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Manoharan M, Mandloi N, Priyadarshini S, Patil A, Gupta R, Iyer L, Gupta R, Chaudhuri A. A Computational Approach Identifies Immunogenic Features of Prognosis in Human Cancers. Front Immunol 2018; 9:3017. [PMID: 30622534 PMCID: PMC6308325 DOI: 10.3389/fimmu.2018.03017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/06/2018] [Indexed: 12/25/2022] Open
Abstract
A large number of tumor intrinsic and extrinsic factors determine long-term survival in human cancers. In this study, we stratified 9120 tumors from 33 cancers with respect to their immune cell content and identified immunogenomic features associated with long-term survival. Our analysis demonstrates that tumors infiltrated by CD8+ T cells expressing higher levels of activation marker (PD1hi) along with TCR signaling genes and cytolytic T cell markers (IL2hi/TNF-αhi/IFN-γhi/GZMA-Bhi) extend survival, whereas survival benefit was absent for tumors infiltrated by anergic and hyperexhausted CD8+ T cells characterized by high expression of CTLA-4, TIM3, LAG3, and genes linked to PI3K signaling pathway. The computational approach of using robust and highly specific gene expression signatures to deconvolute the tumor microenvironment has important clinical applications, such as selecting patients who will benefit from checkpoint inhibitor treatment.
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52
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Changes in the biochemical taste of cytoplasmic and cell-free DNA are major fuels for inflamm-aging. Semin Immunol 2018; 40:6-16. [DOI: 10.1016/j.smim.2018.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
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53
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A novel murine model for contact lens wear reveals clandestine IL-1R dependent corneal parainflammation and susceptibility to microbial keratitis upon inoculation with Pseudomonas aeruginosa. Ocul Surf 2018; 17:119-133. [PMID: 30439473 DOI: 10.1016/j.jtos.2018.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 12/17/2022]
Abstract
PURPOSE Contact lens wear carries a risk of complications, including corneal infection. Solving these complications has been hindered by limitations of existing animal models. Here, we report development of a new murine model of contact lens wear. METHODS C57BL/6 mice were fitted with custom-made silicone-hydrogel contact lenses with or without prior inoculation with Pseudomonas aeruginosa (PAO1-GFP). Contralateral eyes served as controls. Corneas were monitored for pathology, and examined ex vivo using high-magnification, time-lapse imaging. Fluorescent reporter mice allowed visualization of host cell membranes and immune cells. Lens-colonizing bacteria were detected by viable counts and FISH. Direct-colony PCR was used for bacterial identification. RESULTS Without deliberate inoculation, lens-wearing corneas remained free of visible pathology, and retained a clarity similar to non-lens wearing controls. CD11c-YFP reporter mice revealed altered numbers, and distribution, of CD11c-positive cells in lens-wearing corneas after 24 h. Worn lenses showed bacterial colonization, primarily by known conjunctival or skin commensals. Corneal epithelial cells showed vacuolization during lens wear, and after 5 days, cells with phagocyte morphology appeared in the stroma that actively migrated over resident keratocytes that showed altered morphology. Immunofluorescence confirmed stromal Ly6G-positive cells after 5 days of lens wear, but not in MyD88 or IL-1R gene-knockout mice. P. aeruginosa-contaminated lenses caused infectious pathology in most mice from 1 to 13 days. CONCLUSIONS This murine model of contact lens wear appears to faithfully mimic events occurring during human lens wear, and could be valuable for experiments, not possible in humans, that help solve the pathogenesis of lens-related complications.
