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Cannataro R, Caroleo MC, Fazio A, La Torre C, Plastina P, Gallelli L, Lauria G, Cione E. Ketogenic Diet and microRNAs Linked to Antioxidant Biochemical Homeostasis. Antioxidants (Basel) 2019; 8:antiox8080269. [PMID: 31382449 PMCID: PMC6719224 DOI: 10.3390/antiox8080269] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 02/05/2023] Open
Abstract
Recently, we demonstrated the capability of the ketogenic diet (KD) to influence the microRNA (miR) expression profile. Here, we report that KD is able to normalize miR expression in obese subjects when compared with lean subjects. By applying two different bioinformatics tools, we found that, amongst the miRs returning to comparable levels in lean subjects, four of them are linked to antioxidant biochemical pathways specifically, and the others are linked to both antioxidant and anti-inflammatory biochemical pathways. Of particular interest is the upregulation of hsa-miR-30a-5p, which correlates with the decrease of catalase expression protein in red blood cells.
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Affiliation(s)
- Roberto Cannataro
- GalaScreen Laboratories, Mater Domini Hospital 88100 Catanzaro and Department of Pharmacy, Health and Nutrition Sciences, University of Calabria, 87036 Rende (CS), Italy
| | - Maria Cristina Caroleo
- Department of Pharmacy, Health and Nutrition Sciences, University of Calabria, Via Pietro Bucci, 87036 Rende (CS), Italy
| | - Alessia Fazio
- Department of Pharmacy, Health and Nutrition Sciences, University of Calabria, Via Pietro Bucci, 87036 Rende (CS), Italy
| | - Chiara La Torre
- Department of Pharmacy, Health and Nutrition Sciences, University of Calabria, Via Pietro Bucci, 87036 Rende (CS), Italy
| | - Pierluigi Plastina
- Department of Pharmacy, Health and Nutrition Sciences, University of Calabria, Via Pietro Bucci, 87036 Rende (CS), Italy
| | - Luca Gallelli
- Clinical Pharmacology and Pharmacovigilance Operative Unit, Department of Health Science, University of Magna Graecia, Mater Domini Hospital Catanzaro, 88100 Catanzaro, Italy
| | - Graziantonio Lauria
- Department of Pharmacy, Health and Nutrition Sciences, University of Calabria, Via Pietro Bucci, 87036 Rende (CS), Italy
| | - Erika Cione
- Department of Pharmacy, Health and Nutrition Sciences, University of Calabria, Via Pietro Bucci, 87036 Rende (CS), Italy.
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Chumsri S, Serie DJ, Li Z, Pogue-Geile KL, Soyano-Muller AE, Mashadi-Hossein A, Warren S, Lou Y, Colon-Otero G, Knutson KL, Perez EA, Moreno-Aspitia A, Thompson EA. Effects of Age and Immune Landscape on Outcome in HER2-Positive Breast Cancer in the NCCTG N9831 (Alliance) and NSABP B-31 (NRG) Trials. Clin Cancer Res 2019; 25:4422-4430. [PMID: 30808774 DOI: 10.1158/1078-0432.ccr-18-2206] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 12/18/2018] [Accepted: 02/21/2019] [Indexed: 12/17/2022]
Abstract
PURPOSE Young age has been shown to be an independent predictor of poor outcome in breast cancer. In HER2-positive breast cancer, the effects of aging remain largely unknown. EXPERIMENTAL DESIGN A total of 4,547 patients were included [3,132 from North Central Cancer Treatment Group (NCCTG) N9831 and 1,415 from National Surgical Adjuvant Breast and Bowel Project (NSABP) B-31]. Pathologic stromal tumor-infiltrating lymphocyte (sTIL) and molecular tumor infiltrating lymphocyte (mTIL) signatures were evaluated. RESULTS In NCCTG N9831, comparable benefit of trastuzumab was observed in all patients [age ≤ 40; HR, 0.43; 95% confidence interval (CI), 0.28-0.66; P < 0.001; and age > 40; HR, 0.56; 95% CI, 0.45-0.69; P < 0.001]. Similar results were observed in NSABP B-31 (age ≤ 40; HR, 0.45; 95% CI, 0.29-0.68; P < 0.001; and age > 40; HR, 0.42; 95% CI, 0.33-0.54; P < 0.001). Among patients who received chemotherapy alone, younger age was associated with poor outcome in the hormone receptor-positive subset, but not the hormone receptor-negative subset, in both trials. Although there was no association between sTILs and age, a small, but significant increase in mTIL CD45 and some immune subset signatures were observed. Among patients who received chemotherapy alone, patients over 40 years of age with lymphocyte-predominant breast cancer had excellent outcome, with 95% remaining recurrence free at 15 years. CONCLUSIONS Among patients treated with trastuzumab, there was no significant difference in outcome related to age. Our study suggests that trastuzumab can negate the poor prognosis associated with young age.
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MESH Headings
- Adult
- Age Factors
- Aged
- Aged, 80 and over
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/drug therapy
- Breast Neoplasms/immunology
- Breast Neoplasms/mortality
- Breast Neoplasms/pathology
- Chemotherapy, Adjuvant
- Cyclophosphamide/administration & dosage
- Disease-Free Survival
- Doxorubicin/administration & dosage
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Middle Aged
- Neoplasm Recurrence, Local/drug therapy
- Neoplasm Recurrence, Local/immunology
- Neoplasm Recurrence, Local/mortality
- Neoplasm Recurrence, Local/pathology
- Paclitaxel/administration & dosage
- Receptor, ErbB-2/metabolism
- Survival Rate
- Trastuzumab/administration & dosage
- Young Adult
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Affiliation(s)
- Saranya Chumsri
- Division of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, Florida.
| | - Daniel J Serie
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, Florida
| | - Zhuo Li
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, Florida
| | - Katherine L Pogue-Geile
- National Surgical Adjuvant Breast and Bowel Project (now NRG Oncology), Pittsburgh, Pennsylvania
| | | | | | | | - Yanyan Lou
- Division of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, Florida
| | - Gerardo Colon-Otero
- Division of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, Florida
| | - Keith L Knutson
- Department of Immunology, Mayo Clinic, Jacksonville, Florida
| | - Edith A Perez
- Division of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, Florida
- Genentech Inc., South San Francisco, California
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103
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Discovery and Validation of Novel Biomarkers for Detection of Epithelial Ovarian Cancer. Cells 2019; 8:cells8070713. [PMID: 31336942 PMCID: PMC6678810 DOI: 10.3390/cells8070713] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/05/2019] [Accepted: 07/10/2019] [Indexed: 12/13/2022] Open
Abstract
Detection of epithelial ovarian cancer (EOC) poses a critical medical challenge. However, novel biomarkers for diagnosis remain to be discovered. Therefore, innovative approaches are of the utmost importance for patient outcome. Here, we present a concept for blood-based biomarker discovery, investigating both epithelial and specifically stromal compartments, which have been neglected in search for novel candidates. We queried gene expression profiles of EOC including microdissected epithelium and adjacent stroma from benign and malignant tumours. Genes significantly differentially expressed within either the epithelial or the stromal compartments were retrieved. The expression of genes whose products are secreted yet absent in the blood of healthy donors were validated in tissue and blood from patients with pelvic mass by NanoString analysis. Results were confirmed by the comprehensive gene expression database, CSIOVDB (Ovarian cancer database of Cancer Science Institute Singapore). The top 25% of candidate genes were explored for their biomarker potential, and twelve were able to discriminate between benign and malignant tumours on transcript levels (p < 0.05). Among them T-cell differentiation protein myelin and lymphocyte (MAL), aurora kinase A (AURKA), stroma-derived candidates versican (VCAN), and syndecan-3 (SDC), which performed significantly better than the recently reported biomarker fibroblast growth factor 18 (FGF18) to discern malignant from benign conditions. Furthermore, elevated MAL and AURKA expression levels correlated significantly with a poor prognosis. We identified promising novel candidates and found the stroma of EOC to be a suitable compartment for biomarker discovery.
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104
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Bustamante Eduardo M, Popovici V, Imboden S, Aebi S, Ballabio N, Altermatt HJ, Günthert A, Jaggi R. Characterization of molecular scores and gene expression signatures in primary breast cancer, local recurrences and brain metastases. BMC Cancer 2019; 19:549. [PMID: 31174485 PMCID: PMC6556009 DOI: 10.1186/s12885-019-5752-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/27/2019] [Indexed: 12/11/2022] Open
Abstract
Background Breast cancer is a leading cause of cancer-related death in women worldwide. Despite extensive studies in all areas of basic, clinical and applied research, accurate prognosis remains elusive, thus leading to overtreatment of many patients. Diagnosis could be improved by introducing multigene molecular scores in standard clinical practice. Several tests that work with formalin-fixed tissue have become routine. Molecular scores usually include several genes representing processes, response to oestrogens, progestogens and human epidermal growth factor receptor 2 (Her2), respectively, which are combined additively in single values. These multi-gene scores have the advantage of being more robust and reproducible than single-gene scores. Their utility may be further enhanced by combining them with classical diagnostic parameters. Here, we present an exploratory study comparing the RISK and research versions of Oncotype DX recurrence score (RS), Prosigna Risk of Recurrence (ROR) and EndoPredict (EP) with respect to their prognostic potential for ipsilateral recurrence and/or distant relapse in brain, and we compared the scores to the intrinsic subtypes based on PAM50. Methods RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue cores of primary tumours, local recurrences and brain metastases. Gene expression was measured on a NanoString nCounter Analysis System. Intrinsic subtypes and molecular scores were computed according to published literature and RISK, RS, ROR and EP were compared against each other and to the intrinsic subtypes Luminal A (lumA), Luminal B (lumB), Her2-enriched (Her2↑), Basal-like (basal), and Normal-like (normal) of PAM50. Local recurrences and brain metastases were compared to their corresponding primary tumours. Results All four molecular scores were highly correlated. Highest correlations were observed among genes related to proliferation while lower correlations were found among oestrogen-related genes. The scores were significantly higher in primary tumours progressing to brain metastases as compared to recurrence-free primary tumours and primary tumours that relapsed as local recurrences. Conclusions RISK and ROR-P are prognostic for primary tumours metastasizing to the brain. All four scores, RISK, RS, EP and ROR-P failed to discriminate between primary tumours that remained recurrence-free and primary tumours relapsing as local recurrences. Electronic supplementary material The online version of this article (10.1186/s12885-019-5752-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Vlad Popovici
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Sara Imboden
- Department of Gynecology and Obstetrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Stefan Aebi
- Department of Medical Oncology, Cantonal Hospital of Lucerne, Lucerne, Switzerland
| | | | | | | | - Rolf Jaggi
- Department for Biomedical Research, University of Bern, Murtenstrasse, 40, 3008, Bern, Switzerland.
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105
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Montalbo R, Lozano JJ, Izquierdo L, Ingelmo-Torres M, BaÑos C, Palou J, Van der Heijden AG, Medina R, Schmidbauer J, Prat A, Ribal MJ, Alcaraz A, Mengual L. Ability of a urine gene expression classifier to reduce the number of follow-up cystoscopies in bladder cancer patients. Transl Res 2019; 208:73-84. [PMID: 30771285 DOI: 10.1016/j.trsl.2019.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/18/2019] [Accepted: 02/04/2019] [Indexed: 11/28/2022]
Abstract
This study aimed to improve our previous urine gene expression classifiers focusing on the detection of non-high-risk non-muscle-invasive bladder cancer (NMIBC), and develop a new classifier able to decrease the frequency of cystoscopies during bladder cancer (BC) patients' surveillance. A total of 597 urines from BC patients, controls and patients in follow-up for BC (PFBC) were included. The study has 3 phases. In the urinary biomarker discovery phase, 84 urines from BC and control patients were retrospectively included and analyzed by Ribonucleic Acid (RNA) sequencing. In the classifier development phase, a total of 132 selected genes from previous phase were evaluated by nCounter in 214 prospectively collected urines from PFBC (98 with tumor). A diagnostic classifier was generated by logistic regression. Finally, in the classifier validation phase, a multicentric and international cohort of 248 urines (134 BC and 114 nonrecurrent PFBC) was used to validate classifier performance. A total of 521 genes were found differentially expressed between non-high-risk NMIBC samples and all other groups (P < 0.05). An 8-gene diagnostic classifier with an area under curve (AUC) of 0.893 was developed. Validation of this classifier in a cohort of PFBC achieved an overall sensitivity (SN) and a negative predictive value (NPV) of 96% and 97%, respectively (AUC = 0.823). Notably, this accuracy was maintained in non-high-risk NMIBC group (SN = 94%; NPV = 98%). In conclusion, this 8-gene expression classifier has high SN and NPV in a real clinical scenario. The use of this classifier can reduce the number of follow-up cystoscopies in PFBC, although assessing its final place in clinical setting is necessary.
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Affiliation(s)
- Ruth Montalbo
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | | | - Laura Izquierdo
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | - Mercedes Ingelmo-Torres
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | - Carmen BaÑos
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | - Joan Palou
- Department of Urology, Fundació Puigvert, Barcelona, Spain
| | | | - Rafael Medina
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Joerg Schmidbauer
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | - Aleix Prat
- Oncology Department, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Maria J Ribal
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | - Antonio Alcaraz
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | - Lourdes Mengual
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain.
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106
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Expression Concordance of 325 Novel RNA Biomarkers between Data Generated by NanoString nCounter and Affymetrix GeneChip. DISEASE MARKERS 2019; 2019:1940347. [PMID: 31217830 PMCID: PMC6536986 DOI: 10.1155/2019/1940347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 02/09/2019] [Accepted: 02/15/2019] [Indexed: 02/06/2023]
Abstract
Background With the development of new drug combinations and targeted treatments for multiple types of cancer, the ability to stratify categories of patient populations and to develop companion diagnostics has become increasingly important. A panel of 325 RNA biomarkers was selected based on cancer-related biological processes of healthy cells and gene expression changes over time during nonmalignant epithelial cell organization. This "cancer in reverse" approach resulted in a panel of biomarkers relevant for at least 7 cancer types, providing gene expression profiles representing key cellular signaling pathways beyond mutations in "driver genes." Objective. To further investigate this biomarker panel, the objective of the current study is to (1) validate the assay reproducibility for the 325 RNA biomarkers and (2) compare gene expression profiles side by side using two technology platforms. Methods and Results We have mapped the 325 RNA transcripts and in a custom NanoString nCounter expression panel to be compared to all potential probe sets in the Affymetrix Human Genome U133 Plus 2.0. The experiments were conducted with 10 unique biological formalin-fixed paraffin-embedded (FFPE) breast tumor samples. Each site extracted RNA from four sections of 10-micron thick FFPE tissue over three different days by two different operators using an optimized standard operating procedure and quality control criteria. Samples were analyzed using mas5 in BioConductor and NanoStringNorm in R. Pearson correlation showed reproducibility between sites for all 60 samples with r = 0.995 for Affymetrix and r = 0.999 for NanoString. Correlation in multiple days and multiple users was for Affymetrix r = (0.962 - 0.999) and for NanoString r = (0.982 - 0.991). Conclusion The 325 RNA biomarkers showed reproducibility in two technology platforms with moderate to high concordance. Future directions include performing clinical validation studies and generating rationale for patient selection in clinical trials using the technically validated assay.
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107
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Lindberg T, Forreryd A, Bergendorff O, Lindstedt M, Zeller KS. In vitro assessment of mechanistic events induced by structurally related chemical rubber sensitizers. Toxicol In Vitro 2019; 60:144-153. [PMID: 31082492 DOI: 10.1016/j.tiv.2019.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/30/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
Abstract
Allergic contact dermatitis (ACD) is one of the most common forms of immunotoxicity, and increased understanding of how chemicals trigger these adverse reactions is needed in order to treat or design testing strategies to identify and subsequently avoid exposure to such substances. In this study, we investigated the cellular response induced by rubber chemicals in a dendritic cell (DC) model, focusing on the structurally similar chemicals diethylthiocarbamylbenzothiazole sulfide and dimethylthiocarbamylbenzothiazole sulfide, with regard to regulation of microRNA, and messenger RNA expression. Only a few miRNAs were found to be commonly regulated by both rubber chemicals, among them miR1973, while the overall miRNA expression profiles were diverse. Similarly, out of approximately 500 differentially regulated transcripts for each chemical, about 60% overlapped, while remaining were unique. The pathways predicted to be enriched in the cell model by stimulation with the rubber chemicals were linked to immunological events, relevant in the context of ACD. These results suggest that small structural differences can trigger specific activation of the immune system in response to chemicals. The here presented mechanistic data can be valuable in explaining the immunotoxicological events in DC activation after exposure to skin sensitizing chemicals, and can contribute to understanding, preventing and treating ACD.
