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RGS20 Promotes Tumor Progression through Modulating PI3K/AKT Signaling Activation in Penile Cancer. JOURNAL OF ONCOLOGY 2022; 2022:1293622. [PMID: 35498542 PMCID: PMC9042636 DOI: 10.1155/2022/1293622] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 11/20/2022]
Abstract
Regulator of G protein signaling 20 (RGS20) plays an important role in regulating neuronal G protein-coupled receptor signaling; however, its expression and oncogenic function in penile cancer (PC) remains unclear. Here, we observed high RGS20 expression in PC tissues compared to normal/adjacent penile tissues, which was closely associated with tumor stage, nodal status, and pelvic metastasis in our PC cohort. The cellular functional analysis of RGS20 revealed that manipulation of the RGS20 expression markedly affected cell viability, BrdU incorporation, soft agar clonogenesis, caspase-3 activity, and cell migration/invasion in PC cell models. Moreover, RGS20 could interact with PI3K p85α subunit and regulate PI3K/AKT signaling activation in PC cell lines. Knockdown of the PI3K p85α or p110α subunit attenuated cell viability, BrdU incorporation, soft agar clonogenesis, and cell migration/invasion in PC cell lines. In contrast, the overexpression of constitutively activated PI3K p110α mutant restored cell proliferation and cell migration/invasion caused by RGS20 depletion in PC cells. Consistent with the in vitro findings, RGS20 depletion attenuated PI3K/AKT signaling activation and suppressed tumor growth in a murine xenograft model. Importantly, the high RGS20 expression was associated with PI3K/AKT signaling activation and unfavorable progression-free/overall survival, highlighting the clinical relevance of RGS20/PI3K/AKT signaling in PC. In conclusion, the aberrant RGS20 expression may serve as a diagnostic and prognostic marker for PC. RGS20 may promote PC progression through modulating PI3K/AKT signaling activation, which may assist with the development of RGS20-targeting therapeutics in the future.
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102
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Identification and Validation of Immune Cells and Hub Genes in Gastric Cancer Microenvironment. DISEASE MARKERS 2022; 2022:8639323. [PMID: 35422890 PMCID: PMC9005323 DOI: 10.1155/2022/8639323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/24/2022] [Indexed: 12/30/2022]
Abstract
Gastric cancer (GC) is the most common malignant tumor in the digestive system, traditional radiotherapy and chemotherapy are not effective for some patients. The research progress of immunotherapy seems to provide a new way for treatment. However, it is still urgent to predict immunotherapy biomarkers and determine novel therapeutic targets. In this study, the gene expression profiles and clinical data of 407 stomach adenocarcinoma (STAD) patients were downloaded from The Cancer Genome Atlas (TCGA) portal, and the abundance ratio of immune cells in each sample was obtained via the “Cell Type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT)” algorithm. Five immune cells were obtained as a result of abundance comparison, and 295 immune-related genes were obtained through differential gene analysis. Enrichment, protein interaction, and module analysis were performed on these genes. We identified five immune cells associated with infiltration and 20 hub genes, of which five genes were correlated with overall survival. Finally, we used Real-time PCR (RT-PCR) to detect the expression differences of the five hub genes in 18 pairs of GC and adjacent tissues. This research not only provides cellular and gene targets for immunotherapy of GC but also provides new ideas for researchers to explore immunotherapy for various tumors.
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103
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UBR4/POE facilitates secretory trafficking to maintain circadian clock synchrony. Nat Commun 2022; 13:1594. [PMID: 35332162 PMCID: PMC8948264 DOI: 10.1038/s41467-022-29244-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/02/2022] [Indexed: 11/08/2022] Open
Abstract
Ubiquitin ligases control the degradation of core clock proteins to govern the speed and resetting properties of the circadian pacemaker. However, few studies have addressed their potential to regulate other cellular events within clock neurons beyond clock protein turnover. Here, we report that the ubiquitin ligase, UBR4/POE, strengthens the central pacemaker by facilitating neuropeptide trafficking in clock neurons and promoting network synchrony. Ubr4-deficient mice are resistant to jetlag, whereas poe knockdown flies are prone to arrhythmicity, behaviors reflective of the reduced axonal trafficking of circadian neuropeptides. At the cellular level, Ubr4 ablation impairs the export of secreted proteins from the Golgi apparatus by reducing the expression of Coronin 7, which is required for budding of Golgi-derived transport vesicles. In summary, UBR4/POE fulfills a conserved and unexpected role in the vesicular trafficking of neuropeptides, a function that has important implications for circadian clock synchrony and circuit-level signal processing. Although ubiquitin ligases are known to control clock protein degradation, their other roles in clock neurons are unclear. Here the authors report that UBR4 promotes export of neuropeptides from the Golgi for axonal trafficking, which is important for circadian clock synchrony in mice and flies.
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104
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Li S, Sun Y, Sun Y. A Comparative Study of Systems Pharmacology and Gene Chip Technology for Predicting Targets of a Traditional Chinese Medicine Formula in Primary Liver Cancer Treatment. Front Pharmacol 2022; 13:768862. [PMID: 35308212 PMCID: PMC8926147 DOI: 10.3389/fphar.2022.768862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/08/2022] [Indexed: 01/08/2023] Open
Abstract
Background: The systems pharmacology approach is a target prediction model for traditional Chinese medicine and has been used increasingly in recent years. However, the accuracy of this model to other prediction models is yet to be established. Objective: To compare the systems pharmacology modelwithexperimental gene chip technology by using these models to predict targets of a traditional Chinese medicine formulain the treatment of primary liver cancer. Methods: Systems pharmacology and gene chip target predictions were performed for the traditional Chinese medicine formula ZhenzhuXiaojiTang (ZZXJT). A third square alignment was performed with molecular docking. Results: Identification of systems pharmacology accounted for 17% of targets, whilegene chip-predicted outcomes accounted for 19%.Molecular docking showed that the top ten targets (excludingcommon targets) of the system pharmacology model had better binding free energies than the gene chip model using twocommon targets as a benchmark. For both models, the core drugs predictions were more consistent than the core small molecules predictions. Conclusion:In this study, the identified targets of systems pharmacology weredissimilar to those identified by gene chip technology; whereas the core drug and small molecule predictions were similar.
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Affiliation(s)
- Songzhe Li
- Department of Biology, College of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yang Sun
- Department of Biology, College of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yue Sun
- Department of Biology, College of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
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105
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Fernbach S, Spieler EE, Busnadiego I, Karakus U, Lkharrazi A, Stertz S, Hale BG. Restriction factor screening identifies RABGAP1L-mediated disruption of endocytosis as a host antiviral defense. Cell Rep 2022; 38:110549. [PMID: 35320721 PMCID: PMC8939003 DOI: 10.1016/j.celrep.2022.110549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/31/2022] [Accepted: 03/01/2022] [Indexed: 11/26/2022] Open
Abstract
Host interferons (IFNs) powerfully restrict viruses through the action of several hundred IFN-stimulated gene (ISG) products, many of which remain uncharacterized. Here, using RNAi screening, we identify several ISG restriction factors with previously undescribed contributions to IFN-mediated defense. Notably, RABGAP1L, a Tre2/Bub2/Cdc16 (TBC)-domain-containing protein involved in regulation of small membrane-bound GTPases, robustly potentiates IFN action against influenza A viruses (IAVs). Functional studies reveal that the catalytically active TBC domain of RABGAP1L promotes antiviral activity, and the RABGAP1L proximal interactome uncovered its association with proteins involved in endosomal sorting, maturation, and trafficking. In this regard, RABGAP1L overexpression is sufficient to disrupt endosomal function during IAV infection and restricts an early post-attachment, but pre-fusion, stage of IAV cell entry. Other RNA viruses that enter cells primarily via endocytosis are also impaired by RABGAP1L, while entry promiscuous SARS-CoV-2 is resistant. Our data highlight virus endocytosis as a key target for host defenses.
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Affiliation(s)
- Sonja Fernbach
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, ETH and University of Zurich, 8057 Zurich, Switzerland
| | - Eva E Spieler
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, ETH and University of Zurich, 8057 Zurich, Switzerland
| | - Idoia Busnadiego
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Umut Karakus
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Anouk Lkharrazi
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Benjamin G Hale
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland.
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106
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Dolinski AC, Homola JJ, Jankowski MD, Robinson JD, Owen JC. Differential gene expression reveals host factors for viral shedding variation in mallards ( Anas platyrhynchos) infected with low-pathogenic avian influenza virus. J Gen Virol 2022; 103:10.1099/jgv.0.001724. [PMID: 35353676 PMCID: PMC10519146 DOI: 10.1099/jgv.0.001724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Intraspecific variation in pathogen shedding impacts disease transmission dynamics; therefore, understanding the host factors associated with individual variation in pathogen shedding is key to controlling and preventing outbreaks. In this study, ileum and bursa of Fabricius tissues of wild-bred mallards (Anas platyrhynchos) infected with low-pathogenic avian influenza (LPAIV) were evaluated at various post-infection time points to determine genetic host factors associated with intraspecific variation in viral shedding. By analysing transcriptome sequencing data (RNA-seq), we found that LPAIV-infected wild-bred mallards do not exhibit differential gene expression compared to uninfected birds, but that gene expression was associated with cloacal viral shedding quantity early in the infection. In both tissues, immune gene expression was higher in high/moderate shedding birds compared to low shedding birds, and significant positive relationships with viral shedding were observed. In the ileum, expression for host genes involved in viral cell entry was lower in low shedders compared to moderate shedders at 1 day post-infection (DPI), and expression for host genes promoting viral replication was higher in high shedders compared to low shedders at 2 DPI. Our findings indicate that viral shedding is a key factor for gene expression differences in LPAIV-infected wild-bred mallards, and the genes identified in this study could be important for understanding the molecular mechanisms driving intraspecific variation in pathogen shedding.
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Affiliation(s)
- Amanda C. Dolinski
- Department of Fisheries and Wildlife, Michigan State
University, East Lansing, MI
| | - Jared J. Homola
- Department of Fisheries and Wildlife, Michigan State
University, East Lansing, MI
| | - Mark D. Jankowski
- Department of Fisheries and Wildlife, Michigan State
University, East Lansing, MI
- U.S. Environmental Protection Agency, Region 10, Seattle,
WA 98101
| | - John D. Robinson
- Department of Fisheries and Wildlife, Michigan State
University, East Lansing, MI
| | - Jennifer C. Owen
- Department of Fisheries and Wildlife, Michigan State
University, East Lansing, MI
- Department of Large Animal Clinical Sciences, Michigan
State University, East Lansing, MI, USA
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107
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Xin Z, Cai Y, Dang LT, Burke HMS, Revote J, Charitakis N, Bienroth D, Nim HT, Li YF, Ramialison M. MonaGO: a novel gene ontology enrichment analysis visualisation system. BMC Bioinformatics 2022; 23:69. [PMID: 35164667 PMCID: PMC8845231 DOI: 10.1186/s12859-022-04594-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/31/2022] [Indexed: 11/12/2022] Open
Abstract
Background Gene ontology (GO) enrichment analysis is frequently undertaken during exploration of various -omics data sets. Despite the wide array of tools available to biologists to perform this analysis, meaningful visualisation of the overrepresented GO in a manner which is easy to interpret is still lacking. Results Monash Gene Ontology (MonaGO) is a novel web-based visualisation system that provides an intuitive, interactive and responsive interface for performing GO enrichment analysis and visualising the results. MonaGO supports gene lists as well as GO terms as inputs. Visualisation results can be exported as high-resolution images or restored in new sessions, allowing reproducibility of the analysis. An extensive comparison between MonaGO and 11 state-of-the-art GO enrichment visualisation tools based on 9 features revealed that MonaGO is a unique platform that simultaneously allows interactive visualisation within one single output page, directly accessible through a web browser with customisable display options. Conclusion MonaGO combines dynamic clustering and interactive visualisation as well as customisation options to assist biologists in obtaining meaningful representation of overrepresented GO terms, producing simplified outputs in an unbiased manner. MonaGO will facilitate the interpretation of GO analysis and will assist the biologists into the representation of the results. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04594-1.
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Affiliation(s)
- Ziyin Xin
- Faculty of IT, Monash University, Clayton, VIC, Australia
| | - Yujun Cai
- Faculty of IT, Monash University, Clayton, VIC, Australia.,Southeast University, Nanjing, China
| | - Louis T Dang
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.,Systems Biology Institute Australia, Clayton, VIC, Australia
| | - Hannah M S Burke
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.,Systems Biology Institute Australia, Clayton, VIC, Australia
| | - Jerico Revote
- Monash eResearch Centre, Monash University, Melbourne, VIC, Australia
| | | | - Denis Bienroth
- Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Hieu T Nim
- Faculty of IT, Monash University, Clayton, VIC, Australia. .,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia. .,Systems Biology Institute Australia, Clayton, VIC, Australia. .,Murdoch Children's Research Institute, Parkville, VIC, Australia.
| | - Yuan-Fang Li
- Faculty of IT, Monash University, Clayton, VIC, Australia. .,Systems Biology Institute Australia, Clayton, VIC, Australia.