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Jiang Z, Liu Z, Li M, Chen C, Wang X. Immunogenomics Analysis Reveals that TP53 Mutations Inhibit Tumor Immunity in Gastric Cancer. Transl Oncol 2018; 11:1171-1187. [PMID: 30059832 PMCID: PMC6078052 DOI: 10.1016/j.tranon.2018.07.012] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 12/23/2022] Open
Abstract
Although immunotherapy continues to demonstrate efficacy in a variety of refractory cancers, currently, no any immunotherapeutic strategy is clinically used for gastric cancer (GC) except its microsatellite instable subtype. Thus, it is important to identify molecular biomarkers for predicting the responders to GC immunotherapy. TP53 mutations frequently occur in GC and are associated with unfavorable clinical outcomes in GC. We performed a comprehensive characterization of the associations between TP53 mutations and immune activities in GC based on two large-scale GC cancer genomics data. We compared expression and enrichment levels of 787 immune-related genes and 23 immune gene-sets among TP53-mutated GCs, TP53‐wildtype GCs, and normal tissue, and explored the correlations between p53-mediated pathways and immune activities in GC. Strikingly, almost all analyzed immune gene-sets were significantly downregulated in enrichment levels in TP53-mutated GCs compared to TP53‐wildtype GCs. These less active immune pathways and cell types in TP53-mutated GCs included 15 immune cell types and function, tumor-infiltrating lymphocytes, regulatory T cells, immune checkpoint, cytokine and cytokine receptor, human leukocyte antigen, pro‐inflammatory, and parainflammation. Moreover, we identified a number of p53-mediated pathways and proteins that were significantly associated with immune activities in GC. Furthermore, we demonstrated that the TP53 mutation itself could result in the depressed immune activities in GC and other cancer types. We revealed that chromosomal instability was an important mechanism for the depressed tumor immunity in TP53-mutated cancers. Finally, we showed that immune cell infiltration and immune activities were likely positively associated with survival prognosis in GC. Our findings suggest that p53 may play an important role in activating tumor immunity in GC and other cancer types and that the TP53 mutation status could be useful in stratifying cancer patients responsive to a certain immunotherapy.
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Affiliation(s)
- Zehang Jiang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Zhixian Liu
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Mengyuan Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Cai Chen
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China.
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56
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Grothey A, Yoshino T, Bodoky G, Ciuleanu T, Garcia-Carbonero R, García-Alfonso P, Van Cutsem E, Muro K, Mytelka DS, Li L, Lipkovich O, Hsu Y, Sashegyi A, Ferry D, Nasroulah F, Tabernero J. Association of baseline absolute neutrophil counts and survival in patients with metastatic colorectal cancer treated with second-line antiangiogenic therapies: exploratory analyses of the RAISE trial and validation in an electronic medical record data set. ESMO Open 2018; 3:e000347. [PMID: 29713498 PMCID: PMC5922565 DOI: 10.1136/esmoopen-2018-000347] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND In the RAISE trial, ramucirumab+leucovorin/fluorouracil/irinotecan (FOLFIRI) improved the median overall survival (mOS) of patients with previously treated metastatic colorectal cancer versus patients treated with placebo+FOLFIRI but had a higher incidence of neutropaenia, leading to more chemotherapy dose modifications and discontinuations. Thus, we conducted an exploratory post-hoc analysis of RAISE and a retrospective, observational analysis of electronic medical record (EMR) data to determine and verify the association of neutropaenia, baseline absolute neutrophil count (ANC) and survival. METHODS The RAISE analysis used the study safety population (n=1057). IMS Health Oncology Database (IMS EMR) was the source for the real-world data set (n=617). RESULTS RAISE patients with treatment-emergent neutropaenia had improved mOS compared with those without (ramucirumab arm: 16.1 vs 10.7 months, HR=0.57, p<0.0001; placebo arm: 12.7 vs 10.7 months, HR=0.76, p=0.0065). RAISE patients with low ANC versus high baseline ANC also had longer mOS (ramucirumab arm: 15.2 vs 8.9 months, HR=0.49, p<0.0001; placebo arm: 13.2 vs 7.3 months, HR=0.50, p<0.0001). The results were similar for IMS EMR low versus high baseline ANC (bevacizumab+FOLFIRI patients: 14.9 vs 7.7 months, HR=0.59, p<0.0001; FOLFIRI alone: 14.6 vs 5.4 months, HR=0.37, p<0.0001). Patients in the RAISE trial with low baseline ANC were more likely to develop neutropaenia (OR: ramucirumab arm=2.62, p<0.0001; placebo arm=2.16, p=0.0003). CONCLUSION Neutropaenia during treatment, and subsequent dose modifications or discontinuations, do not compromise treatment efficacy. Baseline ANC is a strong prognostic factor for survival and is associated with treatment-emergent neutropaenia in the analysed population. TRIAL REGISTRATION NUMBER NCT01183780, Results.
