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Whole blood co-expression modules associate with metabolic traits and type 2 diabetes: an IMI-DIRECT study. Genome Med 2020; 12:109. [PMID: 33261667 PMCID: PMC7708171 DOI: 10.1186/s13073-020-00806-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/11/2020] [Indexed: 01/04/2023] Open
Abstract
Background The rising prevalence of type 2 diabetes (T2D) poses a major global challenge. It remains unresolved to what extent transcriptomic signatures of metabolic dysregulation and T2D can be observed in easily accessible tissues such as blood. Additionally, large-scale human studies are required to further our understanding of the putative inflammatory component of insulin resistance and T2D. Here we used transcriptomics data from individuals with (n = 789) and without (n = 2127) T2D from the IMI-DIRECT cohorts to describe the co-expression structure of whole blood that mainly reflects processes and cell types of the immune system, and how it relates to metabolically relevant clinical traits and T2D. Methods Clusters of co-expressed genes were identified in the non-diabetic IMI-DIRECT cohort and evaluated with regard to stability, as well as preservation and rewiring in the cohort of individuals with T2D. We performed functional and immune cell signature enrichment analyses, and a genome-wide association study to describe the genetic regulation of the modules. Phenotypic and trans-omics associations of the transcriptomic modules were investigated across both IMI-DIRECT cohorts. Results We identified 55 whole blood co-expression modules, some of which clustered in larger super-modules. We identified a large number of associations between these transcriptomic modules and measures of insulin action and glucose tolerance. Some of the metabolically linked modules reflect neutrophil-lymphocyte ratio in blood while others are independent of white blood cell estimates, including a module of genes encoding neutrophil granule proteins with antibacterial properties for which the strongest associations with clinical traits and T2D status were observed. Through the integration of genetic and multi-omics data, we provide a holistic view of the regulation and molecular context of whole blood transcriptomic modules. We furthermore identified an overlap between genetic signals for T2D and co-expression modules involved in type II interferon signaling. Conclusions Our results offer a large-scale map of whole blood transcriptomic modules in the context of metabolic disease and point to novel biological candidates for future studies related to T2D.
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202
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High-coverage lipidomics for functional lipid and pathway analyses. Anal Chim Acta 2020; 1147:199-210. [PMID: 33485579 DOI: 10.1016/j.aca.2020.11.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022]
Abstract
Rapid advances in front-end separation approaches and analytical technologies have accelerated the development of lipidomics, particularly in terms of increasing analytical coverage to encompass an expanding repertoire of lipids within a single analytical approach. Developments in lipid pathway analysis, however, have somewhat lingered behind, primarily due to (1) the lack of coherent alignment between lipid identifiers in common databases versus that generated from experiments, owing to the differing structural resolution of lipids at molecular level that is specific to the analytical approaches adopted by various laboratories; (2) the immense complexity of lipid metabolic relationships that may entail head group changes, fatty acyls modifications of various forms (e.g. elongation, desaturation, oxidation), as well as active remodeling that demands a multidimensional, panoramic view to take into account all possibilities in lipid pathway analyses. Herein, we discuss current efforts undertaken to address these challenges, as well as alternative form of "pathway analyses" that may be particularly useful for uncovering functional lipid interactions under different biological contexts. Consolidating lipid pathway analyses will be indispensable in facilitating the transition of lipidomics from its prior role of phenotype validation to a hypothesis-generating tool that uncovers novel molecular targets to drive downstream mechanistic pursuits under biomedical settings.
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203
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Tanaka T, Basisty N, Fantoni G, Candia J, Moore AZ, Biancotto A, Schilling B, Bandinelli S, Ferrucci L. Plasma proteomic biomarker signature of age predicts health and life span. eLife 2020; 9:61073. [PMID: 33210602 PMCID: PMC7723412 DOI: 10.7554/elife.61073] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022] Open
Abstract
Older age is a strong shared risk factor for many chronic diseases, and there is increasing interest in identifying aging biomarkers. Here, a proteomic analysis of 1301 plasma proteins was conducted in 997 individuals between 21 and 102 years of age. We identified 651 proteins associated with age (506 over-represented, 145 underrepresented with age). Mediation analysis suggested a role for partial cis-epigenetic control of protein expression with age. Of the age-associated proteins, 33.5% and 45.3%, were associated with mortality and multimorbidity, respectively. There was enrichment of proteins associated with inflammation and extracellular matrix as well as senescence-associated secretory proteins. A 76-protein proteomic age signature predicted accumulation of chronic diseases and all-cause mortality. These data support the use of proteomic biomarkers to monitor aging trajectories and to identify individuals at higher risk of disease to be targeted for in depth diagnostic procedures and early interventions.
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Affiliation(s)
- Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, United States
| | - Nathan Basisty
- The Buck Institute for Research on Aging, Novato, United States
| | - Giovanna Fantoni
- National Institute on Aging, Intramural Research Program, Clinical Research Core, NIH, Baltimore, United States
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, United States
| | - Ann Z Moore
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, United States
| | - Angelique Biancotto
- Precision Immunology, Immunology & Inflammation Research Therapeutic Area, Sanofi, Cambridge, United States
| | | | | | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, United States
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204
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Divergent organ-specific isogenic metastatic cell lines identified using multi-omics exhibit differential drug sensitivity. PLoS One 2020; 15:e0242384. [PMID: 33196681 PMCID: PMC7668614 DOI: 10.1371/journal.pone.0242384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/01/2020] [Indexed: 12/19/2022] Open
Abstract
Background Monitoring and treating metastatic progression remains a formidable task due, in part, to an inability to monitor specific differential molecular adaptations that allow the cancer to thrive within different tissue types. Hence, to develop optimal treatment strategies for metastatic disease, an important consideration is the divergence of the metastatic cancer growing in visceral organs from the primary tumor. We had previously reported the establishment of isogenic human metastatic breast cancer cell lines that are representative of the common metastatic sites observed in breast cancer patients. Methods Here we have used proteomic, RNAseq, and metabolomic analyses of these isogenic cell lines to systematically identify differences and commonalities in pathway networks and examine the effect on the sensitivity to breast cancer therapeutic agents. Results Proteomic analyses indicated that dissemination of cells from the primary tumor sites to visceral organs resulted in cell lines that adapted to growth at each new site by, in part, acquiring protein pathways characteristic of the organ of growth. RNAseq and metabolomics analyses further confirmed the divergences, which resulted in differential efficacies to commonly used FDA approved chemotherapeutic drugs. This model system has provided data that indicates that organ-specific growth of malignant lesions is a selective adaptation and growth process. Conclusions The insights provided by these analyses indicate that the rationale of targeted treatment of metastatic disease may benefit from a consideration that the biology of metastases has diverged from the primary tumor biology and using primary tumor traits as the basis for treatment may not be ideal to design treatment strategies.
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205
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Barel G, Herwig R. NetCore: a network propagation approach using node coreness. Nucleic Acids Res 2020; 48:e98. [PMID: 32735660 PMCID: PMC7515737 DOI: 10.1093/nar/gkaa639] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/22/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
We present NetCore, a novel network propagation approach based on node coreness, for phenotype–genotype associations and module identification. NetCore addresses the node degree bias in PPI networks by using node coreness in the random walk with restart procedure, and achieves improved re-ranking of genes after propagation. Furthermore, NetCore implements a semi-supervised approach to identify phenotype-associated network modules, which anchors the identification of novel candidate genes at known genes associated with the phenotype. We evaluated NetCore on gene sets from 11 different GWAS traits and showed improved performance compared to the standard degree-based network propagation using cross-validation. Furthermore, we applied NetCore to identify disease genes and modules for Schizophrenia GWAS data and pan-cancer mutation data. We compared the novel approach to existing network propagation approaches and showed the benefits of using NetCore in comparison to those. We provide an easy-to-use implementation, together with a high confidence PPI network extracted from ConsensusPathDB, which can be applied to various types of genomics data in order to obtain a re-ranking of genes and functionally relevant network modules.
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Affiliation(s)
- Gal Barel
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
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206
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Byun JK, Park M, Lee S, Yun JW, Lee J, Kim JS, Cho SJ, Jeon HJ, Lee IK, Choi YK, Park KG. Inhibition of Glutamine Utilization Synergizes with Immune Checkpoint Inhibitor to Promote Antitumor Immunity. Mol Cell 2020; 80:592-606.e8. [PMID: 33159855 DOI: 10.1016/j.molcel.2020.10.015] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/21/2020] [Accepted: 10/11/2020] [Indexed: 02/07/2023]
Abstract
Despite its outstanding clinical success, immune checkpoint blockade remains ineffective in many patients. Accordingly, combination therapy capable of achieving greater antitumor immunity is urgently required. Here, we report that limiting glutamine metabolism in cancer cells bolsters the effectiveness of anti-programmed death ligand-1 (PD-L1) antibody. Inhibition of glutamine utilization increased PD-L1 levels in cancer cells, thereby inactivating co-cultured T cells. Under glutamine-limited conditions, reduced cellular GSH levels caused an upregulation of PD-L1 expression by impairing SERCA activity, which activates the calcium/NF-κB signaling cascade. Consequently, in tumors grown in immunocompetent mice, inhibition of glutamine metabolism decreased the antitumor activity of T cells. In combination with anti-PD-L1, however, glutamine depletion strongly promoted the antitumor efficacy of T cells in vitro and in vivo due to simultaneous increases in Fas/CD95 levels. Our results demonstrate the relevance of cancer glutamine metabolism to antitumor immunity and suggest that co-targeting of glutamine metabolism and PD-L1 represents a promising therapeutic approach.
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Affiliation(s)
- Jun-Kyu Byun
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41944, South Korea; Research Institute of Aging and Metabolism, Kyungpook National University, Daegu 41566, South Korea
| | - Mihyang Park
- Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghyeong Lee
- Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu 41566, South Korea
| | - Jae Won Yun
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul 05368, South Korea; Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, South Korea
| | - Jaebon Lee
- Sungkyunkwan University School of Medicine, Seoul 16419, South Korea
| | - Jae Sun Kim
- Sungkyunkwan University School of Medicine, Seoul 16419, South Korea
| | - Sung Jin Cho
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, South Korea
| | - Hui-Jeon Jeon
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, South Korea
| | - In-Kyu Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41944, South Korea; Research Institute of Aging and Metabolism, Kyungpook National University, Daegu 41566, South Korea; Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu 41566, South Korea
| | - Yeon-Kyung Choi
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41944, South Korea; Research Institute of Aging and Metabolism, Kyungpook National University, Daegu 41566, South Korea.
| | - Keun-Gyu Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41944, South Korea; Research Institute of Aging and Metabolism, Kyungpook National University, Daegu 41566, South Korea; Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu 41566, South Korea.
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207
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Molecular specializations of deep cortical layer analogs in songbirds. Sci Rep 2020; 10:18767. [PMID: 33127988 PMCID: PMC7599217 DOI: 10.1038/s41598-020-75773-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022] Open
Abstract
How the evolution of complex behavioral traits is associated with the emergence of novel brain pathways is largely unknown. Songbirds, like humans, learn vocalizations via tutor imitation and possess a specialized brain circuitry to support this behavior. In a comprehensive in situ hybridization effort, we show that the zebra finch vocal robust nucleus of the arcopallium (RA) shares numerous markers (e.g. SNCA, PVALB) with the adjacent dorsal intermediate arcopallium (AId), an avian analog of mammalian deep cortical layers with involvement in motor function. We also identify markers truly unique to RA and thus likely linked to modulation of vocal motor function (e.g. KCNC1, GABRE), including a subset of the known shared markers between RA and human laryngeal motor cortex (e.g. SLIT1, RTN4R, LINGO1, PLXNC1). The data provide novel insights into molecular features unique to vocal learning circuits, and lend support for the motor theory for vocal learning origin.
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208
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Kandemir B, Gulfidan G, Arga KY, Yilmaz B, Kurnaz IA. Transcriptomic profile of Pea3 family members reveal regulatory codes for axon outgrowth and neuronal connection specificity. Sci Rep 2020; 10:18162. [PMID: 33097800 PMCID: PMC7584614 DOI: 10.1038/s41598-020-75089-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
PEA3 transcription factor subfamily is present in a variety of tissues with branching morphogenesis, and play a particularly significant role in neural circuit formation and specificity. Many target genes in axon guidance and cell-cell adhesion pathways have been identified for Pea3 transcription factor (but not for Erm or Er81); however it was not so far clear whether all Pea3 subfamily members regulate same target genes, or whether there are unique targets for each subfamily member that help explain the exclusivity and specificity of these proteins in neuronal circuit formation. In this study, using transcriptomics and qPCR analyses in SH-SY5Y neuroblastoma cells, hypothalamic and hippocampal cell line, we have identified cell type-specific and subfamily member-specific targets for PEA3 transcription factor subfamily. While Pea3 upregulates transcription of Sema3D and represses Sema5B, for example, Erm and Er81 upregulate Sema5A and Er81 regulates Unc5C and Sema4G while repressing EFNB3 in SH-SY5Y neuroblastoma cells. We furthermore present a molecular model of how unique sites within the ETS domain of each family member can help recognize specific target motifs. Such cell-context and member-specific combinatorial expression profiles help identify cell-cell and cell-extracellular matrix communication networks and how they establish specific connections.
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Affiliation(s)
- Başak Kandemir
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
- Biotechnology Graduate Program, Yeditepe University, Kayisdagi, Istanbul, Turkey
- Department of Molecular Biology and Genetics, Baskent University, Ankara, Turkey
| | - Gizem Gulfidan
- Department of Bioengineering, Marmara University, Goztepe, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, Goztepe, Istanbul, Turkey
| | - Bayram Yilmaz
- Biotechnology Graduate Program, Yeditepe University, Kayisdagi, Istanbul, Turkey
- Faculty of Medicine, Yeditepe University, Kayisdagi, Istanbul, Turkey
| | - Isil Aksan Kurnaz
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey.
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey.