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia. .,Systems Biology Institute Australia, Clayton, VIC, Australia. .,Murdoch Children's Research Institute, Parkville, VIC, Australia.
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108
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Wu X, Li W, Luo Z, Chen Y. The molecular mechanism of Ligusticum wallichii for improving idiopathic pulmonary fibrosis: A network pharmacology and molecular docking study. Medicine (Baltimore) 2022; 101:e28787. [PMID: 35147109 PMCID: PMC8830865 DOI: 10.1097/md.0000000000028787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/21/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND At present, there was no evidence that any drugs other than lung transplantation can effectively treat Idiopathic Pulmonary Fibrosis (IPF). Ligusticum wallichii, or Chinese name Chuan xiong has been widely used in different fibrosis fields. Our aim is to use network pharmacology and molecular docking to explore the pharmacological mechanism of the Traditional Chinese medicine (TCM) Ligusticum wallichii to improve IPF. MATERIALS AND METHODS The main chemical components and targets of Ligusticum wallichii were obtained from TCMSP, Swiss Target Prediction and Phammapper databases, and the targets were uniformly regulated in the Uniprot protein database after the combination. The main targets of IPF were obtained through Gencards, OMIM, TTD and DRUGBANK databases, and protein interaction analysis was carried out by using String to build PPI network. Metascape platform was used to analyze its involved biological processes and pathways, and Cytoscape3.8.2 software was used to construct "component-IPF target-pathway" network. And molecular docking verification was conducted through Auto Dock software. RESULTS The active ingredients of Ligusticum wallichii were Myricanone, Wallichilide, Perlolyrine, Senkyunone, Mandenol, Sitosterol and FA. The core targets for it to improve IPF were MAPK1, MAPK14, SRC, BCL2L1, MDM2, PTGS2, TGFB2, F2, MMP2, MMP9, and so on. The molecular docking verification showed that the molecular docking affinity of the core active compounds in Ligusticum wallichii (Myricanone, wallichilide, Perlolyrine) was <0 with MAPK1, MAPK14, and SRC. Perlolyrine has the strongest molecular docking ability, and its docking ability with SRC (-6.59 kJ/mol) is particularly prominent. Its biological pathway to improve IPF was mainly acted on the pathways in cancer, proteoglycans in cancer, and endocrine resistance, etc. CONCLUSIONS This study preliminarily identified the various molecular targets and multiple pathways of Ligusticum wallichii to improve IPF.
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109
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Ito M, Nakano M, Ariyama H, Yamaguchi K, Tanaka R, Semba Y, Sugio T, Miyawaki K, Kikushige Y, Mizuno S, Isobe T, Tanoue K, Taguchi R, Ueno S, Kawano T, Murata M, Baba E, Akashi K. Macrophages are primed to transdifferentiate into fibroblasts in malignant ascites and pleural effusions. Cancer Lett 2022; 532:215597. [PMID: 35150810 DOI: 10.1016/j.canlet.2022.215597] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 11/02/2022]
Abstract
Cancer-associated fibroblasts (CAFs) play an important role in cancer progression. However, the origin of CAFs remains unclear. This study shows that macrophages in malignant ascites and pleural effusions (cavity fluid-associated macrophages: CAMs) transdifferentiate into fibroblast-like cells. CAMs obtained from gastrointestinal cancer patients were sorted by flow cytometry and cultured in vitro. CD45+CD14+ CAMs transdifferentiated into CD45-CD90+ fibroblast-like cells that exhibited spindle shapes. Then, cDNA microarray analysis showed that the CD45-CD90+ fibroblast-like cells (macrophage-derived CAFs: MDCAFs) had a fibroblast-specific gene expression signature and produced growth factors for epithelial cell proliferation. Human colon cancer cells transplanted into immunodeficient mice with MDCAFs formed larger tumors than cancer cells alone. Gene ontology analyses showed the involvement of TGFβ signaling and cell-matrix adhesion in MDCAFs, and transdifferentiation of CAMs into MDCAFs was canceled by inhibiting TGFβ and cell adhesion. Furthermore, the acquired genetic alterations in hematopoietic stem cells (HSCs) were shared in CAMs and MDCAFs. Taken together, CAMs could be a source of CAFs and might originate from HSCs. We propose the transdifferentiation process of CAMs into MDCAFs as a new therapeutic target for fibrosis associated with gastrointestinal cancer.
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Affiliation(s)
- Mamoru Ito
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Michitaka Nakano
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Hiroshi Ariyama
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Kyoko Yamaguchi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Risa Tanaka
- Department of Medical Oncology, Hamanomachi Hospital, Fukuoka, Japan
| | - Yuichiro Semba
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Takeshi Sugio
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Kohta Miyawaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yoshikane Kikushige
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shinichi Mizuno
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Taichi Isobe
- Department of Oncology and Social Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kenro Tanoue
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Ryosuke Taguchi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shohei Ueno
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Takahito Kawano
- Center for Advanced Medical Innovation, Kyushu University, Fukuoka, Japan
| | - Masaharu Murata
- Center for Advanced Medical Innovation, Kyushu University, Fukuoka, Japan
| | - Eishi Baba
- Department of Oncology and Social Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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110
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A Transfer-Learning-Based Deep Convolutional Neural Network for Predicting Leukemia-Related Phosphorylation Sites from Protein Primary Sequences. Int J Mol Sci 2022; 23:ijms23031741. [PMID: 35163663 PMCID: PMC8915183 DOI: 10.3390/ijms23031741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/27/2022] Open
Abstract
As one of the most important post-translational modifications (PTMs), phosphorylation refers to the binding of a phosphate group with amino acid residues like Ser (S), Thr (T) and Tyr (Y) thus resulting in diverse functions at the molecular level. Abnormal phosphorylation has been proved to be closely related with human diseases. To our knowledge, no research has been reported describing specific disease-associated phosphorylation sites prediction which is of great significance for comprehensive understanding of disease mechanism. In this work, focusing on three types of leukemia, we aim to develop a reliable leukemia-related phosphorylation site prediction models by combing deep convolutional neural network (CNN) with transfer-learning. CNN could automatically discover complex representations of phosphorylation patterns from the raw sequences, and hence it provides a powerful tool for improvement of leukemia-related phosphorylation site prediction. With the largest dataset of myelogenous leukemia, the optimal models for S/T/Y phosphorylation sites give the AUC values of 0.8784, 0.8328 and 0.7716 respectively. When transferred learning on the small size datasets, the models for T-cell and lymphoid leukemia also give the promising performance by common sharing the optimal parameters. Compared with other five machine-learning methods, our CNN models reveal the superior performance. Finally, the leukemia-related pathogenesis analysis and distribution analysis on phosphorylated proteins along with K-means clustering analysis and position-specific conversation profiles on the phosphorylation site all indicate the strong practical feasibility of our easy-to-use CNN models.
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111
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Bracci N, de la Fuente C, Saleem S, Pinkham C, Narayanan A, García-Sastre A, Balaraman V, Richt JA, Wilson W, Kehn-Hall K. Rift Valley fever virus Gn V5-epitope tagged virus enables identification of UBR4 as a Gn interacting protein that facilitates Rift Valley fever virus production. Virology 2022; 567:65-76. [PMID: 35032865 PMCID: PMC8877469 DOI: 10.1016/j.virol.2021.12.010] [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: 08/04/2021] [Revised: 11/15/2021] [Accepted: 12/31/2021] [Indexed: 02/03/2023]
Abstract
Rift Valley fever virus (RVFV) is an arbovirus that was first reported in the Rift Valley of Kenya which causes significant disease in humans and livestock. RVFV is a tri-segmented, negative-sense RNA virus consisting of a L, M, and S segments with the M segment encoding the glycoproteins Gn and Gc. Host factors that interact with Gn are largely unknown. To this end, two viruses containing an epitope tag (V5) on the Gn protein in position 105 or 229 (V5Gn105 and V5Gn229) were generated using the RVFV MP-12 vaccine strain as a backbone. The V5-tag insertion minimally impacted Gn functionality as measured by replication kinetics, Gn localization, and antibody neutralization assays. A proteomics-based approach was used to identify novel Gn-binding host proteins, including the E3 ubiquitin-protein ligase, UBR4. Depletion of UBR4 resulted in a significant decrease in RVFV titers and a reduction in viral RNA production.
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Affiliation(s)
- Nicole Bracci
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University,National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Cynthia de la Fuente
- The National Institutes of Health, National Institute of Allergy and Infectious Diseases, DEA,National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Sahar Saleem
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Chelsea Pinkham
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | | | - Velmurugan Balaraman
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University
| | - William Wilson
- National Bio and Agro-Defense Facility, Agricultural Research Service, USDA
| | - Kylene Kehn-Hall
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University,National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University,Center for Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University,Corresponding Author: Kylene Kehn-Hall, Ph.D., Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Integrated Life Sciences Building, 1981 Kraft Drive, Blacksburg, VA 24060 USA,
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112
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Zhang L, Han L, Ma J, Wu T, Wei Y, Zhao L, Tong X. Exploring the synergistic and complementary effects of berberine and paeoniflorin in the treatment of type 2 diabetes mellitus by network pharmacology. Eur J Pharmacol 2022; 919:174769. [DOI: 10.1016/j.ejphar.2022.174769] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 12/08/2021] [Accepted: 01/12/2022] [Indexed: 01/19/2023]
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113
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Hou S, Li Z, Dong J, Gao Y, Chang Z, Ding X, Li S, Li Y, Zeng Y, Xin Q, Wang B, Ni Y, Ning X, Hu Y, Fan X, Hou Y, Li X, Wen L, Zhou B, Liu B, Tang F, Lan Y. Heterogeneity in endothelial cells and widespread venous arterialization during early vascular development in mammals. Cell Res 2022; 32:333-348. [PMID: 35079138 PMCID: PMC8975889 DOI: 10.1038/s41422-022-00615-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022] Open
Abstract
AbstractArteriogenesis rather than unspecialized capillary expansion is critical for restoring effective circulation to compromised tissues in patients. Deciphering the origin and specification of arterial endothelial cells during embryonic development will shed light on the understanding of adult arteriogenesis. However, during early embryonic angiogenesis, the process of endothelial diversification and molecular events underlying arteriovenous fate settling remain largely unresolved in mammals. Here, we constructed the single-cell transcriptomic landscape of vascular endothelial cells (VECs) during the time window for the occurrence of key vasculogenic and angiogenic events in both mouse and human embryos. We uncovered two distinct arterial VEC types, the major artery VECs and arterial plexus VECs, and unexpectedly divergent arteriovenous characteristics among VECs that are located in morphologically undistinguishable vascular plexus intra-embryonically. Using computational prediction and further lineage tracing of venous-featured VECs with a newly developed Nr2f2CrexER mouse model and a dual recombinase-mediated intersectional genetic approach, we revealed early and widespread arterialization from the capillaries with considerable venous characteristics. Altogether, our findings provide unprecedented and comprehensive details of endothelial heterogeneity and lineage relationships at early angiogenesis stages, and establish a new model regarding the arteriogenesis behaviors of early intra-embryonic vasculatures.
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Kim M, Ly SH, Xie Y, Duronio GN, Ford-Roshon D, Hwang JH, Sulahian R, Rennhack JP, So J, Gjoerup O, Talamas JA, Grandclaudon M, Long HW, Doench JG, Sethi NS, Giannakis M, Hahn WC. YAP1 and PRDM14 converge to promote cell survival and tumorigenesis. Dev Cell 2022; 57:212-227.e8. [PMID: 34990589 PMCID: PMC8827663 DOI: 10.1016/j.devcel.2021.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/15/2021] [Accepted: 12/03/2021] [Indexed: 01/26/2023]
Abstract
The transcriptional co-activator YAP1 oncogene is the downstream effector of the Hippo pathway, which regulates tissue homeostasis, organ size, regeneration, and tumorigenesis. Multiple cancers are dependent on sustained expression of YAP1 for cell proliferation, survival, and tumorigenesis, but the molecular basis of this oncogene dependency is not well understood. To identify genes that can functionally substitute for YAP1, we performed a genome-scale genetic rescue screen in YAP1-dependent colon cancer cells expressing an inducible YAP1-specific shRNA. We found that the transcription factor PRDM14 rescued cell proliferation and tumorigenesis upon YAP1 suppression in YAP1-dependent cells, xenografts, and colon cancer organoids. YAP1 and PRDM14 individually activated the transcription of calmodulin 2 (CALM2) and a glucose transporter SLC2A1 upon YAP1 suppression, and CALM2 or SLC2A1 expression was required for the rescue of YAP1 suppression. Together, these findings implicate PRDM14-mediated transcriptional upregulation of CALM2 and SLC2A1 as key components of oncogenic YAP1 signaling and dependency.
