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Nwizu C, Hughes M, Ramseier ML, Navia AW, Shalek AK, Fusi N, Raghavan S, Winter PS, Amini AP, Crawford L. Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579839. [PMID: 38405697 PMCID: PMC10888887 DOI: 10.1101/2024.02.11.579839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Clustering is commonly used in single-cell RNA-sequencing (scRNA-seq) pipelines to characterize cellular heterogeneity. However, current methods face two main limitations. First, they require user-specified heuristics which add time and complexity to bioinformatic workflows; second, they rely on post-selective differential expression analyses to identify marker genes driving cluster differences, which has been shown to be subject to inflated false discovery rates. We address these challenges by introducing nonparametric clustering of single-cell populations (NCLUSION): an infinite mixture model that leverages Bayesian sparse priors to identify marker genes while simultaneously performing clustering on single-cell expression data. NCLUSION uses a scalable variational inference algorithm to perform these analyses on datasets with up to millions of cells. By analyzing publicly available scRNA-seq studies, we demonstrate that NCLUSION (i) matches the performance of other state-of-the-art clustering techniques with significantly reduced runtime and (ii) provides statistically robust and biologically relevant transcriptomic signatures for each of the clusters it identifies. Overall, NCLUSION represents a reliable hypothesis-generating tool for understanding patterns of expression variation present in single-cell populations.
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Affiliation(s)
- Chibuikem Nwizu
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Warren Alpert Medical School of Brown University, Providence, RI, USA
| | | | - Michelle L. Ramseier
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew W. Navia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alex K. Shalek
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Srivatsan Raghavan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Peter S. Winter
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Microsoft Research, Cambridge, MA, USA
- Department of Biostatistics, Brown University, Providence, RI, USA
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Yap CC, Digilio L, McMahon L, Winckler B. "Disruption of Golgi markers by two RILP-directed shRNAs in neurons: a new role for RILP or a neuron-specific off-target phenotype?". J Biol Chem 2023:104916. [PMID: 37315786 PMCID: PMC10362152 DOI: 10.1016/j.jbc.2023.104916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023] Open
Abstract
In neurons, degradation of dendritic cargos requires RAB7 and dynein-mediated retrograde transport to somatic lysosomes. To test if the dynein adaptor RILP (RAB-interacting lysosomal protein) mediated the recruitment of dynein to late endosomes for retrograde transport in dendrites, we obtained several knockdown reagents previously validated in non-neuronal cells. Striking endosomal phenotypes elicited by one shRILP plasmid were not reproduced by another one. Furthermore, we discovered a profound depletion of Golgi/TGN markers for both shRILP plasmids. This Golgi disruption was only observed in neurons and could not be rescued by re-expression of RILP. This Golgi phenotype was also not found in neurons treated with siRILP or gRILP/Cas9. Lastly, we tested if a different RAB protein that interacts with RILP, namely the Golgi-associated RAB34, might be responsible for the loss of Golgi markers. Expression of a dominant-negative RAB34 did indeed cause changes in Golgi staining in a small subset of neurons but manifested as fragmentation rather than loss of staining. Unlike in non-neuronal cells, interference with RAB34 did not cause dispersal of lysosomes in neurons. Based on multiple lines of experimentation, we conclude that the neuronal Golgi phenotype observed with shRILP is likely off-target in this cell type specifically. Any observed disruptions of endosomal trafficking caused by shRILP in neurons might thus be downstream of Golgi disruption. It would be interesting to identify the actual target for this neuronal Golgi phenotype. Cell type-specific off-target phenotypes therefore likely occur in neurons, necessitating re-validation of reagents that were previously validated in other cell types.
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Affiliation(s)
- Chan Choo Yap
- Department of Cell Biology, University of Virginia, 1340 Jefferson Park Avenue, Pinn Hall 3226, Charlottesville, VA 22908, USA.
| | - Laura Digilio
- Department of Cell Biology, University of Virginia, 1340 Jefferson Park Avenue, Pinn Hall 3226, Charlottesville, VA 22908, USA
| | - Lloyd McMahon
- Department of Cell Biology, University of Virginia, 1340 Jefferson Park Avenue, Pinn Hall 3226, Charlottesville, VA 22908, USA
| | - Bettina Winckler
- Department of Cell Biology, University of Virginia, 1340 Jefferson Park Avenue, Pinn Hall 3226, Charlottesville, VA 22908, USA.
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Ye C, Ren S, Sadula A, Guo X, Yuan M, Meng M, Li G, Zhang X, Yuan C. The expression characteristics of transmembrane protein genes in pancreatic ductal adenocarcinoma through comprehensive analysis of bulk and single-cell RNA sequence. Front Oncol 2023; 13:1047377. [PMID: 37265785 PMCID: PMC10229874 DOI: 10.3389/fonc.2023.1047377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 05/02/2023] [Indexed: 06/03/2023] Open
Abstract
Background Transmembrane (TMEM) protein genes are a class of proteins that spans membranes and function to many physiological processes. However, there is very little known about TMEM gene expression, especially in cancer tissue. Using single-cell and bulk RNA sequence may facilitate the understanding of this poorly characterized protein genes in PDAC. Methods We selected the TMEM family genes through the Human Protein Atlas and characterized their expression by single-cell and bulk transcriptomic datasets. Identification of the key TMEM genes was performed through three machine learning algorithms: LASSO, SVM-RFE and RF-SRC. Then, we established TMEM gene riskscore and estimate its implication in predicting survival and response to systematic therapy. Additionally, we explored the difference and impact of TMEM gene expression in PDAC through immunohistochemistry and cell line research. Results 5 key TMEM genes (ANO1, TMEM59, TMEM204, TMEM205, TMEM92) were selected based on the single-cell analysis and machine learning survival outcomes. Patients stratified into the high and low-risk groups based on TMEM riskscore, were observed with distinct overall survival in internal and external datasets. Moreover, through bulk RNA-sequence and immunohistochemical staining we verified the protein expression of TMEM genes in PDAC and revealed TMEM92 as an essential regulator of pancreatic cancer cell proliferation, migration, and invasion. Conclusion Our study on TMEM gene expression and behavior in PDAC has revealed unique characteristics, offering potential for precise therapeutic approaches. Insights into molecular mechanisms expand understanding of PDAC complexity and TMEM gene roles. Such knowledge may inform targeted therapy development, benefiting patients.
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Affiliation(s)
- Chen Ye
- Department of General Surgery, Peking University Third Hospital, Beijing, China
- Department of Hepatobiliary surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Siqian Ren
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | | | - Xin Guo
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Meng Yuan
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Meng Meng
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Gang Li
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Xiaowei Zhang
- Department of Hematology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chunhui Yuan
- Department of General Surgery, Peking University Third Hospital, Beijing, China
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4
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Moon SW, Zhao L, Matloff W, Hobel S, Berger R, Kwon D, Kim J, Toga AW, Dinov ID. Brain structure and allelic associations in Alzheimer's disease. CNS Neurosci Ther 2023; 29:1034-1048. [PMID: 36575854 PMCID: PMC10018103 DOI: 10.1111/cns.14073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD), the most prevalent form of dementia, affects 6.5 million Americans and over 50 million people globally. Clinical, genetic, and phenotypic studies of dementia provide some insights of the observed progressive neurodegenerative processes, however, the mechanisms underlying AD onset remain enigmatic. AIMS This paper examines late-onset dementia-related cognitive impairment utilizing neuroimaging-genetics biomarker associations. MATERIALS AND METHODS The participants, ages 65-85, included 266 healthy controls (HC), 572 volunteers with mild cognitive impairment (MCI), and 188 Alzheimer's disease (AD) patients. Genotype dosage data for AD-associated single nucleotide polymorphisms (SNPs) were extracted from the imputed ADNI genetics archive using sample-major additive coding. Such 29 SNPs were selected, representing a subset of independent SNPs reported to be highly associated with AD in a recent AD meta-GWAS study by Jansen and colleagues. RESULTS We identified the significant correlations between the 29 genomic markers (GMs) and the 200 neuroimaging markers (NIMs). The odds ratios and relative risks for AD and MCI (relative to HC) were predicted using multinomial linear models. DISCUSSION In the HC and MCI cohorts, mainly cortical thickness measures were associated with GMs, whereas the AD cohort exhibited different GM-NIM relations. Network patterns within the HC and AD groups were distinct in cortical thickness, volume, and proportion of White to Gray Matter (pct), but not in the MCI cohort. Multinomial linear models of clinical diagnosis showed precisely the specific NIMs and GMs that were most impactful in discriminating between AD and HC, and between MCI and HC. CONCLUSION This study suggests that advanced analytics provide mechanisms for exploring the interrelations between morphometric indicators and GMs. The findings may facilitate further clinical investigations of phenotypic associations that support deep systematic understanding of AD pathogenesis.