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209
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Guo Y, Mao X, Qiao Z, Chen B, Jin F. A Novel Promoter CpG-Based Signature for Long-Term Survival Prediction of Breast Cancer Patients. Front Oncol 2020; 10:579692. [PMID: 33194705 PMCID: PMC7606941 DOI: 10.3389/fonc.2020.579692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/08/2020] [Indexed: 11/20/2022] Open
Abstract
DNA methylation has been reported as one of the most critical epigenetic aberrations during the tumorigenesis and development of breast cancer (BC). This study explored a novel promoter CpG-based signature for long-term survival prediction of BC patients. We used The Cancer Genome Atlas (TCGA) data as training set, and results were validated in an independent dataset from Gene Expression Omnibus (GEO). First, the differential methylation CpG sites were screened in TCGA dataset, of which the candidate promoter CpG sites were preliminarily identified with the univariate Cox regression analysis and the least absolute shrinkage and selection operator regression analysis. Second, the signature was constructed with stepwise regression analysis and multivariate Cox proportional hazards model, which was validated with the survival analysis of two cohorts each from TCGA and GEO databases. The 10-year receiver operating characteristic curves of risk score presented an area under the curve of over 0.7 for both cohorts. A nomogram was also constructed and released. Moreover, Gene Set Enrichment Analysis was performed to identify the more active pathways in high-risk patients. The CpG sites-target gene correlations and differential methylation regions were further explored. In conclusion, the promoter CpG-based signature exhibited good prognostic prediction efficacy in the long-term overall survival of BC patients.
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Affiliation(s)
| | - Xiaoyun Mao
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
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210
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Lasconi C, Pahl MC, Cousminer DL, Doege CA, Chesi A, Hodge KM, Leonard ME, Lu S, Johnson ME, Su C, Hammond RK, Pippin JA, Terry NA, Ghanem LR, Leibel RL, Wells AD, Grant SFA. Variant-to-Gene-Mapping Analyses Reveal a Role for the Hypothalamus in Genetic Susceptibility to Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol 2020; 11:667-682. [PMID: 33069917 PMCID: PMC7843407 DOI: 10.1016/j.jcmgh.2020.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Inflammatory bowel disease (IBD) is a polygenic disorder characterized principally by dysregulated inflammation impacting the gastrointestinal tract. However, there also is increasing evidence for a clinical association with stress and depression. Given the role of the hypothalamus in stress responses and in the pathogenesis of depression, useful insights could be gleaned from understanding its genetic role in IBD. METHODS We conducted genetic correlation analyses on publicly available genome-wide association study summary statistics for depression and IBD traits to identify genetic commonalities. We used partitioned linkage disequilibrium score regression, leveraging our ATAC sequencing and promoter-focused Capture C data, to measure enrichment of IBD single-nucleotide polymorphisms within promoter-interacting open chromatin regions of human embryonic stem cell-derived hypothalamic-like neurons (HNs). Using the same data sets, we performed variant-to-gene mapping to implicate putative IBD effector genes in HNs. To contrast these results, we similarly analyzed 3-dimensional genomic data generated in epithelium-derived colonoids from rectal biopsy specimens from donors without pathologic disease noted at the time of colonoscopy. Finally, we conducted enrichment pathway analyses on the implicated genes to identify putative IBD dysfunctional pathways. RESULTS We found significant genetic correlations (rg) of 0.122 with an adjusted P (Padj) = 1.4 × 10-4 for IBD: rg = 0.122; Padj = 2.5 × 10-3 for ulcerative colitis and genetic correlation (rg) = 0.094; Padj = 2.5 × 10-3 for Crohn's disease, and significant approximately 4-fold (P = .005) and approximately 7-fold (P = .03) enrichment of IBD single-nucleotide polymorphisms in HNs and colonoids, respectively. We implicated 25 associated genes in HNs, among which CREM, CNTF, and RHOA encode key regulators of stress. Seven genes also additionally were implicated in the colonoids. We observed an overall enrichment for immune and hormonal signaling pathways, and a colonoid-specific enrichment for microbiota-relevant terms. CONCLUSIONS Our results suggest that the hypothalamus warrants further study in the context of IBD pathogenesis.
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Affiliation(s)
- Chiara Lasconi
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Diana L Cousminer
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Claudia A Doege
- Division of Molecular Genetics (Pediatrics), Naomi Berrie Diabetes Center, Columbia University Vagelos College of Physicians and Surgeons, New York, New York
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Kenyaita M Hodge
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Michelle E Leonard
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Matthew E Johnson
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Chun Su
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Reza K Hammond
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - James A Pippin
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | | | | | - Rudolph L Leibel
- Division of Molecular Genetics (Pediatrics), Naomi Berrie Diabetes Center, Columbia University Vagelos College of Physicians and Surgeons, New York, New York
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Department of Pathology, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Philadelphia, Pennsylvania
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania; Division of Diabetes and Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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211
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Jung H, Han S, Lee Y. Transcriptome analysis of alternative splicing in the pathogen life cycle in human foreskin fibroblasts infected with Trypanosoma cruzi. Sci Rep 2020; 10:17481. [PMID: 33060827 PMCID: PMC7566602 DOI: 10.1038/s41598-020-74540-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/05/2020] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma cruzi is an intracellular protozoan parasite that causes Chagas disease as a zoonotic pathogen. The parasite has been shown to remodel expression in the host transcriptome under different conditions. Although alternative splicing (AS) is involved in virtually every biological function in eukaryotes, including cellular differentiation and responses to immune reactions, host AS events that occur as a result of T. cruzi infection have yet to be explored. In this study, we bioinformatically investigated the transcriptome AS dynamics of T. cruzi (Y strain) infected human foreskin fibroblasts using RNA-Seq data captured over four timepoints (4, 24, 48, and 72 h post infection (hpi)). We identified 1768, 399, 250, and 299 differentially expressed exons (AS exons) at 4, 24, 48, and 72 hpi, respectively, showing that host AS mechanism may have a significant role in the intracellular life cycle of the parasite. We present an exon skipping event in HDAC7, which is a candidate gene that is important in the parasite’s cell cycle. To sum up, this bioinformatics analysis of transcriptome may provide new potential insight into AS regulation in human foreskin fibroblast (HFF) cells infected by T. cruzi and into its implication to the parasite life cycle. Moreover, identified AS genes may provide new potential molecular candidates for improving treatment.
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Affiliation(s)
- Hyeim Jung
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.
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212
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Pterostilbene Sensitizes Cisplatin-Resistant Human Bladder Cancer Cells with Oncogenic HRAS. Cancers (Basel) 2020; 12:cancers12102869. [PMID: 33036162 PMCID: PMC7650649 DOI: 10.3390/cancers12102869] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/26/2020] [Accepted: 10/02/2020] [Indexed: 12/28/2022] Open
Abstract
Simple Summary RAS oncoproteins are considered undruggable cancer targets. Nearly 15% of cases of bladder cancer have a mutation of HRAS. The active HRAS contributes to the tumor progression and the risk of recurrence. Using our novel gene expression screening platform, pterostilbene was identified to sensitize cisplatin-resistant bladder cancer cells with HRAS alterations via RAS-related autophagy and cell senescence pathways, suggesting a potentially chemotherapeutic role of pterostilbene for cisplatin treatment of human bladder cancer with oncogenic HRAS. Pterostilbene is a safe and readily available food ingredient in edible plants worldwide. Exploiting the principle of combination therapy on pterostilbene-enhanced biosensitivity to identify undruggable molecular targets for cancer therapy may have a great possibility to overcome the cisplatin resistance of bladder cancer. Our data make HRAS a good candidate for modulation by pterostilbene for targeted cancer therapy in combination with conventional chemotherapeutic agents cisplatin plus gemcitabine. Abstract Analysis of various public databases revealed that HRAS gene mutation frequency and mRNA expression are higher in bladder urothelial carcinoma. Further analysis revealed the roles of oncogenic HRAS, autophagy, and cell senescence signaling in bladder cancer cells sensitized to the anticancer drug cisplatin using the phytochemical pterostilbene. A T24 cell line with the oncogenic HRAS was chosen for further experiments. Indeed, coadministration of pterostilbene increased stronger cytotoxicity on T24 cells compared to HRAS wild-type E7 cells, which was paralleled by neither elevated apoptosis nor induced cell cycle arrest, but rather a marked elevation of autophagy and cell senescence in T24 cells. Pterostilbene-induced autophagy in T24 cells was paralleled by inhibition of class I PI3K/mTOR/p70S6K as well as activation of MEK/ERK (a RAS target) and class III PI3K pathways. Pterostilbene-induced cell senescence on T24 cells was paralleled by increased pan-RAS and decreased phospho-RB expression. Coadministration of PI3K class III inhibitor 3-methyladenine or MEK inhibitor U0126 suppressed pterostilbene-induced autophagy and reversed pterostilbene-enhanced cytotoxicity, but did not affect pterostilbene-elevated cell senescence in T24 cells. Animal study data confirmed that pterostilbene enhanced cytotoxicity of cisplatin plus gemcitabine. These results suggest a therapeutic application of pterostilbene in cisplatin-resistant bladder cancer with oncogenic HRAS.
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213
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Simpson M, Frisbee A, Kumar P, Schwan C, Aktories K, Petri WA. Clostridioides difficile binary toxin (CDT) is recognized by the TLR2/6 heterodimer to induce an NF-κB response. J Infect Dis 2020; 225:1296-1300. [PMID: 33011801 PMCID: PMC8974845 DOI: 10.1093/infdis/jiaa620] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022] Open
Abstract
Clostridioides difficile infection (CDI) represents a significant burden on the health care system, one that is exacerbated by the emergence of binary toxin (CDT)-producing hypervirulent C. difficile strains. Previous work from our lab has shown that TLR2 recognizes CDT to induce inflammation. Here we explore the interactions of CDT with TLR2 and the impact on host immunity during CDI. We found that the TLR2/6 heterodimer, not TLR2/1, is responsible for CDT recognition, and that gene pathways including NF-κB and MAPK downstream of TLR2/6 are upregulated in mice with intact TLR2/6 signaling during CDI.
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Affiliation(s)
- Morgan Simpson
- Department of Pathology, University of Virginia, Charlottesville, Virginia
| | - Alyse Frisbee
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Carsten Schwan
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus Aktories
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - William A Petri
- Department of Pathology, University of Virginia, Charlottesville, Virginia.,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia.,Department of Medicine, University of Virginia, Charlottesville, Virginia
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Chai AWY, Yee PS, Price S, Yee SM, Lee HM, Tiong VKH, Gonçalves E, Behan FM, Bateson J, Gilbert J, Tan AC, McDermott U, Garnett MJ, Cheong SC. Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway. eLife 2020; 9:e57761. [PMID: 32990596 PMCID: PMC7591259 DOI: 10.7554/elife.57761] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023] Open
Abstract
New therapeutic targets for oral squamous cell carcinoma (OSCC) are urgently needed. We conducted genome-wide CRISPR-Cas9 screens in 21 OSCC cell lines, primarily derived from Asians, to identify genetic vulnerabilities that can be explored as therapeutic targets. We identify known and novel fitness genes and demonstrate that many previously identified OSCC-related cancer genes are non-essential and could have limited therapeutic value, while other fitness genes warrant further investigation for their potential as therapeutic targets. We validate a distinctive dependency on YAP1 and WWTR1 of the Hippo pathway, where the lost-of-fitness effect of one paralog can be compensated only in a subset of lines. We also discover that OSCCs with WWTR1 dependency signature are significantly associated with biomarkers of favorable response toward immunotherapy. In summary, we have delineated the genetic vulnerabilities of OSCC, enabling the prioritization of therapeutic targets for further exploration, including the targeting of YAP1 and WWTR1.
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Affiliation(s)
- Annie Wai Yeeng Chai
- Head and Neck Cancer Research Team, Cancer Research Malaysia, Head and Neck Cancer Research TeamSubang Jaya, SelangorMalaysia
| | - Pei San Yee
- Head and Neck Cancer Research Team, Cancer Research Malaysia, Head and Neck Cancer Research TeamSubang Jaya, SelangorMalaysia
| | - Stacey Price
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - Shi Mun Yee
- Head and Neck Cancer Research Team, Cancer Research Malaysia, Head and Neck Cancer Research TeamSubang Jaya, SelangorMalaysia
| | - Hui Mei Lee
- Head and Neck Cancer Research Team, Cancer Research Malaysia, Head and Neck Cancer Research TeamSubang Jaya, SelangorMalaysia
| | - Vivian KH Tiong
- Head and Neck Cancer Research Team, Cancer Research Malaysia, Head and Neck Cancer Research TeamSubang Jaya, SelangorMalaysia
| | - Emanuel Gonçalves
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - Fiona M Behan
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - Jessica Bateson
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - James Gilbert
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - Aik Choon Tan
- Department of Biostatistics and Bioinformatics, Moffitt Cancer CenterTampaUnited States
| | - Ultan McDermott
- Oncology R&D AstraZeneca, CRUK Cambridge InstituteCambridgeUnited Kingdom
| | - Mathew J Garnett
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - Sok Ching Cheong
- Head and Neck Cancer Research Team, Cancer Research Malaysia, Head and Neck Cancer Research TeamSubang Jaya, SelangorMalaysia
- Department of Oral & Maxillofacial Clinical Sciences, Faculty of Dentistry, University of MalayaKuala LumpurMalaysia
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215
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EBF1-Correlated Long Non-coding RNA Transcript Levels in 3rd Trimester Maternal Blood and Risk of Spontaneous Preterm Birth. Reprod Sci 2020; 28:541-549. [PMID: 32959224 DOI: 10.1007/s43032-020-00320-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/14/2020] [Indexed: 12/19/2022]
Abstract
Biomarkers associated with spontaneous preterm birth (sPTB) before labor onset could aid in prediction, triage, and stratification for testing interventions. In this study we examined maternal blood EBF1-correlated long non-coding RNAs (lncRNAs) in relation to sPTB. We retrieved all lncRNA transcripts from a public gene expression dataset (GSE59491) derived from maternal blood in trimesters 2 and 3 from a Canadian cohort with a matched set of sPTB (n = 51) and term births (n = 106). LncRNA transcripts differentially expressed (limma moderated t-tests) in sPTB vs. term were tested for correlations (Pearson) with EBF1 mRNA levels in the same blood samples. Using logistic regression, EBF1-correlated lncRNAs were divided into tertiles and assessed in relation to odds of sPTB. Two lncRNA transcripts in the 3rd trimester maternal blood were differentially expressed between sPTB and term births (all p < 0.001 and FDR < 0.250) and positively and negatively correlated with EBF1 mRNA levels. They were as follows: (1) LINC00094 r = 0.196 (95% CI: 0.039 to 0.344), p = 0.015, and BH adjusted p = 0.022 and (2) LINC00870 r = - 0.303 (95% CI: - 0.441 to - 0.152), p < 0.001, and BH adjusted p < 0.001. As compared with term births, sPTBs were more likely to be in the highest tertile of LINC00870 (odds ratio (OR) = 4.08 (95% CI 1.60, 10.40), p = 0.003) and the lowest tertile of LINC00094 (OR = 5.16 (95% CI 1.96, 13.61), p < 0.001). Two sPTB-associated EBF1-correlated lncRNAs (LINC00870 and LINC00094) had multiple potential enhancers containing EBF1 binding site(s). Our current findings, along with previous reports linking EBF1 and sPTB, motivate additional research on the EBF1 gene-related gene expression and regulation in relation to sPTB within other cohorts and within laboratory-based models.