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Affiliation(s)
- Miju Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Seav Huong Ly
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Gina N Duronio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dane Ford-Roshon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Justin H Hwang
- Masonic Cancer Center and Department of Medicine, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Rita Sulahian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan P Rennhack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan So
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ole Gjoerup
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jessica A Talamas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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Zhang M, Zhou Z, Liu Z, Liu F, Zhao C. Exploring the potential biomarkers for prognosis of glioblastoma via weighted gene co-expression network analysis. PeerJ 2022; 10:e12768. [PMID: 35111402 PMCID: PMC8781321 DOI: 10.7717/peerj.12768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/17/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common malignant tumor in the central system with a poor prognosis. Due to the complexity of its molecular mechanism, the recurrence rate and mortality rate of GBM patients are still high. Therefore, there is an urgent need to screen GBM biomarkers to prove the therapeutic effect and improve the prognosis. RESULTS We extracted data from GBM patients from the Gene Expression Integration Database (GEO), analyzed differentially expressed genes in GEO and identified key modules by weighted gene co-expression network analysis (WGCNA). GSE145128 data was obtained from the GEO database, and the darkturquoise module was determined to be the most relevant to the GBM prognosis by WGCNA (r = - 0.62, p = 0.01). We performed enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to reveal the interaction activity in the selected modules. Then Kaplan-Meier survival curve analysis was used to extract genes closely related to GBM prognosis. We used Kaplan-Meier survival curves to analyze the 139 genes in the darkturquoise module, identified four genes (DARS/GDI2/P4HA2/TRUB1) associated with prognostic GBM. Low expression of DARS/GDI2/TRUB1 and high expression of P4HA2 had a poor prognosis. Finally, we used tumor genome map (TCGA) data, verified the characteristics of hub genes through Co-expression analysis, Drug sensitivity analysis, TIMER database analysis and GSVA analysis. We downloaded the data of GBM from the TCGA database, the results of co-expression analysis showed that DARS/GDI2/P4HA2/TRUB1 could regulate the development of GBM by affecting genes such as CDC73/CDC123/B4GALT1/CUL2. Drug sensitivity analysis showed that genes are involved in many classic Cancer-related pathways including TSC/mTOR, RAS/MAPK.TIMER database analysis showed DARS expression is positively correlated with tumor purity (cor = 0.125, p = 1.07e-02)), P4HA2 expression is negatively correlated with tumor purity (cor =-0.279, p = 6.06e-09). Finally, GSVA analysis found that DARS/GDI2/P4HA2/TRUB1 gene sets are closely related to the occurrence of cancer. CONCLUSION We used two public databases to identify four valuable biomarkers for GBM prognosis, namely DARS/GDI2/P4HA2/TRUB1, which have potential clinical application value and can be used as prognostic markers for GBM.
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Affiliation(s)
- Mengyuan Zhang
- Department of Neurology and Stroke Center, The First Hospital of China Medical University, Shenyang, China
| | - Zhike Zhou
- Department of Geriatrics, The First Hospital of China Medical University, Shenyang, China
| | - Zhouyang Liu
- Department of Neurology and Stroke Center, The First Hospital of China Medical University, Shenyang, China
| | - Fangxi Liu
- Department of Neurology and Stroke Center, The First Hospital of China Medical University, Shenyang, China
| | - Chuansheng Zhao
- Department of Neurology and Stroke Center, The First Hospital of China Medical University, Shenyang, China
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Li CC, Zhang G, Du J, Liu D, Li Z, Ni Y, Zhou J, Li Y, Hou S, Zheng X, Lan Y, Liu B, He A. Pre-configuring chromatin architecture with histone modifications guides hematopoietic stem cell formation in mouse embryos. Nat Commun 2022; 13:346. [PMID: 35039499 PMCID: PMC8764075 DOI: 10.1038/s41467-022-28018-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022] Open
Abstract
The gene activity underlying cell differentiation is regulated by a diverse set of transcription factors (TFs), histone modifications, chromatin structures and more. Although definitive hematopoietic stem cells (HSCs) are known to emerge via endothelial-to-hematopoietic transition (EHT), how the multi-layered epigenome is sequentially unfolded in a small portion of endothelial cells (ECs) transitioning into the hematopoietic fate remains elusive. With optimized low-input itChIP-seq and Hi-C assays, we performed multi-omics dissection of the HSC ontogeny trajectory across early arterial ECs (eAECs), hemogenic endothelial cells (HECs), pre-HSCs and long-term HSCs (LT-HSCs) in mouse embryos. Interestingly, HSC regulatory regions are already pre-configurated with active histone modifications as early as eAECs, preceding chromatin looping dynamics within topologically associating domains. Chromatin looping structures between enhancers and promoters only become gradually strengthened over time. Notably, RUNX1, a master TF for hematopoiesis, enriched at half of these loops is observed early from eAECs through pre-HSCs but its enrichment further increases in HSCs. RUNX1 and co-TFs together constitute a central, progressively intensified enhancer-promoter interactions. Thus, our study provides a framework to decipher how temporal epigenomic configurations fulfill cell lineage specification during development.
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Affiliation(s)
- Chen C Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Guangyu Zhang
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Junjie Du
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Di Liu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Zongcheng Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Yanli Ni
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Jie Zhou
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Yunqiao Li
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Siyuan Hou
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Xiaona Zheng
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
| | - Bing Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China.
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China.
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
| | - Aibin He
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
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SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia. Cell Rep 2022; 38:110233. [PMID: 35021089 PMCID: PMC8796272 DOI: 10.1016/j.celrep.2021.110233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/20/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Acute myeloid leukemia (AML) cells rely on phospho-signaling pathways to gain unlimited proliferation potential. Here, we use domain-focused CRISPR screening and identify the nuclear phosphatase SCP4 as a dependency in AML, yet this enzyme is dispensable in normal hematopoietic progenitor cells. Using CRISPR exon scanning and gene complementation assays, we show that the catalytic function of SCP4 is essential in AML. Through mass spectrometry analysis of affinity-purified complexes, we identify the kinase paralogs STK35 and PDIK1L as binding partners and substrates of the SCP4 phosphatase domain. We show that STK35 and PDIK1L function catalytically and redundantly in the same pathway as SCP4 to maintain AML proliferation and to support amino acid biosynthesis and transport. We provide evidence that SCP4 regulates STK35/PDIK1L through two distinct mechanisms: catalytic removal of inhibitory phosphorylation and by promoting kinase stability. Our findings reveal a phosphatase-kinase signaling complex that supports the pathogenesis of AML.
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From high-throughput to therapeutic: host-directed interventions against influenza viruses. Curr Opin Virol 2022; 53:101198. [PMID: 35030353 PMCID: PMC9086133 DOI: 10.1016/j.coviro.2021.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022]
Abstract
Influenza viruses are simultaneously supported and antagonized by factors within the host cell. This close relationship is the theoretical basis for future antivirals that target the host rather than the virus itself, a concept termed host-directed therapeutics. Genetic screening has led to the identification of host factors capable of modulating influenza virus infections, and these factors represent candidate targets for host-directed antiviral strategies. Despite advances in understanding host targets, however, there are currently no host-directed interventions for influenza viruses in clinical use. In this brief review, we discuss some host factors identified in knockout/knockdown and overexpression screens that could potentially be targeted as host-directed influenza intervention strategies. We further comment on the feasibility of changing gene expression in the respiratory tract with RNA delivery vectors and transient CRISPR-mediated gene targeting.
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Reverdatto S, Prasad A, Belrose JL, Zhang X, Sammons MA, Gibbs KM, Szaro BG. Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate Central Nervous System. BMC Genomics 2022; 23:2. [PMID: 34979916 PMCID: PMC8725369 DOI: 10.1186/s12864-021-08247-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Because some of its CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs, the South African claw-toed frog, Xenopus laevis, offers unique opportunities for exploring differences between regenerative and non-regenerative responses to CNS injury within the same organism. An earlier, three-way RNA-seq study (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) identified genes that regulate chromatin accessibility among those that were differentially expressed in regenerative vs non-regenerative CNS [11]. The current study used whole genome bisulfite sequencing (WGBS) of DNA collected from these same animals at the peak period of axon regeneration to study the extent to which DNA methylation could potentially underlie differences in chromatin accessibility between regenerative and non-regenerative CNS. RESULTS Consistent with the hypothesis that DNA of regenerative CNS is more accessible than that of non-regenerative CNS, DNA from both the regenerative tadpole hindbrain and frog eye was less methylated than that of the non-regenerative frog hindbrain. Also, consistent with observations of CNS injury in mammals, DNA methylation in non-regenerative frog hindbrain decreased after SCI. However, contrary to expectations that the level of DNA methylation would decrease even further with axotomy in regenerative CNS, DNA methylation in these regions instead increased with injury. Injury-induced differences in CpG methylation in regenerative CNS became especially enriched in gene promoter regions, whereas non-CpG methylation differences were more evenly distributed across promoter regions, intergenic, and intragenic regions. In non-regenerative CNS, tissue-related (i.e., regenerative vs. non-regenerative CNS) and injury-induced decreases in promoter region CpG methylation were significantly correlated with increased RNA expression, but the injury-induced, increased CpG methylation seen in regenerative CNS across promoter regions was not, suggesting it was associated with increased rather than decreased chromatin accessibility. This hypothesis received support from observations that in regenerative CNS, many genes exhibiting increased, injury-induced, promoter-associated CpG-methylation also exhibited increased RNA expression and association with histone markers for active promoters and enhancers. DNA immunoprecipitation for 5hmC in optic nerve regeneration found that the promoter-associated increases seen in CpG methylation were distinct from those exhibiting changes in 5hmC. CONCLUSIONS Although seemingly paradoxical, the increased injury-associated DNA methylation seen in regenerative CNS has many parallels in stem cells and cancer. Thus, these axotomy-induced changes in DNA methylation in regenerative CNS provide evidence for a novel epigenetic state favoring successful over unsuccessful CNS axon regeneration. The datasets described in this study should help lay the foundations for future studies of the molecular and cellular mechanisms involved. The insights gained should, in turn, help point the way to novel therapeutic approaches for treating CNS injury in mammals.
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Affiliation(s)
- Sergei Reverdatto
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Aparna Prasad
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Jamie L Belrose
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Morgan A Sammons
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kurt M Gibbs
- Department of Biology & Chemistry, Morehead State University, Morehead, KY, 40351, USA
| | - Ben G Szaro
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA.
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA.
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
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Raza SHA, Liang C, Guohua W, Pant SD, Mohammedsaleh ZM, Shater AF, Alotaibi MA, Khan R, Schreurs N, Cheng G, Mei C, Zan L. Screening and Identification of Muscle-Specific Candidate Genes via Mouse Microarray Data Analysis. Front Vet Sci 2021; 8:794628. [PMID: 34966817 PMCID: PMC8710720 DOI: 10.3389/fvets.2021.794628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/22/2021] [Indexed: 01/17/2023] Open
Abstract
Muscle tissue is involved with every stage of life activities and has roles in biological processes. For example, the blood circulation system needs the heart muscle to transport blood to all parts, and the movement cannot be separated from the participation of skeletal muscle. However, the process of muscle development and the regulatory mechanisms of muscle development are not clear at present. In this study, we used bioinformatics techniques to identify differentially expressed genes specifically expressed in multiple muscle tissues of mice as potential candidate genes for studying the regulatory mechanisms of muscle development. Mouse tissue microarray data from 18 tissue samples was selected from the GEO database for analysis. Muscle tissue as the treatment group, and the other 17 tissues as the control group. Genes expressed in the muscle tissue were different to those in the other 17 tissues and identified 272 differential genes with highly specific expression in muscle tissue, including 260 up-regulated genes and 12 down regulated genes. is the genes were associated with the myofibril, contractile fibers, and sarcomere, cytoskeletal protein binding, and actin binding. KEGG pathway analysis showed that the differentially expressed genes in muscle tissue were mainly concentrated in pathways for AMPK signaling, cGMP PKG signaling calcium signaling, glycolysis, and, arginine and proline metabolism. A PPI protein interaction network was constructed for the selected differential genes, and the MCODE module used for modular analysis. Five modules with Score > 3.0 are selected. Then the Cytoscape software was used to analyze the tissue specificity of differential genes, and the genes with high degree scores collected, and some common genes selected for quantitative PCR verification. The conclusion is that we have screened the differentially expressed gene set specific to mouse muscle to provide potential candidate genes for the study of the important mechanisms of muscle development.
