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Yamaguchi N, Sawano T, Nakatani J, Nakano-Doi A, Nakagomi T, Matsuyama T, Tanaka H. Voluntary running exercise modifies astrocytic population and features in the peri-infarct cortex. IBRO Neurosci Rep 2023; 14:253-263. [PMID: 36880055 PMCID: PMC9984846 DOI: 10.1016/j.ibneur.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Rehabilitative exercise following a brain stroke has beneficial effects on the morphological plasticity of neurons. Particularly, voluntary running exercise after focal cerebral ischemia promotes functional recovery and ameliorates ischemia-induced dendritic spine loss in the peri-infarct motor cortex layer 5. Moreover, neuronal morphology is affected by changes in the perineuronal environment. Glial cells, whose phenotypes may be altered by exercise, are known to play a pivotal role in the formation of this perineuronal environment. Herein, we investigated the effects of voluntary running exercise on glial cells after middle cerebral artery occlusion. Voluntary running exercise increased the population of glial fibrillary acidic protein-positive astrocytes born between post-operative days (POD) 0 and 3 on POD15 in the peri-infarct cortex. After exercise, transcriptomic analysis of post-ischemic astrocytes revealed 10 upregulated and 70 downregulated genes. Furthermore, gene ontology analysis showed that the 70 downregulated genes were significantly associated with neuronal morphology. In addition, exercise reduced the number of astrocytes expressing lipocalin 2, a regulator of dendritic spine density, on POD15. Our results suggest that exercise modifies the composition of astrocytic population and their phenotype.
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Key Words
- ACSA-2, astrocyte cell surface antigen-2
- Astrocytes
- BrdU, 5-bromo-2′-deoxyuridine
- Cerebral ischemia
- DEG, differentially expressed gene
- EDTA, ethylenediaminetetraacetic acid
- FBS, fetal bovine serum
- GFAP, glial fibrillary acidic protein
- GO, gene ontology
- GST-π, glutathione S-transferase-π
- Gstp1, glutathione S-transferase, pi 1
- Gstp2, glutathione S-transferase, pi 2
- Iba1, ionized calcium-binding adapter molecule 1
- Ig, immunoglobulin
- Lcn2, lipocalin 2
- MCAO, middle cerebral artery occlusion
- PBS, phosphate-buffered saline
- PFA, 4% paraformaldehyde
- POD, post-operative day
- Proliferation
- TUNEL, terminal deoxynucleotidyl transferase-mediated dUTP nick 3’-end labeling
- Transcriptome
- Vegfa, vascular endothelial growth factor A
- Voluntary running exercise
- Vtn, vitronectin
- qPCR, quantitative polymerase chain reaction
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Affiliation(s)
- Natsumi Yamaguchi
- Pharmacology Laboratory, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan.,Ritsumeikan Advanced Research Academy, 1 Nishinokyo-Suzaku-cho, Nakagyo-ku, Kyoto 604-8520, Japan
| | - Toshinori Sawano
- Pharmacology Laboratory, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Jin Nakatani
- Pharmacology Laboratory, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Akiko Nakano-Doi
- Institute for Advanced Medical Sciences, Hyogo College of Medicine, 1-1 Mukogawacho, Nishinomiya 663-8501, Japan.,Department of Therapeutic Progress in Brain Diseases, Hyogo College of Medicine, 1-1 Mukogawacho, Nishinomiya 663-8501, Japan
| | - Takayuki Nakagomi
- Institute for Advanced Medical Sciences, Hyogo College of Medicine, 1-1 Mukogawacho, Nishinomiya 663-8501, Japan.,Department of Therapeutic Progress in Brain Diseases, Hyogo College of Medicine, 1-1 Mukogawacho, Nishinomiya 663-8501, Japan
| | - Tomohiro Matsuyama
- Department of Therapeutic Progress in Brain Diseases, Hyogo College of Medicine, 1-1 Mukogawacho, Nishinomiya 663-8501, Japan
| | - Hidekazu Tanaka
- Pharmacology Laboratory, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
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Nousbeck J, McAleer MA, Irvine AD. Peripheral Blood Gene Expression Profile of Infants with Atopic Dermatitis. JID Innov 2023; 3:100165. [PMID: 36699197 PMCID: PMC9868882 DOI: 10.1016/j.xjidi.2022.100165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/06/2022] Open
Abstract
To enhance the understanding of molecular mechanisms and mine previously unidentified biomarkers of pediatric atopic dermatitis, PBMC gene expression profiles were generated by RNA sequencing in infants with atopic dermatitis and age-matched controls. A total of 178 significantly differentially expressed genes (DEGs) (115 upregulations and 63 downregulations) were seen, compared with those in healthy controls. The DEGs identified included IL1β, TNF, TREM1, IL18R1, and IL18RAP. DEGs were validated by real-time RT- qPCR in a larger number of samples from PBMCs of infants with atopic dermatitis aged <12 months. Using the DAVID (Database for Annotation, Visualization and Integrated Discovery) database, functional and pathway enrichment analyses of DEGs were performed. Gene ontology enrichment analysis showed that DEGs were associated with immune responses, inflammatory responses, regulation of immune responses, and platelet activation. Pathway analysis indicated that DEGs were enriched in cytokine‒cytokine receptor interaction, immunoregulatory interactions between lymphoid and nonlymphoid cells, hematopoietic cell lineage, phosphoinositide 3-kinase‒protein kinase B signaling pathway, NK cell‒mediated cytotoxicity, and platelet activation. Furthermore, the protein‒protein interaction network was predicted using the STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) database and visualized with Cytoscape software. Finally, on the basis of the protein‒protein interaction network, 18 hub genes were selected, and two significant modules were obtained. In conclusion, this study sheds light on the molecular mechanisms of pediatric atopic dermatitis and may provide diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Janna Nousbeck
- National Children's Research Centre, Dublin, Ireland.,Clinical Medicine, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Maeve A McAleer
- National Children's Research Centre, Dublin, Ireland.,Department of Paediatric Dermatology, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Alan D Irvine
- National Children's Research Centre, Dublin, Ireland.,Clinical Medicine, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland.,Department of Paediatric Dermatology, Children's Health Ireland at Crumlin, Dublin, Ireland
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Sato T, Head KZ, Li J, Dolin CE, Wilkey D, Skirtich N, Smith K, McCreary DD, Liu S, Beier JI, Singhi AD, McEnaney RM, Merchant ML, Arteel GE. Fibrosis resolution in the mouse liver: Role of Mmp12 and potential role of calpain 1/2. Matrix Biol Plus 2023; 17:100127. [PMID: 36632559 PMCID: PMC9826883 DOI: 10.1016/j.mbplus.2022.100127] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/05/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022] Open
Abstract
Although most work has focused on resolution of collagen ECM, fibrosis resolution involves changes to several ECM proteins. The purpose of the current study was twofold: 1) to examine the role of MMP12 and elastin; and 2) to investigate the changes in degraded proteins in plasma (i.e., the "degradome") in a preclinical model of fibrosis resolution. Fibrosis was induced by 4 weeks carbon tetrachloride (CCl4) exposure, and recovery was monitored for an additional 4 weeks. Some mice were treated with daily MMP12 inhibitor (MMP408) during the resolution phase. Liver injury and fibrosis was monitored by clinical chemistry, histology and gene expression. The release of degraded ECM peptides in the plasma was analyzed using by 1D-LC-MS/MS, coupled with PEAKS Studio (v10) peptide identification. Hepatic fibrosis and liver injury rapidly resolved in this mouse model. However, some collagen fibrils were still present 28d after cessation of CCl4. Despite this persistent collagen presence, expression of canonical markers of fibrosis were also normalized. The inhibition of MMP12 dramatically delayed fibrosis resolution under these conditions. LC-MS/MS analysis identified that several proteins were being degraded even at late stages of fibrosis resolution. Calpains 1/2 were identified as potential new proteases involved in fibrosis resolution. CONCLUSION. The results of this study indicate that remodeling of the liver during recovery from fibrosis is a complex and highly coordinated process that extends well beyond the degradation of the collagenous scar. These results also indicate that analysis of the plasma degradome may yield new insight into the mechanisms of fibrosis recovery, and by extension, new "theragnostic" targets. Lastly, a novel potential role for calpain activation in the degradation and turnover of proteins was identified.
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Affiliation(s)
- Toshifumi Sato
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, United States
| | - Kimberly Z. Head
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Jiang Li
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, United States
| | - Christine E. Dolin
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
| | - Daniel Wilkey
- Department of Medicine, Division of Nephrology and Hypertension, University of Louisville, Louisville, KY 40292, United States
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40292, United States
| | - Nolan Skirtich
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Katelyn Smith
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Dylan D. McCreary
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Sylvia Liu
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, United States
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Juliane I. Beier
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, United States
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15213, United States
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Aatur D. Singhi
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, United States
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Ryan M. McEnaney
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Michael L. Merchant
- Department of Medicine, Division of Nephrology and Hypertension, University of Louisville, Louisville, KY 40292, United States
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40292, United States
| | - Gavin E. Arteel
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, United States
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15213, United States
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Kong L, Huang Y, Zeng X, Ye C, Wu Z, Guo Y, Pan D. Effects of galactosyltransferase on EPS biosynthesis and freeze-drying resistance of Lactobacillus acidophilus NCFM. Food Chem (Oxf) 2022; 5:100145. [PMID: 36573108 PMCID: PMC9789326 DOI: 10.1016/j.fochms.2022.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/01/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
Galactosyltransferase (GalT) is an important enzyme in synthesizing exopolysaccharide (EPS), the major polymer of biofilms protecting cells from severe conditions. However, the contribution to, and regulatory mechanism of GalT, in stressor resistance are still unclear. Herein, we successfully overexpressed GalT in Lactobacillus acidophilus NCFM by genetic engineering. The GalT activity and freeze-drying survival rate of the recombinant strain were significantly enhanced. The EPS yield also increased by 17.8%, indicating a positive relationship between freeze-drying resistance and EPS. RNA-Seq revealed that GalT could regulate the flux of the membrane transport system, pivotal sugar-related metabolic pathways, and promote quorum sensing to facilitate EPS biosynthesis, which enhanced freeze-drying resistance. The findings concretely prove that the mechanism of GalT regulating EPS biosynthesis plays an important role in protecting lactic acid bacteria from freeze-drying stress.
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Key Words
- BP, biological process
- CC, cellular component
- DEG, differentially expressed gene
- ELISA, enzyme linked immunosorbent assay
- EPS, exopolysaccharideS
- Exopolysaccharide
- FT-IR, Fourier transform infrared spectroscopy
- Freeze-drying
- GO, gene ontology
- GalT, galactosyltransferase
- Galactosyltransferase
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LAB, lactic acid bacteria
- LB, Luria-Bertani
- MF, molecular function
- MRS, de Man, Rogosa and Sharpe
- NCBI, National Center for Biotechnology Information GenBank
- Overexpression
- PCR, polymerase chain reaction
- PEP, phosphoenolpyruvate
- PTS, phosphotransferase system
- QS, quorum sensing
- RT-qPCR, real-time quantitative polymerase chain reaction
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Affiliation(s)
- Lingyu Kong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Yuze Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Xiaoqun Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China,Corresponding author at: State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China.
| | - Congyan Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Zhen Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Yuxing Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210097, China
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
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Magalingam KB, Somanath SD, Haleagrahara N, Selvaduray KR, Radhakrishnan AK. Unravelling the neuroprotective mechanisms of carotenes in differentiated human neural cells: Biochemical and proteomic approaches. Food Chem (Oxf) 2022; 4:100088. [PMID: 35415676 DOI: 10.1016/j.fochms.2022.100088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 12/20/2022]
Abstract
Total mixed carotenes (TMC) protect differentiated human neural cells against 6-hydroxydopamine-induced toxicity. TMC elevated the antioxidant enzymes activities and suppressed generation of reactive oxygen species. TMC augmented the dopamine and tyrosine hydroxylase levels. TMC exerted differential protein expression in human neural cells.
Carotenoids, fat-soluble pigments found ubiquitously in plants and fruits, have been reported to exert significant neuroprotective effects against free radicals. However, the neuroprotective effects of total mixed carotenes complex (TMC) derived from virgin crude palm oil have not been studied extensively. Therefore, the present study was designed to establish the neuroprotective role of TMC on differentiated human neural cells against 6-hydroxydopamine (6-OHDA)-induced cytotoxicity. The human neural cells were differentiated using retinoic acid for six days. Then, the differentiated neural cells were pre-treated for 24 hr with TMC before exposure to 6-OHDA. TMC pre-treated neurons showed significant alleviation of 6-OHDA-induced cytotoxicity as evidenced by enhanced activity of the superoxide dismutase (SOD) and catalase (CAT) enzymes. Furthermore, TMC elevated the levels of intra-neuronal dopamine and tyrosine hydroxylase (TH) in differentiated neural cells. The 6-OHDA induced overexpression of α-synuclein was significantly hindered in neural cells pre-treated with TMC. In proteomic analysis, TMC altered the expression of ribosomal proteins, α/β isotypes of tubulins, protein disulphide isomerases (PDI) and heat shock proteins (HSP) in differentiated human neural cells. The natural palm phytonutrient TMC is a potent antioxidant with significant neuroprotective effects against free radical-induced oxidative stress.
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Key Words
- 6-OHDA, 6-hydroxydopamine
- 6-hydroxydopamine
- AD, Alzheimer’s disease
- BCM, beta-carotene-15,15′-monooxygenase
- CAT, catalase
- DRD2, dopamine receptor D2
- Dopamine
- ER, endoplasmic reticulum
- GO, gene ontology
- HSP, Heat shock protein
- HSPA9, Heat shock protein family A (HSP70) member 9
- HSPD1, Heat shock protein family D (HSP60) member 1
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LC-MS/MS, liquid chromatography-double mass spectrometry
- LDH, lactate dehydrogenase
- MCODE, minimal common oncology data elements
- MS, mass spectrometry
- Mixed carotene
- PD, Parkinson's disease
- PDI, protein disulphide isomerases
- PHB2, prohibitin 2
- PPI, protein–protein interaction
- RAN, Ras-related nuclear protein
- ROS, reactive oxygen species
- RPs, ribosomal proteins
- SH-SY5Y neuroblastoma cells
- SOD, superoxide dismutase
- TH, tyrosine hydroxylase
- TMC, total mixed carotene complex
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Yin H, Tao J, Peng Y, Xiong Y, Li B, Li S, Yang H. MSPJ: Discovering potential biomarkers in small gene expression datasets via ensemble learning. Comput Struct Biotechnol J 2022; 20:3783-3795. [PMID: 35891786 PMCID: PMC9304602 DOI: 10.1016/j.csbj.2022.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022] Open
Abstract
In transcriptomics, differentially expressed genes (DEGs) provide fine-grained phenotypic resolution for comparisons between groups and insights into molecular mechanisms underlying the pathogenesis of complex diseases or phenotypes. The robust detection of DEGs from large datasets is well-established. However, owing to various limitations (e.g., the low availability of samples for some diseases or limited research funding), small sample size is frequently used in experiments. Therefore, methods to screen reliable and stable features are urgently needed for analyses with limited sample size. In this study, MSPJ, a new machine learning approach for identifying DEGs was proposed to mitigate the reduced power and improve the stability of DEG identification in small gene expression datasets. This ensemble learning-based method consists of three algorithms: an improved multiple random sampling with meta-analysis, SVM-RFE (support vector machines-recursive feature elimination), and permutation test. MSPJ was compared with ten classical methods by 94 simulated datasets and large-scale benchmarking with 165 real datasets. The results showed that, among these methods MSPJ had the best performance in most small gene expression datasets, especially those with sample size below 30. In summary, the MSPJ method enables effective feature selection for robust DEG identification in small transcriptome datasets and is expected to expand research on the molecular mechanisms underlying complex diseases or phenotypes.
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Key Words
- AUC, area under the ROC curve (AUC)
- DEGs, differentially expressed genes
- Differentially expressed genes
- FDR, false positive rate
- Feature selection
- GA, genetic algorithm
- GEO, Gene Expression Omnibus
- GO, gene ontology
- MSPJ, the Joint method of Meta-analysis, SVM-RFE, and Permutation test
- Machine learning
- RF, random forest
- ROC, receiver operating characteristic
- Random sampling
- SAM, significance analysis of microarrays
- SMDs, standardized mean differences
- SNR, signal noise ratio
- SVM-RFE, support vector machines-recursive feature elimination
- Small sample size
- mRMR, minimum-redundancy-maximum-relevance
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Affiliation(s)
- HuaChun Yin
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing 400037, China.,College of Life Sciences, Chongqing Normal University, Chongqing 401331, China.,Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, The Army Medical University, Chongqing 400038, China
| | - JingXin Tao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Yuyang Peng
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing 400037, China
| | - Ying Xiong
- Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, The Army Medical University, Chongqing 400038, China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Song Li
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing 400037, China.,Guangyang Bay Laboratory, Chongqing Institute for Brain and Intelligence, Chongqing, China
| | - Hui Yang
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing 400037, China.,Guangyang Bay Laboratory, Chongqing Institute for Brain and Intelligence, Chongqing, China
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Albogami S. Comprehensive analysis of gene expression profiles to identify differential prognostic factors of primary and metastatic breast cancer. Saudi J Biol Sci 2022; 29:103318. [PMID: 35677896 PMCID: PMC9168623 DOI: 10.1016/j.sjbs.2022.103318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/17/2022] [Accepted: 05/19/2022] [Indexed: 12/21/2022] Open
Abstract
Breast cancer accounts for nearly half of all cancer-related deaths in women worldwide. However, the molecular mechanisms that lead to tumour development and progression remain poorly understood and there is a need to identify candidate genes associated with primary and metastatic breast cancer progression and prognosis. In this study, candidate genes associated with prognosis of primary and metastatic breast cancer were explored through a novel bioinformatics approach. Primary and metastatic breast cancer tissues and adjacent normal breast tissues were evaluated to identify biomarkers characteristic of primary and metastatic breast cancer. The Cancer Genome Atlas-breast invasive carcinoma (TCGA-BRCA) dataset (ID: HS-01619) was downloaded using the mRNASeq platform. Genevestigator 8.3.2 was used to analyse TCGA-BRCA gene expression profiles between the sample groups and identify the differentially-expressed genes (DEGs) in each group. For each group, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were used to determine the function of DEGs. Networks of protein-protein interactions were constructed to identify the top hub genes with the highest degree of interaction. Additionally, the top hub genes were validated based on overall survival and immunohistochemistry using The Human Protein Atlas. Of the top 20 hub genes identified, four (KRT14, KIT, RAD51, and TTK) were considered as prognostic risk factors based on overall survival. KRT14 and KIT expression levels were upregulated while those of RAD51 and TTK were downregulated in patients with breast cancer. The four proposed candidate hub genes might aid in further understanding the molecular changes that distinguish primary breast tumours from metastatic tumours as well as help in developing novel therapeutics. Furthermore, they may serve as effective prognostic risk markers based on the strong correlation between their expression and patient overall survival.