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Affiliation(s)
| | | | | | - Tudor Ciuleanu
- The Oncology Institute Prof Dr Ion Chiricută and Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | | | | | - Kei Muro
- Aichi Cancer Center Hospital, Nagoya, Japan
| | | | - Li Li
- Eli Lilly and Company, Bridgewater, New Jersey, USA
| | | | - Yanzhi Hsu
- Eli Lilly and Company, Bridgewater, New Jersey, USA
| | | | - David Ferry
- Eli Lilly and Company, Bridgewater, New Jersey, USA
| | | | - Josep Tabernero
- Vall d’Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
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Corbella S, Veronesi P, Galimberti V, Weinstein R, Del Fabbro M, Francetti L. Is periodontitis a risk indicator for cancer? A meta-analysis. PLoS One 2018; 13:e0195683. [PMID: 29664916 PMCID: PMC5903629 DOI: 10.1371/journal.pone.0195683] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/27/2018] [Indexed: 01/22/2023] Open
Abstract
Background The aim of the present systematic review was to evaluate the hypothesis of an association between periodontitis and the development of cancer. Methods Two reviewers independently screened electronic and manual sources for pertinent articles. Primary outcome measures were the occurrence of neoplasm diagnosis in exposed and non-exposed groups, reported to evaluate association between cancer and periodontitis. Results Of the 490 initially retrieved papers 10 were included in the qualitative synthesis and eight in the quantitative synthesis; the eight papers covered six studies. Considering hazard ratios, a statistically significant association was found for all cancers studied (1.14; CI 95%: 1.04, 1.24), digestive tract cancer (1.34; CI 95%: 1.05, 1.72), pancreatic cancer (1.74; CI 95%: 1.21, 2.52), prostate cancer (1.25; CI 95%: 1.04, 1.51), breast cancer (1.11; CI 95%: 1.00, 1.23), corpus uteri cancer (2.20; CI 95%: 1.16, 4.18), lung cancer (1.24; CI 95%: 1.06, 1.45), hematological cancer (1.30; CI 95%: 1.11, 1.53), esophagus / oropharyngeal cancer pooled together (2.25; CI 95%: 1.30, 3.90) and Non-Hodgkin lymphoma (1.30; CI 95%: 1.11, 1.52). Conclusions Despite the sparse scientific evidence and considering the low statistical power of the results, this systematic review revealed a substantial lack of studies with standardized and comparable methods to speculate about the association between periodontitis and cancer; more studies are need in order to explore further the scientific evidence of such correlation.
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Affiliation(s)
- Stefano Corbella
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
- * E-mail:
| | - Paolo Veronesi
- European Institute of Oncology, Division of Senology, Milan, Italy
- Università degli Studi di Milano, Milan, Italy
| | | | - Roberto Weinstein
- Scientific Director D&S ICH Humanitas Dental Center, Rozzano, Milan, Italy
| | - Massimo Del Fabbro
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Luca Francetti
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
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Tamborero D, Rubio-Perez C, Muiños F, Sabarinathan R, Piulats JM, Muntasell A, Dienstmann R, Lopez-Bigas N, Gonzalez-Perez A. A Pan-cancer Landscape of Interactions between Solid Tumors and Infiltrating Immune Cell Populations. Clin Cancer Res 2018; 24:3717-3728. [PMID: 29666300 DOI: 10.1158/1078-0432.ccr-17-3509] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/02/2018] [Accepted: 04/12/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Throughout their development, tumors are challenged by the immune system, and they acquire features to evade its surveillance. A systematic view of these traits, which shed light on how tumors respond to immunotherapies, is still lacking.Experimental Design: Here, we computed the relative abundance of an array of immune cell populations to measure the immune infiltration pattern of 9,174 tumors of 29 solid cancers. We then clustered tumors with similar infiltration pattern to define immunophenotypes. Finally, we identified genomic and transcriptomic traits associated to these immunophenotypes across cancer types.Results: In highly cytotoxic immunophenotypes, we found tumors with low clonal heterogeneity enriched for alterations of genes involved in epigenetic regulation, ubiquitin-mediated proteolysis, antigen presentation, and cell-cell communication, which may drive resistance in combination with the ectopic expression of negative immune checkpoints. Tumors with immunophenotypes of intermediate cytotoxicity are characterized by an upregulation of processes involved in neighboring tissue invasion and remodeling that may foster the recruitment of immunosuppressive cells. Tumors with poorly cytotoxic immunophenotype tend to be of more advanced stages and bear a greater burden of copy number alterations and frequent alterations of cell cycle, hedgehog, β-catenin, and TGFβ pathways, which may cause immune depletion.Conclusions: We provide a comprehensive landscape of the characteristics of solid tumors that may influence (or be influenced by) the characteristics of their immune infiltrate. These results may help interpret the response of solid tumors to immunotherapies and guide the development of novel drug combination strategies. Clin Cancer Res; 24(15); 3717-28. ©2018 AACR.