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Affiliation(s)
| | - Chengcheng Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wang Guohua
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Sameer D Pant
- School of Animal & Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Zuhair M Mohammedsaleh
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Abdullah F Shater
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | | | - Rajwali Khan
- Department of Livestock Management, Breeding and Genetic, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Nicola Schreurs
- Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, China
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Combined Transcriptome and Proteome Profiling for Role of pfEMP1 in Antimalarial Mechanism of Action of Dihydroartemisinin. Microbiol Spectr 2021; 9:e0127821. [PMID: 34908430 PMCID: PMC8672878 DOI: 10.1128/spectrum.01278-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Malaria parasites induce morphological and biochemical changes in the membranes of parasite-infected red blood cells (iRBCs) for propagation. Artemisinin combination therapies are the first-line antiplasmodials in countries of endemicity. However, the mechanism of action of artemisinin is unclear, and drug resistance decreases long-term efficacy. To understand whether artemisinin targets or interacts with iRBC membrane proteins, this study investigated the molecular changes caused by dihydroartemisinin (DHA), an artemisinin derivative, in Plasmodium falciparum 3D7 using a combined transcriptomic and membrane proteomic profiling approach. Optical microscopy and scanning electron microscopy showed that DHA can cause morphological variation in the iRBC membrane. We identified 125 differentially expressed membrane proteins, and functional analysis indicated structural molecule activity and protein export as key biological functions of the two omics studies. DHA treatment decreased the expression of var gene variants PF3D7_0415700 and PF3D7_0900100 dose-dependently. Western blotting and immunofluorescence analysis showed that DHA treatment downregulates the var gene encoding P. falciparum erythrocyte membrane protein-1 (pfEMP1). pfEMP1 knockout significantly increased artemisinin sensitivity. Results showed that pfEMP1 might be involved in the antimalarial mechanism of action of DHA and pfEMP1 or its regulated factors may be further exploited in antiparasitic drug design. The findings are beneficial for elucidating the potential effects of DHA on iRBC membrane proteins and developing new drugs targeting iRBC membrane. IMPORTANCE Malaria parasites induce morphological and biochemical changes in the membranes of parasite-infected red blood cells (iRBCs) for propagation, with artemisinin combination therapies as the first-line treatments. To understand whether artemisinin targets or interacts with iRBC membrane proteins, this study investigated the molecular changes caused by dihydroartemisinin (DHA), an artemisinin derivative, in Plasmodium falciparum 3D7 using a combined transcriptomic and membrane proteomic profiling approach. We found that DHA can cause morphological changes of iRBC membrane. Structural molecule activity and protein export are considered to be the key biological functions based on the two omics studies. pfEMP1 might be involved in the DHA mechanism of action. pfEMP1 or its regulated factors may be further exploited in antiparasitic drug design. The findings are beneficial for elucidating the potential effects of DHA on iRBC membrane proteins and developing new antimalarial drugs targeting iRBC membrane.
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Bresciani E, Carrington B, Yu K, Kim EM, Zhen T, Guzman VS, Broadbridge E, Bishop K, Kirby M, Harper U, Wincovitch S, Dell’Orso S, Sartorelli V, Sood R, Liu P. Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development. Blood Adv 2021; 5:4949-4962. [PMID: 34492681 PMCID: PMC9153008 DOI: 10.1182/bloodadvances.2020003969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/02/2021] [Indexed: 11/20/2022] Open
Abstract
RUNX1 is essential for the generation of hematopoietic stem cells (HSCs). Runx1-null mouse embryos lack definitive hematopoiesis and die in mid-gestation. However, although zebrafish embryos with a runx1 W84X mutation have defects in early definitive hematopoiesis, some runx1W84X/W84X embryos can develop to fertile adults with blood cells of multilineages, raising the possibility that HSCs can emerge without RUNX1. Here, using 3 new zebrafish runx1-/- lines, we uncovered the compensatory mechanism for runx1-independent hematopoiesis. We show that, in the absence of a functional runx1, a cd41-green fluorescent protein (GFP)+ population of hematopoietic precursors still emerge from the hemogenic endothelium and can colonize the hematopoietic tissues of the mutant embryos. Single-cell RNA sequencing of the cd41-GFP+ cells identified a set of runx1-/--specific signature genes during hematopoiesis. Significantly, gata2b, which normally acts upstream of runx1 for the generation of HSCs, was increased in the cd41-GFP+ cells in runx1-/- embryos. Interestingly, genetic inactivation of both gata2b and its paralog gata2a did not affect hematopoiesis. However, knocking out runx1 and any 3 of the 4 alleles of gata2a and gata2b abolished definitive hematopoiesis. Gata2 expression was also upregulated in hematopoietic cells in Runx1-/- mice, suggesting the compensatory mechanism is conserved. Our findings indicate that RUNX1 and GATA2 serve redundant roles for HSC production, acting as each other's safeguard.
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Affiliation(s)
| | | | - Kai Yu
- Oncogenesis and Development Section
| | | | - Tao Zhen
- Oncogenesis and Development Section
| | | | | | | | | | | | - Stephen Wincovitch
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - Raman Sood
- Oncogenesis and Development Section
- Zebrafish Core
| | - Paul Liu
- Oncogenesis and Development Section
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123
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Gao Y, Li Y, Niu Y, Ju H, Chen R, Li B, Song X, Song L. Chemical Characterization, Antitumor, and Immune-Enhancing Activities of Polysaccharide from Sargassum pallidum. Molecules 2021; 26:7559. [PMID: 34946640 PMCID: PMC8709291 DOI: 10.3390/molecules26247559] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 12/24/2022] Open
Abstract
Searching for natural products with antitumor and immune-enhancing activities is an important aspect of cancer research. Sargassum pallidum is an edible brown alga that has been used in Chinese traditional medicine for the treatment of tumors. However, the purification and application of its active components are still insufficient. In the present study, the polysaccharides from S. pallidum (SPPs) with antitumor and immune-enhancing activities were isolated and purified, and five polysaccharide fractions (SPP-0.3, SPP-0.5, SPP-0.7, SPP-1, and SPP-2) were obtained. The ratio of total saccharides, monosaccharide composition, and sulfated contents was determined, and their structures were analyzed by Fourier transform infrared spectroscopy. Moreover, bioactivity analysis showed that all five fractions had significant antitumor activity against three types of cancer cells (A549, HepG2, and B16), and can induce cancer cell apoptosis. In addition, the results indicated that SPPs can enhance the proliferation of immune cells and improve the expression levels of serum cytokines (IL-6, IL-1β, iNOS, and TNF-α). SPP-0.7 was identified as the most active fraction and selected for further purification, and its physicochemical properties and antitumor mechanism were further analyzed. Transcriptome sequencing result showed that SPP-0.7 can significantly induce the cell apoptosis, cytokine secretion, and cellular stress response process, and inhibit the normal physiological processes of cancer cells. Overall, SPPs and SPP-0.7 may be suitable for use as potential candidate agents for cancer therapy.
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Affiliation(s)
- Yi Gao
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Y.G.); (B.L.)
| | - Yizhen Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China; (Y.L.); (Y.N.); (H.J.); (R.C.)
| | - Yunze Niu
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China; (Y.L.); (Y.N.); (H.J.); (R.C.)
| | - Hao Ju
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China; (Y.L.); (Y.N.); (H.J.); (R.C.)
| | - Ran Chen
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China; (Y.L.); (Y.N.); (H.J.); (R.C.)
| | - Bin Li
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Y.G.); (B.L.)
| | - Xiyun Song
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China;
| | - Lin Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao 266042, China
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124
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Pennemann FL, Mussabekova A, Urban C, Stukalov A, Andersen LL, Grass V, Lavacca TM, Holze C, Oubraham L, Benamrouche Y, Girardi E, Boulos RE, Hartmann R, Superti-Furga G, Habjan M, Imler JL, Meignin C, Pichlmair A. Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators. Nat Commun 2021; 12:7009. [PMID: 34853303 PMCID: PMC8636641 DOI: 10.1038/s41467-021-27192-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/02/2021] [Indexed: 12/11/2022] Open
Abstract
The cell intrinsic antiviral response of multicellular organisms developed over millions of years and critically relies on the ability to sense and eliminate viral nucleic acids. Here we use an affinity proteomics approach in evolutionary distant species (human, mouse and fly) to identify proteins that are conserved in their ability to associate with diverse viral nucleic acids. This approach shows a core of orthologous proteins targeting viral genetic material and species-specific interactions. Functional characterization of the influence of 181 candidates on replication of 6 distinct viruses in human cells and flies identifies 128 nucleic acid binding proteins with an impact on virus growth. We identify the family of TAO kinases (TAOK1, -2 and -3) as dsRNA-interacting antiviral proteins and show their requirement for type-I interferon induction. Depletion of TAO kinases in mammals or flies leads to an impaired response to virus infection characterized by a reduced induction of interferon stimulated genes in mammals and impaired expression of srg1 and diedel in flies. Overall, our study shows a larger set of proteins able to mediate the interaction between viral genetic material and host factors than anticipated so far, attesting to the ancestral roots of innate immunity and to the lineage-specific pressures exerted by viruses.
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Affiliation(s)
- Friederike L Pennemann
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Assel Mussabekova
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Christian Urban
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Alexey Stukalov
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Line Lykke Andersen
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Vincent Grass
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Teresa Maria Lavacca
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Cathleen Holze
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Lila Oubraham
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Yasmine Benamrouche
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Enrico Girardi
- CeMM - Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Rasha E Boulos
- Computer Science and Mathematics Department, School of Arts and Science, Lebanese American University, Byblos, Lebanon
| | - Rune Hartmann
- Aarhus University, Department of Molecular Biology and Genetics - Structural Biology, Aarhus, Denmark
| | - Giulio Superti-Furga
- CeMM - Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Matthias Habjan
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Jean-Luc Imler
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Carine Meignin
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Andreas Pichlmair
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany.
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany.
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany.
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125
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Liu J, Fu Q, Liu S. Transcriptional Regulation Based on Network of Autophagy Identifies Key Genes and Potential Mechanisms in Human Osteoarthritis. Cartilage 2021; 13:1431S-1441S. [PMID: 32819149 PMCID: PMC8804715 DOI: 10.1177/1947603520951632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVE Osteoarthritis (OA) is a chronic arthropathy that frequently occurs in the middle-aged and elderly population. The aim of this study was to investigate the molecular mechanism of OA based on autophagy theory. DESIGN We downloaded the gene expression profile from the Gene Expression Omnibus repository. Differentially expressed genes (DEGs) related to the keyword "autophagy" were identified using the scanGEO online analysis tool. DEGs representing the same expression trend were screened using the MATCH function. Clinical synovial specimens were collected for identification, pathological diagnosis, hematoxylin and eosin staining, and real-time polymerase chain reaction analysis. Differential expression of mRNAs in the synovial membrane tissues and chondrocyte monolayer samples from OA patients was used to identify potential OA biomarkers. Protein-protein interactions were established by the STRING website and visualized with Cytoscape. Functional and pathway enrichment analyses were performed using the Metascape database. RESULTS GABARAPL1, GABARAPL2, and ATG13 were obtained as co-expressed autogenes in the 3 data sets. They were all downregulated among OA synovial tissues compared with non-OA synovial tissues (P < 0.01). A protein-protein interaction network was constructed based on these 3 genes and included 63 genes. A functional analysis revealed that these genes were associated with autophagy-related functions. The top hub genes in the protein-protein interaction network were presented. Furthermore, 3 key modules were extracted to be core control modules. CONCLUSIONS These results offer an important molecular understanding of the key transcriptional regulatory genes and modules based on the network of potential autophagy mechanisms in human OA.
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Affiliation(s)
- Jiamei Liu
- Department of Pathology, The Shengjing
Hospital of China Medical University, Shenyang, Liaoning, People’s Republic of
China
| | - Qin Fu
- Department of Orthopedics, The Shengjing
Hospital of China Medical University, Shenyang, Liaoning, People’s Republic of
China
| | - Shengye Liu
- Department of Orthopedics, The Shengjing
Hospital of China Medical University, Shenyang, Liaoning, People’s Republic of
China,Shengye Liu, Department of Orthopedics, The
Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004,
People’s Republic of China.