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Affiliation(s)
- Tim Lindberg
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
| | - Andy Forreryd
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
| | - Ola Bergendorff
- Department of Occupational and Environmental Dermatology, Skåne University Hospital, Lund University, 20502 Malmö, Sweden.
| | - Malin Lindstedt
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
| | - Kathrin S Zeller
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
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108
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Kim EN, Kim CJ, Kim SR, Song JA, Choe H, Kim KB, Choi JS, Oh SJ. High serum CRP influences myocardial miRNA profiles in ischemia-reperfusion injury of rat heart. PLoS One 2019; 14:e0216610. [PMID: 31063484 PMCID: PMC6504103 DOI: 10.1371/journal.pone.0216610] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 04/24/2019] [Indexed: 11/25/2022] Open
Abstract
Objective Prognosis of myocardial infarction tends to be worse when serum C-reactive protein (CRP) level is high. miRNAs are also known to be involved in different pathogeneses of heart diseases such as myocardial infarction. However, how CRP is involved in myocardial infarction has not been fully elucidated. We hypothesized that serum CRP changes the miRNA profile during ischemia-reperfusion injury (IRI) of the myocardium. To confirm this hypothesis, we performed global miRNA expression profiling of myocardium using IRI and CRP infusion rat model. Methods After ligation of the coronary artery of rat hearts, human serum CRP was intravenously injected, and reperfusion was performed (I/R+CRP group, n = 6). Control group consisted of the sham group (n = 3), IV CRP infusion group (CRP only, n = 3), and the I/R-only group (I/R only, n = 5). We evaluated 423 miRNA expression in non-ischemic areas and areas at risk (AAR) of each group using NanoString nCounter miRNA expression assay. Results MiR-124 was downregulated in non-ischemic myocardium in CRP-only group. In AAR, 7 miRNAs were commonly upregulated in both I/R-only and I/R+CRP groups. And additional 6 miRNAs were upregulated in the I/R+CRP group (miR-33, miR-409-3p, miR-384-3p, miR-3562, miR-101a, and miR-340-5p). Similarly, in the non-ischemic areas, 6 miRNAs were commonly upregulated in both I/R-only and I/R+CRP groups, and additional 5 miRNAs changed in the I/R+CRP group (upregulation of miR-3559-5p, miR-499, and miR-21 and downregulation of miR-500 and miR-532-3p). Conclusion We showed that when serum CRP level is high, IRI results in multiple miRNA profile changes not only in ischemic areas but also in non-ischemic myocardium. Our results may provide a strong basis for studying the role of CRP and miRNAs in ischemic heart disease.
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Affiliation(s)
- Eun Na Kim
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
- Asan Laboratory of Perinatal Science, Asan Medical Center, Seoul, Republic of Korea
| | - Chong Jai Kim
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
- Asan Laboratory of Perinatal Science, Asan Medical Center, Seoul, Republic of Korea
| | - So Ra Kim
- Asan Laboratory of Perinatal Science, Asan Medical Center, Seoul, Republic of Korea
| | - Jung-A. Song
- Department of Physiology, Asan-Minnesota Institute for Innovating Transplantation, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Han Choe
- Department of Physiology, Asan-Minnesota Institute for Innovating Transplantation, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Ki-Bong Kim
- Department of Thoracic and Cardiovascular Surgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jae-Sung Choi
- Department of Thoracic and Cardiovascular Surgery, Seoul National University College of Medicine, SMG-SNU Boramae Medical Center, Seoul, Republic of Korea
| | - Se Jin Oh
- Department of Thoracic and Cardiovascular Surgery, Seoul National University College of Medicine, SMG-SNU Boramae Medical Center, Seoul, Republic of Korea
- * E-mail:
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109
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Navas-Delgado I, García-Nieto J, López-Camacho E, Rybinski M, Lavado R, Berciano Guerrero MÁ, Aldana-Montes JF. VIGLA-M: visual gene expression data analytics. BMC Bioinformatics 2019; 20:150. [PMID: 30999846 PMCID: PMC6472185 DOI: 10.1186/s12859-019-2695-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background The analysis of gene expression levels is used in many clinical studies to know how patients evolve or to find new genetic biomarkers that could help in clinical decision making. However, the techniques and software available for these analyses are not intended for physicians, but for geneticists. However, enabling physicians to make initial discoveries on these data would benefit in the clinical assay development. Results Melanoma is a highly immunogenic tumor. Therefore, in recent years physicians have incorporated immune system altering drugs into their therapeutic arsenal against this disease, revolutionizing the treatment of patients with an advanced stage of the cancer. This has led us to explore and deepen our knowledge of the immunology surrounding melanoma, in order to optimize the approach. Within this project we have developed a database for collecting relevant clinical information for melanoma patients, including the storage of patient gene expression levels obtained from the NanoString platform (several samples are taken from each patient). The Immune Profiling Panel is used in this case. This database is being exploited through the analysis of the different expression profiles of the patients. This analysis is being done with Python, and a parallel version of the algorithms is available with Apache Spark to provide scalability as needed. Conclusions VIGLA-M, the visual analysis tool for gene expression levels in melanoma patients is available at http://khaos.uma.es/melanoma/. The platform with real clinical data can be accessed with a demo user account, physician, using password physician_test_7634 (if you encounter any problems, contact us at this email address: mailto: khaos@lcc.uma.es). The initial results of the analysis of gene expression levels using these tools are providing first insights into the patients’ evolution. These results are promising, but larger scale tests must be developed once new patients have been sequenced, to discover new genetic biomarkers.
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Affiliation(s)
- Ismael Navas-Delgado
- Khaos Research, Universidad de Málaga, Málaga, Spain, Arquitecto Francisco Peñalosa 18, Málaga, 29071, Spain.
| | - José García-Nieto
- Khaos Research, Universidad de Málaga, Málaga, Spain, Arquitecto Francisco Peñalosa 18, Málaga, 29071, Spain
| | - Esteban López-Camacho
- Khaos Research, Universidad de Málaga, Málaga, Spain, Arquitecto Francisco Peñalosa 18, Málaga, 29071, Spain
| | - Maciej Rybinski
- Khaos Research, Universidad de Málaga, Málaga, Spain, Arquitecto Francisco Peñalosa 18, Málaga, 29071, Spain
| | - Rocio Lavado
- Unidad de Oncología Intercentros, Hospitales Univesitarios Regional y Virgen de la Victoria de Málaga, Instituto de Investigaciones Biomédicas (IBIMA), Málaga, Spain, Málaga, Spain
| | - Miguel Ángel Berciano Guerrero
- Unidad de Oncología Intercentros, Hospitales Univesitarios Regional y Virgen de la Victoria de Málaga, Instituto de Investigaciones Biomédicas (IBIMA), Málaga, Spain, Málaga, Spain
| | - José F Aldana-Montes
- Khaos Research, Universidad de Málaga, Málaga, Spain, Arquitecto Francisco Peñalosa 18, Málaga, 29071, Spain
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Cammarata I, Martire C, Citro A, Raimondo D, Fruci D, Melaiu O, D'Oria V, Carone C, Peruzzi G, Cerboni C, Santoni A, Sidney J, Sette A, Paroli M, Caccavale R, Milanetti E, Riminucci M, Timperi E, Piconese S, Manzo A, Montecucco C, Scrivo R, Valesini G, Cariani E, Barnaba V. Counter-regulation of regulatory T cells by autoreactive CD8 + T cells in rheumatoid arthritis. J Autoimmun 2019; 99:81-97. [PMID: 30777378 DOI: 10.1016/j.jaut.2019.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 12/21/2022]
Abstract
The mechanisms whereby autoreactive T cells escape peripheral tolerance establishing thus autoimmune diseases in humans remain an unresolved question. Here, we demonstrate that autoreactive polyfunctional CD8+ T cells recognizing self-antigens (i.e., vimentin, actin cytoplasmic 1, or non-muscle myosin heavy chain 9 epitopes) with high avidity, counter-regulate Tregs by killing them, in a consistent percentage of rheumatoid arthritis (RA) patients. Indeed, these CD8+ T cells express a phenotype and gene profile of effector (eff) cells and, upon antigen-specific activation, kill Tregs indirectly in an NKG2D-dependent bystander fashion in vitro. This data provides a mechanistic basis for the finding showing that AE-specific (CD107a+) CD8+ T killer cells correlate, directly with the disease activity score, and inversely with the percentage of activated Tregs, in both steady state and follow-up studies in vivo. In addition, multiplex immunofluorescence imaging analyses of inflamed synovial tissues in vivo show that a remarkable number of CD8+ T cells express granzyme-B and selectively contact FOXP3+ Tregs, some of which are in an apoptotic state, validating hence the possibility that CD8+ Teff cells can counteract neighboring Tregs within inflamed tissues, by killing them. Alternatively, the disease activity score of a different subset of patients is correlated with the expansion of a peculiar subpopulation of autoreactive low avidity, partially-activated (pa)CD8+ T cells that, despite they conserve the conventional naïve (N) phenotype, produce high levels of tumor necrosis factor (TNF)-α and exhibit a gene expression signature of a progressive activation state. Tregs directly correlate with the expansion of this autoreactive (low avidity) paCD8+ TN cell subset in vivo, and efficiently control their differentiation rather their proliferation in vitro. Interestingly, autoreactive high avidity CD8+ Teff cells or low avidity paCD8+ TN cells are significantly expanded in RA patients who would become non-responders or patients who would become responders to TNF-α inhibitor therapy, respectively. These data provide evidence of a previously undescribed role of such mechanisms in the progression and therapy of RA.
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Affiliation(s)
- Ilenia Cammarata
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, 00161, Rome, Italy
| | - Carmela Martire
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, 00161, Rome, Italy
| | - Alessandra Citro
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, 00161, Rome, Italy
| | - Domenico Raimondo
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161, Rome, Italy
| | - Doriana Fruci
- Dipartimento di Ematologia/Oncologia, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy
| | - Ombretta Melaiu
- Dipartimento di Ematologia/Oncologia, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy; Dipartimento di Biologia, Università di Pisa, 56126, Pisa, Italy
| | - Valentina D'Oria
- Core Facility Research Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165, Rome, Italy
| | - Chiara Carone
- Ospedale Civile S. Agostino-Estense, 41126, Modena, Italy
| | - Giovanna Peruzzi
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161, Rome, Italy
| | - Cristina Cerboni
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161, Rome, Italy; Istituto Pasteur - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - Angela Santoni
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161, Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161, Rome, Italy; Istituto Pasteur - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, San Diego, CA, 92121, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, San Diego, CA, 92121, USA
| | - Marino Paroli
- Dipartimento di Scienze e Biotecnologie Medico-Chirurgiche, Sapienza Università di Roma, Polo Pontino, 04100, Latina, Italy
| | - Rosalba Caccavale
- Dipartimento di Scienze e Biotecnologie Medico-Chirurgiche, Sapienza Università di Roma, Polo Pontino, 04100, Latina, Italy
| | - Edoardo Milanetti
- Dipartimento di Fisica, Sapienza Università di Roma, 00185, Rome, Italy
| | - Mara Riminucci
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161, Rome, Italy
| | - Eleonora Timperi
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, 00161, Rome, Italy
| | - Silvia Piconese
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, 00161, Rome, Italy; Istituto Pasteur - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - Antonio Manzo
- Dipartimento di Medicina Interna e Terapia Medica, Fondazione IRCCS Policlinico "San Matteo", Università di Pavia, 27100, Pavia, Italy
| | - Carlomaurizio Montecucco
- Dipartimento di Medicina Interna e Terapia Medica, Fondazione IRCCS Policlinico "San Matteo", Università di Pavia, 27100, Pavia, Italy
| | - Rossana Scrivo
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, 00161, Rome, Italy
| | - Guido Valesini
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, 00161, Rome, Italy
| | | | - Vincenzo Barnaba
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, 00161, Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161, Rome, Italy; Istituto Pasteur - Fondazione Cenci Bolognetti, 00185, Rome, Italy.
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111
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Porsch M, Özdemir E, Wisniewski M, Graf S, Bull F, Hoffmann K, Ignatov A, Haybaeck J, Grosse I, Kalinski T, Nass N. Time resolved gene expression analysis during tamoxifen adaption of MCF-7 cells identifies long non-coding RNAs with prognostic impact. RNA Biol 2019; 16:661-674. [PMID: 30760083 DOI: 10.1080/15476286.2019.1581597] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Acquired tamoxifen resistance is a persistent problem for the treatment of estrogen receptor positive, premenopausal breast cancer patients and predictive biomarkers are still elusive. We here analyzed gene expression changes in a cellular model to identify early and late changes upon tamoxifen exposure and thereby novel prognostic biomarkers. Estrogen receptor positive MCF-7 cells were incubated with 4OH-tamoxifen (10 nM) and gene expression analyzed by array hybridization during 12 weeks. Array results were confirmed by nCounter- and qRT-PCR technique. Pathway enrichment analysis revealed that early responses concerned mainly amine synthesis and NRF2-related signaling and evolved into a stable gene expression pattern within 4 weeks characterized by changes in glucuronidation-, estrogen metabolism-, nuclear receptor- and interferon signaling pathways. As a large number of long non coding RNAs was subject to regulation, we investigated 5 of these (linc01213, linc00632 linc0992, LOC101929547 and XR_133213) in more detail. From these, only linc01213 was upregulated but all were less abundant in estrogen-receptor negative cell lines (MDA-MB 231, SKBR-3 and UACC3199). In a web-based survival analysis linc01213 and linc00632 turned out to have prognostic impact. Linc01213 was investigated further by plasmid-mediated over-expression as well as siRNA down-regulation in MCF-7 cells. Nevertheless, this had no effect on proliferation or expression of tamoxifen regulated genes, but migration was increased. In conclusion, the cellular model identified a set of lincRNAs with prognostic relevance for breast cancer. One of these, linc01213 although regulated by 4OH-tamoxifen, is not a central regulator of tamoxifen adaption, but interferes with the regulation of migration.
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Affiliation(s)
- Martin Porsch
- a Insitute of Computer Science , Martin Luther University Halle-Wittenberg , Halle , Germany.,b Institute of Human Genetics , Martin Luther University Halle-Wittenberg , Halle , Germany.,c German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Leipzig , Germany
| | - Esra Özdemir
- d Institute of Pathology, Otto von Guericke University Magdeburg , Magdeburg , Germany
| | - Martin Wisniewski
- d Institute of Pathology, Otto von Guericke University Magdeburg , Magdeburg , Germany
| | - Sebastian Graf
- a Insitute of Computer Science , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Fabian Bull
- a Insitute of Computer Science , Martin Luther University Halle-Wittenberg , Halle , Germany.,b Institute of Human Genetics , Martin Luther University Halle-Wittenberg , Halle , Germany.,c German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Leipzig , Germany
| | - Katrin Hoffmann
- b Institute of Human Genetics , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Atanas Ignatov
- e Department of Obstetrics and Gynecology , Otto von Guericke University Magdeburg , Magdeburg , Germany
| | - Johannes Haybaeck
- d Institute of Pathology, Otto von Guericke University Magdeburg , Magdeburg , Germany.,f Diagnostic and Research Institute of Pathology , Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz , Graz , Austria.,g Department of Pathology , Medical University of Innsbruck , Innsbruck , Austria
| | - Ivo Grosse
- a Insitute of Computer Science , Martin Luther University Halle-Wittenberg , Halle , Germany.,c German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Leipzig , Germany
| | - Thomas Kalinski
- d Institute of Pathology, Otto von Guericke University Magdeburg , Magdeburg , Germany
| | - Norbert Nass
- d Institute of Pathology, Otto von Guericke University Magdeburg , Magdeburg , Germany
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112
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Mantere O, Trontti K, García-González J, Balcells I, Saarnio S, Mäntylä T, Lindgren M, Kieseppä T, Raij T, Honkanen JK, Vaarala O, Hovatta I, Suvisaari J. Immunomodulatory effects of antipsychotic treatment on gene expression in first-episode psychosis. J Psychiatr Res 2019; 109:18-26. [PMID: 30463035 DOI: 10.1016/j.jpsychires.2018.11.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/25/2018] [Accepted: 11/05/2018] [Indexed: 12/27/2022]
Abstract
Previous studies suggest immunological alterations in patients with first-episode psychosis (FEP). Some studies show that antipsychotic compounds may cause immunomodulatory effects. To evaluate the immunological changes and the possible immunomodulatory effects in FEP, we recruited patients with FEP (n = 67) and matched controls (n = 38), aged 18-40 years, from the catchment area of the Helsinki University Hospital and the City of Helsinki, Finland. Fasting peripheral blood samples were collected between 8 and 10 a.m. in 10 ml PAXgene tubes. We applied the NanoString nCounter in-solution hybridization technology to determine gene expression levels of 147 candidate genes reflecting activation of the immune system. Cases had higher gene expression levels of BDKRB1 and SPP1/osteopontin compared with controls. Of the individual medications used as monotherapy, risperidone was associated with a statistically significant upregulation of 11 immune system genes, including cytokines and cytokine receptors (SPP1, IL1R1, IL1R2), pattern recognition molecules (TLR1, TLR2 and TLR6, dectin-1/CLEC7A), molecules involved in apoptosis (FAS), and some other molecules with functions in immune activation (BDKRB1, IGF1R, CR1). In conclusion, risperidone possessed strong immunomodulatory properties affecting mainly innate immune response in FEP patients, whereas the observed effects of quetiapine and olanzapine were only marginal. Our results further emphasize the importance of understanding the immunomodulatory mechanisms of antipsychotic treatment, especially in terms of specific compounds, doses and duration of medication in patients with severe mental illness. Future studies should evaluate the response pre- and post-treatment, and the possible role of this inflammatory activation for the progression of psychiatric and metabolic symptoms.