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Key Words
- BC, breast cancer
- BP, biological process
- Breast cancer
- CC, cellular component
- CI, confidence interval
- DEG, differentially expressed gene
- Differentially expressed genes
- FDR, false discovery rate
- GEPIA, gene expression profiling interactive analysis
- GO, gene ontology
- HR, hazard ratio
- IDC, infiltrating ductal carcinoma
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MCODE, molecular complex detection
- MF, molecular function
- Metastasis
- OS, overall survival
- Overall survival
- PPI, protein-protein interaction
- Prognostic marker
- Protein-protein interaction
- RNA-Seq, RNA sequencing
- STRING, search tool for the retrieval of interacting genes
- TCGA-BRCA, The Cancer Genome Atlas-breast invasive carcinoma
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Affiliation(s)
- Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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8
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Cao J, Li L, Xiong L, Wang C, Chen Y, Zhang X. Research on the mechanism of berberine in the treatment of COVID-19 pneumonia pulmonary fibrosis using network pharmacology and molecular docking. Phytomed Plus 2022; 2:100252. [PMID: 35403089 PMCID: PMC8895682 DOI: 10.1016/j.phyplu.2022.100252] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 05/14/2023]
Abstract
Purpose Pulmonary fibrosis caused by COVID-19 pneumonia is a serious complication of COVID-19 infection, there is a lack of effective treatment methods clinically. This article explored the mechanism of action of berberine in the treatment of COVID-19 (Corona Virus Disease 2019, COVID-19) pneumonia pulmonary fibrosis with the help of the network pharmacology and molecular docking. Methods We predicted the role of berberine protein targets with the Pharmmapper database and the 3D structure of berberine in the Pubchem database. And GeneCards database was used in order to search disease target genes and screen common target genes. Then we used STRING web to construct PPI interaction network of common target protein. The common target genes were analyzed by GO and KEGG by DAVID database. The disease-core target gene-drug network was established and molecular docking was used for prediction. We also analyzed the binding free energy and simulates molecular dynamics of complexes. Results Berberine had 250 gene targets, COVID-19 pneumonia pulmonary fibrosis had 191 gene targets, the intersection of which was 23 in common gene targets. Molecular docking showed that berberine was associated with CCl2, IL-6, STAT3 and TNF-α. GO and KEGG analysis reveals that berberine mainly plays a vital role by the signaling pathways of influenza, inflammation and immune response. Conclusion Berberine acts on TNF-α, STAT3, IL-6, CCL2 and other targets to inhibit inflammation and the activation of fibrocytes to achieve the purpose of treating COVID-19 pneumonia pulmonary fibrosis.
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Key Words
- ARDS, acute respiratory distress syndrome
- BP, biological process
- Berberine
- CC, cellular component
- CCL2, chemokine ligand2
- COVID-19
- COVID-19 pneumonia
- COVID-19, corona virus disease 2019
- ECM, extracellular matrix
- EMT, epithelial-mesenchymal cell transformation
- FOXM1, forkhead box M1
- Fsp1, fibroblast-specific protein 1
- GO, gene ontology
- HIF-1, hypoxia inducible factor
- IBD, inflammatory bowel disease
- IL-12, interleukin 12
- IL-6, interleukin 6
- JAK, Janus kinase
- KEGG, Kyoto encyclopedia of genes and genomes
- LR-MSCs, mesenchymal stem cells
- MF, molecular function
- MMP14, matrix metalloproteinase 14
- MMP7, matrix metalloproteinase 7
- Molecular docking
- NF-κB, nuclear transcription factor
- NOS, nitric oxide synthase
- Network pharmacology
- OTUB1, deubiquitinase
- PAI-1, plasminogen activator inhibitor 1
- PPI, protein-protein interaction
- Pulmonary fibrosis
- STAT3, transcription activator
- TGF-β, transforming growth factor-β
- TNF-α, tumor necrosis factor-α
- sIL-6R, interleukin 6 receptor
- α-SMA, α-smooth muscle actin
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Affiliation(s)
- Junfeng Cao
- Clinical Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Lianglei Li
- Center for Experimental Technology of Preclinical Medicine, Chengdu Medical College, No.783 Xindu Road, Xindu District, Chengdu, Sichuan 610500, China
| | - Li Xiong
- Clinical Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Chaochao Wang
- Clinical Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Yijun Chen
- Clinical Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Xiao Zhang
- Center for Experimental Technology of Preclinical Medicine, Chengdu Medical College, No.783 Xindu Road, Xindu District, Chengdu, Sichuan 610500, China
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9
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Wan R, Bai L, Cai C, Ya W, Jiang J, Hu C, Chen Q, Zhao B, Li Y. Discovery of tumor immune infiltration-related snoRNAs for predicting tumor immune microenvironment status and prognosis in lung adenocarcinoma. Comput Struct Biotechnol J 2021; 19:6386-6399. [PMID: 34938414 PMCID: PMC8649667 DOI: 10.1016/j.csbj.2021.11.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/15/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022] Open
Abstract
Lung adenocarcinoma (LUAD) has a high mortality rate and is difficult to diagnose and treat in its early stage. Previous studies have demonstrated that small nucleolar RNAs (snoRNAs) play a critical role in tumor immune infiltration and the development of a variety of solid tumors. However, there have been no studies on the correlation between tumor-infiltrating immune-related snoRNAs (TIISRs) and LUAD. In this study, we filtered six immune-related snoRNAs based on the tissue specificity index (TSI) and expression profile of all snoRNAs between all LUAD cell lines from the Cancer Cell Line Encyclopedia and 21 types of immune cells from the Gene Expression Omnibus database. Further, we performed real-time quantitative polymerase chain reaction (RT-qPCR) to validate the expression status of these snoRNAs on peripheral blood mononuclear cells (PBMCs) and lung cancer cell lines. Next, we developed a TIISR signature based on the expression profiles of snoRNAs from 479 LUAD patients filtered by the random survival forest algorithm. We then analyzed the value of this TIISR signature (TIISR risk score) for assessing tumor immune infiltration, immune checkpoint inhibitor (ICI) treatment response, and the prognosis of LUAD between groups with high and low TIISR risk score. Further, we found that the TIISR risk score groups showed significant differences in biological characteristics and that the risk score could be used to assess the level of tumor immune cell infiltration, thereby predicting prognosis and responsiveness to immunotherapy in LUAD patients.
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Key Words
- AUC, area under the curve
- CCLE, Cancer Cell Line Encyclopedia
- FPKM, fragments per kilobase of transcript per million
- GEO, Gene Expression Omnibus
- GO, gene ontology
- GSVA, gene set variation analysis
- HIC, immunohistochemistry
- HR, hazard ratio
- ICIs, immune checkpoints inhibitors
- IF, immunofluorescence
- Immune checkpoints
- LUAD, lung adenocarcinoma
- Lung adenocarcinoma
- NK cell, natural killer cell
- PBMC, Peripheral Blood Mononuclear Cell
- ROC, receiver operating characteristic
- RSF, random survival forest
- RT-qPCR, Real-time Quantitative Polymerase Chain Reaction
- Small nucleolar RNAs
- TCGA, The Cancer Genome Atlas
- TIISR signature
- TIISR, tumor-infiltrating immune-related snoRNA
- TIME, tumor immune microenvironment
- TPM, transcripts per kilobase million
- TSI, tissue specificity index
- Tumor cell immune infiltration
- ncRNA, noncoding RNA
- snoRNAs, small nucleolar RNAs
- ssGSEA, single-sample gene set enrichment analysis
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Affiliation(s)
- Rongjun Wan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Lu Bai
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Changjing Cai
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Wang Ya
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Juan Jiang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Chengping Hu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Qiong Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Bingrong Zhao
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Yuanyuan Li
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
- Corresponding author.
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10
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Jin J, Wahlang B, Thapa M, Head KZ, Hardesty JE, Srivastava S, Merchant ML, Rai SN, Prough RA, Cave MC. Proteomics and metabolic phenotyping define principal roles for the aryl hydrocarbon receptor in mouse liver. Acta Pharm Sin B 2021; 11:3806-3819. [PMID: 35024308 PMCID: PMC8727924 DOI: 10.1016/j.apsb.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/20/2022] Open
Abstract
Dioxin-like molecules have been associated with endocrine disruption and liver disease. To better understand aryl hydrocarbon receptor (AHR) biology, metabolic phenotyping and liver proteomics were performed in mice following ligand-activation or whole-body genetic ablation of this receptor. Male wild type (WT) and Ahr–/– mice (Taconic) were fed a control diet and exposed to 3,3′,4,4′,5-pentachlorobiphenyl (PCB126) (61 nmol/kg by gavage) or vehicle for two weeks. PCB126 increased expression of canonical AHR targets (Cyp1a1 and Cyp1a2) in WT but not Ahr–/–. Knockouts had increased adiposity with decreased glucose tolerance; smaller livers with increased steatosis and perilipin-2; and paradoxically decreased blood lipids. PCB126 was associated with increased hepatic triglycerides in Ahr–/–. The liver proteome was impacted more so by Ahr–/– genotype than ligand-activation, but top gene ontology (GO) processes were similar. The PCB126-associated liver proteome was Ahr-dependent. Ahr principally regulated liver metabolism (e.g., lipids, xenobiotics, organic acids) and bioenergetics, but it also impacted liver endocrine response (e.g., the insulin receptor) and function, including the production of steroids, hepatokines, and pheromone binding proteins. These effects could have been indirectly mediated by interacting transcription factors or microRNAs. The biologic roles of the AHR and its ligands warrant more research in liver metabolic health and disease.
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Key Words
- AHR
- AHR, aryl hydrocarbon receptor
- ALT, alanine transaminase
- ANOVA, analysis of variance
- AST, aspartate transaminase
- AUC, area under the curve
- CAR, constitutive androstane receptor
- CD36, cluster of differentiation 36
- CYP, cytochrome P450
- EPF, enrichment by protein function
- Endocrine disruption
- Environmental liver disease
- FDR, false discovery rate
- FGF21, fibroblast growth factor 21
- GCR, glucocorticoid receptor
- GO, gene ontology
- H&E, hematoxylin-eosin
- HDL, high-density lipoprotein
- HFD, high fat diet
- IGF1, insulin-like growth factor 1
- IL-6, interleukin 6
- IPF, interaction by protein function
- LDL, low-density lipoprotein
- MCP-1, monocyte chemoattractant protein-1
- MUP, major urinary protein
- NAFLD, non-alcoholic fatty liver disease
- NFKBIA, nuclear factor kappa-inhibitor alpha
- Nonalcoholic fatty liver disease
- PAI-1, plasminogen activator inhibitor-1
- PCB, polychlorinated biphenyl
- PCB126
- PLIN2, perilipin-2
- PNPLA3, patatin-like phospholipase domain-containing protein 3
- PPARα, peroxisome proliferator-activated receptor alpha
- PXR, pregnane-xenobiotic receptor
- Perilipin-2
- Pheromones
- SGK1, serum/glucocorticoid regulated kinase
- TAFLD, toxicant-associated fatty liver disease
- TASH, toxicant-associated steatohepatitis
- TAT, tyrosine aminotransferase
- TMT, tandem mass tag
- VLDL, very low-density lipoprotein
- WT, wild type
- ZFP125, zinc finger protein 125
- miR, microRNA
- nHDLc, non-HDL cholesterol
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Oh NA, Hong X, Doulamis IP, Meibalan E, Peiseler T, Melero-Martin J, García-Cardeña G, Del Nido PJ, Friehs I. Abnormal Flow Conditions Promote Endocardial Fibroelastosis Via Endothelial-to-Mesenchymal Transition, Which Is Responsive to Losartan Treatment. JACC Basic Transl Sci 2021; 6:984-999. [PMID: 35024504 PMCID: PMC8733675 DOI: 10.1016/j.jacbts.2021.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022]
Abstract
EFE is a congenital cardiac pathology contributing to increased morbidity and mortality. The pathologic triggers of EFE remain to be characterized. To determine whether abnormal flow promotes EFE development, we used in vivo neonatal rodent surgical models and an in vitro model using human primary endocardial cells We established novel surgical model with flow profiles seen in patients that develop EFE. Static and turbulent flow conditions promoted EFE development in neonatal rodent hearts. Losartan treatment is shown to significantly ameliorate EFE progression and decreases mRNA and protein expression of EndoMT markers in neonatal rodent hearts. RNAseq analysis of human endocardial cells subjected to different flow conditions show that normal flow suppresses gene expression critical for mesenchymal differentiation and Notch signaling.
Endocardial fibroelastosis (EFE) is defined by fibrotic tissue on the endocardium and forms partly through aberrant endothelial-to-mesenchymal transition. However, the pathologic triggers are still unknown. In this study, we showed that abnormal flow induces EFE partly through endothelial-to-mesenchymal transition in a rodent model, and that losartan can abrogate EFE development. Furthermore, we translated our findings to human endocardial endothelial cells, and showed that laminar flow promotes the suppression of genes associated with mesenchymal differentiation. These findings emphasize the role of flow in promoting EFE in endocardial endothelial cells and provide a novel potential therapy to treat this highly morbid condition.
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Key Words
- AR, aortic regurgitation
- EFE, endocardial fibroelastosis
- EndoMT, endothelial-to-mesenchymal transition
- GO, gene ontology
- HLHS, hypoplastic left heart syndrome
- HUEEC, human endocardial endothelial cells
- HUVEC, human umbilical vein endothelial cells
- LSS, laminar shear stress
- LV, left ventricle
- congenital heart disease
- endocardial endothelial cells
- endocardial fibroelastosis
- endothelial-to-mesenchymal transition
- wall shear stress
- α-SMA, alpha-smooth muscle actin
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Affiliation(s)
- Nicholas A Oh
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Cardiothoracic Surgery, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Xuechong Hong
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Ilias P Doulamis
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Elamaran Meibalan
- Laboratory for Systems Mechanobiology, Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Teresa Peiseler
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Juan Melero-Martin
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Guillermo García-Cardeña
- Laboratory for Systems Mechanobiology, Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Pedro J Del Nido
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Ingeborg Friehs
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
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Xu L, Yin L, Qi Y, Tan X, Gao M, Peng J. 3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing. Acta Pharm Sin B 2021; 11:3150-3164. [PMID: 34729306 PMCID: PMC8546856 DOI: 10.1016/j.apsb.2021.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/30/2021] [Accepted: 02/07/2021] [Indexed: 12/12/2022] Open
Abstract
The three-dimensional (3D) conformation of chromatin is integral to the precise regulation of gene expression. The 3D genome and genomic variations in non-alcoholic fatty liver disease (NAFLD) are largely unknown, despite their key roles in cellular function and physiological processes. High-throughput chromosome conformation capture (Hi-C), Nanopore sequencing, and RNA-sequencing (RNA-seq) assays were performed on the liver of normal and NAFLD mice. A high-resolution 3D chromatin interaction map was generated to examine different 3D genome hierarchies including A/B compartments, topologically associated domains (TADs), and chromatin loops by Hi-C, and whole genome sequencing identifying structural variations (SVs) and copy number variations (CNVs) by Nanopore sequencing. We identified variations in thousands of regions across the genome with respect to 3D chromatin organization and genomic rearrangements, between normal and NAFLD mice, and revealed gene dysregulation frequently accompanied by these variations. Candidate target genes were identified in NAFLD, impacted by genetic rearrangements and spatial organization disruption. Our data provide a high-resolution 3D genome interaction resource for NAFLD investigations, revealed the relationship among genetic rearrangements, spatial organization disruption, and gene regulation, and identified candidate genes associated with these variations implicated in the pathogenesis of NAFLD. The newly findings offer insights into novel mechanisms of NAFLD pathogenesis and can provide a new conceptual framework for NAFLD therapy.
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Key Words
- 3C, chromosome conformation capture
- 3D genome
- 3D, three-dimensional
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- Abcg5, ATP-binding cassette sub-family G member 5
- BWA, Burrows-Wheeler Aligner
- CNV, copy number variation
- Camk1d, calcium/calmodulin-dependent protein kinase type 1D
- Chr, chromosome
- Chromatin looping
- DEG, differentially expressed gene
- DEL, deletion
- DI, directionality index
- DUP, duplication
- Elovl6, elongation of very long chain fatty acids protein 6
- FDR, false discovery rate
- FFA, free fatty acid
- Fgfr2, fibroblast growth factor receptor 2
- GCKR, glucokinase regulator
- GO, gene ontology
- GSH, glutathione
- Gadd45g, growth arrest and DNA damage-inducible protein GADD45 gamma
- Grm8, metabotropic glutamate receptor 8
- Gsta1, glutathione S-transferase A1
- H&E, hematoxylin-eosin
- HFD, high-fat diet
- HSD17B13, hydroxysteroid 17-beta dehydrogenase 13
- Hi-C, high-throughput chromosome conformation capture
- IDE, interaction decay exponent
- INS, insertion
- INV, inversion
- IR, inclusion ratio
- IRGM, immunity related GTPase M
- IRS4, insulin receptor substrate 4
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- Kcnma1, calcium-activated potassium channel subunit alpha-1
- LPIN1, lipin 1
- MBOAT7, membrane bound O-acyltransferase domain containing 7
- MDA, malondialdehyde
- NAFLD, non-alcoholic fatty liver disease
- NF1, neurofibromin 1
- NGS, next-generation sequencing
- NOTCH1, notch receptor 1
- ONT, Oxford Nanopore Technologies
- PCA, principal component analysis
- PNPLA3, patatin like phospholipase domain containing 3
- PPP1R3B, protein phosphatase 1 regulatory subunit 3B
- PTEN, phosphatase and tensin homolog
- Pde4b, phosphodiesterase 4B
- Plce1, 1-phosphat-idylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
- Plxnb1, Plexin-B1
- RB1, RB transcriptional corepressor 1
- RNA-seq, RNA-sequencing
- SD, standard deviation
- SOD, superoxide dismutase
- SV, structural variation
- Scd1, acyl-CoA desaturase 1
- Sugct, succinate-hydroxymethylglutarate CoA-transferase
- TAD, topologically associated domain
- TC, total cholesterol
- TG, triglyceride
- TM6SF2, transmembrane 6 superfamily member 2
- TP53, tumor protein p53
- TRA, translocation
- Topologically associated domain
- Transcriptome
- WGS, whole-genome sequencing
- Whole-genome sequencing
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Zhang H, Luo YB, Wu W, Zhang L, Wang Z, Dai Z, Feng S, Cao H, Cheng Q, Liu Z. The molecular feature of macrophages in tumor immune microenvironment of glioma patients. Comput Struct Biotechnol J 2021; 19:4603-18. [PMID: 34471502 DOI: 10.1016/j.csbj.2021.08.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Background Gliomas are one of the most common types of primary tumors in central nervous system. Previous studies have found that macrophages actively participate in tumor growth. Methods Weighted gene co-expression network analysis was used to identify meaningful macrophage-related gene genes for clustering. Pamr, SVM, and neural network were applied for validating clustering results. Somatic mutation and methylation were used for defining the features of identified clusters. Differentially expressed genes (DEGs) between the stratified groups after performing elastic regression and principal component analyses were used for the construction of MScores. The expression of macrophage-specific genes were evaluated in tumor microenvironment based on single cell sequencing analysis. A total of 2365 samples from 15 glioma datasets and 5842 pan-cancer samples were used for external validation of MScore. Results Macrophages were identified to be negatively associated with the survival of glioma patients. Twenty-six macrophage-specific DEGs obtained by elastic regression and PCA were highly expressed in macrophages at single-cell level. The prognostic value of MScores in glioma was validated by the active proinflammatory and metabolic profile of infiltrating microenvironment and response to immunotherapies of samples with this signature. MScores managed to stratify patient survival probabilities in 15 external glioma datasets and pan-cancer datasets, which predicted worse survival outcome. Sequencing data and immunohistochemistry of Xiangya glioma cohort confirmed the prognostic value of MScores. A prognostic model based on MScores demonstrated high accuracy rate. Conclusion Our findings strongly support a modulatory role of macrophages, especially M2 macrophages in glioma progression and warrants further experimental studies.