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126
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Deep Learning Analyses to Delineate the Molecular Remodeling Process after Myocardial Infarction. Cells 2021; 10:cells10123268. [PMID: 34943776 PMCID: PMC8699769 DOI: 10.3390/cells10123268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 02/01/2023] Open
Abstract
Specific proteins and processes have been identified in post-myocardial infarction (MI) pathological remodeling, but a comprehensive understanding of the complete molecular evolution is lacking. We generated microarray data from swine heart biopsies at baseline and 6, 30, and 45 days after infarction to feed machine-learning algorithms. We cross-validated the results using available clinical and experimental information. MI progression was accompanied by the regulation of adipogenesis, fatty acid metabolism, and epithelial-mesenchymal transition. The infarct core region was enriched in processes related to muscle contraction and membrane depolarization. Angiogenesis was among the first morphogenic responses detected as being sustained over time, but other processes suggesting post-ischemic recapitulation of embryogenic processes were also observed. Finally, protein-triggering analysis established the key genes mediating each process at each time point, as well as the complete adverse remodeling response. We modeled the behaviors of these genes, generating a description of the integrative mechanism of action for MI progression. This mechanistic analysis overlapped at different time points; the common pathways between the source proteins and cardiac remodeling involved IGF1R, RAF1, KPCA, JUN, and PTN11 as modulators. Thus, our data delineate a structured and comprehensive picture of the molecular remodeling process, identify new potential biomarkers or therapeutic targets, and establish therapeutic windows during disease progression.
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127
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Marzi A, Jankeel A, Menicucci AR, Callison J, O'Donnell KL, Feldmann F, Pinski AN, Hanley PW, Messaoudi I. Single Dose of a VSV-Based Vaccine Rapidly Protects Macaques From Marburg Virus Disease. Front Immunol 2021; 12:774026. [PMID: 34777392 PMCID: PMC8578864 DOI: 10.3389/fimmu.2021.774026] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Marburg virus (MARV) is a member of the filovirus family that causes hemorrhagic disease with high case fatality rates. MARV is on the priority list of the World Health Organization for countermeasure development highlighting its potential impact on global public health. We developed a vesicular stomatitis virus (VSV)-based vaccine expressing the MARV glycoprotein (VSV-MARV) and previously demonstrated uniform protection of nonhuman primates (NHPs) with a single dose. Here, we investigated the fast-acting potential of this vaccine by challenging NHPs with MARV 14, 7 or 3 days after a single dose vaccination with VSV-MARV. We found that 100% of the animals survived when vaccinated 7 or 14 days and 75% of the animal survived when vaccinated 3 days prior to lethal MARV challenge. Transcriptional analysis of whole blood samples indicated activation of B cells and antiviral defense after VSV-MARV vaccination. In the day -14 and -7 groups, limited transcriptional changes after challenge were observed with the exception of day 9 post-challenge in the day -7 group where we detected gene expression profiles indicative of a recall response. In the day -3 group, transcriptional analysis of samples from surviving NHPs revealed strong innate immune activation. In contrast, the animal that succumbed to disease in this group lacked signatures of antiviral immunity. In summary, our data demonstrate that the VSV-MARV is a fast-acting vaccine suitable for the use in emergency situations like disease outbreaks in Africa.
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Affiliation(s)
- Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Allen Jankeel
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Andrea R Menicucci
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Julie Callison
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Kyle L O'Donnell
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Amanda N Pinski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Patrick W Hanley
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
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128
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Zheng L, Wu Y, Shen L, Liang X, Yang Z, Li S, Li T, Shang W, Shao W, Wang Y, Liu F, Ma L, Jia J. Mechanisms of JARID1B Up-Regulation and Its Role in Helicobacter pylori-Induced Gastric Carcinogenesis. Front Oncol 2021; 11:757497. [PMID: 34778074 PMCID: PMC8581301 DOI: 10.3389/fonc.2021.757497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Abstract
Gastric cancer (GC) is the third leading cause of cancer-related death worldwide. Helicobacter pylori infection can induce GC through a serial cascade of events, with emerging evidence suggesting the important role of epigenetic alterations in the development and progression of the disease. Here, we report on mechanisms responsible for Jumonji AT-rich interactive domain1B (JARID1B) upregulation in GC and its role in the malignant transformation induced by H. pylori infection. We found that upregulation of JARID1B was associated with poorer prognosis, greater tumor purity, and less immune cell infiltration into the tumor. Mechanistically, we showed that the upregulation of JARID1B in human GC was attributed to JARID1B amplification and its induction by H. pylori infection. Furthermore, we identified miR-29c as a negative regulator of JARID1B in GC. H. pylori caused downregulation of miR-29c in human GC and thereby contributed to JARID1B upregulation through relieving posttranscriptional regulation. Functionally, we showed that knockdown of JARID1B reduced GC cell proliferation induced by H. pylori infection. Subsequently, cyclinD1 (CCND1), a key molecule in GC, was shown to be a target gene of JARID1B. In conclusion, these results suggest that JARID1B may be an oncogene upregulated in human GC and could represent a novel therapeutic target to prevent malignant transformation induced by H. pylori infection.
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Affiliation(s)
- Lixin Zheng
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Yujiao Wu
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Li Shen
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Xiuming Liang
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Zongcheng Yang
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Shuyan Li
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Tongyu Li
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Wenjing Shang
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Wei Shao
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Yue Wang
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Fen Liu
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Lin Ma
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Jihui Jia
- Key Laboratory of Experimental Teratology, School of Basic Medical Sciences, Shandong University, Jinan, China.,Shandong Provincial Key Laboratory of Infection and Immunology, School of Basic Medical Sciences, Shandong University, Jinan, China
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129
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Yu M, Su Z, Huang X, Wang X. Single-Cell Sequencing Reveals the Novel Role of Ezh2 in NK Cell Maturation and Function. Front Immunol 2021; 12:724276. [PMID: 34764950 PMCID: PMC8576367 DOI: 10.3389/fimmu.2021.724276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
Natural killer (NK) cells are lymphocytes primarily involved in innate immunity and exhibit important functional properties in antimicrobial and antitumoral responses. Our previous work indicated that the enhancer of zeste homolog 2 (Ezh2) is a negative regulator of early NK cell differentiation and function through trimethylation of histone H3 lysine 27 (H3K27me3). Here, we deleted Ezh2 from immature NK cells and downstream progeny to explore its role in NK cell maturation by single-cell RNA sequencing (scRNA-seq). We identified six distinct NK stages based on the transcriptional signature during NK cell maturation. Conditional deletion of Ezh2 in NK cells resulted in a maturation trajectory toward NK cell arrest in CD11b SP stage 5, which was clustered with genes related to the activating function of NK cells. Mechanistically, we speculated that Ezh2 plays a critical role in NK development by activating AP-1 family gene expression independent of PRC2 function. Our results implied a novel role for the Ezh2-AP-1-Klrg1 axis in altering the NK cell maturation trajectory and NK cell-mediated cytotoxicity.
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Affiliation(s)
- Minghang Yu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Immunology, School of Basic Medical Sciences; Advanced Innovation Center for Human Brain Protection, Beijing Key Laboratory for Cancer Invasion and Metastasis, Department of Oncology, Capital Medical University, Beijing, China
| | - Ziyang Su
- Department of Immunology, School of Basic Medical Sciences; Advanced Innovation Center for Human Brain Protection, Beijing Key Laboratory for Cancer Invasion and Metastasis, Department of Oncology, Capital Medical University, Beijing, China
| | - Xuefeng Huang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Immunology, School of Basic Medical Sciences; Advanced Innovation Center for Human Brain Protection, Beijing Key Laboratory for Cancer Invasion and Metastasis, Department of Oncology, Capital Medical University, Beijing, China
| | - Xi Wang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Immunology, School of Basic Medical Sciences; Advanced Innovation Center for Human Brain Protection, Beijing Key Laboratory for Cancer Invasion and Metastasis, Department of Oncology, Capital Medical University, Beijing, China
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130
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Zou D, Bai J, Lu E, Yang C, Liu J, Wen Z, Liu X, Jin Z, Xu M, Jiang L, Zhang Y, Zhang Y. Identification of Novel Drug Candidate for Epithelial Ovarian Cancer via In Silico Investigation and In Vitro Validation. Front Oncol 2021; 11:745590. [PMID: 34745968 PMCID: PMC8568458 DOI: 10.3389/fonc.2021.745590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/28/2021] [Indexed: 12/24/2022] Open
Abstract
Epithelial ovarian cancer (EOC) has a poor prognosis and high mortality rate; patients are easy to relapse with standard therapies. So, there is an urgent need to develop novel drugs. In this study, differentially expressed genes (DEGs) of EOC were identified in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Enrichment and protein–protein interaction (PPI) analyses were performed. The drug candidate which has the possibility to treat EOC was predicted by Connectivity Map (CMAP) databases. Moreover, molecular docking was selected to calculate the binding affinity between drug candidate and hub genes. The cytotoxicity of drug candidates was assessed by MTT and colony formation analysis, the proteins coded by hub genes were detected by Western blots, and apoptosis analysis was evaluated by flow cytometry. Finally, 296 overlapping DEGs (|log 2 fold change|>1; q-value <0.05), which were principally involved in the cell cycle (p < 0.05), and cyclin-dependent kinase 1 (CDK1) were screened as the significant hub gene from the PPI network. Furthermore, the 21 drugs were extracted from CMAPs; among them, piperlongumine (PL) showed a lower CMAP score (-0.80, -62.92) and was regarded as the drug candidate. Furthermore, molecular docking results between PL and CDK1 with a docking score of –8.121 kcal/mol were close to the known CDK1 inhibitor (–8.24 kcal/mol). Additionally, in vitro experiments showed that PL inhibited proliferation and induced apoptosis via targeting CDK1 in EOC SKOV3 cells. Our results reveal that PL may be a novel drug candidate for EOC by inhibiting cell cycle.
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Affiliation(s)
- Dan Zou
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, China.,Department of Medical Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Jin Bai
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, China.,Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Enting Lu
- Department of Gynecology, First Hospital of China Medical University, Shenyang, China
| | - Chunjiao Yang
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, China
| | - Jiaqing Liu
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, China
| | - Zhenpeng Wen
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, China
| | - Xuqin Liu
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, China
| | - Zi Jin
- The First Department of Oncology, Shenyang Fifth People's Hospital, Shenyang, China
| | - Mengdan Xu
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, China
| | - Lei Jiang
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, China
| | - Ye Zhang
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, China
| | - Yi Zhang
- Department of Gynecology, First Hospital of China Medical University, Shenyang, China
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131
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Wu S, Shao M, Zhang Y, Shi D. Activation of RSK2 upregulates SOX8 to promote methotrexate resistance in gestational trophoblastic neoplasia. J Transl Med 2021; 101:1494-1504. [PMID: 34373588 DOI: 10.1038/s41374-021-00651-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 11/09/2022] Open
Abstract
Resistance to chemotherapy is frequently driven by aberrantly activated kinases in cancer. Herein, we characterized the global phosphoproteomic alterations associated with methotrexate (MTX) resistance in gestational trophoblastic neoplastic (GTN) cells. A total of 1111 phosphosites on 713 proteins were significantly changed, with highly elevated Ribosomal S6 Kinase 2 (RSK2) phosphorylation (pS227) observed in MTX-resistant GTN cells. Activation of RSK2 promoted cell proliferation and survival after MTX treatment in GTN cell models. Interestingly, RSK2 might play an important role in the regulation of reactive oxygen species (ROS) homeostasis, as manipulation of RSK2 activation affected ROS accumulation and SOX8 expression in GTN cells. In addition, overexpression of SOX8 partly rescued cell proliferation and survival in RSK2-depleted MTX-resistant GTN cells, suggesting that SOX8 might serve as a downstream effector of RSK2 to promote MTX resistance in GTN cells. Highly activated RSK2/SOX8 signaling was observed in MTX-resistant GTN specimens. Further, the RSK2 inhibitor BIX02565 effectively reduced SOX8 expression, induced ROS accumulation, and enhanced MTX-induced cytotoxicity in vitro and in vivo. Collectively, our findings suggested that RSK2 activation could promote MTX resistance via upregulating SOX8 and attenuating MTX-induced ROS in GTN cells, which may help to develop experimental therapeutics to treat MTX-resistant GTN.
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Affiliation(s)
- Shaobin Wu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Mingjie Shao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Zhang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, China
| | - Dazun Shi
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, China.