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Affiliation(s)
- Outi Mantere
- Department of Psychiatry, McGill University, Montréal, QC, Canada; Bipolar Disorders Clinic, Douglas Mental Health University Institute, 6875, LaSalle Boulevard Montreal, Quebec, H4H 1R3, Montréal, QC, Canada.
| | - Kalevi Trontti
- Molecular and Integrative Biosciences Research Program, P.O. Box 56, FI-00014, University of Helsinki, Finland
| | - Judit García-González
- Molecular and Integrative Biosciences Research Program, P.O. Box 56, FI-00014, University of Helsinki, Finland
| | - Ingrid Balcells
- Molecular and Integrative Biosciences Research Program, P.O. Box 56, FI-00014, University of Helsinki, Finland
| | - Suvi Saarnio
- Molecular and Integrative Biosciences Research Program, P.O. Box 56, FI-00014, University of Helsinki, Finland
| | - Teemu Mäntylä
- Department of Neuroscience and Biomedical Engineering, and Advanced Magnetic Imaging Center, Aalto NeuroImaging, P.O. Box 12200, FI-00076, Aalto University School of Science, Finland; Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland; Mental Health Unit, National Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland
| | - Maija Lindgren
- Mental Health Unit, National Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland
| | - Tuula Kieseppä
- Department of Psychiatry, Helsinki University and Helsinki University Hospital, P.O. Box 590, FI-00029 HUS, Finland
| | - Tuukka Raij
- Department of Neuroscience and Biomedical Engineering, and Advanced Magnetic Imaging Center, Aalto NeuroImaging, P.O. Box 12200, FI-00076, Aalto University School of Science, Finland; Department of Psychiatry, Helsinki University and Helsinki University Hospital, P.O. Box 590, FI-00029 HUS, Finland
| | - Jarno K Honkanen
- Clinicum, P.O. Box 21, FI-00014, University of Helsinki, Finland
| | - Outi Vaarala
- Clinicum, P.O. Box 21, FI-00014, University of Helsinki, Finland
| | - Iiris Hovatta
- Molecular and Integrative Biosciences Research Program, P.O. Box 56, FI-00014, University of Helsinki, Finland
| | - Jaana Suvisaari
- Mental Health Unit, National Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland
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113
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P'ng C, Green J, Chong LC, Waggott D, Prokopec SD, Shamsi M, Nguyen F, Mak DYF, Lam F, Albuquerque MA, Wu Y, Jung EH, Starmans MHW, Chan-Seng-Yue MA, Yao CQ, Liang B, Lalonde E, Haider S, Simone NA, Sendorek D, Chu KC, Moon NC, Fox NS, Grzadkowski MR, Harding NJ, Fung C, Murdoch AR, Houlahan KE, Wang J, Garcia DR, de Borja R, Sun RX, Lin X, Chen GM, Lu A, Shiah YJ, Zia A, Kearns R, Boutros PC. BPG: Seamless, automated and interactive visualization of scientific data. BMC Bioinformatics 2019; 20:42. [PMID: 30665349 PMCID: PMC6341661 DOI: 10.1186/s12859-019-2610-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 01/04/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND We introduce BPG, a framework for generating publication-quality, highly-customizable plots in the R statistical environment. RESULTS This open-source package includes multiple methods of displaying high-dimensional datasets and facilitates generation of complex multi-panel figures, making it suitable for complex datasets. A web-based interactive tool allows online figure customization, from which R code can be downloaded for integration with computational pipelines. CONCLUSION BPG provides a new approach for linking interactive and scripted data visualization and is available at http://labs.oicr.on.ca/boutros-lab/software/bpg or via CRAN at https://cran.r-project.org/web/packages/BoutrosLab.plotting.general.
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Affiliation(s)
| | - Jeffrey Green
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Daryl Waggott
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | | | | | | | - Felix Lam
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Ying Wu
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Esther H Jung
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | | | - Cindy Q Yao
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Bianca Liang
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Emilie Lalonde
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Syed Haider
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | | | - Kenneth C Chu
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Natalie S Fox
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | | | | | - Clement Fung
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Kathleen E Houlahan
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Jianxin Wang
- Ontario Institute for Cancer Research, Toronto, Canada.,Present address: Center for Computational Research, Buffalo Institute for Genomics and Data Analytics, NYS Center for Excellence in Bioinformatics & Life Science, University at Buffalo, Buffalo, USA
| | | | | | - Ren X Sun
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Xihui Lin
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Aileen Lu
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Amin Zia
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Ryan Kearns
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada. .,Department of Human Genetics, University of California, Los Angeles, USA. .,Department of Urology, University of California, Los Angeles, USA. .,Institute for Precision Health, University of California, Los Angeles, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA.
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114
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Cannataro R, Perri M, Gallelli L, Caroleo MC, De Sarro G, Cione E. Ketogenic Diet Acts on Body Remodeling and MicroRNAs Expression Profile. Microrna 2019; 8:116-126. [PMID: 30474543 DOI: 10.2174/2211536608666181126093903] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/18/2018] [Accepted: 11/16/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND The Ketogenic Diet (KD) promotes metabolic changes and optimizes energy metabolism. It is unknown if microRNAs (miRs) are influenced by KD in obese subjects. The screening of circulating miRs was performed with the FDA approved platform n-counter flex and blood biochemical parameters were dosed by ADVIA 1800. OBJECTIVES The aim of this study was to evaluate mir profile under 6 weeks of biphasic KD in obese subjects. We enrolled 36 obese subjects (18 females and 18 males) in stage 1 of Edmonton Obesity Staging System (EOSS) parameter. RESULT Any correlation was found between biochemical parameter and three miRs, hsa-let-7b-5p, hsa-miR-143-3p and hsa-miR-504-5p influenced in an equal manner in both sexes. The KD resulted safe and ameliorate both biochemical and anthropometric factors in obese subjects re-collocating them into stage 0 of EOSS parameters. CONCLUSION The miRs herein identified under KD might be a useful tool to monitor low carbohydrate nutritional regimens which reflect indirectly the regulatory biochemical mechanisms and cell signaling that orchestrate metabolic and signaling pathways.
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Affiliation(s)
- Roberto Cannataro
- GalaScreen SRL, Department of Pharmacy Health and Nutritional Sciences, University of Calabria, Via Savinio, Edificio Polifunzionale, 87036 Rende (CS), Italy
| | - Mariarita Perri
- GalaScreen SRL, Department of Pharmacy Health and Nutritional Sciences, University of Calabria, Via Savinio, Edificio Polifunzionale, 87036 Rende (CS), Italy
| | - Luca Gallelli
- Department of Health Sciences, University of Magna Graecia, Via Venuta Germaneto, 88100 Catanzaro, Italy
| | - Maria Cristina Caroleo
- Department of Pharmacy Health and Nutritional Sciences, University of Calabria, Via Savinio, Edificio Polifunzionale, 87036 Rende (CS), Italy
| | - Giovambattista De Sarro
- Department of Health Sciences, University of Magna Graecia, Via Venuta Germaneto, 88100 Catanzaro, Italy
| | - Erika Cione
- Department of Pharmacy Health and Nutritional Sciences, University of Calabria, Via Savinio, Edificio Polifunzionale, 87036 Rende (CS), Italy
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115
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Sendorek DH, Lalonde E, Yao CQ, Sabelnykova VY, Bristow RG, Boutros PC. NanoStringNormCNV: pre-processing of NanoString CNV data. Bioinformatics 2019; 34:1034-1036. [PMID: 29112706 DOI: 10.1093/bioinformatics/btx707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/02/2017] [Indexed: 11/14/2022] Open
Abstract
Summary The NanoString System is a well-established technology for measuring RNA and DNA abundance. Although it can estimate copy number variation, relatively few tools support analysis of these data. To address this gap, we created NanoStringNormCNV, an R package for pre-processing and copy number variant calling from NanoString data. This package implements algorithms for pre-processing, quality-control, normalization and copy number variation detection. A series of reporting and data visualization methods support exploratory analyses. To demonstrate its utility, we apply it to a new dataset of 96 genes profiled on 41 prostate tumour and 24 matched normal samples. Availability and implementation NanoStringNormCNV is implemented in R and is freely available at http://labs.oicr.on.ca/boutros-lab/software/nanostringnormcnv. Contact paul.boutros@oicr.on.ca. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dorota H Sendorek
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research
| | - Emilie Lalonde
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research.,Department of Medical Biophysics, University of Toronto
| | - Cindy Q Yao
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research
| | | | - Robert G Bristow
- Department of Medical Biophysics, University of Toronto.,Princess Margaret Cancer Centre, University Health Network
| | - Paul C Boutros
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research.,Department of Medical Biophysics, University of Toronto.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
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116
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Feng S, Bucuvalas JC, Demetris AJ, Burrell BE, Spain KM, Kanaparthi S, Magee JC, Ikle D, Lesniak A, Lozano JJ, Alonso EM, Bray RA, Bridges NE, Doo E, Gebel HM, Gupta NA, Himes RW, Jackson AM, Lobritto SJ, Mazariegos GV, Ng VL, Rand EB, Sherker AH, Sundaram S, Turmelle YP, Sanchez-Fueyo A. Evidence of Chronic Allograft Injury in Liver Biopsies From Long-term Pediatric Recipients of Liver Transplants. Gastroenterology 2018; 155:1838-1851.e7. [PMID: 30144432 PMCID: PMC6279538 DOI: 10.1053/j.gastro.2018.08.023] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 07/26/2018] [Accepted: 08/08/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS A substantial proportion of pediatric liver transplant recipients develop subclinical chronic allograft injury. We studied whether there are distinct patterns of injury based on histopathologic features and identified associated immunologic profiles. METHODS We conducted a cross-sectional study of 157 stable, long-term pediatric recipients of transplanted livers (70 boys; > 6 years old at time of transplantation; mean, 8.9 ± 3.46 years after liver transplantation) who underwent liver biopsy analysis from August 13, 2012, through May 1, 2014. Participants had received livers from a living or deceased donor and had consistently normal results from liver tests. Liver biopsy specimens were scored by a central pathologist; an unsupervised hierarchical cluster analysis of histologic features was used to sort biopsy samples into 3 clusters. We conducted transcriptional and cytometric analyses of liver tissue samples and performed a systems biology analysis that incorporated clinical, serologic, histologic, and transcriptional data. RESULTS The mean level of alanine aminotransferase in participants was 27.6 ± 14.57 U/L, and the mean level of γ-glutamyl transferase was 17.4 ± 7.93 U/L. Cluster 1 was characterized by interface activity (n = 34), cluster 2 was characterized by periportal or perivenular fibrosis without interface activity (n = 45), and cluster 3 had neither feature (n = 78). We identified a module of genes whose expression correlated with levels of alanine aminotransferase, class II donor-specific antibody, portal inflammation, interface activity, perivenular inflammation, portal and perivenular fibrosis, and cluster assignment. The module was enriched in genes that regulate T-cell-mediated rejection (TCMR) of liver and other transplanted organs. Functional pathway analysis showed overrepresentation of TCMR gene sets for cluster 1 but not clusters 2 or 3. CONCLUSION In an analysis of biopsies from an apparently homogeneous group of stable, long-term pediatric liver transplant recipients with consistently normal liver test results, we found evidence of chronic graft injury (inflammation and/or fibrosis). Biopsy samples with interface activity had a gene expression pattern associated with TCMR.
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Affiliation(s)
- Sandy Feng
- Division of Transplantation, Department of Surgery, University of California San Francisco, San Francisco, California.
| | - John C. Bucuvalas
- Pediatric Liver Care Center, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | | | | | | | | | - John C. Magee
- Section of Transplant Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | | | - Andrew Lesniak
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - Juan J. Lozano
- Biomedical Research Center in Hepatic and Digestive Diseases, Carlos III Health Institute, Barcelona, Spain
| | - Estella M. Alonso
- Siragusa Transplantation Center, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL
| | - Robert A. Bray
- Department of Pathology, Emory University Hospital, Atlanta, GA
| | - Nancy E. Bridges
- Transplantation Branch; Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Edward Doo
- Division of Digestive Diseases and Nutrition, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD; Department of Pathology, Emory University Hospital, Atlanta, GA
| | - Howard M. Gebel
- Department of Pathology, Emory University Hospital, Atlanta, GA
| | - Nitika A. Gupta
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Ryan W. Himes
- Section of Gastroenterology, Hepatology, and Nutrition, Texas Children’s Hospital, Houston, TX
| | - Annette M. Jackson
- Division of Immunogenetics and Transplantation Immunology, Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - Steven J. Lobritto
- Center for Liver Diseases and Transplantation, Department of Surgery, Columbia University Medical Center, New York, NY
| | - George V. Mazariegos
- Hillman Center for Pediatric Transplantation, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA
| | - Vicky L. Ng
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Transplant and Regenerative Medicine Center, Toronto, Ontario, Canada
| | - Elizabeth B. Rand
- Liver Transplant Program, The Children’s Hospital of Pennsylvania, Philadelphia, PA
| | - Averell H. Sherker
- Siragusa Transplantation Center, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL
| | - Shikha Sundaram
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, CO
| | - Yumirle P. Turmelle
- Division of Gastroenterology, Hepatology, and Nutrition, St. Louis Children’s Hospital, St. Louis, MO
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117
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Paulose JK, Cassone CV, Cassone VM. Aging, melatonin biosynthesis, and circadian clockworks in the gastrointestinal system of the laboratory mouse. Physiol Genomics 2018; 51:1-9. [PMID: 30444453 DOI: 10.1152/physiolgenomics.00095.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The gastrointestinal (GI) system is vital in its capacities for nutrient and water uptake, immune function, metabolism and detoxification, and stem-cell derived regeneration. Of significance to human health are a myriad of GI disorders associated with aging that integrate with the circadian clock. Here we present data from three groups of mice: young (3 mo old), middle aged (12 mo old), and old aged (24 mo old). Small intestine and colon samples taken every 4 h under light-dark (LD) conditions were assayed for gene expression related to molecular circadian rhythmicity, transcription, cell signaling, and immune function. Transcripts related to melatonin biosynthesis and signaling, as well as melatonin content from stool, were also included, as GI melatonin and aging have been associated in contexts outside of the circadian clock. With respect to circadian genes, the data here are congruent with data from other peripheral tissues: age does not affect the rhythmic expression of core clock genes in the gut. The same can be said for several clock-controlled transcripts. In contrast, diurnal patterns in the expression of nitric oxide synthase 1 and of immune factors irak4 and interleukin-8 were observed in the colon of young mice that were lost in middle-aged and aged animals. Furthermore, the diurnal pattern of melatonin synthesis genes was altered by age, and stool melatonin levels showed significant decline between young mice and aged cohorts. These data expand the evidence for the persistence of the circadian clock throughout the aging process and highlight its importance to health.