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216
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Wood SH, Hindle MM, Mizoro Y, Cheng Y, Saer BRC, Miedzinska K, Christian HC, Begley N, McNeilly J, McNeilly AS, Meddle SL, Burt DW, Loudon ASI. Circadian clock mechanism driving mammalian photoperiodism. Nat Commun 2020; 11:4291. [PMID: 32855407 PMCID: PMC7453030 DOI: 10.1038/s41467-020-18061-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
The annual photoperiod cycle provides the critical environmental cue synchronizing rhythms of life in seasonal habitats. In 1936, Bünning proposed a circadian-based coincidence timer for photoperiodic synchronization in plants. Formal studies support the universality of this so-called coincidence timer, but we lack understanding of the mechanisms involved. Here we show in mammals that long photoperiods induce the circadian transcription factor BMAL2, in the pars tuberalis of the pituitary, and triggers summer biology through the eyes absent/thyrotrophin (EYA3/TSH) pathway. Conversely, long-duration melatonin signals on short photoperiods induce circadian repressors including DEC1, suppressing BMAL2 and the EYA3/TSH pathway, triggering winter biology. These actions are associated with progressive genome-wide changes in chromatin state, elaborating the effect of the circadian coincidence timer. Hence, circadian clock-pituitary epigenetic pathway interactions form the basis of the mammalian coincidence timer mechanism. Our results constitute a blueprint for circadian-based seasonal timekeeping in vertebrates.
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Affiliation(s)
- S H Wood
- Centre for Biological Timing, Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
- Arctic Chronobiology and Physiology Research Group, Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, 9037, Norway
| | - M M Hindle
- The Roslin Institute, and Royal (Dick) School of Veterinary Studies University of Edinburgh, Roslin, Midlothian, EH25 9PRG, UK
| | - Y Mizoro
- Centre for Biological Timing, Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Y Cheng
- UQ Genomics Initiative, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | - B R C Saer
- Centre for Biological Timing, Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - K Miedzinska
- The Roslin Institute, and Royal (Dick) School of Veterinary Studies University of Edinburgh, Roslin, Midlothian, EH25 9PRG, UK
| | - H C Christian
- University of Oxford, Department of Physiology, Anatomy and Genetics, Le Gros Clark Building, South Parks Road, Oxford, OX1 3QX, UK
| | - N Begley
- Centre for Biological Timing, Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - J McNeilly
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, UK
| | - A S McNeilly
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, UK
| | - S L Meddle
- The Roslin Institute, and Royal (Dick) School of Veterinary Studies University of Edinburgh, Roslin, Midlothian, EH25 9PRG, UK
| | - D W Burt
- The Roslin Institute, and Royal (Dick) School of Veterinary Studies University of Edinburgh, Roslin, Midlothian, EH25 9PRG, UK
- UQ Genomics Initiative, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - A S I Loudon
- Centre for Biological Timing, Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.
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217
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HIF-1α and HIF-2α differently regulate tumour development and inflammation of clear cell renal cell carcinoma in mice. Nat Commun 2020; 11:4111. [PMID: 32807776 PMCID: PMC7431415 DOI: 10.1038/s41467-020-17873-3] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
Mutational inactivation of VHL is the earliest genetic event in the majority of clear cell renal cell carcinomas (ccRCC), leading to accumulation of the HIF-1α and HIF-2α transcription factors. While correlative studies of human ccRCC and functional studies using human ccRCC cell lines have implicated HIF-1α as an inhibitor and HIF-2α as a promoter of aggressive tumour behaviours, their roles in tumour onset have not been functionally addressed. Herein we show using an autochthonous ccRCC model that Hif1a is essential for tumour formation whereas Hif2a deletion has only minor effects on tumour initiation and growth. Both HIF-1α and HIF-2α are required for the clear cell phenotype. Transcriptomic and proteomic analyses reveal that HIF-1α regulates glycolysis while HIF-2α regulates genes associated with lipoprotein metabolism, ribosome biogenesis and E2F and MYC transcriptional activities. HIF-2α-deficient tumours are characterised by increased antigen presentation, interferon signalling and CD8+ T cell infiltration and activation. Single copy loss of HIF1A or high levels of HIF2A mRNA expression correlate with altered immune microenvironments in human ccRCC. These studies reveal an oncogenic role of HIF-1α in ccRCC initiation and suggest that alterations in the balance of HIF-1α and HIF-2α activities can affect different aspects of ccRCC biology and disease aggressiveness.
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218
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Chen Y, Wang K, Shang M, Zhao S, Zhang Z, Yang H, Chen Z, Du R, Wang Q, Chen B. Exploration of DNA Methylation-Driven Genes in Papillary Thyroid Carcinoma Based on the Cancer Genome Atlas. J Comput Biol 2020; 28:99-114. [PMID: 32790501 DOI: 10.1089/cmb.2019.0471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although the incidence of thyroid carcinoma is reported to be the highest among malignancies of endocrine system, its diagnosis is still unsatisfactory. This study sought to explore the key DNA methylation-driven genes in the development of papillary thyroid carcinoma (PTC) via a bioinformatic analysis based on the Cancer Genome Atlas (TCGA) database and was validated using the Gene Expression Omnibus (GEO) database. The level 3 DNA methylation, mRNA expression, and clinical data of 499 patients with PTC were obtained from the TCGA database. The R package LIMMA, edgeR, and MethylMix were applied to explore the DNA methylation-driven genes in PTC. The ConsensusPathDB software, DAVID, and STRING databases were used for Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses, as well as protein/protein interaction network construction individually. To verify the result, the explored genes were validated using GSE97466 data set retrieved from the GEO database. Fifty-seven (57) methylation-driven genes were detected via MethylMix based on a beta mixture model that compared the DNA methylation state of tumor tissues with that of the normal tissues. Eventually, three genes (TNFRSF1A, CLDN1, and CASP1) were identified to be the most potential biomarkers for the diagnosis or treatment of PTC. These results suggest the crucial roles of TNFRSF1A, CLDN1, and CASP1 in the tumorigenesis of PTC and provide a vital bioinformatic basis for further experimental validations and clinical applications.
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Affiliation(s)
- Yanwei Chen
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Keke Wang
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Mengyuan Shang
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Shuangshuang Zhao
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Zheng Zhang
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Haizhen Yang
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Zheming Chen
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Rui Du
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Qilong Wang
- Department of Pharmaceutics, School of Pharmacy and Center for Drug/Gene Delivery and Tissue Engineering, Jiangsu University, Zhenjiang, People's Republic of China
| | - Baoding Chen
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
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219
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Wu YP, Lin XD, Chen SH, Ke ZB, Lin F, Chen DN, Xue XY, Wei Y, Zheng QS, Wen YA, Xu N. Identification of Prostate Cancer-Related Circular RNA Through Bioinformatics Analysis. Front Genet 2020; 11:892. [PMID: 32922436 PMCID: PMC7457069 DOI: 10.3389/fgene.2020.00892] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/20/2020] [Indexed: 01/22/2023] Open
Abstract
Background Prostate cancer (PCa) is one of the most common malignant tumors worldwide. Accumulating evidence has suggested that circular RNAs (circRNAs) are involved in the development and progression of various cancers, and they show great potential as novel biomarkers. However, the underlying mechanisms and specific functions of most circRNAs in PCa remain unknown. Here, we aimed to identify circRNAs with potential roles in PCa from the PCa expression profile. Methods We used data downloaded from the Gene Expression Omnibus to identify circRNAs that were differentially expressed between PCa samples and adjacent non-tumor samples. Relative expression levels of identified circRNAs were validated by quantitative real-time PCR. Micro (mi)RNA response elements were predicted by the CircInteractome database, and miRNA target genes were predicted by miRDB, miRTarBase, and TargetScan databases. Gene ontology (GO) enrichment analysis and pathway analysis revealed the potential biological and functional roles of these target genes. A circRNA–miRNA–mRNA interaction network was constructed by Cytoscape. The interaction between circRNAs and miRNAs in PCa was thoroughly reviewed in the PubMed. Finally, the mRNA expression of these genes was validated by the Cancer Genome Atlas (TCGA) and Gene Expression Profiling Interactive Analysis (GEPIA) databases. The expression of proteins encoded by these genes was further validated by the Human protein Atlas (HPA) database. Results A total of 60 circRNAs that were differentially expressed between PCa and healthy samples were screened, of which 15 were annotated. Three circRNAs (hsa_circ_0024353, hsa_circ_0085494, hsa_circ_0031408) certified the criteria were studied. The results of quantitative real-time PCR demonstrated that the expression of hsa_circ_0024353 was significantly downregulated in PC-3 cells when compared with RWPE-1 cells, while the expression of hsa_circ_0031408 and hsa_circ_0085494 was significantly upregulated in PC-3 cells when compared with RWPE-1 cells. GO and Kyoto Encyclopedia of Genes and Genomes analyses found that target genes were mainly enriched in metabolic processes and pathways involving phosphoinositide 3-kinase-Akt signaling, hypoxia-inducible factor-1 signaling, p53 signaling, and the cell cycle. A total of 11 miRNA target genes showing differential expression between PCa and healthy samples were selected, and their mRNA and protein expression were validated by GEPIA and HPA databases, respectively. Of these, PDE7B, DMRT2, and TGFBR3 were identified as potentially playing a role in PCa progression. Finally, three circRNA–miRNA–mRNA interaction axes were predicted by bioinformatics: hsa_circ_0024353–hsa-miR-940–PDE7B, hsa_circ_0024353–hsa-miR-1253–DMRT2, and hsa_circ_0085494–hsa-miR-330-3p–TGFBR3. Conclusion This study identified three circRNA–miRNA–mRNA interaction axes that might provide novel insights into the potential mechanisms underlying PCa development.
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Affiliation(s)
- Yu-Peng Wu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiao-Dan Lin
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Shao-Hao Chen
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Zhi-Bin Ke
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Fei Lin
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Dong-Ning Chen
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xue-Yi Xue
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yong Wei
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Qing-Shui Zheng
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yao-An Wen
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Ning Xu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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220
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Beklen H, Gulfidan G, Arga KY, Mardinoglu A, Turanli B. Drug Repositioning for P-Glycoprotein Mediated Co-Expression Networks in Colorectal Cancer. Front Oncol 2020; 10:1273. [PMID: 32903699 PMCID: PMC7438820 DOI: 10.3389/fonc.2020.01273] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/19/2020] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most fatal types of cancers that is seen in both men and women. CRC is the third most common type of cancer worldwide. Over the years, several drugs are developed for the treatment of CRC; however, patients with advanced CRC can be resistant to some drugs. P-glycoprotein (P-gp) (also known as Multidrug Resistance 1, MDR1) is a well-identified membrane transporter protein expressed by ABCB1 gene. The high expression of MDR1 protein found in several cancer types causes chemotherapy failure owing to efflux drug molecules out of the cancer cell, decreases the drug concentration, and causes drug resistance. As same as other cancers, drug-resistant CRC is one of the major obstacles for effective therapy and novel therapeutic strategies are urgently needed. Network-based approaches can be used to determine specific biomarkers, potential drug targets, or repurposing approved drugs in drug-resistant cancers. Drug repositioning is the approach for using existing drugs for a new therapeutic purpose; it is a highly efficient and low-cost process. To improve current understanding of the MDR-1-related drug resistance in CRC, we explored gene co-expression networks around ABCB1 gene with different network sizes (50, 100, 150, 200 edges) and repurposed candidate drugs targeting the ABCB1 gene and its co-expression network by using drug repositioning approach for the treatment of CRC. The candidate drugs were also assessed by using molecular docking for determining the potential of physical interactions between the drug and MDR1 protein as a drug target. We also evaluated these four networks whether they are diagnostic or prognostic features in CRC besides biological function determined by functional enrichment analysis. Lastly, differentially expressed genes of drug-resistant (i.e., oxaliplatin, methotrexate, SN38) HT29 cell lines were found and used for repurposing drugs with reversal gene expressions. As a result, it is shown that all networks exhibited high diagnostic and prognostic performance besides the identification of various drug candidates for drug-resistant patients with CRC. All these results can shed light on the development of effective diagnosis, prognosis, and treatment strategies for drug resistance in CRC.
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Affiliation(s)
- Hande Beklen
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Gizem Gulfidan
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | | | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom.,Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Beste Turanli
- Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey
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221
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The genetic architecture of human brainstem structures and their involvement in common brain disorders. Nat Commun 2020; 11:4016. [PMID: 32782260 PMCID: PMC7421944 DOI: 10.1038/s41467-020-17376-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
Brainstem regions support vital bodily functions, yet their genetic architectures and involvement in common brain disorders remain understudied. Here, using imaging-genetics data from a discovery sample of 27,034 individuals, we identify 45 brainstem-associated genetic loci, including the first linked to midbrain, pons, and medulla oblongata volumes, and map them to 305 genes. In a replication sample of 7432 participants most of the loci show the same effect direction and are significant at a nominal threshold. We detect genetic overlap between brainstem volumes and eight psychiatric and neurological disorders. In additional clinical data from 5062 individuals with common brain disorders and 11,257 healthy controls, we observe differential volume alterations in schizophrenia, bipolar disorder, multiple sclerosis, mild cognitive impairment, dementia, and Parkinson’s disease, supporting the relevance of brainstem regions and their genetic architectures in common brain disorders. The genetic architecture underlying brainstem regions and how this links to common brain disorders is not well understood. Here, the authors use MRI and GWAS data from 27,034 individuals to identify genetic and morphological brainstem features that influence common brain disorders.