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Affiliation(s)
- Seok Woo Moon
- Department of Neuropsychiatry, Research Institute of Medical ScienceKonkuk University School of MedicineSeoulKorea
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
| | - Lu Zhao
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
| | - William Matloff
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
| | - Sam Hobel
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
| | - Ryan Berger
- Microbiology & ImmunologyUniversity of MichiganAnn ArborMichiganUSA
| | - Daehong Kwon
- Department of Biomedical Science and EngineeringKonkuk UniversitySeoulKorea
| | - Jaebum Kim
- Department of Biomedical Science and EngineeringKonkuk UniversitySeoulKorea
| | - Arthur W. Toga
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
| | - Ivo D. Dinov
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
- Department of Health Behavior and Biological Sciences, Statistics Online Computational Resource (SOCR), Michigan Institute for Data Science (MIDAS)University of MichiganAnn ArborMichiganUSA
- Department of StatisticsUniversity of CaliforniaLos AngelesCaliforniaUSA
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Yang S, Zhang J, Xu Y, Wang J, Zhao H, Lei J, Zhou Y, Chen Y, Wu L, Zhou M, Zheng L, Ji X, Li Y. OIT3 mediates macrophage polarization and facilitates hepatocellular carcinoma progression. Cancer Immunol Immunother 2022; 71:2677-2689. [PMID: 35353239 DOI: 10.1007/s00262-022-03188-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/08/2022] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related mortality; however, effective immunotherapy strategies are limited because of the immunosuppressive tumor microenvironment. Macrophages are essential components of the HCC microenvironment and are related to poor prognosis. Here, we evaluated the attributes of paracancer tissues in tumor immunity and progression using public databases. Based on the abundance of immune cells estimated by CIBERSORT, we performed weighted gene co-expression network analysis and found a specific module associated with M2 macrophages. Through analyzing interaction networks using Cytoscape and public datasets, we identified oncoprotein-induced transcript 3 (OIT3) as a novel marker of M2 macrophages. Overexpression of OIT3 remodeled immune features and reprogrammed the metabolism of M2 macrophages. Moreover, compared with wildtype macrophages, OIT3-overexpressing macrophages further enhanced the migration and invasion of co-cultured cancer cells. Additionally, OIT3-overexpressing macrophages promoted tumorigenesis and cancer development in vivo. Taken together, the findings demonstrate that OIT3 is a novel biomarker of alternatively activated macrophages and facilitates HCC metastasis.
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Affiliation(s)
- Shuai Yang
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
- Department of Pathology, the 958th Hospital, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Jiangang Zhang
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Yanquan Xu
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Jingchun Wang
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Huakan Zhao
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Juan Lei
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Yu Zhou
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Yu Chen
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Lei Wu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Mingyue Zhou
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Lu Zheng
- Department of Hepatobiliary Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
| | - Xiaohui Ji
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China.
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China.
| | - Yongsheng Li
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China.
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China.
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6
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Cen C, Tang J, Su Q, Zhang Z, Yang Z, Mo W. Systemic analysis the expression, prognostic, and immune infiltrates significance of MS4A family in lung cancer. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2025914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Caize Cen
- Department of Clinical Laboratory, First Affiliated Hospital Guangxi Medical University, Nanning, People’s Republic of China
| | - Jiameng Tang
- Department of Clinical Laboratory, First Affiliated Hospital Guangxi Medical University, Nanning, People’s Republic of China
| | - Qisheng Su
- Department of Clinical Laboratory, First Affiliated Hospital Guangxi Medical University, Nanning, People’s Republic of China
| | - Zunni Zhang
- Department of Clinical Laboratory, People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, People’s Republic of China
| | - Zheng Yang
- Department of Clinical Laboratory, First Affiliated Hospital Guangxi Medical University, Nanning, People’s Republic of China
| | - Wuning Mo
- Department of Clinical Laboratory, First Affiliated Hospital Guangxi Medical University, Nanning, People’s Republic of China
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Abstract
Alzheimer's disease (AD) is characterized by the presence of amyloid beta (Aβ) plaques and neurofibrillary tangles (NFTs), neuronal and synaptic loss and inflammation of the central nervous system (CNS). The majority of AD research has been dedicated to the understanding of two major AD hallmarks (i.e. Aβ and NFTs); however, recent genome-wide association studies (GWAS) data indicate neuroinflammation as having a critical role in late-onset AD (LOAD) development, thus unveiling a novel avenue for AD therapeutics. Recent evidence has provided much support to the innate immune system's involvement with AD progression; however, much remains to be uncovered regarding the role of glial cells, specifically microglia, in AD. Moreover, numerous variants in immune and/or microglia-related genes have been identified in whole-genome sequencing and GWAS analyses, including such genes as TREM2, CD33, APOE, API1, MS4A, ABCA7, BIN1, CLU, CR1, INPP5D, PICALM and PLCG2. In this review, we aim to provide an insight into the function of the major LOAD-associated microglia response genes.
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Affiliation(s)
- Lauren A. Jonas
- Weill Cornell, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065, USA,Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tanya Jain
- Weill Cornell, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065, USA,Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yue-Ming Li
- Weill Cornell, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065, USA,Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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8
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Li H, Yang W, Zhang M, He T, Zhou F, G Herman J, Hu L, Guo M. Methylation of TMEM176A, a key ERK signaling regulator, is a novel synthetic lethality marker of ATM inhibitors in human lung cancer. Epigenomics 2021; 13:1403-1419. [PMID: 34558311 DOI: 10.2217/epi-2021-0217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: The role of TMEM176A methylation in lung cancer and its therapeutic application remains unclear. Materials and methods: Nine lung cancer cell lines and 123 cases of cancer tissue samples were employed. Results: TMEM176A was methylated in 53.66% of primary lung cancer. Restoration of TMEM176A expression induced cell apoptosis and G2/M phase arrest, and inhibited colony formation, cell proliferation, migration and invasion. TMEM176A suppressed H1299 cell xenograft growth in mice. Methylation of TMEM176A activated ERK signaling and sensitized H1299 and H23 cells to AZD0156, an ATM inhibitor. Conclusion: The expression of TMEM176A is regulated by promoter region methylation. Methylation of TMEM176A is a potential lung cancer diagnostic marker and a novel synthetic lethal therapeutic marker for AZD0156.
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Affiliation(s)
- Hongxia Li
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Faculty of Environmental & Life Science, Beijing Key Laboratory of Environmental & Oncology, Beijing University of Technology, Beijing, 100124, China
| | - Weili Yang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Meiying Zhang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Tao He
- Department of Pathology, Characteristic Medical Center of The Chinese People's Armed Police Force, Tianjin, 300162, China
| | - Fuyou Zhou
- Department of Thoracic Surgery, Anyang Tumor Hospital, Anyang, 455000, Henan, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Suite 2.18/Research, Pittsburgh, PA 15213, USA
| | - Liming Hu
- Faculty of Environmental & Life Science, Beijing Key Laboratory of Environmental & Oncology, Beijing University of Technology, Beijing, 100124, China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Henan Key Laboratory for Esophageal Cancer Research, Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, China.,State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853, China
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9
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Nouailles G, Wyler E, Pennitz P, Postmus D, Vladimirova D, Kazmierski J, Pott F, Dietert K, Muelleder M, Farztdinov V, Obermayer B, Wienhold SM, Andreotti S, Hoefler T, Sawitzki B, Drosten C, Sander LE, Suttorp N, Ralser M, Beule D, Gruber AD, Goffinet C, Landthaler M, Trimpert J, Witzenrath M. Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19. Nat Commun 2021; 12:4869. [PMID: 34381043 PMCID: PMC8357947 DOI: 10.1038/s41467-021-25030-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/13/2021] [Indexed: 01/08/2023] Open
Abstract
In COVID-19, immune responses are key in determining disease severity. However, cellular mechanisms at the onset of inflammatory lung injury in SARS-CoV-2 infection, particularly involving endothelial cells, remain ill-defined. Using Syrian hamsters as a model for moderate COVID-19, we conduct a detailed longitudinal analysis of systemic and pulmonary cellular responses, and corroborate it with datasets from COVID-19 patients. Monocyte-derived macrophages in lungs exert the earliest and strongest transcriptional response to infection, including induction of pro-inflammatory genes, while epithelial cells show weak alterations. Without evidence for productive infection, endothelial cells react, depending on cell subtypes, by strong and early expression of anti-viral, pro-inflammatory, and T cell recruiting genes. Recruitment of cytotoxic T cells as well as emergence of IgM antibodies precede viral clearance at day 5 post infection. Investigating SARS-CoV-2 infected Syrian hamsters thus identifies cell type-specific effector functions, providing detailed insights into pathomechanisms of COVID-19 and informing therapeutic strategies.
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Affiliation(s)
- Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Pulmonary Inflammation, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
| | - Peter Pennitz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Pulmonary Inflammation, Berlin, Germany
| | - Dylan Postmus
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
| | | | - Julia Kazmierski
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Fabian Pott
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Kristina Dietert
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research, Freie Universität Berlin, Berlin, Germany
| | - Michael Muelleder
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Core Facility - High-Throughput Mass Spectrometry, Berlin, Germany
| | - Vadim Farztdinov
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Core Facility - High-Throughput Mass Spectrometry, Berlin, Germany
| | - Benedikt Obermayer
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Bioinformatics, Berlin, Germany
| | - Sandra-Maria Wienhold
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Pulmonary Inflammation, Berlin, Germany
| | - Sandro Andreotti
- Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
| | - Thomas Hoefler
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Birgit Sawitzki
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Leif E Sander
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Norbert Suttorp
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, UK
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Bioinformatics, Berlin, Germany
| | - Achim D Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Christine Goffinet
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- IRI Life Sciences, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, Berlin, Germany.
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Pulmonary Inflammation, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.
- German Center for Lung Research (DZL), Berlin, Germany.