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Affiliation(s)
- Jiffin K Paulose
- Department of Biology, University of Kentucky , Lexington, Kentucky
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118
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Haider S, Yao CQ, Sabine VS, Grzadkowski M, Stimper V, Starmans MHW, Wang J, Nguyen F, Moon NC, Lin X, Drake C, Crozier CA, Brookes CL, van de Velde CJH, Hasenburg A, Kieback DG, Markopoulos CJ, Dirix LY, Seynaeve C, Rea DW, Kasprzyk A, Lambin P, Lio' P, Bartlett JMS, Boutros PC. Pathway-based subnetworks enable cross-disease biomarker discovery. Nat Commun 2018; 9:4746. [PMID: 30420699 PMCID: PMC6232113 DOI: 10.1038/s41467-018-07021-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/29/2018] [Indexed: 11/29/2022] Open
Abstract
Biomarkers lie at the heart of precision medicine. Surprisingly, while rapid genomic profiling is becoming ubiquitous, the development of biomarkers usually involves the application of bespoke techniques that cannot be directly applied to other datasets. There is an urgent need for a systematic methodology to create biologically-interpretable molecular models that robustly predict key phenotypes. Here we present SIMMS (Subnetwork Integration for Multi-Modal Signatures): an algorithm that fragments pathways into functional modules and uses these to predict phenotypes. We apply SIMMS to multiple data types across five diseases, and in each it reproducibly identifies known and novel subtypes, and makes superior predictions to the best bespoke approaches. To demonstrate its ability on a new dataset, we profile 33 genes/nodes of the PI3K pathway in 1734 FFPE breast tumors and create a four-subnetwork prediction model. This model out-performs a clinically-validated molecular test in an independent cohort of 1742 patients. SIMMS is generic and enables systematic data integration for robust biomarker discovery.
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Affiliation(s)
- Syed Haider
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada.
- Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, United Kingdom.
| | - Cindy Q Yao
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
- Diagnostic Development Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Vicky S Sabine
- Diagnostic Development Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Michal Grzadkowski
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Vincent Stimper
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Maud H W Starmans
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
- Department of Radiation Oncology (Maastro), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jianxin Wang
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Francis Nguyen
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Nathalie C Moon
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Xihui Lin
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Camilla Drake
- Diagnostic Development Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Cheryl A Crozier
- Diagnostic Development Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Cassandra L Brookes
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | | | | | | | | | | | | | - Daniel W Rea
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Arek Kasprzyk
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Philippe Lambin
- Department of Radiation Oncology (Maastro), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Pietro Lio'
- Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, United Kingdom
| | - John M S Bartlett
- Diagnostic Development Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada.
| | - Paul C Boutros
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, M5S 1A8, Canada.
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119
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Fukutani KF, Nascimento-Carvalho CM, Bouzas ML, Oliveira JR, Barral A, Dierckx T, Khouri R, Nakaya HI, Andrade BB, Van Weyenbergh J, de Oliveira CI. In situ Immune Signatures and Microbial Load at the Nasopharyngeal Interface in Children With Acute Respiratory Infection. Front Microbiol 2018; 9:2475. [PMID: 30473680 PMCID: PMC6238668 DOI: 10.3389/fmicb.2018.02475] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022] Open
Abstract
Acute respiratory infection (ARI) is the most frequent cause for hospitalization in infants and young children. Using multiplexed nCounter technology to digitally quantify 600 human mRNAs in parallel with 14 virus- and 5 bacterium-specific RNAs, we characterized viral and bacterial presence in nasopharyngeal aspirates (NPA) of 58 children with ARI and determined the corresponding in situ immune profiles. NPA contained different groups of organisms and these were classified into bacterial (n = 27), viral (n = 5), codetection [containing both viral and bacterial transcripts (n = 21), or indeterminate intermediate where microbial load is below threshold (n = 5)]. We then identified differentially expressed immune transcripts (DEITs) comparing NPAs from symptomatic children vs. healthy controls, and comparing children presenting NPAs with detectable microbial load vs. indeterminate. We observed a strong innate immune response in NPAs, due to the presence of evolutionarily conserved type I Interferon (IFN)-stimulated genes (ISG), which was correlated with total bacterial and/or viral load. In comparison with indeterminate NPAs, adaptive immunity transcripts discriminated among viral, bacterial, and codetected microbial profiles. In viral NPAs, B cell transcripts were significantly enriched among DEITs, while only type III IFN was correlated with viral load. In bacterial NPAs, myeloid cells and coinhibitory transcripts were enriched and significantly correlated with bacterial load. In conclusion, digital nCounter transcriptomics provide a microbial and immunological in situ “snapshot” of the nasopharyngeal interface in children with ARI. This enabled discrimination among viral, bacterial, codetection, and indeterminate transcripts in the samples using non-invasive sampling.
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Affiliation(s)
| | - Cristiana M Nascimento-Carvalho
- School of Medicine, Federal University of Bahia, Salvador, Brazil.,Department of Pediatrics, School of Medicine, Federal University of Bahia, Salvador, Brazil
| | - Maiara L Bouzas
- School of Medicine, Federal University of Bahia, Salvador, Brazil
| | | | - Aldina Barral
- Instituto Gonçalo Moniz-FIOCRUZ, Salvador, Brazil.,School of Medicine, Federal University of Bahia, Salvador, Brazil
| | - Tim Dierckx
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Ricardo Khouri
- Instituto Gonçalo Moniz-FIOCRUZ, Salvador, Brazil.,School of Medicine, Federal University of Bahia, Salvador, Brazil
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Bruno B Andrade
- Instituto Gonçalo Moniz-FIOCRUZ, Salvador, Brazil.,Multinational Organization Network Sponsoring Translational and Epidemiological Research Initiative, Fundação José Silveira, Salvador, Brazil
| | - Johan Van Weyenbergh
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Camila I de Oliveira
- Instituto Gonçalo Moniz-FIOCRUZ, Salvador, Brazil.,School of Medicine, Federal University of Bahia, Salvador, Brazil
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120
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Yu YH, Wilk K, Waldon PL, Intini G. In vivo identification of Bmp2-correlation networks during fracture healing by means of a limb-specific conditional inactivation of Bmp2. Bone 2018; 116:103-110. [PMID: 30048819 PMCID: PMC6613210 DOI: 10.1016/j.bone.2018.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 05/09/2018] [Accepted: 07/21/2018] [Indexed: 12/31/2022]
Abstract
Bmp2 is known to play an essential role in the initiation of fracture healing via periosteal activation. Specifically, activation and subsequent differentiation of periosteal progenitor cells requires Bmp2 signaling for activation of the osteo-chondrogenic pathway. Here, we explored the interactive transcriptional gene-gene interplays between Bmp2 and 150 known candidate genes during fracture repair. We constructed the interactive Bmp2 signaling pathways in vivo, by comparing gene expression levels prior and 24 h post femur fracture, in presence (wild type) and in absence of Bmp2 (Bmp2c/c;Prx1::cre limb-specific conditional knockout). Twenty-six differentially expressed genes (pre- vs. post-fracture), which demonstrated high correlations within each experimental condition, were used to construct the co-expression networks. Topological dynamic shifts across different co-expression networks characterized the 26 differentially expressed genes as non-redundant focal linking hubs, redundant connecting hubs, periphery genes, or non-existent. Top-ranked up- or down-regulated genes were identified and discussed. Protein-protein interactions in public databases support our findings. Thus, the co-expression networks from this study can be used for future experimental hypotheses.
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Affiliation(s)
- Yau-Hua Yu
- Dept. of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA; Dept. of Periodontology, Tufts University School of Dental Medicine, Boston MA, USA.
| | - Katarzyna Wilk
- Dept. of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - PhiAnh L Waldon
- Dept. of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Giuseppe Intini
- Dept. of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USAa.
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121
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Leal LF, Evangelista AF, de Paula FE, Caravina Almeida G, Carloni AC, Saggioro F, Stavale JN, Malheiros SMF, Mançano B, de Oliveira MA, Luu B, Neder L, Taylor MD, Reis RM. Reproducibility of the NanoString 22-gene molecular subgroup assay for improved prognostic prediction of medulloblastoma. Neuropathology 2018; 38:475-483. [PMID: 30155928 DOI: 10.1111/neup.12508] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/22/2018] [Accepted: 07/25/2018] [Indexed: 11/30/2022]
Abstract
Medulloblastoma is the most frequent malignant brain tumor in children. Four medulloblastoma molecular subgroups, MBSHH , MBWNT , MBGRP3 and MBGRP4 , have been identified by integrated high-throughput platforms. Recently, a 22-gene panel NanoString-based assay was developed for medulloblastoma molecular subgrouping, but the robustness of this assay has not been widely evaluated. Mutations in the gene for human telomerase reverse transcriptase (hTERT) have been found in medulloblastomas and are associated with distinct molecular subtypes. This study aimed to implement the 22-gene panel in a Brazilian context, and to associate the molecular profile with patients' clinical-pathological features. Formalin-fixed, paraffin-embedded (FFPE) medulloblastoma samples (n = 104) from three Brazilian centers were evaluated. Expression profiling of the 22-gene panel was performed by NanoString and a Canadian series (n = 240) was applied for training phase. hTERT mutations were analyzed by PCR followed by direct Sanger sequencing and the molecular profile was associated with patients' clinicopathological features. Overall, 65% of the patients were male, average age at diagnosis was 18 years and 7% of the patients presented metastasis at diagnosis. The molecular classification was attained in 100% of the cases, with the following frequencies: MBSHH (n = 51), MBWNT (n = 19), MBGRP4 (n = 19) and MBGRP3 (n = 15). The MBSHH and MBGRP3 subgroups were associated with older and younger patients, respectively. The MBGRP4 subgroup exhibited the lowest 5-year cancer-specific overall survival (OS), yet in the multivariate analysis, only metastasis at diagnosis and surgical resection were associated with OS. hTERT mutations were detected in 29% of the cases and were associated with older patients, increased hTERT expression and MBSHH subgroup. The 22-gene panel provides a reproducible assay for molecular subgrouping of medulloblastoma FFPE samples in a routine setting and is well-suited for future clinical trials.
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Affiliation(s)
- Letícia F Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Flávia E de Paula
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Adriana C Carloni
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Fabiano Saggioro
- Department of Pathology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - João N Stavale
- Department of Pathology, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Bruna Mançano
- Children and Young Adult's Cancer Hospital, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Betty Luu
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Luciano Neder
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - Michael D Taylor
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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122
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Raman AT, Pohodich AE, Wan YW, Yalamanchili HK, Lowry WE, Zoghbi HY, Liu Z. Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations. Nat Commun 2018; 9:3225. [PMID: 30104565 PMCID: PMC6089998 DOI: 10.1038/s41467-018-05627-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/04/2018] [Indexed: 11/09/2022] Open
Abstract
Recent studies have suggested that genes longer than 100 kb are more likely to be misregulated in neurological diseases associated with synaptic dysfunction, such as autism and Rett syndrome. These length-dependent transcriptional changes are modest in MeCP2-mutant samples, but, given the low sensitivity of high-throughput transcriptome profiling technology, here we re-evaluate the statistical significance of these results. We find that the apparent length-dependent trends previously observed in MeCP2 microarray and RNA-sequencing datasets disappear after estimating baseline variability from randomized control samples. This is particularly true for genes with low fold changes. We find no bias with NanoString technology, so this long gene bias seems to be particular to polymerase chain reaction amplification-based platforms. In contrast, authentic long gene effects, such as those caused by topoisomerase inhibition, can be detected even after adjustment for baseline variability. We conclude that accurate characterization of length-dependent (or other) trends requires establishing a baseline from randomized control samples.
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Affiliation(s)
- Ayush T Raman
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, 77030, USA
| | - Amy E Pohodich
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hari Krishna Yalamanchili
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - William E Lowry
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Huda Y Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, 77030, USA. .,Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Zhandong Liu
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA. .,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, 77030, USA. .,Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX, USA.
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123
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Bagnall J, Boddington C, England H, Brignall R, Downton P, Alsoufi Z, Boyd J, Rowe W, Bennett A, Walker C, Adamson A, Patel NMX, O’Cualain R, Schmidt L, Spiller DG, Jackson DA, Müller W, Muldoon M, White MRH, Paszek P. Quantitative analysis of competitive cytokine signaling predicts tissue thresholds for the propagation of macrophage activation. Sci Signal 2018; 11:11/540/eaaf3998. [DOI: 10.1126/scisignal.aaf3998] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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124
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Pensold D, Symmank J, Hahn A, Lingner T, Salinas-Riester G, Downie BR, Ludewig F, Rotzsch A, Haag N, Andreas N, Schubert K, Hübner CA, Pieler T, Zimmer G. The DNA Methyltransferase 1 (DNMT1) Controls the Shape and Dynamics of Migrating POA-Derived Interneurons Fated for the Murine Cerebral Cortex. Cereb Cortex 2018; 27:5696-5714. [PMID: 29117290 DOI: 10.1093/cercor/bhw341] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Indexed: 01/24/2023] Open
Abstract
The proliferative niches in the subpallium generate a rich cellular variety fated for diverse telencephalic regions. The embryonic preoptic area (POA) represents one of these domains giving rise to the pool of cortical GABAergic interneurons and glial cells, in addition to striatal and residual POA cells. The migration from sites of origin within the subpallium to the distant targets like the cerebral cortex, accomplished by the adoption and maintenance of a particular migratory morphology, is a critical step during interneuron development. To identify factors orchestrating this process, we performed single-cell transcriptome analysis and detected Dnmt1 expression in murine migratory GABAergic POA-derived cells. Deletion of Dnmt1 in postmitotic immature cells of the POA caused defective migration and severely diminished adult cortical interneuron numbers. We found that DNA methyltransferase 1 (DNMT1) preserves the migratory shape in part through negative regulation of Pak6, which stimulates neuritogenesis at postmigratory stages. Our data underline the importance of DNMT1 for the migration of POA-derived cells including cortical interneurons.
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Affiliation(s)
- Daniel Pensold
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Judit Symmank
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Anne Hahn
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Thomas Lingner
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany
| | - Gabriela Salinas-Riester
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany
| | - Bryan R Downie
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany
| | - Fabian Ludewig
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany
| | - Anne Rotzsch
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Natja Haag
- Institute of Biochemistry I, University Hospital Jena, 07743 Jena, Germany.,Institute of Human Genetics, University Hospital RWTH Aachen, Aachen, Germany
| | - Nico Andreas
- FACS Core Facility, Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Katrin Schubert
- FACS Core Facility, Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Christian A Hübner
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Tomas Pieler
- Centre for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany
| | - Geraldine Zimmer
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
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125
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Boldrini L, Giordano M, Lucchi M, Melfi F, Fontanini G. Expression profiling and microRNA regulation of the LKB1 pathway in young and aged lung adenocarcinoma patients. Biomed Rep 2018; 9:198-205. [PMID: 30271594 PMCID: PMC6158392 DOI: 10.3892/br.2018.1122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022] Open
Abstract
Lung cancer in young patients appears to have distinct clinicopathological features. The present study focused on the role of the serine/threonine kinase liver kinase B1 (LKB1), a known tumor suppressor gene, and its miRNA regulation in lung adenocarcinoma, particularly in young versus elderly patients. A total of 88 patients with lung adenocarcinoma were retrospectively analysed. A simultaneous quantification was performed of the expression of LKB1 mRNA and 15 microRNAs (miRNA/miRs; miRs −93, −96, −34a, −34c, −214, −33a, −30b, −145, −182, −30c, −183, −29b, −29c, −153 and −138) involved in the LKB1 pathway, as well as of 5 identified target mRNAs [cyclin D1 (CCND1), catenin β-1 (CTNNB1), lysyl oxidase (LOX), yes-associated protein 1 (YAP1) and survivin], using NanoString technology. KRAS mutations were investigated by pyrosequencing analysis. Patients ≤50 years were defined as a younger group, while patients >50 years old as an older group (n=44/group). No difference between the two groups was identified in terms of survival times analysed using the Kaplan-Meier method or KRAS mutations. Subsequently, the LKB1 signalling pathway was focused on, as a target for therapy in lung adenocarcinoma, and assessed with regards to clinicopathological features; we found that LOX levels in adenocarcinoma patients were significantly associated with histological subtype (P=0.03), stage (P<0.0001) and prognosis (P=0.02 for disease-free interval and P=0.005 for overall survival), but not with age. Furthermore, the miRNA target prediction model indicated that miR-93 and miR-30b appeared to have functional binding sites and downregulate the gene expression of LKB1 and LOX, respectively. In conclusion, young patients appeared have similar survival rates to elderly patients. The assessment of LKB1, its downstream genes and its regulation by miRNAs may have an impact on future research on lung adenocarcinoma in young and elderly patients. Further investigations will be necessary to elucidate the potential of this pathway as a novel target for therapy.