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222
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Butzmann A, Sridhar K, Jangam D, Kumar J, Sahoo MK, Shahmarvand N, Warnke R, Rangasamy E, Pinsky BA, Ohgami RS. A comprehensive analysis of RHOA mutation positive and negative angioimmunoblastic T-cell lymphomas by targeted deep sequencing, expression profiling and single cell digital image analysis. Int J Mol Med 2020; 46:1466-1476. [PMID: 32945366 PMCID: PMC7447311 DOI: 10.3892/ijmm.2020.4686] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/22/2020] [Indexed: 11/29/2022] Open
Abstract
Angioimmunoblastic T-cell lymphoma (AITL) is a uniquely aggressive mature T-cell neoplasm. In recent years, recurrent genetic mutations in ras homolog family member A (RHOA), tet methylcytosine dioxygenase 2 (TET2), DNA methyltransferase 3 alpha (DNMT3A) and isocitrate dehydrogenase [NADP(+)] 2 (IDH2) have been identified as associated with AITL. However, a deep molecular study assessing both DNA mutations and RNA expression profile combined with digital image analysis is lacking. The present study aimed to evaluate the significance of molecular and morphologic features by high resolution digital image analysis in several cases of AITL. To do so, a total of 18 separate tissues from 10 patients with AITL were collected and analyzed. The results identified recurrent mutations in RHOA, TET2, DNMT3A, and IDH2, and demonstrated increased DNA mutations in coding, promoter and CCCTC binding factor (CTCF) binding sites in RHOA mutated AITLs vs. RHOA non-mutated cases, as well as increased overall survival in RHOA mutated patients. In addition, single cell computational digital image analysis morphologically characterized RHOA mutated AITL cells as distinct from cells from RHOA mutation negative patients. Computational analysis of single cell morphological parameters revealed that RHOA mutated cells have decreased eccentricity (more circular) compared with RHOA non-mutated AITL cells. In conclusion, the results from the present study expand our understanding of AITL and demonstrate that there are specific cell biological and morphological manifestations of RHOA mutations in cases of AITL.
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Affiliation(s)
| | - Kaushik Sridhar
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Diwash Jangam
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Jyoti Kumar
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Nahid Shahmarvand
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Roger Warnke
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
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Mahmood N, Arakelian A, Muller WJ, Szyf M, Rabbani SA. An enhanced chemopreventive effect of methyl donor S-adenosylmethionine in combination with 25-hydroxyvitamin D in blocking mammary tumor growth and metastasis. Bone Res 2020; 8:28. [PMID: 32714613 PMCID: PMC7376160 DOI: 10.1038/s41413-020-0103-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/05/2020] [Accepted: 05/10/2020] [Indexed: 01/19/2023] Open
Abstract
Therapeutic targeting of metastatic breast cancer still remains a challenge as the tumor cells are highly heterogenous and exploit multiple pathways for their growth and metastatic spread that cannot always be targeted by a single-agent monotherapy regimen. Therefore, a rational approach through simultaneous targeting of several pathways may provide a better anti-cancer therapeutic effect. We tested this hypothesis using a combination of two nutraceutical agents S-adenosylmethionine (SAM) and Vitamin D (Vit. D) prohormone [25-hydroxyvitamin D; '25(OH)D'] that are individually known to exert distinct changes in the expression of genes involved in tumor growth and metastasis. Our results show that both SAM and 25(OH)D monotherapy significantly reduced proliferation and clonogenic survival of a panel of breast cancer cell lines in vitro and inhibited tumor growth, lung metastasis, and breast tumor cell colonization to the skeleton in vivo. However, these effects were significantly more pronounced in the combination setting. RNA-Sequencing revealed that the transcriptomic footprint on key cancer-related signaling pathways is broader in the combination setting than any of the monotherapies. Furthermore, comparison of the differentially expressed genes from our transcriptome analyses with publicly available cancer-related dataset demonstrated that the combination treatment upregulates genes from immune-related pathways that are otherwise downregulated in bone metastasis in vivo. Since SAM and Vit. D are both approved nutraceuticals with known safety profiles, this combination treatment may serve as a novel strategy to reduce breast cancer-associated morbidity and mortality.
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Affiliation(s)
- Niaz Mahmood
- Department of Medicine, McGill University Health Centre, Montréal, QC H4A3J1 Canada
| | - Ani Arakelian
- Department of Medicine, McGill University Health Centre, Montréal, QC H4A3J1 Canada
| | - William J. Muller
- Department of Biochemistry, McGill University, Montréal, QC H3A 1A3 Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6 Canada
| | - Shafaat A. Rabbani
- Department of Medicine, McGill University Health Centre, Montréal, QC H4A3J1 Canada
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224
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Prieto-Fernández E, Lopez-Lopez E, Martin-Guerrero I, Bárcena L, Gonzalez-Lopez M, Aransay AM, Lozano JJ, Benito J, Falcón-Pérez JM, Garcia-Orad A. Variability in Cerebrospinal Fluid MicroRNAs Through Life. Mol Neurobiol 2020; 57:4134-4142. [PMID: 32676987 DOI: 10.1007/s12035-020-02011-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/01/2020] [Indexed: 01/02/2023]
Abstract
The development of the human brain starts in the first weeks of embryo differentiation. However, there are many relevant neurodevelopmental processes that take place after birth and during lifespan. Such a fine and changing scenario requires the coordinated expression of thousands of genes to achieve the proper specialization and inter-connectivity. In this context, microRNAs (miRNAs), which can modulate mRNA stability and translation, are gaining recognition for their involvement in both brain development and neurodevelopmental disorders. Therefore, cerebrospinal fluid (CSF) miRNAs should be perfectly differentiated in relevant age periods. In this study, we aimed to highlight the biological variability of miRNA expression in the CSF throughout life, which is also crucial for biomarker discovery in CNS pathologies, especially in children, where they are desperately needed. We analyzed the CSF microRNAome of 14 healthy children (aged 0-7.4 years) by smallRNA-Seq and compared it with previously published data in adults (N = 7) and elders (N = 11). miR-423-5p and miR-22-3p were overexpressed in the < 1 and > 3 years groups, respectively. Additionally, we detected 18 miRNAs that reached their highest peak of expression at different time-points during the lifespan and sets of miRNAs that were exclusively expressed in a specific age group. On the contrary, miR-191-5p showed stable expression in CSF from the first year of life. Our results remark the complex differential miRNA expression profile that can be observed through life, which underlines the need for including appropriate age-matched controls when the expression of CSF miRNAs is analyzed in different pathological contexts. Graphical abstract.
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Affiliation(s)
- Endika Prieto-Fernández
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of The Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain.
| | - Elixabet Lopez-Lopez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of The Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain. .,BioCruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain.
| | - Idoia Martin-Guerrero
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of The Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain. .,BioCruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain.
| | - Laura Bárcena
- Genome Analysis Platform, CIC bioGUNE, 48160, Derio, Bizkaia, Spain
| | | | - Ana María Aransay
- Genome Analysis Platform, CIC bioGUNE, 48160, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Juan José Lozano
- Bioinformatic Platform, Hospital Clinic, CIBERehd, 08036, Barcelona, Spain
| | - Javier Benito
- Department of Pediatric Emergency, Cruces University Hospital, 48903, Barakaldo, Bizkaia, Spain.,Department of Pediatrics, University of The Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain
| | - Juan Manuel Falcón-Pérez
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science, 48015, Bilbao, Bizkaia, Spain
| | - Africa Garcia-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of The Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain.,BioCruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
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225
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Santos PW, Machado ART, De Grandis R, Ribeiro DL, Tuttis K, Morselli M, Aissa AF, Pellegrini M, Antunes LMG. Effects of sulforaphane on the oxidative response, apoptosis, and the transcriptional profile of human stomach mucosa cells in vitro. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2020; 854-855:503201. [PMID: 32660825 DOI: 10.1016/j.mrgentox.2020.503201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 11/25/2022]
Abstract
Oxidative stress is a critical factor in the pathogenesis of several gastrointestinal diseases. Sulforaphane (SFN), a bioactive compound found in cruciferous vegetables, activates the redox-sensitive nuclear erythroid 2-related factor 2 (NRF2). In addition to its protective role, SFN exerts cytotoxic effects on cancer cells. However, there is a lack of information concerning the toxicity of SFN in normal cells. We investigated the effects of SFN on cell viability, antioxidant defenses, and gene expression in human stomach mucosa cells (MNP01). SFN reduced ROS formation and protected the cells against induced oxidative stress but high concentrations increased apoptosis. An intermediate SFN concentration (8 μM) was chosen for RNA sequencing studies. We observed upregulation of genes of the NRF2 (antioxidant) pathway, the DNA damage response, and apoptosis signaling; whereas SFN downregulated cell cycle and DNA repair pathway genes. SFN may be cytoprotective at low concentrations and cytotoxic at high concentrations.
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Affiliation(s)
- Patrick Wellington Santos
- Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, SP, Brazil
| | - Ana Rita Thomazela Machado
- Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, SP, Brazil
| | - Rone De Grandis
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, SP, Brazil
| | - Diego Luis Ribeiro
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, SP, Brazil
| | - Katiuska Tuttis
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, SP, Brazil
| | - Marco Morselli
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, CA, USA
| | - Alexandre Ferro Aissa
- Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, SP, Brazil
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, CA, USA
| | - Lusânia Maria Greggi Antunes
- Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, SP, Brazil.
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226
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Murach KA, Vechetti IJ, Van Pelt DW, Crow SE, Dungan CM, Figueiredo VC, Kosmac K, Fu X, Richards CI, Fry CS, McCarthy JJ, Peterson CA. Fusion-Independent Satellite Cell Communication to Muscle Fibers During Load-Induced Hypertrophy. FUNCTION 2020; 1:zqaa009. [PMID: 32864621 PMCID: PMC7448100 DOI: 10.1093/function/zqaa009] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 01/06/2023] Open
Abstract
The "canonical" function of Pax7+ muscle stem cells (satellite cells) during hypertrophic growth of adult muscle fibers is myonuclear donation via fusion to support increased transcriptional output. In recent years, however, emerging evidence suggests that satellite cells play an important secretory role in promoting load-mediated growth. Utilizing genetically modified mouse models of delayed satellite cell fusion and in vivo extracellular vesicle (EV) tracking, we provide evidence for satellite cell communication to muscle fibers during hypertrophy. Myogenic progenitor cell-EV-mediated communication to myotubes in vitro influences extracellular matrix (ECM)-related gene expression, which is congruent with in vivo overload experiments involving satellite cell depletion, as well as in silico analyses. Satellite cell-derived EVs can transfer a Cre-induced, cytoplasmic-localized fluorescent reporter to muscle cells as well as microRNAs that regulate ECM genes such as matrix metalloproteinase 9 (Mmp9), which may facilitate growth. Delayed satellite cell fusion did not limit long-term load-induced muscle hypertrophy indicating that early fusion-independent communication from satellite cells to muscle fibers is an underappreciated aspect of satellite cell biology. We cannot exclude the possibility that satellite cell-mediated myonuclear accretion is necessary to maintain prolonged growth, specifically in the later phases of adaptation, but these data collectively highlight how EV delivery from satellite cells can directly contribute to mechanical load-induced muscle fiber hypertrophy, independent of cell fusion to the fiber.
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Affiliation(s)
- Kevin A Murach
- The Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Ivan J Vechetti
- The Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Douglas W Van Pelt
- The Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Samuel E Crow
- The Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Cory M Dungan
- The Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Vandre C Figueiredo
- The Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Kate Kosmac
- The Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Xu Fu
- Department of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Christopher I Richards
- Department of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Christopher S Fry
- The Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Athletic Training and Clinical Nutrition, College of Health Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - John J McCarthy
- The Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Charlotte A Peterson
- The Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY 40536, USA
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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227
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Ciuculete DM, Voisin S, Kular L, Jonsson J, Rask-Andersen M, Mwinyi J, Schiöth HB. meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes. Clin Epigenetics 2020; 12:99. [PMID: 32616021 PMCID: PMC7333393 DOI: 10.1186/s13148-020-00884-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Little is known about how genetics and epigenetics interplay in depression. Evidence suggests that genetic variants may change vulnerability to depression by modulating DNA methylation (DNAm) and non-coding RNA (ncRNA) levels. Therefore, the aim of the study was to investigate the effect of the genetic variation, previously identified in the largest genome-wide association study for depression, on proximal DNAm and ncRNA levels. RESULTS We performed DNAm quantitative trait locus (meQTL) analysis in two independent cohorts (total n = 435 healthy individuals), testing associations between 102 single-nucleotide polymorphisms (SNPs) and DNAm levels in whole blood. We identified and replicated 64 SNP-CpG pairs (padj. < 0.05) with meQTL effect. Lower DNAm at cg02098413 located in the HACE1 promoter conferred by the risk allele (C allele) at rs1933802 was associated with higher risk for depression (praw = 0.014, DNAm = 2.3%). In 1202 CD14+ cells sorted from blood, DNAm at cg02088412 positively correlated with HACE1 mRNA expression. Investigation in postmortem brain tissue of adults diagnosed with major depressive disorder (MDD) indicated 1% higher DNAm at cg02098413 in neurons and lower HACE1 mRNA expression in CA1 hippocampus of MDD patients compared with healthy controls (p = 0.008 and 0.012, respectively). Expression QTL analysis in blood of 74 adolescent revealed that hsa-miR-3664-5p was associated with rs7117514 (SHANK2) (padj. = 0.015, mRNA difference = 5.2%). Gene ontology analysis of the miRNA target genes highlighted implication in neuronal processes. CONCLUSIONS Collectively, our findings from a multi-tissue (blood and brain) and multi-layered (genetic, epigenetic, transcriptomic) approach suggest that genetic factors may influence depression by modulating DNAm and miRNA levels. Alterations at HACE1 and SHANK2 loci imply potential mechanisms, such as oxidative stress in the brain, underlying depression. Our results deepened the knowledge of molecular mechanisms in depression and suggest new epigenetic targets that should be further evaluated.
