acute knockout protocol of Nr2f6 in primary mouse T cells. RESULTS Analyzing these Nr2f6CRISPR/Cas9 knockout T cells, we reproducibly observed a hyper-reactive effector phenotype upon CD3/CD28 stimulation in vitro, highly reminiscent to Nr2f6-/- T cells. Importantly, CRISPR/Cas9-mediated Nr2f6 ablation prior to adoptive cell therapy (ACT) of autologous polyclonal T cells into wild-type tumor-bearing recipient mice in combination with PD-L1 or CTLA-4 tumor immune checkpoint blockade significantly delayed MC38 tumor progression and induced superior survival, thus further validating a T cell-inhibitory function of NR2F6 during tumor progression. CONCLUSIONS These findings indicate that Nr2f6CRISPR/Cas9 knockout T cells are comparable to germline Nr2f6-/- T cells, a result providing an independent confirmation of the immune checkpoint function of lymphatic NR2F6. Taken together, CRISPR/Cas9-mediated acute Nr2f6 gene ablation in primary mouse T cells prior to ACT appeared feasible for potentiating established PD-L1 and CTLA-4 blockade therapies, thereby pioneering NR2F6 inhibition as a sensitizing target for augmented tumor regression. Video abstract.
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Affiliation(s)
- Victoria Klepsch
- Division of Translational Cell Genetics, Medical University of Innsbruck, Peter Mayr Str. 1a, A-6020, Innsbruck, Austria.
| | - Maria Pommermayr
- Division of Translational Cell Genetics, Medical University of Innsbruck, Peter Mayr Str. 1a, A-6020, Innsbruck, Austria
| | - Dominik Humer
- Division of Translational Cell Genetics, Medical University of Innsbruck, Peter Mayr Str. 1a, A-6020, Innsbruck, Austria
| | - Natascha Brigo
- Division of Translational Cell Genetics, Medical University of Innsbruck, Peter Mayr Str. 1a, A-6020, Innsbruck, Austria
- Present address: Department of Internal Medicine II, Medical University of Innsbruck, Anichstraße 35, A-6020, Innsbruck, Austria
| | - Natascha Hermann-Kleiter
- Division of Translational Cell Genetics, Medical University of Innsbruck, Peter Mayr Str. 1a, A-6020, Innsbruck, Austria
| | - Gottfried Baier
- Division of Translational Cell Genetics, Medical University of Innsbruck, Peter Mayr Str. 1a, A-6020, Innsbruck, Austria.
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10
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Polvani S, Pepe S, Milani S, Galli A. COUP-TFII in Health and Disease. Cells 2019; 9:E101. [PMID: 31906104 PMCID: PMC7016888 DOI: 10.3390/cells9010101] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/27/2019] [Accepted: 12/29/2019] [Indexed: 12/14/2022] Open
Abstract
The nuclear receptors (NRs) belong to a vast family of evolutionary conserved proteins acting as ligand-activated transcription factors. Functionally, NRs are essential in embryogenesis and organogenesis and in adulthood they are involved in almost every physiological and pathological process. Our knowledge of NRs action has greatly improved in recent years, demonstrating that both their expression and activity are tightly regulated by a network of signaling pathways, miRNA and reciprocal interactions. The Chicken Ovalbumin Upstream Promoter Transcription Factor II (COUP-TFII, NR2F2) is a NR classified as an orphan due to the lack of a known natural ligand. Although its expression peaks during development, and then decreases considerably, in adult tissues, COUP-TFII is an important regulator of differentiation and it is variably implicated in tissues homeostasis. As such, alterations of its expression or its transcriptional activity have been studied and linked to a spectrum of diseases in organs and tissues of different origins. Indeed, an altered COUP-TFII expression and activity may cause infertility, abnormality in the vascular system and metabolic diseases like diabetes. Moreover, COUP-TFII is actively investigated in cancer research but its role in tumor progression is yet to be fully understood. In this review, we summarize the current understanding of COUP-TFII in healthy and pathological conditions, proposing an updated and critical view of the many functions of this NR.