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10
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Yuan Y, Deng Q, Wei X, Liu Y, Lan Q, Jiang Y, Yu Y, Guo P, Xu J, Yu C, Han L, Cheng M, Wu P, Zhang X, Lai Y, Volpe G, Esteban MA, Yang H, Liu C, Liu L. The Chromatin Accessibility Landscape of Adult Rat. Front Genet 2021; 12:651604. [PMID: 34108989 PMCID: PMC8181391 DOI: 10.3389/fgene.2021.651604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/01/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Yue Yuan
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Qiuting Deng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Xiaoyu Wei
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Yang Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | | | - Yu Jiang
- First Hospital, Jilin University, Changchun, China
| | - Yeya Yu
- BGI-Shenzhen, Shenzhen, China.,BGI College, Zhengzhou University, Zhengzhou, China
| | - Pengcheng Guo
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jiangshan Xu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Cong Yu
- BGI-Shenzhen, Shenzhen, China
| | - Lei Han
- BGI-Shenzhen, Shenzhen, China
| | - Mengnan Cheng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | | | - Xiao Zhang
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Giacomo Volpe
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Miguel A Esteban
- BGI-Shenzhen, Shenzhen, China.,First Hospital, Jilin University, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China.,Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China.,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, China
| | - Chuanyu Liu
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Bay Laboratory, Shenzhen, China
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11
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Han JW, Heo W, Lee D, Kang C, Kim HY, Jun I, So I, Hur H, Lee MG, Jung M, Kim JY. Plasma Membrane Localized GCaMP-MS4A12 by Orai1 Co-Expression Shows Thapsigargin- and Ca 2+-Dependent Fluorescence Increases. Mol Cells 2021; 44:223-232. [PMID: 33935043 PMCID: PMC8112172 DOI: 10.14348/molcells.2021.2031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 11/27/2022] Open
Abstract
Uniquely expressed in the colon, MS4A12 exhibits store-operated Ca2+ entry (SOCE) activity. However, compared to MS4A1 (CD20), a Ca2+ channel and ideal target for successful leukaemia immunotherapy, MS4A12 has rarely been studied. In this study, we investigated the involvement of MS4A12 in Ca2+ influx and expression changes in MS4A12 in human colonic malignancy. Fluorescence of GCaMP-fused MS4A12 (GCaMP-M12) was evaluated to analyse MS4A12 activity in Ca2+ influx. Plasma membrane expression of GCaMP-M12 was achieved by homo- or hetero-complex formation with no-tagged MS4A12 (nt-M12) or Orai1, respectively. GCaMP-M12 fluorescence in plasma membrane increased only after thapsigargin-induced depletion of endoplasmic reticulum Ca2+ stores, and this fluorescence was inhibited by typical SOCE inhibitors and siRNA for Orai1. Furthermore, GCaMP-MS4A12 and Orai1 co-transfection elicited greater plasma membrane fluorescence than GCaMP-M12 co-transfected with nt-M12. Interestingly, the fluorescence of GCaMP-M12 was decreased by STIM1 over-expression, while increased by siRNA for STIM1 in the presence of thapsigargin and extracellular Ca2+. Moreover, immunoprecipitation assay revealed that Orai1 co-expression decreased protein interactions between MS4A12 and STIM1. In human colon tissue, MS4A12 was expressed in the apical region of the colonic epithelium, although its expression was dramatically decreased in colon cancer tissues. In conclusion, we propose that MS4A12 contributes to SOCE through complex formation with Orai1, but does not cooperate with STIM1. Additionally, we discovered that MS4A12 is expressed in the apical membrane of the colonic epithelium and that its expression is decreased with cancer progression.
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Affiliation(s)
- Jung Woo Han
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul 03080, Korea
| | - Woon Heo
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul 03080, Korea
| | - Donghyuk Lee
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul 03080, Korea
| | - Choeun Kang
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul 03080, Korea
| | - Hye-Yeon Kim
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul 03080, Korea
| | - Ikhyun Jun
- The Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Insuk So
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Hyuk Hur
- Department of Surgery, Yonsei University College of Medicine, Seoul 03080, Korea
| | - Min Goo Lee
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul 03080, Korea
| | - Minkyu Jung
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03080, Korea
| | - Joo Young Kim
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul 03080, Korea
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12
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Pavlasova G, Mraz M. The regulation and function of CD20: an "enigma" of B-cell biology and targeted therapy. Haematologica 2021; 105:1494-1506. [PMID: 32482755 PMCID: PMC7271567 DOI: 10.3324/haematol.2019.243543] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/15/2020] [Indexed: 12/26/2022] Open
Abstract
The introduction of anti-CD20 monoclonal antibodies such as rituximab, ofatumumab, or obinutuzumab improved the therapy of B-cell malignancies even though the precise physiological role and regulation of CD20 remains unclear. Furthermore, CD20 expression is highly variable between different B-cell malignancies, patients with the same malignancy, and even between intraclonal subpopulations in an individual patient. Several epigenetic (EZH2, HDAC1/2, HDAC1/4, HDAC6, complex Sin3A-HDAC1) and transcription factors (USF, OCT1/2, PU.1, PiP, ELK1, ETS1, SP1, NFκB, FOXO1, CREM, SMAD2/3) regulating CD20 expression (encoded by MS4A1) have been characterized. CD20 is induced in the context of microenvironmental interactions by CXCR4/SDF1 (CXCL12) chemokine signaling and the molecular function of CD20 has been linked to the signaling propensity of B-cell receptor (BCR). CD20 has also been shown to interact with multiple other surface proteins on B cells (such as CD40, MHCII, CD53, CD81, CD82, and CBP). Current efforts to combine anti-CD20 monoclonal antibodies with BCR signaling inhibitors targeting BTK or PI3K (ibrutinib, acalabrutinib, idelalisib, duvelisib) or BH3-mimetics (venetoclax) lead to the necessity to better understand both the mechanisms of regulation and the biological functions of CD20. This is underscored by the observation that CD20 is decreased in response to the "BCR inhibitor" ibrutinib which largely prevents its successful combination with rituximab. Several small molecules (such as histone deacetylase inhibitors, DNA methyl-transferase inhibitors, aurora kinase A/B inhibitors, farnesyltransferase inhibitors, FOXO1 inhibitors, and bryostatin-1) are being tested to upregulate cell-surface CD20 levels and increase the efficacy of anti-CD20 monoclonal antibodies. Herein, we review the current understanding of CD20 function, and the mechanisms of its regulation in normal and malignant B cells, highlighting the therapeutic implications.
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Affiliation(s)
- Gabriela Pavlasova
- Central European Institute of Technology, Masaryk University, Brno.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Central European Institute of Technology, Masaryk University, Brno .,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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13
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Men X, Su M, Ma J, Mou Y, Dai P, Chen C, Cheng XA. Overexpression of TMEM47 Induces Tamoxifen Resistance in Human Breast Cancer Cells. Technol Cancer Res Treat 2021; 20:15330338211004916. [PMID: 33745390 PMCID: PMC7989118 DOI: 10.1177/15330338211004916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background: Tamoxifen (TAM) is the eminent first-line drug for endocrine therapy of hormone receptor positive premenopausal breast cancer and reduces the risk of recurrence by ∼50%. However, many patients developed TAM resistance and their diseases recurred. Our previous study on transcriptome profile of TAM resistant breast cancer cells revealed that the TMEM47 is one of the most significantly differentially expressed genes. The mechanism of how TMEM47 is involved in TAM resistance was not known. Methods: We constructed a mammal breast cancer cell line, in which TMEM47 was stably overexpressed (TMEM47-OE/MCF-7), to further verify the role of TMEM47 in TAM resistance. siRNA targeting TMEM47 was transfected into TAMR / MCF-7 cells by Liposome. TMEM47 expression was validated on mRNA and protein level by qRT-PCR and western blotting. We tested the cytotoxicity of TAM in the cells. Apoptosis was detected by flow cytometry. Results: Compared to the MCF7 cells, TMEM47 mRNA was significantly up regulated more than 6 folds in the TAMR/MCF7 cells and so its protein. TMEM47 expression level in TMEM47-OE/MCF-7 was similar as in the TAMR/MCF-7 cells. The 50% inhibitory concentration (IC50) value (mean ± SD) of TAM in MCF-7, TAMR/MCF-7 and TMEM47-OE/MCF-7 cells was 1.58 ± 0.19, 2.74 ± 0.24 and 3.12 ± 0.32 µγ/mL, respectively. The apoptosis rates of TAMR/MCF-7 and TMEM47-OE/MCF-7 cell lines were significantly lower than that of MCF-7 cells. After 24 and 48 hours TAM treatments, cell viability was significantly inhibitied in TMEM47 knockdown TAMR/MCF7 cells (P < 0.01). Consistant with the decreased cell viability, the apoptosis rate in TMEM47 knockdown TAMR/MCF-7 cells was significantly increased. Conclusions: Our results suggest that overexpression of TMEM47 in MCF-7 cells acquired TAM resistance to those cells, and knockdown of TMEM47 in TAMR/MCF-7 cells reversed their resistance to TAM. TMEM47 might confer TAM resistance on MCF-7 cells through the inhibition of apoptosis.
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Affiliation(s)
- Xin Men
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, China.,Microbiology Institute of Shaanxi, Xi'an, Shaanxi, China
| | - Mengyang Su
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Jun Ma
- Shaanxi University of Science and Technology, Xi'an, Shaanxi, China
| | - Yueyang Mou
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Penggao Dai
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, China.,Lifegen Co. Ltd., Xi'an, Shaanxi, China
| | - Chao Chen
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Xi An Cheng
- Tongchuan people's Hospital, Tongchuan, Shaanxi, China
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14
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Zarinsefat A, Hartoularos G, Rychkov D, Rashmi P, Chandran S, Vincenti F, Yee CJ, Sarwal MM. Single-Cell RNA Sequencing of Tocilizumab-Treated Peripheral Blood Mononuclear Cells as an in vitro Model of Inflammation. Front Genet 2021; 11:610682. [PMID: 33469465 PMCID: PMC7813999 DOI: 10.3389/fgene.2020.610682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/02/2020] [Indexed: 12/27/2022] Open
Abstract
COVID-19 has posed a significant threat to global health. Early data has revealed that IL-6, a key regulatory cytokine, plays an important role in the cytokine storm of COVID-19. Multiple trials are therefore looking at the effects of Tocilizumab, an IL-6 receptor antibody that inhibits IL-6 activity, on treatment of COVID-19, with promising findings. As part of a clinical trial looking at the effects of Tocilizumab treatment on kidney transplant recipients with subclinical rejection, we performed single-cell RNA sequencing of comparing stimulated PBMCs before and after Tocilizumab treatment. We leveraged this data to create an in vitro cytokine storm model, to better understand the effects of Tocilizumab in the presence of inflammation. Tocilizumab-treated cells had reduced expression of inflammatory-mediated genes and biologic pathways, particularly amongst monocytes. These results support the hypothesis that Tocilizumab may hinder the cytokine storm of COVID-19, through a demonstration of biologic impact at the single-cell level.