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Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden.
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, 3011, Australia
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 171 76, Stockholm, Sweden
| | - Jörgen Jonsson
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden
| | - Mathias Rask-Andersen
- Department of Immunology, Genetic and Pathology, Uppsala University, Uppsala, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
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228
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Liu J, Nie S, Li S, Meng H, Sun R, Yang J, Cheng W. Methylation-driven genes and their prognostic value in cervical squamous cell carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:868. [PMID: 32793712 DOI: 10.21037/atm-19-4577] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Abnormal gene methylation is crucial for tumor progression. This study explored a cluster of methylation-driven genes involved in cervical squamous cell carcinoma (CESC). Methods The data on RNA expression, methylation and clinical outcomes of CESC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Protein-protein interaction (PPI) network was constructed. Gene Ontology (GO) and KEGG analyses were performed to identify the biological functions of methylation-driven genes, and univariable and multivariate Cox analyses to screen out the key prognostic genes. A risk signature was established and its predictive value was evaluated with Kaplan-Meier and ROC curves. The key genes were further investigated by Cox regression analyses, gene set enrichment analysis (GSEA), and methylation site analysis. Additionally, "rms" package was used for establishing nomogram and calibrate curve. Results We found 144 differentially expressed methylation-driven genes. A risk model was constructed with three key prognostic genes (ITGA5, HHEX and S1PR4). The risk score was an independent risk factor for CESC prognosis. Lowly-expressed and hypermethylated ITGA5, highly-expressed and hypomethylated HHEX and S1PR4 were associated with better CESC prognosis. The methylation sites and biological functions enriched in ITGA5, HHEX and S1PR4 were uncovered. Additionally, the nomogram also validated the performance of risk model. Conclusions Methylation-driven ITGA5, HHEX and S1PR4 are associated with CESC development. The three genes might serve as potential targets in the treatment of CESC.
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Affiliation(s)
- Jinhui Liu
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Sipei Nie
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Siyue Li
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huangyang Meng
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui Sun
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Yang
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenjun Cheng
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Oncogene PRR14 promotes breast cancer through activation of PI3K signal pathway and inhibition of CHEK2 pathway. Cell Death Dis 2020; 11:464. [PMID: 32541902 PMCID: PMC7296039 DOI: 10.1038/s41419-020-2640-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/28/2022]
Abstract
Nuclear envelope component PRR14 has been detected to be upregulated in varieties of cancers, especially in breast cancer. But its role in breast carcinogenesis is poorly understood. In this study, we show PRR14 contributes to breast carcinogenesis mainly through overexpression, which derives from elevated transcription and gene amplification. Increased PRR14 expression promotes breast cancer cell proliferation and tumor formation. Biochemical analysis reveals, in addition to previously reported activation of PI3-kinase/Akt/mTOR pathway, PRR14 overexpression regulates cell cycle in breast cancer by inhibiting CHEK2’s activation, followed with the deregulation of DNA damage pathway. In correspondence, CHEK2 and PRR14 show opposite impact on breast cancer patients receiving chemotherapy. Collectively, our study is the first to document the oncogenetic role of PRR14 in breast cancer, which protects cells from apoptosis and stimulates proliferation by activating the PI3-kinase/Akt/mTOR pathway and inhibiting the CHEK2 pathway. Both of these pathways are of great influence in breast cancer and PRR14 appears to be their novel interacting node, which renders patients more resistance to chemotherapy and provides a potential therapeutic target in breast cancer.
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230
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Tian L, Wang SL. Exploring the potential microRNA sponge interactions of breast cancer based on some known interactions. J Bioinform Comput Biol 2020; 18:2050007. [PMID: 32530353 DOI: 10.1142/s0219720020500079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
MicroRNA (miRNA) sponges' regulatory mechanisms play an important role in developing human cancer. Herein, we develop a new method to explore potential miRNA sponge interactions (EPMSIs) for breast cancer. Based on some known interactions, and a matching gene expression profile, EPMSIs explored other potential miRNA sponge interactions for breast cancer. Every interaction is inferred with a value representing interaction intensity. Then, we apply a clustering algorithm called BCPlaid to potential interactions. Ten modules are identified; nine of them are closely associated with biological enrichments. When we employ a classification algorithm to separate normal and tumor samples in each module, each module demonstrates powerful classification performance. Furthermore, EPMSI illustrates a new method to explore the miRNA sponge regulatory network for breast cancer by applying its superior performance.
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Affiliation(s)
- Lei Tian
- School of Information Science and Engineering, Hunan University, Changsha, China
| | - Shu-Lin Wang
- School of Information Science and Engineering, Hunan University, Changsha, China
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231
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Dittmann J, Haydn T, Metzger P, Ward GA, Boerries M, Vogler M, Fulda S. Next-generation hypomethylating agent SGI-110 primes acute myeloid leukemia cells to IAP antagonist by activating extrinsic and intrinsic apoptosis pathways. Cell Death Differ 2020; 27:1878-1895. [PMID: 31831875 PMCID: PMC7244748 DOI: 10.1038/s41418-019-0465-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022] Open
Abstract
Therapeutic efficacy of first-generation hypomethylating agents (HMAs) is limited in elderly acute myeloid leukemia (AML) patients. Therefore, combination strategies with targeted therapies are urgently needed. Here, we discover that priming with SGI-110 (guadecitabine), a next-generation HMA, sensitizes AML cells to ASTX660, a novel antagonist of cellular inhibitor of apoptosis protein 1 and 2 (cIAP1/2) and X-linked IAP (XIAP). Importantly, SGI-110 and ASTX660 synergistically induced cell death in a panel of AML cell lines as well as in primary AML samples while largely sparing normal CD34+ human progenitor cells, underlining the translational relevance of this combination. Unbiased transcriptome analysis revealed that SGI-110 alone or in combination with ASTX660 upregulated the expression of key regulators of both extrinsic and intrinsic apoptosis signaling pathways such as TNFRSF10B (DR5), FAS, and BAX. Individual knockdown of the death receptors TNFR1, DR5, and FAS significantly reduced SGI-110/ASTX660-mediated cell death, whereas blocking antibodies for tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) or FAS ligand (FASLG) failed to provide protection. Also, TNFα-blocking antibody Enbrel had little protective effect on SGI-110/ASTX660-induced cell death. Further, SGI-110 and ASTX660 acted in concert to promote cleavage of caspase-8 and BID, thereby providing a link between extrinsic and intrinsic apoptotic pathways. Consistently, sequential treatment with SGI-110 and ASTX660-triggered loss of mitochondrial membrane potential (MMP) and BAX activation which contributes to cell death, as BAX silencing significantly protected from SGI-110/ASTX660-mediated apoptosis. Together, these events culminated in the activation of caspases-3/-7, nuclear fragmentation, and cell death. In conclusion, SGI-110 and ASTX660 cooperatively induced apoptosis in AML cells by engaging extrinsic and intrinsic apoptosis pathways, highlighting the therapeutic potential of this combination for AML.
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Affiliation(s)
- Jessica Dittmann
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Tinka Haydn
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Patrick Metzger
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University Freiburg, Freiburg im Breisgau, Germany
- Institute of Molecular Medicine and Cell Research (IMMZ), Albert Ludwigs-University Freiburg, Freiburg im Breisgau, Germany
- Faculty of Biology, University Freiburg, Freiburg im Breisgau, Germany
| | | | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University Freiburg, Freiburg im Breisgau, Germany
- Institute of Molecular Medicine and Cell Research (IMMZ), Albert Ludwigs-University Freiburg, Freiburg im Breisgau, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg im Breisgau, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Meike Vogler
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Simone Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt am Main, Germany.
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232
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Li YQ, Chen Y, Fang JY, Jiang SQ, Li P, Li F. Integrated network pharmacology and zebrafish model to investigate dual-effects components of Cistanche tubulosa for treating both Osteoporosis and Alzheimer's Disease. JOURNAL OF ETHNOPHARMACOLOGY 2020; 254:112764. [PMID: 32173426 DOI: 10.1016/j.jep.2020.112764] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Osteoporosis (OP) and Alzheimer's disease (AD) are common geriatric concurrent diseases, and many studies indicate the connection of their pathogenesis. Cistanche tubulosa (Schenk) Wight (CT) is a widely used traditional Chinese medicine and has been extensively applied to treat OP and AD, respectively. However, the active ingredients for both concurrent diseases simultaneously and underlying mechanisms are limited. AIM OF STUDY This work aimed at establishing an effective and reliable network screening method to find dual-effects compounds in CT that can protect AD and OP concurrently. And it will provide new perspectives of the link between OP and AD on molecular mechanisms. MATERIAL AND METHODS The dual-effects of CT were systematically analyzed with integrating multiple databases and extensive analysis at a network pharmacology level. Classified drug-target interaction network was constructed to reveal differences in effects between different types of compounds. To prove the effectiveness of this network, some compounds were selected to verify in Pre-induced OP model and AlCl3-induced AD model of zebrafish according to the topological parameters. RESULTS 22 dual-effects active ingredients in CT were initially screened out via network pharmacology with a closely connection with 81 OP and AD-related targets. Classified network analysis found the better bioactivities of phenylethanoid glycosides and flavonoids. The dual-effects of four selected compounds demonstrated that the network is reasonable and effective, suggesting the dual-effects of the remaining 18 compounds. Moreover, we identified 9 putative targets and two pathways that were significantly related to OP and AD. CONCLUSIONS We successfully identified 22 dual-effects active components in CT. This systematic screening strategy provided a new protocol to objectively discover multi-effects compounds of traditional Chinese medicine, and even a macroscopic perspective that will improve our understanding of the link between OP and AD on molecular mechanisms.
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Affiliation(s)
- Ying-Qi Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Yi Chen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Jia-Yi Fang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Si-Qi Jiang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.
| | - Fei Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; College of Pharmacy, Xinjiang Medical University, Urumqi, 830011, China.
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Meguro A, Yamane T, Takeuchi M, Miyake M, Fan Q, Zhao W, Wang IJ, Mizuki Y, Yamada N, Nomura N, Tsujikawa A, Matsuda F, Hosoda Y, Saw SM, Cheng CY, Tsai TH, Yoshida M, Iijima Y, Teshigawara T, Okada E, Ota M, Inoko H, Mizuki N. Genome-Wide Association Study in Asians Identifies Novel Loci for High Myopia and Highlights a Nervous System Role in Its Pathogenesis. Ophthalmology 2020; 127:1612-1624. [PMID: 32428537 DOI: 10.1016/j.ophtha.2020.05.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 12/19/2022] Open
Abstract
PURPOSE To identify novel susceptibility loci for high myopia. DESIGN Genome-wide association study (GWAS) followed by replication and meta-analysis. PARTICIPANTS A total of 14 096 samples from East and Southeast Asian populations (2549 patients with high myopia and 11 547 healthy controls). METHODS We performed a GWAS in 3269 Japanese individuals (1668 with high myopia and 1601 control participants), followed by replication analysis in a total of 10 827 additional samples (881 with high myopia and 9946 control participants) from Japan, Singapore, and Taiwan. To confirm the biological role of the identified loci in the pathogenesis of high myopia, we performed functional annotation and Gene Ontology (GO) analyses. MAIN OUTCOME MEASURES We evaluated the association of single nucleotide polymorphisms with high myopia and GO terms enriched among genes identified in the current study. RESULTS We identified 9 loci with genome-wide significance (P < 5.0 × 10-8). Three loci were previously reported myopia-related loci (ZC3H11B on 1q41, GJD2 on 15q14, and RASGRF1 on 15q25.1), and the other 6 were novel (HIVEP3 on 1p34.2, NFASC/CNTN2 on 1q32.1, CNTN4/CNTN6 on 3p26.3, FRMD4B on 3p14.1, LINC02418 on 12q24.33, and AKAP13 on 15q25.3). The GO analysis revealed a significant role of the nervous system related to synaptic signaling, neuronal development, and Ras/Rho signaling in the pathogenesis of high myopia. CONCLUSIONS The current study identified 6 novel loci associated with high myopia and demonstrated an important role of the nervous system in the disease pathogenesis. Our findings give new insight into the genetic factors underlying myopia, including high myopia, by connecting previous findings and allowing for a clarified interpretation of the cause and pathophysiologic features of myopia at the molecular level.