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Key Words
- ACC, Adrenocortical carcinoma
- BBB, brain blood barrier
- BLCA, Bladder Urothelial Carcinoma
- BRCA, Breast invasive carcinoma
- CDF, cumulative distribution function
- CESC, Cervical squamous cell carcinoma and endocervical adenocarcinoma
- CGGA, Chinese Glioma Genome Atlas
- CHOL, Cholangiocarcinoma
- CNA, copy number alternations
- CNV, copy number variation
- COAD, Colon adenocarcinoma
- CSF-1, colony-stimulating factor-1
- DLBC, Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
- DMP, differentially methylated position
- ESCA, Esophageal carcinoma
- GBM, glioblastoma
- GEO, Gene Expression Omnibus
- GO, gene ontology
- GSEA, gene set enrichment analysis
- GSVA, gene set variation analysis
- Glioma microenvironment
- HNSC, Head and Neck squamous cell carcinoma
- IGR, intergenic region
- IHC, immunohistochemistry
- IL, interleukin
- Immunotherapy
- KEGG, Kyoto Encyclopaedia of Genes and Genomes
- KICH, Kidney Chromophobe
- KIRC, Kidney renal clear cell carcinoma
- KIRP, Kidney renal papillary cell carcinoma
- LGG, low grade glioma
- LIHC, Liver hepatocellular carcinoma
- LUAD, Lung adenocarcinoma
- LUSC, Lung squamous cell carcinoma
- MMP-2, matrix metalloproteinase-2
- MT1, MMP membrane type 1 matrix metalloprotease
- Machine learning
- Macrophage
- OV, Ovarian serous cystadenocarcinoma
- PAAD, Pancreatic adenocarcinoma
- PAM, partition around medoids
- PCA, principal component analysis
- PCPG, Pheochromocytoma and Paraganglioma
- PRAD, Prostate adenocarcinoma
- Prognostic model
- READ, Rectum adenocarcinoma
- SARC, Sarcoma
- SKCM, Skin Cutaneous Melanoma
- SNP, single-nucleotide polymorphism
- SNV, single-nucleotide variant
- STAD, Stomach adenocarcinoma
- SVM, Support Vector Machines
- TAM, tumor associated macrophage
- TCGA, The Cancer Genome Atlas
- TGF-β, tumor growth factor-β
- THCA, Thyroid carcinoma
- THYM, Thymoma
- TIMP-2, tissue inhibitor of metalloproteinase-2
- TLR2, toll-like receptor 2
- TME, tumor microenvironment
- TNFα, tumor necrosis factor α
- TSS, transcription start site
- UCEC, Uterine Corpus Endometrial Carcinoma
- UCS, Uterine Carcinosarcoma
- WGCNA, weighted gene co-expression network analysis
- pamr, prediction analysis for microarrays
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Gibb AA, Murray EK, Eaton DM, Huynh AT, Tomar D, Garbincius JF, Kolmetzky DW, Berretta RM, Wallner M, Houser SR, Elrod JW. Molecular Signature of HFpEF: Systems Biology in a Cardiac-Centric Large Animal Model. JACC Basic Transl Sci 2021; 6:650-672. [PMID: 34466752 PMCID: PMC8385567 DOI: 10.1016/j.jacbts.2021.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/11/2021] [Accepted: 07/11/2021] [Indexed: 12/30/2022]
Abstract
In this study the authors used systems biology to define progressive changes in metabolism and transcription in a large animal model of heart failure with preserved ejection fraction (HFpEF). Transcriptomic analysis of cardiac tissue, 1-month post-banding, revealed loss of electron transport chain components, and this was supported by changes in metabolism and mitochondrial function, altogether signifying alterations in oxidative metabolism. Established HFpEF, 4 months post-banding, resulted in changes in intermediary metabolism with normalized mitochondrial function. Mitochondrial dysfunction and energetic deficiencies were noted in skeletal muscle at early and late phases of disease, suggesting cardiac-derived signaling contributes to peripheral tissue maladaptation in HFpEF. Collectively, these results provide insights into the cellular biology underlying HFpEF progression.
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Key Words
- BCAA, branched chain amino acids
- DAG, diacylglycerol
- ECM, extracellular matrix
- EF, ejection fraction
- ESI, electrospray ionization
- ETC, electron transport chain
- FC, fold change
- FDR, false discovery rate
- GO, gene ontology
- HF, heart failure
- HFpEF, heart failure with preserved ejection fraction
- HFrEF, heart failure with reduced ejection fraction
- LA, left atrial
- LAV, left atrial volume
- LV, left ventricle/ventricular
- MS/MS, tandem mass spectrometry
- RCR, respiratory control ratio
- RI, retention index
- UPLC, ultraperformance liquid chromatography
- heart failure
- m/z, mass to charge ratio
- metabolomics
- mitochondria
- preserved ejection fraction
- systems biology
- transcriptomics
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Affiliation(s)
- Andrew A. Gibb
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Emma K. Murray
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Deborah M. Eaton
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Anh T. Huynh
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Dhanendra Tomar
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Joanne F. Garbincius
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Devin W. Kolmetzky
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Remus M. Berretta
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Markus Wallner
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
- Division of Cardiology, Medical University of Graz, Graz, Austria
- Center for Biomarker Research in Medicine, CBmed GmbH, Graz, Austria
| | - Steven R. Houser
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - John W. Elrod
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
- Address for correspondence: Dr John W. Elrod, Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, MERB 949, Philadelphia, Pennsylvania 19140, USA.
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Liu Q, Nie R, Li M, Li L, Zhou H, Lu H, Wang X. Identification of subtypes correlated with tumor immunity and immunotherapy in cutaneous melanoma. Comput Struct Biotechnol J 2021; 19:4472-4485. [PMID: 34471493 PMCID: PMC8379294 DOI: 10.1016/j.csbj.2021.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 01/15/2023] Open
Abstract
Because immune checkpoint inhibitors (ICIs) are effective for a subset of melanoma patients, identification of melanoma subtypes responsive to ICIs is crucial. We performed clustering analyses to identify immune subtypes of melanoma based on the enrichment levels of 28 immune cells using transcriptome datasets for six melanoma cohorts, including four cohorts not treated with ICIs and two cohorts treated with ICIs. We identified three immune subtypes (Im-H, Im-M, and Im-L), reproducible in these cohorts. Im-H displayed strong immune signatures, low stemness and proliferation potential, genomic stability, high immunotherapy response rate, and favorable prognosis. Im-L showed weak immune signatures, high stemness and proliferation potential, genomic instability, low immunotherapy response rate, and unfavorable prognosis. The pathways highly enriched in Im-H included immune, MAPK, apoptosis, calcium, VEGF, cell adhesion molecules, focal adhesion, gap junction, and PPAR. The pathways highly enriched in Im-L included Hippo, cell cycle, and ErbB. Copy number alterations correlated inversely with immune signatures in melanoma, while tumor mutation burden showed no significant correlation. The molecular features correlated with favorable immunotherapy response included immune-promoting signatures and pathways of PPAR, MAPK, VEGF, calcium, and glycolysis/gluconeogenesis. Our data recapture the immunological heterogeneity in melanoma and provide clinical implications for the immunotherapy of melanoma.
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Key Words
- Clustering analysis
- DMFS, distant-metastasis free survival
- DSS, disease-specific survival
- EMT, epithelial-mesenchymal transition
- FDR, false discovery rate
- GO, gene ontology
- GSEA, gene-set enrichment analysis
- HLA, human leukocyte antigen
- HRD, homologous recombination deficiency
- ICIs, immune checkpoint inhibitors
- Immune subtypes
- Immunotherapy
- MDSC, myeloid-derived suppressor cell
- Melanoma
- NK, natural killer
- OS, overall survival
- SCNAs, somatic copy number alterations
- TCGA, The Cancer Genome Atlas
- TIME, tumor immune microenvironment
- TMB, tumor mutation burden
- TME, tumor microenvironment
- Tumor immune microenvironment
- WGCNA, weighted gene co-expression network analysis
- ssGSEA, single-sample gene-set enrichment analysis
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Affiliation(s)
- Qian Liu
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Rongfang Nie
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Mengyuan Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Lin Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Haiying Zhou
- Department of Orthopedics, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Hui Lu
- Department of Orthopedics, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
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Ushijima H, Monzaki R, Funakoshi M. Analysis of differentially expressed genes responsible for the suppressive effect of anisomycin on cell proliferation of DLD-1 cells. Biochem Biophys Rep 2021; 27:101038. [PMID: 34151031 PMCID: PMC8190440 DOI: 10.1016/j.bbrep.2021.101038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
Anisomycin is used as a chemical compound that possesses c-Jun N-terminal kinase (JNK)-activating effects. Recently, the potent anti-tumor effects of anisomycin have received much attention. In addition to its JNK-activating effects, anisomycin has been reported to affect gene expression in osteosarcoma, leukemia, hepatocellular carcinoma, ovarian cancer and other cancers. We previously demonstrated that anisomycin induced the degradation of transcription factor GATA-6 in DLD-1 cells (a colorectal cancer cell line) and inhibited their proliferation. However, the details of the gene network involved in the process remain unclear. In this study, we conducted an RNA-seq analysis of differentially expressed genes (DEGs) in anisomycin-treated DLD-1 cells to identify the molecular process of growth-suppressive genes. We found that LAMB3, which regulates cell adhesion and migration, and NFKB2 were down-regulated by anisomycin. In addition, the mRNA expression of several tumor suppressor genes (ATF3, ERRFI1, KLF6, and AKAP12) was transiently enhanced at 3 h after anisomycin treatment. These results suggest that anisomycin blocks a PI3K/Akt-signaling cascade to lead to the suppression of cell growth.
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Affiliation(s)
- Hironori Ushijima
- Department of Analytical Biochemistry, School of Pharmacy, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Shiwa-gun, Iwate, 0283694, Japan
| | - Rina Monzaki
- Department of Analytical Biochemistry, School of Pharmacy, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Shiwa-gun, Iwate, 0283694, Japan
| | - Mika Funakoshi
- Department of Analytical Biochemistry, School of Pharmacy, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Shiwa-gun, Iwate, 0283694, Japan
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Payen VL, Lavergne A, Alevra Sarika N, Colonval M, Karim L, Deckers M, Najimi M, Coppieters W, Charloteaux B, Sokal EM, El Taghdouini A. Single-cell RNA sequencing of human liver reveals hepatic stellate cell heterogeneity. JHEP Rep 2021; 3:100278. [PMID: 34027339 PMCID: PMC8121977 DOI: 10.1016/j.jhepr.2021.100278] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 02/11/2021] [Accepted: 02/28/2021] [Indexed: 02/07/2023] Open
Abstract
Background & Aims The multiple vital functions of the human liver are performed by highly specialised parenchymal and non-parenchymal cells organised in complex collaborative sinusoidal units. Although crucial for homeostasis, the cellular make-up of the human liver remains to be fully elucidated. Here, single-cell RNA-sequencing was used to unravel the heterogeneity of human liver cells, in particular of hepatocytes (HEPs) and hepatic stellate cells (HSCs). Method The transcriptome of ~25,000 freshly isolated human liver cells was profiled using droplet-based RNA-sequencing. Recently published data sets and RNA in situ hybridisation were integrated to validate and locate newly identified cell populations. Results In total, 22 cell populations were annotated that reflected the heterogeneity of human parenchymal and non-parenchymal liver cells. More than 20,000 HEPs were ordered along the portocentral axis to confirm known, and reveal previously undescribed, zonated liver functions. The existence of 2 subpopulations of human HSCs with unique gene expression signatures and distinct intralobular localisation was revealed (i.e. portal and central vein-concentrated GPC3+ HSCs and perisinusoidally located DBH+ HSCs). In particular, these data suggest that, although both subpopulations collaborate in the production and organisation of extracellular matrix, GPC3+ HSCs specifically express genes involved in the metabolism of glycosaminoglycans, whereas DBH+ HSCs display a gene signature that is reminiscent of antigen-presenting cells. Conclusions This study highlights metabolic zonation as a key determinant of HEP transcriptomic heterogeneity and, for the first time, outlines the existence of heterogeneous HSC subpopulations in the human liver. These findings call for further research on the functional implications of liver cell heterogeneity in health and disease. Lay summary This study resolves the cellular landscape of the human liver in an unbiased manner and at high resolution to provide new insights into human liver cell biology. The results highlight the physiological heterogeneity of human hepatic stellate cells. A cell atlas from the near-native transcriptome of >25,000 human liver cells is presented. Hepatocytes were ordered along the portocentral axis to reveal previously undescribed gene expression patterns and zonated liver functions. Two subpopulations of human hepatic stellate cells (HSCs) are reported, characterised by different spatial distribution in the native tissue. Characteristic gene signatures of HSC subpopulations are suggestive of far-reaching functional differences.
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Key Words
- BSA, bovine serum albumin
- CC, cholangiocyte
- CV, central vein
- DEG, differentially expressed gene
- EC, endothelial cell
- ECM, extracellular matrix
- Extracellular matrix
- FFPE, formaldehyde-fixed paraffin embedded
- GAG, glycosaminoglycan
- GEO, Gene Expression Omnibus
- GO, gene ontology
- HEP, hepatocyte
- HLA, human leukocyte antigen
- HRP, horseradish peroxidase
- HSC, hepatic stellate cell
- Hepatocyte
- ISH, in situ hybridisation
- KLR, killer lectin-like receptor
- LP, lymphoid cell
- Liver cell atlas
- MP, macrophage
- MZ, midzonal
- PC, pericentral
- PP, periportal
- PV, portal vein
- TBS, Tris buffered saline
- TSA, tyramide signal amplification
- UMAP, uniform manifold approximation and projection
- UMI, unique molecular identifier
- VIM, vimentin
- Zonation
- scRNA-seq, single-cell RNA-sequencing
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Affiliation(s)
- Valéry L. Payen
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Laboratory of Advanced Drug Delivery and Biomaterials (ADDB), LDRI Institute, Université catholique de Louvain, Brussels, Belgium
| | - Arnaud Lavergne
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Niki Alevra Sarika
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Laboratory of Advanced Drug Delivery and Biomaterials (ADDB), LDRI Institute, Université catholique de Louvain, Brussels, Belgium
| | - Megan Colonval
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Latifa Karim
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Manon Deckers
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Mustapha Najimi
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
| | - Wouter Coppieters
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | | | - Etienne M. Sokal
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Corresponding authors. Address: Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Avenue Mounier 52 Box B1.52.03, 1200 Brussels, Belgium.
| | - Adil El Taghdouini
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Corresponding authors. Address: Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Avenue Mounier 52 Box B1.52.03, 1200 Brussels, Belgium.
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Nazarov PV, Kreis S. Integrative approaches for analysis of mRNA and microRNA high-throughput data. Comput Struct Biotechnol J 2021; 19:1154-1162. [PMID: 33680358 PMCID: PMC7895676 DOI: 10.1016/j.csbj.2021.01.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Review on tools and databases linking miRNA and its mRNA targetome. Databases show little overlap in miRNA targetome predictions suggesting strong contextual effects. Deconvolution and deep learning approaches are promising new approaches to improve miRNA targetome predictions.
Advanced sequencing technologies such as RNASeq provide the means for production of massive amounts of data, including transcriptome-wide expression levels of coding RNAs (mRNAs) and non-coding RNAs such as miRNAs, lncRNAs, piRNAs and many other RNA species. In silico analysis of datasets, representing only one RNA species is well established and a variety of tools and pipelines are available. However, attaining a more systematic view of how different players come together to regulate the expression of a gene or a group of genes requires a more intricate approach to data analysis. To fully understand complex transcriptional networks, datasets representing different RNA species need to be integrated. In this review, we will focus on miRNAs as key post-transcriptional regulators summarizing current computational approaches for miRNA:target gene prediction as well as new data-driven methods to tackle the problem of comprehensively and accurately dissecting miRNome-targetome interactions.
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Key Words
- CCA, canonical correlation analysis
- CDS, coding sequence
- CLASH, cross-linking, ligation and sequencing of hybrids
- CLIP, cross-linking immunoprecipitation
- CNN, convolutional neural network
- Data integration
- GO, gene ontology
- ICA, independent component analysis
- Matrix factorization
- NGS, next-generation sequencing
- NMF, non-negative matrix factorization
- PCA, principal component analysis
- RNASeq, high-throughput RNA sequencing
- TDMD, target RNA-directed miRNA degradation
- TF, transcription factors
- Target prediction
- Transcriptomics
- circRNA, circular RNA
- lncRNA, long non-coding RNA
- mRNA, messenger RNA
- miRNA, microRNA
- microRNA
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Affiliation(s)
- Petr V Nazarov
- Multiomics Data Science Research Group, Department of Oncology & Quantitative Biology Unit, Luxembourg Institute of Health (LIH), Strassen L-1445, Luxembourg
| | - Stephanie Kreis
- Signal Transduction Group, Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
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Eagleson KL, Villaneuva M, Southern RM, Levitt P. Proteomic and mitochondrial adaptations to early-life stress are distinct in juveniles and adults. Neurobiol Stress 2020; 13:100251. [PMID: 33344706 DOI: 10.1016/j.ynstr.2020.100251] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/02/2020] [Accepted: 09/10/2020] [Indexed: 12/26/2022] Open
Abstract
Exposure to early-life stress (ELS) increases risk for poor mental and physical health outcomes that emerge at different stages across the lifespan. Yet, how age interacts with ELS to impact the expression of specific phenotypes remains largely unknown. An established limited-bedding paradigm was used to induce ELS in mouse pups over the early postnatal period. Initial analyses focused on the hippocampus, based on documented sensitivity to ELS in humans and various animal models, and the large body of data reporting anatomical and physiological outcomes in this structure using this ELS paradigm. An unbiased discovery proteomics approach revealed distinct adaptations in the non-nuclear hippocampal proteome in male versus female offspring at two distinct developmental stages: juvenile and adult. Gene ontology and KEGG pathway analyses revealed significant enrichment in proteins associated with mitochondria and the oxidative phosphorylation (OXPHOS) pathway in response to ELS in female hippocampus only. To determine whether the protein adaptations to ELS reflected altered function, mitochondrial respiration (driven through complexes II-IV) and complex I activity were measured in isolated hippocampal mitochondria using a Seahorse X96 Flux analyzer and immunocapture ELISA, respectively. ELS had no effect on basal respiration in either sex at either age. In contrast, ELS increased OXPHOS capacity in juvenile males and females, and reduced OXPHOS capacity in adult females but not adult males. A similar pattern of ELS-induced changes was observed for complex I activity. These data suggest that initial adaptations in juvenile hippocampus due to ELS were not sustained in adults. Mitochondrial adaptations to ELS were also exhibited peripherally by liver. Overall, the temporal distinctions in mitochondrial responses to ELS show that ELS-generated adaptations and outcomes are complex over the lifespan. This may contribute to differences in the timing of appearance of mental and physical disturbances, as well as potential sex differences that influence only select outcomes.