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Affiliation(s)
- Laura Boldrini
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, I-56126 Pisa, Italy
| | - Mirella Giordano
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, I-56126 Pisa, Italy
| | - Marco Lucchi
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, I-56126 Pisa, Italy
| | - Franca Melfi
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, I-56126 Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, I-56126 Pisa, Italy
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126
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Videlock EJ, Mahurkar-Joshi S, Hoffman JM, Iliopoulos D, Pothoulakis C, Mayer EA, Chang L. Sigmoid colon mucosal gene expression supports alterations of neuronal signaling in irritable bowel syndrome with constipation. Am J Physiol Gastrointest Liver Physiol 2018; 315:G140-G157. [PMID: 29565640 PMCID: PMC6109711 DOI: 10.1152/ajpgi.00288.2017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/01/2018] [Accepted: 03/05/2018] [Indexed: 01/31/2023]
Abstract
Peripheral factors likely play a role in at least a subset of irritable bowel syndrome (IBS) patients. Few studies have investigated mucosal gene expression using an unbiased approach. Here, we performed mucosal gene profiling in a sex-balanced sample to identify relevant signaling pathways and gene networks and compare with publicly available profiling data from additional cohorts. Twenty Rome III+ IBS patients [10 IBS with constipation (IBS-C), 10 IBS with diarrhea (IBS-D), 5 men/women each), and 10 age-/sex-matched healthy controls (HCs)] underwent sigmoidoscopy with biopsy for gene microarray analysis, including differential expression, weighted gene coexpression network analysis (WGCNA), gene set enrichment analysis, and comparison with publicly available data. Expression levels of 67 genes were validated in an expanded cohort, including the above samples and 18 additional participants (6 each of IBS-C, IBS-D, HCs) using NanoString nCounter technology. There were 1,270 differentially expressed genes (FDR < 0.05) in IBS-C vs. HCs but none in IBS or IBS-D vs. HCs. WGNCA analysis identified activation of the cAMP/protein kinase A signaling pathway. Nine of 67 genes were validated by the NanoString nCounter technology (FDR < 0.05) in the expanded sample. Comparison with publicly available microarray data from the Mayo Clinic and University of Nottingham supports the reproducibility of 17 genes from the microarray analysis and three of nine genes validated by nCounter in IBS-C vs. HCs. This study supports the involvement of peripheral mechanisms in IBS-C, particularly pathways mediating neuronal signaling. NEW & NOTEWORTHY Peripheral factors play a role in the pathophysiology of irritable bowel syndrome (IBS), which, to date, has been mostly evident in IBS with diarrhea. Here, we show that sigmoid colon mucosal gene expression profiles differentiate IBS with constipation from healthy controls. These profiling data and analysis of additional cohorts also support the concept that peripheral neuronal pathways contribute to IBS pathophysiology.
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Affiliation(s)
- Elizabeth J Videlock
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California , Los Angeles, California
| | - Swapna Mahurkar-Joshi
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California , Los Angeles, California
| | - Jill M Hoffman
- Inflammatory Bowel Disease Research Center, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California , Los Angeles, California
| | - Dimitrios Iliopoulos
- Center for Systems Biomedicine, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California , Los Angeles, California
| | - Charalabos Pothoulakis
- Inflammatory Bowel Disease Research Center, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California , Los Angeles, California
| | - Emeran A Mayer
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California , Los Angeles, California
| | - Lin Chang
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California , Los Angeles, California
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Identification of a neutrophil-related gene expression signature that is enriched in adult systemic lupus erythematosus patients with active nephritis: Clinical/pathologic associations and etiologic mechanisms. PLoS One 2018; 13:e0196117. [PMID: 29742110 PMCID: PMC5942792 DOI: 10.1371/journal.pone.0196117] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 04/08/2018] [Indexed: 11/19/2022] Open
Abstract
Both a lack of biomarkers and relatively ineffective treatments constitute impediments to management of lupus nephritis (LN). Here we used gene expression microarrays to contrast the transcriptomic profiles of active SLE patients with and without LN to identify potential biomarkers for this condition. RNA isolated from whole peripheral blood of active SLE patients was used for transcriptomic profiling and the data analyzed by linear modeling, with corrections for multiple testing. Results were validated in a second cohort of SLE patients, using NanoString technology. The majority of genes demonstrating altered transcript abundance between patients with and without LN were neutrophil-related. Findings in the validation cohort confirmed this observation and showed that levels of RNA abundance in renal remission were similar to active patients without LN. In secondary analyses, RNA abundance correlated with disease activity, hematuria and proteinuria, but not renal biopsy changes. As abundance levels of the individual transcripts correlated strongly with each other, a composite neutrophil score was generated by summing all levels before examining additional correlations. There was a modest correlation between the neutrophil score and the blood neutrophil count, which was largely driven by the dose of glucocorticosteroids and not the proportion of low density and/or activated neutrophils. Analysis of longitudinal data revealed no correlation between baseline neutrophil score or changes over the first year of follow-up with subsequent renal flare or treatment outcomes, respectively. The findings argue that although the neutrophil score is associated with LN, its clinical utility as a biomarker may be limited.
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128
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Mairinger FD, Schmeller J, Borchert S, Wessolly M, Mairinger E, Kollmeier J, Hager T, Mairinger T, Christoph DC, Walter RFH, Eberhardt WEE, Plönes T, Wohlschlaeger J, Jasani B, Schmid KW, Bankfalvi A. Immunohistochemically detectable metallothionein expression in malignant pleural mesotheliomas is strongly associated with early failure to platin-based chemotherapy. Oncotarget 2018; 9:22254-22268. [PMID: 29854276 PMCID: PMC5976462 DOI: 10.18632/oncotarget.24962] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 03/11/2018] [Indexed: 12/13/2022] Open
Abstract
Background Malignant pleural mesothelioma (MPM) is a biologically highly aggressive tumor arising from the pleura with a dismal prognosis. Cisplatin is the drug of choice for the treatment of MPM, and carboplatin seems to have comparable efficacy. Nevertheless, cisplatin treatment results in a response rate of merely 14% and a median survival of less than seven months. Due to their role in many cellular processes, methallothioneins (MTs) have been widely studied in various cancers. The known heavy metal detoxifying effect of MT-I and MT-II may be the reason for heavy metal drug resistance of various cancers including MPM. Methods 105 patients were retrospectively analyzed immunohistochemically for their MT expression levels. Survival analysis was done by Cox-regression, and statistical significance determined using likelihood ratio, Wald test and Score (logrank) tests. Results Cox-regression analyses were done in a linear and logarithmic scale revealing a significant association between expression of MT and shortened overall survival (OS) in a linear (p=0.0009) and logarithmic scale (p=0.0003). Reduced progression free survival (PFS) was also observed for MT expressing tumors (linear: p=0.0134, log: p=0.0152). Conclusion Since both, overall survival and progression-free survival are negatively correlated with detectable MT expression in MPM, our results indicate a possible resistance to platin-based chemotherapy associated with MT expression upregulation, found exclusively in progressive MPM samples. Initial cell culture studies suggest promoter DNA hypomethylation and expression of miRNA-566 a direct regulator of copper transporter SLC31A1 and a putative regulator of MT1A and MT2A gene expression, to be responsible for the drug resistance.
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Affiliation(s)
- Fabian D Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jan Schmeller
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sabrina Borchert
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michael Wessolly
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Elena Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jens Kollmeier
- Department of Pneumology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Thomas Hager
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Thomas Mairinger
- Department of Pathology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Daniel C Christoph
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Internistic Oncology, Kliniken Essen Mitte, Essen, Germany
| | - Robert F H Walter
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Wilfried E E Eberhardt
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Till Plönes
- Department of Thoracic Surgery and Thoracical Endoscopy, Ruhrlandklinik, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Pathology, Diakonissenkrankenhaus Flensburg, Flensburg, Germany
| | - Bharat Jasani
- Department of Pathology, Targos Molecular Pathology GmbH, Kassel, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Agnes Bankfalvi
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Pehme PM, Zhang W, Finik J, Pritchett A, Buthmann J, Dana K, Hao K, Nomura Y. Placental MAOA expression mediates prenatal stress effects on temperament in 12-month-olds. INFANT AND CHILD DEVELOPMENT 2018; 27. [PMID: 30505241 DOI: 10.1002/icd.2094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The placenta adapts to maternal environment and its alterations may have a lasting impact on child's temperament development. Prenatal stress has been linked to both a downregulation of monoamine oxidase A (MAOA) gene expression in the placenta and to difficult temperament. Capitalizing on an ongoing longitudinal study, we analysed data from 95 mother-child dyads to investigate whether MAOA mediates the association between prenatal stress and infant temperament. Prenatal stress was defined as exposure to Superstorm Sandy (Sandy) during pregnancy. Infant temperament was measured by Infant Behaviour Questionnaire-Revised. MAOA gene expression was quantified in placenta tissue. The Smiling and Laughter subscale score was independently associated with Sandy exposure and MAOA placental gene expression. Mediation analysis confirmed that MAOA expression partially mediated the relationship between Sandy and Smiling and Laughter subscale, suggesting that in utero exposure to Sandy could induce lower frequency of smiling and laughter via downregulation of placental MAOA gene expression. These effects could compromise optimal temperamental trajectory and contribute to risk for psychological problems. Placental epigenetic markers can contribute to a multidimensional model of early intervention for high-risk children.
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Affiliation(s)
- Patricia M Pehme
- Clinical Psychology Program, The Graduate Center (CUNY), New York, New York, USA.,Department of Psychology, Queens College (CUNY), New York, New York, USA
| | - Wei Zhang
- Clinical Psychology Program, The Graduate Center (CUNY), New York, New York, USA.,Department of Psychology, Queens College (CUNY), New York, New York, USA
| | - Jackie Finik
- Department of Psychology, Queens College (CUNY), New York, New York, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,CUNY Graduate School of Public Health and Health Policy, New York, New York, USA
| | - Alexandra Pritchett
- Clinical Psychology Program, The Graduate Center (CUNY), New York, New York, USA.,Department of Psychology, Queens College (CUNY), New York, New York, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jessica Buthmann
- Department of Psychology, Queens College (CUNY), New York, New York, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Behavioral and Cognitive Neuroscience Program, The Graduate Center (CUNY), New York, New York, USA
| | - Kathryn Dana
- Clinical Psychology Program, The Graduate Center (CUNY), New York, New York, USA.,Department of Psychology, Queens College (CUNY), New York, New York, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yoko Nomura
- Clinical Psychology Program, The Graduate Center (CUNY), New York, New York, USA.,Department of Psychology, Queens College (CUNY), New York, New York, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,CUNY Graduate School of Public Health and Health Policy, New York, New York, USA.,Behavioral and Cognitive Neuroscience Program, The Graduate Center (CUNY), New York, New York, USA
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130
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Koh J, Hogue JA, Roman SA, Scheri RP, Fradin H, Corcoran DL, Sosa JA. Transcriptional profiling reveals distinct classes of parathyroid tumors in PHPT. Endocr Relat Cancer 2018; 25:407-420. [PMID: 29475894 PMCID: PMC5826637 DOI: 10.1530/erc-17-0470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 02/01/2018] [Indexed: 12/20/2022]
Abstract
The clinical presentation of primary hyperparathyroidism (PHPT) varies widely, although the underlying mechanistic reasons for this disparity remain unknown. We recently reported that parathyroid tumors can be functionally segregated into two distinct groups on the basis of their relative responsiveness to ambient calcium, and that patients in these groups differ significantly in their likelihood of manifesting bone disability. To examine the molecular basis for this phenotypic variation in PHPT, we compared the global gene expression profiles of calcium-sensitive and calcium-resistant parathyroid tumors. RNAseq and proteomic analysis identified a candidate set of differentially expressed genes highly correlated with calcium-sensing capacity. Subsequent quantitative assessment of the expression levels of these genes in an independent cohort of parathyroid tumors confirmed that calcium-sensitive tumors cluster in a discrete transcriptional profile group. These data indicate that PHPT is not an etiologically monolithic disorder and suggest that divergent molecular mechanisms could drive the observed phenotypic differences in PHPT disease course, provenance, and outcome.
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Affiliation(s)
- James Koh
- Dept. of Surgery, Duke University Medical Center, Durham, NC
- Duke Clinical Research Institute, Duke University Medical Center
- To whom reprint requests should be addressed: James Koh, Ph.D., Department of Surgery, Duke University Medical Center, Durham, NC 27710, Phone: 919-684-0892, FAX: 919-681-6622,
| | - Joyce A. Hogue
- Dept. of Surgery, Duke University Medical Center, Durham, NC
| | | | | | | | | | - Julie A. Sosa
- Dept. of Surgery, Duke University Medical Center, Durham, NC
- Dept. of Medicine, Duke University
- Duke Cancer Institute, Duke University Medical Center
- Duke Clinical Research Institute, Duke University Medical Center
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131
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Zhang W, Li Q, Deyssenroth M, Lambertini L, Finik J, Ham J, Huang Y, Tsuchiya KJ, Pehme P, Buthmann J, Yoshida S, Chen J, Nomura Y. Timing of prenatal exposure to trauma and altered placental expressions of hypothalamic-pituitary-adrenal axis genes and genes driving neurodevelopment. J Neuroendocrinol 2018; 30:e12581. [PMID: 29423924 PMCID: PMC5939590 DOI: 10.1111/jne.12581] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/30/2018] [Accepted: 02/03/2018] [Indexed: 12/17/2022]
Abstract
Prenatal maternal stress increases the risk for negative developmental outcomes in offspring; however, the underlying biological mechanisms remain largely unexplored. In the present study, alterations in placental gene expression associated with maternal stress were examined to clarify the potential underlying epi/genetic mechanisms. Expression levels of 40 selected genes involved in regulating foetal hypothalamic-pituitary-adrenal axis and neurodevelopment were profiled in placental tissues collected from a birth cohort established around the time of Superstorm Sandy. Objective prenatal traumatic stress was defined as whether mothers were exposed to Superstorm Sandy during pregnancy. Among the 275 mother-infant dyads, 181 dyads were delivered before Superstorm Sandy (ie, Control), 66 dyads were exposed to Superstorm Sandy during the first trimester (ie, Early Exposure) and 28 were exposed to Superstorm Sandy during the second or third trimester (ie, Mid-Late Exposure). Across all trimesters, expression of HSD11B2, MAOA, ZNF507 and DYRK1A was down-regulated among those exposed to Superstorm Sandy during pregnancy. Furthermore, trimester-specific differences were also observed: exposure during early gestation was associated with down-regulation of HSD11B1 and MAOB and up-regulation of CRHBP; exposure during mid-late gestation was associated with up-regulation of SRD5A3. The findings of the present study suggest that placental gene expression may be altered in response to traumatic stress exposure during pregnancy, and the susceptibility of these genes is dependent on the time of the exposure during pregnancy. Further studies should aim to clarify the biological mechanisms that underlie trimester-specific exposure by evaluating the differential impact on offspring neurodevelopment later in childhood.
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Affiliation(s)
- Wei Zhang
- Queens College, CUNY, Psychology, New York, NY, United States
| | - Qian Li
- Icahn School of Medicine at Mount Sinai, Department of Environmental Medicine and Public Health, New York, NY, USA
| | - Maya Deyssenroth
- Icahn School of Medicine at Mount Sinai, Department of Environmental Medicine and Public Health, New York, NY, USA
| | - Luca Lambertini
- Icahn School of Medicine at Mount Sinai, Department of Environmental Medicine and Public Health, New York, NY, USA
| | - Jackie Finik
- Queens College, CUNY, Psychology, New York, NY, United States
- The Graduate Center, CUNY, Psychology, New York, NY, United States
- Graduate School of Public Health and Health Policy, CUNY, New York, NY, United State
| | - Jacob Ham
- Icahn School of Medicine at Mount Sinai, Psychiatry, New York, NY, United States
| | - Yongling Huang
- The Graduate Center, CUNY, Psychology, New York, NY, United States
| | - Kenji J Tsuchiya
- Hamamatsu University School of Medicine, Research Center for Child Mental Development, Shizuoka, Japan
| | - Patricia Pehme
- Queens College, CUNY, Psychology, New York, NY, United States
- The Graduate Center, CUNY, Psychology, New York, NY, United States
| | - Jessica Buthmann
- Queens College, CUNY, Psychology, New York, NY, United States
- The Graduate Center, CUNY, Psychology, New York, NY, United States
| | - Sachiko Yoshida
- Department of Environmental & Life Sciences, Toyohashi University of Technology, Toyohashi, Japan
| | - Jia Chen
- Icahn School of Medicine at Mount Sinai, Department of Environmental Medicine and Public Health, New York, NY, USA
| | - Yoko Nomura
- Queens College, CUNY, Psychology, New York, NY, United States
- Icahn School of Medicine at Mount Sinai, Department of Environmental Medicine and Public Health, New York, NY, USA
- The Graduate Center, CUNY, Psychology, New York, NY, United States
- Icahn School of Medicine at Mount Sinai, Psychiatry, New York, NY, United States
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132
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Strickland MR, Koller EJ, Deng DZ, Ceballos-Diaz C, Golde TE, Chakrabarty P. Ifngr1 and Stat1 mediated canonical Ifn-γ signaling drives nigrostriatal degeneration. Neurobiol Dis 2018; 110:133-141. [PMID: 29196213 PMCID: PMC5748010 DOI: 10.1016/j.nbd.2017.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/20/2017] [Accepted: 11/27/2017] [Indexed: 12/21/2022] Open
Abstract
Brain expression of AAV-Ifn-γ leads to reactive gliosis, nigrostriatal degeneration and midbrain calcification in wild type mice. This mouse model phenocopies idiopathic basal ganglia calcification which is associated with Parkinsonian symptoms. To understand how the nigro-striatal pathway is selectively vulnerable to Ifn-γ, we determined if the phenotype is driven by canonical signaling intermediates, Ifngr1 and Stat1. Using focused bioinformatic analysis and rotarod testing, we show that neuroinflammation and motor abnormalities precede the appearance of midbrain neuropathologies in the brains of Ifn-γ mouse model. To test whether canonical Ifn-γ signaling is a key driver of progressive nigrostriatal degeneration, we overexpressed Ifn-γ in the brains of Ifngr1-/- and Stat1-/- mice. Expression of Ifn-γ in Ifngr1-/- mice did not result in any neuroinflammation, midbrain calcinosis or nigrostriatal degenerative pathology. Interestingly, in Stat1-/- mice, Ifn-γ expression resulted in gliosis without recapitulating the neurodegenerative phenotype. Overall, our data shows that canonical Ifn-γ signaling triggers midbrain calcinosis and nigrostriatal neurodegeneration, providing mechanistic insights into cytokine-driven selective neuronal vulnerability. Our study establishes the broader relevance of inflammatory signaling in neurodegenerative diseases and can potentially identify novel immunological targets for Parkinsonian syndromes.