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Affiliation(s)
- David Tamborero
- Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain. .,Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carlota Rubio-Perez
- Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain.,Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Radhakrishnan Sabarinathan
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Josep M Piulats
- Department of Medical Oncology, Institut Català d'Oncologia-IDIBELL, CIBERONC, Barcelona, Spain
| | - Aura Muntasell
- Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Rodrigo Dienstmann
- Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Sage Bionetworks, Seattle, Washington
| | - Nuria Lopez-Bigas
- Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain.,Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Abel Gonzalez-Perez
- Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain. .,Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
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59
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Galipeau PC, Oman KM, Paulson TG, Sanchez CA, Zhang Q, Marty JA, Delrow JJ, Kuhner MK, Vaughan TL, Reid BJ, Li X. NSAID use and somatic exomic mutations in Barrett's esophagus. Genome Med 2018; 10:17. [PMID: 29486792 PMCID: PMC5830331 DOI: 10.1186/s13073-018-0520-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/09/2018] [Indexed: 12/18/2022] Open
Abstract
Background Use of aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs) has been shown to protect against tetraploidy, aneuploidy, and chromosomal alterations in the metaplastic condition Barrett’s esophagus (BE) and to lower the incidence and mortality of esophageal adenocarcinoma (EA). The esophagus is exposed to both intrinsic and extrinsic mutagens resulting from gastric reflux, chronic inflammation, and exposure to environmental carcinogens such as those found in cigarettes. Here we test the hypothesis that NSAID use inhibits accumulation of point mutations/indels during somatic genomic evolution in BE. Methods Whole exome sequences were generated from 82 purified epithelial biopsies and paired blood samples from a cross-sectional study of 41 NSAID users and 41 non-users matched by sex, age, smoking, and continuous time using or not using NSAIDs. Results NSAID use reduced overall frequency of point mutations across the spectrum of mutation types, lowered the frequency of mutations even when adjusted for both TP53 mutation and smoking status, and decreased the prevalence of clones with high variant allele frequency. Never smokers who consistently used NSAIDs had fewer point mutations in signature 17, which is commonly found in EA. NSAID users had, on average, a 50% reduction in functional gene mutations in nine cancer-associated pathways and also had less diversity in pathway mutational burden compared to non-users. Conclusions These results indicate NSAID use functions to limit overall mutations on which selection can act and supports a model in which specific mutant cell populations survive or expand better in the absence of NSAIDs. Electronic supplementary material The online version of this article (10.1186/s13073-018-0520-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia C Galipeau
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Kenji M Oman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Thomas G Paulson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Carissa A Sanchez
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Qing Zhang
- Bioinformatics Shared Resource, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Jerry A Marty
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Mary K Kuhner
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA, 98195-5065, USA
| | - Thomas L Vaughan
- Department of Epidemiology, University of Washington, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Brian J Reid
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA.,Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA, 98195-5065, USA.,Department of Medicine, University of Washington, Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Xiaohong Li
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA.
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Liu Z, Li M, Jiang Z, Wang X. A Comprehensive Immunologic Portrait of Triple-Negative Breast Cancer. Transl Oncol 2018; 11:311-329. [PMID: 29413765 PMCID: PMC5884188 DOI: 10.1016/j.tranon.2018.01.011] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 12/21/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a high-risk malignancy due to its high capacity for invasion and lack of targeted therapy. Immunotherapy continues to demonstrate efficacy in a variety of cancers, and thus may be a promising strategy for TNBC given the limited therapeutic options currently available for TNBC. In this study, we performed an exhaustive analysis of immunogenic signatures in TNBC based on 2 large-scale breast cancer (BC) genomic data. We compared enrichment levels of 26 immune cell activities and pathways among TNBC, non-TNBC, and normal tissue, and within TNBCs of different genotypic or phenotypic features. We found that almost all analyzed immune activities and pathways had significantly higher enrichment levels in TNBC than non-TNBC. Elevated enrichment of these immune activities and pathways was likely to be associated with better survival prognosis in TNBC. This study demonstrated that TNBC likely exhibits the strongest immunogenicity among BC subtypes, and thus warrants the immunotherapeutic option for TNBC.