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132
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Fan H, Ren Z, Xu C, Wang H, Wu Z, Rehman ZU, Wu S, Sun MA, Bao W. Chromatin Accessibility and Transcriptomic Alterations in Murine Ovarian Granulosa Cells upon Deoxynivalenol Exposure. Cells 2021; 10:2818. [PMID: 34831041 PMCID: PMC8616273 DOI: 10.3390/cells10112818] [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: 08/25/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 11/26/2022] Open
Abstract
Deoxynivalenol (DON) is a common environmental toxin that is secreted by fusarium fungi that frequently contaminates feedstuff and food. While the detrimental effects of DON on human and animal reproductive systems have been well recognized, the underlying mechanism remains poorly understood. Ovarian granulosa cells (GCs), which surround oocytes, are crucial for regulating oocyte development, mainly through the secretion of hormones such as estrogen and progesterone. Using an in vitro model of murine GCs, we characterized the cytotoxic effects of DON and profiled genome-wide chromatin accessibility and transcriptomic alterations after DON exposure. Our results suggest that DON can induce decreased viability and growth, increased apoptosis rate, and disrupted hormone secretion. In total, 2533 differentially accessible loci and 2675 differentially expressed genes were identified that were associated with Hippo, Wnt, steroid biosynthesis, sulfur metabolism, and inflammation-related pathways. DON-induced genes usually have a concurrently increased occupancy of active histone modifications H3K4me3 and H3K27ac in their promoters. Integrative analyses identified 35 putative directly affected genes including Adrb2 and Fshr, which are key regulators of follicular growth, and revealed that regions with increased chromatin accessibility are enriched with the binding motifs for NR5A1 and NR5A2, which are important for GCs. Moreover, DON-induced inflammatory response is due to the activation of the NF-κB and MAPK signaling pathways. Overall, our results provide novel insights into the regulatory elements, genes, and key pathways underlying the response of ovarian GCs to DON cytotoxicity.
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Affiliation(s)
- Hairui Fan
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Zhanshi Ren
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Chao Xu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Haifei Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Zhengchang Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Zia ur Rehman
- Faculty of Animal Husbandry and Veterinary Sciences, College of Veterinary Sciences, The University of Agriculture Peshawar, Peshawar 25000, Pakistan;
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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133
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Meng H, Zhao MM, Yang RY, Deng XF, Zhang HY, Choi YM, An IS, An SK, Dong YM, He YF, Li L, Guo MM, Yi F. Salvianolic acid B regulates collagen synthesis: Indirect influence on human dermal fibroblasts through the microvascular endothelial cell pathway. J Cosmet Dermatol 2021; 21:3007-3015. [PMID: 34648670 DOI: 10.1111/jocd.14516] [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: 05/22/2021] [Accepted: 09/28/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Salvianolic acid B (SAB) is one of the main active ingredients of Salvia Miltiorrhiza. It has significant skin anti-aging, whitening, and sun protection properties. AIMS The study aimed at studying the mechanism underlying the effect of salvianolic acid Bon collagen synthesis, which has good anti-aging efficacy and modulates microcirculation. METHODS This study employed available public databases, bioinformatics methodologies, and the inverse docking approach to explore the effectiveness of SAB in the regulating collagen synthesis, and then used an human dermal fibroblast (HDF)- Human dermal microvascular endothelial cell (HDMEC) in vitro model to validate the predicted mechanism of SAB in influencing collagen synthesis. RESULTS The results showed that NO production in SAB-treated HDMEC-conditioned medium was increased compared to that in control media, and the same tendency was also observed for growth factor production. SAB also upregulated HDMEC cellular eNOS and VEGF. When SAB-treated HDMEC conditioned medium was transferred to HDFs, the expression of collagen I, collagen III, and elastin in HDFs was upregulated and MMP-1 was downregulated. CONCLUSIONS The results show that SAB regulates collagen through the HDMEC-HDF pathway. Furthermore, the mechanisms might be closely related to the microcirculation factors NO and VEGF.
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Affiliation(s)
- Hong Meng
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, China.,Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China
| | - Meng-Meng Zhao
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, China.,Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China
| | - Ru-Ya Yang
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, China.,Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China
| | - Xiao-Feng Deng
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, China.,Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China
| | - Hong-Yan Zhang
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, China.,Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China
| | - Yeong-Min Choi
- Korea Institute for Skin and Clinical Sciences, Gene Cell Pharm Corporation, Seoul, Korea
| | - In-Sook An
- Korea Institute for Skin and Clinical Sciences, Gene Cell Pharm Corporation, Seoul, Korea
| | - Sung-Kwan An
- Department of Cosmetics Engineering, Research Institute for Molecular-Targeted Drugs, Konkuk University, Seoul, Korea
| | - Yin-Mao Dong
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, China.,Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China
| | - Yi-Fan He
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, China.,Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China
| | - Li Li
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, China.,Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China
| | - Miao-Miao Guo
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, China.,Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China
| | - Fan Yi
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, China.,Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China
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134
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Martin-Sancho L, Tripathi S, Rodriguez-Frandsen A, Pache L, Sanchez-Aparicio M, McGregor MJ, Haas KM, Swaney DL, Nguyen TT, Mamede JI, Churas C, Pratt D, Rosenthal SB, Riva L, Nguyen C, Beltran-Raygoza N, Soonthornvacharin S, Wang G, Jimenez-Morales D, De Jesus PD, Moulton HM, Stein DA, Chang MW, Benner C, Ideker T, Albrecht RA, Hultquist JF, Krogan NJ, García-Sastre A, Chanda SK. Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy. Nat Microbiol 2021; 6:1319-1333. [PMID: 34556855 PMCID: PMC9683089 DOI: 10.1038/s41564-021-00964-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/18/2021] [Indexed: 02/07/2023]
Abstract
The fate of influenza A virus (IAV) infection in the host cell depends on the balance between cellular defence mechanisms and viral evasion strategies. To illuminate the landscape of IAV cellular restriction, we generated and integrated global genetic loss-of-function screens with transcriptomics and proteomics data. Our multi-omics analysis revealed a subset of both IFN-dependent and independent cellular defence mechanisms that inhibit IAV replication. Amongst these, the autophagy regulator TBC1 domain family member 5 (TBC1D5), which binds Rab7 to enable fusion of autophagosomes and lysosomes, was found to control IAV replication in vitro and in vivo and to promote lysosomal targeting of IAV M2 protein. Notably, IAV M2 was observed to abrogate TBC1D5-Rab7 binding through a physical interaction with TBC1D5 via its cytoplasmic tail. Our results provide evidence for the molecular mechanism utilised by IAV M2 protein to escape lysosomal degradation and traffic to the cell membrane, where it supports IAV budding and growth.
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Affiliation(s)
- Laura Martin-Sancho
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Shashank Tripathi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Infectious Disease Research, Microbiology & Cell Biology Department, Indian Institute of Science, Bangalore, India
| | - Ariel Rodriguez-Frandsen
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lars Pache
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Maite Sanchez-Aparicio
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael J McGregor
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Kelsey M Haas
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Thong T Nguyen
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - João I Mamede
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Christopher Churas
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Dexter Pratt
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sara B Rosenthal
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Laura Riva
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Courtney Nguyen
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Nish Beltran-Raygoza
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Stephen Soonthornvacharin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Guojun Wang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Jimenez-Morales
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
| | - Paul D De Jesus
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Hong M Moulton
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - David A Stein
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Max W Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chris Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judd F Hultquist
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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135
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Comprehensive molecular characterization of pediatric radiation-induced high-grade glioma. Nat Commun 2021; 12:5531. [PMID: 34545084 PMCID: PMC8452624 DOI: 10.1038/s41467-021-25709-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
Radiation-induced high-grade gliomas (RIGs) are an incurable late complication of cranial radiation therapy. We performed DNA methylation profiling, RNA-seq, and DNA sequencing on 32 RIG tumors and an in vitro drug screen in two RIG cell lines. We report that based on DNA methylation, RIGs cluster primarily with the pediatric receptor tyrosine kinase I high-grade glioma subtype. Common copy-number alterations include Chromosome (Ch.) 1p loss/1q gain, and Ch. 13q and Ch. 14q loss; focal alterations include PDGFRA and CDK4 gain and CDKN2A and BCOR loss. Transcriptomically, RIGs comprise a stem-like subgroup with lesser mutation burden and Ch. 1p loss and a pro-inflammatory subgroup with greater mutation burden and depleted DNA repair gene expression. Chromothripsis in several RIG samples is associated with extrachromosomal circular DNA-mediated amplification of PDGFRA and CDK4. Drug screening suggests microtubule inhibitors/stabilizers, DNA-damaging agents, MEK inhibition, and, in the inflammatory subgroup, proteasome inhibitors, as potentially effective therapies. Radiation-induced high-grade gliomas (RIGs) are an incurable late complication of cranial radiation therapy. In the largest study to date, we report the results of DNA methylation profiling, RNA-Seq and genomic sequencing of 32 RIG tumors, and an in vitro drug screen in two RIG cell lines.
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136
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Integrative Transcriptome Profiling Reveals SKA3 as a Novel Prognostic Marker in Non-Muscle Invasive Bladder Cancer. Cancers (Basel) 2021; 13:cancers13184673. [PMID: 34572901 PMCID: PMC8470398 DOI: 10.3390/cancers13184673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 01/03/2023] Open
Abstract
Approximately 80% of all new bladder cancer patients are diagnosed with non-muscle invasive bladder cancer (NMIBC). However, approximately 15% of them progress to muscle-invasive bladder cancer (MIBC), for which prognosis is poor. The current study aimed to improve diagnostic accuracy associated with clinical outcomes in NMIBC patients. Nevertheless, it has been challenging to identify molecular biomarkers that accurately predict MIBC progression because this disease is complex and heterogeneous. Through integrative transcriptome profiling, we showed that high SKA3 expression is associated with poor clinical outcomes and MIBC progression. We performed RNA sequencing on human tumor tissues to identify candidate biomarkers in NMIBC. We then selected genes with prognostic significance by analyzing public datasets from multiple cohorts of bladder cancer patients. We found that SKA3 was associated with NMIBC pathophysiology and poor survival. We analyzed public single-cell RNA-sequencing (scRNA-seq) data for bladder cancer to dissect transcriptional tumor heterogeneity. SKA3 was expressed in an epithelial cell subpopulation expressing genes regulating the cell cycle. Knockdown experiments confirmed that SKA3 promotes bladder cancer cell proliferation by accelerating G2/M transition. Hence, SKA3 is a new prognostic marker for predicting NMIBC progression. Its inhibition could form part of a novel treatment lowering the probability of bladder cancer progression.
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137
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Zhan Y, Zhang Y, Zhang S, Coughlan H, Baldoni PL, Jacquelot N, Cao WHJ, Preston S, Louis C, Rautela J, Pellegrini M, Wicks IP, Alexander WS, Harrison LC, Lew AM, Smyth GK, Nutt SL, Chopin M. Differential requirement for the Polycomb repressor complex 2 in dendritic cell and tissue-resident myeloid cell homeostasis. Sci Immunol 2021; 6:eabf7268. [PMID: 34533976 DOI: 10.1126/sciimmunol.abf7268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Yifan Zhan
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia.,Drug Discovery, Shanghai Huaota Biopharma, Shanghai, China
| | - Yuxia Zhang
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia.,Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Shengbo Zhang
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Hannah Coughlan
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Pedro L Baldoni
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicolas Jacquelot
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Wang H J Cao
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Simon Preston
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Cynthia Louis
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jai Rautela
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Marc Pellegrini
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ian P Wicks
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Warren S Alexander
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Leonard C Harrison
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew M Lew
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia.,Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Gordon K Smyth
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,School of Mathematics and Statistics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Stephen L Nutt
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michaël Chopin
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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138
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Browning LM, Miller C, Kuczma M, Pietrzak M, Jing Y, Rempala G, Muranski P, Ignatowicz L, Kraj P. Bone Morphogenic Proteins Are Immunoregulatory Cytokines Controlling FOXP3 + T reg Cells. Cell Rep 2021; 33:108219. [PMID: 33027660 DOI: 10.1016/j.celrep.2020.108219] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 07/28/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022] Open
Abstract
Bone morphogenic proteins (BMPs) are members of the transforming growth factor β (TGF-β) cytokine family promoting differentiation, homeostasis, and self-renewal of multiple tissues. We show that signaling through the bone morphogenic protein receptor 1α (BMPR1α) sustains expression of FOXP3 in Treg cells in peripheral lymphoid tissues. BMPR1α signaling promotes molecular circuits supporting acquisition and preservation of Treg cell phenotype and inhibiting differentiation of pro-inflammatory effector Th1/Th17 CD4+ T cell. Mechanistically, increased expression of KDM6B (JMJD3) histone demethylase, an antagonist of the polycomb repressive complex 2, underlies lineage-specific changes of T cell phenotypes associated with abrogation of BMPR1α signaling. These results reveal that BMPs are immunoregulatory cytokines mediating maturation and stability of peripheral FOXP3+ regulatory T cells (Treg cells) and controlling generation of iTreg cells. Thus, we establish that BMPs, a large cytokine family, are an essential link between stromal tissues and the adaptive immune system involved in sustaining tissue homeostasis by promoting immunological tolerance.