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Key Words
- AA, antimycin A
- ADP, adenosine diphosphate
- CI, confidence interval
- Complex I activity
- ELS, early-life stress
- Early-life stress
- FCCP, carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone
- GO, gene ontology
- HCD, high energy C-trap dissociation
- Hippocampus
- Liver
- MS/MS, tandem mass spectrometry
- Mitochondrial respiration
- OCR, oxygen consumption rate
- OXPHOS, oxidative phosphorylation
- P, postnatal day
- Proteomics
- SCX, strong cation exchange
- iTRAQ, isobaric tag for relative and absolute quantitation
- oligo, oligomycin
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Zhang Z, Li L, Li M, Wang X. The SARS-CoV-2 host cell receptor ACE2 correlates positively with immunotherapy response and is a potential protective factor for cancer progression. Comput Struct Biotechnol J. 2020;18:2438-2444. [PMID: 32905022 PMCID: PMC7462778 DOI: 10.1016/j.csbj.2020.08.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/23/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 29 million people and has caused more than 900,000 deaths worldwide as of September 14, 2020. The SARS-CoV-2 human cell receptor ACE2 has recently received extensive attention for its role in SARS-CoV-2 infection. Many studies have also explored the association between ACE2 and cancer. However, a systemic investigation into associations between ACE2 and oncogenic pathways, tumor progression, and clinical outcomes in pan-cancer remains lacking. Using cancer genomics datasets from the Cancer Genome Atlas (TCGA) program, we performed computational analyses of associations between ACE2 expression and antitumor immunity, immunotherapy response, oncogenic pathways, tumor progression phenotypes, and clinical outcomes in 13 cancer cohorts. We found that ACE2 upregulation was associated with increased antitumor immune signatures and PD-L1 expression, and favorable anti-PD-1/PD-L1/CTLA-4 immunotherapy response. ACE2 expression levels inversely correlated with the activity of cell cycle, mismatch repair, TGF-β, Wnt, VEGF, and Notch signaling pathways. Moreover, ACE2 expression levels had significant inverse correlations with tumor proliferation, stemness, and epithelial-mesenchymal transition. ACE2 upregulation was associated with favorable survival in pan-cancer and in multiple individual cancer types. These results suggest that ACE2 is a potential protective factor for cancer progression. Our data may provide potential clinical implications for treating cancer patients infected with SARS-CoV-2.
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Key Words
- ACE2 expression
- ACE2, angiotensin-converting enzyme 2
- CESC, cervical squamous-cell carcinoma
- COAD, colon adenocarcinoma
- DFI, disease-free interval
- DSS, disease-specific survival
- EMT, epithelial-mesenchymal transition
- ESCA, esophageal carcinoma
- FDR, false discovery rate
- GO, gene ontology
- GSEA, gene set enrichment analysis
- HNSC, head and neck squamous cell carcinoma
- KIRC, kidney renal clear cell carcinoma
- KIRP, kidney renal papillary cell carcinoma
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- OS, overall survival
- OV, ovarian carcinoma
- PAAD, pancreatic adenocarcinoma
- PFI, progression-free interval
- Pan-cancer
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SKCM, skin cutaneous melanoma
- Survival prognosis
- TCGA, The Cancer Genome Atlas
- TF, transcription factor
- THYM, thymoma
- Tumor immunity and immunotherapy
- Tumor progression
- UCEC, uterine corpus endometrial carcinoma
- WGCNA, weighted gene co-expression network analysis
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McCabe MC, Hill RC, Calderone K, Cui Y, Yan Y, Quan T, Fisher GJ, Hansen KC. Alterations in extracellular matrix composition during aging and photoaging of the skin. Matrix Biol Plus 2020; 8:100041. [PMID: 33543036 PMCID: PMC7852213 DOI: 10.1016/j.mbplus.2020.100041] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/02/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
Human skin is composed of the cell-rich epidermis, the extracellular matrix (ECM) rich dermis, and the hypodermis. Within the dermis, a dense network of ECM proteins provides structural support to the skin and regulates a wide variety of signaling pathways which govern cell proliferation and other critical processes. Both intrinsic aging, which occurs steadily over time, and extrinsic aging (photoaging), which occurs as a result of external insults such as solar radiation, cause alterations to the dermal ECM. In this study, we utilized both quantitative and global proteomics, alongside single harmonic generation (SHG) and two-photon autofluorescence (TPAF) imaging, to assess changes in dermal composition during intrinsic and extrinsic aging. We find that both intrinsic and extrinsic aging result in significant decreases in ECM-supporting proteoglycans and structural ECM integrity, evidenced by decreasing collagen abundance and increasing fibril fragmentation. Intrinsic aging also produces changes distinct from those produced by photoaging, including reductions in elastic fiber and crosslinking enzyme abundance. In contrast, photoaging is primarily defined by increases in elastic fiber-associated protein and pro-inflammatory proteases. Changes associated with photoaging are evident even in young (mid 20s) sun-exposed forearm skin, indicating that proteomic evidence of photoaging is present decades prior to clinical signs of photoaging. GO term enrichment revealed that both intrinsic aging and photoaging share common features of chronic inflammation. The proteomic data has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD015982. Intrinsic aging and photoaging both decrease ECM-supporting proteoglycans and structural ECM. Intrinsic aging produces reductions in elastic fiber and crosslinking enzyme abundance. Photoaging results in increases in pro-inflammatory proteases and elastic fiber abundance. Intrinsic aging and photoaging share common features associated with chronic inflammation. Proteomic changes associated with photoaging are evident decades prior to clinical aging signs.
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Key Words
- AUC, area under the curve
- Aging
- CE, cornified envelope
- CNBr, cyanogen bromide
- Collagen
- ECM, extracellular matrix
- Extracellular matrix
- GO, gene ontology
- Photoaging
- Proteomics
- QconCATs, quantitative concatemers
- SHG, single harmonic generation
- Skin
- TPAF, two-photon autofluorescence
- UV, ultraviolet
- iECM, insoluble ECM
- sECM, soluble ECM
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Affiliation(s)
- Maxwell C. McCabe
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Ryan C. Hill
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Kenneth Calderone
- Department of Dermatology, University of Michigan, 1150 W. Medical Center Drive, Medical Science I R6447, Ann Arbor, MI 48109, USA
| | - Yilei Cui
- Department of Dermatology, University of Michigan, 1150 W. Medical Center Drive, Medical Science I R6447, Ann Arbor, MI 48109, USA
| | - Yan Yan
- Department of Dermatology, University of Michigan, 1150 W. Medical Center Drive, Medical Science I R6447, Ann Arbor, MI 48109, USA
| | - Taihao Quan
- Department of Dermatology, University of Michigan, 1150 W. Medical Center Drive, Medical Science I R6447, Ann Arbor, MI 48109, USA
| | - Gary J. Fisher
- Department of Dermatology, University of Michigan, 1150 W. Medical Center Drive, Medical Science I R6447, Ann Arbor, MI 48109, USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, 12801 E 17th Ave., Aurora, CO 80045, USA
- Corresponding author.
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Campos TL, Korhonen PK, Sternberg PW, Gasser RB, Young ND. Predicting gene essentiality in Caenorhabditis elegans by feature engineering and machine-learning. Comput Struct Biotechnol J 2020; 18:1093-1102. [PMID: 32489524 PMCID: PMC7251299 DOI: 10.1016/j.csbj.2020.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023] Open
Abstract
Defining genes that are essential for life has major implications for understanding critical biological processes and mechanisms. Although essential genes have been identified and characterised experimentally using functional genomic tools, it is challenging to predict with confidence such genes from molecular and phenomic data sets using computational methods. Using extensive data sets available for the model organism Caenorhabditis elegans, we constructed here a machine-learning (ML)-based workflow for the prediction of essential genes on a genome-wide scale. We identified strong predictors for such genes and showed that trained ML models consistently achieve highly-accurate classifications. Complementary analyses revealed an association between essential genes and chromosomal location. Our findings reveal that essential genes in C. elegans tend to be located in or near the centre of autosomal chromosomes; are positively correlated with low single nucleotide polymorphim (SNP) densities and epigenetic markers in promoter regions; are involved in protein and nucleotide processing; are transcribed in most cells; are enriched in reproductive tissues or are targets for small RNAs bound to the argonaut CSR-1. Based on these results, we hypothesise an interplay between epigenetic markers and small RNA pathways in the germline, with transcription-based memory; this hypothesis warrants testing. From a technical perspective, further work is needed to evaluate whether the present ML-based approach will be applicable to other metazoans (including Drosophila melanogaster) for which comprehensive data sets (i.e. genomic, transcriptomic, proteomic, variomic, epigenetic and phenomic) are available.
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Key Words
- CDS, coding sequence
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
- Caenorhabditis elegans
- ES, Essentiality Score
- EST, expressed sequence tag
- Essential genes
- Essentiality predictions
- GBM, Gradient Boosting Method
- GFF, general feature format
- GLM, Generalised Linear Model
- GO, gene ontology
- ML, machine-learning
- Machine-learning
- NN, Artificial Neural Network
- PPI, protein-protein interaction
- PR-AUC, Area Under the Precision-Recall Curve
- RF, Random Forest
- RNAi, RNA interference
- ROC-AUC, Area Under the Receiver Operating Characteristic Curve
- SNP, single nucleotide polymorphism
- SPLS, Sparse Partial Least Squares
- SVM, Support-Vector Machine
- TEA, Tissue Enrichment Analysis tool (WormBase)
- TSS, transcription start site
- VCF, variant call file
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.,Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
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Xiang H, Zhang J, Lin C, Zhang L, Liu B, Ouyang L. Targeting autophagy-related protein kinases for potential therapeutic purpose. Acta Pharm Sin B 2020; 10:569-581. [PMID: 32322463 PMCID: PMC7161711 DOI: 10.1016/j.apsb.2019.10.003] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/06/2019] [Accepted: 09/09/2019] [Indexed: 02/08/2023] Open
Abstract
Autophagy, defined as a scavenging process of protein aggregates and damaged organelles mediated by lysosomes, plays a significant role in the quality control of macromolecules and organelles. Since protein kinases are integral to the autophagy process, it is critically important to understand the role of kinases in autophagic regulation. At present, intervention of autophagic processes by small-molecule modulators targeting specific kinases has becoming a reasonable and prevalent strategy for treating several varieties of human disease, especially cancer. In this review, we describe the role of some autophagy-related kinase targets and kinase-mediated phosphorylation mechanisms in autophagy regulation. We also summarize the small-molecule kinase inhibitors/activators of these targets, highlighting the opportunities of these new therapeutic agents.
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Key Words
- 4E-BP1, eukaryotic translation initiation factor 4E-binding protein
- AKT1, AKT serine/threonine kinase 1
- AMBRA1, autophagy/beclin-1 regulator 1
- AMPK, AMP-activated protein kinase
- ARF, auxin response factor gene
- ATG, autophagy-related protein
- Autophagy
- Autophagy-related kinase
- CaMKK2, calcium/calmodulin-dependent protein kinase kinase 2
- DAPK, death associated protein kinase
- FIP200, FAK family kinase-interacting protein of 200 kDa
- GAP, GTPase-activating protein
- GO, gene ontology
- GSK3α, glycogen synthase kinase 3 alpha
- HMGB1, high mobility group protein B1
- Human disease therapy
- JNK1, C-Jun N-terminal kinase
- LC3, microtubule-associated protein 1 light chain 3
- LKB1, serine/threonine-protein kinase stk11
- LPS, lipopolysaccharide
- LRRK2, leucine rich repeat kinase 2
- PD, Parkinson's disease
- PI, phosphatidylinositol
- PI3 kinase, phosphoinositide 3-kinase
- PI3P, phosphatidylinositol triphosphate
- PIM2, proviral insertion in murine lymphomas 2
- PINK1, PTEN-induced putative kinase 1
- PIP2, phosphatidylinositol-4,5-bisphosphate
- PKACα, a protein kinase cAMP-activated catalytic subunit alpha
- PKCα, protein kinase C alpha type
- PKD1, polycystin-1
- PPIs, protein–protein interactions
- PROTAC, proteolysis targeting chimeras
- PTMs, post-translational modifications
- Phosphorylation
- Protein kinases
- Rheb, the RAS homolog enriched in brain
- Small-molecule kinase inhibitors/activators
- TAK1, transforming growth factor activated kinase-1
- TFEB, transcription factor EB
- TNBC, triple-negative breast cancer
- TSC1/2, tuberous sclerosis complex proteins 1/2
- ULK complex, ULK1–mATG13–FIP200–ATG101 complex
- ULK1, unc-51-like kinase 1
- UVRAG, ultraviolet resistance-associated gene
- mTOR, mammalian target of rapamycin
- mTORC1, mammalian target of rapamycin complex 1
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Affiliation(s)
- Honggang Xiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Jifa Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Congcong Lin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Lan Zhang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
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Li L, Feng Q, Wang X. PreMSIm: An R package for predicting microsatellite instability from the expression profiling of a gene panel in cancer. Comput Struct Biotechnol J 2020; 18:668-675. [PMID: 32257050 PMCID: PMC7113609 DOI: 10.1016/j.csbj.2020.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/06/2020] [Accepted: 03/08/2020] [Indexed: 01/10/2023] Open
Abstract
Microsatellite instability (MSI) is a genomic property of the cancers with defective DNA mismatch repair and is a useful marker for cancer diagnosis and treatment in diverse cancer types. In particular, MSI has been associated with the active immune checkpoint blockade therapy response in cancer. Most of computational methods for predicting MSI are based on DNA sequencing data and a few are based on mRNA expression data. Using the RNA-Seq pan-cancer datasets for three cancer cohorts (colon, gastric, and endometrial cancers) from The Cancer Genome Atlas (TCGA) program, we developed an algorithm (PreMSIm) for predicting MSI from the expression profiling of a 15-gene panel in cancer. We demonstrated that PreMSIm had high prediction performance in predicting MSI in most cases using both RNA-Seq and microarray gene expression datasets. Moreover, PreMSIm displayed superior or comparable performance versus other DNA or mRNA-based methods. We conclude that PreMSIm has the potential to provide an alternative approach for identifying MSI in cancer.
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Key Words
- ACC, adrenocortical carcinoma
- AUC, area under the curve
- Algorithm
- BLCA, bladder urothelial carcinoma
- BRCA, breast invasive carcinoma
- CESC, cervical squamous cell carcinoma and endocervical adenocarcinoma
- CHOL, cholangiocarcinoma
- COAD, colon adenocarcinoma
- CV, cross validation
- Cancer
- Classification
- DLBC, lymphoid neoplasm diffuse large B-cell lymphoma
- ESCA, esophageal carcinoma
- GBM, glioblastoma multiforme
- GEO, Gene Expression Omnibus
- GO, gene ontology
- Gene expression profiling
- HNSC, head and neck squamous cell carcinoma
- KICH, kidney chromophobe
- KIRC, kidney renal clear cell carcinoma
- KIRP, kidney renal papillary cell carcinoma
- LAML, acute myeloid leukemia
- LGG, brain lower grade glioma
- LIHC, liver hepatocellular carcinoma
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- MESO, mesothelioma
- MSI, microsatellite instability
- MSS, microsatellite stability
- Machine learning
- Microsatellite instability
- OV, ovarian serous cystadenocarcinoma
- PAAD, pancreatic adenocarcinoma
- PCPG, pheochromocytoma and paraganglioma
- PPI, protein-protein interaction
- PRAD, prostate adenocarcinoma
- READ, rectum adenocarcinoma
- RF, random forest
- ROC, receiver operating characteristic
- SARC, sarcoma
- SKCM, skin cutaneous melanoma
- STAD, stomach adenocarcinoma
- SVM, support vector machine
- TCGA, The Cancer Genome Atlas
- TGCT, testicular germ cell tumors
- THCA, thyroid carcinoma
- THYM, thymoma
- UCEC, uterine corpus endometrial carcinoma
- UCS, uterine carcinosarcoma
- UVM, uveal melanoma
- XGBoost, extreme gradient boosting
- k-NN, k-nearest neighbor
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Affiliation(s)
- Lin Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Qiushi Feng
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
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Aloui C, Barlier C, Awounou D, Claverol S, Fagan J, Cognasse F, Garraud O, Laradi S. Data from differentially expressed proteins in platelet components associated with adverse transfusion reactions. Data Brief 2019; 25:104013. [PMID: 31297409 PMCID: PMC6598860 DOI: 10.1016/j.dib.2019.104013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/03/2019] [Accepted: 05/10/2019] [Indexed: 01/12/2023] Open
Abstract
The presented dataset was used for the study focused on the search for differentially expressed proteins in blood platelet components (PCs) associated with adverse transfusion reactions (ATRs). Pellets of ATR platelet components and their controls were subjected to high-throughput proteomics analysis using a Q Exactive high-resolution tandem mass spectrometer. The data reported here constitutes an extension of “Differential protein expression of blood platelet components associated with adverse transfusion reactions” article Aloui et al., 2018. The reported data herein have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD003510 for the pooled platelet components (PPCs) and PXD008886 for the apheresis platelet components (SDA-PCs) associated with ATRs.