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Affiliation(s)
- Zhixian Liu
- Department of Basic Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Mengyuan Li
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Zehang Jiang
- Department of Basic Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaosheng Wang
- Department of Basic Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
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siRNA Library Screening Identifies a Druggable Immune-Signature Driving Esophageal Adenocarcinoma Cell Growth. Cell Mol Gastroenterol Hepatol 2018; 5:569-590. [PMID: 29930979 PMCID: PMC6009761 DOI: 10.1016/j.jcmgh.2018.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/12/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Effective therapeutic approaches are urgently required to tackle the alarmingly poor survival outcomes in esophageal adenocarcinoma (EAC) patients. EAC originates from within the intestinal-type metaplasia, Barrett's esophagus, a condition arising on a background of gastroesophageal reflux disease and associated inflammation. METHODS This study used a druggable genome small interfering RNA (siRNA) screening library of 6022 siRNAs in conjunction with bioinformatics platforms, genomic studies of EAC tissues, somatic variation data of EAC from The Cancer Genome Atlas data of EAC, and pathologic and functional studies to define novel EAC-associated, and targetable, immune factors. RESULTS By using a druggable genome library we defined genes that sustain EAC cell growth, which included an unexpected immunologic signature. Integrating Cancer Genome Atlas data with druggable siRNA targets showed a striking concordance and an EAC-specific gene amplification event associated with 7 druggable targets co-encoded at Chr6p21.1. Over-representation of immune pathway-associated genes supporting EAC cell growth included leukemia inhibitory factor, complement component 1, q subcomponent A chain (C1QA), and triggering receptor expressed on myeloid cells 2 (TREM2), which were validated further as targets sharing downstream signaling pathways through genomic and pathologic studies. Finally, targeting the triggering receptor expressed on myeloid cells 2-, C1q-, and leukemia inhibitory factor-activated signaling pathways (TYROBP-spleen tyrosine kinase and JAK-STAT3) with spleen tyrosine kinase and Janus-activated kinase inhibitor fostamatinib R788 triggered EAC cell death, growth arrest, and reduced tumor burden in NOD scid gamma mice. CONCLUSIONS These data highlight a subset of genes co-identified through siRNA targeting and genomic studies of expression and somatic variation, specifically highlighting the contribution that immune-related factors play in support of EAC development and suggesting their suitability as targets in the treatment of EAC.
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Key Words
- ATCC, American Type Culture Collection
- BE, Barrett’s esophagus
- Barrett’s Esophagus
- EAC, esophageal adenocarcinoma
- ERBB2, erb-b2 receptor tyrosine kinase 2
- ESCC, esophageal squamous cell carcinoma
- Esophageal Adenocarcinoma
- FCS, fetal calf serum
- GEM, gene expression microarray
- GERD, gastroesophageal reflux disease
- GO, gene ontology
- HGD, high-grade dysplastic
- IL, interleukin
- Inflammation
- JAK-STAT, Janus kinase/signal transducer-and-activator of transcription
- LIF, leukemia inhibitory factor
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
- PBS, phosphate-buffered saline
- RA, rheumatoid arthritis
- SV, somatic variation
- SYK, spleen tyrosine kinase
- TCGA, The Cancer Genome Atlas
- TREM2, triggering receptor expressed on myeloid cells 2
- Therapeutic Targets
- VEGFA, vascular endothelial growth factor A
- mRNA, messenger RNA
- siRNA, small interfering RNA
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Cieślik M, Chinnaiyan AM. Cancer transcriptome profiling at the juncture of clinical translation. Nat Rev Genet 2017; 19:93-109. [PMID: 29279605 DOI: 10.1038/nrg.2017.96] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methodological breakthroughs over the past four decades have repeatedly revolutionized transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples. These transcriptomes provide a link between cellular phenotypes and their molecular underpinnings, such as mutations. In the context of cancer, this link represents an opportunity to dissect the complexity and heterogeneity of tumours and to discover new biomarkers or therapeutic strategies. Here, we review the rationale, methodology and translational impact of transcriptome profiling in cancer.
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Affiliation(s)
- Marcin Cieślik
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan.,Comprehensive Cancer Center, University of Michigan.,Department of Urology, University of Michigan.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
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63
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Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol 2017; 18:220. [PMID: 29141660 PMCID: PMC5688663 DOI: 10.1186/s13059-017-1349-1] [Citation(s) in RCA: 2481] [Impact Index Per Article: 354.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 10/10/2017] [Indexed: 12/12/2022] Open
Abstract
Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene signature-based method, and use it to infer 64 immune and stromal cell types. We harmonized 1822 pure human cell type transcriptomes from various sources and employed a curve fitting approach for linear comparison of cell types and introduced a novel spillover compensation technique for separating them. Using extensive in silico analyses and comparison to cytometry immunophenotyping, we show that xCell outperforms other methods. xCell is available at http://xCell.ucsf.edu/.