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Affiliation(s)
- Michael R Strickland
- Center for Translational Research in Neurodegenerative Diseases, University of Florida, Gainesville, FL 32610, United States
| | - Emily J Koller
- Center for Translational Research in Neurodegenerative Diseases, University of Florida, Gainesville, FL 32610, United States; Department of Neuroscience, University of Florida, Gainesville, FL 32610, United States
| | - Doris Z Deng
- Center for Translational Research in Neurodegenerative Diseases, University of Florida, Gainesville, FL 32610, United States
| | - Carolina Ceballos-Diaz
- Center for Translational Research in Neurodegenerative Diseases, University of Florida, Gainesville, FL 32610, United States; Department of Neuroscience, University of Florida, Gainesville, FL 32610, United States
| | - Todd E Golde
- Center for Translational Research in Neurodegenerative Diseases, University of Florida, Gainesville, FL 32610, United States; Department of Neuroscience, University of Florida, Gainesville, FL 32610, United States; McKnight Brain Institute, University of Florida, Gainesville, FL 32610, United States
| | - Paramita Chakrabarty
- Center for Translational Research in Neurodegenerative Diseases, University of Florida, Gainesville, FL 32610, United States; Department of Neuroscience, University of Florida, Gainesville, FL 32610, United States; McKnight Brain Institute, University of Florida, Gainesville, FL 32610, United States.
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133
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Walter RFH, Mairinger FD, Werner R, Vollbrecht C, Hager T, Schmid KW, Wohlschlaeger J, Christoph DC. Folic-acid metabolism and DNA-repair phenotypes differ between neuroendocrine lung tumors and associate with aggressive subtypes, therapy resistance and outcome. Oncotarget 2018; 7:20166-79. [PMID: 27064343 PMCID: PMC4991445 DOI: 10.18632/oncotarget.7737] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 01/30/2016] [Indexed: 02/02/2023] Open
Abstract
Purpose 25% of all lung cancer cases are neuroendocrine (NELC) including typical (TC) and atypical carcinoid (AC), large-cell neuroendocrine (LCNEC) and small cell lung cancer (SCLC). Prognostic and predictive biomarkers are lacking. Experimental Design Sixty patients were used for nCounter mRNA expression analysis of the folic-acid metabolism (ATIC, DHFR, FOLR1, FPGS, GART, GGT1, SLC19A1, TYMS) and DNA-repair (ERCC1, MLH1, MSH2, MSH6, XRCC1). Phenotypic classification classified tumors (either below or above the median expression level) with respect to the folic acid metabolism or DNA repair. Results Expression of FOLR1, FPGS, MLH1 and TYMS (each p<0.0001) differed significantly between all four tumor types. FOLR1 and FPGS associated with tumor differentiation (both p<0.0001), spread to regional lymph nodes (FOLR1 p=0.0001 and FPGS p=0.0038), OS and PFS (FOLR1 p<0.0050 for both and FPGS p<0.0004 for OS). Phenotypic sorting revealed the Ft-phenotype to be the most prominent expression profile in carcinoids, whereas SCLC presented nearly univocal with the fT and LCNEC with fT or ft. These results were significant for tumor subtype (p<0.0001). Conclusions The assessed biomarkers and phenotypes allow for risk stratification (OS, PFS), diagnostic classification and enhance the biological understanding of the different subtypes of neuroendocrine tumors revealing potential new therapy options and clarifying known resistance mechanisms.
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Affiliation(s)
- Robert Fred Henry Walter
- Ruhrlandklinik Essen, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Fabian Dominik Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, Division of Molecular Pathology, Charité, Berlin, Germany
| | - Robert Werner
- Department of Pathology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Claudia Vollbrecht
- Institute of Pathology, Division of Molecular Pathology, Charité, Berlin, Germany
| | - Thomas Hager
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, Ev.-Luth. Diakonissenkrankenhaus Flensburg, Flensburg, Germany
| | - Daniel Christian Christoph
- Department of Medical Oncology, West German Cancer Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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134
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Llovera G, Benakis C, Enzmann G, Cai R, Arzberger T, Ghasemigharagoz A, Mao X, Malik R, Lazarevic I, Liebscher S, Ertürk A, Meissner L, Vivien D, Haffner C, Plesnila N, Montaner J, Engelhardt B, Liesz A. The choroid plexus is a key cerebral invasion route for T cells after stroke. Acta Neuropathol 2017; 134:851-868. [PMID: 28762187 DOI: 10.1007/s00401-017-1758-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 07/27/2017] [Accepted: 07/27/2017] [Indexed: 11/28/2022]
Abstract
Neuroinflammation contributes substantially to stroke pathophysiology. Cerebral invasion of peripheral leukocytes-particularly T cells-has been shown to be a key event promoting inflammatory tissue damage after stroke. While previous research has focused on the vascular invasion of T cells into the ischemic brain, the choroid plexus (ChP) as an alternative cerebral T-cell invasion route after stroke has not been investigated. We here report specific accumulation of T cells in the peri-infarct cortex and detection of T cells as the predominant population in the ipsilateral ChP in mice as well as in human post-stroke autopsy samples. T-cell migration from the ChP to the peri-infarct cortex was confirmed by in vivo cell tracking of photoactivated T cells. In turn, significantly less T cells invaded the ischemic brain after photothrombotic lesion of the ipsilateral ChP and in a stroke model encompassing ChP ischemia. We detected a gradient of CCR2 ligands as the potential driving force and characterized the neuroanatomical pathway for the intracerebral migration. In summary, our study demonstrates that the ChP is a key invasion route for post-stroke cerebral T-cell invasion and describes a CCR2-ligand gradient between cortex and ChP as the potential driving mechanism for this invasion route.
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Affiliation(s)
- Gemma Llovera
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Corinne Benakis
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Gaby Enzmann
- Theodor Kocher Institute, University of Bern, Freiestrasse 1, 3012, Bern, Switzerland
| | - Ruiyao Cai
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Thomas Arzberger
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 23, 81377, Munich, Germany
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilians-Universität, Nussbaumstraße 7, 80336, Munich, Germany
| | - Alireza Ghasemigharagoz
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Xiang Mao
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Rainer Malik
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Ivana Lazarevic
- Theodor Kocher Institute, University of Bern, Freiestrasse 1, 3012, Bern, Switzerland
| | - Sabine Liebscher
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig-Maximilians-University, Grosshaderner Str. 9, 82152, Munich, Germany
| | - Ali Ertürk
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Lilja Meissner
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Denis Vivien
- INSERM, UMR-S U919, Institut National de la Santé Et de la Recherche Médicale (INSERM), Team Serine Proteases and Pathophysiology of the Neurovascular Unit, GIP CYCERON, University Caen Basse-Normandie, 14074, Caen Cedex, France
| | - Christof Haffner
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Nikolaus Plesnila
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Joan Montaner
- Neurovascular Research Laboratory, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Britta Engelhardt
- Theodor Kocher Institute, University of Bern, Freiestrasse 1, 3012, Bern, Switzerland
| | - Arthur Liesz
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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135
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Boldrini L, Giordano M, Niccoli C, Melfi F, Lucchi M, Mussi A, Fontanini G. Role of microRNA-33a in regulating the expression of PD-1 in lung adenocarcinoma. Cancer Cell Int 2017; 17:105. [PMID: 29176936 PMCID: PMC5693599 DOI: 10.1186/s12935-017-0474-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/09/2017] [Indexed: 12/28/2022] Open
Abstract
Background MiRNAs are vital in functioning as either oncogenes or tumor suppressors in the cell cycle. Target transcripts for immune checkpoint molecules such as PD-1/PD-L1 and (programmed cell death-1/its ligand and cytotoxic T-lymphocyte antigen 4) have proven to be beneficial against several solid tumors, including lung adenocarcinoma. Methods Simultaneous quantification of the expression level of miR-33a and PD-1, PD-L1 and CTLA4 mRNAs with NanoString technology was performed in 88 lung adenocarcinoma specimens. A cohort of 323 lung adenocarcinoma patients from the cancer genome atlas (TCGA) database was further analyzed, in order to test our hypothesis. Potential interference of PD-1, PD-L1 and CTLA4 gene expression by miR-33a was predicted using the microRNA target prediction program RNA22. Results High miR-33a expression was significantly associated with younger (p = 0.005), female (p = 0.04), patients with low grade (p < 0.0001), early stage (p = 0.03) tumors, and better survival. The hypothesis of the involvement of miR-33a in PD-1/PD-L1/CTLA4 mechanisms was corroborated by the finding of putative miR-33a binding sites in all three genes using the RNA22 method. We found an inverse correlation between miR-33a and PD-1 levels (p = 0.01), as well as for PD-L1 (p = 0.01) and CTLA4 (p = 0.03) expression, and a significant better prognosis for patients with high miR-33a/low PD-1. TCGA database analysis confirmed that miR-33a high levels were associated with low PD-1 expression and with longer survival on a larger population. Conclusions Our study emphasizes the notion of a potential value of miR-33a as a favorable prognostic marker through PD-1 regulation.
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Affiliation(s)
- Laura Boldrini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Roma 57, 56126 Pisa, Italy
| | - Mirella Giordano
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Roma 57, 56126 Pisa, Italy
| | - Cristina Niccoli
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Roma 57, 56126 Pisa, Italy
| | - Franca Melfi
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Roma 57, 56126 Pisa, Italy
| | - Marco Lucchi
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Roma 57, 56126 Pisa, Italy
| | - Alfredo Mussi
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Roma 57, 56126 Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Roma 57, 56126 Pisa, Italy
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136
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Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma. Nat Commun 2017; 8:990. [PMID: 29042553 PMCID: PMC5645359 DOI: 10.1038/s41467-017-01217-9] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 08/30/2017] [Indexed: 01/04/2023] Open
Abstract
Many high-grade serous carcinomas (HGSCs) of the pelvis are thought to originate in the distal portion of the fallopian tube. Serous tubal intra-epithelial carcinoma (STIC) lesions are the putative precursor to HGSC and identifiable in ~ 50% of advanced stage cases. To better understand the molecular etiology of HGSCs, we report a multi-center integrated genomic analysis of advanced stage tumors with and without STIC lesions and normal tissues. The most significant focal DNA SCNAs were shared between cases with and without STIC lesions. The RNA sequence and the miRNA data did not identify any clear separation between cases with and without STIC lesions. HGSCs had molecular profiles more similar to normal fallopian tube epithelium than ovarian surface epithelium or peritoneum. The data suggest that the molecular features of HGSCs with and without associated STIC lesions are mostly shared, indicating a common biologic origin, likely to be the distal fallopian tube among all cases.High-grade serous carcinomas (HGSCs) are associated with precursor lesions (STICs) in the fallopian epithelium in only half of the cases. Here the authors report the molecular analysis of HGSCs with and without associated STICs and show similar profiles supporting a common origin for all HGSCs.
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137
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Lawler K, Papouli E, Naceur-Lombardelli C, Mera A, Ougham K, Tutt A, Kimbung S, Hedenfalk I, Zhan J, Zhang H, Buus R, Dowsett M, Ng T, Pinder SE, Parker P, Holmberg L, Gillett CE, Grigoriadis A, Purushotham A. Gene expression modules in primary breast cancers as risk factors for organotropic patterns of first metastatic spread: a case control study. Breast Cancer Res 2017; 19:113. [PMID: 29029636 PMCID: PMC5640935 DOI: 10.1186/s13058-017-0881-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 07/12/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Metastases from primary breast cancers can involve single or multiple organs at metastatic disease diagnosis. Molecular risk factors for particular patterns of metastastic spread in a clinical population are limited. METHODS A case-control design including 1357 primary breast cancers was used to study three distinct clinical patterns of metastasis, which occur within the first six months of metastatic disease: bone and visceral metasynchronous spread, bone-only, and visceral-only metastasis. Whole-genome expression profiles were obtained using whole genome (WG)-DASL assays from formalin-fixed paraffin-embedded (FFPE) samples. A systematic protocol was developed for handling FFPE samples together with stringent data quality controls to identify robust expression profiling data. A panel of published and novel gene sets were tested for association with these specific patterns of metastatic spread and odds ratios (ORs) were calculated. RESULTS Metasynchronous metastasis to bone and viscera was found in all intrinsic breast cancer subtypes, while immunohistochemically (IHC)-defined receptor status and specific IntClust subgroups were risk factors for visceral-only or bone-only first metastases. Among gene modules, those related to proliferation increased the risk of metasynchronous metastasis (OR (95% CI) = 2.3 (1.1-4.8)) and visceral-only first metastasis (OR (95% CI) = 2.5 (1.2-5.1)) but not bone-only metastasis (OR (95% CI) = 0.97 (0.56-1.7)). A 21-gene module (BV) was identified in estrogen-receptor-positive breast cancers with metasynchronous metastasis to bone and viscera (area under the curve = 0.77), and its expression increased the risk of bone and visceral metasynchronous spread in this population. BV was further orthogonally validated with NanoString nCounter in primary breast cancers, and was reproducible in their matched lymph nodes metastases and an external cohort. CONCLUSION This case-control study of WG-DASL global expression profiles from FFPE tumour samples, after careful quality control and RNA selection, revealed that gene modules in the primary tumour have differing risks for clinical patterns of metasynchronous first metastases. Moreover, a novel gene module was identified as a putative risk factor for metasynchronous bone and visceral first metastatic spread, with potential implications for disease monitoring and treatment planning.