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Affiliation(s)
- Akira Meguro
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Advanced Medicine for Ocular Diseases, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takahiro Yamane
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Advanced Medicine for Ocular Diseases, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masaki Takeuchi
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Advanced Medicine for Ocular Diseases, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Science, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Qiao Fan
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Republic of Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Republic of Singapore
| | - Wanting Zhao
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Republic of Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Republic of Singapore
| | - I-Jong Wang
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yuki Mizuki
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Norihiro Yamada
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naoko Nomura
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Akitaka Tsujikawa
- Department of Ophthalmology and Visual Science, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yoshikatsu Hosoda
- Department of Ophthalmology and Visual Science, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Seang-Mei Saw
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Republic of Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Republic of Singapore
| | - Ching-Yu Cheng
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Republic of Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Republic of Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore; Ophthalmology & Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Tzu-Hsun Tsai
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
| | - Masao Yoshida
- Department of Public Health, Kyorin University School of Medicine, Tokyo, Japan
| | - Yasuhito Iijima
- Department of Ophthalmology, Aoto Eye Clinic, Yokohama, Japan
| | - Takeshi Teshigawara
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Advanced Medicine for Ocular Diseases, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Ophthalmology, Yokosuka Chuoh Eye Clinic, Yokosuka, Japan; Department of Ophthalmology, Tsurumi Chuoh Eye Clinic, Yokohama, Japan
| | - Eiichi Okada
- Department of Ophthalmology, Okada Eye Clinic, Yokohama, Japan
| | - Masao Ota
- Department of Advanced Medicine for Ocular Diseases, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hidetoshi Inoko
- Department of Molecular Life Science, Division of Molecular Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Nobuhisa Mizuki
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Advanced Medicine for Ocular Diseases, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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Bahrami S, Steen NE, Shadrin A, O’Connell K, Frei O, Bettella F, Wirgenes KV, Krull F, Fan CC, Dale AM, Smeland OB, Djurovic S, Andreassen OA. Shared Genetic Loci Between Body Mass Index and Major Psychiatric Disorders: A Genome-wide Association Study. JAMA Psychiatry 2020; 77:503-512. [PMID: 31913414 PMCID: PMC6990967 DOI: 10.1001/jamapsychiatry.2019.4188] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/30/2019] [Indexed: 01/02/2023]
Abstract
Importance People with major psychiatric disorders (MPDs) have a 10- to 20-year shorter life span than the rest of the population, and this difference is mainly due to comorbid cardiovascular diseases. Genome-wide association studies have identified common variants involved in schizophrenia (SCZ), bipolar disorder (BIP), and major depression (MD) and body mass index (BMI), a key cardiometabolic risk factor. However, genetic variants jointly influencing MPD and BMI remain largely unknown. Objective To assess the extent of the overlap between the genetic architectures of MPDs and BMI and identify genetic loci shared between them. Design, Setting, and Participants Using a conditional false discovery rate statistical framework, independent genome-wide association study data on individuals with SCZ (n = 82 315), BIP (n = 51 710), MD (n = 480 359), and BMI (n = 795 640) were analyzed. The UK Biobank cohort (n = 29 740) was excluded from the MD data set to avoid sample overlap. Data were collected from August 2017 to May 2018, and analysis began July 2018. Main Outcomes and Measures The primary outcomes were a list of genetic loci shared between BMI and MPDs and their functional pathways. Results Genome-wide association study data from 1 380 284 participants were analyzed, and the genetic correlation between BMI and MPDs varied (SCZ: r for genetic = -0.11, P = 2.1 × 10-10; BIP: r for genetic = -0.06, P = .0103; MD: r for genetic = 0.12, P = 6.7 × 10-10). Overall, 63, 17, and 32 loci shared between BMI and SCZ, BIP, and MD, respectively, were analyzed at conjunctional false discovery rate less than 0.01. Of the shared loci, 34% (73 of 213) in SCZ, 52% (36 of 69) in BIP, and 57% (56 of 99) in MD had risk alleles associated with higher BMI (conjunctional false discovery rate <0.05), while the rest had opposite directions of associations. Functional analyses indicated that the overlapping loci are involved in several pathways including neurodevelopment, neurotransmitter signaling, and intracellular processes, and the loci with concordant and opposite association directions pointed mostly to different pathways. Conclusions and Relevance In this genome-wide association study, extensive polygenic overlap between BMI and SCZ, BIP, and MD were found, and 111 shared genetic loci were identified, implicating novel functional mechanisms. There was mixture of association directions in SCZ and BMI, albeit with a preponderance of discordant ones.
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Affiliation(s)
- Shahram Bahrami
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Nils Eiel Steen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Alexey Shadrin
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Kevin O’Connell
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Oleksandr Frei
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Francesco Bettella
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | | | - Florian Krull
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Chun C. Fan
- Department of Radiology, University of California, San Diego, La Jolla
- Department of Cognitive Science, University of California, San Diego, La Jolla
| | - Anders M Dale
- Department of Radiology, University of California, San Diego, La Jolla
- Multimodal Imaging Laboratory, University of California, San Diego, La Jolla
- Department of Psychiatry, University of California, San Diego, La Jolla
- Department of Neurosciences, University of California, San Diego, La Jolla
| | - Olav B. Smeland
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- NORMENT Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ole A. Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
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Jannuzzi AT, Arslan S, Yilmaz AM, Sari G, Beklen H, Méndez L, Fedorova M, Arga KY, Karademir Yilmaz B, Alpertunga B. Higher proteotoxic stress rather than mitochondrial damage is involved in higher neurotoxicity of bortezomib compared to carfilzomib. Redox Biol 2020; 32:101502. [PMID: 32244176 PMCID: PMC7115161 DOI: 10.1016/j.redox.2020.101502] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/02/2020] [Accepted: 03/07/2020] [Indexed: 02/07/2023] Open
Abstract
Proteasome inhibitors have great success for their therapeutic potential against hematologic malignancies. First generation proteasome inhibitor bortezomib induced peripheral neuropathy is considered as a limiting factor in chemotherapy and its second-generation counterpart carfilzomib is associated with lower rates of neurotoxicity. The mitochondrial toxicity (mitotoxicity) hypothesis arises from studies with animal models of bortezomib induced peripheral neuropathy. However, molecular mechanisms are not fully elucidated and the role of mitotoxicity in bortezomib and carfilzomib induced neurotoxicity has not been investigated comparatively. Herein, we characterized the neurotoxic effects of bortezomib and carfilzomib at the molecular level in human neuronal cells using LC-MS/MS analysis, flow cytometry, RT-qPCR, confocal microscopy and western blotting. We showed that bortezomib and carfilzomib affected the human neuronal proteome differently, and bortezomib caused higher proteotoxic stress via protein oxidation, protein K48-ubiquitination, heat shock protein expression upregulation and reduction of mitochondria membrane potential. Bortezomib and carfilzomib did not affect the gene expression levels related to mitochondrial dynamics (optic atrophy 1; OPA1, mitofusin 1; MFN1, mitofusin 2; MFN2, fission 1; FIS1, dynamin-related protein 1; DRP1) and overall mitophagy rate whereas, PINK1/Parkin mediated mitophagy gene expressions were altered with both drugs. Bortezomib and carfilzomib caused downregulation of the contents of mitochondrial oxidative phosphorylation complexes, voltage-dependent anion channel 1 (VDAC1) and uncoupling protein 2 (UCP2) similarly. Our findings suggest that, both drugs induce mitotoxicity besides proteotoxic stress in human neuronal cells and the higher incidence of neurotoxicity with bortezomib than carfilzomib is not directly related to mitochondrial pathways.
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Affiliation(s)
- Ayse Tarbin Jannuzzi
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey; Department of Biochemistry, School of Medicine / Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Sema Arslan
- Department of Biochemistry, School of Medicine / Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Ayse Mine Yilmaz
- Department of Biochemistry, School of Medicine / Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Gulce Sari
- Department of Biochemistry, School of Medicine / Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Hande Beklen
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Lucía Méndez
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Germany; Institute of Marine Research, Spanish Council for Scientific Research, (IIM-CSIC), Vigo, Spain
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Germany
| | | | - Betul Karademir Yilmaz
- Department of Biochemistry, School of Medicine / Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey.
| | - Buket Alpertunga
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey.
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Zhang ZJ, Wu WY, Hou JJ, Zhang LL, Li FF, Gao L, Wu XD, Shi JY, Zhang R, Long HL, Lei M, Wu WY, Guo DA, Chen KX, Hofmann LA, Ci ZH. Active constituents and mechanisms of Respiratory Detox Shot, a traditional Chinese medicine prescription, for COVID-19 control and prevention: Network-molecular docking-LC-MS E analysis. JOURNAL OF INTEGRATIVE MEDICINE 2020; 18:229-241. [PMID: 32307268 PMCID: PMC7195604 DOI: 10.1016/j.joim.2020.03.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Lung-toxin Dispelling Formula No. 1, referred to as Respiratory Detox Shot (RDS), was developed based on a classical prescription of traditional Chinese medicine (TCM) and the theoretical understanding of herbal properties within TCM. Therapeutic benefits of using RDS for both disease control and prevention, in the effort to contain the coronavirus disease 2019 (COVID-19), have been shown. However, the biochemically active constituents of RDS and their mechanisms of action are still unclear. The goal of the present study is to clarify the material foundation and action mechanism of RDS. METHODS To conduct an analysis of RDS, an integrative analytical platform was constructed, including target prediction, protein-protein interaction (PPI) network, and cluster analysis; further, the hub genes involved in the disease-related pathways were identified, and the their corresponding compounds were used for in vitro validation of molecular docking predictions. The presence of these validated compounds was also measured in samples of the RDS formula to quantify the abundance of the biochemically active constituents. In our network pharmacological study, a total of 26 bioinformatic programs and databases were used, and six networks, covering the entire Zang-fu viscera, were constructed to comprehensively analyze the intricate connections among the compounds-targets-disease pathways-meridians of RDS. RESULTS For all 1071 known chemical constituents of the nine ingredients in RDS, identified from established TCM databases, 157 passed drug-likeness screening and led to 339 predicted targets in the constituent-target network. Forty-two hub genes with core regulatory effects were extracted from the PPI network, and 134 compounds and 29 crucial disease pathways were implicated in the target-constituent-disease network. Twelve disease pathways attributed to the Lung-Large Intestine meridians, with six and five attributed to the Kidney-Urinary Bladder and Stomach-Spleen meridians, respectively. One-hundred and eighteen candidate constituents showed a high binding affinity with SARS-coronavirus-2 3-chymotrypsin-like protease (3CLpro), as indicated by molecular docking using computational pattern recognition. The in vitro activity of 22 chemical constituents of RDS was validated using the 3CLpro inhibition assay. Finally, using liquid chromatography mass spectrometry in data-independent analysis mode, the presence of seven out of these 22 constituents was confirmed and validated in an aqueous decoction of RDS, using reference standards in both non-targeted and targeted approaches. CONCLUSION RDS acts primarily in the Lung-Large Intestine, Kidney-Urinary Bladder and Stomach-Spleen meridians, with other Zang-fu viscera strategically covered by all nine ingredients. In the context of TCM meridian theory, the multiple components and targets of RDS contribute to RDS's dual effects of health-strengthening and pathogen-eliminating. This results in general therapeutic effects for early COVID-19 control and prevention.
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Affiliation(s)
- Zi-Jia Zhang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wen-Yong Wu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Jun Hou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lin-Lin Zhang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Fei-Fei Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Gao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing-Dong Wu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing-Ying Shi
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Zhang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua-Li Long
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Min Lei
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wan-Ying Wu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - De-An Guo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Kai-Xian Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | | | - Zhong-Hua Ci
- World Health Science Organization, Leesburg, VA 20176, USA
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Sexually dimorphic DNA-methylation in cardiometabolic health: A systematic review. Maturitas 2020; 135:6-26. [DOI: 10.1016/j.maturitas.2020.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/03/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023]
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Johansson P, Klein-Hitpass L, Budeus B, Kuhn M, Lauber C, Seifert M, Roeder I, Pförtner R, Stuschke M, Dührsen U, Eckstein A, Dürig J, Küppers R. Identifying Genetic Lesions in Ocular Adnexal Extranodal Marginal Zone Lymphomas of the MALT Subtype by Whole Genome, Whole Exome and Targeted Sequencing. Cancers (Basel) 2020; 12:cancers12040986. [PMID: 32316399 PMCID: PMC7225979 DOI: 10.3390/cancers12040986] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022] Open
Abstract
The pathogenesis of ocular adnexal marginal zone lymphomas of mucosa-associated lymphatic tissue-type (OAML) is not fully understood. We performed whole genome sequencing (WGS) and/or whole exome sequencing (WES) for 13 cases of OAML and sequenced 38 genes selected from this analysis in a large cohort of 82 OAML. Besides confirmation of frequent mutations in the genes transducin beta like 1 X-linked receptor 1 (TBL1XR1) and cAMP response element binding protein (CREBBP), we newly identifed JAK3 as a frequently mutated gene in OAML (11% of cases). In our retrospective cohort, JAK3 mutant cases had a shorter progression-free survival compared with unmutated cases. Other newly identified genes recurrently mutated in 5-10% of cases included members of the collagen family (collagen type XII alpha 1/2 (COL12A1, COL1A2)) and DOCK8. Evaluation of the WGS data of six OAML did not reveal translocations or a current infection of the lymphoma cells by viruses. Evaluation of the WGS data for copy number aberrations confirmed frequent loss of TNFAIP3, and revealed recurrent gains of the NOTCH target HES4, and of members of the CEBP transcription factor family. Overall, we identified several novel genes recurrently affected by point mutations or copy number alterations, but our study also indicated that the landscape of frequently (>10% of cases) mutated protein-coding genes in OAML is now largely known.
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Affiliation(s)
- Patricia Johansson
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (U.D.); (J.D.)
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany; (L.K.-H.); (B.B.); (R.K.)
- Correspondence: ; Tel.: +49-201-723-85845
| | - Ludger Klein-Hitpass
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany; (L.K.-H.); (B.B.); (R.K.)
| | - Bettina Budeus
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany; (L.K.-H.); (B.B.); (R.K.)
| | - Matthias Kuhn
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany; (M.K.); (C.L.); (M.S.); (I.R.)
| | - Chris Lauber
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany; (M.K.); (C.L.); (M.S.); (I.R.)
| | - Michael Seifert
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany; (M.K.); (C.L.); (M.S.); (I.R.)
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany; (M.K.); (C.L.); (M.S.); (I.R.)
| | - Roman Pförtner
- Department of Oral and Cranio-Maxillofacial Surgery, Kliniken Essen-Mitte, Evang. Huyssens-Stiftung/Knappschaft GmbH, University Hospital of Essen, 45136 Essen, Germany;
| | - Martin Stuschke
- Department of Radiotherapy, University Hospital Essen, 45147 Essen, Germany;
| | - Ulrich Dührsen
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (U.D.); (J.D.)
| | - Anja Eckstein
- Department of Ophthalmology, Molecular Ophthalmology Group, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Jan Dürig
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (U.D.); (J.D.)
- German Cancer Consortium (DKTK), 45147 Essen, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany; (L.K.-H.); (B.B.); (R.K.)