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Affiliation(s)
- Dvir Aran
- Institute for Computational Health Sciences, University of California, San Francisco, California, 94158, USA.
| | - Zicheng Hu
- Institute for Computational Health Sciences, University of California, San Francisco, California, 94158, USA
| | - Atul J Butte
- Institute for Computational Health Sciences, University of California, San Francisco, California, 94158, USA.
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Wang R, Bhat-Nakshatri P, Padua MB, Prasad MS, Anjanappa M, Jacobson M, Finnearty C, Sefcsik V, McElyea K, Redmond R, Sandusky G, Penthala N, Crooks PA, Liu J, Zimmers T, Nakshatri H. Pharmacological Dual Inhibition of Tumor and Tumor-Induced Functional Limitations in a Transgenic Model of Breast Cancer. Mol Cancer Ther 2017; 16:2747-2758. [PMID: 28978719 DOI: 10.1158/1535-7163.mct-17-0717] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/12/2017] [Accepted: 09/21/2017] [Indexed: 12/17/2022]
Abstract
Breast cancer progression is associated with systemic effects, including functional limitations and sarcopenia without the appearance of overt cachexia. Autocrine/paracrine actions of cytokines/chemokines produced by cancer cells mediate cancer progression and functional limitations. The cytokine-inducible transcription factor NF-κB could be central to this process, as it displays oncogenic functions and is integral to the Pax7:MyoD:Pgc-1β:miR-486 myogenesis axis. We tested this possibility using the MMTV-PyMT transgenic mammary tumor model and the NF-κB inhibitor dimethylaminoparthenolide (DMAPT). We observed deteriorating physical and functional conditions in PyMT+ mice with disease progression. Compared with wild-type mice, tumor-bearing PyMT+ mice showed decreased fat mass, impaired rotarod performance, and reduced grip strength as well as increased extracellular matrix (ECM) deposition in muscle. Contrary to acute cachexia models described in the literature, mammary tumor progression was associated with reduction in skeletal muscle stem/satellite-specific transcription factor Pax7. Additionally, we observed tumor-induced reduction in Pgc-1β in muscle, which controls mitochondrial biogenesis. DMAPT treatment starting at 6 to 8 weeks age prior to mammary tumor occurrence delayed mammary tumor onset and tumor growth rates without affecting metastasis. DMAPT overcame cancer-induced functional limitations and improved survival, which was accompanied with restoration of Pax7, Pgc-1β, and mitochondria levels and reduced ECM levels in skeletal muscles. In addition, DMAPT restored circulating levels of 6 out of 13 cancer-associated cytokines/chemokines changes to levels seen in healthy animals. These results reveal a pharmacological approach for overcoming cancer-induced functional limitations, and the above-noted cancer/drug-induced changes in muscle gene expression could be utilized as biomarkers of functional limitations. Mol Cancer Ther; 16(12); 2747-58. ©2017 AACR.
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Affiliation(s)
- Ruizhong Wang
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Maria B Padua
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Mayuri S Prasad
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Manjushree Anjanappa
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Max Jacobson
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Courtney Finnearty
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Victoria Sefcsik
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kyle McElyea
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Rachael Redmond
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - George Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Narsimha Penthala
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Peter A Crooks
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jianguo Liu
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Teresa Zimmers
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana. .,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana.,Richard L Roudebush VA Medical Center, Indianapolis, Indiana
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65
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Lasry A, Aran D, Butte AJ, Ben-Neriah Y. Cancer Cell-Autonomous Parainflammation Mimics Immune Cell Infiltration. Cancer Res 2017; 77:3740-3744. [PMID: 28667073 PMCID: PMC5518753 DOI: 10.1158/0008-5472.can-16-3383] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/26/2017] [Accepted: 05/19/2017] [Indexed: 12/21/2022]
Abstract
Parainflammation is a unique variant of inflammation, characterized by epithelial-autonomous activation of inflammatory response. Parainflammation has been shown to strongly promote mouse gut tumorigenesis upon p53 loss. In a recent study, we explored the prevalence of parainflammation in human cancer and determined its relationship to certain molecular and clinical parameters affecting treatment and prognosis. Parainflammation can be identified from a 40-gene signature and is found in both carcinoma cell lines and a variety of primary tumors, independently of tumor microenvironment. Here, we discuss the implications of our findings in analyses of tumor microenvironment, suggesting that as tumor cell gene expression may often mimic immune and inflammatory infiltration, caution should be applied when interpreting tumor expression data. We also address the connection between parainflammation and prevalence of p53 mutations in specific types of tumors, and cancer prevention by regular usage of NSAIDs. We suggest that parainflammation may serve as a novel biomarker for screening patients who may particularly benefit from NSAID treatment. Cancer Res; 77(14); 3740-4. ©2017 AACR.