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Affiliation(s)
- Chaker Aloui
- French Blood Bank (EFS) Auvergne-Rhône-Alpes, Saint-Etienne, France.,GIMAP-EA3064, University of Lyon, Saint-Etienne, France
| | - Céline Barlier
- French Blood Bank (EFS) Auvergne-Rhône-Alpes, Saint-Etienne, France
| | - Danielle Awounou
- French Blood Bank (EFS) Auvergne-Rhône-Alpes, Saint-Etienne, France
| | - Stéphane Claverol
- Proteome Platform, CGFB, University of Bordeaux Segalen, Bordeaux, France
| | - Jocelyne Fagan
- French Blood Bank (EFS) Auvergne-Rhône-Alpes, Saint-Etienne, France.,GIMAP-EA3064, University of Lyon, Saint-Etienne, France
| | - Fabrice Cognasse
- French Blood Bank (EFS) Auvergne-Rhône-Alpes, Saint-Etienne, France.,GIMAP-EA3064, University of Lyon, Saint-Etienne, France
| | - Olivier Garraud
- GIMAP-EA3064, University of Lyon, Saint-Etienne, France.,National Institute of Blood Transfusion (INTS), Paris, France
| | - Sandrine Laradi
- French Blood Bank (EFS) Auvergne-Rhône-Alpes, Saint-Etienne, France.,GIMAP-EA3064, University of Lyon, Saint-Etienne, France
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Lacey M, Baribault C, Ehrlich KC, Ehrlich M. Data showing atherosclerosis-associated differentially methylated regions are often at enhancers. Data Brief 2019; 23:103812. [PMID: 31372457 PMCID: PMC6660590 DOI: 10.1016/j.dib.2019.103812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 12/22/2022] Open
Abstract
Atherosclerosis involves phenotypic modulation and transdifferentiation of vascular smooth muscle cells (SMCs). Data are given in tabular or figure format that illustrate genome-wide DNA methylation alterations in atherosclerotic vs. control aorta (athero DMRs). Data based upon publicly available chromatin state profiles are also shown for normal aorta, monocyte, and skeletal muscle tissue-specific DMRs and for aorta-specific chromatin features (enhancer chromatin, promoter chromatin, repressed chromatin, actively transcribed chromatin). Athero hypomethylated and hypermethylated DMRs as well as epigenetic and transcription profiles are described for the following genes: ACTA2, MYH10, MYH11 (SMC-associated genes); SMAD3 (a signaling gene for SMCs and other cell types); CD79B and SH3BP2 (leukocyte-associated genes); and TBX20 and genes in the HOXA, HOXB, HOXC, and HOXD clusters (T-box and homeobox developmental genes). The data reveal strong correlations between athero hypermethylated DMRs and regions of enhancer chromatin in aorta, which are discussed in the linked research article “Atherosclerosis-associated differentially methylated regions can reflect the disease phenotype and are often at enhancers” (M. Lacey et al., 2019).
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Key Words
- Atherosclerosis
- DMR, differentially methylated region
- DNA methylation
- Differentially methylated regions (DMRs)
- Enhancers
- GO, gene ontology
- Monocytes
- PBMC, peripheral blood mononuclear cells
- PMD, percent methylation difference
- SkM, skeletal muscle
- Smooth muscle
- athero hypermeth DMR, atherosclerosis-associated hypermethylated DMR
- athero hypometh DMR, atherosclerosis-associated hypomethylated DMR
- ctl, control
- enh, enhancer chromatin
- mod, moderate
- prom, promoter chromatin
- repr, repressed
- txn chromatin, chromatin with the histone marks of actively transcribed chromatin
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Affiliation(s)
- Michelle Lacey
- Tulane Cancer Center, Tulane University Health Sciences Center, LA 70112, USA.,Department of Mathematics, Tulane University, New Orleans, LA 70118, USA
| | - Carl Baribault
- Tulane Cancer Center, Tulane University Health Sciences Center, LA 70112, USA
| | - Kenneth C Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, USA
| | - Melanie Ehrlich
- Tulane Cancer Center, Tulane University Health Sciences Center, LA 70112, USA.,Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, USA.,Hayward Genetics Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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27
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Qi S, Guo L, Yan S, Lee RJ, Yu S, Chen S. Hypocrellin A-based photodynamic action induces apoptosis in A549 cells through ROS-mediated mitochondrial signaling pathway. Acta Pharm Sin B 2019; 9:279-293. [PMID: 30972277 PMCID: PMC6437636 DOI: 10.1016/j.apsb.2018.12.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/15/2018] [Accepted: 11/28/2018] [Indexed: 12/31/2022] Open
Abstract
Over recent decades, many studies have reported that hypocrellin A (HA) can eliminate cancer cells with proper irradiation in several cancer cell lines. However, the precise molecular mechanism underlying its anticancer effect has not been fully defined. HA-mediated cytotoxicity and apoptosis in human lung adenocarcinoma A549 cells were evaluated after photodynamic therapy (PDT). A temporal quantitative proteomics approach by isobaric tag for relative and absolute quantitation (iTRAQ) 2D liquid chromatography with tandem mass spectrometric (LC–MS/MS) was introduced to help clarify molecular cytotoxic mechanisms and identify candidate targets of HA-induced apoptotic cell death. Specific caspase inhibitors were used to further elucidate the molecular pathway underlying apoptosis in PDT-treated A549 cells. Finally, down-stream apoptosis-related protein was evaluated. Apoptosis induced by HA was associated with cell shrinkage, externalization of cell membrane phosphatidylserine, DNA fragmentation, and mitochondrial disruption, which were preceded by increased intracellular reactive oxygen species (ROS) generations. Further studies showed that PDT treatment with 0.08 µmol/L HA resulted in mitochondrial disruption, pronounced release of cytochrome c, and activation of caspase-3, -9, and -7. Together, HA may be a possible therapeutic agent directed toward mitochondria and a promising photodynamic anticancer candidate for further evaluation.
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Key Words
- ACN, acetonitrile
- CLSM, confocal laser scanning confocal microscopy
- DCFH-DA, 2′,7′-dichlorofuorescin diacetate
- DMEM, Dulbecco׳s modified Eagle׳s medium
- Dox, doxorubicin
- ECL, enhanced chemiluminescence
- FCCP, carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone
- FDR, false discovery rate
- GO, gene ontology
- HA, hypocrellin A
- HRP, horseradish peroxidase
- Hypocrellin A
- IAA, iodoacetamide
- IKK, IκB kinase complex
- JC-1, 5,5′,6,6′-tetrachloro-1,1′,3,3′-tetraethyl-benzimidazolcarbocyanine iodide
- LC–MS/MS
- MMP, mitochondrial membrane potential
- MPT, mitochondrial permeability transition
- NAC, N-acetyl-l-cysteine
- OCR, oxygen consumption rate
- PDT, photodynamic therapy
- PI, propidium iodide
- PS, photosensitizer
- Photodynamic therapy
- Proteomic
- ROS, reactive oxygen species
- Reactive oxygen species
- SCX, strong cation exchange
- TCM, traditional Chinese medicinal
- TEM, transmission electron microscope
- TFA, trifluoroacetic acid
- UA, urea
- iTRAQ
- iTRAQ, isobaric tag for relative and absolute quantitation
- z-IETD-fmk, z-Ile-Glu-Asp-fluoromethylketone
- z-LEHD-fmk, z-Leu-Glu(OMe)-His-Asp(OMe)-fluoromethylketone
- z-VAD-fmk, z-Val-Ala-Asp-fluoromethylketone
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Affiliation(s)
- Shanshan Qi
- Jiangsu Province Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
| | - Lingyuan Guo
- Jiangsu Province Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Shuzhen Yan
- Jiangsu Province Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Robert J. Lee
- College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
| | - Shuqin Yu
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Corresponding author. Tel./fax: +86 25 8559 1050.
| | - Shuanglin Chen
- Jiangsu Province Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Corresponding author. Tel.: +86 25 8589 1265.
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Maas AE, Blanco-Bercial L, Lo A, Tarrant AM, Timmins-Schiffman E. Variations in Copepod Proteome and Respiration Rate in Association with Diel Vertical Migration and Circadian Cycle. Biol Bull 2018; 235:30-42. [PMID: 30160998 DOI: 10.1086/699219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The diel vertical migration of zooplankton is a process during which individuals spend the night in surface waters and retreat to depth during the daytime, with substantial implications for carbon transport and the ecology of midwater ecosystems. The physiological consequences of this daily pattern have, however, been poorly studied beyond investigations of speed and the energetic cost of swimming. Many other processes are likely influenced, such as fuel use, energetic trade-offs, underlying diel (circadian) rhythms, and antioxidant responses. Using a new reference transcriptome, proteomic analyses were applied to compare the physiological state of a migratory copepod, Pleuromamma xiphias, immediately after arriving to the surface at night and six hours later. Oxygen consumption was monitored semi-continuously to explore underlying cyclical patterns in metabolic rate under dark-dark conditions. The proteomic analysis suggests a distinct shift in physiology that reflects migratory exertion and changes in metabolism. These proteomic analyses are supported by the respiration experiments, which show an underlying cycle in metabolic rate, with a peak at dawn. This project generates molecular tools (transcriptome and proteome) that will allow for more detailed understanding of the underlying physiological processes that influence and are influenced by diel vertical migration. Further, these studies suggest that P. xiphias is a tractable model for continuing investigations of circadian and diel vertical migration influences on plankton physiology. Previous studies did not account for this cyclic pattern of respiration and may therefore have unrepresented respiratory carbon fluxes from copepods by about 24%.
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Key Words
- ACN, acetonitrile
- ANOSIM, analysis of similarity
- BATS, Bermuda Atlantic Time Series
- BUSCO, Benchmarking Universal Single-Copy Orthologs
- DM, dry mass
- DVM, diel vertical migration
- FFT-NLLS, fast Fourier transform non-linear least squares
- GO, gene ontology
- MESA, maximum entropy spectral analysis
- NAD+, oxidized nicotinamide adenine dinucleotide
- NAD, nicotinamide adenine dinucleotide
- NADH, reduced nicotinamide adenine dinucleotide
- NMDS, non-metric multidimensional scaling
- NSAF, normalized spectral abundance factor
- RT, room temperature
- TTP, Trans Proteomic Pipeline
- nr, non-redundant database
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Duggan SP, Garry C, Behan FM, Phipps S, Kudo H, Kirca M, Zaheer A, McGarrigle S, Reynolds JV, Goldin R, Kalloger SE, Schaeffer DF, Long A, Strid J, Kelleher D. siRNA Library Screening Identifies a Druggable Immune-Signature Driving Esophageal Adenocarcinoma Cell Growth. Cell Mol Gastroenterol Hepatol 2018; 5:569-90. [PMID: 29930979 DOI: 10.1016/j.jcmgh.2018.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/12/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Effective therapeutic approaches are urgently required to tackle the alarmingly poor survival outcomes in esophageal adenocarcinoma (EAC) patients. EAC originates from within the intestinal-type metaplasia, Barrett's esophagus, a condition arising on a background of gastroesophageal reflux disease and associated inflammation. METHODS This study used a druggable genome small interfering RNA (siRNA) screening library of 6022 siRNAs in conjunction with bioinformatics platforms, genomic studies of EAC tissues, somatic variation data of EAC from The Cancer Genome Atlas data of EAC, and pathologic and functional studies to define novel EAC-associated, and targetable, immune factors. RESULTS By using a druggable genome library we defined genes that sustain EAC cell growth, which included an unexpected immunologic signature. Integrating Cancer Genome Atlas data with druggable siRNA targets showed a striking concordance and an EAC-specific gene amplification event associated with 7 druggable targets co-encoded at Chr6p21.1. Over-representation of immune pathway-associated genes supporting EAC cell growth included leukemia inhibitory factor, complement component 1, q subcomponent A chain (C1QA), and triggering receptor expressed on myeloid cells 2 (TREM2), which were validated further as targets sharing downstream signaling pathways through genomic and pathologic studies. Finally, targeting the triggering receptor expressed on myeloid cells 2-, C1q-, and leukemia inhibitory factor-activated signaling pathways (TYROBP-spleen tyrosine kinase and JAK-STAT3) with spleen tyrosine kinase and Janus-activated kinase inhibitor fostamatinib R788 triggered EAC cell death, growth arrest, and reduced tumor burden in NOD scid gamma mice. CONCLUSIONS These data highlight a subset of genes co-identified through siRNA targeting and genomic studies of expression and somatic variation, specifically highlighting the contribution that immune-related factors play in support of EAC development and suggesting their suitability as targets in the treatment of EAC.
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Key Words
- ATCC, American Type Culture Collection
- BE, Barrett’s esophagus
- Barrett’s Esophagus
- EAC, esophageal adenocarcinoma
- ERBB2, erb-b2 receptor tyrosine kinase 2
- ESCC, esophageal squamous cell carcinoma
- Esophageal Adenocarcinoma
- FCS, fetal calf serum
- GEM, gene expression microarray
- GERD, gastroesophageal reflux disease
- GO, gene ontology
- HGD, high-grade dysplastic
- IL, interleukin
- Inflammation
- JAK-STAT, Janus kinase/signal transducer-and-activator of transcription
- LIF, leukemia inhibitory factor
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
- PBS, phosphate-buffered saline
- RA, rheumatoid arthritis
- SV, somatic variation
- SYK, spleen tyrosine kinase
- TCGA, The Cancer Genome Atlas
- TREM2, triggering receptor expressed on myeloid cells 2
- Therapeutic Targets
- VEGFA, vascular endothelial growth factor A
- mRNA, messenger RNA
- siRNA, small interfering RNA
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30
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Faggionato D, Serb JM. Strategy to Identify and Test Putative Light-Sensitive Non-Opsin G-Protein-Coupled Receptors: A Case Study. Biol Bull 2017; 233:70-82. [PMID: 29182499 DOI: 10.1086/694842] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The rise of high-throughput RNA sequencing (RNA-seq) and de novo transcriptome assembly has had a transformative impact on how we identify and study genes in the phototransduction cascade of non-model organisms. But the advantage provided by the nearly automated annotation of RNA-seq transcriptomes may at the same time hinder the possibility for gene discovery and the discovery of new gene functions. For example, standard functional annotation based on domain homology to known protein families can only confirm group membership, not identify the emergence of new biochemical function. In this study, we show the importance of developing a strategy that circumvents the limitations of semiautomated annotation and apply this workflow to photosensitivity as a means to discover non-opsin photoreceptors. We hypothesize that non-opsin G-protein-coupled receptor (GPCR) proteins may have chromophore-binding lysines in locations that differ from opsin. Here, we provide the first case study describing non-opsin light-sensitive GPCRs based on tissue-specific RNA-seq data of the common bay scallop Argopecten irradians (Lamarck, 1819). Using a combination of sequence analysis and three-dimensional protein modeling, we identified two candidate proteins. We tested their photochemical properties and provide evidence showing that these two proteins incorporate 11-cis and/or all-trans retinal and react to light photochemically. Based on this case study, we demonstrate that there is potential for the discovery of new light-sensitive GPCRs, and we have developed a workflow that starts from RNA-seq assemblies to the discovery of new non-opsin, GPCR-based photopigments.
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Key Words
- Bta-RHO, bovine rhodopsin
- EL, extracellular loop
- FPKM, fragments per kilobase of exon per million fragments mapped
- GO, gene ontology
- GPCR, G-protein-coupled receptor
- Gr, gustatory receptor
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- TM, transmembrane helix
- Tpa-OPNGq1, Todarodes pacificus, rhodopsin
- mRNA, messenger RNA
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31
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Hongo Y, Yasuda N, NagaI S. Identification of Genes for Synthesis of the Blue Pigment, Biliverdin IXα, in the Blue Coral Heliopora coerulea. Biol Bull 2017; 232:71-81. [PMID: 28654333 DOI: 10.1086/692661] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Heliopora coerulea is the only species in the subclass Octocorallia that has a crystalline aragonite skeleton. The skeleton has been reported to contain the blue pigment, biliverdin IXα, which is formed by heme oxygenase (HO) during heme decomposition. There is little information regarding gene expression in H. coerulea; therefore, the biosynthesis pathway for biliverdin IXα is poorly understood. To identify the genes related to heme synthesis and degradation, metatranscripts of H. coerulea and its symbiont Symbiodinium spp. were sequenced and separated from the host- and symbiont-derived sequences. From the metatranscriptome analyses, all genes for heme synthesis and three HOs were isolated from the host and symbiont. From our phylogenetic and amino acid analysis, we noted that one of the HO isoforms in the host coral was predicted to possess HO activity. However, biliverdin reductase, which reduces biliverdin to bilirubin, was not identified in the present study. Similarly, biliverdin reductase was not identified in the transcripts of the red coral Corallium rubrum, a species that also belongs to Octocorallia. However, genes related to heme synthesis and HO were found in C. rubrum. We speculate that Heliopora coerulea can produce biliverdin and accumulate it in the skeleton, while red corals and other Octocorallia species cannot. Further information from molecular studies of H. coerulea will provide insights into the synthesis of biliverdin IXα, the blue pigment in the hard crystalline aragonite skeleton, and will be fundamental to future ecological and physiological studies.
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Key Words
- ALA, 5-aminolevulinic acid
- DDBJ, DNA Data Bank of Japan
- GO, gene ontology
- HO, heme oxygenase
- ROS, reactive oxygen species
- contig (from contiguous), a group of DNA segments that overlap and, as one, depict a consensus region of DNA
- hcHO-1, 2, 3, three isoforms of heme oxygenase in Heliopora coerulea
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Lo YH, Chung E, Li Z, Wan YW, Mahe MM, Chen MS, Noah TK, Bell KN, Yalamanchili HK, Klisch TJ, Liu Z, Park JS, Shroyer NF. Transcriptional Regulation by ATOH1 and its Target SPDEF in the Intestine. Cell Mol Gastroenterol Hepatol 2016; 3:51-71. [PMID: 28174757 PMCID: PMC5247424 DOI: 10.1016/j.jcmgh.2016.10.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/13/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND & AIMS The transcription factor atonal homolog 1 (ATOH1) controls the fate of intestinal progenitors downstream of the Notch signaling pathway. Intestinal progenitors that escape Notch activation express high levels of ATOH1 and commit to a secretory lineage fate, implicating ATOH1 as a gatekeeper for differentiation of intestinal epithelial cells. Although some transcription factors downstream of ATOH1, such as SPDEF, have been identified to specify differentiation and maturation of specific cell types, the bona fide transcriptional targets of ATOH1 still largely are unknown. Here, we aimed to identify ATOH1 targets and to identify transcription factors that are likely to co-regulate gene expression with ATOH1. METHODS We used a combination of chromatin immunoprecipitation and messenger RNA-based high-throughput sequencing (ChIP-seq and RNA-seq), together with cell sorting and transgenic mice, to identify direct targets of ATOH1, and establish the epistatic relationship between ATOH1 and SPDEF. RESULTS By using unbiased genome-wide approaches, we identified more than 700 genes as ATOH1 transcriptional targets in adult small intestine and colon. Ontology analysis indicated that ATOH1 directly regulates genes involved in specification and function of secretory cells. De novo motif analysis of ATOH1 targets identified SPDEF as a putative transcriptional co-regulator of ATOH1. Functional epistasis experiments in transgenic mice show that SPDEF amplifies ATOH1-dependent transcription but cannot independently initiate transcription of ATOH1 target genes. CONCLUSIONS This study unveils the direct targets of ATOH1 in the adult intestines and illuminates the transcriptional events that initiate the specification and function of intestinal secretory lineages.