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Affiliation(s)
- Simone Polvani
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, Gastroenterology Unit, University of Florence, viale Pieraccini 6, 50139 Firenze, Italy; (S.P.); (S.M.)
- Department of Experimental and Clinical Medicine, University of Florence, largo Brambilla 50, 50139 Firenze, Italy
| | - Sara Pepe
- Istituto per la Ricerca, la Prevenzione e la rete Oncologica (ISPRO), viale Pieraccini 6, 50139 Firenze, Italy;
- Department of Medical Biotechnologies, University of Siena, via M. Bracci 16, 53100 Siena, Italy
| | - Stefano Milani
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, Gastroenterology Unit, University of Florence, viale Pieraccini 6, 50139 Firenze, Italy; (S.P.); (S.M.)
| | - Andrea Galli
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, Gastroenterology Unit, University of Florence, viale Pieraccini 6, 50139 Firenze, Italy; (S.P.); (S.M.)
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11
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Klepsch V, Moschen AR, Tilg H, Baier G, Hermann-Kleiter N. Nuclear Receptors Regulate Intestinal Inflammation in the Context of IBD. Front Immunol 2019; 10:1070. [PMID: 31139192 PMCID: PMC6527601 DOI: 10.3389/fimmu.2019.01070] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/26/2019] [Indexed: 12/26/2022] Open
Abstract
Gastrointestinal (GI) homeostasis is strongly dependent on nuclear receptor (NR) functions. They play a variety of roles ranging from nutrient uptake, sensing of microbial metabolites, regulation of epithelial intestinal cell integrity to shaping of the intestinal immune cell repertoire. Several NRs are associated with GI pathologies; therefore, systematic analysis of NR biology, the underlying molecular mechanisms, and regulation of target genes can be expected to help greatly in uncovering the course of GI diseases. Recently, an increasing number of NRs has been validated as potential drug targets for therapeutic intervention in patients with inflammatory bowel disease (IBD). Besides the classical glucocorticoids, especially PPARγ, VDR, or PXR-selective ligands are currently being tested with promising results in clinical IBD trials. Also, several pre-clinical animal studies are being performed with NRs. This review focuses on the complex biology of NRs and their context-dependent anti- or pro-inflammatory activities in the regulation of gastrointestinal barrier with special attention to NRs already pharmacologically targeted in clinic and pre-clinical IBD treatment regimens.
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Affiliation(s)
- Victoria Klepsch
- Translational Cell Genetics, Department of Pharmacology and Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander R. Moschen
- Department of Internal Medicine I, Gastroenterology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Gottfried Baier
- Translational Cell Genetics, Department of Pharmacology and Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Natascha Hermann-Kleiter
- Translational Cell Genetics, Department of Pharmacology and Genetics, Medical University of Innsbruck, Innsbruck, Austria
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12
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Alexandre PA, Naval-Sanchez M, Porto-Neto LR, Ferraz JBS, Reverter A, Fukumasu H. Systems Biology Reveals NR2F6 and TGFB1 as Key Regulators of Feed Efficiency in Beef Cattle. Front Genet 2019; 10:230. [PMID: 30967894 PMCID: PMC6439317 DOI: 10.3389/fgene.2019.00230] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/04/2019] [Indexed: 11/20/2022] Open
Abstract
Systems biology approaches are used as strategy to uncover tissue-specific perturbations and regulatory genes related to complex phenotypes. We applied this approach to study feed efficiency (FE) in beef cattle, an important trait both economically and environmentally. Poly-A selected RNA of five tissues (adrenal gland, hypothalamus, liver, skeletal muscle and pituitary) of eighteen young bulls, selected for high and low FE, were sequenced (Illumina HiSeq 2500, 100 bp, pared-end). From the 17,354 expressed genes considering all tissues, 1,335 were prioritized by five selection categories (differentially expressed, harboring SNPs associated with FE, tissue-specific, secreted in plasma and key regulators) and used for network construction. NR2F6 and TGFB1 were identified and validated by motif discovery as key regulators of hepatic inflammatory response and muscle tissue development, respectively, two biological processes demonstrated to be associated with FE. Moreover, we indicated potential biomarkers of FE, which are related to hormonal control of metabolism and sexual maturity. By using robust methodologies and validation strategies, we confirmed the main biological processes related to FE in Bos indicus and indicated candidate genes as regulators or biomarkers of superior animals.