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Affiliation(s)
- Arya Zarinsefat
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - George Hartoularos
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Dmitry Rychkov
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Priyanka Rashmi
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Sindhu Chandran
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Flavio Vincenti
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Chun J. Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Minnie M. Sarwal
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
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15
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Ma Y, Jun GR, Chung J, Zhang X, Kunkle BW, Naj AC, White CC, Bennett DA, De Jager PL, Mayeux R, Haines JL, Pericak‐Vance MA, Schellenberg GD, Farrer LA, Lunetta KL. CpG-related SNPs in the MS4A region have a dose-dependent effect on risk of late-onset Alzheimer disease. Aging Cell 2019; 18:e12964. [PMID: 31144443 PMCID: PMC6612647 DOI: 10.1111/acel.12964] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 04/04/2019] [Accepted: 04/13/2019] [Indexed: 01/22/2023] Open
Abstract
CpG‐related single nucleotide polymorphisms (CGS) have the potential to perturb DNA methylation; however, their effects on Alzheimer disease (AD) risk have not been evaluated systematically. We conducted a genome‐wide association study using a sliding‐window approach to measure the combined effects of CGSes on AD risk in a discovery sample of 24 European ancestry cohorts (12,181 cases, 12,601 controls) from the Alzheimer's Disease Genetics Consortium (ADGC) and replication sample of seven European ancestry cohorts (7,554 cases, 27,382 controls) from the International Genomics of Alzheimer's Project (IGAP). The potential functional relevance of significant associations was evaluated by analysis of methylation and expression levels in brain tissue of the Religious Orders Study and the Rush Memory and Aging Project (ROSMAP), and in whole blood of Framingham Heart Study participants (FHS). Genome‐wide significant (p < 5 × 10−8) associations were identified with 171 1.0 kb‐length windows spanning 932 kb in the APOE region (top p < 2.2 × 10−308), five windows at BIN1 (top p = 1.3 × 10−13), two windows at MS4A6A (top p = 2.7 × 10−10), two windows near MS4A4A (top p = 6.4 × 10−10), and one window at PICALM (p = 6.3 × 10‐9). The total number of CGS‐derived CpG dinucleotides in the window near MS4A4A was associated with AD risk (p = 2.67 × 10−10), brain DNA methylation (p = 2.15 × 10−10), and gene expression in brain (p = 0.03) and blood (p = 2.53 × 10−4). Pathway analysis of the genes responsive to changes in the methylation quantitative trait locus signal at MS4A4A (cg14750746) showed an enrichment of methyltransferase functions. We confirm the importance of CGS in AD and the potential for creating a functional CpG dosage‐derived genetic score to predict AD risk.
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Affiliation(s)
- Yiyi Ma
- Department of Medicine (Biomedical Genetics) Boston University School of Medicine Boston Massachusetts
- Center for Translational & Computational Neuroimmunology, Multiple Sclerosis Clinical Care and Research Center, Division of Neuroimmunology, Department of Neurology Columbia University Medical Center New York New York
| | - Gyungah R. Jun
- Department of Medicine (Biomedical Genetics) Boston University School of Medicine Boston Massachusetts
- Department of Biostatistics Boston University School of Public Health Boston Massachusetts
- Department of Ophthalmology Boston University School of Medicine Boston Massachusetts
| | - Jaeyoon Chung
- Department of Medicine (Biomedical Genetics) Boston University School of Medicine Boston Massachusetts
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics) Boston University School of Medicine Boston Massachusetts
- Department of Biostatistics Boston University School of Public Health Boston Massachusetts
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine University of Miami Miami Florida
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology, and Informatics University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania
- Department of Pathology and Laboratory Medicine University of Pennsylvania Philadelphia Pennsylvania
| | - Charles C. White
- Program in Translational NeuroPsychiatric Genomics Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Boston Massachusetts
- Program in Medical and Population Genetics Broad Institute Cambridge Massachusetts
| | - David A Bennett
- Rush Alzheimer’s Disease Center Rush University Medical Center Chicago Illinois
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Multiple Sclerosis Clinical Care and Research Center, Division of Neuroimmunology, Department of Neurology Columbia University Medical Center New York New York
- Program in Translational NeuroPsychiatric Genomics Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Boston Massachusetts
- Program in Medical and Population Genetics Broad Institute Cambridge Massachusetts
| | - Richard Mayeux
- Department of Neurology and Sergievsky Center Columbia University New York New York
| | - Jonathan L. Haines
- Department of Epidemiology and Biostatistics Case Western Reserve University Cleveland Ohio
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine University of Miami Miami Florida
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine University of Pennsylvania Philadelphia Pennsylvania
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics) Boston University School of Medicine Boston Massachusetts
- Department of Biostatistics Boston University School of Public Health Boston Massachusetts
- Department of Ophthalmology Boston University School of Medicine Boston Massachusetts
- Department of Neurology Boston University School of Medicine Boston Massachusetts
- Department of Epidemiology Boston University School of Public Health Boston Massachusetts
| | - Kathryn L. Lunetta
- Department of Biostatistics Boston University School of Public Health Boston Massachusetts
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16
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Bossel Ben-Moshe N, Hen-Avivi S, Levitin N, Yehezkel D, Oosting M, Joosten LAB, Netea MG, Avraham R. Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells. Nat Commun 2019; 10:3266. [PMID: 31332193 PMCID: PMC6646406 DOI: 10.1038/s41467-019-11257-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 07/03/2019] [Indexed: 12/20/2022] Open
Abstract
Complex interactions between different host immune cell types can determine the outcome of pathogen infections. Advances in single cell RNA-sequencing (scRNA-seq) allow probing of these immune interactions, such as cell-type compositions, which are then interpreted by deconvolution algorithms using bulk RNA-seq measurements. However, not all aspects of immune surveillance are represented by current algorithms. Here, using scRNA-seq of human peripheral blood cells infected with Salmonella, we develop a deconvolution algorithm for inferring cell-type specific infection responses from bulk measurements. We apply our dynamic deconvolution algorithm to a cohort of healthy individuals challenged ex vivo with Salmonella, and to three cohorts of tuberculosis patients during different stages of disease. We reveal cell-type specific immune responses associated not only with ex vivo infection phenotype but also with clinical disease stage. We propose that our approach provides a predictive power to identify risk for disease, and human infection outcomes. Complex interactions between different host immune cell types can determine the outcome of pathogen infections. Here, Avraham and colleagues present a deconvolution algorithm that uses single-cell RNA and bulk RNA sequencing measurements of pathogen-infected cells to predict disease risk outcomes.
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Affiliation(s)
- Noa Bossel Ben-Moshe
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Shelly Hen-Avivi
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Natalia Levitin
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Dror Yehezkel
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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17
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Mehdizadeh E, Khalaj-Kondori M, Shaghaghi-Tarakdari Z, Sadigh-Eteghad S, Talebi M, Andalib S. Association of MS4A6A, CD33, and TREM2 gene polymorphisms with the late-onset Alzheimer's disease. ACTA ACUST UNITED AC 2019; 9:219-225. [PMID: 31799158 PMCID: PMC6879710 DOI: 10.15171/bi.2019.27] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/22/2019] [Accepted: 04/09/2019] [Indexed: 12/14/2022]
Abstract
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Introduction: Alzheimer’s disease (AD), which is a progressive neurodegenerative disorder, causes structural and functional brain disruption. MS4A6A, TREM2, and CD33 gene polymorphisms loci have been found to be associated with the pathobiology of late-onset AD (LOAD). In the present study, we tested the hypothesis of association of LOAD with rs983392, rs75932628, and rs3865444 polymorphisms in MS4A6A, TREM2, CD33 genes, respectively.
Methods: In the present study, 113 LOAD patients and 100 healthy unrelated age- and gender-matched controls were selected. DNA was extracted from blood samples by the salting-out method and the genotyping was performed by RFLP-PCR. Electrophoresis was carried out on agarose gel. Sequencing was thereafter utilized for the confirmation of the results.
Results: Only CD33 rs3865444 polymorphism revealed a significant difference in the genotypic frequencies of GG (P = 0.001) and GT (P = 0.001), and allelic frequencies of G (P = 0.033) and T (P = 0.03) between LOAD patients and controls.
Conclusion: The evidence from the present study suggests that T allele of CD33 rs3865444 polymorphism is associated with LOAD in the studied Iranian population.
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Affiliation(s)
- Elham Mehdizadeh
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Zeinab Shaghaghi-Tarakdari
- Department of Genetics, Animal Biology Group, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Saeed Sadigh-Eteghad
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahnaz Talebi
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sasan Andalib
- Neuroscience Research Center, Poursina Hospital, Guilan University of Medical Sciences, Rasht, Iran.,Department of Neurosurgery, Poursina Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran.,Department of Nuclear Medicine, Odense University Hospital, Odense, Denmark.,Center for Applied Neuroscience, Brain Research - Interdisciplinary Guided Excellence, BRIDGE, Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.,Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.,Department of Psychiatry, Psychiatry in the Region of Southern Denmark, Odense, Denmark
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18
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Nikolac Perkovic M, Pivac N. Genetic Markers of Alzheimer's Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1192:27-52. [PMID: 31705489 DOI: 10.1007/978-981-32-9721-0_3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease is a complex and heterogeneous, severe neurodegenerative disorder and the predominant form of dementia, characterized by cognitive disturbances, behavioral and psychotic symptoms, progressive cognitive decline, disorientation, behavioral changes, and death. Genetic background of Alzheimer's disease differs between early-onset familial Alzheimer's disease, other cases of early-onset Alzheimer's disease, and late-onset Alzheimer's disease. Rare cases of early-onset familial Alzheimer's diseases are caused by high-penetrant mutations in genes coding for amyloid precursor protein, presenilin 1, and presenilin 2. Late-onset Alzheimer's disease is multifactorial and associated with many different genetic risk loci (>20), with the apolipoprotein E ε4 allele being a major genetic risk factor for late-onset Alzheimer's disease. Genetic and genomic studies offer insight into many additional genetic risk loci involved in the genetically complex nature of late-onset Alzheimer's disease. This review highlights the contributions of individual loci to the pathogenesis of Alzheimer's disease and suggests that their exact contribution is still not clear. Therefore, the use of genetic markers of Alzheimer's disease, for monitoring development, time course, treatment response, and prognosis of Alzheimer's disease, is still far away from the clinical application, because the contribution of genetic variations to the relative risk of developing Alzheimer's disease is limited. In the light of prediction and prevention of Alzheimer's disease, a novel approach could be found in the form of additive genetic risk scores, which combine additive effects of numerous susceptibility loci.