- German Cancer Consortium (DKTK), 45147 Essen, Germany
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Mahmood N, Arakelian A, Khan HA, Tanvir I, Mazar AP, Rabbani SA. uPAR antibody (huATN-658) and Zometa reduce breast cancer growth and skeletal lesions. Bone Res 2020; 8:18. [PMID: 32337090 PMCID: PMC7165173 DOI: 10.1038/s41413-020-0094-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 01/16/2020] [Accepted: 02/22/2020] [Indexed: 12/12/2022] Open
Abstract
Urokinase plasminogen activator receptor (uPAR) is implicated in tumor growth and metastasis due to its ability to activate latent growth factors, proteases, and different oncogenic signaling pathways upon binding to different ligands. Elevated uPAR expression is correlated with the increased aggressiveness of cancer cells, which led to its credentialing as an attractive diagnostic and therapeutic target in advanced solid cancer. Here, we examine the antitumor effects of a humanized anti-uPAR antibody (huATN-658) alone and in combination with the approved bisphosphonate Zometa (Zoledronic acid) on skeletal lesion through a series of studies in vitro and in vivo. Treatment with huATN-658 or Zometa alone significantly decreased human MDA-MB-231 cell proliferation and invasion in vitro, effects which were more pronounced when huATN-658 was combined with Zometa. In vivo studies demonstrated that huATN-658 treatment significantly reduced MDA-MB-231 primary tumor growth compared with controls. In a model of breast tumor-induced bone disease, huATN-658 and Zometa were equally effective in reducing skeletal lesions. The skeletal lesions were significantly reduced in animals receiving the combination of huATN-658 + Zometa compared with monotherapy treatment. These effects were due to a significant decrease in osteoclastic activity and tumor cell proliferation in the combination treatment group. Transcriptome analysis revealed that combination treatment significantly changes the expression of genes from signaling pathways implicated in tumor progression and bone remodeling. Results from these studies provide a rationale for the continued development of huATN-658 as a monotherapy and in combination with currently approved agents such as Zometa in patients with metastatic breast cancer.
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Affiliation(s)
- Niaz Mahmood
- Department of Medicine, McGill University, Montréal, QC H4A3J1 Canada
| | - Ani Arakelian
- Department of Medicine, McGill University, Montréal, QC H4A3J1 Canada
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240
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Queiroz FC, Vargas AMP, Oliveira MGA, Comarela GV, Silveira SA. ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces. BMC Bioinformatics 2020; 21:143. [PMID: 32293241 PMCID: PMC7158050 DOI: 10.1186/s12859-020-3474-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/27/2020] [Indexed: 12/15/2022] Open
Abstract
Background Protein-protein interactions (PPIs) are fundamental in many biological processes and understanding these interactions is key for a myriad of applications including drug development, peptide design and identification of drug targets. The biological data deluge demands efficient and scalable methods to characterize and understand protein-protein interfaces. In this paper, we present ppiGReMLIN, a graph based strategy to infer interaction patterns in a set of protein-protein complexes. Our method combines an unsupervised learning strategy with frequent subgraph mining in order to detect conserved structural arrangements (patterns) based on the physicochemical properties of atoms on protein interfaces. To assess the ability of ppiGReMLIN to point out relevant conserved substructures on protein-protein interfaces, we compared our results to experimentally determined patterns that are key for protein-protein interactions in 2 datasets of complexes, Serine-protease and BCL-2. Results ppiGReMLIN was able to detect, in an automatic fashion, conserved structural arrangements that represent highly conserved interactions at the specificity binding pocket of trypsin and trypsin-like proteins from Serine-protease dataset. Also, for the BCL-2 dataset, our method pointed out conserved arrangements that include critical residue interactions within the conserved motif LXXXXD, pivotal to the binding specificity of BH3 domains of pro-apoptotic BCL-2 proteins towards apoptotic suppressors. Quantitatively, ppiGReMLIN was able to find all of the most relevant residues described in literature for our datasets, showing precision of at least 69% up to 100% and recall of 100%. Conclusions ppiGReMLIN was able to find highly conserved structures on the interfaces of protein-protein complexes, with minimum support value of 60%, in datasets of similar proteins. We showed that the patterns automatically detected on protein interfaces by our method are in agreement with interaction patterns described in the literature.
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Affiliation(s)
- Felippe C Queiroz
- Department of Computer Science, Universidade Federal de Viçosa, Av Peter Henry Rolfs, Viçosa, MG, Brazil.
| | - Adriana M P Vargas
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av Peter Henry Rolfs, Viçosa, MG, Brazil
| | - Maria G A Oliveira
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av Peter Henry Rolfs, Viçosa, MG, Brazil.,Instituto de Biotecnologia aplicada a Agropecuaria, BIOAGRO-UFV, Av Peter Henry Rolfs, Viçosa MG, Brazil
| | - Giovanni V Comarela
- Department of Computer Science, Universidade Federal do Espírito Santo, Av Fernando Ferrari, Vitória, ES, Brazil
| | - Sabrina A Silveira
- Department of Computer Science, Universidade Federal de Viçosa, Av Peter Henry Rolfs, Viçosa, MG, Brazil.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
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241
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Karolak JA, Gambin T, Rydzanicz M, Polakowski P, Ploski R, Szaflik JP, Gajecka M. Accumulation of sequence variants in genes of Wnt signaling and focal adhesion pathways in human corneas further explains their involvement in keratoconus. PeerJ 2020; 8:e8982. [PMID: 32328353 PMCID: PMC7164425 DOI: 10.7717/peerj.8982] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Background Keratoconus (KTCN) is a protrusion and thinning of the cornea, resulting in loss of visual acuity. The etiology of KTCN remains unclear. The purpose of this study was to assess the potential involvement of new genetic variants in KTCN etiology based on both the genomic and transcriptomic findings recognized in the same corneal tissues. Methods Corneal tissues derived from five unrelated Polish individuals with KTCN were examined using exome sequencing (ES), followed by enrichment analyses. For comparison purposes, the datasets comprising ES data of five randomly selected Polish individuals without ocular abnormalities and five Polish patients with high myopia were used. Expression levels of selected genes from the overrepresented pathways were obtained from the previous RNA-Seq study. Results Exome capture discovered 117 potentially relevant variants that were further narrowed by gene overrepresentation analyses. In each of five patients, the assessment of functional interactions revealed rare (MAF ≤ 0.01) DNA variants in at least one gene from Wnt signaling (VANGL1, WNT1, PPP3CC, LRP6, FZD2) and focal adhesion (BIRC2, PAK6, COL4A4, PPP1R12A, PTK6) pathways. No genes involved in pathways enriched in KTCN corneas were overrepresented in our control sample sets. Conclusions The results of this first pilot ES profiling of human KTCN corneas emphasized that accumulation of sequence variants in several genes from Wnt signaling and/or focal adhesion pathways might cause the phenotypic effect and further points to a complex etiology of KTCN.
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Affiliation(s)
- Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Piotr Polakowski
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Jacek P Szaflik
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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242
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Wang HT, Smallwood J, Mourao-Miranda J, Xia CH, Satterthwaite TD, Bassett DS, Bzdok D. Finding the needle in a high-dimensional haystack: Canonical correlation analysis for neuroscientists. Neuroimage 2020; 216:116745. [PMID: 32278095 DOI: 10.1016/j.neuroimage.2020.116745] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/12/2020] [Accepted: 03/12/2020] [Indexed: 12/12/2022] Open
Abstract
The 21st century marks the emergence of "big data" with a rapid increase in the availability of datasets with multiple measurements. In neuroscience, brain-imaging datasets are more commonly accompanied by dozens or hundreds of phenotypic subject descriptors on the behavioral, neural, and genomic level. The complexity of such "big data" repositories offer new opportunities and pose new challenges for systems neuroscience. Canonical correlation analysis (CCA) is a prototypical family of methods that is useful in identifying the links between variable sets from different modalities. Importantly, CCA is well suited to describing relationships across multiple sets of data, such as in recently available big biomedical datasets. Our primer discusses the rationale, promises, and pitfalls of CCA.
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Affiliation(s)
- Hao-Ting Wang
- Department of Psychology, University of York, Heslington, York, United Kingdom; Sackler Center for Consciousness Science, University of Sussex, Brighton, United Kingdom.
| | - Jonathan Smallwood
- Department of Psychology, University of York, Heslington, York, United Kingdom
| | - Janaina Mourao-Miranda
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, United Kingdom; Max Planck University College London Centre for Computational Psychiatry and Ageing Research, University College London, London, United Kingdom
| | - Cedric Huchuan Xia
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Theodore D Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Danielle S Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Physics & Astronomy, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Danilo Bzdok
- Department of Psychiatry, Psychotherapy and Psychosomatics, RWTH Aachen University, Germany; JARA-BRAIN, Jülich-Aachen Research Alliance, Germany; Parietal Team, INRIA, Neurospin, Bat 145, CEA Saclay, 91191, Gif-sur-Yvette, France; Department of Biomedical Engineering, Montreal Neurological Institute, Faculty of Medicine, McGill University, Montreal, Canada; Mila - Quebec Artificial Intelligence Institute, Canada.
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243
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Nalbantoglu S, Abu-Asab M, Suy S, Collins S, Amri H. Metabolomics-Based Biosignatures of Prostate Cancer in Patients Following Radiotherapy. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 23:214-223. [PMID: 31009330 DOI: 10.1089/omi.2019.0006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabolomics offers new promise for research on prostate cancer (PCa) and its personalized treatment. Metabolomic profiling of radiation-treated PCa patients is particularly important to reveal their new metabolomic status, and evaluate the radiation effects. In addition, bioinformatics-integrated metabolomics-based approaches for disease profiling and assessment of therapy could help develop precision biomarkers in a context of PCa. We report mass spectrometry-based untargeted (global) serum metabolomics findings from patients with PCa (n = 55) before and after treatment with stereotactic body radiation therapy (SBRT), and intensity-modulated radiation therapy (IMRT) with SBRT, and using parsimony phylogenetic analysis. Importantly, the radiation-treated serum metabolome of patients represented a unique robust cluster on a cladogram that was distinct from the pre-RT metabolome. The altered radiation responsive serum metabolome was defined by predominant aberrations in the metabolic pathways of nitrogen, pyrimidine, purine, porphyrin, alanine, aspartate, glutamate, and glycerophospholipid. Our findings collectively suggest that global metabolomics integrated with parsimony phylogenetics offer a unique and robust systems biology analytical platform for powerful unbiased determination of radiotherapy (RT)-associated biosignatures in patients with PCa. These new observations call for future translational research for evaluation of metabolomic biomarkers in PCa prognosis specifically, and response to radiation treatment broadly. Radiation metabolomics is an emerging specialty of systems sciences and clinical medicine that warrants further research and educational initiatives.
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Affiliation(s)
- Sinem Nalbantoglu
- 1 Department of Biochemistry, Cellular and Molecular Biology, School of Medicine, Georgetown University, Washington, District of Columbia.,2 TUBITAK Marmara Research Center, Institute of Gene Engineering and Biotechnology, Molecular Oncology Laboratory, Gebze, Kocaeli, Turkey
| | - Mones Abu-Asab
- 3 Section of Ultrastructural Biology, NEI/NIH, Bethesda, Maryland
| | - Simeng Suy
- 4 Department of Radiation Oncology, School of Medicine, Georgetown University, Washington, District of Columbia
| | - Sean Collins
- 4 Department of Radiation Oncology, School of Medicine, Georgetown University, Washington, District of Columbia
| | - Hakima Amri
- 1 Department of Biochemistry, Cellular and Molecular Biology, School of Medicine, Georgetown University, Washington, District of Columbia
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244
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Dungan CM, Peck BD, Walton RG, Huang Z, Bamman MM, Kern PA, Peterson CA. In vivo analysis of γH2AX+ cells in skeletal muscle from aged and obese humans. FASEB J 2020; 34:7018-7035. [PMID: 32246795 DOI: 10.1096/fj.202000111rr] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 12/25/2022]
Abstract
Over the past 20 years, various identifiers of cellular senescence have been used to quantify the abundance of these cells in different tissues. These include classic markers such as p16, senescence-associated β-gal, and γH2AX, in addition to more recent markers (Sudan Black B and HMGB1). In vivo data on the usefulness of these markers in skeletal muscle are very limited and inconsistent. In the present study, we attempted to identify senescent cells in frozen human skeletal muscle biopsies using these markers to determine the effects of age and obesity on senescent cell burden; however, we were only able to assess the abundance of DNA-damaged nuclei using γH2AX immunohistochemistry. The abundance of γH2AX+ cells, including satellite cells, was not higher in muscle from old compared to young individuals; however, γH2AX+ cells were higher with obesity. Additionally, terminally differentiated, postmitotic myofiber nuclei from obese individuals had elevated γH2AX abundance compared to muscle from lean individuals. Analyses of gene expression support the conclusion that the elevated DNA damage and the senescence-associated secretory phenotype are preferentially associated with obesity in skeletal muscle. These data implicate obesity as a larger contributor to DNA damage in skeletal muscle than aging; however, more sensitive senescence markers for human skeletal muscle are needed to determine if these cells are in fact senescent.
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Affiliation(s)
- Cory M Dungan
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY, USA.,Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
| | - Bailey D Peck
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY, USA.,Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
| | - R Grace Walton
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY, USA.,Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
| | - Zhengyan Huang
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Marcas M Bamman
- Department of Cell, Developmental, and Integrative Biology, School of Medicine, University of Alabama, Birmingham, AL, USA.,Geriatric Research, Education, and Clinical Center, Birmingham VA Medical Center, Birmingham, AL, USA
| | - Philip A Kern
- Department of Internal Medicine/Endocrinology, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Charlotte A Peterson
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY, USA.,Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
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245
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Volozonoka L, Rots D, Kempa I, Kornete A, Rezeberga D, Gailite L, Miskova A. Genetic landscape of preterm birth due to cervical insufficiency: Comprehensive gene analysis and patient next-generation sequencing data interpretation. PLoS One 2020; 15:e0230771. [PMID: 32214361 PMCID: PMC7098624 DOI: 10.1371/journal.pone.0230771] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/07/2020] [Indexed: 01/10/2023] Open
Abstract
Preterm delivery is both a traumatizing experience for the patient and a burden on the healthcare system. A condition distinguishable by its phenotype in prematurity is cervical insufficiency, where certain cases exhibit a strong genetic component. Despite genomic advancements, little is known about the genetics of human cervix remodeling during pregnancy. Using selected gene approaches, a few studies have demonstrated an association of common gene variants with cervical insufficiency. However, until now, no study has employed comprehensive methods to investigate this important subject matter. In this study, we asked: i) are there genes reliably linked to cervical insufficiency and, if so, what are their roles? and ii) what is the proportion of cases of non-syndromic cervical insufficiency attributable to these genetic variations? We performed next-generation sequencing on 21 patients with a clinical presentation of cervical insufficiency. To assist the sequencing data interpretation, we retrieved all known genes implicated in cervical functioning through a systematic literature analysis and additional gene searches. These genes were then classified according to their relation to the questions being posed by the study. Patients' sequence variants were filtered for pathogenicity and assigned a likelihood of being contributive to phenotype development. Gene extraction and analysis revealed 12 genes primarily linked to cervical insufficiency, the majority of which are known to cause collagenopathies. Ten patients carried disruptive variants potentially contributive to the development of non-syndromic cervical insufficiency. Pathway enrichment analysis of variant genes from our cohort revealed an increased variation burden in genes playing roles in tissue mechanical and biomechanical properties, i.e. collagen biosynthesis and cell-extracellular matrix communications. Consequently, the proposed idea of cervical insufficiency being a subtle form of collagenopathy, now strengthened by our genetic findings, might open up new opportunities for improved patient evaluation and management.