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Affiliation(s)
- Lauren M Browning
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Caroline Miller
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Michal Kuczma
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Maciej Pietrzak
- Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, USA
| | - Yu Jing
- Center for Bioelectrics, Old Dominion University, Norfolk, VA 23529, USA
| | - Grzegorz Rempala
- College of Public Health, Ohio State University, Columbus, OH 43210, USA
| | - Pawel Muranski
- Columbia University Medical Center, New York, NY 10032, USA
| | - Leszek Ignatowicz
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Piotr Kraj
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA.
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139
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Cuthbert JM, Russell SJ, Polejaeva IA, Meng Q, White KL, Benninghoff AD. Comparing mRNA and sncRNA profiles during the maternal-to-embryonic transition in bovine IVF and scNT embryos. Biol Reprod 2021; 105:1401-1415. [PMID: 34514499 DOI: 10.1093/biolre/ioab169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/09/2021] [Accepted: 09/02/2021] [Indexed: 12/14/2022] Open
Abstract
Production of embryos with high developmental competence by somatic cell nuclear transfer (scNT) is far less efficient than for in vitro fertilized (IVF) embryos, likely due to an accumulation of errors in genome reprogramming that results in aberrant expression of RNA transcripts, including messenger RNAs (mRNA) and, possibly, microRNAs (miRNA). Thus, our objectives were to use RNAseq to determine the dynamics of mRNA expression in early developing scNT and IVF embryos in the context of the maternal-to-embryonic transition (MET) and to correlate apparent transcriptional dysregulation in cloned embryos with miRNA expression profiles. Comparisons between scNT and IVF embryos indicated large scale transcriptome differences, which were most evident at the 8-cell and morula stages for genes associated with biological functions critical for the MET. For two miRNAs previously identified as differentially expressed in scNT morulae, miR-34a and miR-345, negative correlations with some predicted mRNA targets were apparent, though not widespread among the majority of predicted targets. Moreover, although large-scale aberrations in expression of mRNAs were evident during the MET in cattle scNT embryos, these changes were not consistently correlated with aberrations in miRNA expression at the same developmental stage, suggesting that other mechanisms controlling gene expression may be involved.
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Affiliation(s)
- Jocelyn M Cuthbert
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, Utah 84322, USA
| | - Stewart J Russell
- CReATe Fertility Centre, 790 Bay St. #1100, Toronto, M5G 1N8, Canada
| | - Irina A Polejaeva
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, Utah 84322, USA
| | - Qinggang Meng
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, Utah 84322, USA
| | - Kenneth L White
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, Utah 84322, USA
| | - Abby D Benninghoff
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, Utah 84322, USA
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140
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Shi Z, Liu J, Wang F, Li Y. Integrated analysis of Solute carrier family-2 members reveals SLC2A4 as an independent favorable prognostic biomarker for breast cancer. Channels (Austin) 2021; 15:555-568. [PMID: 34488531 PMCID: PMC8425726 DOI: 10.1080/19336950.2021.1973788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Most of Solute carrier family-2 (SLC2) members play a key role of facilitative transporters, and glucose transporter (GLUT) proteins encoded by SLC2s can transport hexoses or polyols. However, the function and mechanism of SLC2s remain unclear in human cancers. Here, we explored the dysregulated expression, prognostic values, epigenetic, genetic alterations, and biomolecular network of SLC2s in human cancers. According to the data from public-omicsrepository, SLC2A4 (GLUT4) was found to be significantly downregulated in most cancers, and higher messenger RNA (mRNA) expression of SLC2A4 significantly associated with better prognosis of breast cancer (BRCA) patients. Moreover, DNA hypermethylation in the promoter of SLC2A4 may affect the regulation of its mRNA expression, and SLC2A4 was strongly correlated with pathways, including the translocation of SLC2A4 to the plasma membrane and PID INSULIN PATHWAY. In conclusion, these results provide insight into SLC2s in human cancers and suggest that SLC2A4 could be an unfavorable prognostic biomarker for the survival of BRCA patients.
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Affiliation(s)
- Zhenyu Shi
- Department of Predictive Medicine,Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, HenanUniversity,Kaifeng,China
| | - Jiahao Liu
- Department of Predictive Medicine,Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, HenanUniversity,Kaifeng,China
| | - Fei Wang
- Department of Predictive Medicine,Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, HenanUniversity,Kaifeng,China
| | - Yongqiang Li
- Department of Predictive Medicine,Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, HenanUniversity,Kaifeng,China
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141
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Rhoades NS, Hendrickson SM, Prongay K, Haertel A, Gill L, Edwards RA, Garzel L, Slifka MK, Messaoudi I. Growth faltering regardless of chronic diarrhea is associated with mucosal immune dysfunction and microbial dysbiosis in the gut lumen. Mucosal Immunol 2021; 14:1113-1126. [PMID: 34158595 PMCID: PMC8379072 DOI: 10.1038/s41385-021-00418-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 02/04/2023]
Abstract
Despite the impact of childhood diarrhea on morbidity and mortality, our understanding of its sequelae has been significantly hampered by the lack of studies that examine samples across the entire intestinal tract. Infant rhesus macaques are naturally susceptible to human enteric pathogens and recapitulate the hallmarks of diarrheal disease such as intestinal inflammation and growth faltering. Here, we examined intestinal biopsies, lamina propria leukocytes, luminal contents, and fecal samples from healthy infants and those experiencing growth faltering with distant acute or chronic active diarrhea. We show that growth faltering in the presence or absence of active diarrhea is associated with a heightened systemic and mucosal pro-inflammatory state centered in the colon. Moreover, polyclonal stimulation of colonic lamina propria leukocytes resulted in a dampened cytokine response, indicative of immune exhaustion. We also detected a functional and taxonomic shift in the luminal microbiome across multiple gut sites including the migration of Streptococcus and Prevotella species between the small and large intestine, suggesting a decompartmentalization of gut microbial communities. Our studies provide valuable insight into the outcomes of diarrheal diseases and growth faltering not attainable in humans and lays the groundwork to test interventions in a controlled and reproducible setting.
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Affiliation(s)
- Nicholas S Rhoades
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Sara M Hendrickson
- Division of Neuroscience, Oregon National Primate Research Center, Portland, OR, USA
| | - Kamm Prongay
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University West Campus, Portland, OR, USA
| | - Andrew Haertel
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University West Campus, Portland, OR, USA
| | - Leanne Gill
- California National Primate Research Center, Davis, Davis, CA, USA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Laura Garzel
- California National Primate Research Center, Davis, Davis, CA, USA
| | - Mark K Slifka
- Division of Neuroscience, Oregon National Primate Research Center, Portland, OR, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA.
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142
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Xu J, Huang QY, Ge CJ. Identification of prognostic long intergenic non-coding RNAs as competing endogenous RNAs with KRAS mutations in colorectal cancer. Oncol Lett 2021; 22:717. [PMID: 34429757 PMCID: PMC8371979 DOI: 10.3892/ol.2021.12978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/28/2021] [Indexed: 01/17/2023] Open
Abstract
Colorectal cancer (CRC) is recognized as a common type of human cancer, and KRAS mutations are correlated with poor CRC survival outcomes. The evaluation and prediction of CRC results remain challenging. In the present study, RNA sequencing and clinical data from The Cancer Genome Atlas were used to identify KRAS mutation-related prognostic long intergenic non-coding RNAs (lincRNAs) in CRC. Significantly dysregulated lincRNAs and independent prognostic lincRNAs with KRAS mutations in CRC were identified. Two lincRNAs with KRAS mutations, LINC00265 and AL390719.2, were selected as key prognostic lincRNAs for both 10- and 5-year survival rates. In addition, competing endogenous (ce)RNA models were constructed to comprehensively assess the oncogenic performance of the two key lincRNAs. The ceRNA models suggested that LINC00265 and AL390719.2 are critical for the cell cycle and cancer pathways. Finally, reverse transcription-quantitative PCR was used to validate the ceRNA models in 12 pairs of CRC tissue samples. These prognostic lincRNAs may provide novel biomarkers for the prognostic prediction of CRC. The ceRNA model may also demonstrate the underlying mechanism of these lincRNAs in CRC.
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Affiliation(s)
- Jun Xu
- Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443000, P.R. China
| | - Qiu-Yun Huang
- Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443000, P.R. China
| | - Cun-Jin Ge
- Department of Gastroenterology, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443000, P.R. China
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143
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Identification of COVID-19 prognostic markers and therapeutic targets through meta-analysis and validation of Omics data from nasopharyngeal samples. EBioMedicine 2021; 70:103525. [PMID: 34392148 PMCID: PMC8358265 DOI: 10.1016/j.ebiom.2021.103525] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
Background While our battle with the COVID-19 pandemic continues, a multitude of Omics data have been generated from patient samples in various studies. Translation of these data into clinical interventions against COVID-19 remains to be accomplished. Exploring host response to COVID-19 in the upper respiratory tract can unveil prognostic markers and therapeutic targets. Methods We conducted a meta-analysis of published transcriptome and proteome profiles of respiratory samples of COVID-19 patients to shortlist high confidence upregulated host factors. Subsequently, mRNA overexpression of selected genes was validated in nasal swabs from a cohort of COVID-19 positive/negative, symptomatic/asymptomatic individuals. Guided by this analysis, we sought to check for potential drug targets. An FDA-approved drug, Auranofin, was tested against SARS-CoV-2 replication in cell culture and Syrian hamster challenge model. Findings The meta-analysis and validation in the COVID-19 cohort revealed S100 family genes (S100A6, S100A8, S100A9, and S100P) as prognostic markers of severe COVID-19. Furthermore, Thioredoxin (TXN) was found to be consistently upregulated. Auranofin, which targets Thioredoxin reductase, was found to mitigate SARS-CoV-2 replication in vitro. Furthermore, oral administration of Auranofin in Syrian hamsters in therapeutic as well as prophylactic regimen reduced viral replication, IL-6 production, and inflammation in the lungs. Interpretation Elevated mRNA level of S100s in the nasal swabs indicate severe COVID-19 disease, and FDA-approved drug Auranofin mitigated SARS-CoV-2 replication in preclinical hamster model. Funding This study was supported by the DBT-IISc partnership program (DBT (IED/4/2020-MED/DBT)), the Infosys Young Investigator award (YI/2019/1106), DBT-BIRAC grant (BT/CS0007/CS/02/20) and the DBT-Wellcome Trust India Alliance Intermediate Fellowship (IA/I/18/1/503613) to ST lab.
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144
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White K, Esparza M, Liang J, Bhat P, Naidoo J, McGovern BL, Williams MAP, Alabi BR, Shay J, Niederstrasser H, Posner B, García-Sastre A, Ready J, Fontoura BMA. Aryl Sulfonamide Inhibits Entry and Replication of Diverse Influenza Viruses via the Hemagglutinin Protein. J Med Chem 2021; 64:10951-10966. [PMID: 34260245 PMCID: PMC8900595 DOI: 10.1021/acs.jmedchem.1c00304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Influenza viruses cause approximately half a million deaths every year worldwide. Vaccines are available but partially effective, and the number of antiviral medications is limited. Thus, it is crucial to develop therapeutic strategies to counteract this major pathogen. Influenza viruses enter the host cell via their hemagglutinin (HA) proteins. The HA subtypes of influenza A virus are phylogenetically classified into groups 1 and 2. Here, we identified an inhibitor of the HA protein, a tertiary aryl sulfonamide, that prevents influenza virus entry and replication. This compound shows potent antiviral activity against diverse H1N1, H5N1, and H3N2 influenza viruses encoding HA proteins from both groups 1 and 2. Synthesis of derivatives of this aryl sulfonamide identified moieties important for antiviral activity. This compound may be considered as a lead for drug development with the intent to be used alone or in combination with other influenza A virus antivirals to enhance pan-subtype efficacy.