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Affiliation(s)
- Pâmela A. Alexandre
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Marina Naval-Sanchez
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Laercio R. Porto-Neto
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - José Bento S. Ferraz
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Antonio Reverter
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Heidge Fukumasu
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
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Grywalska E, Pasiarski M, Góźdź S, Roliński J. Immune-checkpoint inhibitors for combating T-cell dysfunction in cancer. Onco Targets Ther 2018; 11:6505-6524. [PMID: 30323625 PMCID: PMC6177399 DOI: 10.2147/ott.s150817] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Under normal conditions, the immune system responds effectively to both external and internal threats without damaging healthy tissues. Cells undergoing a neoplastic transformation are one such threat. An efficient activation of T cells is enabled by T-cell receptor (TCR) interactions with antigen-presenting class I and class II molecules of the major histocompatibility complex (MHC), co-stimulatory molecules, and cytokines. After threatening stimuli are removed from the body, the host's immune response ceases, which prevents tissue damage or chronic inflammation. The recognition of foreign antigens is highly selective, which requires multistep regulation to avoid reactions against the antigens of healthy cells. This multistep regulation includes central and peripheral tolerance toward the body's own antigens. Here, we discuss T-cell dysfunction, which leads to poor effector function against foreign antigens, including cancer. We describe selected cellular receptors implicated in T-cell dysfunction and discuss how immune-checkpoint inhibitors can help overcome T-cell dysfunction in cancer treatment.
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Affiliation(s)
- Ewelina Grywalska
- Department of Clinical Immunology and Immunotherapy, Medical University of Lublin, Lublin, Poland,
| | - Marcin Pasiarski
- Department of Hematology, Holy Cross Oncology Center of Kielce, Kielce, Poland.,Faculty of Health Sciences, Jan Kochanowski University, Kielce, Poland
| | - Stanisław Góźdź
- Faculty of Health Sciences, Jan Kochanowski University, Kielce, Poland.,Department of Oncology, Holy Cross Oncology Center of Kielce, Kielce, Poland
| | - Jacek Roliński
- Department of Clinical Immunology and Immunotherapy, Medical University of Lublin, Lublin, Poland,
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Sayour EJ, Mitchell DA. Immunotherapy for Pediatric Brain Tumors. Brain Sci 2017; 7:brainsci7100137. [PMID: 29065490 PMCID: PMC5664064 DOI: 10.3390/brainsci7100137] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/20/2017] [Accepted: 10/18/2017] [Indexed: 12/20/2022] Open
Abstract
Malignant brain tumors are the most common cause of solid cancer death in children. New targeted therapies are vital to improve treatment outcomes, but must be developed to enable trafficking across the blood brain barrier (BBB). Since activated T cells cross the BBB, cancer immunotherapy can be harnessed to unlock the cytotoxic potential of the immune system. However, standard of care treatments (i.e., chemotherapy and radiation) applied concomitant to pediatric brain tumor immunotherapy may abrogate induction of immunotherapeutic responses. This review will discuss the development of immunotherapies within this paradigm using emerging approaches being investigated in phase I/II trials in children with refractory brain tumors, including checkpoint inhibitors, vaccine immunotherapy, and adoptive cell therapy.
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Affiliation(s)
- Elias J Sayour
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lilian S. Wells Department of Neurosurgery, 1149 South Newell Drive, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Duane A Mitchell
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lilian S. Wells Department of Neurosurgery, 1149 South Newell Drive, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
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15
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Acute myocardial infarction or stroke in occult colorectal cancer: Epiphenomena of the degree of epigenetic deregulation of SEPT9 gene? Immunol Lett 2016; 181:116-117. [PMID: 27838469 DOI: 10.1016/j.imlet.2016.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/06/2016] [Accepted: 11/07/2016] [Indexed: 02/06/2023]
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