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Key Words
- ATOH1
- ATOH1, atonal homolog 1
- Atoh1Flag
- Atoh1GFP
- CRC, colorectal cancer
- ChIP, chromatin immunoprecipitation
- ChIP-seq, chromatin immunoprecipitation sequencing
- DBZ, dibenzazepine
- FACS, fluorescence-activated cell sorting
- FDR, false-discovery rate
- GFP, green fluorescent protein
- GO, gene ontology
- Gfi1, growth factor independent 1
- ISC, intestinal stem cell
- Intestinal Epithelium
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- QES, Q-enrichment-score
- RT-qPCR, reverse-transcription quantitative polymerase chain reaction
- SPDEF
- Spdef, SAM pointed domain containing ETS transcription factor
- TRE-Spdef
- TSS, transcription start site
- Transcription
- Villin-creER
- mRNA, messenger RNA
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Affiliation(s)
- Yuan-Hung Lo
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Eunah Chung
- Division of Pediatric Urology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Zhaohui Li
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas
| | - Maxime M. Mahe
- Department of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Min-Shan Chen
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Taeko K. Noah
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kristin N. Bell
- Graduate Program in Molecular Developmental Biology, University of Cincinnati, Cincinnati, Cincinnati, Ohio
| | | | - Tiemo J. Klisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Zhandong Liu
- Department of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Joo-Seop Park
- Division of Pediatric Urology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Joo-Seop Park, PhD, Divisions of Pediatric Urology and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.Divisions of Pediatric Urology and Developmental BiologyCincinnati Children's Hospital Medical CenterCincinnatiOhio
| | - Noah F. Shroyer
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, Texas
- Division of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas
- Correspondence Address correspondence to: Noah F. Shroyer, PhD, Division of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas.Division of MedicineSection of Gastroenterology and HepatologyBaylor College of MedicineHoustonTexas
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Okada T, Takahashi H, Suzuki Y, Sugano S, Noji M, Kenmoku H, Toyota M, Kanaya S, Kawahara N, Asakawa Y, Sekita S. Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing. Genom Data 2016; 10:4-11. [PMID: 27625990 PMCID: PMC5011178 DOI: 10.1016/j.gdata.2016.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/02/2016] [Accepted: 08/02/2016] [Indexed: 10/27/2022]
Abstract
Ephedra plants are taxonomically classified as gymnosperms, and are medicinally important as the botanical origin of crude drugs and as bioresources that contain pharmacologically active chemicals. Here we show a comparative analysis of the transcriptomes of aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing by RNA-Seq. De novo assembly of short cDNA sequence reads generated 23,358, 13,373, and 28,579 contigs longer than 200 bases from aerial stems, roots, or both aerial stems and roots, respectively. The presumed functions encoded by these contig sequences were annotated by BLAST (blastx). Subsequently, these contigs were classified based on gene ontology slims, Enzyme Commission numbers, and the InterPro database. Furthermore, comparative gene expression analysis was performed between aerial stems and roots. These transcriptome analyses revealed differences and similarities between the transcriptomes of aerial stems and roots in E. sinica. Deep transcriptome sequencing of Ephedra should open the door to molecular biological studies based on the entire transcriptome, tissue- or organ-specific transcriptomes, or targeted genes of interest.
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Affiliation(s)
- Taketo Okada
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan
| | - Hironobu Takahashi
- Institute of Pharmacognosy, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Noji
- Institute of Pharmacognosy, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Hiromichi Kenmoku
- Institute of Pharmacognosy, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Masao Toyota
- Institute of Pharmacognosy, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Shigehiko Kanaya
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Nobuo Kawahara
- Tsukuba Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba, Ibaraki 305-0843, Japan
| | - Yoshinori Asakawa
- Institute of Pharmacognosy, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Setsuko Sekita
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan
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Liberini CG, Borner T, Boyle CN, Lutz TA. The satiating hormone amylin enhances neurogenesis in the area postrema of adult rats. Mol Metab 2016; 5:834-843. [PMID: 27688997 PMCID: PMC5034493 DOI: 10.1016/j.molmet.2016.06.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 06/22/2016] [Accepted: 06/27/2016] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVE Adult neurogenesis in the subgranular zone and subventricular zone is generally accepted, but its existence in other brain areas is still controversial. Circumventricular organs, such as the area postrema (AP) have recently been described as potential neurogenic niches in the adult brain. The AP is the major site of action of the satiating hormone amylin. Amylin has been shown to promote the formation of neuronal projections originating from the AP in neonatal rodents but the role of amylin in adult neurogenesis remains unknown. METHODS To test this, we first performed an RNA-sequencing of the AP of adult rats acutely injected with either amylin (20 μg/kg), amylin plus the amylin receptor antagonist AC187 (500 μg/kg) or vehicle. Second, animals were subcutaneously equipped with minipumps releasing either amylin (50 μg/kg/day) or vehicle for 3 weeks to assess cell proliferation and differentiation with the 5'-bromo-2-deoxyuridine (BrdU) technique. RESULTS Acute amylin injections affected genes involved in pathways and processes that control adult neurogenesis. Amylin consistently upregulated NeuroD1 transcript and protein in the adult AP, and this effect was blocked by the co-administration of AC187. Further, chronic amylin treatment increased the number of newly proliferated AP-cells and significantly promoted their differentiation into neurons rather than astrocytes. CONCLUSION Our findings revealed a novel role of the satiating hormone amylin in promoting neurogenesis in the AP of adult rats.
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Key Words
- AP, area postrema
- Adult neurogenesis
- Amylin
- Area postrema
- BrdU
- BrdU, 5′-bromo-2-deoxyuridine
- CR, calretinin
- CTR, calcitonin receptor
- CVO, circumventricular organs
- Circumventricular organs
- ERK1/2, extracellular signal-regulated kinase 1 and 2
- EphRs, ephrin receptors
- FDR, false discovery rate
- GO, gene ontology
- ME, median eminence
- NGS, next generation sequencing
- NSC, neural stem cells
- NeuroD, neuronal differentiation
- NeuroD1, neuronal differentiation-1
- RAMP, receptor activity-modifying protein
- Wnt, Wingless-Type MMTV Integration Site Family
- bHLH, basic helix-loop-helix
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Affiliation(s)
- Claudia G Liberini
- Institute of Veterinary Physiology, Vetsuisse Faculty University of Zurich (UZH), 8057 Zurich, Switzerland; Zurich Centre for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland; Zurich Centre for Clinical Studies, Vetsuisse Faculty University of Zurich, 8057 Zurich, Switzerland
| | - Tito Borner
- Institute of Veterinary Physiology, Vetsuisse Faculty University of Zurich (UZH), 8057 Zurich, Switzerland; Zurich Centre for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
| | - Christina N Boyle
- Institute of Veterinary Physiology, Vetsuisse Faculty University of Zurich (UZH), 8057 Zurich, Switzerland.
| | - Thomas A Lutz
- Institute of Veterinary Physiology, Vetsuisse Faculty University of Zurich (UZH), 8057 Zurich, Switzerland; Zurich Centre for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
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Heidecker B, Kittleson MM, Kasper EK, Wittstein IS, Champion HC, Russell SD, Baughman KL, Hare JM. Transcriptomic Analysis Identifies the Effect of Beta-Blocking Agents on a Molecular Pathway of Contraction in the Heart and Predicts Response to Therapy. JACC Basic Transl Sci 2016; 1:107-121. [PMID: 30167508 PMCID: PMC6113163 DOI: 10.1016/j.jacbts.2016.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/23/2016] [Accepted: 02/23/2016] [Indexed: 01/04/2023]
Abstract
Over the last decades, beta-blockers have been a key component of heart failure therapy. However, currently there is no method to identify patients who will benefit from beta-blocking therapy versus those who will be unresponsive or worsen. Furthermore, there is an unmet need to better understand molecular mechanisms through which heart failure therapies, such as beta-blockers, improve cardiac function, in order to design novel targeted therapies. Solving these issues is an important step towards personalized medicine. Here, we present a comprehensive transcriptomic analysis of molecular pathways that are affected by beta-blocking agents and a transcriptomic biomarker to predict therapy response.
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Key Words
- AR, adrenergic receptor
- EF, ejection fraction
- EMB, endomyocardial biopsy
- GO, gene ontology
- HF, heart failure
- MYH, myosin heavy chain
- MiPP, Misclassified Penalized Posteriors
- SAM, significance analysis of microarrays
- SERCA, sarcoplasmic reticulum calcium-dependent ATPase
- TBB, transcriptomic-based biomarker
- beta-blocking agents
- biomarker
- gene expression
- heart failure
- transcriptomics
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Affiliation(s)
| | | | | | | | | | | | | | - Joshua M. Hare
- University of Miami, Miami, Florida
- Reprint requests and correspondence: Dr. Joshua M. Hare, Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Biomedical Research Building, 1501 NW 10th Avenue, Room, 910 P.O. Box 016960 (R-125), Miami, Florida 33136.
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Milan E, Perini T, Resnati M, Orfanelli U, Oliva L, Raimondi A, Cascio P, Bachi A, Marcatti M, Ciceri F, Cenci S. A plastic SQSTM1/p62-dependent autophagic reserve maintains proteostasis and determines proteasome inhibitor susceptibility in multiple myeloma cells. Autophagy 2016; 11:1161-78. [PMID: 26043024 PMCID: PMC4590585 DOI: 10.1080/15548627.2015.1052928] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
Multiple myeloma (MM) is the paradigmatic proteasome inhibitor (PI) responsive cancer, but many patients fail to respond. An attractive target to enhance sensitivity is (macro)autophagy, recently found essential to bone marrow plasma cells, the normal counterpart of MM. Here, integrating proteomics with hypothesis-driven strategies, we identified the autophagic cargo receptor and adapter protein, SQSTM1/p62 as an essential component of an autophagic reserve that not only synergizes with the proteasome to maintain proteostasis, but also mediates a plastic adaptive response to PIs, and faithfully reports on inherent PI sensitivity. Lentiviral engineering revealed that SQSTM1 is essential for MM cell survival and affords specific PI protection. Under basal conditions, SQSTM1-dependent autophagy alleviates the degradative burden on the proteasome by constitutively disposing of substantial amounts of ubiquitinated proteins. Indeed, its inhibition or stimulation greatly sensitized to, or protected from, PI-induced protein aggregation and cell death. Moreover, under proteasome stress, myeloma cells selectively enhanced SQSTM1 de novo expression and reset its vast endogenous interactome, diverting SQSTM1 from signaling partners to maximize its association with ubiquitinated proteins. Saturation of such autophagic reserve, as indicated by intracellular accumulation of undigested SQSTM1-positive aggregates, specifically discriminated patient-derived myelomas inherently susceptible to PIs from primarily resistant ones. These aggregates correlated with accumulation of the endoplasmic reticulum, which comparative proteomics identified as the main cell compartment targeted by autophagy in MM. Altogether, the data integrate autophagy into our previously established proteasome load-versus-capacity model, and reveal SQSTM1 aggregation as a faithful marker of defective proteostasis, defining a novel prognostic and therapeutic framework for MM.
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Key Words
- APC, allophycocyanin
- Ab, antibody
- BM, bone marrow
- Baf A1, bafilomycin A1
- Btz, bortezomib
- ER, endoplasmic reticulum
- ERGIC, ER-Golgi intermediate compartment
- GO, gene ontology
- HCQ, hydroxychloroquine
- IP, immunoprecipitation
- Ig, immunoglobulin
- LC-MS/MS, liquid chromatography–tandem mass spectrometry
- MM, multiple myeloma
- PBS, phosphate-buffered saline
- PC, plasma cell
- PI, proteasome inhibitor
- Rapa, rapamycin
- SILAC, stable isotope labeling in cell culture
- SQSTM1
- UPR, unfolded protein response
- UPS, ubiquitin-proteasome system
- Ub, ubiquitin
- aggregate
- amc, 7-amino-4-methylcoumarin
- autophagy
- bortezomib
- endoplasmic reticulum
- multiple myeloma
- p62
- pAb, polyclonal antibody
- plasma cells
- proteasome
- proteasome inhibitors
- proteostasis
- ubiquitin
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Affiliation(s)
- Enrico Milan
- a San Raffaele Scientific Institute; Division of Genetics and Cell Biology ; Milan , Italy
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Zhang SF, Wang XY, Fu ZQ, Peng QH, Zhang JY, Ye F, Fu YF, Zhou CY, Lu WG, Cheng XD, Xie X. TXNDC17 promotes paclitaxel resistance via inducing autophagy in ovarian cancer. Autophagy 2016; 11:225-38. [PMID: 25607466 DOI: 10.1080/15548627.2014.998931] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Paclitaxel is recommended as a first-line chemotherapeutic agent against ovarian cancer, but drug resistance becomes a major limitation of its success clinically. The key molecule or mechanism associated with paclitaxel resistance in ovarian cancer still remains unclear. Here, we showed that TXNDC17 screened from 356 differentially expressed proteins by LC-MS/MS label-free quantitative proteomics was more highly expressed in paclitaxel-resistant ovarian cancer cells and tissues, and the high expression of TXNDC17 was associated with poorer prognostic factors and exhibited shortened survival in 157 ovarian cancer patients. Moreover, paclitaxel exposure induced upregulation of TXNDC17 and BECN1 expression, increase of autophagosome formation, and autophagic flux that conferred cytoprotection for ovarian cancer cells from paclitaxel. TXNDC17 inhibition by siRNA or enforced overexpression by a pcDNA3.1(+)-TXNDC17 plasmid correspondingly decreased or increased the autophagy response and paclitaxel resistance. Additionally, the downregulation of BECN1 by siRNA attenuated the activation of autophagy and cytoprotection from paclitaxel induced by TXNDC17 overexpression in ovarian cancer cells. Thus, our findings suggest that TXNDC17, through participation of BECN1, induces autophagy and consequently results in paclitaxel resistance in ovarian cancer. TXNDC17 may be a potential predictor or target in ovarian cancer therapeutics.
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Key Words
- 95% CI, 95% confidence interval
- ALDOC, aldolase C, fructose-bisphosphate
- ATG5, autophagy-related 5
- BECN1
- BECN1, Beclin 1, autophagy-related
- BafA1, bafilomycin A1
- CNN3, calponin 3, acidic
- DAPI, 4', 6-diamidino-2-phenylindole
- FLNA, filamin A, α
- GO, gene ontology
- GenMAPP, gene microarray pathway profiler
- HBSS, Hank's balanced salt solution
- HR, hazard ratio
- KEGG, Kyoto encyclopedia of genes and genome
- LC-MS/MS, liquid chromatography-mass spectrometry/ mass spectrometry
- MAP1LC3B/LC3B, microtubule-associated protein 1 light chain 3 β
- OS, overall survival
- PFS, progression-free survival
- PGAM1, phosphoglycerate mutase 1 (brain)
- SQSTM1, sequestosome 1
- TNF, tumor necrosis factor
- TXN, thioredoxin
- TXNDC17
- TXNDC17, thioredoxin domain containing 17
- UTP23, small subunit (SSU) processome component, homolog (yeast)
- autophagy
- ovarian cancer
- paclitaxel resistance
- siRNA, short interfering RNA
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Affiliation(s)
- Song-Fa Zhang
- a Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine ; Zhejiang University ; Hangzhou , China
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Zhang J, Shao J, Wu X, Mao Q, Wang Y, Gao F, Kong W, Liang Z. Type I interferon related genes are common genes on the early stage after vaccination by meta-analysis of microarray data. Hum Vaccin Immunother 2015; 11:739-45. [PMID: 25839220 DOI: 10.1080/21645515.2015.1008884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The objective of this study was to find common immune mechanism across different kinds of vaccines. A meta-analysis of microarray datasets was performed using publicly available microarray Gene Expression Omnibus (GEO) and Array Express data sets of vaccination records. Seven studies (out of 35) were selected for this meta-analysis. A total of 447 chips (145 pre-vaccination and 302 post-vaccination) were included. Significance analysis of microarrays (SAM) program was used for screening differentially expressed genes (DEGs). Functional pathway enrichment for the DEGs was conducted in DAVID Gene Ontology (GO) database. Twenty DEGs were identified, of which 10 up-regulated genes involved immune response. Six of which were type I interferon (IFN) related genes, including LY6E, MX1, OAS3, IFI44L, IFI6 and IFITM3. Ten down-regulated genes mainly mediated negative regulation of cell proliferation and cell motion. Results of a subgroup analysis showed that although the kinds of genes varied widely between days 3 and 7 post vaccination, the pathways between them are basically the same, such as immune response and response to viruses, etc. For an independent verification of these 6 type I IFN related genes, peripheral blood mononuclear cells (PBMCs) were collected at baseline and day 3 after the vaccination from 8 Enterovirus 71(EV71) vaccinees and were assayed by RT-PCR. Results showed that the 6 DEGs were also upregulated in EV71 vaccinees. In summary, meta-analysis methods were used to explore the immune mechanism of vaccines and results indicated that the type I IFN related genes and corresponding pathways were common in early immune responses for different kinds of vaccines.
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Key Words
- CPE, cytopathogenic effect
- DCs, dendritic cells
- DEGs, differentially expressed genes
- EV71, enterovirus 71
- GEO, Gene Expression Omnibus
- GO, gene ontology
- IFN, interferon
- PBMCs, peripheral blood mononuclear cells
- PRRs, pattern recognition receptors
- SAM, significance analysis of microarrays
- TLRs, Toll-like receptors
- immune mechanism
- meta-analysis
- microarray
- type I interferon
- vaccine
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Affiliation(s)
- Junnan Zhang
- a National Institutes for Food and Drug Control ; Beijing , P.R. China
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Gan Y, Zheng S, Baak JP, Zhao S, Zheng Y, Luo N, Liao W, Fu C. Prediction of the anti-inflammatory mechanisms of curcumin by module-based protein interaction network analysis. Acta Pharm Sin B 2015; 5:590-5. [PMID: 26713275 PMCID: PMC4675814 DOI: 10.1016/j.apsb.2015.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/14/2015] [Accepted: 09/11/2015] [Indexed: 12/16/2022] Open
Abstract
Curcumin, the medically active component from Curcuma longa (Turmeric), is widely used to treat inflammatory diseases. Protein interaction network (PIN) analysis was used to predict its mechanisms of molecular action. Targets of curcumin were obtained based on ChEMBL and STITCH databases. Protein–protein interactions (PPIs) were extracted from the String database. The PIN of curcumin was constructed by Cytoscape and the function modules identified by gene ontology (GO) enrichment analysis based on molecular complex detection (MCODE). A PIN of curcumin with 482 nodes and 1688 interactions was constructed, which has scale-free, small world and modular properties. Based on analysis of these function modules, the mechanism of curcumin is proposed. Two modules were found to be intimately associated with inflammation. With function modules analysis, the anti-inflammatory effects of curcumin were related to SMAD, ERG and mediation by the TLR family. TLR9 may be a potential target of curcumin to treat inflammation.