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Affiliation(s)
- Matea Nikolac Perkovic
- Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka 54, Zagreb, 10000, Croatia
| | - Nela Pivac
- Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka 54, Zagreb, 10000, Croatia.
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19
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Huang T, Huang X, Shi B, Liang X, Luo J, Yao M. Relationship among MS4A8 expression, its variants, and the immune response in a porcine model of Salmonella. CANADIAN JOURNAL OF ANIMAL SCIENCE 2018. [DOI: 10.1139/cjas-2017-0037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Salmonella colonization often establishes carrier status in infected animals, which decreases their performance. Salmonella-carrying pigs shed large amounts of bacteria in their feces, and thus they have a negative economic impact on the swine industry. The MS4A8 gene (membrane-spanning 4-domains A8) was significantly activated, by up to 119-fold, in peripheral blood after Salmonella inoculation of pigs. The present study analyzed the correlation of peripheral blood expression level and a genetic variant of porcine MS4A8 with Salmonella-infection traits. The result indicated that MS4A8 expression levels correlated significantly with Salmonella shedding counts. Both the expression of MS4A8 and fecal shedding counts correlated with leukocytes, lymphocytes, monocytes, segmented neutrophils, and banded neutrophils. A novel single nucleotide polymorphism of porcine MS4A8 (nonsynonymous, Val > Ala) was associated with Salmonella shedding counts and average daily gain (ADG) of body weight. The TT genotype had higher fecal shedding counts, leukocyte counts, and lymphocyte counts than the TC and CC genotypes. The CC genotype had higher level of ADG than the TC and TT genotype (p < 0.05). Those results indicated that MS4A8 is intriguing and could be used as a prospective genetic marker for Salmonella susceptibility.
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Affiliation(s)
- Tinghua Huang
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
| | - Xiali Huang
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
| | - Bomei Shi
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
| | - Xiongyan Liang
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
| | - Jingbo Luo
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
| | - Min Yao
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
- College of Animal Science, Yangtze University, Jingzhou, Hubei 434025, People’s Republic of China
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Epigenetic silencing of TMEM176A activates ERK signaling in human hepatocellular carcinoma. Clin Epigenetics 2018; 10:137. [PMID: 30400968 PMCID: PMC6219251 DOI: 10.1186/s13148-018-0570-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/21/2018] [Indexed: 12/14/2022] Open
Abstract
Background The role of TMEM176A in human hepatocellular carcinoma (HCC) is unknown. This study explored the epigenetic regulation and function of TMEM176A in human HCC. Materials and methods Twelve HCC cell lines and 126 cases of primary cancer were analyzed. Methylation-specific PCR, immunohistochemistry, flow cytometry, and xenograft mouse models were employed. Results TMEM176A was highly expressed in SNU387, SNU182, Huh1, and SNU475 cells; reduced expression was observed in HepG2 and PLC/PRF/5 cells; and no expression was found in SNU449, HBXF344, SMMC7721, Huh7, and LM3 cells. Unmethylation of the TMEM176A promoter was detected in SNU387, SNU182, Huh1, and SNU475 cells; partial methylation was observed in HepG2 and PLC/PRF/5 cells; and complete methylation was found in SNU449, HBXF344, SMMC7721, Huh7, and LM3 cells. Upon treatment with 5-Aza-2-deoxycytidine, re-expression of TMEM176A was detected in SNU449, HBXF344, SMMC7721, Huh7, and LM3 cells; increased expression of TMEM176A was observed in HepG2 and PLC/PRF/5 cells; and no expression changes were found in SNU387, SNU182, Huh1, and SNU475 cells. The TMEM176A promoter region was methylated in 75.4% (95/126) of primary human HCC. Reduced expression of TMEM176A was associated with promoter region methylation (P < 0.05). No association was found between TMEM176A promoter methylation and age, gender, HBV infection, liver cirrhosis, tumor size, lymph node metastasis, vessel cancerous embolus, number of lesions, and TNM stage (all P > 0.05). These results demonstrated that the expression of TMEM176A is regulated by promoter region methylation. Methylation of the TMEM176A promoter was significantly associated with tumor cell differentiation (P < 0.05) and was an independent prognostic factor for poor 3-year overall survival (OS, P < 0.05). TMEM176A expression induced cell apoptosis; inhibited cell proliferation, migration, and invasion; suppressed human HCC cell xenograft growth in mice; and inhibited ERK signaling in HCC cells. Conclusion The promoter region of TMEM176A is frequently methylated in human HCC, and the expression of TMEM176A is regulated by promoter region methylation. Methylation of the TMEM176A promoter may serve as a diagnostic and prognostic marker in HCC. TMEM176A suppresses HCC growth by inhibiting the ERK signaling pathway.
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Stem Cells as Potential Targets of Polyphenols in Multiple Sclerosis and Alzheimer's Disease. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1483791. [PMID: 30112360 PMCID: PMC6077677 DOI: 10.1155/2018/1483791] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/19/2018] [Indexed: 12/16/2022]
Abstract
Alzheimer's disease (AD) and multiple sclerosis are major neurodegenerative diseases, which are characterized by the accumulation of abnormal pathogenic proteins due to oxidative stress, mitochondrial dysfunction, impaired autophagy, and pathogens, leading to neurodegeneration and behavioral deficits. Herein, we reviewed the utility of plant polyphenols in regulating proliferation and differentiation of stem cells for inducing brain self-repair in AD and multiple sclerosis. Firstly, we discussed the genetic, physiological, and environmental factors involved in the pathophysiology of both the disorders. Next, we reviewed various stem cell therapies available and how they have proved useful in animal models of AD and multiple sclerosis. Lastly, we discussed how polyphenols utilize the potential of stem cells, either complementing their therapeutic effects or stimulating endogenous and exogenous neurogenesis, against these diseases. We suggest that polyphenols could be a potential candidate for stem cell therapy against neurodegenerative disorders.
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Ma J, Zhang W, Tan L, Wang HF, Wan Y, Sun FR, Tan CC, Yu JT, Tan L, Alzheimer's Disease Neuroimaging Initiative. MS4A6A genotypes are associated with the atrophy rates of Alzheimer's disease related brain structures. Oncotarget 2018; 7:58779-58788. [PMID: 27244883 PMCID: PMC5312275 DOI: 10.18632/oncotarget.9563] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/26/2016] [Indexed: 11/25/2022] Open
Abstract
Membrane-spanning 4-domains, subfamily A, member 6A (MS4A6A) has been identified as susceptibility loci of Alzheimer's disease (AD) by several recent genome-wide association studies (GWAS), whereas little is known about the potential roles of these variants in the brain structure and function of AD. In this study, we included a total of 812 individuals from the Alzheimer's disease Neuroimaging Initiative (ADNI) database. Using multiple linear regression models, we found MS4A6A genotypes were strongly related to atrophy rate of left middle temporal (rs610932: Pc = 0.017, rs7232: Pc = 0.022), precuneus (rs610932: Pc = 0.015) and entorhinal (rs610932, Pc = 0.022) on MRI in the entire group. In the subgroup analysis, MS4A6A SNPs were significantly accelerated the percentage of volume loss of middle temporal, precuneus and entorhinal, especially in the MCI subgroup. These findings reveal that MS4A6A genotypes affect AD specific brain structures which supported the possible role of MS4A6A polymorphisms in influencing AD-related neuroimaging phenotypes.
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Affiliation(s)
- Jing Ma
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Wei Zhang
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Lin Tan
- College of Medicine and Pharmaceutics, Ocean University of China, Qingdao, China
| | - Hui-Fu Wang
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Yu Wan
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Fu-Rong Sun
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Chen-Chen Tan
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Jin-Tai Yu
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China.,College of Medicine and Pharmaceutics, Ocean University of China, Qingdao, China
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23
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Aberrant expression of CD20 in thyroid cancer and its clinicopathologic significance. Hum Pathol 2017; 71:74-83. [PMID: 29079175 DOI: 10.1016/j.humpath.2017.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/05/2017] [Accepted: 10/13/2017] [Indexed: 11/21/2022]
Abstract
CD20 is the first-line diagnostic marker of B-cells, which serves as the target of the therapeutic monoclonal antibodies in B-cell lymphomas and leukemias. Recently, aberrant CD20 expression has been described in a small series of papillary thyroid carcinomas (PTCs). We aimed to evaluate CD20 immunoexpression and to perform clinicopathologic correlation in a large set of thyroid tumors, including a cohort of high-grade thyroid cancer. A total of 625 cases of thyroid tumor comprised tissue microarrays of 538 PTCs and 47 follicular adenomas, and whole-slide sections of 40 aggressive thyroid carcinomas (10 radioiodine-refractory PTCs and 8 poorly differentiated, 5 anaplastic, and 17 medullary thyroid carcinomas) were immunostained with anti-CD20 monoclonal antibody. BRAFV600E mutation was tested by direct sequencing in 478 cancers. Our study found that a small subset of PTCs (<10%, mainly of classic variant) exhibited aberrant membranous expression of CD20. These tumors displayed less aggressive histological features and had a lower prevalence of BRAFV600E mutation. We also discovered that CD20 expression was maintained in 6%-20% of aggressive thyroid cancers but not observed in follicular adenomas. All CD20-positive tumor cells were negative for CD79a and PAX5. Aberrant expression of CD20 by thyroid cancer cells may present a diagnostic pitfall in cytologic evaluation of thyroid and cervical masses. Residual expression of CD20 in aggressive cancers may offer promise for translational implications, which merits further experimental investigation.