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Affiliation(s)
- Katherine Lawler
- School of Cancer Studies, CRUK King’s Health Partners Centre, King’s College London, Guy’s Campus, London, SE1 1UL UK
- Institute for Mathematical and Molecular Biomedicine, King’s College London, Hodgkin Building, Guy’s Campus, London, SE1 1UL UK
| | - Efterpi Papouli
- NIHR Comprehensive Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, WC2R 2LS UK
| | - Cristina Naceur-Lombardelli
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
| | - Anca Mera
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
- Cancer Epidemiology Unit, King’s College London, Guy’s Hospital, Great Maze Pond, London, SE1 9RT UK
| | - Kayleigh Ougham
- Cancer Bioinformatics, King’s College London, Innovation Centre, Cancer Centre at Guy’s Hospital, London, SE1 9RT UK
| | - Andrew Tutt
- Breast Cancer Now Research Unit, Innovation Centre, Cancer Centre at Guy’s Hospital, King’s Health Partners AHSC, King’s College London, Faculty of Life Sciences and Medicine, London, SE1 9RT UK
| | - Siker Kimbung
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Jun Zhan
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education of Beijing, Beijing, People’s Republic of China, Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Hongquan Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education of Beijing, Beijing, People’s Republic of China, Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Richard Buus
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Mitch Dowsett
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Tony Ng
- School of Cancer Studies, CRUK King’s Health Partners Centre, King’s College London, Guy’s Campus, London, SE1 1UL UK
- Breast Cancer Now Research Unit, Innovation Centre, Cancer Centre at Guy’s Hospital, King’s Health Partners AHSC, King’s College London, Faculty of Life Sciences and Medicine, London, SE1 9RT UK
- Richard Dimbleby Department of Cancer Research, Randall Division of Cell and Molecular Biophysics, King’s College London, Guy’s Campus, London, SE1 1UL UK
- UCL Cancer Institute, Paul O’Gorman Building, University College London, London, WC1E 6DD UK
| | - Sarah E. Pinder
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
| | - Peter Parker
- School of Cancer Studies, CRUK King’s Health Partners Centre, King’s College London, Guy’s Campus, London, SE1 1UL UK
- London Research Institute, Lincoln’s Inn Fields, London, WC2A 3LY UK
| | - Lars Holmberg
- Cancer Epidemiology Unit, King’s College London, Guy’s Hospital, Great Maze Pond, London, SE1 9RT UK
- Uppsala University, Department of Surgical Sciences, Uppsala University Hospital, 751 85 Uppsala, Sweden
| | - Cheryl E. Gillett
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
| | - Anita Grigoriadis
- School of Cancer Studies, CRUK King’s Health Partners Centre, King’s College London, Guy’s Campus, London, SE1 1UL UK
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
- Cancer Bioinformatics, King’s College London, Innovation Centre, Cancer Centre at Guy’s Hospital, London, SE1 9RT UK
- Breast Cancer Now Research Unit, Innovation Centre, Cancer Centre at Guy’s Hospital, King’s Health Partners AHSC, King’s College London, Faculty of Life Sciences and Medicine, London, SE1 9RT UK
| | - Arnie Purushotham
- School of Cancer Studies, CRUK King’s Health Partners Centre, King’s College London, Guy’s Campus, London, SE1 1UL UK
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
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Antoniali G, Serra F, Lirussi L, Tanaka M, D'Ambrosio C, Zhang S, Radovic S, Dalla E, Ciani Y, Scaloni A, Li M, Piazza S, Tell G. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. Nat Commun 2017; 8:797. [PMID: 28986522 PMCID: PMC5630600 DOI: 10.1038/s41467-017-00842-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 07/28/2017] [Indexed: 01/31/2023] Open
Abstract
Mammalian apurinic/apyrimidinic endonuclease 1 is a DNA repair enzyme involved in genome stability and expression of genes involved in oxidative stress responses, tumor progression and chemoresistance. However, the molecular mechanisms underlying the role of apurinic/apyrimidinic endonuclease 1 in these processes are still unclear. Recent findings point to a novel role of apurinic/apyrimidinic endonuclease 1 in RNA metabolism. Through the characterization of the interactomes of apurinic/apyrimidinic endonuclease 1 with RNA and other proteins, we demonstrate here a role for apurinic/apyrimidinic endonuclease 1 in pri-miRNA processing and stability via association with the DROSHA-processing complex during genotoxic stress. We also show that endonuclease activity of apurinic/apyrimidinic endonuclease 1 is required for the processing of miR-221/222 in regulating expression of the tumor suppressor PTEN. Analysis of a cohort of different cancers supports the relevance of our findings for tumor biology. We also show that apurinic/apyrimidinic endonuclease 1 participates in RNA-interactomes and protein-interactomes involved in cancer development, thus indicating an unsuspected post-transcriptional effect on cancer genes. APE1 plays an important role in the cellular response to oxidative stress, and mutations are linked to tumor progression and chemoresistance. Here, the authors characterize the interactions of APE1 with RNA and demonstrate a role in microRNA processing.
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Affiliation(s)
- Giulia Antoniali
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy
| | - Fabrizio Serra
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.,Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, I.R.C.C.S., via Franco Gallini 2, Aviano (PN), 33081, Italy
| | - Lisa Lirussi
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.,Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Sykehusveien 27, Nordbyhagen, 1474, Norway
| | - Mikiei Tanaka
- Laboratory of Biochemistry, National Heart Lung and Blood Institute, National Institutes of Health, 50 South Drive, MSC-8012, Bethesda, MD, 20892-8012, USA
| | - Chiara D'Ambrosio
- Proteomics and Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment (ISPAAM) National Research Council (CNR) of Italy, via Argine 1085, Naples, 80147, Italy
| | - Shiheng Zhang
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | | | - Emiliano Dalla
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy
| | - Yari Ciani
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment (ISPAAM) National Research Council (CNR) of Italy, via Argine 1085, Naples, 80147, Italy
| | - Mengxia Li
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
| | - Silvano Piazza
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy. .,Bioinformatics Core Facility, Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 18, Povo, Trento, TN, 38123, Italy.
| | - Gianluca Tell
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.
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139
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Zhang W, Finik J, Dana K, Glover V, Ham J, Nomura Y. Prenatal Depression and Infant Temperament: The Moderating Role of Placental Gene Expression. INFANCY 2017; 23:211-231. [PMID: 30393466 DOI: 10.1111/infa.12215] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Prior research has demonstrated the link between maternal depression during pregnancy (i.e., prenatal depression) and increased neurodevelopmental dysregulation in offspring. However, little is known about the roles of key hypothalamic-pituitary axis regulatory genes in the placenta modulating this association. This study will examine whether placental gene expression levels of 11β-hydroxysteroid dehydrogenase type 2 (HSD11B2), glucocorticoid receptor (NR3C1), and mineralocorticoid receptor (NR3C2) can help elucidate the underlying mechanisms linking prenatal depression to infant temperament, particularly in infants with high negativity and low emotion regulation. Stored placenta tissues (N = 153) were used to quantify messenger ribonucleic acid levels of HSD11B2, NR3C1, and NR3C2. Assessments of prenatal depression and infant temperament at 6 months of age were ascertained via maternal report. Results found that prenatal depression was associated with increased Negative Affectivity (p < .05) after controlling for postnatal depression and psychosocial characteristics. Furthermore, the association between prenatal depression and Negative Affectivity was moderated by gene expression levels of HSD11B2, NR3C1, and NR3C2 such that greater gene expression significantly lessened the association between prenatal depression and Negative Affectivity. Our findings suggest that individual differences in placental gene expression may be used as an early marker of susceptibility or resilience to prenatal adversity.
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Affiliation(s)
| | - Jackie Finik
- Queens College, CUNY and Icahn School of Medicine at Mount Sinai and Graduate School of Public Health and Health Policy, CUNY
| | - Kathryn Dana
- Queens College, CUNY and The Graduate Center, CUNY
| | | | - Jacob Ham
- Icahn School of Medicine at Mount Sinai
| | - Yoko Nomura
- Queens College, CUNY and Icahn School of Medicine at Mount Sinai and The Graduate Center, CUNY
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140
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Colombo C, Belfiore A, Paielli N, De Cecco L, Canevari S, Laurini E, Fermeglia M, Pricl S, Verderio P, Bottelli S, Fiore M, Stacchiotti S, Palassini E, Gronchi A, Pilotti S, Perrone F. β-Catenin in desmoid-type fibromatosis: deep insights into the role of T41A and S45F mutations on protein structure and gene expression. Mol Oncol 2017. [PMID: 28627792 PMCID: PMC5664003 DOI: 10.1002/1878-0261.12101] [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] [Indexed: 12/30/2022] Open
Abstract
Desmoid‐type fibromatosis (DF) is a rare mesenchymal lesion with high risk of local recurrence. Specific β‐catenin mutations (S45F) appeared to be related to this higher risk compared to T41A‐mutated or wild‐type (WT). We explored the influence of both mutations and WT on structure stability and affinity of β‐catenin for α‐catenin and the pattern of gene expression that may influence DF behavior. Using 33 surgically resected primary DFs harboring T41A (n = 14), S45F (n = 10), or WT (n = 9), we performed a comparative molecular analysis by protein/protein interaction modeling, gene expression by DASL microarrays, human inflammation gene panel, and assessment of immune system‐based biomarkers by immunohistochemistry. Mutated proteins were more stable than WT and formed a weaker complex with α‐catenin. Consensus unsupervised gene clustering revealed the presence of two DF group‐mutated (T41A + S45F) and WT (P = 0.0047). The gene sets ‘Inflammatory‐Defense‐Humoral Immune Response’ and ‘Antigen Binding’ were significantly enriched in T41A. The deregulation of 16 inflammation‐related genes was confirmed. Low numbers of T cells and tumor‐associated macrophages (TAM) infiltrating the tumors and low/absent PD‐1/PD‐L1 expression were also identified. We demonstrated that mutated DFs (T41A or S45F) and WT are two distinct molecular subgroups with regard to β‐catenin stability, α‐catenin affinity, and gene expression profiling. A different inflammation signature characterized the two mutated groups, suggesting mediation either by T41A or by S45F. Finally, all mutated cases showed a low number of TIL and TAM cells and a low or absent expression of PD‐1 and PD‐L1 consistent with β‐catenin activation insensitive to checkpoint blockade.
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Affiliation(s)
- Chiara Colombo
- Sarcoma Service, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Antonino Belfiore
- Laboratory of Experimental Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Nicholas Paielli
- Laboratory of Experimental Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Loris De Cecco
- Functional Genomics and Bioinformatics, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvana Canevari
- Functional Genomics and Bioinformatics, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, University of Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, University of Trieste, Italy
| | - Sabrina Pricl
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, University of Trieste, Italy
| | - Paolo Verderio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Stefano Bottelli
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Marco Fiore
- Sarcoma Service, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Silvia Stacchiotti
- Adult Mesenchymal Tumor Medical Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Elena Palassini
- Adult Mesenchymal Tumor Medical Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Alessandro Gronchi
- Sarcoma Service, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Silvana Pilotti
- Laboratory of Experimental Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Federica Perrone
- Laboratory of Experimental Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
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141
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Park C, Cho J, Lee J, Kang SY, An JY, Choi MG, Lee JH, Sohn TS, Bae JM, Kim S, Kim ST, Park SH, Park JO, Kang WK, Sohn I, Jung SH, Kang MS, Kim KM. Host immune response index in gastric cancer identified by comprehensive analyses of tumor immunity. Oncoimmunology 2017; 6:e1356150. [PMID: 29147610 DOI: 10.1080/2162402x.2017.1356150] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/05/2017] [Accepted: 07/07/2017] [Indexed: 12/13/2022] Open
Abstract
Tumor infiltrating lymphocytes (TIL) in Epstein-Barr virus (EBV)-associated/microsatellite-unstable (MSI) gastric carcinomas (GC) constitute immune-active principal cellular components of tumor microenvironment and contribute to better prognosis. With the remarkable success of cancer immunotherapies, there is an urgent need for a comprehensive understanding of tumor-immune interactions in patients with GC in the context of host immune response. To identify GC subtype-specific immune response gene set, we tested differentially expressed genes for MSI and EBV+ GC subtypes in randomly selected test set (n = 278) in merged ACRG-SMC microarray and TCGA RNA sequencing data set. We identified Host ImmunE Response index (HIERÏ) consisting of 29 immune genes classifying GC patients into robust 3 groups with prognostic significance. Immune-high cluster 1 was enriched with PD-L1High/EBV+/MSI/TILHigh with the best clinical outcome while immune-low cluster 3 displayed worst outcome and exemplified with PD-L1Low/EBV-/MSS. The results were validated in the same cohort (n = 279) and independent cohort (n = 181) with RNA from formalin-fixed paraffin-embedded (FFPE) tissue. Unexpectedly, nearly half of GC in cluster 1 were EBV-/MSS and 10% of cluster 3 GC were EBV+/MSI GC patients, suggesting that in addition to EBV+/MSI GC subtypes, EBV-/MSS subtype also constitutes almost half of high immune cluster and would be a good candidate for immune checkpoint inhibitor therapy. In contrary, almost 10% of EBV+/MSI GC patients may not respond to immune checkpoint inhibitor therapy. Thus, our HIERÏ gene signature demonstrates the potential to subclassify tumor immunity levels, predict prognosis and help immunotherapeutic decisions.
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Affiliation(s)
- Charny Park
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Clinical Genome Analysis and Precision Medicine Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Junhun Cho
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Pathology, Soonchunhyang University Cheonan Hospital, Soonchunhyang University College of Medicine, Cheonan, Korea
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - So Young Kang
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji Yeong An
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Min Gew Choi
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jun Ho Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Sung Sohn
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Moon Bae
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Se Hoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Oh Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Ki Kang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Insuk Sohn
- Biostatistics and Clinical Epidemiology Center, Samsung Medical Center, Seoul, Korea
| | - Sin Ho Jung
- Biostatistics and Clinical Epidemiology Center, Samsung Medical Center, Seoul, Korea
| | - Myung-Soo Kang
- Samsung Biomedical Research Institute (SBRI), Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University and Samsung Medical Center, Seoul, Korea.,Lifetech Institute of iNtRON Biotechnology, Seongnam, Korea
| | - Kyoung-Mee Kim
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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142
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Petralia F, Aushev VN, Gopalakrishnan K, Kappil M, W Khin N, Chen J, Teitelbaum SL, Wang P. A new method to study the change of miRNA-mRNA interactions due to environmental exposures. Bioinformatics 2017; 33:i199-i207. [PMID: 28881990 PMCID: PMC5870720 DOI: 10.1093/bioinformatics/btx256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
MOTIVATION Integrative approaches characterizing the interactions among different types of biological molecules have been demonstrated to be useful for revealing informative biological mechanisms. One such example is the interaction between microRNA (miRNA) and messenger RNA (mRNA), whose deregulation may be sensitive to environmental insult leading to altered phenotypes. The goal of this work is to develop an effective data integration method to characterize deregulation between miRNA and mRNA due to environmental toxicant exposures. We will use data from an animal experiment designed to investigate the effect of low-dose environmental chemical exposure on normal mammary gland development in rats to motivate and evaluate the proposed method. RESULTS We propose a new network approach-integrative Joint Random Forest (iJRF), which characterizes the regulatory system between miRNAs and mRNAs using a network model. iJRF is designed to work under the high-dimension low-sample-size regime, and can borrow information across different treatment conditions to achieve more accurate network inference. It also effectively takes into account prior information of miRNA-mRNA regulatory relationships from existing databases. When iJRF is applied to the data from the environmental chemical exposure study, we detected a few important miRNAs that regulated a large number of mRNAs in the control group but not in the exposed groups, suggesting the disruption of miRNA activity due to chemical exposure. Effects of chemical exposure on two affected miRNAs were further validated using breast cancer human cell lines. AVAILABILITY AND IMPLEMENTATION R package iJRF is available at CRAN. CONTACTS pei.wang@mssm.edu or susan.teitelbaum@mssm.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vasily N Aushev
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kalpana Gopalakrishnan
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maya Kappil
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nyan W Khin
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susan L Teitelbaum
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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143
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Jing Y, Chavez V, Ban Y, Acquavella N, El-Ashry D, Pronin A, Chen X, Merchan JR. Molecular Effects of Stromal-Selective Targeting by uPAR-Retargeted Oncolytic Virus in Breast Cancer. Mol Cancer Res 2017; 15:1410-1420. [PMID: 28679779 DOI: 10.1158/1541-7786.mcr-17-0016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/21/2017] [Accepted: 06/29/2017] [Indexed: 12/22/2022]
Abstract
The tumor microenvironment (TME) is a relevant target for novel biological therapies. MV-m-uPA and MV-h-uPA are fully retargeted, species-specific, oncolytic measles viruses (MV) directed against murine or human urokinase receptor (PLAUR/uPAR), expressed in tumor and stromal cells. The effects of stromal-selective targeting by uPAR-retargeted MVs were investigated. In vitro infection, virus-induced GFP expression, and cytotoxicity by MV-h-uPA and MV-m-uPA were demonstrated in human and murine cancer cells and cancer-associated fibroblasts in a species-specific manner. In a murine fibroblast/human breast cancer 3D coculture model, selective fibroblast targeting by MV-m-uPA inhibited breast cancer cell growth. Systemic administration of murine-specific MV-m-uPA in mice bearing human MDA-MB-231 xenografts was associated with a significant delay in tumor progression and improved survival compared with controls. Experiments comparing tumor (MV-h-uPA) versus stromal (MV-m-uPA) versus combined virus targeting showed that tumor and stromal targeting was associated with improved tumor control over the other groups. Correlative studies confirmed in vivo viral targeting of tumor stroma by MV-m-uPA, increased apoptosis, and virus-induced differential regulation of murine stromal genes associated with inflammatory, angiogenesis, and survival pathways, as well as indirect regulation of human cancer pathways, indicating viral-induced modulation of tumor-stroma interactions. These data demonstrate the feasibility of stromal-selective targeting by an oncolytic MV, virus-induced modulation of tumor-stroma pathways, and subsequent tumor growth delay. These findings further validate the critical role of stromal uPAR in cancer progression and the potential of oncolytic viruses as antistromal agents.Implications: The current report demonstrates for the first time the biological, in vitro, and in vivo antitumor and molecular effects of stromal selective targeting by an oncolytic virus. Mol Cancer Res; 15(10); 1410-20. ©2017 AACR.