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Affiliation(s)
- Ludmila Volozonoka
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Dmitrijs Rots
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Inga Kempa
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Anna Kornete
- Department of Obstetrics and Gynecology, Riga Stradins University, Riga, Latvia
| | - Dace Rezeberga
- Department of Obstetrics and Gynecology, Riga Stradins University, Riga, Latvia
| | - Linda Gailite
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Anna Miskova
- Department of Obstetrics and Gynecology, Riga Stradins University, Riga, Latvia
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246
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Dong H, Zhou W, Wang P, Zuo E, Ying X, Chai S, Fei T, Jin L, Chen C, Ma G, Liu H. Comprehensive Analysis of the Genetic and Epigenetic Mechanisms of Osteoporosis and Bone Mineral Density. Front Cell Dev Biol 2020; 8:194. [PMID: 32269995 PMCID: PMC7109267 DOI: 10.3389/fcell.2020.00194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/09/2020] [Indexed: 01/11/2023] Open
Abstract
Osteoporosis is a skeletal disorder characterized by a systemic impairment of bone mineral density (BMD). Genome-wide association studies (GWAS) have identified hundreds of susceptibility loci for osteoporosis and BMD. However, the vast majority of susceptibility loci are located in non-coding regions of the genome and provide limited information about the genetic mechanisms of osteoporosis. Herein we performed a comprehensive functional analysis to investigate the genetic and epigenetic mechanisms of osteoporosis and BMD. BMD and osteoporosis are found to share many common susceptibility loci, and the corresponding susceptibility genes are significantly enriched in bone-related biological pathways. The regulatory element enrichment analysis indicated that BMD and osteoporosis susceptibility loci are significantly enriched in 5′UTR and DNase I hypersensitive sites (DHSs) of peripheral blood immune cells. By integrating GWAS and expression Quantitative Trait Locus (eQTL) data, we found that 15 protein-coding genes are regulated by the osteoporosis and BMD susceptibility loci. Our analysis provides new clues for a better understanding of the pathogenic mechanisms and offers potential therapeutic targets for osteoporosis.
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Affiliation(s)
- Hui Dong
- Department of Oral Prosthodontics, School of Stomatology, Dalian Medical University, Dalian, China.,Department of Stomatology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Pingping Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Enjun Zuo
- Department of Oral Prosthodontics, School of Stomatology, Dalian Medical University, Dalian, China
| | - Xiaoxia Ying
- Department of Oral Prosthodontics, School of Stomatology, Dalian Medical University, Dalian, China
| | - Songling Chai
- Department of Oral Prosthodontics, School of Stomatology, Dalian Medical University, Dalian, China
| | - Tao Fei
- Department of Oral Prosthodontics, School of Stomatology, Dalian Medical University, Dalian, China
| | - Laidi Jin
- Department of Oral Prosthodontics, School of Stomatology, Dalian Medical University, Dalian, China
| | - Chen Chen
- Department of Oral Prosthodontics, School of Stomatology, Dalian Medical University, Dalian, China
| | - Guowu Ma
- Department of Oral Prosthodontics, School of Stomatology, Dalian Medical University, Dalian, China
| | - Huiying Liu
- Department of Oral Prosthodontics, School of Stomatology, Dalian Medical University, Dalian, China
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247
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Arantes MR, Peijnenburg A, Hendriksen PJM, Stoopen G, Almeida TS, Souza TM, Farias DF, Carvalho AFU, Rocha TM, Leal LKAM, Vasconcelos IM, Oliveira JTA. In vitro toxicological characterisation of the antifungal compound soybean toxin (SBTX). Toxicol In Vitro 2020; 65:104824. [PMID: 32165152 DOI: 10.1016/j.tiv.2020.104824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/13/2020] [Accepted: 03/08/2020] [Indexed: 12/18/2022]
Abstract
Soybean toxin (SBTX) is a protein isolated from soybean seeds and composed of two polypeptide subunits (17 and 27 kDa). SBTX has in vitro activity against phytopathogenic fungi such as Cercospora sojina, Aspergillus niger, and Penicillium herguei, and yeasts like Candida albicans, C. parapsilosis, Kluyveromyces marxiannus, and Pichia membranifaciens. The present study aimed to analyze in vitro whether SBTX causes any side effects on non-target bacterial and mammalian cells that could impede its potential use as a novel antifungal agent. SBTX at 100 μg/mL and 200 μg/mL did not hinder the growth of the bacteria Salmonella enterica (subspecies enterica serovar choleraesuis), Bacillus subtilis (subspecies spizizenii) and Staphylococcus aureus. Moreover, SBTX at concentrations up to 500 μg/mL did not significantly affect the viability of erythrocytes, neutrophils, and human intestinal Caco-2 cells. To study whether SBTX could induce relevant alterations in gene expression, in vitro DNA microarray experiments were conducted in which differentiated Caco-2 cells were exposed for 24 h to 100 μg/mL or 200 μg/mL SBTX. SBTX up-regulated genes involved in cell cycle and immune response pathways, but down-regulated genes that play a role in cholesterol biosynthesis and platelet degranulation pathways. Thus, although SBTX did not affect bacteria, nor induced cytotoxity in mammalian cells, it affected some biological pathways in the human Caco-2 cell line that warrants further investigation.
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Affiliation(s)
- Mariana Reis Arantes
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60020-181 Fortaleza, CE, Brazil
| | - Ad Peijnenburg
- WFSR, Wageningen University and Research Centre, P.O. Box 230, 6700 AE Wageningen, the Netherlands.
| | - Peter J M Hendriksen
- WFSR, Wageningen University and Research Centre, P.O. Box 230, 6700 AE Wageningen, the Netherlands.
| | - Geert Stoopen
- WFSR, Wageningen University and Research Centre, P.O. Box 230, 6700 AE Wageningen, the Netherlands.
| | - Thiago Silva Almeida
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60020-181 Fortaleza, CE, Brazil
| | - Terezinha Maria Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht 6229, ER, the Netherlands.
| | - Davi Felipe Farias
- Department of Molecular Biology, Federal University of Paraíba, 58051-900 Joao Pessoa, PB, Brazil.
| | | | | | | | - Ilka Maria Vasconcelos
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60020-181 Fortaleza, CE, Brazil.
| | - Jose Tadeu Abreu Oliveira
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60020-181 Fortaleza, CE, Brazil.
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248
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Exhausted phenotype of follicular CD8 T cells in CVID. J Allergy Clin Immunol 2020; 146:912-915.e13. [PMID: 32169377 DOI: 10.1016/j.jaci.2020.02.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/25/2020] [Accepted: 02/28/2020] [Indexed: 01/10/2023]
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249
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Wu W, Zhang Z, Li F, Deng Y, Lei M, Long H, Hou J, Wu W. A Network-Based Approach to Explore the Mechanisms of Uncaria Alkaloids in Treating Hypertension and Alleviating Alzheimer's Disease. Int J Mol Sci 2020; 21:ijms21051766. [PMID: 32143538 PMCID: PMC7084279 DOI: 10.3390/ijms21051766] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 02/06/2023] Open
Abstract
Uncaria alkaloids are the major bioactive chemicals found in the Uncaria genus, which have a long history of clinical application in treating cardiovascular and mental diseases in traditional Chinese medicine (TCM). However, there are gaps in understanding the multiple targets, pathways, and biological activities of Uncaria alkaloids. By constructing the interactions among drug-targets-diseases, network pharmacology provides a systemic methodology and a novel perspective to present the intricate connections among drugs, potential targets, and related pathways. It is a valuable tool for studying TCM drugs with multiple indications, and how these multi-indication drugs are affected by complex interactions in the biological system. To better understand the mechanisms and targets of Uncaria alkaloids, we built an integrated analytical platform based on network pharmacology, including target prediction, protein-protein interaction (PPI) network, topology analysis, gene enrichment analysis, and molecular docking. Using this platform, we revealed the underlying mechanisms of Uncaria alkaloids' anti-hypertensive effects and explored the possible application of Uncaria alkaloids in preventing Alzheimer's disease. These results were further evaluated and refined using biological experiments. Our study provides a novel strategy for understanding the holistic pharmacology of TCM, as well as for exploring the multi-indication properties of TCM beyond its traditional applications.
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Affiliation(s)
- Wenyong Wu
- Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Pudong New District, Shanghai 201203, China; (W.W.); (Z.Z.); (F.L.); (Y.D.); (M.L.); (H.L.)
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zijia Zhang
- Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Pudong New District, Shanghai 201203, China; (W.W.); (Z.Z.); (F.L.); (Y.D.); (M.L.); (H.L.)
| | - Feifei Li
- Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Pudong New District, Shanghai 201203, China; (W.W.); (Z.Z.); (F.L.); (Y.D.); (M.L.); (H.L.)
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yanping Deng
- Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Pudong New District, Shanghai 201203, China; (W.W.); (Z.Z.); (F.L.); (Y.D.); (M.L.); (H.L.)
| | - Min Lei
- Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Pudong New District, Shanghai 201203, China; (W.W.); (Z.Z.); (F.L.); (Y.D.); (M.L.); (H.L.)
| | - Huali Long
- Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Pudong New District, Shanghai 201203, China; (W.W.); (Z.Z.); (F.L.); (Y.D.); (M.L.); (H.L.)
| | - Jinjun Hou
- Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Pudong New District, Shanghai 201203, China; (W.W.); (Z.Z.); (F.L.); (Y.D.); (M.L.); (H.L.)
- Correspondence: (J.H.); (W.W.); Tel.: +86-021-5080-2351 (J.H.)
| | - Wanying Wu
- Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Pudong New District, Shanghai 201203, China; (W.W.); (Z.Z.); (F.L.); (Y.D.); (M.L.); (H.L.)
- Correspondence: (J.H.); (W.W.); Tel.: +86-021-5080-2351 (J.H.)
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Kim A, Yoon D, Lim Y, Roh HJ, Kim S, Park CI, Kim HS, Cha HJ, Choi YH, Kim DH. Co-Expression Network Analysis of Spleen Transcriptome in Rock Bream ( Oplegnathus fasciatus) Naturally Infected with Rock Bream Iridovirus (RBIV). Int J Mol Sci 2020; 21:ijms21051707. [PMID: 32131541 PMCID: PMC7084886 DOI: 10.3390/ijms21051707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/12/2022] Open
Abstract
Rock bream iridovirus (RBIV) is a notorious agent that causes high mortality in aquaculture of rock bream (Oplegnathus fasciatus). Despite severity of this virus, no transcriptomic studies on RBIV-infected rock bream that can provide fundamental information on protective mechanism against the virus have been reported so far. This study aimed to investigate physiological mechanisms between host and RBIV through transcriptomic changes in the spleen based on RNA-seq. Depending on infection intensity and sampling time point, fish were divided into five groups: uninfected healthy fish at week 0 as control (0C), heavy infected fish at week 0 (0H), heavy mixed RBIV and bacterial infected fish at week 0 (0MH), uninfected healthy fish at week 3 (3C), and light infected fish at week 3 (3L). We explored clusters from 35,861 genes with Fragments Per Kilo-base of exon per Million mapped fragments (FPKM) values of 0.01 or more through signed co-expression network analysis using WGCNA package. Nine of 22 modules were highly correlated with viral infection (|gene significance (GS) vs. module membership (MM) |> 0.5, p-value < 0.05). Expression patterns in selected modules were divided into two: heavy infected (0H and 0MH) and control and light-infected groups (0C, 3C, and 3L). In functional analysis, genes in two positive modules (5448 unigenes) were enriched in cell cycle, DNA replication, transcription, and translation, and increased glycolysis activity. Seven negative modules (3517 unigenes) built in this study showed significant decreases in the expression of genes in lymphocyte-mediated immune system, antigen presentation, and platelet activation, whereas there was significant increased expression of endogenous apoptosis-related genes. These changes lead to RBIV proliferation and failure of host defense, and suggests the importance of blood cells such as thrombocytes and B cells in rock bream in RBIV infection. Interestingly, a hub gene, pre-mRNA processing factor 19 (PRPF19) showing high connectivity (kME), and expression of this gene using qRT-PCR was increased in rock bream blood cells shortly after RBIV was added. It might be a potential biomarker for diagnosis and vaccine studies in rock bream against RBIV. This transcriptome approach and our findings provide new insight into the understanding of global rock bream-RBIV interactions including immune and pathogenesis mechanisms.
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Affiliation(s)
- Ahran Kim
- Department of Chemistry, Center for Proteome Biophysics, and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (A.K.); (D.Y.); (S.K.)
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
| | - Dahye Yoon
- Department of Chemistry, Center for Proteome Biophysics, and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (A.K.); (D.Y.); (S.K.)
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong 27709, Korea
| | - Yunjin Lim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
- Hazardous Substances Analysis Division, Gwangju Regional Office of Food and Drug Safety, Gwangju 61012, Korea
| | - Heyong Jin Roh
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
| | - Suhkmann Kim
- Department of Chemistry, Center for Proteome Biophysics, and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (A.K.); (D.Y.); (S.K.)
| | - Chan-Il Park
- Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, Tongyeong 53064, Korea;
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea;
| | - Hee-Jae Cha
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Korea;
| | - Yung Hyun Choi
- Department of Biochemistry, College of Oriental Medicine, Dongeui University, Busan 47227, Korea;
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
- Correspondence: ; Tel.: +82-51-629-5945
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