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Affiliation(s)
- Audrey Lasry
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Dvir Aran
- Institute for Computational Health Sciences, University of California, San Francisco, California
| | - Atul J Butte
- Institute for Computational Health Sciences, University of California, San Francisco, California
| | - Yinon Ben-Neriah
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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66
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Human MSCs promotes colorectal cancer epithelial-mesenchymal transition and progression via CCL5/β-catenin/Slug pathway. Cell Death Dis 2017; 8:e2819. [PMID: 28542126 PMCID: PMC5520690 DOI: 10.1038/cddis.2017.138] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/06/2017] [Accepted: 02/17/2017] [Indexed: 12/12/2022]
Abstract
Mesenchymal stem cells (MSCs) extensively interact with cancer cells and other stroma cells in the tumor microenvironment. However, the role of MSCs in colorectal cancer (CRC) progression and metastasis is controversial. This study was designed to identify the role of inflammation-activated-MSCs in CRC development. Our results show that tumor necrosis factor (TNF)-α-preactivated-hMSCs significantly promote the progression of colon cancer cells by enhancing cell proliferation, epithelial–mesenchymal transition, migration, and invasion. TNF-α-primed-hMSCs secrete high level of CCL5, which interacts with its receptor CCR1 expressed in colon cancer cells. Interestingly, the stimulation of colon cancer cell progression by TNF-α-primed hMSCs is associated with the upregulation ofβ-catenin signaling pathway. Blockingβ-catenin pathway significantly decreases the TNF-α-primed-conditioned medium or CCL5-mediated cancer cell progression by decreasing the enhancement of Slug, suggesting that the CCL5/β-catenin/Slug pathway plays a critical role in hMSC-mediated cancer progression. Furthermore,in vivomodel in nude mice confirms the ability of hMSCs to promote the proliferation and progression of colon cancer cells, and the upregulation of CCl5/β-catenin/Slug pathway. Taken together, the present study has demonstrated a novel pathway involving CCl5/CCR1/β-catenin/Slug, via which hMSCs promotes CRC development.
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67
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Menendez JA, Alarcón T. Senescence-Inflammatory Regulation of Reparative Cellular Reprogramming in Aging and Cancer. Front Cell Dev Biol 2017; 5:49. [PMID: 28529938 PMCID: PMC5418360 DOI: 10.3389/fcell.2017.00049] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/18/2017] [Indexed: 12/16/2022] Open
Abstract
The inability of adult tissues to transitorily generate cells with functional stem cell-like properties is a major obstacle to tissue self-repair. Nuclear reprogramming-like phenomena that induce a transient acquisition of epigenetic plasticity and phenotype malleability may constitute a reparative route through which human tissues respond to injury, stress, and disease. However, tissue rejuvenation should involve not only the transient epigenetic reprogramming of differentiated cells, but also the committed re-acquisition of the original or alternative committed cell fate. Chronic or unrestrained epigenetic plasticity would drive aging phenotypes by impairing the repair or the replacement of damaged cells; such uncontrolled phenomena of in vivo reprogramming might also generate cancer-like cellular states. We herein propose that the ability of senescence-associated inflammatory signaling to regulate in vivo reprogramming cycles of tissue repair outlines a threshold model of aging and cancer. The degree of senescence/inflammation-associated deviation from the homeostatic state may delineate a type of thresholding algorithm distinguishing beneficial from deleterious effects of in vivo reprogramming. First, transient activation of NF-κB-related innate immunity and senescence-associated inflammatory components (e.g., IL-6) might facilitate reparative cellular reprogramming in response to acute inflammatory events. Second, para-inflammation switches might promote long-lasting but reversible refractoriness to reparative cellular reprogramming. Third, chronic senescence-associated inflammatory signaling might lock cells in highly plastic epigenetic states disabled for reparative differentiation. The consideration of a cellular reprogramming-centered view of epigenetic plasticity as a fundamental element of a tissue's capacity to undergo successful repair, aging degeneration or malignant transformation should provide challenging stochastic insights into the current deterministic genetic paradigm for most chronic diseases, thereby increasing the spectrum of therapeutic approaches for physiological aging and cancer.