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Affiliation(s)
- Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Matthew Esparza
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Jue Liang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Prasanna Bhat
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Jacinth Naidoo
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Briana L McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Michael A P Williams
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Busola R Alabi
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Jerry Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Hanspeter Niederstrasser
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Bruce Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Joseph Ready
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
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145
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Taftaf R, Liu X, Singh S, Jia Y, Dashzeveg NK, Hoffmann AD, El-Shennawy L, Ramos EK, Adorno-Cruz V, Schuster EJ, Scholten D, Patel D, Zhang Y, Davis AA, Reduzzi C, Cao Y, D'Amico P, Shen Y, Cristofanilli M, Muller WA, Varadan V, Liu H. ICAM1 initiates CTC cluster formation and trans-endothelial migration in lung metastasis of breast cancer. Nat Commun 2021; 12:4867. [PMID: 34381029 PMCID: PMC8358026 DOI: 10.1038/s41467-021-25189-z] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor cell (CTC) clusters mediate metastasis at a higher efficiency and are associated with lower overall survival in breast cancer compared to single cells. Combining single-cell RNA sequencing and protein analyses, here we report the profiles of primary tumor cells and lung metastases of triple-negative breast cancer (TNBC). ICAM1 expression increases by 200-fold in the lung metastases of three TNBC patient-derived xenografts (PDXs). Depletion of ICAM1 abrogates lung colonization of TNBC cells by inhibiting homotypic tumor cell-tumor cell cluster formation. Machine learning-based algorithms and mutagenesis analyses identify ICAM1 regions responsible for homophilic ICAM1-ICAM1 interactions, thereby directing homotypic tumor cell clustering, as well as heterotypic tumor-endothelial adhesion for trans-endothelial migration. Moreover, ICAM1 promotes metastasis by activating cellular pathways related to cell cycle and stemness. Finally, blocking ICAM1 interactions significantly inhibits CTC cluster formation, tumor cell transendothelial migration, and lung metastasis. Therefore, ICAM1 can serve as a novel therapeutic target for metastasis initiation of TNBC. Circulating tumor cell (CTC) clusters are more efficient at mediating metastasis as compared to single cells and are associated with poor prognosis in breast cancer. Here, the authors show that ICAM1 is enriched in CTC clusters and its loss suppresses cell-cell interaction and CTC cluster formation, and propose ICAM1 as a therapeutic target for treating breast cancer metastasis.
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Affiliation(s)
- Rokana Taftaf
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xia Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Salendra Singh
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Yuzhi Jia
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nurmaa K Dashzeveg
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Andrew D Hoffmann
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lamiaa El-Shennawy
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Erika K Ramos
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Valery Adorno-Cruz
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Emma J Schuster
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David Scholten
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Dhwani Patel
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Youbin Zhang
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Andrew A Davis
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Carolina Reduzzi
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yue Cao
- Department of Electrical and Computer Engineering, TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA
| | - Paolo D'Amico
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - William A Muller
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Vinay Varadan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Huiping Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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146
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Liu X, Xu F, Ren L, Zhao F, Huang Y, Wei L, Wang Y, Wang C, Fan Z, Mei S, Song J, Zhao Z, Cen S, Liang C, Wang J, Guo F. MARCH8 inhibits influenza A virus infection by targeting viral M2 protein for ubiquitination-dependent degradation in lysosomes. Nat Commun 2021; 12:4427. [PMID: 34285233 PMCID: PMC8292393 DOI: 10.1038/s41467-021-24724-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/30/2021] [Indexed: 01/05/2023] Open
Abstract
The membrane-associated RING-CH (MARCH) proteins are E3 ligases that regulate the stability of various cellular membrane proteins. MARCH8 has been reported to inhibit the infection of HIV-1 and a few other viruses, thus plays an important role in host antiviral defense. However, the antiviral spectrum and the underlying mechanisms of MARCH8 are incompletely defined. Here, we demonstrate that MARCH8 profoundly inhibits influenza A virus (IAV) replication both in vitro and in mice. Mechanistically, MARCH8 suppresses IAV release through redirecting viral M2 protein from the plasma membrane to lysosomes for degradation. Specifically, MARCH8 catalyzes the K63-linked polyubiquitination of M2 at lysine residue 78 (K78). A recombinant A/Puerto Rico/8/34 virus carrying the K78R M2 protein shows greater replication and more severe pathogenicity in cells and mice. More importantly, we found that the M2 protein of the H1N1 IAV has evolved to acquire non-lysine amino acids at positions 78/79 to resist MARCH8-mediated ubiquitination and degradation. Together, our data support the important role of MARCH8 in host anti-IAV intrinsic immune defense by targeting M2, and suggest the inhibitory pressure of MARCH8 on H1N1 IAV transmission in the human population.
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Affiliation(s)
- Xiaoman Liu
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fei Zhao
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu Huang
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Liang Wei
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yingying Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Conghui Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhangling Fan
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shan Mei
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jingdong Song
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhendong Zhao
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chen Liang
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Canada
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. .,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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147
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Cox N, Crozet L, Holtman IR, Loyher PL, Lazarov T, White JB, Mass E, Stanley ER, Elemento O, Glass CK, Geissmann F. Diet-regulated production of PDGFcc by macrophages controls energy storage. Science 2021; 373:373/6550/eabe9383. [PMID: 34210853 DOI: 10.1126/science.abe9383] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 05/13/2021] [Indexed: 12/12/2022]
Abstract
The mechanisms by which macrophages regulate energy storage remain poorly understood. We identify in a genetic screen a platelet-derived growth factor (PDGF)/vascular endothelial growth factor (VEGF)-family ortholog, Pvf3, that is produced by macrophages and is required for lipid storage in fat-body cells of Drosophila larvae. Genetic and pharmacological experiments indicate that the mouse Pvf3 ortholog PDGFcc, produced by adipose tissue-resident macrophages, controls lipid storage in adipocytes in a leptin receptor- and C-C chemokine receptor type 2-independent manner. PDGFcc production is regulated by diet and acts in a paracrine manner to control lipid storage in adipose tissues of newborn and adult mice. At the organismal level upon PDGFcc blockade, excess lipids are redirected toward thermogenesis in brown fat. These data identify a macrophage-dependent mechanism, conducive to the design of pharmacological interventions, that controls energy storage in metazoans.
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Affiliation(s)
- Nehemiah Cox
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lucile Crozet
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Inge R Holtman
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
| | - Pierre-Louis Loyher
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tomi Lazarov
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Jessica B White
- Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Elvira Mass
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Developmental Biology of the Immune System, LIMES Institute, University of Bonn, 53115 Bonn, Germany
| | - E Richard Stanley
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA.,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
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148
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Gu Z, Sun Y, Wu F. Mechanism of Growth Regulation of Yeast Involving Hydrogen Sulfide From S-Propargyl-Cysteine Catalyzed by Cystathionine-γ-Lyase. Front Microbiol 2021; 12:679563. [PMID: 34276612 PMCID: PMC8285084 DOI: 10.3389/fmicb.2021.679563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022] Open
Abstract
Pathogenic fungi are recognized as a progressive threat to humans, particularly those with the immunocompromised condition. The growth of fungi is controlled by several factors, one of which is signaling molecules, such as hydrogen sulfide (H2S), which was traditionally regarded as a toxic gas without physiological function. However, recent studies have revealed that H2S is produced enzymatically and endogenously in several species, where it serves as a gaseous signaling molecule performing a variety of critical biological functions. However, the influence of this endogenous H2S on the biological activities occurring within the pathogenic fungi, such as transcriptomic and phenotypic alternations, has not been elucidated so far. Therefore, the present study was aimed to decipher this concern by utilizing S-propargyl-cysteine (SPRC) as a novel and stable donor of H2S and Saccharomyces cerevisiae as a fungal model. The results revealed that the yeast could produce H2S by catabolizing SPRC, which facilitated the growth of the yeast cells. This implies that the additional intracellularly generated H2S is generated primarily from the enhanced sulfur-amino-acid-biosynthesis pathways and serves to increase the growth rate of the yeast, and presumably the growth of the other fungi as well. In addition, by deciphering the implicated pathways and analyzing the in vitro enzymatic activities, cystathionine-γ-lyase (CYS3) was identified as the enzyme responsible for catabolizing SPRC into H2S in the yeast, which suggested that cystathionine-γ-lyase might play a significant role in the regulation of H2S-related transcriptomic and phenotypic alterations occurring in yeast. These findings provide important information regarding the mechanism underlying the influence of the gaseous signaling molecules such as H2S on fungal growth. In addition, the findings provide a better insight to the in vivo metabolism of H2S-related drugs, which would be useful for the future development of anti-fungal drugs.
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Affiliation(s)
- Zhongkai Gu
- The Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yufan Sun
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Department of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Feizhen Wu
- The Institute of Biomedical Sciences, Fudan University, Shanghai, China
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149
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Adorno-Cruz V, Hoffmann AD, Liu X, Dashzeveg NK, Taftaf R, Wray B, Keri RA, Liu H. ITGA2 promotes expression of ACLY and CCND1 in enhancing breast cancer stemness and metastasis. Genes Dis 2021; 8:493-508. [PMID: 34179312 PMCID: PMC8209312 DOI: 10.1016/j.gendis.2020.01.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/22/2020] [Accepted: 01/26/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer metastasis is largely incurable and accounts for 90% of breast cancer deaths, especially for the aggressive basal-like or triple negative breast cancer (TNBC). Combining patient database analyses and functional studies, we examined the association of integrin family members with clinical outcomes as well as their connection with previously identified microRNA regulators of metastasis, such as miR-206 that inhibits stemness and metastasis of TNBC. Here we report that the integrin receptor CD49b-encoding ITGA2, a direct target of miR-206, promotes breast cancer stemness and metastasis. ITGA2 knockdown suppressed self-renewal related mammosphere formation and pluripotency marker expression, inhibited cell cycling, compromised migration and invasion, and therefore decreased lung metastasis of breast cancer. ITGA2 overexpression reversed miR-206-caused cell cycle arrest in G1. RNA sequencing analyses revealed that ITGA2 knockdown inhibits genes related to cell cycle regulation and lipid metabolism, including CCND1 and ACLY as representative targets, respectively. Knockdown of CCND1 or ACLY inhibits mammosphere formation of breast cancer cells. Overexpression of CCND1 rescues the phenotype of ITGA2 knockdown-induced cell cycle arrest. ACLY-encoded ATP citrate lyase is essential to maintain cellular acetyl-CoA levels. CCND1 knockdown further mimics ITGA2 knockdown in abolishing lung colonization of breast cancer cells. We identified that the low levels of miR-206 as well as high expression levels of ITGA2, ACLY and CCND1 are associated with an unfavorable relapse-free survival of the patients with estrogen receptor-negative or high grade breast cancer, especially basal-like or TNBC, possibly serving as potential biomarkers of cancer stemness and therapeutic targets of breast cancer metastasis.
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Affiliation(s)
- Valery Adorno-Cruz
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 11318, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrew D. Hoffmann
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Xia Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- University of Kentucky, College of Medicine, Lexington, KY 40536, USA
| | - Nurmaa K. Dashzeveg
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rokana Taftaf
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Brian Wray
- Bioinformatic Core, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ruth A. Keri
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 11318, USA
- Department of Genetics and Genome Sciences, The Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, OH 11318, USA
| | - Huiping Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Medicine, The Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Pathology and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 11318, USA
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150
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Clapes T, Polyzou A, Prater P, Sagar, Morales-Hernández A, Ferrarini MG, Kehrer N, Lefkopoulos S, Bergo V, Hummel B, Obier N, Maticzka D, Bridgeman A, Herman JS, Ilik I, Klaeylé L, Rehwinkel J, McKinney-Freeman S, Backofen R, Akhtar A, Cabezas-Wallscheid N, Sawarkar R, Rebollo R, Grün D, Trompouki E. Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration. Nat Cell Biol 2021; 23:704-717. [PMID: 34253898 PMCID: PMC8492473 DOI: 10.1038/s41556-021-00707-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
Abstract
Haematopoietic stem cells (HSCs) are normally quiescent, but have evolved mechanisms to respond to stress. Here, we evaluate haematopoietic regeneration induced by chemotherapy. We detect robust chromatin reorganization followed by increased transcription of transposable elements (TEs) during early recovery. TE transcripts bind to and activate the innate immune receptor melanoma differentiation-associated protein 5 (MDA5) that generates an inflammatory response that is necessary for HSCs to exit quiescence. HSCs that lack MDA5 exhibit an impaired inflammatory response after chemotherapy and retain their quiescence, with consequent better long-term repopulation capacity. We show that the overexpression of ERV and LINE superfamily TE copies in wild-type HSCs, but not in Mda5-/- HSCs, results in their cycling. By contrast, after knockdown of LINE1 family copies, HSCs retain their quiescence. Our results show that TE transcripts act as ligands that activate MDA5 during haematopoietic regeneration, thereby enabling HSCs to mount an inflammatory response necessary for their exit from quiescence.
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Affiliation(s)
- Thomas Clapes
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Aikaterini Polyzou
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Pia Prater
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Sagar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Medicine II, Gastroenterology, Hepatology, Endocrinology and Infectious Diseases, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | | | - Natalie Kehrer
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Stylianos Lefkopoulos
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Veronica Bergo
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Nadine Obier
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Daniel Maticzka
- Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Josip S Herman
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Würzburg Institute of Systems Immunology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Ibrahim Ilik
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Lhéanna Klaeylé
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Rolf Backofen
- Department of Computer Science, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Nina Cabezas-Wallscheid
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
- Medical Research Council (MRC), University of Cambridge, Cambridge, UK
| | - Rita Rebollo
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, Villeurbanne, France
| | - Dominic Grün
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Würzburg Institute of Systems Immunology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany.
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