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Affiliation(s)
- Yuqi Jing
- Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Valery Chavez
- Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Yuguang Ban
- Division of Biostatistics and Bioinformatics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Nicolas Acquavella
- Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Doraya El-Ashry
- Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Alexey Pronin
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
| | - Xi Chen
- Division of Biostatistics and Bioinformatics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Jaime R Merchan
- Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida.
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144
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Mariano VS, Leal LF, Pastrez PRA, Silva EM, Reis RM, Longatto-Filho A. Lung cancer samples preserved in liquid medium: One step beyond cytology. Diagn Cytopathol 2017; 45:915-921. [PMID: 28589673 DOI: 10.1002/dc.23743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 04/19/2017] [Accepted: 04/20/2017] [Indexed: 12/14/2022]
Abstract
Lung cancer is one of the most common cancer types in men and women worldwide with a high mortality rate. World Health Organization (WHO) classification has accepted biopsy as the primary sample for lung cancer diagnosis, pathological classification and molecular testing for management of patients, yet, the use of alternative sampling procedures is highly encouraged. Bronchial cytological samples require a less invasive collection technique and may be suitable for pathological and molecular analysis and storage in liquid medium. Furthermore, the molecular analysis of bronchial cytological samples allows the detection of molecular biomarkers, which may be useful for the selection of molecular targeted therapies. Thus, the purpose of this review is to describe the usefulness of bronchial cytological samples preserved in liquid medium from lung cancer patients for pathological diagnosis and molecular investigation.
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Affiliation(s)
| | - Letícia Ferro Leal
- Barretos Cancer Hospital/Pio XII Foundation, Molecular Oncology Research Center, Brazil
| | | | - Estela Maria Silva
- Barretos Cancer Hospital/Pio XII Foundation, Molecular Oncology Research Center, Brazil
| | - Rui Manuel Reis
- Barretos Cancer Hospital/Pio XII Foundation, Molecular Oncology Research Center, Brazil.,Research Institute of Life and Health Sciences (ICVS), University of Minho, Braga, Portugal.,ICVS/3B's - Associated Laboratory to the Government of Portugal, Braga/Guimarães, Portugal
| | - Adhemar Longatto-Filho
- Barretos Cancer Hospital/Pio XII Foundation, Molecular Oncology Research Center, Brazil.,Research Institute of Life and Health Sciences (ICVS), University of Minho, Braga, Portugal.,ICVS/3B's - Associated Laboratory to the Government of Portugal, Braga/Guimarães, Portugal.,Medical Laboratory of Medical Investigation (LIM) 14, Department of Pathology, Faculty of Medicine, University of São Paulo, Brazil
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145
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Ling B, Watt K, Banerjee S, Newsted D, Truesdell P, Adams J, Sidhu SS, Craig AWB. A novel immunotherapy targeting MMP-14 limits hypoxia, immune suppression and metastasis in triple-negative breast cancer models. Oncotarget 2017; 8:58372-58385. [PMID: 28938563 PMCID: PMC5601659 DOI: 10.18632/oncotarget.17702] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/22/2017] [Indexed: 12/12/2022] Open
Abstract
Matrix metalloproteinase-14 (MMP-14) is a clinically relevant target in metastatic cancers due to its role in tumor progression and metastasis. Since active MMP-14 is localized on the cell surface, it is amenable to antibody-mediated blockade in cancer, and here we describe our efforts to develop novel inhibitory anti-MMP-14 antibodies. A phage-displayed synthetic humanized Fab library was screened against the extracellular domain of MMP-14 and a panel of MMP14-specific Fabs were identified. A lead antibody that inhibits the catalytic domain of MMP-14 (Fab 3369) was identified and treatment of MDA-MB-231 breast cancer cells with Fab 3369 led to significant loss of extracellular matrix degradation and cell invasion abilities. In mammary orthotopic tumor xenograft assays, MMP-14 blockade by IgG 3369 limited tumor growth and metastasis. Analysis of tumor tissue sections revealed that MMP-14 blockade limited tumor neoangiogenesis and hypoxia. Similar effects of MMP-14 blockade in syngeneic 4T1 mammary tumors were observed, along with increased detection of cytotoxic immune cell markers. In conclusion, we show that immunotherapies targeting MMP-14 can limit immune suppression, tumor progression, and metastasis in triple-negative breast cancer.
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Affiliation(s)
- Binbing Ling
- Department of Biomedical and Molecular Sciences, Queen's University, Cancer Biology and Genetics Division, Queen's Cancer Research Institute, Kingston, ON, Canada
| | - Kathleen Watt
- Department of Biomedical and Molecular Sciences, Queen's University, Cancer Biology and Genetics Division, Queen's Cancer Research Institute, Kingston, ON, Canada
| | | | - Daniel Newsted
- Department of Biomedical and Molecular Sciences, Queen's University, Cancer Biology and Genetics Division, Queen's Cancer Research Institute, Kingston, ON, Canada
| | - Peter Truesdell
- Department of Biomedical and Molecular Sciences, Queen's University, Cancer Biology and Genetics Division, Queen's Cancer Research Institute, Kingston, ON, Canada
| | - Jarrett Adams
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Andrew W B Craig
- Department of Biomedical and Molecular Sciences, Queen's University, Cancer Biology and Genetics Division, Queen's Cancer Research Institute, Kingston, ON, Canada
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146
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Mairinger FD, Werner R, Flom E, Schmeller J, Borchert S, Wessolly M, Wohlschlaeger J, Hager T, Mairinger T, Kollmeier J, Christoph DC, Schmid KW, Walter RFH. miRNA regulation is important for DNA damage repair and recognition in malignant pleural mesothelioma. Virchows Arch 2017; 470:627-637. [PMID: 28466156 DOI: 10.1007/s00428-017-2133-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/10/2017] [Accepted: 04/13/2017] [Indexed: 01/06/2023]
Abstract
Platin-containing regimes are currently considered as state-of-the-art therapies in malignant pleural mesotheliomas (MPM) but show dissatisfying response rates ranging from 6 to 16% only. Still, the reasons for the rather poor efficacy remain largely unknown. A clear stratification of patients based on new biomarkers seems to be a promising approach to enhance clinical management, which would be a long-needed improvement for MPM patients but does not seem likely soon unless new biomarkers can be validated. Twenty-four formalin-fixed, paraffin-embedded (FFPE) tumour specimens were subjected to a miRNA expression screening of 800 important miRNAs using digital quantification via the nCounter technique (NanoString). We defined a small subset of miRNAs regulating the key enzymes involved in the repair of platin-associated DNA damage. Particularly, the TP53 pathway network for DNA damage recognition as well as genes related to the term "BRCAness" are the main miRNA targets within this context. The TP53 pathway network for DNA damage recognition as well as genes related to the term "BRCAness" are the main players for risk stratification in patients suffering from this severe disease. Taking the specific molecular profile of the tumour into account can help to enhance the clinical management prospectively and to smooth the way to better response prediction.
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Affiliation(s)
- Fabian Dominik Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany.
| | - Robert Werner
- Institute of Pathology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Elena Flom
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Jan Schmeller
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Sabrina Borchert
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Michael Wessolly
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Thomas Hager
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Thomas Mairinger
- Institute of Pathology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Jens Kollmeier
- Institute of Pneumology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Daniel Christian Christoph
- Department of Medical Oncology, West German Cancer Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Robert Fred Henry Walter
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany.,Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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147
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Kappel A, Keller A. miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects. Clin Chem Lab Med 2017; 55:636-647. [PMID: 27987355 DOI: 10.1515/cclm-2016-0467] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/01/2016] [Indexed: 12/27/2022]
Abstract
microRNAs (miRNAs) are short non-coding RNA molecules that regulate gene expression in eukaryotes. Their differential abundance is indicative or even causative for a variety of pathological processes including cancer or cardiovascular disorders. Due to their important biological function, miRNAs represent a promising class of novel biomarkers that may be used to diagnose life-threatening diseases, and to monitor disease progression. Further, they may guide treatment selection or dosage of drugs. miRNAs from blood or derived fractions are particularly interesting candidates for routine laboratory applications, as they can be measured in most clinical laboratories already today. This assures a good accessibility of respective tests. Albeit their great potential, miRNA-based diagnostic tests have not made their way yet into the clinical routine, and hence no standardized workflows have been established to measure miRNAs for patients' benefit. In this review we summarize the detection technologies and workflow options that exist to measure miRNAs, and we describe the advantages and disadvantages of each of these options. Moreover, we also provide a perspective on data analysis aspects that are vital for translation of raw data into actionable diagnostic test results.
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Affiliation(s)
- Andreas Kappel
- Siemens Healthcare GmbH, Guenther-Scharowsky-Str.1, Erlangen
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbruecken
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148
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Walter RFH, Vollbrecht C, Werner R, Wohlschlaeger J, Christoph DC, Schmid KW, Mairinger FD. microRNAs are differentially regulated between MDM2-positive and negative malignant pleural mesothelioma. Oncotarget 2017; 7:18713-21. [PMID: 26918730 PMCID: PMC4951323 DOI: 10.18632/oncotarget.7666] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/02/2016] [Indexed: 12/14/2022] Open
Abstract
Background Malignant pleural mesothelioma (MPM) is a highly aggressive tumour first-line treated with a combination of cisplatin and pemetrexed. MDM2 and P14/ARF (CDKN2A) are upstream regulators of TP53 and may contribute to its inactivation. In the present study, we now aimed to define the impact of miRNA expression on this mechanism. Material and Methods 24 formalin-fixed paraffin-embedded (FFPE) tumour specimens were used for miRNA expression analysis of the 800 most important miRNAs using the nCounter technique (NanoString). Significantly deregulated miRNAs were identified before a KEGG-pathway analysis was performed. Results 17 miRNAs regulating TP53, 18 miRNAs regulating MDM2, and 11 miRNAs directly regulating CDKN2A are significantly downregulated in MDM2-expressing mesotheliomas. TP53 is downregulated in MDM2-negative tumours through miRNAs with a miSVR prediction score of 11.67, RB1 with a prediction score of 8.02, MDM2 with a prediction score of 4.50 and CDKN2A with a prediction score of 1.27. Conclusion MDM2 expression seems to impact miRNA expression levels in MPM. Especially, miRNAs involved in TP53-signaling are strongly decreased in MDM2-positive mesotheliomas. A better understanding of its tumour biology may open the chance for new therapeutic approaches and thereby augment patients' outcome.
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Affiliation(s)
- Robert Fred Henry Walter
- Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Claudia Vollbrecht
- Institute of Pathology, University Hospital Cologne, Germany.,Institute of Pathology, Division of Molecular Pathology, Charité, Berlin, Germany
| | - Robert Werner
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Daniel Christian Christoph
- Department of Medical Oncology, West German Cancer Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Fabian Dominik Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, Division of Molecular Pathology, Charité, Berlin, Germany
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149
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Bayani J, Yao CQ, Quintayo MA, Yan F, Haider S, D’Costa A, Brookes CL, van de Velde CJH, Hasenburg A, Kieback DG, Markopoulos C, Dirix L, Seynaeve C, Rea D, Boutros PC, Bartlett JMS. Molecular stratification of early breast cancer identifies drug targets to drive stratified medicine. NPJ Breast Cancer 2017; 3:3. [PMID: 28649643 PMCID: PMC5445616 DOI: 10.1038/s41523-016-0003-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 12/13/2016] [Accepted: 12/13/2016] [Indexed: 12/28/2022] Open
Abstract
Many women with hormone receptor-positive early breast cancer can be managed effectively with endocrine therapies alone. However, additional systemic chemotherapy treatment is necessary for others. The clinical challenges in managing high-risk women are to identify existing and novel druggable targets, and to identify those who would benefit from these therapies. Therefore, we performed mRNA abundance analysis using the Tamoxifen and Exemestane Adjuvant Multinational (TEAM) trial pathology cohort to identify a signature of residual risk following endocrine therapy and pathways that are potentially druggable. A panel of genes compiled from academic and commercial multiparametric tests as well as genes of importance to breast cancer pathogenesis was used to profile 3825 patients. A signature of 95 genes, including nodal status, was validated to stratify endocrine-treated patients into high-risk and low-risk groups based on distant relapse-free survival (DRFS; Hazard Ratio = 5.05, 95% CI 3.53-7.22, p = 7.51 × 10-19). This risk signature was also found to perform better than current multiparametric tests. When the 95-gene prognostic signature was applied to all patients in the validation cohort, including patients who received adjuvant chemotherapy, the signature remained prognostic (HR = 4.76, 95% CI 3.61-6.28, p = 2.53× 10-28). Functional gene interaction analyses identified six significant modules representing pathways involved in cell cycle control, mitosis and receptor tyrosine signaling; containing a number of genes with existing targeted therapies for use in breast or other malignancies. Thus the identification of high-risk patients using this prognostic signature has the potential to also prioritize patients for treatment with these targeted therapies.
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Affiliation(s)
- Jane Bayani
- Ontario Institute for Cancer Research, Toronto, ON Canada
| | - Cindy Q. Yao
- Ontario Institute for Cancer Research, Toronto, ON Canada
| | | | - Fu Yan
- Ontario Institute for Cancer Research, Toronto, ON Canada
| | - Syed Haider
- Ontario Institute for Cancer Research, Toronto, ON Canada
| | | | - Cassandra L. Brookes
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | | | | | | | | | - Luc Dirix
- St. Augustinus Hospital, Antwerp, Belgium
| | | | - Daniel Rea
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - Paul C. Boutros
- Ontario Institute for Cancer Research, Toronto, ON Canada
- University of Toronto, Toronto, Canada
| | - John M. S. Bartlett
- Ontario Institute for Cancer Research, Toronto, ON Canada
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
- University of Toronto, Toronto, Canada
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150
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Chen Y, Liu D, Liu P, Chen Y, Yu H, Zhang Q. Identification of biomarkers of intrahepatic cholangiocarcinoma via integrated analysis of mRNA and miRNA microarray data. Mol Med Rep 2017; 15:1051-1056. [PMID: 28098904 PMCID: PMC5367350 DOI: 10.3892/mmr.2017.6123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 11/07/2016] [Indexed: 01/06/2023] Open
Abstract
The present study aimed to identify potential therapeutic targets of intrahepatic cholangiocarcinoma (ICC) via integrated analysis of gene (transcript version) and microRNA (miRNA/miR) expression. The miRNA microarray dataset GSE32957 contained miRNA expression data from 16 ICC, 7 mixed type of combined hepatocellular-cholangiocarcinoma (CHC), 2 hepatic adenoma, 3 focal nodular hyperplasia (FNH) and 5 healthy liver tissue samples, and 2 cholangiocarcinoma cell lines. In addition, the mRNA microarray dataset GSE32879 contained mRNA expression data from 16 ICC, 7 CHC, 2 hepatic adenoma, 5 FNH and 7 healthy liver tissue samples. The datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and miRNAs (DEMs) in ICC samples compared with healthy liver tissues were identified via the limma package, following data preprocessing. Genes that exhibited alternative splicing (AS) in ICC samples were identified via AltAnalyze software. Functional enrichment analysis of DEGs was performed using the Database for Annotation, Visualization and Integrated Analysis. Target genes of DEMs were identified using the TargetScan database. The regulatory association between DEMs and any overlaps among DEGs, alternative splicing genes (ASGs) and target genes of DEMs were retrieved, and a network was visualized using the Cytoscape software. A total of 2,327 DEGs, 70 DEMs and 623 ASGs were obtained. Functional enrichment analysis indicated that DEGs were primarily enriched in biological processes and pathways associated with cell activity or the immune system. A total of 63 overlaps were obtained among DEGs, ASGs and target genes of DEMs, and a regulation network that contained 243 miRNA-gene regulation pairs was constructed between these overlaps and DEMs. The overlapped genes, including sprouty-related EVH1 domain containing 1, protein phosphate 1 regulatory subunit 12A, chromosome 20 open reading frame 194, and DEMs, including hsa-miR-96, hsa-miR-1 and hsa-miR-25, may be potential therapeutic targets for the future treatment of ICC.
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Affiliation(s)
- Yaqing Chen
- Department of VIP Ward, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Dan Liu
- Department of Ultrasonic Imaging, Zhuhai People's Hospital, Zhuhai, Guangdong 519000, P.R. China
| | - Pengfei Liu
- Department of Lymphoma, Sino‑US Center of Lymphoma and Leukemia, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Yajing Chen
- Department of Internal Medicine, Baoding Xiongxian County Hospital, Baoding, Hebei 071000, P.R. China
| | - Huiling Yu
- Department of Gastroenterology, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Quan Zhang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
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