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Key Words
- Anti-inflammatory
- Curcumin
- Cytoscape
- ETS, erythroblast transformation-specific
- GO, gene ontology
- Gene ontology enrichment analysis
- IFNs, interferons
- IL, interleukin
- JAK-STAT, Janus kinase-STAT
- MAPK, mitogen-activated protein kinase
- MCODE, molecular complex detection
- Module
- Molecular complex detection
- Molecular mechanism
- NF-κB, nuclear factor kappa B
- PIN, protein interaction network
- PPIs, protein–protein interactions
- Protein interaction network
- STATs, signal transducer and activator of transcription complexes
- TLR, toll-like receptor
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Róna G, Borsos M, Ellis JJ, Mehdi AM, Christie M, Környei Z, Neubrandt M, Tóth J, Bozóky Z, Buday L, Madarász E, Bodén M, Kobe B, Vértessy BG. Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation. Cell Cycle 2015; 13:3551-64. [PMID: 25483092 DOI: 10.4161/15384101.2014.960740] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Phosphorylation by the cyclin-dependent kinase 1 (Cdk1) adjacent to nuclear localization signals (NLSs) is an important mechanism of regulation of nucleocytoplasmic transport. However, no systematic survey has yet been performed in human cells to analyze this regulatory process, and the corresponding cell-cycle dynamics have not yet been investigated. Here, we focused on the human proteome and found that numerous proteins, previously not identified in this context, are associated with Cdk1-dependent phosphorylation sites adjacent to their NLSs. Interestingly, these proteins are involved in key regulatory events of DNA repair, epigenetics, or RNA editing and splicing. This finding indicates that cell-cycle dependent events of genome editing and gene expression profiling may be controlled by nucleocytoplasmic trafficking. For in-depth investigations, we selected a number of these proteins and analyzed how point mutations, expected to modify the phosphorylation ability of the NLS segments, perturb nucleocytoplasmic localization. In each case, we found that mutations mimicking hyper-phosphorylation abolish nuclear import processes. To understand the mechanism underlying these phenomena, we performed a video microscopy-based kinetic analysis to obtain information on cell-cycle dynamics on a model protein, dUTPase. We show that the NLS-adjacent phosphorylation by Cdk1 of human dUTPase, an enzyme essential for genomic integrity, results in dynamic cell cycle-dependent distribution of the protein. Non-phosphorylatable mutants have drastically altered protein re-import characteristics into the nucleus during the G1 phase. Our results suggest a dynamic Cdk1-driven mechanism of regulation of the nuclear proteome composition during the cell cycle.
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Key Words
- Cdc28, cyclin-dependent protein kinase (Cdk) encoded by CDC28
- Cdk1, cyclin-dependent kinase 1
- GO, gene ontology
- NES, nuclear export signal
- NLS, nuclear localization signal
- SNP, single nucleotide polymorphisms
- SV40, Simian virus 40
- UBA1, Ubiquitin-activating enzyme E1
- UNG2, Human Uracil-DNA glycosylase 2
- cNLS, classical nuclear localization signal
- cell cycle
- dNTP, deoxyribonucleotide triphosphate
- dTTP, deoxythymidine triphosphate
- dUMP, deoxyuridine monophosphate
- dUTP, deoxyuridine triphosphate
- dUTPase
- importin
- phosphorylation
- trafficking
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Affiliation(s)
- Gergely Róna
- a Institute of Enzymology; RCNS; Hungarian Academy of Sciences ; Budapest , Hungary
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Huang J, Schriefer AE, Yang W, Cliften PF, Rudnick DA. Identification of an epigenetic signature of early mouse liver regeneration that is disrupted by Zn-HDAC inhibition. Epigenetics 2015; 9:1521-31. [PMID: 25482284 DOI: 10.4161/15592294.2014.983371] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Liver regeneration has been well studied with hope of discovering strategies to improve liver disease outcomes. Nevertheless, the signals that initiate such regeneration remain incompletely defined, and translation of mechanism-based pro-regenerative interventions into new treatments for hepatic diseases has not yet been achieved. We previously reported the isoform-specific regulation and essential function of zinc-dependent histone deacetylases (Zn-HDACs) during mouse liver regeneration. Those data suggest that epigenetically regulated anti-proliferative genes are deacetylated and transcriptionally suppressed by Zn-HDAC activity or that pro-regenerative factors are acetylated and induced by such activity in response to partial hepatectomy (PH). To investigate these possibilities, we conducted genome-wide interrogation of the liver histone acetylome during early PH-induced liver regeneration in mice using acetyL-histone chromatin immunoprecipitation and next generation DNA sequencing. We also compared the findings of that study to those seen during the impaired regenerative response that occurs with Zn-HDAC inhibition. The results reveal an epigenetic signature of early liver regeneration that includes both hyperacetylation of pro-regenerative factors and deacetylation of anti-proliferative and pro-apoptotic genes. Our data also show that administration of an anti-regenerative regimen of the Zn-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA) not only disrupts gene-specific pro-regenerative changes in liver histone deacetylation but also reverses PH-induced effects on histone hyperacetylation. Taken together, these studies offer new insight into and suggest novel hypotheses about the epigenetic mechanisms that regulate liver regeneration.
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Affiliation(s)
- Jiansheng Huang
- a Department of Pediatrics ; Washington University School of Medicine ; St. Louis , MO USA
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Zhou L, Shang Y, Jin Z, Zhang W, Lv C, Zhao X, Liu Y, Li N, Liang J. UHRF1 promotes proliferation of gastric cancer via mediating tumor suppressor gene hypermethylation. Cancer Biol Ther 2015; 16:1241-51. [PMID: 26147747 DOI: 10.1080/15384047.2015.1056411] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Epigenetic changes play significant roles in cancer development. UHRF1, an epigenetic regulator, has been shown to be overexpressed and to coordinate tumor suppressor gene (TSG) silencing in several cancers. In a previous study, we found that UHRF1 promoted gastric cancer (GC) invasion and metastasis. However, the role and underlying mechanism of UHRF1 in GC carcinogenesis remain largely unknown. In the present study, we investigated UHRF1 expression and function in GC proliferation and explored its downstream regulatory mechanism. The results demonstrated that UHRF1 overexpression was an independent and significant predictor of GC prognosis. Downregulation of UHRF1 suppressed GC proliferation and growth in vitro and in vivo, and UHRF1 upregulation showed opposite effects. Furthermore, downregulation of UHRF1 reactivated 7 TSGs, including CDX2, CDKN2A, RUNX3, FOXO4, PPARG, BRCA1 and PML, via promoter demethylation. These results provide insight into the GC proliferation process, and suggest that targeting UHRF1 represents a new therapeutic approach to block GC development.
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Key Words
- BRCA, breast cancer
- CDH4, cadherin 4
- CDKN2A, cyclin-dependent kinase inhibitor 2A
- CDX2, caudal type homeobox 2
- DNA methylation
- DNMT, DNA methyltransferase
- FOXO, forkhead box O
- GAPDH, glyceraldehyde 3-phosphate dehydrogenase
- GC, gastric cancer
- GO, gene ontology
- MSP, methylation-specific PCR
- NC, negative control
- PBS, phosphate buffered saline
- PI, propidium iodide
- PLA, Chinese People's Liberation Army
- PML, promyelocytic leukemia
- PPARG,peroxisome proliferator-activated receptor gamma
- RB, retinoblastoma protein
- RUNX3, runt-related transcription factor 3
- TSG, tumor suppressor gene
- UHRF1
- UHRF1, ubiquitin-like containing PHD ring finger 1
- gastric cancer
- mRNA, messenger RNA
- proliferation
- qRT-PCR, quantitative reverse transcription–polymerase chain reaction
- shRNA, short hairpin RNA
- tumor suppressor gene
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Affiliation(s)
- Lin Zhou
- a Department of Medical Affairs ; The 88th Hospital of PLA ; Tai'an , China
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Ikeda K, Tomimoto S, Tsuchiya S, Hamagami KI, Shintani N, Sugimoto Y, Ichikawa A, Kasai A, Nakazawa T, Nagayasu K, Hayata-Takano A, Baba A, Hashimoto H. Comparative gene expression profiles in pancreatic islets associated with agouti yellow mutation and PACAP overexpression in mice. Biochem Biophys Rep 2015; 2:179-183. [PMID: 29124161 PMCID: PMC5668656 DOI: 10.1016/j.bbrep.2015.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 11/19/2022] Open
Abstract
In diabetes mellitus, pituitary adenylate cyclase-activating polypeptide (PACAP) has insulinotropic and glucose-lowering properties. We previously demonstrated that transgenic mice overexpressing PACAP in pancreatic β-cells (PACAP-Tg) show attenuated pancreatic islet hyperplasia and hyperinsulinemia in type 2 diabetic models. To explore the underlying mechanisms, here we crossed PACAP-Tg mice with lethal yellow agouti (KKAy) diabetic mice, and performed gene chip analysis of laser capture microdissected pancreatic islets from four F1 offspring genotypes (wild-type, PACAP-Tg, KKAy, and PACAP-Tg:KKAy). We identified 1371 probes with >16-fold differences between at least one pair of genotypes, and classified the probes into five clusters with characteristic expression patterns. Gene ontology enrichment analysis showed that genes involved in the terms ribosome and intracellular organelles such as ribonucleoprotein complex, mitochondrion, and chromosome organization were significantly enriched in clusters characterized by up-regulated genes in PACAP-Tg:KKAy mice compared with KKAy mice. These results may provide insight into the mechanisms of diabetes that accompany islet hyperplasia and amelioration by PACAP. PACAP overexpressed in KKAy diabetic mice is known to exert antidiabetic effects. We performed gene chip analysis of pancreatic islets in these mice. Gene ontology analysis was performed for genes classified into five clusters. Genes involved in the terms ribosome, mitochondrion, and chromosome were enriched. These pathways may be involved in the mechanism by which PACAP ameliorates diabetes.
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Affiliation(s)
- Kazuya Ikeda
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Research Fellow of the Japan Society for the Promotion of Science, Japan
| | - Shuhei Tomimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Soken Tsuchiya
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Pharmaceutical Biochemistry, Kumamoto University Graduate School of Pharmaceutical Sciences, Oe-Honmachi, Kumamoto 862-0973, Japan
| | - Ken-Ichi Hamagami
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norihito Shintani
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yukihiko Sugimoto
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Pharmaceutical Biochemistry, Kumamoto University Graduate School of Pharmaceutical Sciences, Oe-Honmachi, Kumamoto 862-0973, Japan
| | - Atsushi Ichikawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Institute for Biosciences, Mukogawa Women's University, 11-68 Koshien-Kyubancho, Nishinomiya-shi, Hyogo 663-8179, Japan
| | - Atsushi Kasai
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takanobu Nakazawa
- iPS Cell-based Research Project on Brain Neuropharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazuki Nagayasu
- iPS Cell-based Research Project on Brain Neuropharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Atsuko Hayata-Takano
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akemichi Baba
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Faculty of Pharmaceutical Sciences, Hyogo University of Health Science, 1-3-6 Minatojima, Chuo-ku, Kobe, Hyogo 650-8530, Japan
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,iPS Cell-based Research Project on Brain Neuropharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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Bertucci F, Finetti P, Mamessier E, Pantaleo MA, Astolfi A, Ostrowski J, Birnbaum D. PDL1 expression is an independent prognostic factor in localized GIST. Oncoimmunology 2015; 4:e1002729. [PMID: 26155391 DOI: 10.1080/2162402x.2014.1002729] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 01/18/2023] Open
Abstract
Gastrointestinal stromal tumors (GIST) are the most frequently occurring digestive sarcomas. The prognosis of localized GIST is heterogeneous, notably for patients with an Armed Forces Institute of Pathology (AFIP) intermediate or high risk of relapse. Despite imatinib effectiveness, it is crucial to develop therapies able to overcome the resistance mechanisms. The immune system represents an attractive prognostic and therapeutic target. The Programmed cell Death 1 (PD1)/programmed cell death ligand 1 (PDL1) pathway is a key inhibitor of the immune response; recently, anti-PD1 and anti-PDL1 drugs showed very promising results in patients with solid tumors. However, PDL1 expression has never been studied in GIST. Our objective was to analyze PDL1 expression in a large series of clinical samples. We analyzed mRNA expression data of 139 operated imatinib-untreated localized GIST profiled using DNA microarrays and searched for correlations with histoclinical features including postoperative metastatic relapse. PDL1 expression was heterogeneous across tumors and was higher in AFIP low-risk than in high-risk samples, and in samples without than with metastatic relapse. PDL1 expression was associated with immunity-related parameters such as T-cell-specific and CD8+ T-cell-specific gene expression signatures and probabilities of activation of interferon α (IFNα), IFNγ, and tumor necrosis factor α (TNFα) pathways, suggesting positive correlation with a cytotoxic T-cell response. In multivariate analysis, the PDL1-low group was associated with a higher metastatic risk independently of the AFIP classification and the KIT mutational status. In conclusion, PDL1 expression refines the prediction of metastatic relapse in localized GIST and might improve our ability to better tailor adjuvant imatinib. In the metastatic setting, PDL1 expression might guide the use of PDL1 inhibitors, alone or associated with tyrosine kinase inhibitors.
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Key Words
- AFIP, Armed Forces Institute of Pathology
- DNA microarray
- FDR, false discovery rate
- GEO, gene expression omnibus
- GES, gene expression signatures
- GIST
- GIST, gastrointestinal stromal tumors
- GO, gene ontology
- IHC, immunohistochemistry
- ISH, in situ hybridization
- MFS, metastasis-free survival
- MHC, major histocompatibility complex
- NCBI, National Center for Biotechnology Information
- NK cells, natural killer cells
- PCA, principal component analysis
- PD1, programmed cell death 1
- PDGFRA, platelet-derived growth factor receptor α
- PDL1
- PDL1, programmed cell death ligand 1
- REMARK, REcommendations for tumor MARKer
- RMA, robust multichip average
- ROC, receiver operating characteristic
- TILs, tumor-infiltrating lymphocytes
- Treg, regulatory T cells
- WT, wild type
- gene expression
- immune response
- prognosis
- qRT-PCR, quantitative reverse transcription-polymerase chain reaction
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Affiliation(s)
- François Bertucci
- Department of Molecular Oncology; Institut Paoli-Calmettes; Centre de Recherche en Cancérologie de Marseille ; UMR1068 Inserm; Marseille, France ; Aix-Marseille University ; Marseille, France ; French Sarcoma Group ; Lyon, France
| | - Pascal Finetti
- Department of Molecular Oncology; Institut Paoli-Calmettes; Centre de Recherche en Cancérologie de Marseille ; UMR1068 Inserm; Marseille, France
| | - Emilie Mamessier
- Department of Molecular Oncology; Institut Paoli-Calmettes; Centre de Recherche en Cancérologie de Marseille ; UMR1068 Inserm; Marseille, France
| | - Maria Abbondanza Pantaleo
- Department of Specialized, Experimental and Diagnostic Medicine; Sant'Orsola-Malpighi Hospital ; Bologna, Italy
| | - Annalisa Astolfi
- Giorgio Prodi Cancer Research Center; University of Bologna ; Bologna, Italy
| | - Jerzy Ostrowski
- Department of Gastroenterology and Hepatology; Cancer Center-Institute and Medical Center of Postgraduate Education ; Warsaw, Poland
| | - Daniel Birnbaum
- Department of Molecular Oncology; Institut Paoli-Calmettes; Centre de Recherche en Cancérologie de Marseille ; UMR1068 Inserm; Marseille, France
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Hillman SL, Finer S, Smart MC, Mathews C, Lowe R, Rakyan VK, Hitman GA, Williams DJ. Novel DNA methylation profiles associated with key gene regulation and transcription pathways in blood and placenta of growth-restricted neonates. Epigenetics 2015; 10:50-61. [PMID: 25496377 PMCID: PMC4622857 DOI: 10.4161/15592294.2014.989741] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fetal growth is determined by the feto-placental genome interacting with the maternal in utero environment. Failure of this interplay leads to poor placental development and fetal growth restriction (FGR), which is associated with future metabolic disease. We investigated whether whole genome methylation differences existed in umbilical cord blood and placenta, between gestational-matched, FGR, and appropriately grown (AGA) neonates. Using the Infinium HumanMethylation450 BeadChip®, we found that DNA from umbilical cord blood of FGR born at term (n = 19) had 839 differentially methylated positions (DMPs) that reached genome-wide significance compared with AGA (n = 18). Using gestational age as a continuous variable, we identified 76,249 DMPs in cord blood (adj. P < 0.05) of which 121 DMPs were common to the 839 DMPs and were still evident when comparing 12 FGR with 12 AGA [39.9 ± 1.2 vs. 40.0 ± 1.0 weeks (mean ± SD), respectively]. A total of 53 DMPs had a β methylation difference >10% and 25 genes were co-methylated more than twice within 1000 base pairs. Gene Ontology (GO) analysis of DMPs supported their involvement in gene regulation and transcription pathways related to organ development and metabolic function. A similar profile of DMPs was found across different cell types in the cord blood. At term, no DMPs between FGR and AGA placentae reached genome-wide significance, validated with an external dataset. GO analysis of 284 pre-term, placental DMPs associated with autophagy, oxidative stress and hormonal responses. Growth restricted neonates have distinct DNA methylation profiles in pre-term placenta and in cord blood at birth, which may predispose to future adult disease.
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Key Words
- AGA, appropriately grown offspring
- BMI, body mass index
- CG, cytosine phosphate guanine loci
- DMP, differentially methylated positions
- DNA methylation
- FDR, false discovery rate
- FGR, fetal growth restriction
- GO, gene ontology
- HOMA, homeostasis model assessment
- ICR1, imprinting control region 1
- MODY, maturity onset diabetes of the young
- Marmal-aid
- T2DM, type 2 diabetes mellitus
- UCL, University College London
- UCLH, University College London Hospital
- UCSC, University of California Santa Cruz
- fetal growth restriction
- fetal origins of adult disease
- placenta
- transcription factor
- umbilical cord
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Affiliation(s)
- Sara L Hillman
- a Institute for Women's Health ; University College London ; London , UK
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Abstract
As a widely used warm-season turfgrass in landscapes and golf courses, bermudagrass encounters multiple abiotic stresses during the growth and development. Physiology analysis indicated that abiotic stresses induced the accumulation of ROS and decline of photosynthesis, resulting in increased cell damage and inhibited growth. Proteomic and metabolomic approaches showed that antioxidant enzymes and osmoprotectant contents (sugar, sucrose, dehydrin, proline) were extensively changed under abiotic stress conditions. Exogenous application of small molecules, such as ABA, NO, CaCl2, H2S, polyamine and melatonin, could effectively alleviate damages caused by multiple abiotic stresses, including drought, salt, heat and cold. Based on high through-put RNA seq analysis, genes involved in ROS, transcription factors, hormones, and carbohydrate metabolisms were largely enriched. The data indicated that small molecules induced the accumulation of osmoprotectants and antioxidants, kept cell membrane integrity, increased photosynthesis and kept ion homeostasis, which protected bermudagrass from damages caused by abiotic stresses.