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Affiliation(s)
- Javier A Menendez
- Metabolism and Cancer Group, Program Against Cancer Therapeutic Resistance, Catalan Institute of OncologyGirona, Spain.,Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI)Girona, Spain.,METABOSTEMBarcelona, Spain
| | - Tomás Alarcón
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Barcelona, Spain.,Computational and Mathematical Biology Research Group, Centre de Recerca MatemàticaBarcelona, Spain.,Departament de Matemàtiques, Universitat Autònoma de BarcelonaBarcelona, Spain.,Barcelona Graduate School of MathematicsBarcelona, Spain
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68
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Koliaraki V, Pallangyo CK, Greten FR, Kollias G. Mesenchymal Cells in Colon Cancer. Gastroenterology 2017; 152:964-979. [PMID: 28111227 DOI: 10.1053/j.gastro.2016.11.049] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/17/2016] [Accepted: 11/23/2016] [Indexed: 02/07/2023]
Abstract
Mesenchymal cells in the intestine comprise a variety of cell types of diverse origins, functions, and molecular markers. They provide mechanical and structural support and have important functions during intestinal organogenesis, morphogenesis, and homeostasis. Recent studies of the human transcriptome have revealed their importance in the development of colorectal cancer, and studies from animal models have provided evidence for their roles in the pathogenesis of colitis-associated cancer and sporadic colorectal cancer. Mesenchymal cells in tumors, called cancer-associated fibroblasts, arise via activation of resident mesenchymal cell populations and the recruitment of bone marrow-derived mesenchymal stem cells and fibrocytes. Cancer-associated fibroblasts have a variety of activities that promote colon tumor development and progression; these include regulation of intestinal inflammation, epithelial proliferation, stem cell maintenance, angiogenesis, extracellular matrix remodeling, and metastasis. We review the intestinal mesenchymal cell-specific pathways that regulate these processes, with a focus on their roles in mediating interactions between inflammation and carcinogenesis. We also discuss how increasing our understanding of intestinal mesenchymal cell biology and function could lead to new strategies to identify and treat colitis-associated cancers.
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Affiliation(s)
| | - Charles K Pallangyo
- Muhimbili University of Health and Allied Sciences, School of Medicine, Dar es Salaam, Tanzania
| | - Florian R Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany; German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany.
| | - George Kollias
- Biomedical Sciences Research Centre "Alexander Fleming," Vari, Greece; Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
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69
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Tsilimigras MCB, Fodor A, Jobin C. Carcinogenesis and therapeutics: the microbiota perspective. Nat Microbiol 2017; 2:17008. [PMID: 28225000 PMCID: PMC6423540 DOI: 10.1038/nmicrobiol.2017.8] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/10/2017] [Indexed: 12/18/2022]
Abstract
Cancer arises from the acquisition of multiple genetic and epigenetic changes in host cells over the span of many years, promoting oncogenic traits and carcinogenesis. Most cancers develop following random somatic alterations of key oncogenic genes, which are favoured by a number of risk factors, including lifestyle, diet and inflammation. Importantly, the environment where tumours evolve provides a unique source of signalling cues that affects cancer cell growth, survival, movement and metastasis. Recently, there has been increased interest in how the microbiota, the collection of microorganisms inhabiting the host body surface and cavities, shapes a micro-environment for host cells that can either promote or prevent cancer formation. The microbiota, particularly the intestinal biota, plays a central role in host physiology, and the composition and activity of this consortium of microorganisms is directly influenced by known cancer risk factors such as lifestyle, diet and inflammation. In this REVIEW, we discuss the pro- and anticarcinogenic role of the microbiota, as well as highlighting the therapeutic potential of microorganisms in tumourigenesis. The broad impacts, and, at times, opposing roles of the microbiota in carcinogenesis serve to illustrate the complex and sometimes conflicted relationship between microorganisms and the host-a relationship that could potentially be harnessed for therapeutic benefits.
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Affiliation(s)
- Matthew C. B. Tsilimigras
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, USA
| | - Anthony Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida 32611, USA
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida 32611, USA
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Abstract
Understanding a tumor’s complex cellular heterogeneity will be crucial for the development of better treatment strategies. A new study suggests a novel method for the in silico dissociation of solid tumors and presents novel insights that have implications for immunotherapy in cancer. Please see the related Research article: www.dx.doi.org/10.1186/s13059-016-1028-7.
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Affiliation(s)
- Dvir Aran
- Institute for Computational Health Sciences, University of California, Mission Hall, 550 16th Street, 4th Floor, Box 0110, San Francisco, CA, 94158-2549, USA
| | - Atul J Butte
- Institute for Computational Health Sciences, University of California, Mission Hall, 550 16th Street, 4th Floor, Box 0110, San Francisco, CA, 94158-2549, USA.
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