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Mokhtarzadeh A, Hassanpour S, Vahid ZF, Hejazi M, Hashemi M, Ranjbari J, Tabarzad M, Noorolyai S, de la Guardia M. Nano-delivery system targeting to cancer stem cell cluster of differentiation biomarkers. J Control Release 2017; 266:166-186. [PMID: 28941992 DOI: 10.1016/j.jconrel.2017.09.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 02/07/2023]
Abstract
Cancer stem cells (CSCs) are one of the most important origins of cancer progression and metastasis. CSCs have unique self-renewal properties and diverse cell membrane receptors that induced the resistance to the conventional chemotherapeutic agents. Therefore, the therapeutic removal of CSCs could result in the cancer cure with lack of recurrence and metastasis. In this regard, targeting CSCs in accordance to their specific biomarkers is a talented attitude in cancer therapy. Various CSCs surface biomarkers have been described, which some of them exhibited similarities on different cancer cell types, while the others are cancer specific and have just been reported on one or a few types of cancers. In this review, the importance of CSCs in cancer development and therapeutic response has been stated. Different CSCs cluster of differentiation (CD) biomarkers and their specific function and applications in the treatment of cancers have been discussed, Special attention has been made on targeted nano-delivery systems. In this regard, several examples have been illustrated concerning specific natural and artificial ligands against CSCs CD biomarkers that could be decorated on various nanoparticulated drug delivery systems to enhance therapeutic index of chemotherapeutic agents or anticancer gene therapy. The outlook of CSCs biomarkers discovery and therapeutic/diagnostic applications was discussed.
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Affiliation(s)
- Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biochemistry, Higher Education Institute of Rab-Rashid, Tabriz, Iran
| | - Soodabeh Hassanpour
- Department of Biochemistry, Higher Education Institute of Rab-Rashid, Tabriz, Iran
| | | | | | - Maryam Hashemi
- Nanotechnology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Javad Ranjbari
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Tabarzad
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Saeed Noorolyai
- Department of Biochemistry, Higher Education Institute of Rab-Rashid, Tabriz, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain.
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25
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Genetics of Alzheimer's disease: From pathogenesis to clinical usage. J Clin Neurosci 2017; 45:1-8. [PMID: 28869135 DOI: 10.1016/j.jocn.2017.06.074] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/19/2017] [Indexed: 01/27/2023]
Abstract
Alzheimer's disease (AD) is the most common type of dementia and has caused a major global health concern. Understanding the etiology of AD can be beneficial for the diagnosis and intervention of this disease. Genetics plays a vital role in the pathogenesis of AD. Research methods in genetics such as the linkage analysis, study of candidate genes, genome-wide association study (GWAS), and next-generation sequencing (NGS) technology help us map the genetic information in AD, which can not only provide a new insight into the pathogenesis of AD but also be beneficial for early targeted intervention of AD. This review summarizes the pathogenesis as well as the diagnostic and therapeutic value of genetics in AD.
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Wang Y, Zhang Y, Herman JG, Linghu E, Guo M. Epigenetic silencing of TMEM176A promotes esophageal squamous cell cancer development. Oncotarget 2017; 8:70035-70048. [PMID: 29050260 PMCID: PMC5642535 DOI: 10.18632/oncotarget.19550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 06/27/2017] [Indexed: 12/30/2022] Open
Abstract
The function of human transmembrane protein 176A (TMEM176A) in cancer remains unclear. To understand the function and mechanism of TMEM176A in human esophageal cancer development, 13 esophageal cancer cell lines and 267 cases of primary esophageal squamous cell cancer (ESCC) samples were analyzed by methylation specific PCR (MSP), flow cytometry, immunohistochemistry and transfection assays. TMEM176A was highly expressed in BIC1 cells and loss of TMEM176A expression was found in TE1, TE3, TE13, KYSE140, KYSE180, KYSE410, KYSE450, KYSE520, Segl, KYSE150, YES2 and COLO680N cells. Complete methylation was detected in TE1, TE3, TE13, KYSE140, KYSE180, KYSE410, KYSE450, KYSE520, Segl, KYSE150, YES2 and COLO680N cells, while unmethylation was detected in BIC1 cells. Restoration of TMEM176A expression was induced by 5-aza-2’-deoxycytidine treatment in methylated cell lines. TMEM176A was methylated in 66.7% (178/267) of primary esophageal cancer samples, and promoter region methylation was significantly associated with tumor differentiation (p<0.001) and loss off/reduced expression of TMEM176A (p<0.05). Methylation of TMEM176A was significantly associated with poor 5-year overall survival (p < 0.05). Cox proportional hazards model analysis suggest that TMEM176A methylation is an independent prognostic factor for poor 5-years OS. TMEM176A inhibited cell invasion and migration, and induced apoptosis in esophageal cancer cells. TMEM176A suppressed esophageal cancer cell growth both in vitro and in vivo. In conclusion, TMEM176A is frequently methylated in human ESCC and the expression of TMEM176A is regulated by promoter region methylation. TMEM176A methylation may serve as a diagnostic and prognostic marker in ESCC. TMEM176A is a potential tumor suppressor in human ESCC.
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Affiliation(s)
- Ying Wang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China.,Department of Gastroenterology, The Affiliated Fu Xing Hospital of Capital Medical University, Beijing 100038, China
| | - You Zhang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Enqiang Linghu
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China
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27
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Gao D, Han Y, Yang Y, Herman JG, Linghu E, Zhan Q, Fuks F, Lu ZJ, Guo M. Methylation of TMEM176A is an independent prognostic marker and is involved in human colorectal cancer development. Epigenetics 2017; 12:575-583. [PMID: 28678648 DOI: 10.1080/15592294.2017.1341027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common malignancy and the fourth most common cause of cancer related death worldwide. This study was designed to find tumor suppressors involved in CRC development by performing RNA-seq. Eight CRC cell lines and 130 cases of primary CRC samples were used. RNA-seq, methylation-specific PCR (MSP), flow cytometry, transwell assays, and a xenograft mouse model were used. Reduction of TMEM176A expression was confirmed in human CRC cells by RNA-seq. TMEM176A was expressed in LS180 and SW620 cells, loss of TMEM176A expression was observed in LOVO, HCT116, RKO, and DLD1 cells, and reduced TMEM176A expression was found in HT29 and SW480 cells. Unmethylation of the TMEM176A promoter was found in LS180 and SW620 cells, whereas complete methylation was found in LOVO, HCT116, RKO, and DLD1 cells, and partial methylation was found in HT29 and SW480 cells. Promoter region methylation correlated with loss of/reduced expression of TMEM176A. Re-expression of TMEM176A was induced by 5-aza-2'-deoxycytidine. TMEM176A was methylated in 50.77% of primary colorectal cancers. Methylation of TMEM176A was associated with tumor metastasis (P<0.05) and was an independent prognostic factor for 5-year overall survival (OS) according to Cox proportional hazards model analysis (P<0.05). TMEM176A induced apoptosis and inhibited cell migration and invasion in CRC cells. TMEM176A suppressed CRC cell growth both in vitro and in vivo. Our results suggest that expression of TMEM176A is regulated by promoter region methylation. TMEM176A methylation is an independent prognostic marker for 5-year OS in CRC, and may act as a tumor suppressor in CRC.
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Affiliation(s)
- Dan Gao
- a Department of Gastroenterology & Hepatology , Chinese PLA General Hospital , Beijing , China.,b School of Medicine, Nankai University , Tianjin , China
| | - Yingjie Han
- a Department of Gastroenterology & Hepatology , Chinese PLA General Hospital , Beijing , China.,b School of Medicine, Nankai University , Tianjin , China
| | - Yang Yang
- c MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing , China
| | - James G Herman
- d The Hillman Cancer Center, University of Pittsburgh Cancer Institute , Pittsburgh , PA , USA
| | - Enqiang Linghu
- a Department of Gastroenterology & Hepatology , Chinese PLA General Hospital , Beijing , China
| | - Qimin Zhan
- e Laboratory of Molecular Oncology , Peking University Cancer Hospital & Institute , Beijing , China
| | - François Fuks
- f Laboratory of Cancer Epigenetics , Free University of Brussels (U.L.B.) , Brussels , Belgium
| | - Zhi John Lu
- c MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing , China
| | - Mingzhou Guo
- a Department of Gastroenterology & Hepatology , Chinese PLA General Hospital , Beijing , China
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28
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Sanyal R, Polyak MJ, Zuccolo J, Puri M, Deng L, Roberts L, Zuba A, Storek J, Luider JM, Sundberg EM, Mansoor A, Baigorri E, Chu MP, Belch AR, Pilarski LM, Deans JP. MS4A4A: a novel cell surface marker for M2 macrophages and plasma cells. Immunol Cell Biol 2017; 95:611-619. [PMID: 28303902 DOI: 10.1038/icb.2017.18] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/24/2017] [Accepted: 03/13/2017] [Indexed: 01/05/2023]
Abstract
MS4A4A is a member of the membrane-spanning, four domain family, subfamily A (MS4A) that includes CD20 (MS4A1), FcRβ (MS4A2) and Htm4 (MS4A3). Like the first three members of this family, transcription of MS4A4A appears to be limited to hematopoietic cells. To evaluate expression of the MS4A4A protein in hematopoietic cell lineages and subsets we generated monoclonal antibodies against extracellular epitopes for use in flow cytometry. In human peripheral blood we found that MS4A4A is expressed at the plasma membrane in monocytes but not in granulocytes or lymphocytes. In vitro differentiation of monocytes demonstrated that MS4A4A is expressed in immature but not activated dendritic cells, and in macrophages generated in the presence of interleukin-4 ('alternatively activated' or M2 macrophages) but not by interferon-γ and lipopolysaccharide ('classically' activated or M1 macrophages). MS4A4A was expressed in the U937 monocytic cell line only after differentiation. In normal bone marrow, MS4A4A was expressed in mature monocytes but was undetected, or detected at only a low level, in myeloid/monocytic precursors, as well as their malignant counterparts in patients with various subtypes of myeloid leukemia. Although MS4A4A was not expressed in healthy B lymphocytes, it was highly expressed in normal plasma cells, CD138+ cells from multiple myeloma patients, and bone marrow B cells from a patient with mantle cell lymphoma. These findings suggest immunotherapeutic potential for MS4A4A antibodies in targeting alternatively activated macrophages such as tumor-associated macrophages, and in the treatment of multiple myeloma and mantle cell lymphoma.