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Key Words
- ABA, abscisic acid
- GO, gene ontology
- JA, jasmonate
- JAZ, jasmonate ZIM-domain.
- NCED, 9-cis-epoxycarotenoid dioxygenase
- NO, nitrogen oxide
- PYR/PYL, pyrabactin resistance/PYR like
- RCAR, regulatory component of ABA receptors
- ROS, reactive oxygen species
- SnRK2, SNF1-related protein kinases 2
- TCA, tricarboxylicacid
- abiotic stress
- bermudagrass
- melatonin
- small molecule
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Affiliation(s)
- Zhulong Chan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan, China
- Correspondence to: Zhulong Chan;
| | - Haitao Shi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan, China
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Ritelli M, Chiarelli N, Zoppi N, Dordoni C, Quinzani S, Traversa M, Venturini M, Calzavara-Pinton P, Colombi M. Insights in the etiopathology of galactosyltransferase II (GalT-II) deficiency from transcriptome-wide expression profiling of skin fibroblasts of two sisters with compound heterozygosity for two novel B3GALT6 mutations. Mol Genet Metab Rep 2014. [PMID: 28649518 PMCID: PMC5471164 DOI: 10.1016/j.ymgmr.2014.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mutations in B3GALT6, encoding the galactosyltransferase II (GalT-II) involved in the synthesis of the glycosaminoglycan (GAG) linkage region of proteoglycans (PGs), have recently been associated with a spectrum of connective tissue disorders, including spondyloepimetaphyseal dysplasia with joint laxity type 1 (SEMDJL1) and Ehlers–Danlos-like syndrome. Here, we report on two sisters compound heterozygous for two novel B3GALT6 mutations that presented with severe short stature and progressive kyphoscoliosis, joint hypermobility and laxity, hyperextensible skin, platyspondyly, short ilia, and elbow malalignment. Microarray-based transcriptome analysis revealed the differential expression of several genes encoding extracellular matrix (ECM) structural components, including COMP, SPP1, COL5A1, and COL15A1, enzymes involved in GAG synthesis and in ECM remodeling, such as CSGALNACT1, CHPF, LOXL3, and STEAP4, signaling transduction molecules of the TGFβ/BMP pathway, i.e., GDF6, GDF15, and BMPER, and transcription factors of the HOX and LIM families implicated in skeletal and limb development. Immunofluorescence analyses confirmed the down-regulated expression of some of these genes, in particular of the cartilage oligomeric matrix protein and osteopontin, encoded by COMP and SPP1, respectively, and showed the predominant reduction and disassembly of the heparan sulfate specific GAGs, as well as of the PG perlecan and type III and V collagens. The key role of GalT-II in GAG synthesis and the crucial biological functions of PGs are consistent with the perturbation of many physiological functions that are critical for the correct architecture and homeostasis of various connective tissues, including skin, bone, cartilage, tendons, and ligaments, and generates the wide phenotypic spectrum of GalT-II-deficient patients. Clinical features/molecular characterization of two patients with spondyloepimetaphyseal dysplasia with joint laxity type 1 Identification of two novel B3GALT6 mutations First report of transcriptome-wide gene expression profiling on GalT-II-deficient fibroblasts Immunofluorescence studies of several ECM structural components in GalT-II-deficient cells Enlargement of the knowledge on the GalT-II deficiency’s molecular pathogenesis
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Key Words
- ATCS, adducted-thumb club foot syndrome
- Abs, antibodies
- B3GALT6
- BMP, bone morphogenetic proteins
- C4ST, chondroitin 4-sulfotransferase
- C6ST, chondroitin 6-sulfotransferase
- COLLI, type I collagen
- COLLIII, type III collagen
- COLLV, type V collagen
- COLLs, collagens
- COMP, cartilage oligomeric matrix protein
- CS, chondroitin sulfate
- CSGALNACT1, chondroitin sulfate N-acetylgalactosaminyltransferase 1
- CTDs, connective tissue disorders
- Cartilage oligomeric matrix protein
- ChPF, chondroitin polymerizing factor
- ChSy, chondroitin synthase
- D4ST, dermatan 4 sulfotransferase 1
- DCN, decorin
- DEGs, differentially expressed genes
- DS, dermatan sulfate
- ECM, extracellular matrix
- EDS, Ehlers–Danlos syndrome
- Ehlers–Danlos syndrome
- FN, fibronectin
- GAGs, glycosaminoglycans
- GO, gene ontology
- Gal, galactose
- GalNAc, N-acetylgalactosamine
- GalNAc4S-6ST, GalNAc 4-sulfate 6-O-sulfotransferase
- GalNAcT, β1,4-N-acetylgalactosaminyltransferase
- GalNAcT-16, N-acetylgalactosaminyltransferase 16
- GalT-I/II, galactosyltransferase I and II
- GalT-II deficiency
- GlcA, glucuronic acid
- GlcAT, glucuronosyltransferase
- GlcNAc, N-acetylglucosamine
- GlcNAcT, α1,4-N-acetylglucosaminyltransferase
- HA, hyaluronic acid
- HAS2, hyaluronan synthase 2
- HOX, homeobox gene family
- HPO, human phenotype ontology
- HS, heparan sulfate
- Hep, heparin
- IF, immunofluorescence microscopy studies
- IdoA, iduronic acid
- OPN, osteopontin
- Osteopontin
- PGs, proteoglycans
- PTC, premature termination codon of translation
- SEMDJL1, spondyloepimetaphyseal dysplasia with joint laxity type 1
- Spondyloepimetaphyseal dysplasia with joint laxity type 1
- TNs, tenascins
- Xyl, xylose
- XylT, xylosyltransferase
- qPCR, quantitative polymerase chain reaction
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Affiliation(s)
- Marco Ritelli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Nicola Chiarelli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Nicoletta Zoppi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Chiara Dordoni
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Stefano Quinzani
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Michele Traversa
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Marina Venturini
- Division of Dermatology, Department of Clinical and Experimental Sciences, Spedali Civili University Hospital, Brescia, Italy
| | - Piergiacomo Calzavara-Pinton
- Division of Dermatology, Department of Clinical and Experimental Sciences, Spedali Civili University Hospital, Brescia, Italy
| | - Marina Colombi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
- Corresponding author at: Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
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Brant JO, Riva A, Resnick JL, Yang TP. Influence of the Prader-Willi syndrome imprinting center on the DNA methylation landscape in the mouse brain. Epigenetics 2014; 9:1540-56. [PMID: 25482058 PMCID: PMC4623435 DOI: 10.4161/15592294.2014.969667] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/23/2014] [Accepted: 08/25/2014] [Indexed: 11/19/2022] Open
Abstract
Reduced representation bisulfite sequencing (RRBS) was used to analyze DNA methylation patterns across the mouse brain genome in mice carrying a deletion of the Prader-Willi syndrome imprinting center (PWS-IC) on either the maternally- or paternally-inherited chromosome. Within the ~3.7 Mb imprinted Angelman/Prader-Willi syndrome (AS/PWS) domain, 254 CpG sites were interrogated for changes in methylation due to PWS-IC deletion. Paternally-inherited deletion of the PWS-IC increased methylation levels ~2-fold at each CpG site (compared to wild-type controls) at differentially methylated regions (DMRs) associated with 5' CpG island promoters of paternally-expressed genes; these methylation changes extended, to a variable degree, into the adjacent CpG island shores. Maternal PWS-IC deletion yielded little or no changes in methylation at these DMRs, and methylation of CpG sites outside of promoter DMRs also was unchanged upon maternal or paternal PWS-IC deletion. Using stringent ascertainment criteria, ~750,000 additional CpG sites were also interrogated across the entire mouse genome. This analysis identified 26 loci outside of the imprinted AS/PWS domain showing altered DNA methylation levels of ≥25% upon PWS-IC deletion. Curiously, altered methylation at 9 of these loci was a consequence of maternal PWS-IC deletion (maternal PWS-IC deletion by itself is not known to be associated with a phenotype in either humans or mice), and 10 of these loci exhibited the same changes in methylation irrespective of the parental origin of the PWS-IC deletion. These results suggest that the PWS-IC may affect DNA methylation at these loci by directly interacting with them, or may affect methylation at these loci through indirect downstream effects due to PWS-IC deletion. They further suggest the PWS-IC may have a previously uncharacterized function outside of the imprinted AS/PWS domain.
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Key Words
- AS, Angelman Syndrome
- AS-IC, Angelman Syndrome Imprinting Center
- AS-SRO, Angelman Syndrome Shortest Region of deletion Overlap
- BGS, Sodium Bisulfite Genomic Sequencing
- BISSCA, Bisulfite Sequencing Comparative Analysis
- CGI, CpG Island
- DH, DNase I Hypersensitive
- DMR, Differentially Methylated Region
- DNA methylation
- EtOH, Ethanol
- GO, gene ontology
- IC, Imprinting Center
- ICR, Imprinting Control Region
- IPA, Ingenuity Pathway Analysis ®
- PWS, Prader-Willi Syndrome
- PWS-IC, Prader-Willi Syndrome Imprinting Center
- PWS-SRO, Prader-Willi Syndrome Shortest Region of deletion Overlap
- RRBS, Reduced Representation Bisulfite Sequencing
- SDS, Sodium Dodecyl Sulfate
- SLIM, Sliding Linear Model
- TBE, Tris/Borate/EDTA
- Tris, Trisaminomethane
- UTR, untranslated region
- angelman syndrome
- genomic imprinting
- imprinting center
- lncRNA, long non-coding RNA
- mat, maternally-inherited allele
- pat, paternally-inherited allele
- prader-Willi syndrome
- reduced representation bisulfite sequencing
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Affiliation(s)
- Jason O Brant
- Department of Biochemistry and Molecular Biology; University of Florida; Gainesville, FL USA
- Center for Epigenetics; University of Florida; Gainesville, FL USA
| | - Alberto Riva
- Department of Molecular Genetics and Microbiology; University of Florida; Gainesville, FL USA
- Genetics Institute; University of Florida; Gainesville, FL USA
| | - James L Resnick
- Department of Molecular Genetics and Microbiology; University of Florida; Gainesville, FL USA
- Center for Epigenetics; University of Florida; Gainesville, FL USA
- Genetics Institute; University of Florida; Gainesville, FL USA
| | - Thomas P Yang
- Department of Biochemistry and Molecular Biology; University of Florida; Gainesville, FL USA
- Center for Epigenetics; University of Florida; Gainesville, FL USA
- Genetics Institute; University of Florida; Gainesville, FL USA
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Lesjak MS, Marchan R, Stewart JD, Rempel E, Rahnenführer J, Hengstler JG. EDI3 links choline metabolism to integrin expression, cell adhesion and spreading. Cell Adh Migr 2014; 8:499-508. [PMID: 25482527 PMCID: PMC4594537 DOI: 10.4161/cam.29284] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Endometrial carcinoma differential 3 (EDI3) was the first member of the glycerophosphodiesterase (GDE) protein family shown to be associated with cancer. Our initial work demonstrated that endometrial and ovarian cancer patients with primary tumors overexpressing EDI3 had a higher risk of developing metastasis and decreased survival. Further analysis indicated that EDI3 cleaves glycerophosphocholine to choline and glycerol-3-phosphate, increases the levels of active PKC, and enhances the migratory activity of tumor cells. Despite these initial findings, EDI3 remained mainly uncharacterized. Therefore, to obtain an overview of processes in which EDI3 may be involved, gene array analysis was performed using MCF-7 breast cancer cells after EDI3 knockdown compared with a non-targeting control siRNA. Several biological motifs were altered, including an enrichment of genes involved in integrin-mediated signaling. More specifically, silencing of EDI3 in MCF-7 and OVCAR-3 cells was associated with reduced expression of the key receptor subunit integrin β1, leading to decreased cell attachment and spreading accompanied by delayed formation of cell protrusions. To confirm these results, we stably overexpressed EDI3 in MCF-7 cells which led to elevated integrin β1 expression associated with enhanced cell attachment and spreading - two processes critical for metastasis. In conclusion, our data provide further insight into the role of EDI3 during cancer progression.
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Key Words
- DAG, diacylglycerol
- DHAP, dihydroxyacetone phosphate
- ECM, extracellular matrix
- EDI3
- EDI3, Endometrial carcinoma differential 3
- ER, estrogen receptor
- FN, fibronectin
- GDE, glycerophosphodiesterase
- GDE5
- GO, gene ontology
- GPC, glycerophosphocholine
- PA, phosphatidic acid
- PC, phosphocholine
- PKC, protein kinase C
- PLD, phospholipase D
- PtdCho, phosphatidylcholine
- adhesion
- choline metabolism
- glycerophosphodiesterase
- integrins
- metastasis
- migration
- spreading
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Affiliation(s)
- Michaela S Lesjak
- a Department of Systems Toxicology ; Leibniz Research Centre for Working Environment and Human Factors ; Dortmund , Germany
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Szeto CYY, Lin CH, Choi SC, Yip TTC, Ngan RKC, Tsao GSW, Li Lung M. Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA-microRNA regulatory network in nasopharyngeal carcinoma model systems. FEBS Open Bio 2014; 4:128-40. [PMID: 24490137 PMCID: PMC3907684 DOI: 10.1016/j.fob.2014.01.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 01/09/2014] [Accepted: 01/09/2014] [Indexed: 01/28/2023] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a prevalent malignancy in Southeast Asia among the Chinese population. Aberrant regulation of transcripts has been implicated in many types of cancers including NPC. Herein, we characterized mRNA and miRNA transcriptomes by RNA sequencing (RNASeq) of NPC model systems. Matched total mRNA and small RNA of undifferentiated Epstein–Barr virus (EBV)-positive NPC xenograft X666 and its derived cell line C666, well-differentiated NPC cell line HK1, and the immortalized nasopharyngeal epithelial cell line NP460 were sequenced by Solexa technology. We found 2812 genes and 149 miRNAs (human and EBV) to be differentially expressed in NP460, HK1, C666 and X666 with RNASeq; 533 miRNA–mRNA target pairs were inversely regulated in the three NPC cell lines compared to NP460. Integrated mRNA/miRNA expression profiling and pathway analysis show extracellular matrix organization, Beta-1 integrin cell surface interactions, and the PI3K/AKT, EGFR, ErbB, and Wnt pathways were potentially deregulated in NPC. Real-time quantitative PCR was performed on selected mRNA/miRNAs in order to validate their expression. Transcript sequence variants such as short insertions and deletions (INDEL), single nucleotide variant (SNV), and isomiRs were characterized in the NPC model systems. A novel TP53 transcript variant was identified in NP460, HK1, and C666. Detection of three previously reported novel EBV-encoded BART miRNAs and their isomiRs were also observed. Meta-analysis of a model system to a clinical system aids the choice of different cell lines in NPC studies. This comprehensive characterization of mRNA and miRNA transcriptomes in NPC cell lines and the xenograft provides insights on miRNA regulation of mRNA and valuable resources on transcript variation and regulation in NPC, which are potentially useful for mechanistic and preclinical studies. Using RNASeq we characterized the mRNA and miRNA transcriptomes in NPC and NP models. 2812 Genes and 149 miRNAs (human and EBV) were differentially expressed in NPC vs NP models. 533 miRNA–mRNA target pairs were inversely regulated in HK1, C666, and X666 vs NP460. ECM, β1 integrin, PI3K/AKT, EGFR, ErbB, and Wnt pathways appeared to be deregulated in NPC. A novel TP53 mutation was identified in NP460, HK1, and C666.
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Key Words
- AIP, aryl hydrocarbon receptor interacting protein
- BAX, BCL2-asscoiated X protein
- CIITA, class II, major histocompatibility complex, transactivator
- DKK1, Dickkopf-Like protein 1
- EBV, Epstein–Barr virus
- ECM, extracellular matrix
- EGFR, epidermal growth factor receptor
- EGR1, early growth response 1
- FBLN2, fibulin 2
- GADD45, growth arrest and DNA-damage-inducible
- GNG11, guanine nucleotide binding protein (G protein), Gamma 11
- GO, gene ontology
- GSTP1, glutathione S-transferase pi 1
- IL18, interleukin 18
- INDEL, insertion and deletion
- LMP1, Epstein–Barr virus latent membrane protein 1
- LTBP2, latent transforming growth factor beta binding protein 2
- MDM2, MDM2 oncogene, E3 ubiquitin protein ligase
- MET, met proto-oncogene
- MMP19, matrix metallopeptidase 19
- NGS, next-generation sequencing
- NPC, nasopharyngeal carcinoma
- Nasopharyngeal carcinoma
- Nasopharyngeal cell lines/xenograft (NP460, HK1, C666, X666)
- PI3K, phosphoinositide 3-kinase
- PTEN, phosphatase and tensin homolog
- RNA sequencing
- RNASeq, RNA sequencing
- SNP, single nucleotide polymorphism
- TNFRSF9, tumour necrosis factor receptor superfamily, member 9
- TP53
- Transcriptome analysis
- UTR, untranslated region
- miRNA, microRNA
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Affiliation(s)
- Carol Ying-Ying Szeto
- Center for Nasopharyngeal Cancer Research, The University of Hong Kong, PR China ; Department of Clinical Oncology, The University of Hong Kong, PR China
| | - Chi Ho Lin
- Centre for Genomic Sciences, The University of Hong Kong, PR China
| | - Siu Chung Choi
- Centre for Genomic Sciences, The University of Hong Kong, PR China
| | - Timothy T C Yip
- Center for Nasopharyngeal Cancer Research, The University of Hong Kong, PR China ; Department of Clinical Oncology, Queen Elizabeth Hospital, PR China
| | - Roger Kai-Cheong Ngan
- Center for Nasopharyngeal Cancer Research, The University of Hong Kong, PR China ; Department of Clinical Oncology, Queen Elizabeth Hospital, PR China
| | - George Sai-Wah Tsao
- Center for Nasopharyngeal Cancer Research, The University of Hong Kong, PR China ; Department of Anatomy, The University of Hong Kong, PR China
| | - Maria Li Lung
- Center for Nasopharyngeal Cancer Research, The University of Hong Kong, PR China ; Department of Clinical Oncology, The University of Hong Kong, PR China
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