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Affiliation(s)
- Ratna Sanyal
- Department of Biochemistry and Molecular Biology, and Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Maria J Polyak
- Department of Biochemistry and Molecular Biology, and Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Jonathan Zuccolo
- Department of Biochemistry and Molecular Biology, and Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Mandip Puri
- Department of Biochemistry and Molecular Biology, and Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Lili Deng
- Department of Biochemistry and Molecular Biology, and Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Luc Roberts
- Department of Biochemistry and Molecular Biology, and Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Ania Zuba
- Department of Biochemistry and Molecular Biology, and Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Jan Storek
- Departments of Medicine and Oncology, University of Calgary, Calgary, Alberta, Canada
| | - Joanne M Luider
- Calgary Laboratory Services, Foothills Medical Centre, Calgary, Alberta, Canada
| | - Ellen M Sundberg
- Calgary Laboratory Services, Foothills Medical Centre, Calgary, Alberta, Canada
| | - Adnan Mansoor
- Calgary Laboratory Services, Foothills Medical Centre, Calgary, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Eva Baigorri
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Michael P Chu
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Andrew R Belch
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Linda M Pilarski
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Julie P Deans
- Department of Biochemistry and Molecular Biology, and Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
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29
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Braud M, Magee DA, Park SDE, Sonstegard TS, Waters SM, MacHugh DE, Spillane C. Genome-Wide microRNA Binding Site Variation between Extinct Wild Aurochs and Modern Cattle Identifies Candidate microRNA-Regulated Domestication Genes. Front Genet 2017; 8:3. [PMID: 28197171 PMCID: PMC5281612 DOI: 10.3389/fgene.2017.00003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 01/09/2017] [Indexed: 12/21/2022] Open
Abstract
The domestication of cattle from the now-extinct wild aurochs (Bos primigenius) involved selection for physiological and behavioral traits, with underlying genetic factors that remain largely unknown. Non-coding microRNAs have emerged as key regulators of the spatio-temporal expression of target genes controlling mammalian growth and development, including in livestock species. During the domestication process, selection of mutational changes in miRNAs and/or miRNA binding sites could have provided a mechanism to generate some of the traits that differentiate domesticated cattle from wild aurochs. To investigate this, we analyzed the open reading frame DNA sequence of 19,994 orthologous protein-coding gene pairs from extant Bos taurus genomes and a single extinct B. primigenius genome. We identified miRNA binding site polymorphisms in the 3′ UTRs of 1,620 of these orthologous genes. These 1,620 genes with altered miRNA binding sites between the B. taurus and B. primigenius lineages represent candidate domestication genes. Using a novel Score Site ratio metric we have ranked these miRNA-regulated genes according to the extent of divergence between miRNA binding site presence, frequency and copy number between the orthologous genes from B. taurus and B. primigenius. This provides an unbiased approach to identify cattle genes that have undergone the most changes in miRNA binding (i.e., regulation) between the wild aurochs and modern-day cattle breeds. In addition, we demonstrate that these 1,620 candidate domestication genes are enriched for roles in pigmentation, fertility, neurobiology, metabolism, immunity and production traits (including milk quality and feed efficiency). Our findings suggest that directional selection of miRNA regulatory variants was important in the domestication and subsequent artificial selection that gave rise to modern taurine cattle.
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Affiliation(s)
- Martin Braud
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of Ireland Galway, University Road Galway, Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin Dublin, Ireland
| | - Stephen D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre Dublin, Ireland
| | | | - Sinead M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc Dunsany, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College DublinDublin, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College DublinDublin, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of Ireland Galway, University Road Galway, Ireland
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30
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Abstract
Alzheimer's disease (AD) is a progressive, neurodegenerative disease and the most common form of dementia in elderly people. It is an emerging public health problem that poses a huge societal burden. Linkage analysis was the first milestone in unraveling the mutations in APP, PSEN1, and PSEN2 that cause early-onset AD, followed by the discovery of apolipoprotein E-ε4 allele as the only one genetic risk factor for late-onset AD. Genome-wide association studies have revolutionized genetic research and have identified over 20 genetic loci associated with late-onset AD. Recently, next-generation sequencing technologies have enabled the identification of rare disease variants, including unmasking small mutations with intermediate risk of AD in PLD3, TREM2, UNC5C, AKAP9, and ADAM10. This review provides an overview of the genetic basis of AD and the relationship between these risk genes and the neuropathologic features of AD. An understanding of genetic mechanisms underlying AD pathogenesis and the potentially implicated pathways will lead to the development of novel treatment for this devastating disease.
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Affiliation(s)
- Mohan Giri
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, People’s Republic of China
| | - Man Zhang
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, People’s Republic of China
| | - Yang Lü
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, People’s Republic of China
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Macias-Garcia A, Heizmann B, Sellars M, Marchal P, Dali H, Pasquali JL, Muller S, Kastner P, Chan S. Ikaros Is a Negative Regulator of B1 Cell Development and Function. J Biol Chem 2016; 291:9073-86. [PMID: 26841869 DOI: 10.1074/jbc.m115.704239] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Indexed: 12/19/2022] Open
Abstract
B1 B cells secrete most of the circulating natural antibodies and are considered key effector cells of the innate immune response. However, B1 cell-associated antibodies often cross-react with self-antigens, which leads to autoimmunity, and B1 cells have been implicated in cancer. How B1 cell activity is regulated remains unclear. We show that the Ikaros transcription factor is a major negative regulator of B1 cell development and function. Using conditional knock-out mouse models to delete Ikaros at different locations, we show that Ikaros-deficient mice exhibit specific and significant increases in splenic and bone marrow B1 cell numbers, and that the B1 progenitor cell pool is increased ∼10-fold in the bone marrow. Ikaros-null B1 cells resemble WT B1 cells at the molecular and cellular levels, but show a down-regulation of signaling components important for inhibiting proliferation and immunoglobulin production. Ikaros-null B1 cells hyper-react to TLR4 stimulation and secrete high amounts of IgM autoantibodies. These results indicate that Ikaros is required to limit B1 cell homeostasis in the adult.
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Affiliation(s)
- Alejandra Macias-Garcia
- From the Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Beate Heizmann
- From the Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France,
| | - MacLean Sellars
- From the Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Patricia Marchal
- From the Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Hayet Dali
- Institut de Biologie Moléculaire et Cellulaire (IBMC), CNRS UPR3572, 67000 Strasbourg, France
| | - Jean-Louis Pasquali
- From the Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France, Institut de Biologie Moléculaire et Cellulaire (IBMC), CNRS UPR3572, 67000 Strasbourg, France, UFR Médecine, Université de Strasbourg, 67000 Strasbourg, France
| | - Sylviane Muller
- Institut de Biologie Moléculaire et Cellulaire (IBMC), CNRS UPR3572, 67000 Strasbourg, France, Institut d'Etudes Avancées, Université de Strasbourg, 67000 Strasbourg, France, and
| | - Philippe Kastner
- From the Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France, Faculté de Médecine, Université de Strasbourg, 67000 Strasbourg, France
| | - Susan Chan
- From the Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France,
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Barral S, Cheng R, Reitz C, Vardarajan B, Lee J, Kunkle B, Beecham G, Cantwell LS, Pericak-Vance MA, Farrer LA, Haines JL, Goate AM, Foroud T, Boerwinkle E, Schellenberg GD, Mayeux R. Linkage analyses in Caribbean Hispanic families identify novel loci associated with familial late-onset Alzheimer's disease. Alzheimers Dement 2015; 11:1397-1406. [PMID: 26433351 PMCID: PMC4690771 DOI: 10.1016/j.jalz.2015.07.487] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 06/08/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022]
Abstract
INTRODUCTION We performed linkage analyses in Caribbean Hispanic families with multiple late-onset Alzheimer's disease (LOAD) cases to identify regions that may contain disease causative variants. METHODS We selected 67 LOAD families to perform genome-wide linkage scan. Analysis of the linked regions was repeated using the entire sample of 282 families. Validated chromosomal regions were analyzed using joint linkage and association. RESULTS We identified 26 regions linked to LOAD (HLOD ≥3.6). We validated 13 of the regions (HLOD ≥2.5) using the entire family sample. The strongest signal was at 11q12.3 (rs2232932: HLODmax = 4.7, Pjoint = 6.6 × 10(-6)), a locus located ∼2 Mb upstream of the membrane-spanning 4A gene cluster. We additionally identified a locus at 7p14.3 (rs10255835: HLODmax = 4.9, Pjoint = 1.2 × 10(-5)), a region harboring genes associated with the nervous system (GARS, GHRHR, and NEUROD6). DISCUSSION Future sequencing efforts should focus on these regions because they may harbor familial LOAD causative mutations.
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Affiliation(s)
- Sandra Barral
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA; Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA; Department of Neurology, Columbia University Medical Center and New York Presbyterian Hospital, New York, NY, USA
| | - Rong Cheng
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA; Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA
| | - Christiane Reitz
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA; Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA; Department of Neurology, Columbia University Medical Center and New York Presbyterian Hospital, New York, NY, USA; Department of Epidemiology, School of Public Health, Columbia University, New York, NY, USA
| | - Badri Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA; Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA; Department of Neurology, Columbia University Medical Center and New York Presbyterian Hospital, New York, NY, USA
| | - Joseph Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA; Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA; Department of Epidemiology, School of Public Health, Columbia University, New York, NY, USA
| | - Brian Kunkle
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Gary Beecham
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Laura S Cantwell
- Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Lindsay A Farrer
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; Department of Medicine (Biomedical Genetics), Boston University School of Medicine and Public Health, Boston, MA, USA; Department of Neurology, Boston University School of Medicine and Public Health, Boston, MA, USA; Department of Ophthalmology, Boston University School of Medicine and Public Health, Boston, MA, USA; Department of Epidemiology, Boston University School of Medicine and Public Health, Boston, MA, USA
| | - Jonathan L Haines
- Department of Epidemiology & Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Alison M Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences (EHGES), University of Texas School of Public Health at Houston, Houston, TX, USA; Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA; Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA; Department of Neurology, Columbia University Medical Center and New York Presbyterian Hospital, New York, NY, USA; Department of Epidemiology, School of Public Health, Columbia University, New York, NY, USA.
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Cuajungco MP, Silva J, Habibi A, Valadez JA. The mucolipin-2 (TRPML2) ion channel: a tissue-specific protein crucial to normal cell function. Pflugers Arch 2015; 468:177-92. [PMID: 26336837 DOI: 10.1007/s00424-015-1732-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/25/2015] [Accepted: 08/27/2015] [Indexed: 12/26/2022]
Abstract
The discovery of the TRPML subfamily of ion channels has created an exciting niche in the fields of membrane trafficking, signal transduction, autophagy, and metal homeostasis. The TRPML protein subfamily consists of three members, TRPML1, TRPML2, and TRPML3, which are encoded by MCOLN1, MCOLN2, and MCOLN3 genes, respectively. They are non-selective cation channels with six predicted transmembrane domains and intracellular amino- and carboxyl-terminus regions. They localize to the plasma membrane, endosomes, and lysosomes of cells. TRPML1 is associated with the human lysosomal storage disease known as mucolipidosis type IV (MLIV), but TRPML2 and TRPML3 have not been linked with a human disease. Although TRPML1 is expressed in many tissues, TRPML3 is expressed in a varied but limited set of tissues, while TRPML2 has a more limited expression pattern where it is mostly detected in lymphoid and myeloid tissues. This review focuses on TRPML2 because it appears to play an important, yet unrecognized role in the immune system. While the evidence has been mostly indirect, we present and discuss relevant data that strengthen the connection of TRPML2 with cellular immunity. We also discuss the functional redundancy between the TRPML proteins, and how such features could be exploited as a potential therapeutic strategy for MLIV disease. We present evidence that TRPML2 expression may complement certain phenotypic alterations in MLIV cells and briefly examine the challenges of functional complementation. In conclusion, the function of TRPML2 still remains obscure, but emerging data show that it may serve a critical role in immune cell development and inflammatory responses.
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Affiliation(s)
- Math P Cuajungco
- Department of Biological Science, California State University Fullerton, 800 N. State College Blvd., Fullerton, CA, 92831, USA. .,Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, CA, 92831, USA.
| | - Joshua Silva
- Department of Biological Science, California State University Fullerton, 800 N. State College Blvd., Fullerton, CA, 92831, USA
| | - Ania Habibi
- Department of Biological Science, California State University Fullerton, 800 N. State College Blvd., Fullerton, CA, 92831, USA
| | - Jessica A Valadez
- Department of Biological Science, California State University Fullerton, 800 N. State College Blvd., Fullerton, CA, 92831, USA
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Wes PD, Holtman IR, Boddeke EW, Möller T, Eggen BJ. Next generation transcriptomics and genomics elucidate biological complexity of microglia in health and disease. Glia 2015; 64:197-213. [DOI: 10.1002/glia.22866] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 05/11/2015] [Indexed: 12/11/2022]
Affiliation(s)
| | - Inge R. Holtman
- Department of NeuroscienceSection Medical Physiology, University of Groningen, University Medical Center GroningenGroningen The Netherlands
| | - Erik W.G.M. Boddeke
- Department of NeuroscienceSection Medical Physiology, University of Groningen, University Medical Center GroningenGroningen The Netherlands
| | | | - Bart J.L. Eggen
- Department of NeuroscienceSection Medical Physiology, University of Groningen, University Medical Center GroningenGroningen The Netherlands
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Chistiakov DA, Bobryshev YV, Orekhov AN. Changes in transcriptome of macrophages in atherosclerosis. J Cell Mol Med 2015; 19:1163-73. [PMID: 25973901 PMCID: PMC4459832 DOI: 10.1111/jcmm.12591] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/16/2015] [Indexed: 12/20/2022] Open
Abstract
Macrophages display significant phenotypic heterogeneity. Two growth factors, macrophage colony-stimulating factor and chemokine (C-X-C motif) ligand 4, drive terminal differentiation of monocytes to M0 and M4 macrophages respectively. Compared to M0 macrophages, M4 cells have a unique transcriptome, with expression of surface markers such as S100A8, mannose receptor CD206 and matrix metalloproteinase 7. M4 macrophages did not express CD163, a scavenger receptor for haemoglobin/haptoglobin complex. Depending on the stimuli, M0 macrophages could polarize towards the proinflammatory M1 subset by treatment with lipopolysaccharide or interferon-γ. These macrophages produce a range of proinflammatory cytokines, nitric oxide, reactive oxygen species and exhibit high chemotactic and phagocytic activity. The alternative M2 type could be induced from M0 macrophage by stimulation with interleukin (IL)-4. M2 macrophages express high levels of CD206 and produce anti-inflammatory cytokines IL-10 and transforming growth factor-β. M1, M2 and M4 macrophages could be found in atherosclerotic plaques. In the plaque, macrophages are subjected to the intensive influence not only by cytokines and chemokines but also with bioactive lipids such as cholesterol and oxidized phospholipids. Oxidized phospholipids induce a distinct Mox phenotype in murine macrophages that express a unique panel of antioxidant enzymes under control of the redox-regulated transcription factor Klf2, resistant to lipid accumulation. In unstable human lesions, atheroprotective M(Hb) and HA-mac macrophage subsets could be found. These two subsets are induced by the haemoglobin/haptoglobin complex, highly express haeme oxygenase 1 and CD163, and are implicated in clearance of haemoglobin and erythrocyte remnants. In atherogenesis, the macrophage phenotype is plastic and could therefore be switched to proinflammatory (i.e. proatherogenic) and anti-inflammatory (i.e. atheroprotective). The aim of this review was to characterize changes in macrophage transcriptome in atherosclerosis and discuss key markers that characterize different phenotypes of macrophages present in atherosclerotic lesions.
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Affiliation(s)
- Dimitry A Chistiakov
- Department of Medical Nanobiotechnology, Pirogov Russian State Medical University, Moscow, Russia
| | - Yuri V Bobryshev
- Faculty of Medicine and St Vincent's Centre for Applied Medical Research, University of New South Wales, Sydney, NSW, Australia.,School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia.,Institute for Atherosclerosis Research, Skolkovo Innovative Center, Moscow, Russia
| | - Alexander N Orekhov
- Institute for Atherosclerosis Research, Skolkovo Innovative Center, Moscow, Russia.,Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Sciences, Moscow, Russia.,Department of Biophysics, Biological Faculty, Moscow State University, Moscow, Russia
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Ma J, Yu JT, Tan L. MS4A Cluster in Alzheimer's Disease. Mol Neurobiol 2014; 51:1240-8. [PMID: 24981432 DOI: 10.1007/s12035-014-8800-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 06/22/2014] [Indexed: 01/13/2023]
Abstract
Several variants within membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated the association of Alzheimer's disease (AD) by serial recent genome-wide association studies (GWAS). As cell membrane proteins, MS4A family members are found to participate in the regulation of calcium signaling which have been widely discussed in neurodegeneration and AD. Besides, although the MS4A family members are poorly characterized, an important role in immunity has already been identified for several members of this cluster (such as MS4A1, MS4A2, and MS4A4B), indicating the possible involvement of MS4A gene cluster in AD pathogenesis. In this article, we briefly summarize the structure, localization, and function of MS4A gene cluster, review recent genetic and expression findings concerning the association of MS4A gene cluster with AD pathogenesis, and also speculate the possible roles of MS4A gene cluster in this disease. Based on the contributing effects of MS4A gene cluster in AD pathogenesis, targeting MS4A gene cluster might provide new opportunities for AD treatment.
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Affiliation(s)
- Jing Ma
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
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Interferon induction of IFITM proteins promotes infection by human coronavirus OC43. Proc Natl Acad Sci U S A 2014; 111:6756-61. [PMID: 24753610 DOI: 10.1073/pnas.1320856111] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
IFNs are a family of cytokines that are essential for the antiviral response in vertebrates. Not surprisingly, viruses have adapted to encode virulence factors to cope with the IFN response. Intriguingly, we show here that all three types of interferons, IFN-α, IFN-γ, and IFN-λ, efficiently promote infection by a human coronavirus, HCoV-OC43, one of the major etiological agents of common cold, through the induction of IFN-inducible transmembrane (IFITM) proteins. IFITMs typically exert their antiviral function by inhibiting the entry of a broad spectrum of viruses into their host cells, presumably by trapping and degrading invading virions within the endocytic compartments. In contrast, HCoV-OC43 uses IFN-induced human IFITM2 or IFITM3 as an entry factor to facilitate its infection of host cells. Reverse genetics analyses suggest that the structural motifs critical for the IFITM proteins' enhancement of HCoV-OC43 infection are distinct from those required for inhibiting infection by other viruses. We also present evidence showing that IFITM family members work as homo- and hetero-oligomers to modulate virus entry. The observed enhancement of HCoV-OC43 infection by IFNs may underlie the propensity of the virus to invade the lower respiratory tract under inflammatory conditions.
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